Novel Gene Targets Associated with Amyotrophic Lateral Sclerosis and Methods of Use Thereof

Novel gene targets and methods of use thereof for the diagnosis and treatment of Amyotrophic Lateral Sclerosis are provided.

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Description

This application is a continuation application of U.S. application Ser. No. 13/638,237 filed Nov. 7, 2012, now U.S. Pat. No. 8,969,005 which is §371 Application of PCT/US2011/30178 filed Mar. 28, 2011 which in turn claims priority to U.S. Provisional Application No. 61/318,328, filed Mar. 28, 2010, the entire disclosure if each being incorporated herein by reference as though set forth in full.

Pursuant to 35 U.S.C. §202(c) it is acknowledged that the U.S. Government has rights in the invention described, which was made in part with funds from the National Institutes of Health, Grant Numbers 1DP2OD004417-01 and 1RO1NS065317.

FIELD OF THE INVENTION

The present invention relates to the fields of medicine, protein folding and neurobiology. More specifically, the invention provides a series of genes and alterations therein associated with pathogenesis of amyotrophic lateral sclerosis (ALS). These molecules have utility in diagnostic assays and also in screening assays for identifying agents useful for the treatment of disorders associated with aberrant protein aggregation, particularly in (ALS).

BACKGROUND OF THE INVENTION

Several publications and patent documents are cited throughout the specification in order to describe the state of the art to which this invention pertains. Each of these citations is incorporated by reference herein as though set forth in full.

The United States and other countries around the world are experiencing a demographic sea change owing to the rapidly growing elderly and ‘Baby Boomer’ populations (Trojanowski, (2008) Neurosignals 16: 5-10). Our astonishing biomedical advances in the last half-century have greatly increased our life expectancy. But as a consequence of living longer, our population now faces an increase in the incidence of neurodegenerative diseases. These truly disastrous disorders include Alzheimer's, Huntington's, Parkinson's, amyotrophic lateral sclerosis (ALS) and the frontal temporal dementias (Forman et al. (2004) Nat. Med. 10:1055-1063).

In the future, personalized genome sequencing will become routine, empowering us to define the genetic basis of many human diseases. Currently, however, complete genome sequencing for individuals to discover rare pathogenic mutations is still too costly and time consuming. Thus, more creative approaches are needed for disease gene discovery; moreover, even once genes are revealed, the need for innovative approaches to elucidate causality remains critical.

ALS, also known as Lou Gehrig's disease, is a devastating adult-onset neurodegenerative disease that attacks upper and lower motor neurons (Cleveland and Rothstein, 2001). A progressive and ultimately fatal muscle paralysis ensues, usually causing death within 2 to 5 years of disease onset. ALS is mostly sporadic, but approximately 10% of cases are familial. Pathogenic mutations in several genes have been linked to familial and sporadic ALS, including SOD1, TARDBP, FUS/TLS, VAPB, OPTN and others (Van Damme and Robberecht, 2009). Two of these genes, TARDBP (which encodes TDP-43) and FUS/TLS (FUS) are notable because they encode related RNA-binding proteins (Lagier-Tourenne and Cleveland, 2009). Moreover, both of these proteins have been identified as components of pathological inclusions in neurons of ALS patients (Kwiatkowski et al., 2009; Neumann et al., 2006; Vance et al., 2009). Indeed, an emerging concept suggested by the association of FUS and TDP-43 to ALS is that defects in RNA metabolism might contribute to disease pathogenesis. Accordingly, genes encoding proteins involved in RNA metabolism may provide a new avenue to pursue in the development of efficacious therapeutic targets useful for the treatment of these devastating neurological disorders.

SUMMARY OF THE INVENTION

We have identified several RNA binding proteins in a functional yeast screen which appear to play a role in TDP-43 mediated cellular toxicity and aberrant protein aggregation. These data have resulted in methods for predicting an increased risk of an individual for developing amyotrophic lateral sclerosis (ALS) disease. In one embodiment, the method entails obtaining a nucleic acid sample encoding EWSR1 from said individual and determining whether or not said EWSR1 comprises a mutation selected from the group consisting of a missense mutation in exon 16 (1532 G>C giving rise to a Gly511Ala alteration), and a missense mutation in exon 17 (1655 C>T giving rise to a Pro522Leu alteration) relative to wild-type EWSR1 encoding nucleic acids, wherein the presence of at least one mutation in said EWSR1 encoding nucleic acid when compared to wild type EWSR1 encoding nucleic acids obtained from patients not having ALS is indicative of an increased risk of developing ALS. In another embodiment of the invention, the method entails obtaining a nucleic acid sample encoding TAF15 from said individual and determining whether or not said TAF15 comprises a mutation selected from the group consisting of a missense mutation in exon 14 (1172 G>A giving rise to a Gly391Glu alteration) and in exon 15 (1222C>T giving rise to a Arg408Cys) relative to wild-type TAF15 encoding nucleic acids, wherein the presence of said at least one mutation in said TAF15 encoding nucleic acid when compared to wild type TAF15 encoding nucleic acids obtained from patients not having ALS is indicative of an increased risk of ALS. In preferred embodiments the methods described above are useful for predicting an increased risk for development of early onset ALS.

Diagnostic kits for performing the methods mentioned above comprising reagents suitable for isolation of DNA, and reagents suitable for detection of said mutation containing EWSR1 and TAF15 nucleic acid also form an embodiment of the invention.

In yet another aspect, the invention entails a method identifying agents which inhibit TDP-43 associated complex formation with at least one RNA binding protein listed in Table 1. Particularly preferred targets include EWSR1, TAF15, TIA1, DAZ1, DAZ2, DAZ3, DAZAP1, HNRNPA0, and RBM14. An exemplary method comprises providing a cell which expresses TDP-43 and said RNA binding protein, the expression being associated with increased cellular toxicity and cytoplasmic aggregate formation. Contacting the cell with an effective amount of an agent; and measuring cellular toxicity and/or aggregate formation in the presence of said agent relative to a non-treated control cell, wherein a decrease in cellular toxicity identifies an agent which reduces TDP-43-RNA binding protein mediated cellular toxicity and cytoplasmic aggregate formation. Agents identified using these screening methods are also encompassed within the present invention.

Also provided are isolated nucleic acids encoding the altered EWSR and TAF15 proteins described herein. Such isolated nucleic acids can be affixed to a solid support, or introduced into a host cell for screening agents that may have efficacy for the treatment of ALS.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D. A yeast functional screen identifies human RRM proteins with properties similar to FUS and TDP-43. (FIG. 1A) When expressed in yeast, TDP-43 and FUS form multiple cytoplasmic aggregates (top) and are toxic (bottom). (FIG. 1B) We designed a yeast functional screen to identify additional human RRM proteins that aggregate and are toxic in yeast. A library of 132 different human ORFs encoding the proteins as YFP fusions was individually transformed into yeast cells. (FIG. 1C) Examples of various localization patterns in yeast cells of human RRM proteins. Some proteins were localized diffusely throughout the cytoplasm (TUT1 and DND1) and others were localized diffusely in the nucleus (PPIE and DNAJC17). Some formed multiple foci in the nucleus (RBM39) and several others resembled FUS and TDP-43, which formed multiple cytoplasmic foci (EWSR1, HNRNPA0, DAZ1). (FIG. 1D) Spotting assays to assess the toxicity of human RRM proteins. Transformants were grown on synthetic media containing either glucose (control, RRM gene “off”) or galactose (to induce expression of candidate ORFs, RRM gene “on”). Some proteins were very toxic when overexpressed (DAZ1, ELAV1, FUS, TDP-43) while others were moderately toxic (EWSR1) and others were not toxic (PPIE and DNAJC17). See Table 1 and Table 2 for toxicity and aggregation scores.

FIGS. 2A-2G. Missense mutations in EWSR1 and TAF15 in ALS patients. (FIG. 2A) Comparison of FUS, EWSR1, and TAF15 demonstrates similar domain architecture. All three proteins contain a single RRM, a glycine-rich domain, a predicted prion-domain, RGG domains, and a C-terminal PY-motif, which can function as an NLS (Dormann et al., 2010). Mutations in FUS and TDP-43 are selected examples of those similar to variants found in EWSR1 and TAF15. (FIG. 2B, FIG. 2C) DNA sequence analysis of EWSR1 in ALS patients identified 2 missense mutations (shown are electropherograms highlighting the sequence variants). (FIG. 2B) A single base substitution (asterisk; SEQ ID NO: 5) changing the wild-type guanine at 1532 to cytosine (c.1532 G>C), alanine substituting for glycine (p.G511A). (FIG. 2C) Another mutation in an ALS case: c.1655 C>T (SEQ ID NO: 6), leucine substituted for proline (p.P552L). (FIG. 2D) Sequence alignment of amino acids 505 to 564 of EWSR1 from diverse vertebrate species indicates that the mutated residues in EWSR1 are highly conserved. Identical amino acids have a black background, similar amino acids are gray, and mutation sites are red. (Human, mouse, opossum: SEQ ID NO: 7; dog: SEQ ID NO: 8; frog: SEQ ID NO: 9; zebrafish: SEQ ID NO: 10) (FIG. 2E, FIG. 2F) DNA sequence analysis of TAF15 in ALS patients identified 3 missense mutations. (FIG. 2E) A TAF15 mutation in an ALS case: c.1172 G>A (SEQ ID NO: 11), glutamic acid substituted for glycine (p.G391E). (FIG. 2F) Another TAF15 mutation in an ALS case: c.1222 C>T (SEQ ID NO: 12), histidine substituted for arginine (p.R408C). An additional TAF15 variant (c.1418G>A, p.Gly473Glu), identified in the ALS cohort from Mayo Clinic is shown in FIG. 1A. (FIG. 1G) Sequence alignment of amino acids 358 to 416 of TAF15 from diverse vertebrate species indicates that the mutated residues in TAF15 are highly conserved. Identical amino acids have a black background, similar amino acids are gray, and mutation sites are red. (Human, mouse, dog: SEQ ID NO: 13; chicken: SEQ ID NO: 14; frog: SEQ ID NO: 15)

FIGS. 3A-3D. EWSR1 and TAF15 are aggregation-prone proteins. FIG. 3A) GST-TDP-43, GST-FUS, GST-EWSR-1 or GST-TAF15 (3 μM) were incubated in the presence or absence of TEV protease at 25° C. for 0-90 min with agitation. Note that very little aggregation occurs in the absence of TEV protease. The extent of aggregation was determined by turbidity. Values represent means±SEM (n=3). FIG. 3B) GST-TDP-43, GST-FUS, GST-EWSR1 or GST-TAF15 (3 μM) were incubated in the presence of TEV protease at 25° C. for 0-60 min. At the indicated times, reactions were processed for sedimentation analysis. Pellet and supernatant fractions were resolved by SDS-PAGE and stained with Coomassie Brilliant Blue. The amount of protein in the pellet fraction was determined by densitometry in comparison to known quantities of the appropriate protein. Values represent means±SEM (n=3). A human RRM protein, DND1, which did not aggregate and was not toxic in yeast (FIG. 1c,d), was also soluble and did not form aggregates in this assay (data not shown). FIG. 3C) GST-TDP-43, GST-FUS, GST-EWSR-1 or GST-TAF15 (3 μM) were incubated in the presence of TEV protease at 25° C. for 0-60 min. At various times, reactions were processed for EM. Small arrows denote small pore-shaped oligomers and large arrows denote linear polymers. Bar, 500 nm. FIG. 3D) Gallery of TDP-43, FUS, EWSR1 and TAF15 oligomers formed during aggregation reactions. Bar, 50 nm.

FIGS. 4A-4D. EWSR1 and TAF15 confer neurodegeneration in Drosophila. (FIG. 4A, FIG. 4B, FIG. 4C) EWSR1 and TAF15 cause neural degeneration and dysfunction in Drosophila. FIG. 4A) Toxicity of various human RRM proteins in the eye. EWSR1 and TAF15 cause degeneration and disruption of the retinal structure, akin to TDP-43 (also see (Elden et al., 2010)). Control is driver line alone gmr-GAL4/+. TDP-43 is gmr-GAL4/UAS-TDP-43-YFP. EWSR1 is gmr-GAL4/UAS-EWSR1. TAF15 is gmr-GAL4/UAS-TAF15 (grown at 29° C.). FIG. 4B, FIG. 4C) Progressive loss of climbing behavior upon expression of TDP-43, EWSR1 and TAF15 in the nervous system (elav, FIG. 4B) or selectively in motor neurons (D42, FIG. 4C). FIG. 4D) Upregulation of other RRM proteins does not cause neurodegeneration in Drosophila. As a specificity control for the neurodegenerative phenotype conferred by upregulation of TDP-43, EWSR1, and TAF15 in Drosophila (see FIG. 4A), we tested the effects of upregulating the fly counterparts of two other human RRM proteins in the eye using the GAL4-UAS system. The human homologues fail to aggregate or confer toxicity in yeast—neither fly counterpart conferred neurodegeneration in Drosophila.

FIGS. 5A-5G. ALS-linked EWSR1 and TAF15 mutations promote cytoplasmic localization in motor neurons. Embryonic stem cell derived neurons were transduced with doxycycline (Dox) inducible lentiviruses expressing wild-type (WT) or ALS-linked mutants of EWSR1 (FIG. 5A-5C) or TAF15 (FIG. 5D-5F), each carrying FLAG and myc epitope tags in their amino- and carboxy-termini, respectively. Five days after induction of expression by Dox, the localization of the proteins was visualized by immunofluorescence microscopy with anti-FLAG antibody (red); nuclei were visualized by DAPI staining (blue). The localization of endogenous EWSR1 and TAF15 was performed with anti-EWSR1 and anti-TAF15 specific antibodies (red) in non-transduced neurons. Induced expression of WT EWSR1 (FIG. 5A) or TAF15 (FIG. 5D) led to a slight increase in the accumulation of proteins in the cytoplasm and neuronal processes of transduced cells. The ALS-linked patient mutations (FIG. 5A, FIG. 5D) resulted in an increase in the mislocalization of EWSR1 and TAF15 to the cytoplasm and processes. Percentage of cells showing staining in the cytoplasm and processes are indicated in c (EWSR1 endogenous and transduced WT and mutants) and f (TAF15 endogenous and transduced WT and mutants). For EWSR1: *, P<0.005; **, P<0.01 (localization of EWSR1 variants compared to WT, Student's t test). For TAF15: *, P<0.004 (localization of TAF15 variants compared to WT, Student's t test). At least 100 cells were counted for each sample, with the observer blinded to the identity of the sample and each experiment was performed three independent times. Expression levels of transduced proteins were determined by immunoblots with anti-FLAG antibodies of cell lysates from EWSR1 WT and mutants (FIG. 5B) and TAF15 WT and mutants (FIG. 5E) five days after Dox induction. Vector indicates transduction of cells with empty lentivirus. Immunoblots for GAPDH were used as loading controls. The expression levels of transduced proteins were comparable between WT and mutants. (FIG. 5G, FIG. 5H) Mutant EWSR1 is mislocalized to the neurites of primary neurons cultured from mouse spinal cord. Primary mouse neuron cultures were transfected with WT or mutant EWSR1, stained with α-EWSR1 (red) and α-doublecortin (green). FIG. 5G) Endogenous EWSR1 is almost exclusively localized within the nucleus of neurons. Overexpression of WT EWSR1 shows primarily localization within the nucleus or cytoplasm of neurons, with rare neurites containing EWSR1. In contrast, the ALS-linked mutant forms of EWSR1 showed increased mislocalization into the neurites, including dendrites and axons. FIG. 5H) Quantitation of mislocalization of endogenous transfected WT or mutant EWSR1 into neuronal processes. A variant that was also identified in both an ALS case and a healthy control, G584S, does not affect localization in this assay. #, P<0.002 (localization of EWSR1 variants compared to WT, Student's t test). Error bars=mean±S.E.M. Scale bar, 5 μm for FIG. 5A and FIG. 5D; 10 μm for FIG. 5G.

 DETAILED DESCRIPTION OF THE INVENTION

Amyotrophic lateral sclerosis (ALS) is a devastating human neurodegenerative disease. The causes of ALS are poorly understood, although mutations in two related RNA-binding proteins, TDP-43 and FUS/TLS, have been linked to the disease. Both proteins aggregated and caused toxicity in yeast cells. Including FUS/TLS and TDP-43, the human proteome contains at least 226 RNA-binding proteins. In accordance with the present invention, a yeast functional screen was designed to identify new genes associated with the pathogenesis of ALS. To find additional proteins with properties like TDP-43 and FUS/TLS we expressed 133 RNA-binding proteins in yeast and identified 35 that formed aggregates and were toxic. Further computational analysis revealed the presence of a prion-like domain in FUS, TDP-43 and 8 others. We sequenced two of these genes, EWSR1 (Ewing sarcoma breakpoint region 1) and TAF15 (RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68 kDa), in 600 ALS patients and identified three mutations (G511A, P552L, G584S) in EWSR1 and two mutations in TAF15 (R388H and G391E). None of these variants were found in over 800 control individuals.

Functional evidence reveals that EWSR1 and TAF15 have similar in vitro and in vivo properties as TDP-43 and FUS, can confer neurodegeneration in Drosophila, and we show that disease-associated variants affect localization of the respective proteins in motor neurons, a disease relevant cell type. The additional genes identified in the yeast functional screen, coupled with prion domain prediction analysis, now provide a powerful resource to facilitate ALS disease gene discovery which in turn can lead to the development of therapeutics that have efficacy for the treatment of this deadly disease.

DEFINITIONS

“Amyotrophic lateral sclerosis (ALS)” is a progressive neurodegenerative disease that affects nerve cells in the brain and the spinal cord. Motor neurons reach from the brain to the spinal cord and from the spinal cord to the muscles throughout the body. The progressive degeneration of the motor neurons in ALS eventually leads to their death. When the motor neurons die, the ability of the brain to initiate and control muscle movement is lost. With voluntary muscle action progressively affected, patients in the later stages of the disease may become totally paralyzed.

A “proteinopathy” is a disease which is characterized by accumulation of toxic insoluble protein aggregates in cells. Exemplary disorders, include, without limitation, ALS, FTD, FTLD-U, Alzheimer's disease, Huntington's disease, Parkinson's disease, and other motor neuron diseases.

Ewing sarcoma breakpoint region 1 (EWSR1) encodes a multifunctional protein that is involved in various cellular processes, including gene expression, cell signaling, and RNA processing and transport. The protein includes an N-terminal transcriptional activation domain and a C-terminal RNA-binding domain. Chromosomal translocations between this gene and various genes encoding transcription factors result in the production of chimeric proteins that are involved in tumorigenesis. Mutations in this gene, specifically a t(11;22)(q24;q12) translocation, are known to cause Ewing sarcoma as well as neuroectodermal and various other tumors. Alternative splicing of this gene results in multiple transcript variants.

TAF15 (RNA polymerase II, TATA box binding protein (TBP)-associated factor) is a 68 kDa single strand DNA/RNA binding protein and forms part of the TFIID and RNA polymerase II complex of proteins which assemble on the promoter to form a pre-initiation complex (PIC); TFIID is composed of a TATA-box-binding protein (TBP) and a number of TBP-associated factors (TAFIIS). TAF15 shows homology with EWSR1 and FUS.

