Patents by Inventor Jonathan Ma

Jonathan Ma 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: 20250064981
    Abstract: Nucleic acid molecules, compositions, recombinant AAV (rAAV) particles, kits, and methods are described herein for delivering a base editor (or “nucleobase editor”) to cells, e.g., via AAV vectors. In particular, the disclosure provides compositions, methods, and uses for delivery of adenine base editors and cytosine base editors in a single AAV vector (or genome). Further described herein are improved AAV vectors containing size-minimized regulatory components that enable, e.g., the packaging of base editors. Provided herein are methods and compositions for delivering base editor proteins to a cell or tissue in a single recombinant AAV (rAAV) vector. Contemplated herein are improved methods and compositions for delivering these base editors in vivo, in a single rAAV particle. Further provided herein are base editors and compositions and cells comprising these base editors.
    Type: Application
    Filed: October 25, 2024
    Publication date: February 27, 2025
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Jonathan Ma Levy, Jessie Rose Davis, Tony P. Huang, Isaac Witte
  • Patent number: 12031126
    Abstract: The present disclosure provides systems, compositions, and methods for simultaneously editing both strands of a double-stranded DNA sequence at a target site to be edited. In some aspects, the systems comprise a first and second prime editor complex, wherein each of the first and second prime editor complexes comprises (1) a prime editor comprising (i) a nucleic acid programmable DNA binding protein (napDNAbp), and (ii) a polypeptide having an RNA-dependent DNA polymerase activity; and (2) a pegRNA comprising a spacer sequence, gRNA core, a DNA synthesis template, and a primer binding site, wherein the DNA synthesis template encodes a desired DNA sequence or a complement thereof, wherein the desired DNA sequence and the complement thereof form a duplex comprising an edited portion which integrates into the target site to be edited. In some aspects, the systems comprise a first, second, third, and fourth prime editor complex, each comprising a prime editor and a PEgRNA.
    Type: Grant
    Filed: December 8, 2023
    Date of Patent: July 9, 2024
    Assignees: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone, Jonathan Ma Levy, Xin Gao, Christopher J. Podracky
  • Publication number: 20240158779
    Abstract: The present disclosure provides systems, compositions, and methods for simultaneously editing both strands of a double-stranded DNA sequence at a target site to be edited. In some aspects, the systems comprise a first and second prime editor complex, wherein each of the first and second prime editor complexes comprises (1) a prime editor comprising (i) a nucleic acid programmable DNA binding protein (napDNAbp), and (ii) a polypeptide having an RNA-dependent DNA polymerase activity; and (2) a pegRNA comprising a spacer sequence, gRNA core, a DNA synthesis template, and a primer binding site, wherein the DNA synthesis template encodes a desired DNA sequence or a complement thereof, wherein the desired DNA sequence and the complement thereof form a duplex comprising an edited portion which integrates into the target site to be edited. In some aspects, the systems comprise a first, second, third, and fourth prime editor complex, each comprising a prime editor and a PEgRNA.
    Type: Application
    Filed: December 8, 2023
    Publication date: May 16, 2024
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone, Jonathan Ma Levy, Xin Gao, Christopher J. Podracky
  • Patent number: 11912985
    Abstract: The present disclosure provides systems, compositions, and methods for simultaneously editing both strands of a double-stranded DNA sequence at a target site to be edited. Further provided herein are pharmaceutical compositions, polynucleotides, vectors, cells, and kits for simultaneously editing both strands of a double-stranded DNA sequence.
