Patents by Inventor Orit Rozenblatt-Rosen

Orit Rozenblatt-Rosen 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).

  • Patent number: 11332736
    Abstract: The present invention provides methods and tools for analyzing genetic interactions. The subject matter disclosed herein is generally directed to single cell genomics and proteomics. In one embodiment provided is a method of cell and nuclei hashing using sample barcodes. In another embodiment are method of performing genomewide CRISPR perturbation screens.
    Type: Grant
    Filed: December 7, 2018
    Date of Patent: May 17, 2022
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology
    Inventors: Aviv Regev, Orit Rozenblatt-Rosen, Jellert Gaublomme, Bo Li, Kathryn Geiger-Schuller, Pratiksha Thakore
  • Publication number: 20220105135
    Abstract: The present invention is generally directed to identifying genes and cell types that are correlated with tumor progression in the tumor microenvironment. PENK was identified as a therapeutic target that is positively correlated with tumor time and size. Targeting PENK can enhance anti-tumor immunity. Opioid signaling can be modulated to enhance anti-tumor immunity. The present invention is also generally directed to interacting cells in the tumor microenvironment and using the identified interactions to enhance anti-tumor immunity in cancer. Identified interactions can be modulated using therapeutic agents. Immune cells resistant to suppression can be used for adoptive cell transfer.
    Type: Application
    Filed: October 5, 2021
    Publication date: April 7, 2022
    Inventors: Meromit Singer, Aviv Regev, Orit Rozenblatt-Rosen, Davide Mangani, Ana Carrizosa Anderson, Vijay K. Kuchroo, Linglin Huang
  • Patent number: 11214797
    Abstract: The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.
    Type: Grant
    Filed: April 27, 2018
    Date of Patent: January 4, 2022
    Assignees: The Broad Institute, Inc., Massachusetts Institute of Technology, The Regents of the University of California
    Inventors: Aviv Regev, Brittany Adamson, Brian Cleary, Le Cong, Atray Dixit, Jellert Gaublomme, Eric S. Lander, Thomas Norman, Oren Parnas, Orit Rozenblatt-Rosen, Alexander K. Shalek, Jonathan Weissman
  • Publication number: 20210395821
    Abstract: Techniques Nuc-seq, Div-Seq, and Dronc-Seq are allow for unbiased analysis of any complex tissue. Nuc-Seq, a scalable single nucleus RNA-Seq method, can sensitively identify closely related cell types, including within the adult hippocampus. Div-seq combines Nuc-Seq with EdU-mediated labeling of proliferating cells, allowing tracking of transcriptional dynamics of newborn neurons in an adult neurogenic region in the hippocampus. Dronc-Seq uses a microfluidic device to co-encapsulate individual nuclei in reverse emulsion aqueous droplets in an oil medium together with one uniquely barcoded mRNA-capture bead.
    Type: Application
    Filed: November 13, 2018
    Publication date: December 23, 2021
    Inventors: Naomi Habib, Aviv Regev, Eugene Drokhlyansky, Anindita Basu, Inbal Avraham-Davidi, Orit Rozenblatt-Rosen, David A. Weitz
  • Publication number: 20210171938
    Abstract: The present invention provides methods and tools for analyzing genetic interactions. The subject matter disclosed herein is generally directed to single cell genomics and proteomics. In one embodiment provided is a method of cell and nuclei hashing using sample barcodes. In another embodiment are method of performing genomewide CRISPR perturbation screens.
    Type: Application
    Filed: December 7, 2018
    Publication date: June 10, 2021
    Inventors: Aviv Regev, Orit Rozenblatt-Rosen, Jellert Gaublomme, Bo Li, Kathryn Geiger-Schuller
  • Publication number: 20210115407
    Abstract: Provided herein are methods and compositions for identifying ionocytes from respiratory epithelial cells, and uses of such cells for treatment of inflammatory lung disease. Also provided herein are methods and compositions for modulating respiratory tract epithelial cell proliferation, differentiation, maintenance, and/or function.
    Type: Application
    Filed: April 12, 2018
    Publication date: April 22, 2021
    Inventors: Jayaraj Rajagopal, Aviv Regev, Moshe Biton, Adam Haber, Daniel Montoro, Orit Rozenblatt-Rosen
  • Publication number: 20210102168
    Abstract: The present invention is generally directed to identify interacting cells in the tumor microenvironment and using the identified interactions to enhance anti-tumor immunity in cancer. Identified interactions can be modulated using therapeutic agents. Immune cells resistant to suppression can be used for adoptive cell transfer. The present invention is also generally directed to cell types and genes that are correlated to time of tumor growth and tumor size.