When the terms “prevent,” “preventing,” or “prevention” are used herein in connection with a given treatment for ALS, they mean that the treated subject either does not develop a clinically observable level ALS at all, or the condition develops more slowly and/or to a lesser degree in the subject than it would have absent the treatment. These terms are not limited solely to a situation in which the subject experiences no aspect ALS whatsoever. For example, a treatment will be said to have “prevented” ALS if it is given to a subject at risk of developing a ALS and results in the subject's experiencing fewer and/or milder symptoms of the proteinopathy than otherwise expected. A treatment can “prevent” ALS when the subject displays only mild overt symptoms of ALS. “Prevention” does not imply that there must have been no symptoms of ALS in any cell of a subject.

The phrase “consisting essentially of” when referring to a particular nucleotide or amino acid means a sequence having the properties of a given SEQ ID NO. For example, when used in reference to an amino acid sequence, the phrase includes the sequence per se and molecular modifications that would not affect the functional and novel characteristics of the sequence.

With regard to nucleic acids used in the invention, the term “isolated nucleic acid” is sometimes employed. This term, when applied to DNA, refers to a DNA molecule that is separated from sequences with which it is immediately contiguous (in the 5′ and 3′ directions) in the naturally occurring genome of the organism from which it was derived. For example, the “isolated nucleic acid” may comprise a DNA molecule inserted into a vector, such as a plasmid or virus vector, or integrated into the genomic DNA of a prokaryote or eukaryote. An “isolated nucleic acid molecule” may also comprise a cDNA molecule. An isolated nucleic acid molecule inserted into a vector is also sometimes referred to herein as a recombinant nucleic acid molecule.

With respect to RNA molecules, the term “isolated nucleic acid” primarily refers to an RNA molecule encoded by an isolated DNA molecule as defined above. Alternatively, the term may refer to an RNA molecule that has been sufficiently separated from RNA molecules with which it would be associated in its natural state (i.e., in cells or tissues), such that it exists in a “substantially pure” form.

By the use of the term “enriched” in reference to nucleic acid it is meant that the specific DNA or RNA sequence constitutes a significantly higher fraction (2-5 fold) of the total DNA or RNA present in the cells or solution of interest than in normal cells or in the cells from which the sequence was taken. This could be caused by a person by preferential reduction in the amount of other DNA or RNA present, or by a preferential increase in the amount of the specific DNA or RNA sequence, or by a combination of the two. However, it should be noted that “enriched” does not imply that there are no other DNA or RNA sequences present, just that the relative amount of the sequence of interest has been significantly increased.

The term “vector” relates to a single or double stranded circular nucleic acid molecule that can be infected, transfected or transformed into cells and replicate independently or within the host cell genome. A circular double stranded nucleic acid molecule can be cut and thereby linearized upon treatment with restriction enzymes. An assortment of vectors, restriction enzymes, and the knowledge of the nucleotide sequences that are targeted by restriction enzymes are readily available to those skilled in the art, and include any replicon, such as a plasmid, cosmid, bacmid, phage or virus, to which another genetic sequence or element (either DNA or RNA) may be attached so as to bring about the replication of the attached sequence or element. A nucleic acid molecule of the invention can be inserted into a vector by cutting the vector with restriction enzymes and ligating the two pieces together.

Many techniques are available to those skilled in the art to facilitate transformation, transfection, or transduction of the expression construct into a prokaryotic or eukaryotic organism. The terms “transformation”, “transfection”, and “transduction” refer to methods of inserting a nucleic acid and/or expression construct into a cell or host organism. These methods involve a variety of techniques, such as treating the cells with high concentrations of salt, an electric field, or detergent, to render the host cell outer membrane or wall permeable to nucleic acid molecules of interest, microinjection, PEG-fusion, and the like.

The term “promoter element” describes a nucleotide sequence that is incorporated into a vector that, once inside an appropriate cell, can facilitate transcription factor and/or polymerase binding and subsequent transcription of portions of the vector DNA into mRNA. In one embodiment, the promoter element of the present invention precedes the 5′ end of the TDP-43 or genetic modifier encoding nucleic acid molecule such that the latter is transcribed into mRNA. Host cell machinery then translates mRNA into a polypeptide. As mentioned hereinbelow, a variety of transgenic organisms are contemplated for use in the screening assays of the invention.

Those skilled in the art will recognize that a nucleic acid vector can contain nucleic acid elements other than the promoter element and the genetic modulator encoding nucleic acid molecule. These other nucleic acid elements include, but are not limited to, origins of replication, ribosomal binding sites, nucleic acid sequences encoding drug resistance enzymes or amino acid metabolic enzymes, and nucleic acid sequences encoding secretion signals, localization signals, or signals useful for polypeptide purification.

A “replicon” is any genetic element, for example, a plasmid, cosmid, bacmid, plastid, phage or virus, that is capable of replication largely under its own control. A replicon may be either RNA or DNA and may be single or double stranded.

An “expression operon” refers to a nucleic acid segment that may possess transcriptional and translational control sequences, such as promoters, enhancers, translational start signals (e.g., ATG or AUG codons), polyadenylation signals, terminators, and the like, and which facilitate the expression of a polypeptide coding sequence in a host cell or organism.

As used herein, the terms “reporter,” “reporter system”, “reporter gene,” or “reporter gene product” shall mean an operative genetic system in which a nucleic acid comprises a gene that encodes a product that when expressed produces a reporter signal that is a readily measurable, e.g., by biological assay, immunoassay, radio immunoassay, or by colorimetric, fluorogenic, chemiluminescent or other methods. The nucleic acid may be either RNA or DNA, linear or circular, single or double stranded, antisense or sense polarity, and is operatively linked to the necessary control elements for the expression of the reporter gene product. The required control elements will vary according to the nature of the reporter system and whether the reporter gene is in the form of DNA or RNA, but may include, but not be limited to, such elements as promoters, enhancers, translational control sequences, poly A addition signals, transcriptional termination signals and the like.

The introduced nucleic acid may or may not be integrated (covalently linked) into nucleic acid of the recipient cell or organism. In bacterial, yeast, zebrafish, worm, insect and mammalian cells, for example, the introduced nucleic acid may be maintained as an episomal element or independent replicon such as a plasmid. Alternatively, the introduced nucleic acid may become integrated into the nucleic acid of the recipient cell or organism and be stably maintained in that cell or organism and further passed on or inherited to progeny cells or organisms of the recipient cell or organism. Finally, the introduced nucleic acid may exist in the recipient cell or host organism only transiently.

The term “selectable marker gene” refers to a gene that when expressed confers a selectable phenotype, such as antibiotic resistance, on a transformed cell.

The term “operably linked” means that the regulatory sequences necessary for expression of the coding sequence are placed in the DNA molecule in the appropriate positions relative to the coding sequence so as to effect expression of the coding sequence. This same definition is sometimes applied to the arrangement of transcription units and other transcription control elements (e.g. enhancers) in an expression vector.

The terms “recombinant organism” or “transgenic organism” refer to organisms which have a new combination of genes or nucleic acid molecules. A new combination of genes or nucleic acid molecules can be introduced into an organism using a wide array of nucleic acid manipulation techniques available to those skilled in the art. The term “organism” relates to any living being comprised of a least one cell. An organism can be as simple as one eukaryotic cell or as complex as a mammal. Therefore, the phrase “a recombinant organism” encompasses a recombinant cell, as well as eukaryotic and prokaryotic organism.

The term “isolated protein” or “isolated and purified protein” is sometimes used herein. This term refers primarily to a protein produced by expression of an isolated nucleic acid molecule of the invention. Alternatively, this term may refer to a protein that has been sufficiently separated from other proteins with which it would naturally be associated, so as to exist in “substantially pure” form. “Isolated” is not meant to exclude artificial or synthetic mixtures with other compounds or materials, or the presence of impurities that do not interfere with the fundamental activity, and that may be present, for example, due to incomplete purification, addition of stabilizers, or compounding into, for example, immunogenic preparations or pharmaceutically acceptable preparations.

Methods of Using Nucleic Acids Encoding Mutated RNA Binding Proteins in Assays for Diagnosing an Increased Risk of ALS

The identification of mutations in EWSR1 and TAF15 encoding nucleic acids and their association with ALS facilitates the development of a diagnostic assay for identifying patients having an increased risk of developing ALS. Mutation containing EWSR1 and TAF15 nucleic acids, including those described in Example I may be used for a variety of purposes in accordance with the present invention. DNA, RNA, or fragments of these nucleic acids may be used as probes to detect the presence of and/or expression of the same in patient samples. Such assays include but are not limited to: (1) in situ hybridization; (2) Southern hybridization (3) northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR).

Assays for detecting mutation containing EWSR1 and TAF15 nucleic acids may be conducted on any type of biological sample, including but not limited to body fluids (including blood, urine, serum, gastric lavage), any type of cell (such as brain cells, white blood cells, mononuclear cells) or body tissue.

In most embodiments for screening for the presence of nucleic acids encoding mutated EWSR1 and TAF15, nucleic acid in the sample will initially be amplified, e.g. using PCR, to increase the amount of the templates as compared to other sequences present in the sample. This allows the target sequences to be detected with a high degree of sensitivity if they are present in the sample. This initial step may be avoided by using highly sensitive array techniques that are becoming increasingly important in the art. Alternatively, new detection technologies can overcome this limitation and enable analysis of small samples containing as little as 1 μg of total RNA. Using Resonance Light Scattering (RLS) technology, as opposed to traditional fluorescence techniques, multiple reads can detect low quantities of mRNAs using biotin labeled hybridized targets and anti-biotin antibodies. Another alternative to PCR amplification involves planar wave guide technology (PWG) to increase signal-to-noise ratios and reduce background interference. Reagents for performing both techniques are commercially available from Qiagen Inc. (USA). Also encompassed by the present invention are methods for high throughput sequencing DNA isolated from patients. Such methods are well known to those of skill in the art.

Kits and Articles of Manufacture

Any of the aforementioned products can be incorporated into a kit which can contain nucleic acids encoding mutation containing EWSR1 and TAF15 molecules or other such markers immobilized on a Gene Chip. PCR primers and other suitable reagents can be designed using the following GenBank Accession Nos. EWSR1 mRNA: NM—013986.3 EWSR1 protein: NP— 053733.2; TAF15 mRNA: NM— 139215.1 and TAF15 proteinNP—631961.1—for sequence information. One embodiment of the kit comprises primers and reagents suitable for performance of PCR. Other reagents can include oligonucleotides, polypeptides with and without the mutations described above for use as controls, an antibody, a label, marker, or reporter, a pharmaceutically acceptable carrier, instructions for use, a container, a vessel for administration, an assay substrate, or any combination thereof.

Screening Assays for Identifying Agents which Modulate Cellular Toxicity and Aberrant Protein Aggregation Having Efficacy for the Treatment of ALS

The methods described herein include methods (also referred to herein as “screening assays”) for identifying compounds that modulate (i.e., increase or decrease) complex formation mediated by the RNA binding proteins identified herein (e.g., Table I, particularly ESWR1 and TAF15). Such compounds include, e.g., polypeptides, peptides, antibodies, peptidomimetics, peptoids, small inorganic molecules, small non-nucleic acid organic molecules, nucleic acids (e.g., anti-sense nucleic acids, siRNA, oligonucleotides, synthetic oligonucleotides), carbohydrates, or other agents that bind to the target proteins and have a stimulatory or inhibitory effect thereon. Compounds thus identified can be used to modulate the expression or activity of these proteins in a therapeutic protocol.

In general, screening assays involve assaying the effect of a test agent on expression or activity of a target nucleic acid or target protein in a test sample (i.e., a sample containing the target nucleic acid or target protein). Expression or activity in the presence of the test compound or agent can be compared to expression or activity in a control sample (i.e., a sample containing the target protein that is incubated under the same conditions, but without the test compound). A change in the expression or activity of the target nucleic acid or target protein in the test sample compared to the control indicates that the test agent or compound modulates expression or activity of the target nucleic acid or target protein and is a candidate agent.

Compounds to be screened or identified using any of the methods described herein can include various chemical classes, though typically small organic molecules having a molecular weight in the range of 50 to 2,500 daltons. These compounds can comprise functional groups necessary for structural interaction with proteins (e.g., hydrogen bonding), and typically include at least an amine, carbonyl, hydroxyl, or carboxyl group, and preferably at least two of the functional chemical groups. These compounds often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures (e.g., purine core) substituted with one or more of the above functional groups.

Compounds can be identified from a number of potential sources, including: chemical libraries, natural product libraries, and combinatorial libraries comprised of random peptides, oligonucleotides, or organic molecules. Chemical libraries consist of diverse chemical structures, some of which are analogs of known compounds or analogs or compounds that have been identified as “hits” or “leads” in other drug discovery screens, while others are derived from natural products, and still others arise from non-directed synthetic organic chemistry. Natural product libraries re collections of microorganisms, animals, plants, or marine organisms which are used to create mixtures for screening by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms, or (2) extraction of plants or marine organisms. Natural product libraries include polypeptides, non-ribosomal peptides, and variants (non-naturally occurring) thereof. For a review, see Science 282:63-68 (1998). Combinatorial libraries are composed or large numbers of peptides, oligonucleotides, or organic compounds as a mixture. These libraries are relatively easy to prepare by traditional automated synthesis methods, PCR, cloning, or proprietary synthetic methods. Of particular interest are non-peptide combinatorial libraries. Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries. For a review of combinatorial chemistry and libraries created therefrom, see Myers, Curr. Opin. Biotechnol. 8:701-707 (1997). Identification of test compounds through the use of the various libraries herein permits subsequent modification of the test compound “hit” or “lead” to optimize the capacity of the “hit” or “lead” to prevent or suppress aberrant TDP-43-RNA binding protein complex formation.

In one embodiment, assays are provided for screening candidate or test molecules that are substrates of a target protein or a biologically active portion thereof in a cell. In another embodiment, the assays are for screening candidate or test compounds that disrupt complex formation between EWSR1 TAF15 and other proteins.

In one embodiment, a cell-based assay is employed in which a cell, such as the yeast cells described in Example I, is contacted with a test compound. The ability of the test compound to modulate complex formation between EWSR1 and/or TAF15 and TDP-43 and resulting cellular toxicity is then determined. Other cells of mammalian origin, e.g., rat, mouse, or human are also suitable for this purpose.

The ability of the test compound to bind to a target protein or modulate target protein binding to a compound, e.g., a target protein substrate, can also be evaluated. This can be accomplished, for example, by coupling the compound, e.g., the substrate, with a radioisotope or enzymatic label such that binding of the compound, e.g., the substrate, to the target protein can be determined by detecting the labeled compound, e.g., substrate, in a complex. Alternatively, the target protein can be coupled with a radioisotope or enzymatic label to monitor the ability of a test compound to modulate target protein binding to a target protein substrate in a complex. For example, compounds (e.g., target protein substrates) can be labeled with 1251 35S, 14C, or 3H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting. Alternatively, compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.

The ability of a compound to interact with target protein with or without the labeling of any of the interactants can be evaluated. For example, a microphysiometer can be used to detect the interaction of a compound with a target protein without the labeling of either the compound or the target protein (McConnell et al., Science 257:1906-1912, 1992). As used herein, a “microphysiometer” (e.g., Cytosensor™) is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS). Changes in this acidification rate can be used as an indicator of the interaction between a compound and a target protein.

In yet another embodiment, a cell-free assay is provided in which a target protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the target protein or biologically active portion thereof is evaluated. In general, biologically active portions of target proteins to be used in assays described herein include fragments that participate in interactions with other molecules, e.g., fragments with high surface probability scores.

Cell-free assays involve preparing a reaction mixture of the target proteins and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex that can be removed and/or detected. The ability of a target protein to bind to a target molecule can be determined using real-time Biomolecular Interaction Analysis (BIA) (e.g., Sjolander et al., Anal. Chem., 63:2338-2345, 1991, and Szabo et al., Cuff. Opin. Struct. Biol., 5:699-705, 1995). “Surface plasmon resonance” or “BIA” detects biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore). Changes in the mass at the binding surface (indicative of a binding event) result in alterations of the refractive index of light near the surface (the optical phenomenon of surface plasmon resonance (SPR)), resulting in a detectable signal which can be used as an indication of real-time reactions between biological molecules.

In several of these assays, the target proteins or the test substance is anchored onto a solid phase. The target protein/test compound complexes anchored on the solid phase can be detected at the end of the reaction. Generally, the target proteins are anchored onto a solid surface, and the test compound (which is not anchored) can be labeled, either directly or indirectly, with detectable labels discussed herein. It may be desirable to immobilize either the target protein, an anti-target protein antibody, or its target molecule to facilitate separation of complexed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a test compound to a target protein, or interaction of a target protein with a target molecule in the presence and absence of a test compound, can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microliter plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein can be provided that adds a domain that allows one or both of the proteins to be bound to a matrix. For example, glutathione-S-transferase/target protein fusion proteins or glutathione-S-transferase/target fusion proteins can be adsorbed onto glutathione Sepharose™ beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized microtiter plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein. The mixture is then incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, and the complex determined either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of target protein binding or activity determined using standard techniques.

Other techniques for immobilizing a target protein on matrices include using conjugation of biotin and streptavidin. Biotinylated target protein can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, IU.), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).

To conduct the assay, the non-immobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that any complexes formed will remain immobilized on the solid surface. The complexes anchored on the solid surface can be detected in a number of ways. Where the previously non-immobilized component is pre-labeled, the presence of a label immobilized on the surface indicates that complexes were formed. Where the previously non-immobilized component is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the immobilized component (the antibody, in turn, can be directly labeled or indirectly labeled with, e.g., a labeled anti-Ig antibody).

In some cases, the assay is performed utilizing antibodies reactive with target protein, but which do not interfere with binding of the target protein to its target molecule. Such antibodies can be derivatized to the wells of the plate, and unbound target protein trapped in the wells by antibody conjugation. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the target protein or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the target protein.

Alternatively, cell-free assays can be conducted in a liquid phase. In such an assay, the reaction products are separated from unreacted components, by any of a number of standard techniques, including but not limited to: differential centrifugation (see, for example, Rivas and Minton, Trends Biochem. Sci., 18:284-7, 1993); chromatography (gel filtration chromatography, ion-exchange chromatography); electrophoresis (e.g., Ausubel et al., eds. Current Protocols in Molecular Biology 1999, J. Wiley: New York.); and immunoprecipitation (see, for example, Ausubel et al., eds., 1999, Current Protocols in Molecular Biology, J. Wiley: New York). Such resins and chromatographic techniques are known to one skilled in the art (e.g., Heegaard, J. MoI. Recognit, 11: 141-148, 1998; Hage et al., J. Chromatogr. B. Biomed. Sci. Appl, 699:499-525, 1997). Further, fluorescence energy transfer may also be conveniently utilized, as described herein, to detect binding without further purification of the complex from solution.

The assay can include contacting the target protein or a biologically active portion thereof with a known compound that binds to the target protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the target protein, wherein determining the ability of the test compound to interact with the target protein includes determining the ability of the test compound to preferentially bind to the target protein or biologically active portion thereof, or to modulate the activity of a target molecule, as compared to the known compound.