    Type: Grant
    Filed: November 7, 2022
    Date of Patent: February 27, 2024
    Assignees: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Andrew Vito Anzalone, Jonathan Ma Levy, Xin Gao, Christopher J. Podracky
  • Publication number: 20230220374
    Abstract: The present disclosure provides systems, compositions, and methods for simultaneously editing both strands of a double-stranded DNA sequence at a target site to be edited. In some aspects, the systems comprise a first and second prime editor complex, wherein each of the first and second prime editor complexes comprises (1) a prime editor comprising (i) a nucleic acid programmable DNA binding protein (napDNAbp), and (ii) a polypeptide having an RNA-dependent DNA polymerase activity; and (2) a pegRNA comprising a spacer sequence, gRNA core, a DNA synthesis template, and a primer binding site, wherein the DNA synthesis template encodes a desired DNA sequence or a complement thereof, wherein the desired DNA sequence and the complement thereof form a duplex comprising an edited portion which integrates into the target site to be edited. In some aspects, the systems comprise a first, second, third, and fourth prime editor complex, each comprising a prime editor and a PEgRNA.
    Type: Application
    Filed: November 7, 2022
    Publication date: July 13, 2023
    Applicants: THE BROAD INSTITUTE, INC., PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: David R. Liu, Andrew Vito Anzalone, Jonathan Ma Levy, Xin Gao, Christopher J. Podracky
  • Publication number: 20230159913
    Abstract: The disclosure provides methods of deaminating adenosine and cytosine bases in a target nucleic acid sequence in an USH2A gene comprising contacting the USH2A gene with a base editor in association with a guide RNA (gRNA). In some aspects, base editing is used to restore US2HA function by disrupting a splice site in the USH2A gene sequence to induce skipping of an exon containing a mutation, while in other embodiments, base editing is used to restore US2HA function by correcting a point mutation e.g., in an exon) so as to correct mutations. The disclosure also provides complexes of adenosine base editors and guide RNAs, and complexes of cytidine base editors and guide RNAs. The disclosure further provides pharmaceutical compositions and cells comprising these complexes. The disclosure also provides vectors encoding these complexes, base editors, and gRNAs. In some embodiments, the methods and compositions provided herein are used to treat Usher syndrome and autosomal recessive retinitis pigmentosa (arRP).
    Type: Application
    Filed: April 27, 2021
    Publication date: May 25, 2023
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College, Massachusetts Eye and Ear Infirmary
    Inventors: David R. Liu, Jonathan Ma Levy, Wei Hsi Yeh, Jason Comander, Yuki Tachida, Eric A. Pierce, Qin Liu, Nachiket Pendse
  • Publication number: 20220249697
    Abstract: Provided herein are methods of delivering “split” Cas9 protein or nucleobase editors into a cell, e.g., via a recombinant adeno-associated vims (rAAV), to form a complete and functional Cas9 protein or nucleobase editor. The Cas9 protein or the nucleobase editor is split into two sections, each fused with one part of an intein system (e.g., intein-N and intein-C encoded by the dnaE-n and dnaE-c genes, respectively). Upon co-expression, the two sections of the Cas9 protein or nucleobase editor are ligated together via intein-mediated protein splicing. Nucleic acid molecules encoding the N-terminal portion of a Cas9 protein or a nucleobase editor fused to an intein, and nucleic acid molecules encoding the C-terminal portion of a Cas9 protein or nucleobase editor, are provided. Recombinant AAV vectors (e.
    Type: Application
    Filed: May 20, 2020
    Publication date: August 11, 2022
    Applicants: The Broad Institute, Inc., President and Fellows of Harvard College
    Inventors: David R. Liu, Jonathan Ma Levy, Wei Hsi Yeh
  • Publication number: 20220213507
    Abstract: Provided herein are methods of delivering “split” Cas9 protein or nucleobase editors into a cell, e.g., via a recombinant adeno-associated virus (rAAV), to form a complete and functional Cas9 protein or nucleobase editor. The Cas9 protein or the nucleobase editor is split into two sections, each fused with one part of an intein system (e.g., intein-N and intein-C encoded by dnaEn and dnaEc, respectively). Upon co-expression, the two sections of the Cas9 protein or nucleobase editor are ligated together via intein-mediated protein splicing. Recombinant AAV vectors and particles for the delivery of the split Cas9 protein or nucleobase editor, and methods of using such AAV vectors and particles are also provided.
