Patents Assigned to The Broad Institute
  • Multi-effector CRISPR based diagnostic systems
    Patent number: 11898142
    Abstract: The embodiments disclosed herein utilized RNA targeting effectors to provide a robust CRISPR-based diagnostic with attomolar sensitivity. Embodiments disclosed herein can detect both DNA and RNA with comparable levels of sensitivity and can differentiate targets from non-targets based on single base pair differences. Moreover, the embodiments disclosed herein can be prepared in freeze-dried format for convenient distribution and point-of-care (POC) applications. Such embodiments are useful in multiple scenarios in human health including, for example, viral detection, bacterial strain typing, sensitive genotyping, and detection of disease-associated cell free DNA.
    Type: Grant
    Filed: September 7, 2018
    Date of Patent: February 13, 2024
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows Harvard College
    Inventors: Feng Zhang, Jonathan Gootenberg, Omar Abudayyeh
  • Substituted macrocyclic indole derivatives
    Patent number: 11891404
    Abstract: The present invention relates to substituted macrocyclic indole derivatives of general formula (I): in which R1, R2, R3, R4, R5, R6, A and L are as defined herein, methods of preparing said compounds, intermediate compounds useful for preparing said compounds, pharmaceutical compositions and combinations comprising said compounds, and the use of said compounds for manufacturing pharmaceutical compositions for the treatment or prophylaxis of diseases, in particular of hyperproliferative disorders, as a sole agent or in combination with other active ingredients.
    Type: Grant
    Filed: September 8, 2022
    Date of Patent: February 6, 2024
    Assignees: Bayer Aktiengesellschaft, Bayer Pharma Aktiengesellschaft, The Broad Institute, Inc.
    Inventors: Kai Thede, Anne Mengel, Clara Christ, Joachim Kuhnke, Sarah Anna Liesa Johannes, Philipp Buchgraber, Ulrich Klar, Ulrike Rauh, Stefan Kaulfuss, Amaury Ernesto Fernandez-Montalvan, Nicolas Werbeck, Ursula Moenning, Katrin Nowak-Reppel, Sven Wittrock, David McKinney, Michael H. Serrano-Wu, Chris Lemke, Mark Fitzgerald, Christopher Nasveschuk, Kiel Lazarski, Steven James Ferrara, Laura Furst, Guo Wei, Patrick Ryan McCarren, Rebecca Ann Harvey
  • SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS
    Publication number: 20240035007
    Abstract: The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems.
    Type: Application
    Filed: December 27, 2022
    Publication date: February 1, 2024
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, University of Tokyo, President and Fellows of Harvard College
    Inventors: Silvana KONERMANN, Alexandro TREVINO, Mark BRIGHAM, Fei RAN, Patrick HSU, Chie-yu LIN, Osamu NUREKI, Hiroshi NISHIMASU, Ryuichiro ISHITANI, Feng ZHANG
  • DELIVERY, ENGINEERING AND OPTIMIZATION OF SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION AND THERAPEUTIC APPLICATIONS
    Publication number: 20240035048
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are delivery systems and tissues or organ which are targeted as sites for delivery. Also provided are vectors and vector systems some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity and to edit or modify a target site in a genomic locus of interest to alter or improve the status of a disease or a condition.
    Type: Application
    Filed: June 30, 2023
    Publication date: February 1, 2024
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventor: Feng ZHANG
  • CRYSTAL STRUCTURE OF CRISPR CPF1
    Publication number: 20240035006
    Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.