A target protein can, in vivo, interact with one or more cellular or extracellular macromolecules, such as proteins. For the purposes of this discussion, such cellular and extracellular macromolecules are referred to herein as “binding partners.” Compounds that disrupt such interactions are useful for regulating the activity thereof. Such compounds can include, but are not limited, to molecules such as antibodies, peptides, and small molecules. In general, target proteins for use in identifying agents that disrupt interactions are the target proteins identified herein. To identify compounds that interfere with the interaction between the target protein and its binding partner(s), a reaction mixture containing the target protein and the binding partner is prepared, under conditions and for a time sufficient, to allow the two products to form a complex. To test an inhibitory agent, the reaction mixture is provided in the presence (test sample) and absence (control sample) of the test compound. The test compound can be initially included in the reaction mixture, or can be added at a time subsequent to the addition of the target gene and its cellular or extracellular binding partner. Control reaction mixtures are incubated without the test compound or with a control compound. The formation of complexes between the target protein and the cellular or extracellular binding partner is then detected. The formation of a complex in the control reaction, and less formation of complex in the reaction mixture containing the test compound, indicates that the compound interferes with the interaction of the target protein and the interactive binding partner. Such compounds are candidate compounds for inhibiting the expression or activity or a target protein. Additionally, complex formation within reaction mixtures containing the test compound and normal target protein can also be compared to complex formation within reaction mixtures containing the test compound and mutant target gene product. This comparison can be important in those cases wherein it is desirable to identify compounds that disrupt interactions of mutant but not normal target protein.

Binding assays can be carried out in a liquid phase or in heterogenous formats. In one type of heterogeneous assay system, either the target protein or the interactive cellular or extracellular binding partner, is anchored onto a solid surface (e.g., a microtiter plate), while the non-anchored species is labeled, either directly or indirectly. The anchored species can be immobilized by non-covalent or covalent attachments. Alternatively, an immobilized antibody specific for the species to be anchored can be used to anchor the species to the solid surface.

To conduct the assay, the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed (e.g., by washing) and any complexes formed will remain immobilized on the solid surface. Where the non-immobilized species is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the non-immobilized species is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the initially non-immobilized species (the antibody, in turn, can be directly labeled or indirectly labeled with, e.g., a labeled anti-Ig antibody). Depending upon the order of addition of reaction components, test compounds that inhibit complex formation or that disrupt preformed complexes can be detected.

In another embodiment, modulators of target expression (RNA or protein) are identified. For example, a cell or cell-free mixture is contacted with a test compound and the expression of target mRNA (e.g., EWSR1 encoding mRNA) or protein evaluated relative to the level of expression of target mRNA or protein in the absence of the test compound. When expression of target mRNA or protein is greater in the presence of the test compound than in its absence, the test compound is identified as a stimulator (candidate compound) of target mRNA or protein expression. Alternatively, when expression of target mRNA or protein is less (statistically significantly less) in the presence of the test compound than in its absence, the test compound is identified as an inhibitor (candidate compound) of target mRNA or protein expression. The level of target mRNA or protein expression can be determined by methods described herein and methods known in the art such as Northern blot or Western blot for detecting target mRNA or protein.

In another aspect, the methods described herein pertain to a combination of two or more of the assays described herein. For example, a modulating agent can be identified using a cell-based or a cell-free assay, and the ability of the agent to modulate the activity of a target protein can be confirmed in vivo, e.g., in an animal such as an animal model for ALS. This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent (compound) identified as described herein (e.g., a target protein modulating agent, an anti sense nucleic acid molecule, an siRNA, a target protein-specific antibody, or a target protein-binding partner) in an appropriate animal model to determine the efficacy, toxicity, side effects, or mechanism of action, of treatment with such an agent. Furthermore, novel agents identified by the above-described screening assays can be used for treatments as described herein.

Compounds that modulate target protein expression or activity (target protein modulators) can be tested for their ability to affect metabolic effects associated with the target protein, e.g., with decreased expression or activity of target protein using methods known in the art and methods described herein. For example, the ability of a compound to modulate EWSR1 and/or TAF15/TDP-43 complex formation and associated toxicity can be tested using an in vitro or in vivo model for ALS.

The compounds identified above can be synthesized by any chemical or biological method. The compounds identified above can also be pure, or may be in a heterologous composition (e.g., a pharmaceutical composition), and can be prepared in an assay-, physiologic, or pharmaceutically-acceptable diluent or carrier (see below).

Pharmaceutical Compositions

A compound that is found to prevent or suppress aberrant TDP-43-EWSR1 and/or TAF15 complex formation and cytotoxicity in a cell can be formulated as a pharmaceutical composition, e.g., for administration to a subject to treat ALS.

A pharmaceutical composition typically includes a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. The composition can include a pharmaceutically acceptable salt, e.g., an acid addition salt or a base addition salt (see e.g., Berge et al., J. Pharm. Sci. 66:1-19, 1977).

The compound can be formulated according to standard methods. Pharmaceutical formulation is a well-established art, and is further described, e.g., in Gennaro (ed.), Remington: The Science and Practice of Pharmacy, 20th ed., Lippincott, Williams & Wilkins (2000) (ISBN: 0683306472); Ansel et al., Pharmaceutical Dosage Forms and Drug Delivery Systems, 7th Ed., Lippincott Williams & Wilkins Publishers (1999) (ISBN: 0683305727); and Kibbe (ed.), Handbook of Pharmaceutical Excipients American Pharmaceutical Association, 3rd ed. (2000) (ISBN: 091733096X). In one embodiment, a compound that prevents or suppresses aberrant TDP-43-RNA binding protein complex formation and cytotoxicity in a cell can be formulated with excipient materials, such as sodium chloride, sodium dibasic phosphate heptahydrate, sodium monobasic phosphate, and a stabilizer. It can be provided, for example, in a buffered solution at a suitable concentration and can be stored at 2-8° C. The pharmaceutical compositions may be in a variety of forms. These include, for example, liquid, semi-solid and solid dosage forms, such as liquid solutions {e.g., injectable and infusible solutions), dispersions or suspensions, tablets, capsules, pills, powders, liposomes and suppositories. The preferred form can depend on the intended mode of administration and therapeutic application. Typically compositions for the agents described herein are in the form of injectable or infusible solutions.

Such compositions can be administered by a parenteral mode (e.g., intravenous, subcutaneous, intraperitoneal, or intramuscular injection). The phrases “parenteral administration” and “administered parenterally” as used herein mean modes of administration other than enteral and topical administration, usually by injection, and include, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural, intracerebral, intracranial, intracarotid and intrasternal injection and infusion.

The composition can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable for stable storage at high concentration. Sterile injectable solutions can be prepared by incorporating an agent described herein in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating a compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying that yields a powder of a compound plus any additional desired ingredient from a previously sterile-filtered solution thereof. The proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prolonged absorption of injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, monostearate salts and gelatin.

In certain embodiments, the compound can be prepared with a carrier that will protect the compound against rapid release, such as a controlled release formulation, including implants, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known. See, e.g., Sustained and Controlled Release Drug Delivery Systems, J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978. A compound identified as one that prevents or suppresses aberrant TDP-43-RNA binding protein complex formation and cytotoxicity in a cell can be modified, e.g., with a moiety that improves its stabilization and/or retention in circulation, e.g., in blood, serum, or other tissues, e.g., by at least 1.5, 2, 5, 10, or 50 fold. The modified compound can be evaluated to assess whether it can reach treatment sites of interest.

For example, the compound can be associated with a polymer, e.g., a substantially non-antigenic polymer, such as a polyalkylene oxide or a polyethylene oxide. Suitable polymers will vary substantially by weight. Polymers having molecular number average weights ranging from about 200 to about 35,000 Daltons (or about 1,000 to about 15,000, and 2,000 to about 12,500) can be used. For example, a compound can be conjugated to a water soluble polymer, e.g., a hydrophilic polyvinyl polymer, e.g., polyvinylalcohol or polyvinylpyrrolidone. A non-limiting list of such polymers include polyalkylene oxide homopolymers such as polyethylene glycol (PEG) or polypropylene glycols, polyoxyethylenated polyols, copolymers thereof and block copolymers thereof, provided that the water solubility of the block copolymers is maintained.

Additional useful polymers include polyoxyalkylenes such as polyoxyethylene, polyoxypropylene, and block copolymers of polyoxyethylene and polyoxypropylene (Pluronics); polymethacrylates; carbomers; and branched or unbranched polysaccharides. When the compound is used in combination with a second agent (e.g., any additional therapies for a proteinopathy such as a decongestant or Rilutek®), the two agents can be formulated separately or together. For example, the respective pharmaceutical compositions can be mixed, e.g., just prior to administration, and administered together or can be administered separately, e.g., at the same or different times as elaborated below.

The following materials and methods are provided to facilitate the practice of the present invention.

Plasmids, Yeast Strains and Media

The yeast strain used in the human RRM screen and follow-up analyses was BY4741 [genotype, Mata his3Δ1 leu2Δ0 met15Δ0 ura3Δ0]. Strains were manipulated and media prepared using standard techniques (Guthrie and Fink, 2002). EWSR1 and TAF15 expression constructs were generated by Gateway® cloning (Invitrogen), starting with entry clones in pDONR221 and shuttled from entry clones into a modified PGW vector (for motor neuron transfection experiments), created by incorporating the Gateway B cassette into the Sma1 site of the PGW vector using the Gateway conversion kit (Invitrogen). ALS patient mutations in EWSR1 and TAF15 were introduced by site-directed mutagenesis using the QuickChange Site Directed Mutagenesis kit (Stratagene).

Human RNA Binding Protein Plasmid Library

We constructed a library of yeast expression plasmids containing 133 unique human RRM-containing open reading frames (ORFs). The ORFs were obtained from the human ORFeome collection (Open Biosystems) as Gateway® entry clones in plasmid pDONR223. We selected 133 unique clones contained within the library predicted to encode RRM-domain proteins (PFAM ID PF00076). ORFs from the entry clones were shuttled into the 2-micron galactose-inducible yeast expression plasmid pAG426Gal-ccdB-EYFP by Gateway® LR cloning reaction (Alberti et al., 2007) to generate C-terminally tagged RRM-protein-YFP fusions. Restriction digest and DNA sequencing were used to confirm the integrity of each expression construct.

Yeast Transformation and Spotting Assays

The PEG/lithium acetate method was used to transform yeast with each plasmid DNA from the RRM ORF library (Ito et al., 1983). For spotting assays, yeast cells were grown overnight at 30° C. in liquid media containing raffinose (SRaf/-Ura) until log or mid-log phase. Cultures were then normalized for OD600, serially diluted and spotted onto synthetic solid media containing glucose or galactose lacking uracil, and were grown at 30° C. for 2-3 d.

Microscopy

For fluorescence microscopy experiments, single colony isolates of the yeast strains were grown to mid-log phase in SRaf/-Ura media at 30° C. Cultures were spun down and resuspended in the same volume of SGal/-Ura to induce expression of the TDP-43 constructs. Cultures were induced with galactose for 4-6 h and processed for microscopy. Images were obtained using an Olympus IX70 inverted microscope and a Photometrics CoolSnap HQ 12-bit CCD camera.

Prion-Prediction Algorithm

Proteins were parsed into prion-like and non-prion-like regions using a Hidden Markov Model developed to identify regions that have the unusual amino acid composition characteristic of yeast prions (Alberti et al., 2009; Cushman et al., 2010). Prion-like regions of length ≧60 were given a prion-domain score, defined as the maximum log-likelihood for the prion-like state vs. the non-prion-like state over any 60 consecutive amino acids within the regions (Alberti et al., 2009). Among the 21,873 human genes analyzed (Ensembl GrCh37.59), 246 had prion-like regions of length ≧60, and were ranked by prion-domain score. For genes with multiple transcripts, the longest one was used, with the one with lowest Ensembl Transcript ID used in case of ties.

Sequencing EWSR1 and TAF15 Genes in ALS Patients and Controls

Genomic DNA from non-Latino Caucasian individuals with sporadic ALS (N=552) was obtained from the Coriell Institute for Medical Research (Coriell, Camden, N.J.) distributed in 96-well plates NDPT025, NDPT026, NDPT030, NDPT100, NDPT103, and NDPT106. Additional genomic DNA samples from patients verified to meet El Escorial criteria for definite or probable ALS by a neurologist (N=258) or with neuropathologic findings consistent with ALS (N=88) were obtained from the University of Pennsylvania (PENN) Center for Neurodegenerative Disease Research (CNDR). All subjects were collected with PENN Institutional Review Board approval. The racial background of the PENN subjects was 90% non-Latino Caucasian, 5% Black, and 5% mixed or other. The PENN subjects were 57% male and had an average age of onset of 57 years (8-89) and an average duration of disease of 4 years (range 1-46). A family history of ALS (FALS) was present in 29 of 250 patients (11.6%) for which family history was available. Mutations in SOD1 and FUS/TLS were excluded in all the familial ALS cases and TARDBP mutations excluded in all PENN cases. All cases with potentially pathogenic variants in EWSR1 and TAF15 were also sequenced for TARDBP, FUS, and SOD1.

679 neurologically normal control samples from Coriell were distributed in 96-well plates NDPT084, NDPT090, NDPT093, NDPT094, NDPT095, NDPT096, NDPT098, and NDPT099. An additional 90 neurologically normal control samples were obtained from the Children's Hospital of Philadelphia (CHOP). 179 DNA samples from cognitively normal individuals >60 years of age were obtained from the National Cell Repository for Alzheimer's Disease (NCRAD, Indianapolis, Ind.).

We sequenced exons 15-18 of EWSR1 and exons 13-16 of TAF15, which encode the C-terminal domains of EWSR1 and TAF15, respectively. EWSR1 was sequenced in 817 ALS cases (N=514 Coriell and N=303 PENN) and 1,082 controls. TAF15 was sequenced in 610 ALS cases (N=406 Coriell and N=204 PENN) and 982 controls. Bidirectional sequencing was performed by separately amplifying EWSR1 exons 15-16, 17, and 18 and TAF15 exons 13-15 and 16 from samples using the polymerase chain reaction (PCR). PCR primers and cycling conditions used for amplification and sequencing are available upon request. Amplicons were purified, processed and sequenced using Big-Dye® Terminator v3.1 sequencing (Applied Biosystems). All variants identified were confirmed by repeat sequencing. Sequence analysis was performed using Sequencher DNA Software.

SNP Genotyping

DNA samples from 4811 de-identified healthy control subject of European ancestry who were recruited from the Children's Hospital of Philadelphia (CHOP) Health Care Networks (parents of children cared for at CHOP) were screened for mutations in the EWSR and TAF15 genes, using a custom designed TaqMan SNP genotyping assay from Applied Biosystems. PCR and reporter primer sequences are available upon request.

A total of 10 ng of DNA was used as a template for the PCR reactions. Samples were run on the 7900HT analyzer from Applied Biosystems, after pooling three samples per run to expedite the screening process. Along with the pooled samples, each 384-well plate contained a positive and non-template control (NTC). Subsequent end-point allelic discrimination was performed, using SDSv2.4 software from Applied Biosystems. To ensure mutations were captured from the pooled approach, a test plate was run with mixtures of 1 heterozygous (het) positive and 1 homozygous (horn) negative sample; 1 het pos and 2 horn neg; and 1 het pos and 3 horn neg. The positive alleles were detected in all pools and a mixture of 3 unknowns was ultimately chosen for the study.

Genetic Analysis of EWSR1 and TAF15 Genes in ALS Replication Series from Mayo Clinic

The Mayo Clinic ALS replication series consisted of 105 unrelated ALS patients (56 males, 49 females) from a consecutive clinical case series seen at Mayo Clinic Florida by the ALS Center in the period 2008-2010 and 20 pathologically confirmed ALS patients selected from the Mayo Clinic Florida Brain Bank (7 males, 13 females). All patients agreed to be in the study and biological samples were obtained after informed consent. Mutations in SOD1, FUS/TLS or TARDBP were previously excluded in all patients included in this patient series (add reference to DeJesus-Hernandez et al., Human Mutation, 2010). The average age of onset in our clinical patient population was 57.2±10.6 years (range 17-78 years), while the average age at death in pathologically confirmed samples was 68.9±12.1 years (range 46-83 years). 16.0% of patients showed a positive family history of ALS defined as having at least one affected relative within 3 generations. DNA samples of 812 healthy control individuals (range 51-99 years) were also ascertained at the Department of Neurology at Mayo Clinic Florida and 92 autopsy samples of neurologically normal individuals were selected from the Mayo Clinic Florida Brain Bank. The racial background of all ALS patients and controls was non-Latino Caucasian.

For all 125 ALS patient included in this replication series PCR amplification was performed for exons 17-18 of EWSR1 and exons 15-16 of TAF15, using primers designed to flanking intronic sequences using Qiagen products (Qiagen, Valencia, Calif., USA) (PCR conditions and primer sequences available on request). PCR products were purified using the Ampure system (Agencourt Bioscience Corporation, Beverly, Mass., USA) and sequenced using Big dye terminator V.3.1 products (Applied Biosystems, Foster City, Calif., USA). Sequencing products were purified using the CleanSEQ method (Agencourt) and analyzed on an ABI 3730 DNA analyzer (Applied Biosystems). Sequence analysis was performed using Sequencher software (Gene Codes, Ann Arbor, Mich., USA). All variants identified were confirmed by repeat sequencing. The Gly473Glu variant in TAF15 was further genotyped in the 904 control individuals from Mayo Clinic using a custom designed TaqMan SNP genotyping assay (ABI).

EWSR1 and TAF15 Protein Purification

TDP-43 and FUS were purified as described (Johnson et al., 2009; Sun et al., 2010). EWSR1 and TAF15 were expressed and purified from E. coli as GST-tagged proteins. EWSR1 and TAF15 were cloned into GV13 to yield GST-TEV-EWSR1 or GST-TEV-TAF15, and overexpressed in E. coli BL21 Star (Invitrogen). Protein was purified over a glutathione-sepharose column (GE) according to manufacturer's instructions. GST-EWSR1 and GST-TAF15 were eluted from the glutathione sepharose with 50 mM Tris-HCl pH 7.4, 100 mM potassium acetate, 200 mM trehalose, 0.5 mM EDTA and 20 mM glutathione. After purification, proteins were concentrated to 10 μM or greater using Amicon Ultra-4 centrifugal filter units (10 kDa molecular weight cut-off; Millipore). Protein was then filtered through a 0.22 μm filter to remove any aggregated material. After filtration, the protein concentration was determined by Bradford assay (Bio-Rad) and the proteins were used immediately for aggregation reactions.

EWSR1 and TAF15 In Vitro Aggregation Assays

Filtered, purified GST-EWSR1 and GST-TAF15 proteins were used immediately for aggregation assays. Aggregation was initiated by the addition of TEV protease (Invitrogen) to EWSR1 or TAF15 (3 μM) in assembly buffer (AB): 50 mM TrisHCl pH 7.4, 100 mM potassium acetate, 200 mM trehalose, 0.5 mM EDTA and 20 mM glutathione. Aggregation reactions were incubated at 25° C. for 0-90 min with agitation at 700 rpm in an Eppendorf Thermomixer. No aggregation occurred unless TEV protease was added to separate GST from EWSR1 or TAF15. Turbidity was used to assess aggregation by measuring absorbance at 395 nm. For sedimentation analysis, reactions were centrifuged at 16,100 g for 20 min at 25° C. Supernatant and pellet fractions were then resolved by SDS-PAGE and stained with Coomassie Brilliant Blue, and the amount in either fraction determined by densitometry in comparison to known quantities of EWSR1 or TAF15. For electron microscopy (EM) of in vitro aggregation reactions, protein samples (20 μl of a 3 μM solution) were adsorbed onto glow-discharged 300-mesh Formvar/carboncoated copper grid (Electron Microscopy Sciences) and stained with 2% (w/v) aqueous uranyl acetate. Excess liquid was removed, and grids were allowed to air dry. Samples were viewed using a JEOL 1010 transmission electron microscope.