    Type: Application
    Filed: October 5, 2020
    Publication date: April 8, 2021
    Inventors: Meromit Singer, Aviv Regev, Orit Rozenblatt-Rosen, Davide Mangani, Ana Carrizosa Anderson, Vijay K. Kuchroo, Linglin Huang
  • Publication number: 20210047694
    Abstract: The present invention is generally directed to a colorectal (CRC) cell atlas that provides methods of predicting outcomes of cancer patients and therapeutic targets for treating patients in need thereof. The atlas may be used to predict a response to immunotherapy, in particular checkpoint blockade therapy and adoptive cell transfer. Disclosed herein are previously unidentified gene programs in tumors that can be used to predict response and provide for therapeutic targets that can be used to shift a tumor to a responsive phenotype.
    Type: Application
    Filed: August 17, 2020
    Publication date: February 18, 2021
    Inventors: Aviv Regev, Nir Hacohen, Vijay K. Kuchroo, Ana Carrizosa Anderson, Orit Rozenblatt-Rosen, Jonathan Chen, Karin Pelka, Matan Hofree
  • Publication number: 20200390786
    Abstract: Described herein are compositions and methods of using single-cell RNA-sequencing to identify treatment resistance in patients with ovarian cancer. Also, described herein are compositions and methods for treatment targeting resistance in patients with ovarian cancer.
    Type: Application
    Filed: March 30, 2018
    Publication date: December 17, 2020
    Inventors: Levi Garraway, Benjamin Izar, Aviv Regev, Orit Rozenblatt-Rosen, Asaf Rotem, Elizabeth Stover, Itay Tirosh
  • Publication number: 20200362334
    Abstract: The present disclosure provides compositions, systems, and methods for pooled screening of perturbations correlating to a phenotype. The present disclosure also provides for methods of in vivo perturbation screening. The present disclosure also provides for high-throughput sample multiplexing. The present disclosure also provides for methods to determine the clonal effects associated with millions of genetic perturbation combinations using standard pooled screening reagents.
    Type: Application
    Filed: December 7, 2018
    Publication date: November 19, 2020
    Inventors: Aviv Regev, Atray Dixit, Orit Rozenblatt-Rosen
  • Publication number: 20200347449
    Abstract: Provided herein are methods of recovering single nuclei from a tissue sample comprising chopping or dounce homogenizing the tissue sample in a nuclear extraction buffer at 4° C. to produce a tissue homogenate; centrifuging the tissue homogenate to produce a nuclear pellet; resuspending the nuclear pellet in a nuclear resuspension buffer comprising bovine serum albumin, RNase inhibitor, and salts to produce a resuspension; and filtering the resuspension through a strainer, wherein the single nuclei are present in a supernatant passed through the strainer. The invention also provides a method of single cell sequencing comprising extracting nuclei from a population of cells under conditions that preserve a portion of the outer nuclear envelope and rough endoplasmic reticulum; sorting single nuclei into separate reaction vessels; extracting RNA from the single nuclei; generating a cDNA library, whereby gene expression data from single cells are obtained. The tissue sample may be fresh or frozen.
    Type: Application
    Filed: May 1, 2020
    Publication date: November 5, 2020
    Inventor: Orit Rozenblatt-Rosen
  • Publication number: 20200347456
    Abstract: The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The novel gene signatures predict overall survival in cancer and can be targeted therapeutically. Specifically, disclosed is a resistance program identified by a comprehensive single-cell profiling study in melanoma patients, which was validated in two large validation cohorts. Using a large-scale in silico prediction, CDK4/6 inhibitors were identified as a class of drugs that may reverse this resistance program. These predictions were validated in melanoma cell lines, patient-derived co-culture models, and melanoma in vivo models, which show that the combination of abemaciclib and immune checkpoint blockade (ICB) overcome intrinsic drug resistance. The present invention provides for detecting an immunotherapy resistance signature and modulating the signature with CDK4/6 inhibition.
    Type: Application
    Filed: October 2, 2018
    Publication date: November 5, 2020
    Inventors: Aviv Regev, Orit Rozenblatt-Rosen, Benjamin Izar, Livnat Jerby, Asaf Rotem
  • Publication number: 20200157633
    Abstract: The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The novel gene signatures predict overall survival in cancer and can be targeted therapeutically.
