Patents by Inventor John Stamatoyannopoulos

John Stamatoyannopoulos has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20240066148
    Abstract: The presently disclosed subject matter provides for expression cassettes that allow for expression of a globin gene or a functional portion thereof, vectors comprising thereof, and cells transduced with such expression cassettes and vectors. The presently disclosed subject matter further provides methods for treating a hemoglobinopathy in a subject comprising administering an effective amount of such transduced cells to the subject.
    Type: Application
    Filed: January 26, 2023
    Publication date: February 29, 2024
    Applicants: MEMORIAL SLOAN-KETTERING CANCER CENTER, UNIVERSITY OF WASHINGTON
    Inventors: Michel Sadelain, Isabelle Riviere, Jorge Mansilla-Soto, Xiuyan Wang, George Stamatoyannopoulos, John Stamatoyannopoulos, Mingdong Liu
  • Patent number: 11900600
    Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.
    Type: Grant
    Filed: October 10, 2022
    Date of Patent: February 13, 2024
    Assignee: Altius Institute for Biomedical Sciences
    Inventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Alexander Muratov, Wouter Meuleman, William Kerwin
  • Publication number: 20230399660
    Abstract: The present disclosure provides genome engineering proteins, e.g., nucleic acid binding domains and/or functional domains that have a net positive charge and are cell permeable and can be introduced into the cells without the use of a carrier such as micelles, vesicles, liposomes, and the like.
    Type: Application
    Filed: October 22, 2021
    Publication date: December 14, 2023
    Inventors: Alexander J. Federation, Kyle Siebenthall, Aidan Quigley, Alister PW Funnell, John A. Stamatoyannopoulos
  • Patent number: 11788101
    Abstract: Provided herein are methods for identifying high potency genomic insulator elements that can be used in a vector composition e.g., that are useful for preventing unwanted expression of neighboring genes, such as proto-oncogenes, when administered to a subject in need thereof. Also provided herein are methods for treating disease and methods for administering a nucleic acid to a subject using such vectors.
    Type: Grant
    Filed: January 31, 2020
    Date of Patent: October 17, 2023
    Assignee: UNIVERSITY OF WASHINGTON
    Inventors: George Stamatoyannopoulos, John Stamatoyannopoulos
  • Publication number: 20230274423
    Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.
    Type: Application
    Filed: October 10, 2022
    Publication date: August 31, 2023
    Inventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Alexander Muratov, Wouter Meuleman, William Kerwin
  • Publication number: 20230257722
    Abstract: DNA cleaving enzymes are disclosed. The DNA cleaving enzymes are fused to a heterologous DNA binding domain that is designed to bind to a target nucleic acid sequence. Nucleic acids and expression cassettes encoding the DNA cleaving enzymes are also provided. Methods for genome editing using the DNA cleaving enzymes, fusion proteins, and compositions thereof are disclosed herein.
    Type: Application
    Filed: June 26, 2019
    Publication date: August 17, 2023
    Inventors: John A. Stamatoyannopoulos, Fyodor Urnov, Jocelynn Pearl, Sean Thomas
  • Patent number: 11717579
    Abstract: The presently disclosed subject matter provides for expression cassettes that allow for expression of a globin gene or a functional portion thereof, vectors comprising thereof, and cells transduced with such expression cassettes and vectors. The presently disclosed subject matter further provides methods for treating a hemoglobinopathy in a subject comprising administering an effective amount of such transduced cells to the subject.