Drosophila Experiments

Transgenic flies expressing human EWSR1 and TAF15 were generated by standard techniques using the pUAST vector. TDP-43 transgenic flies are described in (Elden et al., 2010). To direct transgene expression to the eye, gmr-GAL4 driver was used. To direct expression to motor neurons, D42-GAL4 driver was used. Locomotor activity was assessed using a climbing assay as described in (Elden et al.).

EWSR1 and TAF15 Plasmids and Cell Culture

TAF15 and EWS wild type and mutants were amplified by PCR using the following primers: hTAF15 specific primers (Forward, hTAF15SpeIKozMFlagf 5′-CCC GGG ACT AGT CAC CAT GGA CTA CAA GGA CGA CGA TGA CAA AAT GTC GGA TTC TGG AAG T-3′ (SEQ ID NO: 1); Reverse, hTAF15MycNotIr 5′CAC GCG GCC GCC TAC AGA TCC TCT TTC TGA GAT GAG TTT TTG TTC GTA TGG TCG GTT GCG C-3′SEQ ID NO: 2), hEWS specific primers (Forward, hEWSKozMFlagf 5′-TCA CCA TGG ACT ACA AGG ACG ACG ATG ACA AAA TGG CGT CCA CGG ATT ACA G-3′(SEQ ID NO: 3); Reverse, hEWSMycNotIr 5′-CAC GCG GCC GCC TAC AGA TCC TCT TCT GAG ATG AGT TTT TGT TCG TAG GGC CGA TCT CTG-3′ SEQ ID NO: 4). PCR amplified fragments were cloned into the pEN-Tmcs entry vector using T4 DNA ligase (Promega) and recombined by LR-clonase (Invitrogen) into pSILK-Neo destination vector (Signaling-gateway) to obtain pSILK-TAF15/EWS wild type and mutants plasmids. Mouse embryonic stem cells (ES) were maintained in ES medium (DMEM, 15% FBS, 1× Penicillin/streptomycin, 1× Glutamax, 1× Non-essential amino acid, 1× Sodium Pyruvate, 0.1 mM beta-mercaptoethanol, 1000 u/ml LIF, 25 μM PD98059) on a gelatinized plate without feeder cells. For differentiation, the protocol of Wichterle, H. and colleagues was followed (Wichterle et al., 2009). Briefly, 1×106 ES cells were cultured with ADFNK medium (45% Advanced DMEM/F12, 45% Neurobasal medium, 10% knockout serum replacement, 1× Penicillin/streptomycin, 1× L-Glutamine, 0.1 mM beta-mercaptoethanol) for five days to form embryonic bodies (EBs)—small floating aggregates of ES cells. EBs were utilized for neurons culture on day 6 of differentiation. ES cells differentiated into neuron were dissociated into single cells and plated on a Poly-L-lysine/laminin coated 12-well chamber or Nunc 8-well chambers with ADFNB+GDNF medium (49% Advanced DMEM/F12, 49% Neurobasal medium, 2% B27 supplement, 1× Penicillin/streptomycin, 1× L-Glutamine, 5 ng/ml GDNF).

Lentivirus Production and Transduction

The pSLIK expression lentivector was transfected along with lentivirus packaging and pseudotyping plasmids into 293T cells using Lipofectamine 2000 reagent (Invitrogen) following manufacturer's instructions. 293T cells were cultured in DMEM (GIBCO Invitrogen) and 10% Fetal plex serum (Gemini). Plasmids were cotransfected by using 6 μg of pSLIK plasmid, 4.5 μg of the packaging plasmid psPAX2 (Addgene) and 3 μg of the vesicular stomatitis virus (VSV) G envelope plasmid pMD2 (Addgene) diluted in Opti-MEM (Gibco Invitrogen). The viral supernatant was collected 48 h after transfection, passed through 0.45 μm-pore size filters and concentrated by ultracentrifugation onto a 20% sucrose gradients using SW41 rotor (Beckman) at 20,000 rpm for 2 hrs at 4° C. Viral pellets were resuspended in ADFNB medium and stored in aliquots at −80° C. For transduction, cells were mixed with the virus at a low MOI to ensure <30% infection frequency such that the majority of transduced cells contained single viral integrants. Four micrograms of polybrene/ml (Sigma) was included and cells were plated on either a 12-well chamber or Nunc 8-well chambers (56815-1PAK; Fisher). To induce protein expression, 1 μg/ml Doxycycline (DOX; Milipore) was added to the cells 24 hrs after transduction and for five days.

Immunofluorescence Analysis

For immunostaining, neurons were washed 3× with 1× PBS, fixed for 30 min with 3.7% paraformaldehyde, permeabilized using 0.1% Triton X-100 for 10 min, blocked with 3% BSA in PBS for 15 min and incubated overnight at 4° C. with primary antibodies as follows: anti-TAF15 (1:3,000; Bethyl, A300-A308), anti-EWS (1:4,000; Santa cruz, sc-28327), anti-FLAG M2 (1:5,000; Sigma, F1804-1MG). Cells were washed 3× with 1× PBS and incubated with either Alexa-Fluor 555 goat anti-rabbit IgG (1:1,000; MolecularProbes, A21429) or Alexa-Fluor 555 goat anti-mouse IgG (1:1,000; MolecularProbes, A21424). Cells were mounted with prolong plus DAPI (Invitrogen) and were visualized with an Olympus BX-60 microscope. Images were recorded with a Spot Digital camera.

Cell Fractionation and Immunoblot Analysis

For Western blot analysis, 5×105 cells of neurons, transduced with pSLIK lentivectors expressing TAF15 or EWS wild type and mutants and induced with 1 μg/ml DOX for 5 days, were lysed using RIPA buffer (0.1% SDS, 0.5% Deoxycholate, 1% NP-40, 150 mM NaCl, 50 mM Tris-HCl pH 8.0) for 10 min on ice and centrifuged at 13,000 rpm for 10 min to obtain the soluble fractions. Pellets were lysed with Urea buffer (7M Urea, 2M Thiourea, 4% CHAPS, 30 mM Tris pH 8.5) and were sonicated to obtain the insoluble fractions. Cell lysates were separated by Nu-PAGE (4-12% gradient gels; Invitrogen), transferred to nitrocellulose membranes and analyzed by Western blotting with ECL plus detection reagents (GE Healthcare). Primary antibodies used were as follows: anti-FLAG M2 (1:10,000; Sigma), anti-GAPDH (1:20,000; Sigma). A secondary anti-mouse Ig HRP antibody was used at a dilution of 1:10,000. Membranes were developed using X-ray film (Kodak).

Mouse Primary Motor Neuron Transfection and Immunofluorescence

Primary neuron cultures were transfected after 5 days in vitro using Lipofectamine LTX with PLUS reagent (Invitrogen) according to the manufacturers protocol in media lacking antibiotics. Media was replaced 12 hours following transfection with media containing antibiotics. Cells were harvested for immunoflourescence 96 hours after transfection, briefly, cultures were washed in PBS and fixed in 4% paraformaldehyde 15 min, then washed in 1× PBS 4×. Cells were blocked for 1 h in blocking solution (2% Fetal Bovine Serum, 0.02% Triton X-100, 1× PBS), and then incubated 1 h in primary antibody at RT. Cells were then washed 3× in PBS, then incubated with secondary antibody 1 h RT. Cells were then washed with blocking solution and mounted in Vectashield mounting media with DAPI (Vector). Antibodies used were: α-EWSR1 mouse antibody (Santa Cruz), 1:1000; α-TAF15 rabbit antibody (Bethyl Laboratories), α-Doublecortin goat antibody (Santa Cruz) 1:500; Cy-3 conjugated α-mouse IgG (Jackson Immunoresearch), 1:250; and Cy-3 conjugated α-rabbit IgG (Jackson Immunoresearch), 1:250; and Cy-2 conjugated α-goat IgG (Jackson Immunoresearch), 1:250. Cells were visualized by light microscopy. Localization of endogenous, or transfected wild-type or mutant EWSR1 was quantified using blinded analysis of random fields of cells. The number of neurons with EWSR1 staining in processes was divided by the total number of neurons counted to yield the percent of neurons with EWSR1 in neuronal processes. More than 50 neurons were analyzed for each condition. Neurons were identified using morphology and doublecortin staining.

Immunohistochemistry

Formalin-fixed, paraffin-embedded human spinal cord sections were deparaffinized before pretreatment using heat antigen retrieval with Bull's Eye Decloaker (BioCare Medical). Endogenous peroxidase was then blocked with 3% hydrogen peroxide in PBS for 10 minutes. After washing with 0.1% PBST blocking was performed with 10% goat serum, 0.5% PBST for 30-60 minutes at 25° C. Sections were incubated with mouse anti-EWSR1 (1:125; Santa Cruz Biotechnology) or rabbit anti-TAF15 (1:250; Bethyl Laboratories) in 0.1% PBST overnight at 4° C. After washing with 0.1% PBST, sections were incubated with biotinylated goat anti-mouse or rabbit IgG (1:200; Vector Laboratories) for 1 hour at 25° C. After washing with 0.1% PBST, sections were then incubated with Vectastain ABC (Vector Laboratories) for 45 minutes. After washing with 0.1% PBST followed by 0.1M Tris (pH 7.5) and 0.3M NaCl. Peroxidase activity was then detected with DAB (Sigma). Detailed immunohistochemistry protocols are available on the world wide web at med.PENN.edu/mcrc/histology_core/.

Statistical Analysis

Two-tailed Fisher's exact tests were used to evaluate genetic association between EWSR1 and TAF15 sequence variants and ALS.

The following examples are provided to illustrate certain embodiments of the invention. They are not intended to limit the invention in any way.

Example 1 A Yeast Functional Screen Identifies New ALS Disease Genes

Here we report a simple yeast functional screen to identify human proteins with similar properties as TDP-43 and FUS, combined with genetic analysis in human ALS patients, for mutations in two genes from this screen, EWSR1 and TAF15. We show that EWSR1 and TAF15 have similar in vitro and in vivo properties as TDP-43 and FUS and the disease-associated variants affect localization in motor neurons. The identification of mutations in two additional RNA binding proteins underscores a key role for RNA metabolism defects in ALS and suggests that this class of aggregation-prone RNA binding proteins might contribute very broadly to the disease. Having established the effectiveness of this approach in predicting new ALS disease genes, the yeast functional screen promises to facilitate ALS disease gene discovery.

TDP-43 and FUS are both RNA recognition motif (RRM)-containing proteins (RRM proteins) (Lagier-Tourenne and Cleveland, 2009) and both form cytoplasmic inclusions and are toxic when expressed in yeast (FIG. 1a and (Johnson et al., 2008; Johnson et al., 2009)). Including FUS and TDP-43, there are least 213 RRM proteins (PFAM ID PF00076) present in the human proteome (Table 2). This raised the question of whether other human RRM proteins would show properties like TDP-43 and FUS (e.g. aggregation-prone and toxic in yeast), and, if so, could these properties predict that these genes are potential ALS disease genes? We therefore designed a simple yeast functional screen to identify such genes (FIG. 1b). Of the 213 human RRM proteins, we were able to obtain a gene clone for 132. We cloned these 132 different human RRM-containing open reading frames (ORFs) into yeast expression vectors as YFP fusion proteins, under the control of a galactose-inducible promoter, and individually transformed them into yeast cells. We have previously found that the addition of the YFP tag to TDP-43 and FUS does not affect the aggregation or toxicity properties ((Johnson et al., 2008; Johnson et al., 2009; Sun et al., 2010) and data not shown). Fluorescence microscopy was used to determine the localization of each protein (nuclear, cytoplasmic, diffuse, foci; FIG. 1c and Table 2) and spotting assays were used to assess toxicity (FIG. 1d and Table 2). Some proteins localized to the nucleus (39/132) whereas others were diffusely localized in the cytoplasm (27/132). Interestingly, several others formed multiple foci in the cytoplasm in a pattern strikingly similar to that of FUS and TDP-43 (52/132). Of the proteins that accumulated in the cytoplasm, 35 were also toxic, including FUS and TDP-43 (Table 1). Thus, 35 of 132 human RRM proteins behave like FUS and TDP-43 in yeast cells.

TABLE 1 Human RRM proteins with similar properties as FUS and TDP-43 when expressed in yeast. Toxicity Prion Prion Score domain domain Name Description (1-4) score rank 1. BOLL boule-like (Drosophila) 2 2. CPSF6 cleavage and polyadenylation specific factor 2.5 3. DAZ1 deleted in azoospermia 1 2.5 14 143 4. DAZ2 deleted in azoospermia 2 3 14 143 5. DAZ3 deleted in azoospermia 3 3.5 15 136 6. DAZAP1 DAZ associated protein 1 2 12 198 7. ELAVL1 ELAV (embryonic lethal, abnormal vision)-like 1 1 8. ELAVL2 ELAV (embryonic lethal, abnormal vision)-like 2 1 9. ELAVL3 ELAV (embryonic lethal, abnormal vision)-like 3 2.5 10. ELAVL4 ELAV (embryonic lethal, abnormal vision)-like 4 1 11. ENOX1 ecto-NOX disulfide-thiol exchanger 1 2.5 12. EWSR1 Ewing sarcoma breakpoint region 1 3.5 32 25 13. FUS fusion (involved in malignant liposarcoma) 1.5 38 13 14. G3BP1 Ras-GTPase-activating protein 2 15. HNRNPA0 heterogeneous nuclear ribonucleoprotein 1 21 81 16. HNRNPM heterogeneous nuclear ribonucleoprotein 3 17. IGF2BP2 IGF-II mRNA-binding protein 2 2.5 18. IGF2BP3 IGF-II mRNA-binding protein 3 2.5 19. MSI2 musashi homolog 2 2 20. RALYL RNA binding protein-like 2.5 21. RBM12B RNA binding motif protein 3.5 22. RBM14 RNA binding motif protein 2 16 117 23. RBM4 RNA binding motif protein 3 24. RBM41 RNA binding motif protein 2.5 25. RBM4B RNA binding motif protein 2.5 26. RBM5 RNA binding motif protein 3 27. RBM9 RNA binding motif protein 3.5 28. RBMS1 RNA binding motif, single stranded interacting protein 2 29. RBMS2 RNA binding motif, single stranded interacting protein 2 30. RBPMS RNA binding motif, single stranded interacting protein 3 31. ROD1 regulator of differentiation 1 32. SNRPA small nuclear ribonucleoprotein polypeptide 2 33. SNRPB2 small nuclear ribonucleoprotein polypeptide 2 34. TARDBP TAR DNA binding protein (TDP-43) 1.5 27 43 35. TIA1 cytotoxic granule-associated RNA binding protein 2 23 55

A list of 35 human RRM proteins that formed cytoplasmic aggregates and were toxic when expressed in yeast. Toxicity was scored from 1 (most toxic) to 4 (not toxic). Prion domain score, based on 10,11, indicates the maximum log-likelihood for prion-like amino acid composition vs. non-prion-like amino acid composition in any 60 consecutive amino acid window contained in a region parsed as prion-like by the Hidden Markov Model. No prion score indicates that no region of length ≧60 was parsed as prion-like. Prion domain rank is out of 21,873 human proteins.