    Type: Application
    Filed: November 14, 2022
    Publication date: February 1, 2024
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, University of Tokyo, The United States of America, as Represented by the Secretary Dept of Health and Human Services
    Inventors: Takashi Yamano, Hiroshi Nishimasu, Bernd Zetsche, Ian Slaymaker, Yinqing Li, Iana Fedorova, Kira Makarova, Linyi Gao, Eugene Koonin, Feng Zhang, Osamu Nureki
  • Method of treating autoimmune disease with lymphocyte antigen CD5-like (CD5L) protein
    Patent number: 11884717
    Abstract: Described herein are methods for suppressing an immune response in a subject, e.g., a subject with an autoimmune disease, by administering to the subject a therapeutically effective amount of recombinant CD5L, CD5L homodimers and/or CD5L:p40 heterodimers, or nucleic acids encoding any of these. Also described are methods for enhancing an immune response in a subject, e.g., a subject with cancer, infection, or an immune deficiency, by administering to the subject a therapeutically effective amount of an antibody or antigen-binding fragment thereof that binds specifically to CD5L, D5L homodimers and/or CD5L:p40 heterodimers, and inhibits their binding to the IL-23 receptor, or inhibits formation of the CD5L homodimer and/or CD5L:p40 heterodimer, or inhibitory nucleic acids that target CD5L and/or p40.
    Type: Grant
    Filed: April 9, 2021
    Date of Patent: January 30, 2024
    Assignees: The Brigham and Women's Hospital, Inc., The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventors: Vijay K. Kuchroo, Chao Wang, Aviv Regev, Karthik Shekhar
  • TRANSCRIPTOMICS WITH ELECTROPHYSIOLOGICAL RECORDING
    Publication number: 20240019353
    Abstract: Disclosed herein are methods and systems for correlating continuous physiological processes (e.g., electrophysiological activity) and biomolecular processes (e.g., gene expression) in cells within a tissue. Also disclosed herein are methods for preparing a tissue for continuous electrophysiological recording. Further disclosed herein are systems comprising nanoelectronic devices within cells in a tissue, wherein each nanoelectronic device comprises a unique electronic barcode. The methods and systems described herein comprise any tissue with electrical activity (e.g., brain tissue, heart tissue, nervous system tissue, muscle tissue, pancreas tissue, or gastrointestinal tract tissue). Additionally disclosed herein are methods for disease modeling, methods for discovering a target for treating a disease, and methods for drug screening.
    Type: Application
    Filed: October 27, 2021
    Publication date: January 18, 2024
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Xiao Wang, Jia Liu
  • Proteomic analysis with nucleic acid identifiers
    Patent number: 11873483
    Abstract: The disclosure provides methods and compositions useful for labeling of target molecules with origin-specific nucleic acid identifiers (for example, barcodes), which can be used subsequently to identify, quantify, or otherwise characterize a feature or activity of target molecules originating from a particular discreet volume. Such target molecules can include polypeptides expressed by cells, in which nucleic acid molecules encoding the polypeptides are labeled with the same, or matched, origin-specific nucleic acid identifiers.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: January 16, 2024
    Assignees: The Broad Institute, Inc., ÉCOLE SUPERIEURE DE PHYSIQUE ET DE CHIMIE INDUSTRIELLES DE LA VILLE DE PARIS (ESPCI PARIS TECH)
    Inventors: Robert Nicol, Andrew David Griffiths, Baptiste Saudemont, Timothy V. Kirk
  • N-[2-({4-[3-(ANILINO)-4-OXO-4,5,6,7-TETRAHYDRO-1H-PYRROLO[3,2-C]PYRIDIN-2-YL]PYRIDIN-3-YL)OXY)ETHYL]PROP-2-ENAMIDE DERIVATIVES AND SIMILAR COMPOUNDS AS EGFR INHIBITORS FOR THE TREATMENT OF CANCER
    Publication number: 20230416249
    Abstract: Compounds of formula (I) processes for their production and their use as pharmaceuticals.
    Type: Application
    Filed: May 10, 2023
    Publication date: December 28, 2023
    Applicants: Bayer Aktiengesellschaft, Bayer Pharma Aktiengesellschaft, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.