    Type: Application
    Filed: March 30, 2018
    Publication date: May 21, 2020
    Inventors: Aviv Regev, Orit Rozenblatt-Rosen, Benjamin Izar, Livnat Jerby, Asaf Rotem
  • Publication number: 20200102386
    Abstract: This invention relates generally to compositions and methods for modulating complement component 3 (C3) activity or expression to treat, control or otherwise influence tumors and tissues, including cells and cell types of the tumors and tissues, and malignant, microenvironmental, or immunologic states of the tumor cells and tissues. The invention also relates to methods of diagnosing, prognosing and/or staging of tumors, tissues and cells.
    Type: Application
    Filed: June 14, 2018
    Publication date: April 2, 2020
    Inventors: Aviv Regev, Ana Carrizosa Anderson, Ayshwarya Subramanian, Orit Rozenblatt-Rosen
  • Publication number: 20200023007
    Abstract: This invention relates generally to compositions and methods for modulating complement component 3 (C3) activity or expression to treat, control or otherwise influence tumors and tissues, including cells and cell types of the tumors and tissues, and malignant, microenvironmental, or immunologic states of the tumor cells and tissues. The invention also relates to methods of diagnosing, prognosing and/or staging of tumors, tissues and cells.
    Type: Application
    Filed: June 14, 2019
    Publication date: January 23, 2020
    Inventors: Aviv Regev, Ana Carrizosa Anderson, Ayshwarya Subramanian, Orit Rozenblatt-Rosen
  • Publication number: 20190367964
    Abstract: Described herein are compositions and methods of disaggregating a tissue sample into single cells.
    Type: Application
    Filed: February 2, 2017
    Publication date: December 5, 2019
    Applicants: DANA-FARBER CANCER INSTITUTE, INC., THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, PRESIDENT AND FELLOWS OF HARVARD COLLEGE
    Inventors: Benjamin Izar, Levi Garraway, Asaf Rotem, Aviv Regev, Alexander Shalek, Marc Wadsworth, Sanjay Prakadan, Orit Rozenblatt-Rosen, Itay Tirosh
  • Publication number: 20190263912
    Abstract: An atlas of intestinal epithelial cells, intestinal epithelial stem cells and intestinal immune cells identifies new cell populations, markers, networks, and responses to stimuli. Intestinal T cells drive intestinal epithelial cell differentiation and activity. Accordingly, disclosed are methods of modulating intestinal epithelial cell differentiation, maintenance and/or function, related methods for the treatment of disease, including IBD. Also disclosed are methods and kits for identifying cell types, their differentiation, homeostasis and activation.
    Type: Application
    Filed: November 7, 2017
    Publication date: August 29, 2019
    Inventors: Adam Haber, Moshe Biton, Rebecca H. Herbst, Karthik Shekhar, Christopher Smillie, Orit Rozenblatt-Rosen, Ramnik Xavier, Aviv Regev, Jose Ordovas-Montanes, Alexander K. Shalek, Noga Rogel
  • Publication number: 20190085324
    Abstract: The present invention provides tools and methods for the systematic analysis of genetic interactions, including higher order interactions. The present invention provides tools and methods for combinatorial probing of cellular circuits, for dissecting cellular circuitry, for delineating molecular pathways, and/or for identifying relevant targets for therapeutics development.
    Type: Application
    Filed: April 27, 2018
    Publication date: March 21, 2019
    Inventors: Aviv Regev, Brittany Adamson, Brian Cleary, Le Cong, Atray Dixit, Jellert Gaublomme, Eric S. Lander, Thomas Norman, Oren Parnas, Orit Rozenblatt-Rosen, Alexander K. Shalek, Jonathan Weissman
  • Publication number: 20180100201
    Abstract: This invention relates generally to compositions and methods for identifying genes and gene networks that respond to, modulate, control or otherwise influence tumors and tissues, including cells and cell types of the tumors and tissues, and malignant, microenvironmental, or immunologic states of the tumor cells and tissues. The invention also relates to methods of diagnosing, prognosing and/or staging of tumors, tissues and cells, and provides compositions and methods of modulating expression of genes and gene networks of tumors, tissues and cells, as well as methods of identifying, designing and selecting appropriate treatment regimens. The invention also relates to the modulation of complement activity to shift cellular immunity and obtain an effective therapeutic response.
    Type: Application
    Filed: December 17, 2017
    Publication date: April 12, 2018
    Inventors: Levi A. Garraway, Benjamin Izar, Sanjay Prakadan, Aviv Regev, Orit Rozenblatt-Rosen, Alexander K. Shalek, Mario Suva, Itay Tirosh, Andrew Venteicher, Marc H. Wadsworth II, Bradley Bernstein, Anuraag Parikh, Sidharth Puram