TABLE 2 Gene Ensembl Chromo- Prion Domain Name Gene ID some Description Score ELAVL1 ENSG0000 19 ELAV (embryonic lethal, abnormal vision, Drosophila)- — 0066044 like 1 (Hu antigen R) [Source: HGNC Symbol; Acc: 3312] ELAVL2 ENSG0000 9 ELAV (embryonic lethal, abnormal vision, Drosophila)- — 0107105 like 2 (Hu antigen B) [Source: HGNC Symbol; Acc: 3313] ELAVL4 ENSG0000 1 ELAV (embryonic lethal, abnormal vision, Drosophila)- — 0162374 like 4 (Hu antigen D) [Source: HGNC Symbol; Acc: 3315] HNRNPA0 ENSG0000 5 heterogeneous nuclear ribonucleoprotein A0 20.6 0177733 [Source: HGNC Symbol; Acc: 5030] ROD1 ENSG0000 9 ROD1 regulator of differentiation 1 (S. pombe) — 0119314 [Source: HGNC Symbol; Acc: 10253] FUS ENSG0000 16 fused in sarcoma [Source: HGNC Symbol; Acc: 4010] 37.6 0089280 TARDBP ENSG0000 1 TAR DNA binding protein [Source: HGNC 26.5 0120948 Symbol; Acc: 11571] BOLL ENSG0000 2 bol, boule-like (Drosophila) [Source: HGNC — 0152430 Symbol; Acc: 14273] DAZAP1 ENSG0000 19 DAZ associated protein 1 [Source: HGNC 11.7 0071626 Symbol; Acc: 2683] G3BP1 ENSG0000 5 GTPase activating protein (SH3 domain) binding protein — 0145907 1 [Source: HGNC Symbol; Acc: 30292] MSI2 ENSG0000 17 musashi homolog 2 (Drosophila) [Source: HGNC — 0153944 Symbol; Acc: 18585] RBM14 ENSG0000 11 RNA binding motif protein 14 [Source: HGNC 16.1 0239306 Symbol; Acc: 14219] RBMS1 ENSG0000 2 RNA binding motif, single stranded interacting protein 1 — 0153250 [Source: HGNC Symbol; Acc: 9907] RBMS2 ENSG0000 12 RNA binding motif, single stranded interacting protein 2 — 0076067 [Source: HGNC Symbol; Acc: 9909] SNRPA ENSG0000 19 small nuclear ribonucleoprotein polypeptide A — 0077312 [Source: HGNC Symbol; Acc: 11151] SNRPB2 ENSG0000 20 small nuclear ribonucleoprotein polypeptide B″ — 0125870 [Source: HGNC Symbol; Acc: 11155] TIA1 ENSG0000 2 TIA1 cytotoxic granule-associated RNA binding protein 23.2 0116001 [Source: HGNC Symbol; Acc: 11802] CPSF6 ENSG0000 12 microRNA 1279 [Source: HGNC Symbol; Acc: 35357] — 0111605 DAZ1 ENSG0000 Y deleted in azoospermia 1 [Source: HGNC 14.1 0188120 Symbol; Acc: 2682] ELAVL3 ENSG0000 19 ELAV (embryonic lethal, abnormal vision, Drosophila)- — 0196361 like 3 (Hu antigen C) [Source: HGNC Symbol; Acc: 3314] ENOX1 ENSG0000 13 ecto-NOX disulfide-thiol exchanger 1 [Source: HGNC — 0120658 Symbol; Acc: 25474] IGF2BP2 ENSG0000 3 insulin-likegrowth factor 2 mRNA binding protein 2 — 0073792 [Source: HGNC Symbol; Acc: 28867] IGF2BP3 ENSG0000 7 insulin-likegrowth factor 2 mRNA binding protein 3 — 0136231 [Source: HGNC Symbol; Acc: 28868] RALYL ENSG0000 8 RALY RNA binding protein-like [Source: HGNC — 0184672 Symbol; Acc: 27036] RBM41 ENSG0000 X RNA binding motif protein 41 [Source: HGNC — 0089682 Symbol; Acc: 25617] RBM4B ENSG0000 11 RNA binding motif protein 4B [Source: HGNC — 0173914 Symbol; Acc: 28842] DA22 ENSG0000 Y deleted in azoospermia 2 [Source: HGNC 14.1 0205944 Symbol; Acc: 15964] HNRNPM ENSG0000 19 heterogeneous nuclear ribonucleoprotein M — 0099783 [Source: HGNC Symbol; Acc: 5046] RBM4 ENSG0000 11 RNA binding motif protein 4 [Source: HGNC — 0173933 Symbol; Acc: 9901] RBM5 ENSG0000 3 RNA binding motif protein 5 [Source: HGNC — 0003756 Symbol; Acc: 9902] RBPMS ENSG0000 8 RNA binding protein with multiple splicing — 0157110 [Source: HGNC Symbol; Acc: 19097] DAZ3 ENSG0000 Y deleted in azoospermia 3 [Source: HGNC 14.6 0187191 Symbol; Acc: 15965] EWSR1 ENSG0000 22 Ewing sarcoma breakpoint region 1 [Source: HGNC 32.4 0182944 Symbol; Acc: 3508] RBM12B ENSG0000 8 RNA binding motif protein 12B [Source: HGNC — 0183808 Symbol; Acc: 32310] RBM9 ENSG0000 22 RNA binding motif protein 9 [Source: HGNC — 0100320 Symbol; Acc: 9906] A1CF ENSG0000 10 APOBEC1 complementation factor [Source: HGNC — 0148584 Symbol; Acc: 24086] AC005774.2 ENSG0000 16 Fox-1 homolog A (Ataxin-2-binding protein — 0078328 1)(Hexaribonucleotide-binding protein 1) HNRPDL ENSG0000 4 heterogeneous nuclear ribonucleoprotein D-like 31.5 0152795 [Source: HGNC Symbol; Acc: 5037] MYEF2 ENSG0000 15 myelin expression factor 2 [Source: HGNC — 0104177 Symbol; Acc: 17940] PABPC1 ENSG0000 8 poly(A) binding protein, cytoplasmic 1 [Source: HGNC — 0070756 Symbol; Acc: 8554] PABPC5 ENSG0000 X poly(A) binding protein, cytoplasmic 5 [Source: HGNC — 0174740 Symbol; Acc: 13629] PSPC1 ENSG0000 13 paraspeckle component 1 [Source: HGNC 10   0121390 Symbol; Acc: 20320] RBM11 ENSG0000 21 RNA binding motif protein 11 [Source: HGNC — 0185272 Symbol; Acc: 9897] RBM15 ENSG0000 1 RNA binding motif protein 15 [Source: HGNC — 0162775 Symbol; Acc: 14959] RBM28 ENSG0000 7 RNA binding motif protein 28 [Source: HGNC — 0106344 Symbol; Acc: 21863] RBM3 ENSG0000 X RNA binding motif (RNP1, RRM) protein 3 — 0102317 [Source: HGNC Symbol; Acc: 9900] RBM47 ENSG0000 4 RNA binding motif protein 47 [Source: HGNC — 0163694 Symbol; Acc: 30358] RNPS1 ENSG0000 16 RNA binding protein S1, serine-rich domain — 0205937 [Source: HGNC Symbol; Acc: 10080] SFRS1 ENSG0000 17 splicing factor, arginine/serine-rich 1 [Source: HGNC — 0136450 Symbol; Acc: 10780] SFRS13B ENSG0000 6 splicing factor, arginine/serine-rich 13B [Source: HGNC — 0154548 Symbol; Acc: 21220] SFRS7 ENSG0000 2 splicing factor, arginine/serine-rich 7, 35 kDa — 0115875 [Source: HGNC Symbol; Acc: 10789] ZNF638 ENSG0000 2 zinc finger protein 638 [Source: HGNC — 0075292 Symbol; Acc: 17894] RBM46 ENSG0000 4 RNA binding motif protein 46 [Source: HGNC — 0151962 Symbol; Acc: 28401] AC008073.5 ENSG0000 2 Pre-mRNA branch site protein p14 (SF3b 14 kDa — 0115128 subunit) [Source: UniProtKB/Swiss-Prot; Acc: Q9Y3B4] BRUNOL6 ENSG0000 15 CUGBP, Elav-like family member 6 [Source: HGNC — 0140488 Symbol; Acc: 14059] CELF5 ENSG0000 19 CUGBP, Elav-like family member 5 [Source: HGNC — 0161082 Symbol; Acc: 14058] CIRBP ENSG0000 19 cold inducible RNA binding protein [Source: HGNC — 0099622 Symbol; Acc: 1982] CPEB3 ENSG0000 10 cytoplasmic polyadenylation element binding protein 3 — 0107864 [Source: HGNC Symbol; Acc: 21746] CUGBP2 ENSG0000 10 CUGBP, Elav-like family member 2 [Source: HGNC — 0048740 Symbol; Acc: 2550] DND1 ENSG0000 5 dead end homolog 1 (zebrafish) [Source: HGNC — 0183403 Symbol; Acc: 23799] EIF4B ENSG0000 12 eukaryotic translation initiation factor 4B [Source: HGNC — 0063046 Symbol; Acc: 3285] ESRP1 ENSG0000 8 epithelial splicing regulatory protein 1 [Source: HGNC — 0104413 Symbol; Acc: 25966] HNRNPA1 ENSG0000 12 heterogeneous nuclear ribonucleoprotein A1-like 3 28.2 0135486 [Source: HGNC Symbol; Acc: 31015] HNRNPF ENSG0000 10 heterogeneous nuclear ribonucleoprotein F — 0169813 [Source: HGNC Symbol; Acc: 5039] HNRNPR ENSG0000 1 heterogeneous nuclear ribonucleoprotein R — 0125944 [Source: HGNC Symbol; Acc: 5047] NCBP2 ENSG0000 3 nuclear cap binding protein subunit 2, 20 kDa — 0114503 [Source: HGNC Symbol; Acc: 7659] PTBP1 ENSG0000 19 polypyrimidine tract binding protein 1 [Source: HGNC — 0011304 Symbol; Acc: 9583] RAVER1 ENSG0000 19 ribonucleoprotein, PTB-binding 1 [Source: HGNC — 0161847 Symbol; Acc: 30296] RBM15B ENSG0000 3 RNA binding motif protein 15B [Source: HGNC — 0179837 Symbol; Acc: 24303] RBM26 ENSG0000 13 RNA binding motif protein 26 [Source: HGNC — 0139746 Symbol; Acc: 20327] RBM42 ENSG0000 19 RNA binding motif protein 42 [Source: HGNC — 0126254 Symbol; Acc: 28117] RRP7A ENSG0000 22 ribosomal RNA processing 7 homolog B (S. cerevisiae) — 0189306 [Source: HGNC Symbol; Acc: 30454] SF3B4 ENSG0000 1 splicing factor 3b, subunit 4, 49 kDa [Source: HGNC — 0143368 Symbol; Acc: 10771] SFRS2 ENSG0000 17 splicing factor, arginine/serine-rich 2 [Source: HGNC — 0161547 Symbol; Acc: 10783] SYNCRIP ENSG0000 6 synaptotagmin binding, cytoplasmic RNA interacting — 0135316 protein [Source: HGNC Symbol; Acc: 16918] TRNAU1AP ENSG0000 1 tRNA selenocysteine 1 associated protein 1 — 0180098 [Source: HGNC Symbol; Acc: 30813] TUT1 ENSG0000 11 terminal uridylyl transferase 1, U6 snRNA-specific — 0149016 [Source: HGNC Symbol; Acc: 26184] U2AF1 ENSG0000 21 U2 small nuclear RNA auxiliary factor 1 [Source: HGNC — 0160201 Symbol; Acc: 12453] U2AF2 ENSG0000 19 U2 small nuclear RNA auxiliary factor 2 [Source: HGNC — 0063244 Symbol; Acc: 23156] NONO ENSG0000 X non-POU domain containing, octamer-binding — 0147140 [Source: HGNC Symbol; Acc: 7871] RBMY1F ENSG0000 Y RNA binding motif protein, Y-linked, family 1, member — 0169800 F [Source: HGNC Symbol; Acc: 23974] AC004381.6 ENSG0000 16 Putative RNA exonuclease NEF-sp (EC 3.1.—.—) — 0005189 [Source: UniProtKB/Swiss-Prot; Acc: Q96IC2] C14orf156 ENSG0000 14 SRA stem-loop-interacting RNA-binding protein, — 0119705 mitochondrial Precursor [Source: UniProtKB/Swiss- Prot; Acc: Q9GZT3] CPEB4 ENSG0000 5 cytoplasmic polyadenylation element binding protein 4 — 0113742 [Source: HGNC Symbol; Acc: 21747] CSTF2T ENSG0000 10 cleavage stimulation factor, 3′ pre-RNA, subunit 2, 14   0177613 64 kDa, tau variant [Source: HGNC Symbol; Acc: 17086] DAZ4 ENSG0000 Y deleted in azoospermia 4 [Source: HGNC 14.1 0205916 Symbol; Acc: 15966] EIF3G ENSG0000 19 eukaryotic translation initiation factor 3, subunit G — 0130811 [Source: HGNC Symbol; Acc: 3274] ESRP2 ENSG0000 16 epithelial splicing regulatory protein 2 [Source: HGNC — 0103067 Symbol; Acc: 26152] HNRNPA3 ENSG0000 2 heterogeneous nuclear ribonucleoprotein A3 27.2 0170144 [Source: HGNC Symbol; Acc: 24941] HTATSF1 ENSG0000 X HIV-1 Tat specific factor 1 [Source: HGNC — 0102241 Symbol; Acc: 5276] PUF60 ENSG0000 8 poly-U binding splicing factor 60 KDa [Source: HGNC — 0179950 Symbol; Acc: 17042] RBM33 ENSG0000 7 RNA binding motif protein 33 [Source: HGNC 12.9 0184863 Symbol; Acc: 27223] RDBP ENSG0000 6 Negative elongation factor E (NELF-E)(RNA-binding — 0204356 protein RD) [Source: UniProtKB/Swiss-Prot; Acc: P18615] PTBP2 ENSG0000 1 polypyrimidine tract binding protein 2 [Source: HGNC — 0117569 Symbol; Acc: 17662] G3BP2 ENSG0000 4 GTPase activating protein (SH3 domain) binding protein — 0138757 2 [Source: HGNC Symbol; Acc: 30291] HNRNPC ENSG0000 14 heterogeneous nuclear ribonucleoprotein C (C1/C2) — 0092199 [Source: HGNC Symbol; Acc: 5035] RBMX ENSG0000 X RNA binding motif protein, X-linked [Source: HGNC — 0147274 Symbol; Acc: 9910] CPSF7 ENSG0000 11 cleavage and polyadenylation specific factor 7, 59 kDa — 0149532 [Source: HGNC Symbol; Acc: 30098] RBM39 ENSG0000 20 RNA binding motif protein 39 [Source: HGNC — 0131051 Symbol; Acc: 15923] SFRS11 ENSG0000 1 splicing factor, arginine/serine-rich 11 [Source: HGNC — 0116754 Symbol; Acc: 10782] SFRS12 ENSG0000 5 splicing factor, arginine/serine-rich 12 [Source: HGNC — 0153914 Symbol; Acc: 17882] SFRS4 ENSG0000 1 splicing factor, arginine/serine-rich 4 [Source: HGNC — 0116350 Symbol; Acc: 10786] SFRS5 ENSG0000 14 splicing factor, arginine/serine-rich 5 [Source: HGNC — 0100650 Symbol; Acc: 10787] RBM34 ENSG0000 1 RNA binding motif protein 34 [Source: HGNC — 0188739 Symbol; Acc: 28965] TRA2A ENSG0000 7 transformer 2 alpha homolog (Drosophila) — 0164548 [Source: HGNC Symbol; Acc: 16645] RBM7 ENSG0000 11 RNA binding motif protein 7 [Source: HGNC — 0076053 Symbol; Acc: 9904] ZCRB1 ENSG0000 12 zinc finger CCHC-type and RNA binding motif 1 — 0139168 [Source: HGNC Symbol; Acc: 29620] HNRNPA2B1 ENSG0000 7 heterogeneous nuclear ribonucleoprotein A2/B1 29.9 0122566 [Source: HGNC Symbol; Acc: 5033] HNRNPD ENSG0000 4 heterogeneous nuclear ribonucleoprotein D (AU-rich 30.6 0138668 element RNA binding protein 1, 37 kDa) DNAJC17 ENSG0000 15 DnaJ (Hsp40) homolog, subfamily C, member 17 — 0104129 [Source: HGNC Symbol; Acc: 25556] EIF4H ENSG0000 7 eukaryotic translation initiation factor 4H [Source: HGNC — 0106682 Symbol; Acc: 12741] ENOX2 ENSG0000 X ecto-NOX disulfide-thiol exchanger 2 [Source: HGNC — 0165675 Symbol; Acc: 2259] HNRPLL ENSG0000 2 heterogeneous nuclear ribonucleoprotein L-like — 0143889 [Source: HGNC Symbol; Acc: 25127] MKI67IP ENSG0000 2 MKI67 (FHA domain) interacting nucleolar — 0155438 phosphoprotein [Source: HGNC Symbol; Acc: 17838] PABPC3 ENSG0000 13 poly(A) binding protein, cytoplasmic 3 [Source: HGNC — 0151846 Symbol; Acc: 8556] POLDIP3 ENSG0000 22 polymerase (DNA-directed), delta interacting protein 3 — 0100227 [Source: HGNC Symbol; Acc: 23782] PPIE ENSG0000 1 peptidylprolyl isomerase E (cyclophilin E) — 0084072 [Source: HGNC Symbol; Acc: 9258] PPIL4 ENSG0000 6 peptidylprolyl isomerase (cyclophilin)-like 4 — 0131013 [Source: HGNC Symbol; Acc: 15702] RBM10 ENSG0000 X RNA binding motif protein 10 [Source: HGNC — 0182872 Symbol; Acc: 9896] RBM12 ENSG0000 20 RNA binding motif protein 12 [Source: HGNC — 0244462 Symbol; Acc: 9898] RBM16 ENSG0000 6 RNA binding motif protein 16 [Source: HGNC — 0213079 Symbol; Acc: 20959] RBM17 ENSG0000 10 RNA binding motif protein 17 [Source: HGNC — 0134453 Symbol; Acc: 16944] RBM19 ENSG0000 12 RNA binding motif protein 19 [Source: HGNC — 0122965 Symbol; Acc: 29098] RBM22 ENSG0000 5 RNA binding motif protein 22 [Source: HGNC — 0086589 Symbol; Acc: 25503] RBM23 ENSG0000 14 RNA binding motif protein 23 [Source: HGNC — 0100461 Symbol; Acc: 20155] RBM45 ENSG0000 2 RNA binding motif protein 45 [Source: HGNC — 0155636 Symbol; Acc: 24468] RBM8A ENSG0000 1 RNA binding motif protein 8A [Source: HGNC — 0131795 Symbol; Acc: 9905] RBMY1A1 ENSG0000 Y RNA binding motif protein, Y-linked, family 1, member — 0234414 C [Source: HGNC Symbol; Acc: 9914] SFRS13A ENSG0000 1 splicing factor, arginine/serine-rich 13A [Source: HGNC — 0188529 Symbol; Acc: 16713] SFRS6 ENSG0000 20 splicing factor, arginine/serine-rich 6 [Source: HGNC — 0124193 Symbol; Acc: 10788] SNRNP35 ENSG0000 12 small nuclear ribonucleoprotein 35 kDa (U11/U12) — 0184209 [Source: HGNC Symbol; Acc: 30852] zinc finger (CCCH type), RNA-binding motif and ZRSR2 ENSG0000 X serine/arginine rich 2 [Source: HGNC — 0169249 Symbol; Acc: 23019] AC015631.1 ENSG0000 4 Polyadenylate-binding protein 4-like (Poly(A)-binding — 0250177 protein 4-like)(PABP-4-like) AC021224.2 ENSG0000 18 Putative uncharacterized protein ENSP00000383298 21.6 0215492 [Source: UniProtKB/TrEMBL; Acc: C9JCD7] AC021534.1 ENSG0000 17 Fox-1 homolog C [Source: UniProtKB/Swiss- — 0167281 Prot; Acc: A6NFN3] AC021593.2 ENSG0000 17 Trinucleotide repeat-containing gene 6C protein 15.4 0078687 [Source: UniProtKB/Swiss-Prot; Acc: Q9HCJ0] AC027139.2 ENSG0000 15 — 0215042 AC132219.2 ENSG0000 8 — 0231942 CELF1 ENSG0000 11 CUGBP, Elav-like family member 1 [Source: HGNC — 0149187 Symbol; Acc: 2549] CELF4 ENSG0000 18 CUGBP, Elav-like family member 4 [Source: HGNC 12.8 0101489 Symbol; Acc: 14015] CNOT4 ENSG0000 7 CCR4-NOT transcription complex, subunit 4 — 0080802 [Source: HGNC Symbol; Acc: 7880] CPEB2 ENSG0000 4 cytoplasmic polyadenylation element binding protein 2 — 0137449 [Source: HGNC Symbol; Acc: 21745] CSTF2 ENSG0000 X cleavage stimulation factor, 3′ pre-RNA, subunit 2, 15.7 0101811 64 kDa [Source: HGNC Symbol; Acc: 2484] DAZL ENSG0000 3 deleted in azoospermia-like [Source: HGNC — 0092345 Symbol; Acc: 2685] EIF3B ENSG0000 7 eukaryotic translation initiation factor 3, subunit B — 0106263 [Source: HGNC Symbol; Acc: 3280] GRSF1 ENSG0000 4 G-rich RNA sequence binding factor 1 [Source: HGNC — 0132463 Symbol; Acc: 4610] HNRNPA1L2 ENSG0000 13 heterogeneous nuclear ribonucleoprotein A1-like 2 22.8 0139675 [Source: HGNC Symbol; Acc: 27067] HNRNPAB ENSG0000 5 heterogeneous nuclear ribonucleoprotein A/B 27.3 0197451 [Source: HGNC Symbol; Acc: 5034] HNRNPCL1 ENSG0000 1 heterogeneous nuclear ribonucleoprotein C-like 1 — 0179172 [Source: HGNC Symbol; Acc: 29295] HNRNPH1 ENSG0000 5 heterogeneous nuclear ribonucleoprotein H1 (H) 22.3 0169045 [Source: HGNC Symbol; Acc: 5041] HNRNPH2 ENSG0000 X heterogeneous nuclear ribonucleoprotein H2 (H′) 17.5 0126945 [Source: HGNC Symbol; Acc: 5042] HNRNPH3 ENSG0000 10 heterogeneous nuclear ribonucleoprotein H3 (2H9) 14   0096746 [Source: HGNC Symbol; Acc: 5043] HNRNPL ENSG0000 19 heterogeneous nuclear ribonucleoprotein L — 0104824 [Source: HGNC Symbol; Acc: 5045] IGF2BP1 ENSG0000 17 insulin-like growth factor 2 mRNA binding protein 1 — 0159217 [Source: HGNC Symbol; Acc: 28866] LARP7 ENSG0000 4 La ribonucleoprotein domain family, member 7 — 0174720 [Source: HGNC Symbol; Acc: 24912] MSI1 ENSG0000 12 musashi homolog 1 (Drosophila) [Source: HGNC — 0135097 Symbol; Acc: 7330] MTHFSD ENSG0000 16 methenyltetrahydrofolate synthetase domain containing — 0103248 [Source: HGNC Symbol; Acc: 25778] NCBP2L ENSG0000 X nuclear cap binding protein subunit 2-like — 0170935 [Source: HGNC Symbol; Acc: 31795] NCL ENSG0000 2 nucleolin [Source: HGNC Symbol; Acc: 7667] — 0115053 NOL8 ENSG0000 9 nucleolar protein 8 [Source: HGNC Symbol; Acc: 23387] — 0198000 PABPC1L ENSG0000 20 poly(A) binding protein, cytoplasmic 1-like — 0101104 [Source: HGNC Symbol; Acc: 15797] PABPC1L2A ENSG0000 X poly(A) binding protein, cytoplasmic 1-like 2A — 0186288 [Source: HGNC Symbol; Acc: 27989] PABPC1L2B ENSG0000 X poly(A) binding protein, cytoplasmic 1-like 2B — 0184388 [Source: HGNC Symbol; Acc: 31852] PABPC4 ENSG0000 1 poly(A) binding protein, cytoplasmic 4 (inducible form) — 0090621 [Source: HGNC Symbol; Acc: 8557] PABPN1 ENSG0000 14 poly (A) binding protein, nuclear 1 [Source: HGNC — 0100836 Symbol; Acc: 8565] PABPN1L ENSG0000 16 poly(A) binding protein, nuclear 1-like (cytoplasmic) — 0205022 [Source: HGNC Symbol; Acc: 37237] PPARGC1A ENSG0000 4 peroxisome proliferator-activated receptor gamma, — 0109819 coactivator 1 alpha [Source: HGNC Symbol; Acc: 9237] PPARGC1B ENSG0000 5 peroxisome proliferator-activated receptor gamma, — 0155846 coactivator 1 beta [Source: HGNC Symbol; Acc: 30022] PPRC1 ENSG0000 10 peroxisome proliferator-activated receptor gamma, — 0148840 coactivator-related 1 [Source: HGNC Symbol; Acc: 30025] RALY ENSG0000 20 RNA binding protein, autoantigenic (hnRNP_associated — 0125970 with lethal yellow homolog (mouse)) RAVER2 ENSG0000 1 ribonucleoprotein, PTB-binding 2 [Source: HGNC — 0162437 Symbol; Acc: 25577] RBM18 ENSG0000 9 RNA binding motif protein 18 [Source: HGNC — 0119446 Symbol; Acc: 28413] RBM24 ENSG0000 6 RNA binding motif protein 24 [Source: HGNC — 0112183 Symbol; Acc: 21539] RBM25 ENSG0000 14 RNA binding motif protein 25 [Source: HGNC — 0119707 Symbol; Acc: 23244] RBM27 ENSG0000 5 RNA binding motif protein 27 [Source: HGNC — 0091009 Symbol; Acc: 29243] RBM38 ENSG0000 20 RNA binding motif protein 38 [Source: HGNC — 0132819 Symbol; Acc: 15818] RBM44 ENSG0000 2 RNA binding motif protein 44 [Source: HGNC — 0177483 Symbol; Acc: 24756] RBMS2P1 ENSG0000 12 RNA binding motif, single stranded interacting protein 2 — 0213250 pseudogene 1 [Source: HGNC Symbol; Acc: 30994] RBMS3 ENSG0000 3 RNA binding motif, single stranded interacting protein 3 — 0144642 [Source: HGNC Symbol; Acc: 13427] RBMX2 ENSG0000 X RNA binding motif protein, X-linked 2 [Source: HGNC — 0134597 Symbol; Acc: 24282] RBMXL1 ENSG0000 1 RNA binding motif protein, X-linked-like 1 — 0213516 [Source: HGNC Symbol; Acc: 25073] RBMXL2 ENSG0000 11 RNA binding motif protein, X-linked-like 2 — 0170748 [Source: HGNC Symbol; Acc: 17886] RBMXL3 ENSG0000 X RNA binding motif protein, X-linked-like 3 — 0175718 [Source: HGNC Symbol; Acc: 26859] RBMY1B ENSG0000 Y RNA binding motif protein, Y-linked, family 1, member — 0242875 B [Source: HGNC Symbol; Acc: 23914] RBMY1D ENSG0000 Y RNA binding motif protein, Y-linked, family 1, member — 0244395 D [Source: HGNC Symbol; Acc: 23915] RBMY1E ENSG0000 Y RNA binding motif protein, Y-linked, family 1, member — 0242389 E [Source: HGNC Symbol; Acc: 23916] RBMY1J ENSG0000 Y RNA binding motif protein, Y-linked, family 1, member J — 0226941 [Source: HGNC Symbol; Acc: 23917] RBPMS2 ENSG0000 15 RNA binding protein with multiple splicing 2 — 0166831 [Source: HGNC Symbol; Acc: 19098] RNPC3 ENSG0000 1 RNA-binding region (RNP1, RRM) containing 3 — 0185946 [Source: HGNC Symbol; Acc: 18666] RP11- ENSG0000 11 Transcriptional coactivator CoAZ — 658F2.1 0248643 [Source: UniProtKB/TrEMBL; Acc: B0LM41] SAFB ENSG0000 19 scaffold attachment factor B [Source: HGNC — 0160633 Symbol; Acc: 10520] SAFB2 ENSG0000 19 scaffold attachment factor B2 [Source: HGNC — 0130254 Symbol; Acc: 21605] SART3 ENSG0000 12 squamous cell carcinoma antigen recognized by T cells — 0075856 3 [Source: HGNC Symbol; Acc: 16860] SETD1A ENSG0000 16 SET domain containing 1A [Source: HGNC — 0099381 Symbol; Acc: 29010] SETD1B ENSG0000 12 SET domain containing 1B [Source: HGNC — 0139718 Symbol; Acc: 29187] SFPQ ENSG0000 1 splicing factor proline/glutamine-rich [Source: HGNC 20.8 0116560 Symbol; Acc: 10774] SFRS15 ENSG0000 21 splicing factor, arginine/serine-rich 15 [Source: HGNC — 0156304 Symbol; Acc: 19304] SFRS2B ENSG0000 11 splicing factor, arginine/serine-rich 2B [Source: HGNC — 0180771 Symbol; Acc: 16988] SFRS3 ENSG0000 6 splicing factor, arginine/serine-rich 3 [Source: HGNC — 0112081 Symbol; Acc: 10785] SFRS9 ENSG0000 12 splicing factor, arginine/serine-rich 9 [Source: HGNC — 0111786 Symbol; Acc: 10791] SLTM ENSG0000 15 SAFB-like, transcription modulator [Source: HGNC — 0137776 Symbol; Acc: 20709] SNRNP70 ENSG0000 19 small nuclear ribonucleoprotein 70 kDa (U1) — 0104852 [Source: HGNC Symbol; Acc: 11150] SPEN ENSG0000 1 spen homolog, transcriptional regulator (Drosophila) — 0065526 [Source: HGNC Symbol; Acc: 17575] SR140 ENSG0000 3 U2-associated protein SR140 (140 kDa Ser/Arg-rich — 0163714 domain protein) [Source: UniProtKB/Swiss- Prot; Acc: O15042] SSB ENSG0000 2 Sjogren syndrome antigen B (autoantigen La) — 0138385 [Source: HGNC Symbol; Acc: 11316] TAF15 ENSG0000 17 TAF15 RNA polymerase II, TATA box binding protein 33.2 0172660 (TBP)-associated factor, 68 kDa [Source: HGNC Symbol; Acc: 11547] TDRD10 ENSG0000 1 tudor domain containing 10 [Source: HGNC — 0163239 Symbol; Acc: 25316] THOC4 ENSG0000 17 THO complex 4 [Source: HGNC Symbol; Acc: 19071] — 0183684 TIAL1 ENSG0000 10 TIA1 cytotoxic granule-associated RNA binding protein- 13.5 0151923 like 1 [Source: HGNC Symbol; Acc: 11804] TNRC4 ENSG0000 1 CUGBP, Elav-like family member 3 [Source: HGNC — 0159409 Symbol; Acc: 11967] TRA2B ENSG0000 3 transformer 2 beta homolog (Drosophila) — 0136527 [Source: HGNC Symbol; Acc: 10781] UHMK1 ENSG0000 1 U2AF homology motif (UHM) kinase 1 [Source: HGNC — 0152332 Symbol; Acc: 19683] ZRSR1 ENSG0000 5 zinc finger (CCCH type), RNA-binding motif and — 0212643 serine/arginine rich 1 [Source: HGNC Symbol; Acc: 12456] Prion Domain Tested Toxicity Gene Prion Domain Rank Among in Yeast in Yeast Localiztion in Name Rank RRM Proteins Screen Screen (1-4) Yeast Screen ELAVL1 — — yes 1 cytoplasm, multiple foci ELAVL2 — — yes 1 cytoplasm, multiple foci ELAVL4 — — yes 1 cytoplasm, multiple foci HNRNPA0 81 16 yes 1 cytoplasm, multiple foci ROD1 — — yes 1 cytoplasm, multiple foci FUS 13  1 yes 1.5 cytoplasm, multiple foci TARDBP 43 10 yes 1.5 cytoplasm, multiple foci BOLL — — yes 2 cytoplasm, multiple foci DAZAP1 198  30 yes 2 cytoplasm, multiple foci G3BP1 — — yes 2 cytoplasm, multiple foci MSI2 — — yes 2 cytoplasm, multiple foci RBM14 117  18 yes 2 cytoplasm, multiple foci RBMS1 — — yes 2 cytoplasm, multiple foci RBMS2 — — yes 2 cytoplasm, multiple foci SNRPA — — yes 2 cytoplasm, multiple foci SNRPB2 — — yes 2 cytoplasm, multiple foci TIA1 55 11 yes 2 cytoplasm, multiple foci CPSF6 — — yes 2.5 cytoplasm, multiple foci DAZ1 143 23 yes 2.5 cytoplasm, multiple foci ELAVL3 — — yes 2.5 cytoplasm, multiple foci ENOX1 — — yes 2.5 cytoplasm, multiple foci IGF2BP2 — — yes 2.5 cytoplasm, multiple foci IGF2BP3 — — yes 2.5 cytoplasm, multiple foci RALYL — — yes 2.5 cytoplasm, multiple foci RBM41 — — yes 2.5 cytoplasm, multiple foci RBM4B — — yes 2.5 cytoplasm, multiple foci DA22 143  23 yes 3 cytoplasm, multiple foci HNRNPM — — yes 3 cytoplasm, multiple foci RBM4 — — yes 3 cytoplasm, multiple foci RBM5 — — yes 3 cytoplasm, multiple foci RBPMS — — yes 3 cytoplasm, multiple foci DAZ3 136  21 yes 3.5 cytoplasm, multiple foci EWSR1 25  3 yes 3.5 cytoplasm, multiple foci RBM12B — — yes 3.5 cytoplasm, multiple foci RBM9 — — yes 3.5 cytoplasm, multiple foci A1CF — — yes 4 cytoplasm, multiple foci AC005774.2 — — yes 4 cytoplasm, multiple foci HNRPDL 28  4 yes 4 cytoplasm, multiple foci MYEF2 — — yes 4 cytoplasm, multiple foci PABPC1 — — yes 4 cytoplasm, multiple foci PABPC5 — — yes 4 cytoplasm, multiple foci PSPC1 226  31 yes 4 cytoplasm, multiple foci RBM11 — — yes 4 cytoplasm, multiple foci RBM15 — — yes 4 cytoplasm, multiple foci RBM28 — — yes 4 cytoplasm, multiple foci RBM3 — — yes 4 cytoplasm, multiple foci RBM47 — — yes 4 cytoplasm, multiple foci RNPS1 — — yes 4 cytoplasm, multiple foci SFRS1 — — yes 4 cytoplasm, multiple foci SFRS13B — — yes 4 cytoplasm, multiple foci SFRS7 — — yes 4 cytoplasm, multiple foci ZNF638 — — yes 4 cytoplasm, multiple foci RBM46 — — yes 3 cytoplasm, diffuse AC008073.5 — — yes 4 cytoplasm, diffuse BRUNOL6 — — yes 4 cytoplasm, diffuse CELF5 — — yes 4 cytoplasm, diffuse CIRBP — — yes 4 cytoplasm, diffuse CPEB3 — — yes 4 cytoplasm, diffuse CUGBP2 — — yes 4 cytoplasm, diffuse DND1 — — yes 4 cytoplasm, diffuse EIF4B — — yes 4 cytoplasm, diffuse ESRP1 — — yes 4 cytoplasm, diffuse HNRNPA1 38  7 yes 4 cytoplasm, diffuse HNRNPF — — yes 4 cytoplasm, diffuse HNRNPR — — yes 4 cytoplasm, diffuse NCBP2 — — yes 4 cytoplasm, diffuse PTBP1 — — yes 4 cytoplasm, diffuse RAVER1 — — yes 4 cytoplasm, diffuse RBM15B — — yes 4 cytoplasm, diffuse RBM26 — — yes 4 cytoplasm, diffuse RBM42 — — yes 4 cytoplasm, diffuse RRP7A — — yes 4 cytoplasm, diffuse SF3B4 — — yes 4 cytoplasm, diffuse SFRS2 — — yes 4 cytoplasm, diffuse SYNCRIP — — yes 4 cytoplasm, diffuse TRNAU1AP — — yes 4 cytoplasm, diffuse TUT1 — — yes 4 cytoplasm, diffuse U2AF1 — — yes 4 cytoplasm, diffuse U2AF2 — — yes 4 cytoplasm, diffuse NONO — — yes 4 ER membrane RBMY1F — — yes 3 no expression AC004381.6 — — yes 4 no expression C14orf156 — — yes 4 no expression CPEB4 — — yes 4 no expression CSTF2T 148    25.5 yes 4 no expression DAZ4 143  23 yes 4 no expression EIF3G — — yes 4 no expression ESRP2 — — yes 4 no expression HNRNPA3 41  9 yes 4 no expression HTATSF1 — — yes 4 no expression PUF60 — — yes 4 no expression RBM33 172  28 yes 4 no expression RDBP — — yes 4 no expression PTBP2 — — yes 1.5 nucleus, multiple foci G3BP2 — — yes 2 nucleus, multiple foci HNRNPC — — yes 2.5 nucleus, multiple foci RBMX — — yes 3 nucleus, multiple foci CPSF7 — — yes 4 nucleus, multiple foci RBM39 — — yes 4 nucleus, multiple foci SFRS11 — — yes 4 nucleus, multiple foci SFRS12 — — yes 4 nucleus, multiple foci SFRS4 — — yes 4 nucleus, multiple foci SFRS5 — — yes 4 nucleus, multiple foci RBM34 — — yes 1 nucleus, diffuse TRA2A — — yes 2 nucleus, diffuse RBM7 — — yes 3 nucleus, diffuse ZCRB1 — — yes 3 nucleus, diffuse HNRNPA2B1 32  6 yes 3.5 nucleus, diffuse HNRNPD 30  5 yes 3.5 nucleus, diffuse DNAJC17 — — yes 4 nucleus, diffuse EIF4H — — yes 4 nucleus, diffuse ENOX2 — — yes 4 nucleus, diffuse HNRPLL — — yes 4 nucleus, diffuse MKI67IP — — yes 4 nucleus, diffuse PABPC3 — — yes 4 nucleus, diffuse POLDIP3 — — yes 4 nucleus, diffuse PPIE — — yes 4 nucleus, diffuse PPIL4 — — yes 4 nucleus, diffuse RBM10 — — yes 4 nucleus, diffuse RBM12 — — yes 4 nucleus, diffuse RBM16 — — yes 4 nucleus, diffuse RBM17 — — yes 4 nucleus, diffuse RBM19 — — yes 4 nucleus, diffuse RBM22 — — yes 4 nucleus, diffuse RBM23 — — yes 4 nucleus, diffuse RBM45 — — yes 4 nucleus, diffuse RBM8A — — yes 4 nucleus, diffuse RBMY1A1 — — yes 4 nucleus, diffuse SFRS13A — — yes 4 nucleus, diffuse SFRS6 — — yes 4 nucleus, diffuse SNRNP35 — — yes 4 nucleus, diffuse ZRSR2 — — yes 4 nucleus, diffuse AC015631.1 — — no NA NA AC021224.2 68 14 no NA NA AC021534.1 — — no NA NA AC021593.2 124  20 no NA NA AC027139.2 — — no NA NA AC132219.2 — — no NA NA CELF1 — — no NA NA CELF4 176  29 no NA NA CNOT4 — — no NA NA CPEB2 — — no NA NA CSTF2 122  19 no NA NA DAZL — — no NA NA EIF3B — — no NA NA GRSF1 — — no NA NA HNRNPA1L2 57 12 no NA NA HNRNPAB 39  8 no NA NA HNRNPCL1 — — no NA NA HNRNPH1 63 13 no NA NA HNRNPH2 98 17 no NA NA HNRNPH3 147    25.5 no NA NA HNRNPL — — no NA NA IGF2BP1 — — no NA NA LARP7 — — no NA NA MSI1 — — no NA NA MTHFSD — — no NA NA NCBP2L — — no NA NA NCL — — no NA NA NOL8 — — no NA NA PABPC1L — — no NA NA PABPC1L2A — — no NA NA PABPC1L2B — — no NA NA PABPC4 — — no NA NA PABPN1 — — no NA NA PABPN1L — — no NA NA PPARGC1A — — no NA NA PPARGC1B — — no NA NA PPRC1 — — no NA NA RALY — — no NA NA RAVER2 — — no NA NA RBM18 — — no NA NA RBM24 — — no NA NA RBM25 — — no NA NA RBM27 — — no NA NA RBM38 — — no NA NA RBM44 — — no NA NA RBMS2P1 — — no NA NA RBMS3 — — no NA NA RBMX2 — — no NA NA RBMXL1 — — no NA NA RBMXL2 — — no NA NA RBMXL3 — — no NA NA RBMY1B — — no NA NA RBMY1D — — no NA NA RBMY1E — — no NA NA RBMY1J — — no NA NA RBPMS2 — — no NA NA RNPC3 — — no NA NA RP11- — — no NA NA 658F2.1 SAFB — — no NA NA SAFB2 — — no NA NA SART3 — — no NA NA SETD1A — — no NA NA SETD1B — — no NA NA SFPQ 79 15 no NA NA SFRS15 — — no NA NA SFRS2B — — no NA NA SFRS3 — — no NA NA SFRS9 — — no NA NA SLTM — — no NA NA SNRNP70 — — no NA NA SPEN — — no NA NA SR140 — — no NA NA SSB — — no NA NA TAF15 22  2 no NA NA TDRD10 — — no NA NA THOC4 — — no NA NA TIAL1 158  27 no NA NA TNRC4 — — no NA NA TRA2B — — no NA NA UHMK1 — — no NA NA ZRSR1 — — no NA NA A Table of all 213 human RRM proteins. 132 of these were tested for aggregation and toxicity in yeast. Prion Domain scores and ranks are given for all RRM proteins. Rank is out of all 21,873 human proteins. Toxicity score: 1 = Very toxic, 4 = not toxic