    Type: Grant
    Filed: March 3, 2017
    Date of Patent: August 8, 2023
    Assignees: MEMORIAL SLOAN-KETTERING CANCER CENTER, UNIVERSITY OF WASHINGTON
    Inventors: Michel Sadelain, Isabelle Riviere, Jorge Mansilla-Soto, Xiuyan Wang, George Stamatoyannopoulos, John Stamatoyannopoulos, Mingdong Liu
  • Publication number: 20230227513
    Abstract: The present disclosure provides methods and compositions for modulating expression of a target gene in a cell by reducing binding of an endogenous transcription factor to a regulatory sequence of the target gene. The method includes introducing into the cell a DNA binding polypeptide (DBF) that binds a sequence in regulatory region of a target gene bound by a transcription factor (TF), thereby displacing the TF and modulating expression of the target gene. The DBF may be designed to bind a sequence comprising the binding site for the TF and additional nucleotides present on one or both sides of the sequence. Accordingly, the DBF specifically binds to binding site for the TF in the target gene but not in other genes that are also regulated by binding of the TF but do not include the nucleotides present on one or both sides of the sequence.
    Type: Application
    Filed: October 14, 2020
    Publication date: July 20, 2023
    Inventors: JENNIFER M. CHERONE, ALISTER PW FUNNELL, JOHN A. STAMATOYANNOPOULOS
  • Publication number: 20230134592
    Abstract: Methods, compositions, kits, and systems are provided for identifying regions of genomic DNA bound to a protein. The methods may include contacting genomic DNA with an adenine methyltransferase (A-MTase), where the A-MTase causes methylation of adenine residues in regions of the genomic DNA not bound to a protein; and conducting single molecule long read sequencing of the contacted genomic DNA to detect locations in the genomic DNA lacking methylated adenine residues to identify regions of genomic DNA bound to a protein. The bound regions may be nucleosome positions and the methods may determinenucleosome positions in genomic DNA. Also provided are methods for visualization of regions of chromatin not bound to a protein and spatially available as a substrate for an adenine methyltransferase (A-MTase) in a cell by visualizing location of methylated adenines after contacting the cells with the A-MTase.
    Type: Application
    Filed: April 2, 2021
    Publication date: May 4, 2023
    Inventors: John A. Stamatoyannopoulos, Andrew B. Stergachis
  • Publication number: 20220411822
    Abstract: Provided herein are expression cassettes comprising at least one copy of an enhancer element, wherein the enhancer element comprises or consists essentially of a nucleotide sequence at least 50% identical to any one of SEQ ID NOs: 1-10 and vectors comprising the expression cassettes. Also provided herein are cells transduced with the expression cassettes or the vectors. Further described herein are pharmaceutical compositions comprising an effective amount of one or more of: the cell, the expression cassette, or the vector of this disclosure. Also disclosed herein are methods of treating a hemoglobinopathy in a subject, comprising administering an effective amount of the pharmacological compositions described herein.
    Type: Application
    Filed: January 22, 2021
    Publication date: December 29, 2022
    Inventors: NIKOLETA PSATHA, JEFF VIERSTA, GRIGORIOS GEORGOLOPOULOS, JOHN A. STAMATOYANNOPOULOS
  • Publication number: 20220397526
    Abstract: Disclosed herein are methods of detecting a target nucleic acid sequence, determining the localization of the target nucleic acid sequence, and/or quantifying the number of target nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH.
    Type: Application
    Filed: May 4, 2022
    Publication date: December 15, 2022
    Inventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Vivek Nandakumar
  • Publication number: 20220372089
    Abstract: The present disclosure provides genome engineering proteins, e.g., nucleic acid binding domains and/or functional domains that have a net positive charge and are cell permeable and can be introduced into the cells without the use of a carrier such as micelles, vesicles, liposomes, and the like.
    Type: Application
    Filed: April 23, 2020
    Publication date: November 24, 2022
    Inventors: ALEXANDER J. FEDERATION, JOHN A. STAMATOYANNOPOULOS
  • Patent number: 11501429
    Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.
    Type: Grant
    Filed: July 19, 2018
    Date of Patent: November 15, 2022
    Assignee: Altius Institute for Biomedical Sciences
    Inventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Alexander Muratov, Wouter Meuleman, William Kerwin
  • Publication number: 20220306699
    Abstract: Provided herein are polypeptides, compositions comprising the polypeptides and methods for genome editing and gene regulation (e.g., activation and/or repression) using the polypeptides or the compositions comprising the polypeptides, such as, DNA binding domains derived from the genus of Ralstonia. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a TALE protein, such as, a Xanthomonas TALE protein. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a DNA binding protein derived from bacteria of the genus Ralstonia.