    Inventors: Stephan SIEGEL, Franziska SIEGEL, Volker SCHULZE, Markus BERGER, Keith GRAHAM, Ulrich KLAR, Jeremie Xavier G. MORTIER, Detlev SÜLZLE, Ulf BÖMER, Daniel KORR, Jens SCHRÖDER, Matthew MEYERSON, Heidi GREULICH, Bethany KAPLAN
  • SUBSTITUTED 3,6-DIHYDRO-2H-1,3,4-OXADIAZIN-2-ONES FOR THE TREATMENT OF SARCOMA
    Publication number: 20230405015
    Abstract: The present invention provides a method of treatment of sarcoma comprising administering to a patient in need thereof a compound of general formula (I), in which R1, R2, R3, and R4, are as defined herein, alone or in pharmaceutical compositions or combinations comprising said compounds as a sole agent or in combination with other active ingredients.
    Type: Application
    Filed: August 31, 2023
    Publication date: December 21, 2023
    Applicants: Bayer Aktiengesellschaft, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.
    Inventors: Martin LANGE, Stefan KAULFUSS, Charlotte Christine KOPITZ, Heidi GREULICH, Xiaoyun WU, Matthew MEYERSON
  • DELIVERY, ENGINEERING AND OPTIMIZATION OF SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION AND THERAPEUTIC APPLICATIONS
    Publication number: 20230399662
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are delivery systems and tissues or organ which are targeted as sites for delivery. Also provided are vectors and vector systems some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity and to edit or modify a target site in a genomic locus of interest to alter or improve the status of a disease or a condition.
    Type: Application
    Filed: June 30, 2023
    Publication date: December 14, 2023
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventor: Feng ZHANG
  • Proteomics and spatial patterning using antenna networks
    Patent number: 11841371
    Abstract: The application relates to methods and systems for proteomics and spatial mapping of biomolecules using a next generation sequencing readout to decipher biomolecular and cellular interaction networks. Specifically, disclosed are antenna networks generated by conjugating DNA antennas to proteins. The antennas carry a unique antenna identifier (UAI) sequence that can provide spatial location of the network, as well as biomolecules by transfer of the UAI to reporter oligonucleotides associated with other antennas and biomolecules. The methods and systems are also applicable to single cells.
    Type: Grant
    Filed: March 13, 2019
    Date of Patent: December 12, 2023
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventors: Aviv Regev, Jellert Gaublomme
  • Compositions and methods related to di-substituted bicyclo[2.2.1] heptanamine-containing compounds
    Patent number: 11840495
    Abstract: The present disclosure relates to compositions and methods related to bicyclo[2.2.1] heptanamine-containing compounds and salts.
    Type: Grant
    Filed: December 23, 2021
    Date of Patent: December 12, 2023
    Assignees: The Broad Institute, Inc., Instituto Carlos Slim de la Salud, A.C., Brigham and Women's Hospital, Inc.
    Inventors: Brian T. Chamberlain, David Kornfilt, Florence F. Wagner, Maria Alimova, Anna Greka, Joseph Growney
  • Compositions and methods for diagnosing, evaluating and treating cancer by means of the DNA methylation status
    Patent number: 11834718
    Abstract: The present invention relates to methods of determining a cancer treatment prognosis for a subject in need thereof by evaluating epigenetic and genetic changes within a tumor sample from the subject. The present invention further provides methods of treating cancer in a subject by evaluating epigenetic and genetic changes within a tumor sample from the subject. In addition, the present invention provides methods of screening test agents to identify agents that decrease tumor cell plasticity.
    Type: Grant
    Filed: September 10, 2020
    Date of Patent: December 5, 2023
    Assignees: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard College
    Inventors: Mark Kendell Clement, Gad Getz, Dan-Avi Landau, Alexander Meissner, Catherine Ju-Ying Wu
  • METHODS AND COMPOSITIONS FOR PRIME EDITING NUCLEOTIDE SEQUENCES
    Publication number: 20230383289
    Abstract: Compositions and methods are provided herein for conducting prime editing of a target DNA molecule (e.g., a genome) that enables the incorporation of a nucleotide change and/or targeted mutagenesis. The compositions include fusion proteins comprising nucleic acid programmable DNA binding proteins (napDNAbp) and a polymerase (e.g., reverse transcriptase), which is guided to a specific DNA sequence by a modified guide RNA, named an PEgRNA. The PEgRNA has been altered (relative to a standard guide RNA) to comprise an extended portion that provides a DNA synthesis template sequence which encodes a single strand DNA flap which is synthesized by the polymerase of the fusion protein and which becomes incorporated into the target DNA molecule.