    Type: Application
    Filed: March 11, 2022
    Publication date: July 7, 2022
    Applicant: President and Fellows of Harvard College
    Inventors: David R. Liu, Jonathan Ma Levy, Wei Hsi Yeh
  • Patent number: 11306324
    Abstract: Provided herein are methods of delivering “split” Cas9 protein or nucleobase editors into a cell, e.g., via a recombinant adeno-associated virus (rAAV), to form a complete and functional Cas9 protein or nucleobase editor. The Cas9 protein or the nucleobase editor is split into two sections, each fused with one part of an intein system (e.g., intein-N and intein-C encoded by dnaEn and dnaEc, respectively). Upon co-expression, the two sections of the Cas9 protein or nucleobase editor are ligated together via intein-mediated protein splicing. Recombinant AAV vectors and particles for the delivery of the split Cas9 protein or nucleobase editor, and methods of using such AAV vectors and particles are also provided.
    Type: Grant
    Filed: October 13, 2017
    Date of Patent: April 19, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: David R. Liu, Jonathan Ma Levy, Wei Hsi Yeh
  • Publication number: 20210032275
    Abstract: Methods for forming a Ge-containing film on a substrate comprise the steps of introducing a vapor of a cyclic Ge(II) silylamido precursor into a reactor having the substrate disposed therein and depositing at least part of the cyclic Ge(II) silylamido precursor onto the substrate to form the Ge-containing film using a vapor deposition method. The cyclic Ge(II) silylamido precursor is [SiMe3-(N—)—SiMe2-(N—)—SiMe3]Ge(II) or [tBu-(N—)—SiMe2-(N—)-tBu]Ge(II).
    Type: Application
    Filed: July 30, 2020
    Publication date: February 4, 2021
    Inventors: Naohisa NAKAGAWA, Jean-Marc GIRARD, Raphael ROCHAT, Takio KIZU, Jonathan MA, Vitaly NESTEROV
  • Patent number: 10827014
    Abstract: An online system predicts the user's activity on the online system during a future time interval (e.g., the next day). The system collects activity data, such as actions that the user has taken on the system. The system predicts whether the user is likely to be active during the future time interval based on features extracted from the activity data. This system determines selection of notifications and delivery of notifications based on the predicted time when the user is likely to be active on the online system. The system further records the user's past interactions with notifications, such as whether the user viewed the notification, whether the user interacted with a content item associated with the notification, and so on. If system determines a rate of delivery of notifications to the user based on the frequency of past user interactions with notifications.
    Type: Grant
    Filed: April 22, 2019
    Date of Patent: November 3, 2020
    Assignee: Facebook, Inc.
    Inventors: Li Ju, Matthew Bryan Folz, Ramanathan Palaniappan, Jonathan Ma, Pawel Bara
  • Patent number: 10313461
    Abstract: An online system predicts the user's activity on the online system during a future time interval (e.g., the next day). The system collects activity data, such as actions that the user has taken on the system. The system predicts whether the user is likely to be active during the future time interval based on features extracted from the activity data. This system determines selection of notifications and delivery of notifications based on the predicted time when the user is likely to be active on the online system. The system further records the user's past interactions with notifications, such as whether the user viewed the notification, whether the user interacted with a content item associated with the notification, and so on. If system determines a rate of delivery of notifications to the user based on the frequency of past user interactions with notifications.
    Type: Grant
    Filed: November 17, 2016
    Date of Patent: June 4, 2019
    Assignee: Facebook, Inc.
    Inventors: Li Ju, Matthew Bryan Folz, Ramanathan Palaniappan, Jonathan Ma, Pawel Bara
  • Patent number: 10116758
    Abstract: An online system predicts the user's activity on the online system during a future time interval (e.g., the next day). The system collects activity data, such as actions that the user has taken on the system. The system predicts whether the user is likely to be active during the future time interval based on features extracted from the activity data. This system determines selection of notifications and delivery of notifications based on the predicted time when the user is likely to be active on the online system. The system further records the user's past interactions with notifications, such as whether the user viewed the notification, whether the user interacted with a content item associated with the notification, and so on. If system determines a rate of delivery of notifications to the user based on the frequency of past user interactions with notifications.