TABLE 3 EWSR1 sequencing Chromosomic DNA Genomic DNA Coding DNA Predicted Protein aALS Samples bSequenced Controls NC_000022.10 NG_023240.1 NM_001163285.1 NP_001156757.1 (n = 817) (n = 1082) g.29694840G>C g.35843G>C c.1532G>C p.G511A 1.22E−03 (1) 0 g.29695020C>A g.36023C>A NC NC 1.22E−03 (1) 0 g.29695132A>G g.36135A>G NC NC 1.22E−03 (1) 0 g.29695189A>G g.36192A>G NC NC 1.22E−03 (1) 0 g.29695301C>T g.36304C>T c.1655C>T p.P552L 1.22E−03 (1) 0 g.29695662C>T g.36665C>T c.1749C>T NC 1.22E−03 (1) 0 g.29695663G>A g.36666G>A c.1750G>A p.G584S 1.22E−03 (1) 0 g.29694847C>T g.35850C>T c.1539C>T NC 0 9.24E−04 (1) g.29694892A>G g.35895A>G NC NC 0 2.77E−03 (3) g.29694995C>T g.35998C>T NC NC 0 9.24E−04 (1) g.29695032G>A g.36035G>A NC NC 0 9.24E−04 (1) g.29695082A>G g.36085A>G NC NC 0 9.24E−04 (1) g.29695737C>T g.36740C>T c.1824C>T NC 0 9.24E−04 (1) g.29695771C>G g.36774C>G c.1858C>G NC 0 9.24E−04 (1) g.29695816C>T g.36819C>T c.1903C>T p.R635C 0 9.24E−04 (1) EWSR1 sequencing Chromosomic DNA cSNP Controls NC_000022.10 (n = 4608) ID Dx AAO. y FH Source g.29694840G>C 0 ND10314 ALS 50 Alzheimer Coriell g.29695020C>A NA ND10157 ALS 51 No Coriell g.29695132A>G NA ND903-1 ALS 51 No CNDR g.29695189A>G NA ND12124 ALS 48 No Coriell g.29695301C>T 0 ND1038-1 ALS 36 No CNDR g.29695662C>T NA ND745-1 ALS 71 No CNDR g.29695663G>A 2.17E−04 (1) ND10828 ALS 51 No Coriell g.29694847C>T NA CHOP1H11 Healthy NA NA CHOP g.29694892A>G NA CHOP1G10 Healthy NA NA CHOP CHOP2E01 Healthy NA NA CHOP pl1G09 Healthy NA NA CNDR g.29694995C>T NA ND02652 Healthy NA NA Coriell g.29695032G>A NA N009739 Healthy NA NA Coriell g.29695082A>G NA CHOP2E05 Healthy NA NA CHOP g.29695737C>T NA CHOP2B02 Healthy NA NA CHOP g.29695771C>G NA ND07270 Healthy NA NA Coriell g.29695816C>T NA ND10777 Healthy NA NA Coriell TAF15 sequencing Chromosomic DNA Genomic DNA Coding DNA Predicted Protein aALS Samples bSequenced Controls NC_000017.10 NG_023279.1 NM_139215.1 NP_631961.1 (n = 610) (n = 982) g.34171358G>A g.39871G>A c.1163G>A p.R388H 6.56E−03 (4) 1.02E−03 (1) g.34171367G>A g.39880G>A c.1172G>A p.G391E 1.64E−03 (1) 0 g.34171525C>T g.40038C>T c.1222C>T p.R408C 1.64E−03 (1) 0 g.34171635C>T g.40148C>T c.1332C>T NC 1.64E−03 (1) 0 g.34171749T>C g.40262T>C c.1446T>C NC 1.64E−03 (1) 0 g.34171212T>A g.39725T>A NC NC 0 1.02E−03 (1) g.34171216G>A g.39729G>A NC NC 0 1.02E−03 (1) TAF15 sequencing Chromosomic DNA cSNP Controls NC_000017.10 (n = 4608) ID Dx AAO. y FH Source g.34171358G>A NA 1995-164 ALS NA NA CNDR 2001-163 ALS NA NA CNDR 2007-029 ALS 54 NA CNDR ND08531 ALS 47 No Coriell g.34171367G>A 0 ND989-1 ALS NA Other ND CNDR g.34171525C>T 0 2008-162 ALS NA NA CNDR g.34171635C>T NA 2007-127 ALS 69 NA CNDR g.34171749T>C NA ND634-1 ALS 57 Other ND CNDR g.34171212T>A NA ND01658 Healthy NA NA Coriell g.34171216G>A NA CHOP1B06 Healthy NA NA CHOP Abbreviations: AAO, age at onset; ALS, amyotrophic lateral sclerosis; Dx, diagnosis; FH, family history; ID, identifier, NA, not available; NC, no change. aFrequency in 817 ALS cases for EWSR1 or 610 for TAF15; numbers in parentheses indicate counts. bFrequency in our 1,082 sequenced control cases for EWSR1 and 982 for TAF15; numbers in parentheses indicate counts. cFrequency in our 4,608 SNP genotyped control cases; numbers in parentheses indicate counts. Note that for EWSR1, we identified variant G584S once in an A| R388H four times in ALS cases and once in sequenced controls. The other missense variants (G511A and P552L for EWSR1; G391E and R408C for TAF15) were not present in the controls (5,690 for EWSR1 and 5,590 for TAF15) nor in publicly available SNP databases.