    Type: Application
    Filed: May 31, 2023
    Publication date: November 30, 2023
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone, James William Nelson
  • CRISPR-CAS COMPONENT SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION
    Publication number: 20230374527
    Abstract: The invention provides for systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for selecting specific cells by introducing precise mutations utilizing the CRISPR/Cas system.
    Type: Application
    Filed: April 13, 2023
    Publication date: November 23, 2023
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventor: Feng Zhang
  • OPTIMIZED CRISPR-CAS DOUBLE NICKASE SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION
    Publication number: 20230374550
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.
    Type: Application
    Filed: February 6, 2023
    Publication date: November 23, 2023
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Feng ZHANG, Patrick HSU, Chie-yu LIN, Fei RAN
  • COMPOSITIONS AND METHODS OF USE OF CRISPR-CAS SYSTEMS IN NUCLEOTIDE REPEAT DISORDERS
    Publication number: 20230365950
    Abstract: The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are delivery systems and tissues or organ which are targeted as sites for delivery. Also provided are vectors and vector systems some of which encode one or more components of a SIN CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing SIN CRISPR complex formation in eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity and to edit or modify a target site in a genomic locus of interest to alter or improve the status of a disease or a condition.
    Type: Application
    Filed: February 8, 2023
    Publication date: November 16, 2023
    Applicants: The Broad Institute, Inc., Massachusetts Institute of Technology, University of Iowa Research Foundation
    Inventors: Feng ZHANG, Beverly DAVIDSON, Chie-Yu LIN, Edgardo RODRIGUEZ
  • 2,4,5-TRISUBSTITUTED 1,2,4-TRIAZOLONES USEFUL AS INHIBITORS OF DHODH
    Publication number: 20230365524
    Abstract: The present invention provides triazolone compounds of general formula (I): in which R1, R2, R3, R4, and R5 are as defined herein, methods of preparing said compounds, intermediate compounds useful for preparing said compounds, pharmaceutical compositions and combinations comprising said compounds and the use of said compounds for manufacturing pharmaceutical compositions for the treatment and prophylaxis of diseases, in particular hyperproliferative disorders, as a sole agent or in combination with other active ingredients.
    Type: Application
    Filed: April 20, 2023
    Publication date: November 16, 2023
    Applicants: Bayer Aktiengesellschaft, Bayer Pharma Aktiengesellschaft, The Broad Institute, Inc., President and Fellows of Harvard College, The General Hospital Corporation
    Inventors: Stefan Nikolaus GRADL, Duy NGUYEN, Knut EIS, Judith GÜNTHER, Timo STELLFELD, Andreas JANZER, Sven CHRISTIAN, Thomas MÜLLER, Sherif El SHEIKH, Han Jie ZHOU, Changjia ZHAO, David B. SYKES, Steven James FERRARA, Kery LIU, Michael KRÖBER, Claudia MERZ, Michael NIEHUES, Martina SCHÄFER, Katja ZIMMERMANN, Carl Friedrich NISING
  • Methods for characterizing bladder cancer
    Patent number: 11814687
    Abstract: The present invention features methods for characterizing mutational profiles in patients with bladder cancer.
    Type: Grant
    Filed: August 7, 2020
    Date of Patent: November 14, 2023
    Assignees: The Broad Institute, Inc., The General Hospital Corporation, Baylor College of Medicine, The Brigham and Women's Hospital, Inc., Northwestern University, The Johns Hopkins University, United States Government as represented by the U.S. Department of Veterans Affairs
    Inventors: Jaegil Kim, Gad Getz, Seth Paul Lerner, David Kwiatkowski, Joshua Meeks, Joaquim Bellmunt, David McConkey