    Type: Grant
    Filed: November 17, 2016
    Date of Patent: October 30, 2018
    Assignee: Facebook, Inc.
    Inventors: Li Ju, Matthew Bryan Folz, Ramanathan Palaniappan, Jonathan Ma, Pawel Bara
  • Publication number: 20180139294
    Abstract: An online system predicts the user's activity on the online system during a future time interval (e.g., the next day). The system collects activity data, such as actions that the user has taken on the system. The system predicts whether the user is likely to be active during the future time interval based on features extracted from the activity data. This system determines selection of notifications and delivery of notifications based on the predicted time when the user is likely to be active on the online system. The system further records the user's past interactions with notifications, such as whether the user viewed the notification, whether the user interacted with a content item associated with the notification, and so on. If system determines a rate of delivery of notifications to the user based on the frequency of past user interactions with notifications.
    Type: Application
    Filed: November 17, 2016
    Publication date: May 17, 2018
    Inventors: Li Ju, Matthew Bryan Folz, Ramanathan Palaniappan, Jonathan Ma, Pawel Bara
  • Publication number: 20180139295
    Abstract: An online system predicts the user's activity on the online system during a future time interval (e.g., the next day). The system collects activity data, such as actions that the user has taken on the system. The system predicts whether the user is likely to be active during the future time interval based on features extracted from the activity data. This system determines selection of notifications and delivery of notifications based on the predicted time when the user is likely to be active on the online system. The system further records the user's past interactions with notifications, such as whether the user viewed the notification, whether the user interacted with a content item associated with the notification, and so on. If system determines a rate of delivery of notifications to the user based on the frequency of past user interactions with notifications.
    Type: Application
    Filed: November 17, 2016
    Publication date: May 17, 2018
    Inventors: Li Ju, Matthew Bryan Folz, Ramanathan Palaniappan, Jonathan Ma, Pawel Bara
  • Publication number: 20180127780
    Abstract: Provided herein are methods of delivering “split” Cas9 protein or nucleobase editors into a cell, e.g., via a recombinant adeno-associated virus (rAAV), to form a complete and functional Cas9 protein or nucleobase editor. The Cas9 protein or the nucleobase editor is split into two sections, each fused with one part of an intein system (e.g., intein-N and intein-C encoded by dnaEn and dnaEc, respectively). Upon co-expression, the two sections of the Cas9 protein or nucleobase editor are ligated together via intein-mediated protein splicing. Recombinant AAV vectors and particles for the delivery of the split Cas9 protein or nucleobase editor, and methods of using such AAV vectors and particles are also provided.
    Type: Application
    Filed: October 13, 2017
    Publication date: May 10, 2018
    Inventors: David R. Liu, Jonathan Ma Levy, Wei Hsi Yeh
  • Publication number: 20110011394
    Abstract: Aerosolized food products can be of sufficient size to deposit in the mouth without easily entering into the respiratory tract and of small enough size so as to allow for suspension in air. An apparatus (110) incorporating an aerosol generating device and food products can allow for the aerosolization of the food products and the delivery thereof in a matter suitable for inhalation or deposition and subsequent ingestion. The food delivery apparatus (110) represents a novel means of delivering food to the mouths of humans and animals. Indeed, the apparatus (110) of the invention is designed to produce, transport, and direct aerosolized food particles of sufficient size to deposit in the mouth without substantial exposure or entry into the respiratory tract and of small enough size so as to allow for suspension in air.
    Type: Application
    Filed: October 8, 2008
    Publication date: January 20, 2011
    Inventors: David A. Edwards, Jonathan Ma, Jonathan Jacques Kamler, José Sanchez