To focus this list further, we used a bioinformatics approach. In addition to the RRM domain, FUS and TDP-43 share a glycine-rich domain and a bioinformatics-predicted prion-like domain (Cushman et al., 2010). Like prion domains found in fungal prion proteins (e.g. Sup35, Ure2, and Rnq1), these domains are enriched in uncharged polar amino acids (such as asparagine, glutamine and tyrosine) and glycine (Alberti et al., 2009). In TDP-43, the predicted prion domain overlaps the glycine-rich domain; in FUS, a QQSY-rich region defines the prion domain, although there is some overlap with the glycine rich domain. The prion domain is a shared feature that may be important, given the prion-like aggregation propensity of many proteins associated with human neurodegenerative disease (Aguzzi and Rajendran, 2009). Remarkably, using an algorithm to score 21,873 human proteins for likelihood of harboring a prion domain, FUS and TDP-43 ranked 13th and 43rd, respectively. We therefore interrogated the list of human RRM proteins to identify whether others ranked highly using the prion domain prediction algorithm (Alberti et al., 2009). Interestingly, 31 of the 213 human RRM proteins ranked in the top 250 (Table 2). Among these, FUS and TDP-43 ranked 1st and 10th, respectively. Of the 35 proteins that were toxic and formed cytoplasmic inclusions in the cytoplasm in yeast, 10, including FUS and TDP-43, scored highly for a prion-like domain (Table 1). Thus, using the combined yeast screen and prion-like domain analysis, we narrowed the list of RRM proteins by 13-fold (132 human RRM proteins→35 that aggregate and are toxic in yeast→10 that also contain prion domain). Further, that of human RRM proteins, FUS ranks #1 and TDP-43 ranks #10, indicated that the other human RRM proteins with prion domains ranked #2-9 should be a top priority for analysis. We therefore focused on these proteins because they shared similar functional and structural features with FUS and TDP-43: 1) formed cytoplasmic accumulations, 2) were toxic in yeast, and 3) contained a predicted prion-like domain.

With this list of ten “FUS- and TDP-43-like” proteins in hand, we sought to test the hypothesis that these additional RRM proteins might contribute to ALS. One of these proteins, EWSR1 (Ewing sarcoma breakpoint region 1), in addition to being a homologue of FUS, revealed a localization pattern in yeast remarkably similar to that of TDP-43 and FUS (FIG. 1c). Spotting assays showed that EWSR1 expression was also toxic, albeit not as toxic as TDP-43 and FUS (FIG. 1d). Using the prion domain prediction algorithm, EWSR1 ranked 25th out of 21,873 human proteins and 3rd out of 213 human RRM proteins (Table 1). Furthermore, EWSR1 contains notably similar domain architecture to FUS: like FUS, EWSR1 contains a single RRM, a glycine-rich region, an N-terminal prion domain, RGG domains, and a C-terminal PY-motif (FIG. 2a). Given these striking commonalities in structure, predicted prion domain, and behavior in yeast, we sought to identify EWSR1 mutations in ALS patients.

Since almost all known pathogenic mutations in FUS and TDP-43 are located in the C-terminal domains of the proteins (Lagier-Tourenne and Cleveland, 2009), we focused on the last four exons of the EWSR1 gene (exons 15-18; NM—001163285). These exons comprise the RGG- and PY-motif-containing C-terminal domain, which are important for nuclear localization of FUS and EWSR1 (Araya et al., 2003; Dormann et al., 2010; Shaw et al., 2009; Zakaryan and Gehring, 2006). Complete sequencing of these exons was performed in 817 individuals diagnosed with ALS (see Methods for patient and control demographic information) and in 1,082 geographically-matched healthy population control individuals (see Methods for details). We followed up this analysis with Taqman SNP genotyping of any patient-specific mutations in 4,608 healthy individuals (Table 3). This approach identified two patient specific missense variants in EWSR1 in two unrelated ALS patients with sporadic disease (FIG. 2b-d, Table 3). Missense variants were identified in exon 16 (c.1532G>C, p.Gly511Ala) and exon 17 (c.1655C>T, p.Pro522Leu). These individuals had disease onset of 50 years and 36 years, respectively. Neither of these were present in 1,082 sequenced controls nor in the 4,608 targeted SNP genotyped controls, strongly supporting clinical significance of these variants. Overall, these specific genetic variants in EWSR1 were detected in 2 out of 817 ALS cases and 0 out of 5,690 controls (P=0.015). Furthermore, none of these variants were present in public SNP databases (e.g. dbSNP), eight HapMAP individuals sequenced (Ng et al., 2009b), or the 1000 Genomes Project (http://browser.1000genomes.org/index.html). Notably, the two variants are located in highly conserved regions of EWSR1 (FIG. 2d). Since the EWSR1 variants were identified in sporadic ALS cases, familial evidence for segregation with disease was not possible; however TARDBP and FUS mutations have also been confirmed in apparent sporadic ALS cases (Lagier-Tourenne et al., 2010). In addition, the parents of the affected individuals were not available to determine if the mutations occurred de novo or were inherited.

Because the yeast expression library of RRM proteins did not contain every human RRM protein, we analyzed additional proteins that were not included in the yeast screen for features similar to TDP-43, FUS, and EWSR1. We gave top priority to TAF15 (RNA polymerase II, TATA box binding protein (TBP)-associated factor, 68 kDa) because it belongs to the same protein family as FUS and EWSR1 (TET family) and is remarkably similar to those two proteins, especially within the RRM, glycine-rich domain, and C-terminal RGG domain- and PY-motif-containing region (FIG. 2a). Curiously, all three genes have been implicated in chromosomal translocations in cancer (Tan and Manley, 2009). Like FUS and EWSR1, TAF15 ranks very high using the prion domain prediction algorithm (ranked 2nd out of 213 human RRM proteins). Given these commonalities, we proceeded to sequence exons 13-16 of TAF15 (NM—139215), which encode the C-terminal region analogous to where we found EWSR1 variants and to where many FUS mutations are located. We performed complete sequencing of these exons in 610 individuals diagnosed with ALS (see Methods for patient and control demographic information) and in 982 geographically-matched healthy population control individuals. This analysis was followed up by Taqman SNP genotyping of patient specific mutations in 4,608 healthy individuals (Table 3). In TAF15, we found two patient-specific missense variants (FIG. 2e-g, Table 3), one in exon 14 (c.1172G>A, p.Gly391Glu) and the other in exon 15 (c.1222C>T, p.Arg408Cys). These variants were found in individuals with ages of onset of sporadic ALS of 67 years and 47 years, respectively. As for EWSR1, the TAF15 variants were not found in the large cohort of control individuals (982 control individuals sequenced and 4,608 analyzed by targeted SNP genotyping). Familial segregation studies were not possible. Overall, these specific missense variants in TAF15 were detected in 2 out of 610 ALS cases and 0 out of 5,590 population controls (P=0.01).

In the process of sequencing these genes in ALS cases and controls, we also identified several synonomous and noncoding variants as summarized in Table 3. In addition, we identified two missense variants that were present in both patients and controls (EWSR1 c. 1750G>A, p.G584S and TAF15 c.1163G>A, p.R388H) as well as one variant present only in a single control (EWSR1 c.1903C>T, p.R635C). The presence of these variants in control individuals suggests that these likely represent rare benign variants, although these studies alone cannot not exclude the possibility that they represent disease variants with reduced penetrance. In contrast, the four patient-specific variants in EWSR1 (G511A and P552L) and TAF15 (G391E and R408C) were not found in >5,000 healthy controls, and together with the functional evidence below, strongly suggests that these are disease-specific mutations. Finally, we also analyzed EWSR1 and TAF15 in an independent ALS cohort from the Mayo Clinic. We screened 125 ALS patients and identified one missense variant in TAF15 (c.1418G>A, p.Gly473Glu) in an individual with age of onset of 68. This variant was not present in the 982 sequenced controls or in an additional 904 SNP-genotyped controls. Thus, taken together, we identified 2 missense variants in EWSR1 and 3 missense variants in TAF15 (FIG. 2a) in ALS patients that were not present in a very large number of healthy controls.

Although these studies highlight a potential role for EWSR1 and TAF15 in ALS pathogenesis, we next sought functional evidence that these proteins have properties similar to TDP-43 and FUS. First, do EWSR1 and TAF15 spontaneously aggregate in vitro as do TDP-43 and FUS (Johnson et al., 2009; Li et al., 2010b)? Second, do these proteins confer neurodegeneration when expressed in the nervous system, as for TDP-43 (Elden et al., 2010; Hanson et al., 2010; Li et al., 2010a; Lu et al., 2009; Ritson et al., 2010)? Third, can the ALS-associated variants in EWSR1 and TAF15 perturb protein localization in neurons, as for some ALS-linked TDP-43 and FUS mutations (Barmada et al., 2010; Dormann et al., 2010; Kabashi et al., 2010; Kwiatkowski et al., 2009; Vance et al., 2009)?

Bacterially expressed glutathione S-transferase (GST) tagged EWSR1 and TAF15 were purified as soluble proteins under native conditions, as previously done for TDP-43 and FUS (Johnson et al., 2009; Sun et al., 2010). Upon addition of Tobacco Etch Virus (TEV) protease to specifically remove the N-terminal GST tag EWSR1 and TAF15 rapidly aggregated at 25° C. with gentle agitation. The proteins aggregated with kinetics similar to FUS and slightly more rapidly than TDP-43, assessed by turbidity (FIG. 3a) and the amount that entered the pellet fraction after centrifugation (FIG. 3B). If TEV protease was omitted, then little aggregation occurred (FIG. 3a, b). Electron microscopy revealed that EWSR1 and TAF15 rapidly accessed oligomeric forms (FIG. 3c), which would frequently adopt a pore-like conformation (FIG. 3c, small arrows; 3d), similar to those formed by TDP-43 and FUS (FIG. 3c, d) (Johnson et al., 2009; Sun et al., 2010). Furthermore, EWSR1 and TAF15 also assembled into linear polymers with a cross-sectional diameter of ˜15-20 nm (FIG. 3c, large arrows) that increased in length over time and would often become tangled into large masses by 60 min (FIG. 3c). In general, the morphology of EWSR1 and TAF15 aggregates were more similar to FUS than to TDP-43, which over this time frame formed shorter polymers that would clump together to form large masses (FIG. 3c) (Johnson et al., 2009). Importantly, a human RRM protein, DND1, which did not aggregate and was not toxic in yeast (FIG. 1c, d) also remained soluble and did not aggregate in this in vitro assay (data not shown), providing evidence that in vitro aggregation is not a property shared by all RRM proteins. Thus, similar to TDP-43 and FUS, and concordant with the yeast data, EWSR1 and TAF15 are inherently aggregation-prone proteins.

To analyze the effects of these proteins in the nervous system, we used Drosophila. We and others have previously shown that directing TDP-43 expression to the fly nervous system causes neurodegeneration (Elden et al., 2010; Hanson et al., 2010; Li et al., 2010a; Lu et al., 2009; Ritson et al., 2010). A series of transgenic lines were generated that expressed wild type (WT) human EWSR1 and TAF15. Directing expression of these proteins to the eye of the fly caused degeneration of the structure (FIG. 4a) and led to progressive loss of motility when directed to motor neurons (FIG. 4b). As for the in vitro aggregation assay, the effect was specific because two other unrelated RRM proteins, the human counterparts of which did not aggregate and are not toxic in yeast, did not confer neurodegeneration when upregulated in Drosophila (FIG. 4d). Thus, EWSR1 and TAF15 possess activity sufficient to confer neurodegeneration in the nervous system, in a manner similar to that of TDP-43. Importantly, these experiments do not indicate per se that these molecules cause disease. Rather, they provide evidence that they have similar properties as the known ALS disease-causing genes TDP-43 and FUS.

The preceding experiments provide evidence that the wild type versions of EWSR1 and TAF15 have similar properties as TDP-43 and FUS; they aggregate in vitro, confer toxicity in yeast and neurodegeneration in Drosophila. This aggregation and toxicity in yeast and flies that we observe with the WT protein may or may not be directly disease-related; the key point is that, in addition to sharing similar structural features to TDP-43 and FUS, EWSR1 and TAF15 also share similar functional features. To provide evidence that these variants might be pathogenic, we next asked if and how they affected the protein.

We had previously found that some ALS-linked TDP-43 mutations increase aggregation and toxicity in vitro and in yeast cells (Johnson et al., 2009) and enhance neurodegeneration in Drosophila (Elden et al., 2010). On the other hand, in recent experiments with FUS, we find that ALS-linked FUS mutants do not aggregate more rapidly than WT in vitro and in yeast, and are not more toxic than WT in yeast (Sun et al., 2010). Moreover, ALS-linked mutations located in the C-terminal PY-motif of FUS have been shown to disrupt nuclear localization rather than affecting aggregation propensity in mammalian cells (Dormann et al., 2010). As with FUS, we found that the ALS-linked variants in EWSR1 and TAF15 did not increase aggregation or toxicity in yeast and also did not enhance neurodegeneration compared to WT when upregulated in Drosophila (data not shown). However, ALS-linked mutations in TDP-43 and FUS have been shown to disrupt protein localization, leading to enhanced cytoplasmic accumulation of ALS-linked variants (Barmada et al., 2010; Dormann et al., 2010; Kabashi et al., 2010; Kwiatkowski et al., 2009; Vance et al., 2009). Given this common feature, we assessed the effects of the EWSR1 and TAF15 variants on subcellular localization. We used cell cultures of embryonic stem (ES) cell-derived neurons and primary motor neurons isolated from mouse embryos. Transduction of WT EWSR1 and TAF15 in the ES-derived neuronal cultures resulted in a mostly nuclear pattern, with occasional localization to the cytoplasm (FIG. 5a). Strikingly, all four patient specific EWSR1 and TAF15 variants analyzed resulted in a significant increase in cytoplasmic accumulation, as well as a pattern of coarse neuritic staining that was less prevalent with the WT proteins (FIG. 5a,b,d,e). Immunoblotting confirmed that the transduced WT and variant proteins were expressed at similar levels (FIG. 5c,f).

We observed similar effects on the localization of EWSR1 when WT or the mutant forms were transfected into primary motor neurons cultured from mouse embryos. WT EWSR1 primarily localized to the nucleus, whereas the ALS-specific variants resulted in increased cytoplasmic and neuritic accumulation (FIG. 5g,h). We also tested EWSR1 variant G584S, which was found in both ALS patients and controls (1/817 ALS patients and 1/5,690 controls). Importantly, in contrast to the patient-specific variants, EWSR1 G584S did not enhance cytoplasmic or neuritic accumulation in this assay, providing additional evidence that this variant is not likely to be pathogenic (FIG. 5g,h). As additional variants in EWSR1 and TAF15 are identified, this functional assay will be useful for assessing their potential pathogenicity. Thus, like ALS-linked TDP-43 and FUS mutations, the ALS-linked variants of EWSR1 and TAF15 can also promote cytoplasmic accumulation of the protein in motor neurons, a disease relevant cell type, providing further evidence in support of the pathogenicity of these variants. Interestingly, in addition to the PY-motif, which can function as a NLS (Zakaryan and Gehring, 2006), sequences in the last RGG domain of EWSR1 have also been shown to be required for proper nuclear localization (Shaw et al., 2009). Notably, one of the two EWSR1 variants found is located in this domain, as are all three TAF15 variants (FIG. 2a), suggesting that perhaps these mutations perturb the function of this RGG domain in a way that decreases its ability to interact efficiently with the nuclear localization machinery, resulting in the enhanced cytoplasmic localization observed in the cell cultures (FIG. 5). While the other EWSR1 variant, G511A, is located in a RGG domain that has been suggested not to be required for nuclear localization (Shaw et al., 2009), in other contexts this domain has been shown to also contribute to nuclear localization (Araya et al., 2003).