    Type: Application
    Filed: June 26, 2019
    Publication date: September 29, 2022
    Inventors: John A. Stamatoyannopoulos, Fyodor Urnov, Sean Thomas
  • Publication number: 20220290188
    Abstract: The present disclosure provides polypeptides, compositions thereof, and methods for suppressing expression of a target gene such as PDCD1, CTLA4, LAG3, or TIM-3. The polypeptides disclosed herein include a DNA binding domain (DBD) that binds to a sequence of the target gene and a transcriptional repressor domain that suppresses expression of the target gene. The transcriptional repressor domain may be a known transcriptional repressor or may be a novel transcriptional repressor disclosed herein. Also disclosed herein are novel transcriptional repressors that are conjugated to a heterologous DNA binding domain and mediate suppression of expression of a target gene bound by the DNA binding domain.
    Type: Application
    Filed: August 6, 2020
    Publication date: September 15, 2022
    Inventors: Fyodor Urnov, John A. Stamatoyannopoulos, Joycelynn Pearl, Matthew Wilken, Christie Ciarlo, Shon Green
  • Publication number: 20220220171
    Abstract: The present disclosure provides genome engineering proteins, e.g., nucleic acid binding domains and/or functional domains that have a net positive charge and are cell permeable and can be introduced into the cells without the use of a carrier such as micelles, vesicles, liposomes, and the like.
    Type: Application
    Filed: April 23, 2020
    Publication date: July 14, 2022
    Inventors: ALEXANDER J. FEDERATION, JOHN A. STAMATOYANNOPOULOS
  • Patent number: 11353400
    Abstract: Disclosed herein are methods of detecting a target nucleic acid sequence, determining the localization of the target nucleic acid sequence, and/or quantifying the number of target nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH.
    Type: Grant
    Filed: July 19, 2017
    Date of Patent: June 7, 2022
    Assignee: Altius Institute for Biomedical Sciences
    Inventors: John A. Stamatoyannopoulos, Shreeram Akilesh, Vivek Nandakumar
  • Publication number: 20220010366
    Abstract: Provided herein are methods and compositions for use in detecting on-target and/or off-target cleavage of genomic DNA in a cell by a nuclease. The on-target and off-target cleavage is detected by using oligonucleotides that bind to the single-stranded 3?-overhang created at the cleavage site. The nuclease may be an engineered nuclease comprising a nucleic acid binding domain that binds to a target nucleic acid of interest.
    Type: Application
    Filed: November 18, 2019
    Publication date: January 13, 2022
    Inventors: John Stamatoyannopoulos, Pavel Zrazhevskiy
  • Publication number: 20210371847
    Abstract: Provided herein are DNA binding domains comprising a plurality of repeat units, wherein each repeat unit is expanded or contracted in length. Also provided herein are DNA binding domains comprising a plurality of repeat units, wherein each repeat unit is separated from a neighboring repeat unit by a linker. In certain aspects, the linker includes a recognition site. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a TALE protein. The TALE protein may be a Xanthomonas TALE protein.
    Type: Application
    Filed: June 26, 2019
    Publication date: December 2, 2021
    Inventors: Fyodor Urnov, John A. Stamatoyannopoulos
  • Publication number: 20210310058
    Abstract: Disclosed herein are methods of detecting a target viral nucleic acid sequence, determining the localization of the target viral nucleic acid sequence, and/or quantifying the number of target viral nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH or viral Nano-FISH.
    Type: Application
    Filed: July 19, 2018
    Publication date: October 7, 2021
    Inventors: Shreeram AKILESH, John A. STAMATOYANNOPOULOS, Alessandra SULLIVAN, William KERWIN, Tobias RAGOCZY, Pavel ZRAZHEVSKIY