Abstract: The present disclosure provides polynucleotides, vector systems, cells, and methods for amplifying expression of proteins, such as AAV Rep and Cap proteins or therapeutic proteins (e.g., an antibody). Increased expression of AAV Rep and Cap proteins is useful in increasing production of recombinant AAV virions. Also provided herein are vector systems for inducing amplification of expression of AAV Rep and Cap proteins. Also provided herein are vector systems for inducing amplification of expression of therapeutic proteins. Inducible expression of therapeutic proteins is useful in increasing production of therapeutic proteins.

Abstract: Disclosed herein are engineered RNAs and compositions comprising the same for treatment of diseases or conditions in a subject. Also disclosed herein are methods of treating diseases or conditions in a subject by administering engineered RNAs, polynucleotides encoding the described engineered RNAs, or pharmaceutical compositions described here.

Abstract: Disclosed herein are engineered latent guide RNAs targeting LRRK2 and compositions comprising the same for treatment of diseases or conditions (e.g. Parkinson's Disease) in a subject. Also disclosed herein are methods of treating diseases or conditions (e.g. Parkinson's Disease) in a subject by administering engineered latent guide RNAs or pharmaceutical compositions described herein.

Abstract: Provided are compositions and methods for silencing suppressor tRNAs. Further provided are compositions and methods for silencing suppressor tRNAs during AAV production for producing virions comprising sequences coding for suppressor tRNAs.

Abstract: Disclosed herein are engineered AAV VP capsid polypeptides with the ability to assemble into virus particles and having improved tissue tropism to eye tissues, for example, retinal tissues, retinal pigment epithelial cells, or photoreceptor cells. The capsids are engineered using the high throughput discovery system described herein. In certain embodiments, provided herein are recombinant adeno-associated virus (AAV) VP capsid polypeptides having at least one mutation in a 581 to 589 region of the VP capsid polypeptide, corresponding to residues 581 to residue 589 of a VP1 polypeptide of SEQ ID NO: 1.

Abstract: Provided herein are engineered guides configured, upon hybridization to target RNA molecules, to form double stranded RNA substrates comprising (i) a region comprising at least one structural feature; and (ii) a first internal loop and a second internal loop, wherein the double stranded RNA substrates recruit RNA editing entities and facilitate chemical modifications of base nucleotides in the target RNA molecules. Also provided herein are compositions, vectors, and cells comprising the engineered guides disclosed herein. Also provided herein are methods of introducing the engineered guides described herein into cells and methods of treating a disease or condition in a subject in need thereof comprising administering to the subject the engineered guides, polynucleotides encoding the engineered guides, delivery vehicles comprising such engineered guides or such polynucleotides, or pharmaceutical compositions comprising any one of these as described herein.

Abstract: Systems and methods for generating a polymer sequence for a biological molecule having one or more target biological properties are provided. A plurality of target metric values for one or more target biological properties of a biological molecule and a seed for a nucleic acid or amino acid sequence for the biological molecule are inputted into a conditional generator model of a conditional generative adversarial network to obtain as output from the conditional generator model a nucleic acid or amino acid sequence for the biological molecule that is predicted by the conditional generator model to confer on the biological molecule the one or more target biological properties approximating the plurality of target metric values.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise steps of: (a) forming a plurality of first vessels each comprising: (i) a single cell, and (ii) a single solid support; (b) copying onto the single solid support: (i) a first copy of a first cell polynucleotide from the single cell, and (ii) a second copy of a second cell polynucleotide from the single cell; (c) forming a plurality of second vessels each comprising (i) a single solid support from the plurality of first vessels, and (ii) a barcoded polynucleotide; and (d) amplifying (i) the first copy and the second copy with a first primer set, and (ii) the barcode with a second primer set, wherein a primer of the first primer set is complementary to a primer of the second set; and (e) forming first and second single cell barcoded sequences.

Abstract: Provided herein are methods for target gene sequencing and single cell barcoding in conjunction with analysis of gene expression in single cells. In some embodiments, the target gene is an immune molecule, such as an antibody or TCR. In some embodiments, the methods can be used to carry out transcriptome sequencing, e.g., RNA sequencing, to capture transcriptome of single cells paired with full receptor immune receptor sequences such that information about the immune repertoire and transcriptome of a cell can be determined. Also provided are polynucleotide libraries for use in carrying out transcriptome analysis and immune molecule, e.g., antibody or TCR, sequencing.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. The methods and compositions can be used to pair any two sequences originating from a single cell, such as heavy and light chain antibody sequences, alpha and beta chain T-cell receptor sequences, or gamma and delta chain T-cell receptor sequences, for antibody and T-cell receptor discovery, disease and immune diagnostics, and low error sequencing.