Discussion

In an effort to streamline the identification of new ALS disease genes, we devised a simple yeast functional screen to define additional RRM proteins with properties shared by the known ALS disease genes FUS and TDP-43. This screen resulted in the enrichment of 35 proteins that behave like FUS and TDP-43 in yeast (cytoplasmic inclusions and toxicity), ten of which contain a predicted prion domain (see Table 1). Indeed, the combination of yeast screen and prion prediction algorithm enabled us to significantly focus our list of candidate genes ˜13-fold. As evidence of the usefulness of this approach to define genes with a role in ALS, we identified two patient-specific missense variants in one of these genes, EWSR1, in unrelated ALS patients and three patient-specific missense variants in a homologous gene, TAF15, in three additional ALS patients. Further, we provide in vitro and in vivo evidence that these proteins have functional properties similar to those of TDP-43 and FUS: they can confer neurodegeneration in Drosophila, and the ALS-linked mutations can alter protein subcellular localization in motor neurons. While familial segregation could not be assessed, the absence of the variants in a very large number of healthy controls, as well as the shared structural evidence with known ALS genes, and functional in vitro data strongly support the notion that these variants in EWSR1 and TAF15 represent pathogenic disease mutations for ALS. Thus, we suggest that EWSR1 and TAF15 now join FUS and TDP-43 as RNA-binding proteins linked to ALS, further underscoring a central role for perturbations in RNA metabolism as fundamental to ALS pathogenesis. In a broader sense, these findings suggest that there may be a delicate balance in RNA processing within motor neurons such that slight perturbations from any one of several different aggregation-prone RNA-binding proteins could lead to neurodegeneration. Indeed, select ALS-linked mutations in TDP-43 increase aggregation of the protein (Johnson et al., 2009); ALS-linked mutations in FUS, EWSR1, and TAF15 might do so as well, although it is possible that these mutations could contribute to disease by distinct mechanisms (Dormann et al., 2010; Ling et al., 2010).

These findings predict that additional aggregation-prone RRM or other RNA binding proteins, like EWSR1, TAF15, FUS, and TDP-43, contribute to ALS. Notably, the prion domain algorithm ranked FUS, TAF15, and EWSR1 1st, 2nd, and 3rd out of 213 RRM proteins, respectively, and ranked TDP-43 10th. We suggest that genes ranked 4th through 9th should now be given top priority for genetic analysis in ALS patient populations. Next generation sequencing and exon capture approaches will eventually become routine in personalized medicine, (Biesecker, 2010; Ng et al., 2009a; Ng et al., 2009b) and promises to identify all genetic contributors to ALS; this approach, coupled with functional biochemical and functional studies shown, will empower elucidation of all of the genetic contributors to ALS. Meanwhile, the list of ALS candidate genes that we provide here (Table 1 and Table 2), generated by the combination of the yeast functional screen and prion domain prediction, will be a powerful resource, which promises to facilitate efforts to identify new ALS disease genes and spur innovative new diagnostic and therapeutic approaches.

Example II Diagnostic Assays for Detecting Increased Risk of Developing ALS

The information herein above can be applied clinically to patients for diagnosing an increased susceptibility for developing ALS, and for therapeutic intervention. Diagnostic compositions, including microarrays, and methods can be designed to identify the mutation containing EWSR1 and TAF15 genes described herein in nucleic acids from a patient to assess susceptibility for developing ALS. This can occur after a patient arrives in the clinic; the patient has blood drawn, and using the diagnostic methods described herein, a clinician can detect the aberrant nucleic acids associated with ALS if present. The nucleic acid obtained from the patient sample, which can optionally be amplified prior to assessment, will be used to diagnose a patient with an increased or decreased susceptibility for developing ALS. Kits for performing the diagnostic method of the invention are also provided herein. Such kits comprise a microarray comprising at least one probe or primer provided herein in and the necessary reagents for assessing the patient samples as described above. As discussed at length in Example I, the presence of particular mutations in the EWSR1 and TAF15 genes respectively is significantly associated with ALS, in certain instances early onset ALS. The identification of these mutations in a patient sample serves to identify those that possess an altered risk for developing ALS. The information provided herein allows for therapeutic intervention at earlier times in disease progression that previously possible.

Example III Screening Assays for the Identification of Agents which Modulate Pathological TDP-43-EWSR1 and/or TAF15 Complex Formation

Certain aspects of the present disclosure provide methods of screening for a candidate drug (agent or compound) or a genetic factor that modulates TDP-43-EWSR1-TAF-15-RNA interactions and associated pathology. Various types of candidate drugs may be screened by the methods described herein and the effects on the function or activity or localization of the molecules assessed alone or in combination. Compounds to be screened include nucleic acids, polypeptides, small molecule compounds, and peptidomimetics. In some cases, genetic agents can be screened by contacting the yeast cell with a nucleic acid construct coding for a gene. For example, one may screen cDNA libraries expressing a variety of genes, to identify other genes that modulate these interactions. For example, the identified drugs may modulate TDP-43-EWSR1-TAF15-RNA complex formation, subcellular localization and/or neuronal cell morphology or viability. Accordingly, irrespective of the exact mechanism of action, drugs identified by the screening methods described herein are expected to provide therapeutic benefit to patients suffering from ALS.

Screening methods described herein use may employ the yeast cells or the drosophila cells described in Example I. Candidate drugs can be screened from large libraries of synthetic or natural compounds. One example is an FDA approved library of compounds that can be used by humans. In addition, compound libraries are commercially available from a number of companies including but not limited to Maybridge Chemical Co. (Trevillet, Cornwall, UK), Comgenex (Princeton, N.J.), Microsource (New Milford, Conn.), Aldrich (Milwaukee, Wis.), AKos Consulting and Solutions GmbH (Basel, Switzerland), Ambinter (Paris, France), Asinex (Moscow, Russia), Aurora (Graz, Austria), BioFocus DPI, Switzerland, Bionet (Camelford, UK), ChemBridge, (San Diego, Calif.), ChemDiv, (San Diego, Calif.), Chemical Block Lt, (Moscow, Russia), ChemStar (Moscow, Russia), Exclusive Chemistry, Ltd (Obninsk, Russia), Enamine (Kiev, Ukraine), Evotec (Hamburg, Germany), Indofme (Hillsborough, N.J.), Interbioscreen (Moscow, Russia), Interchim (Montlucon, France), Life Chemicals, Inc. (Orange, Conn.), Microchemistry Ltd. (Moscow, Russia), Otava, (Toronto, ON), PharmEx Ltd. (Moscow, Russia), Princeton Biomolecular (Monmouth Junction, N.J.), Scientific Exchange (Center Ossipee, N.H.), Specs (Delft, Netherlands), TimTec (Newark, Del.), Toronto Research Corp. (North York ON), UkrOrgSynthesis (Kiev, Ukraine), Vitas-M, (Moscow, Russia), Zelinsky Institute, (Moscow, Russia), and Bicoll (Shanghai, China).

Combinatorial libraries are available and can be prepared. Libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are commercially available or can be readily prepared by methods well known in the art. It is proposed that compounds isolated from natural sources, such as animals, bacteria, fungi, plant sources, including leaves and bark, and marine samples may be assayed as candidates for the presence of potentially useful pharmaceutical agents. It will be understood that the pharmaceutical agents to be screened could also be derived or synthesized from chemical compositions or man-made compounds.

For example, the yeast or drosophila cells in Example 1 can be incubated in the presence and absence of a test compound the effect of the compound on TDP-43/EWSR1/TAF15/RNA complex formation and associated cellular toxicity assessed. Agents so identified could then be tested in whole animal models of ALS to assess in vivo efficacy.

Agents identified using the screening assays described herein are also encompassed by the present invention

REFERENCES

  • Aguzzi, A., and Rajendran, L. (2009). The transcellular spread of cytosolic amyloids, prions, and prionoids. Neuron 64, 783-790.
  • Alberti, S., Gitler, A. D., and Lindquist, S. (2007). A suite of Gateway® cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast (Chichester, England) 24, 913-919.
  • Alberti, S., Halfmann, R., King, O., Kapila, A., and Lindquist, S. (2009). A systematic survey identifies prions and illuminates sequence features of prionogenic proteins. Cell 137, 146-158.
  • Araya, N., Hirota, K., Shimamoto, Y., Miyagishi, M., Yoshida, E., Ishida, J., Kaneko, S., Kaneko, M., Nakajima, T., and Fukamizu, A. (2003). Cooperative interaction of EWS with CREB-binding protein selectively activates hepatocyte nuclear factor 4-mediated transcription. J Biol Chem 278, 5427-5432.
  • Barmada, S. J., Skibinski, G., Korb, E., Rao, E. J., Wu, J. Y., and Finkbeiner, S. (2010). Cytoplasmic mislocalization of TDP-43 is toxic to neurons and enhanced by a mutation associated with familial amyotrophic lateral sclerosis. J Neurosci 30, 639-649.
  • Biesecker, L. G. (2010). Exome sequencing makes medical genomics a reality. Nat Genet 42, 13-14.
  • Cleveland, D. W., and Rothstein, J. D. (2001). From Charcot to Lou Gehrig: deciphering selective motor neuron death in ALS. Nat Rev Neurosci 2, 806-819.
  • Cushman, M., Johnson, B. S., King, O. D., Gitler, A. D., and Shorter, J. (2010). Prion-like disorders: blurring the divide between transmissibility and infectivity. J Cell Sci 123, 1191-1201.
  • Dormann, D., Rodde, R., Edbauer, D., Bentmann, E., Fischer, I., Hruscha, A., Than, M. E., Mackenzie, I. R., Capell, A., Schmid, B., et al. (2010). ALS-associated fused in sarcoma (FUS) mutations disrupt Transportin-mediated nuclear import. EMBO J.
  • Elden, A. C., Kim, H. J., Hart, M. P., Chen-Plotkin, A. S., Johnson, B. S., Fang, X., Armakola, M., Geser, F., Greene, R., Lu, M. M., et al. (2010). Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS. Nature 466, 1069-1075.
  • Guthrie, C., and Fink, G. R. (2002). Methods in Ezymology: Guide to Yeast Genetics and Molecular and Cell Biology. Academic Press 169.
  • Hanson, K. A., Kim, S. H., Wassarman, D. A., and Tibbetts, R. S. (2010). Ubiquilin modifies TDP-43 toxicity in a Drosophila model of amyotrophic lateral sclerosis (ALS). J Biol Chem 285, 11068-11072.
  • Ito, H., Fukuda, Y., Murata, K., and Kimura, A. (1983). Transformation of intact yeast cells treated with alkali cations. J Bacteriol 153, 163-168.
  • Johnson, B. S., McCaffery, J. M., Lindquist, S., and Gitler, A. D. (2008). A yeast TDP-43 proteinopathy model: Exploring the molecular determinants of TDP-43 aggregation and cellular toxicity. Proc Natl Acad Sci USA 105, 6439-6444.
  • Johnson, B. S., Snead, D., Lee, J. J., McCaffery, J. M., Shorter, J., and Gitler, A. D. (2009). TDP-43 is intrinsically aggregation-prone, and amyotrophic lateral sclerosis-linked mutations accelerate aggregation and increase toxicity. J Biol Chem 284, 20329-20339.
  • Kabashi, E., Lin, L., Tradewell, M. L., Dion, P. A., Bercier, V., Bourgouin, P., Rochefort, D., Bel Hadj, S., Durham, H. D., Vande Velde, C., et al. (2010). Gain and loss of function of ALS-related mutations of TARDBP (TDP-43) cause motor deficits in vivo. Hum Mol Genet 19, 671-683.
  • Kwiatkowski, T. J., Jr., Bosco, D. A., Leclerc, A. L., Tamrazian, E., Vanderburg, C. R., Russ, C., Davis, A., Gilchrist, J., Kasarskis, E. J., Munsat, T., et al. (2009). Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science 323, 1205-1208.
  • Lagier-Tourenne, C., and Cleveland, D. W. (2009). Rethinking ALS: the FUS about TDP-43. Cell 136, 1001-1004.
  • Lagier-Tourenne, C., Polymenidou, M., and Cleveland, D. W. (2010). TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. Hum Mol Genet.
  • Li, Y., Ray, P., Rao, E. J., Shi, C., Guo, W., Chen, X., Woodruff, E. A., 3rd, Fushimi, K., and Wu, J. Y. (2010a). A Drosophila model for TDP-43 proteinopathy. Proc Natl Acad Sci USA 107, 3169-3174.
  • Li, Y., Sun, L., Cai, T., Zhang, Y., Lv, S., Wang, Y., and Ye, L. (2010b). alpha-Synuclein overexpression during manganese-induced apoptosis in SH-SY5Y neuroblastoma cells. Brain Res Bull 81, 428-433.
  • Ling, S. C., Albuquerque, C. P., Han, J. S., Lagier-Tourenne, C., Tokunaga, S., Zhou, H., and Cleveland, D. W. (2010). ALS-associated mutations in TDP-43 increase its stability and promote TDP-43 complexes with FUS/TLS. Proc Natl Acad Sci USA.
  • Lu, Y., Ferris, J., and Gao, F. B. (2009). Frontotemporal dementia and amyotrophic lateral sclerosis-associated disease protein TDP-43 promotes dendritic branching. Mol Brain 2, 30.
  • Neumann, M., Sampathu, D. M., Kwong, L. K., Truax, A. C., Micsenyi, M. C., Chou, T. T., Bruce, J., Schuck, T., Grossman, M., Clark, C. M., et al. (2006). Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314, 130-133.
  • Ng, S. B., Buckingham, K. J., Lee, C., Bigham, A. W., Tabor, H. K., Dent, K. M., Huff, C. D., Shannon, P. T., Jabs, E. W., Nickerson, D. A., et al. (2009a). Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42, 30-35.
  • Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., et al. (2009b). Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272-276.
  • Ritson, G. P., Custer, S. K., Freibaum, B. D., Guinto, J. B., Geffel, D., Moore, J., Tang, W., Winton, M. J., Neumann, M., Trojanowski, J. Q., et al. (2010). TDP-43 mediates degeneration in a novel Drosophila model of disease caused by mutations in VCP/p 97. J Neurosci 30, 7729-7739.
  • Shaw, D. J., Morse, R., Todd, A. G., Eggleton, P., Lorson, C. L., and Young, P. J. (2009). Identification of a tripartite import signal in the Ewing Sarcoma protein (EWS). Biochem Biophys Res Commun 390, 1197-1201.
  • Sun, Z., Diaz, Z., Chesi, A., Ramos, D., Shorter, J., and Gitler, A. D. (2010). Defining pathogenic features of the ALS disease protein FUS/TLS. Manuscript submitted.
  • Tan, A. Y., and Manley, J. L. (2009). The TET family of proteins: functions and roles in disease. J Mol Cell Biol 1, 82-92.
  • Van Damme, P., and Robberecht, W. (2009). Recent advances in motor neuron disease. Curr Opin Neurol 22, 486-492.
  • Vance, C., Rogelj, B., Hortobagyi, T., De Vos, K. J., Nishimura, A. L., Sreedharan, J., Hu, X., Smith, B., Ruddy, D., Wright, P., et al. (2009). Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science 323, 1208-1211.
  • Wichterle, H., Peljto, M., and Nedelec, S. (2009). Xenotransplantation of embryonic stem cell-derived motor neurons into the developing chick spinal cord. Methods Mol Biol 482, 171-183.
  • Zakaryan, R. P., and Gehring, H. (2006). Identification and characterization of the nuclear localization/retention signal in the EWS proto-oncoprotein. J Mol Biol 363, 27-38.

While the invention has been described in detail and with reference to specific examples thereof, it will be apparent to one skilled in the art that various changes and modifications can be made therein without departing from the spirit and scope thereof.

Claims

1. A method for predicting an increased risk of an individual for developing amyotrophic lateral sclerosis (ALS) disease, said method comprising: obtaining a nucleic acid sample encoding EWSR1 from said individual and determining whether or not said EWSR1 comprises a mutation selected from the group consisting of

i) a missense mutation in exon 16 at 1532 G>C causing a Gly511Ala alteration, and
ii) a missense mutation in exon 17 at 1655 C>T causing a Pro522Leu alteration, relative to wild-type EWSR1 encoding nucleic acids, wherein the presence of at least one mutation in said EWSR1 encoding nucleic acid when compared to wild type EWSR1 encoding nucleic acids obtained from patients not having ALS is indicative of an increased risk of ALS.

2. (canceled)

3. The method of claim 1, wherein said method predicts an increased risk of early onset ALS.

4. The method of claim 1, wherein said nucleic acid is obtained from a blood, tissue or skin sample.

5. The method of claim 1, wherein said mutations are detected using an EWSR1 specific probe or primer.

6. A diagnostic kit for performing the method of claim 5, comprising reagents suitable for isolation of DNA, and reagents suitable for detection of said mutation containing EWSR1 nucleic acids.

7. A method for identifying agents which inhibit TDP-43 associated complex formation with at least one RNA binding protein listed in Table 1, comprising:

a) providing a cell which expresses TDP-43 and said RNA binding protein, said expression being associated with increased cellular toxicity and cytoplasmic aggregate formation;
b) contacting said cell with an effective amount of an agent; and
c) measuring cellular toxicity and/or aggregate formation in the presence of said agent relative to a non-treated control cell, wherein a decrease in cellular toxicity identifies an agent which reduces TDP-43-RNA binding protein mediated cellular toxicity and cytoplasmic aggregate formation.

8. The method of claim 7, wherein said cell is a Saccharomyces cerevisiae or Drosophila cell.

9. The method of claim 7, wherein said RNA binding protein is EWSR1, said EWSR1 optionally comprising at least one missense mutation.

10. The method of claim 7, wherein said RNA binding protein is TAF15, said TAF15 optionally comprising at least one missense mutation.

11. An agent identified via the method of claim 8 or claim 9.

12. An isolated nucleic acid encoding an altered EWSR1 protein comprising a genetic alteration selected from the group consisting of

i) a missense mutation in exon 16 at 1532 G>C causing a Gly511Ala alteration, and
ii) a missense mutation in exon 17 at 1655 C>T causing a Pro522Leu alteration.

13. An isolated altered EWSR1 protein encoded by the nucleic acid of claim 12.

14. (canceled)

15. (canceled)

16. The nucleic acid of claim 12 affixed to a solid support.

17. A vector comprising the nucleic acid of claim 12.

18. A host cell comprising the vector of claim 17.

19. The host cell of claim 18 which is a drosophila cell or a yeast cell.

Patent History
Publication number: 20150252424
Type: Application
Filed: Mar 3, 2015
Publication Date: Sep 10, 2015
Inventor: Aaron D. Gitler (Foster City, CA)
Application Number: 14/637,116
Classifications
International Classification: C12Q 1/68 (20060101); C07K 14/47 (20060101); G01N 33/50 (20060101);