Abstract: Provided in some aspects are compositions of cells for treating subjects with disease and conditions such as non-Hodgkin's lymphoma (NHL), and related methods, compositions, uses and articles of manufacture. In some embodiments, the disease or condition is a B-cell non-Hodgkin lymphoma (B-cell NHL). The cells generally express recombinant receptors such as chimeric antigen receptors (CARs) for targeting an antigen, such as CD 19, on cells of the lymphoma.

Abstract: Provided in some aspects are compositions of cells for treating subjects with disease and conditions such as multiple myeloma (MM), and related methods, compositions, uses and articles of manufacture. In some embodiments, the disease or condition is a relapsed or refractory multiple myeloma (r/r MM). The cells generally express recombinant receptors such as chimeric antigen receptors (CARs) for targeting an antigen, such as BCMA, on cells of the myeloma.

Abstract: This invention relates to novel anti-HIV antibodies that can be used in the treatment and detection of human immunodeficiency virus (HIV). These antibodies exhibit a high degree of sensitivity and can provide a broad range of specificity.

Abstract: Provided herein are methods and compositions for single cell characterization using affinity-oligonucleotide conjugates.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise steps of: (a) forming a plurality of first vessels each comprising: (i) a single cell, and (ii) a single solid support; (b) copying onto the single solid support: (i) a first copy of a first cell polynucleotide from the single cell, and (ii) a second copy of a second cell polynucleotide from the single cell; (c) forming a plurality of second vessels each comprising (i) a single solid support from the plurality of first vessels, and (ii) a barcoded polynucleotide; and (d) amplifying (i) the first copy and the second copy with a first primer set, and (ii) the barcode with a second primer set, wherein a primer of the first primer set is complementary to a primer of the second set; and (e) forming first and second single cell barcoded sequences.

Abstract: Provided herein are methods and compositions for single cell characterization using affinity-oligonucleotide conjugates. In some aspects, such methods may comprise attaching a first vessel barcoded polynucleotide to an oligonucleotide portion of an affinity-oligonucleotide conjugate, which binds to a target antigen expressed by a single cell that is isolated in a single vessel. In some aspects, the oligonucleotide portion of the affinity-oligonucleotide conjugate may comprise an antigen identification sequence (AID). In some aspects, the oligonucleotide portion of the affinity-oligonucleotide conjugate may further comprise an affinity molecular barcode (AMB) sequence. In some aspects, such methods may further comprise lysing the single cell and attaching a second vessel barcoded polynucleotide to a cell polynucleotide from the single cell.

Abstract: This invention relates to novel anti-HIV antibodies that can be used in the treatment and detection of human immunodeficiency virus (HIV). These antibodies exhibit a high degree of sensitivity and can provide a broad range of specificity.

Abstract: Provided herein are methods and compositions for high-throughput T-cell receptor target identification of natively paired T-cell receptor sequences.

Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise steps of: (a) forming a plurality of first vessels each comprising: (i) a single cell, and (ii) a single solid support; (b) copying onto the single solid support: (i) a first copy of a first cell polynucleotide from the single cell, and (ii) a second copy of a second cell polynucleotide from the single cell; (c) forming a plurality of second vessels each comprising (i) a single solid support from the plurality of first vessels, and (ii) a barcoded polynucleotide; and (d) amplifying (i) the first copy and the second copy with a first primer set, and (ii) the barcode with a second primer set, wherein a primer of the first primer set is complementary to a primer of the second set; and (e) forming first and second single cell barcoded sequences.

Abstract: Provided are methods for assessing nucleic acid sequences integrated into a genome of a genetically engineered cell, such as a genetically engineered cell used in cell therapy. Cells are generally genetically engineered to express a recombinant protein, such as a recombinant receptor, via introduction of a polynucleotide and integration of certain sequences in the polynucleotide, such as recombinant sequences, into the genome of the cell. In some aspects, the provided methods can be used to distinguish integrated nucleic acids and non-integrated, residual nucleic acids.