Patents by Inventor Ramnik Xavier
Ramnik Xavier 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).
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Publication number: 20240108689Abstract: The subject matter disclosed herein is generally directed to pathogenic Th1 cells whose phenotype is dependent on IL-23R signaling. Th1 cell specific therapeutic targets and gene programs are disclosed herein. In particular, inhibition of CD160 reduces Th1 cell pathogenicity.Type: ApplicationFiled: January 21, 2022Publication date: April 4, 2024Inventors: Vijay K. Kuchroo, Ramnik Xavier, Mathias Pawlak, David DeTomaso, Nir Yosef
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Publication number: 20240024381Abstract: Microbes expressing cholesterol oxidoreductase (COR) proteins, methods of engineering the microbes expressing COR proteins, compositions and methods of using the microbes are provided.Type: ApplicationFiled: March 6, 2023Publication date: January 25, 2024Inventors: Douglas Kenny, Hera Vlamakis, Ramnik Xavier, Emily Balskus, Damian Plichta
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Patent number: 11806372Abstract: This application provides for methods of treatment for IBD, especially in subjects who have R. gnavus species or R. gnavus group IBD strains as a component of their microbiome. The application also provides for methods of diagnosing IBD, as well as kits for use in the claimed methods.Type: GrantFiled: April 20, 2018Date of Patent: November 7, 2023Assignees: The Broad Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard CollegeInventors: Andrew Brantley Hall, Ramnik Xavier, Curtis Huttenhower, Moran Yassour, Hera Vlamakis
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Patent number: 11725011Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.Type: GrantFiled: November 20, 2020Date of Patent: August 15, 2023Assignees: THE GENERAL HOSPITAL CORPORATION, DANA-FARBER CANCER INSTITUTE, INC., THE BROAD INSTITUTE, INC.Inventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
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Publication number: 20230234959Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.Type: ApplicationFiled: March 27, 2023Publication date: July 27, 2023Applicants: THE BROAD INSTITUTE, INC., DANA-FARBER CANCER INSTITUTE, INC., THE GENERAL HOSPITAL CORPORATIONInventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
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Patent number: 11633436Abstract: Microbes expressing cholesterol oxidoreductase (COR) proteins, methods of engineering the microbes expressing COR proteins, compositions and methods of using the microbes are provided.Type: GrantFiled: September 18, 2020Date of Patent: April 25, 2023Assignees: The Broad Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard CollegeInventors: Douglas Kenny, Hera Vlamakis, Ramnik Xavier, Emily Balskus, Damian Plichta
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Publication number: 20220305016Abstract: The present disclosure provides methods of treating and/or preventing osteoporosis using salt-inducible kinase (SIK) inhibitors. Also provided are methods of using SIK inhibitors for increasing the function of osteocytes, increasing the number of osteoblasts, increasing the activity of osteoblasts, inhibiting the resorption of a bone, decreasing the number of osteoclasts, inhibiting the activity of osteoclasts, increasing the mass of a bone, down-regulating the expression of the gene SOST, and/or inhibiting the activity of sclerostin. The SIK inhibitors may be combined with Src inhibitors or CSF I R inhibitors. Exemplary SIK inhibitors include the compounds of the formula: (I), (II), (III), (IV), (V) or (VI).Type: ApplicationFiled: January 21, 2022Publication date: September 29, 2022Applicants: The General Hospital Corporation, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.Inventors: Marc Wein, Henry Kronenberg, Thomas Sundberg, Ramnik Xavier, Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Alykhan Shamji
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Publication number: 20220293215Abstract: A system and method for prediction of immunodominant epitopes is provided herein. MHCII peptidomics was used to discover complex bacterial epitopes and host antigen processing pathways. Novel insights into the features of antigenicity are leveraged to build an algorithm for prediction of immunodominant epitopes. Use of immunodominant epitopes is described.Type: ApplicationFiled: June 27, 2018Publication date: September 15, 2022Inventors: Ramnik Xavier, Daniel B. Graham, Chengwei Luo
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Patent number: 11382908Abstract: Disclosed herein are compounds for the treatment of inflammatory bowel disease. Additionally, provided herein are compositions and methods for using these compounds and compositions in the treatment of inflammatory bowel disease in a subject.Type: GrantFiled: September 26, 2018Date of Patent: July 12, 2022Assignees: The Broad Institute, Inc., The General Hospital Corporation, President and Fellows of Harvard CollegeInventors: Elizaveta Leshchiner, Zhifang Cao, Jason Rush, Michael Durney, Alykhan Shamji, Daniel Graham, Stuart L. Schreiber, Ramnik Xavier
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Publication number: 20220143148Abstract: The present invention provides novel compositions and methods based on the discovery of the mechanisms and gene expression programs associated with homeostatic ILC2s and proinflammatory ILC2s that drive tissue inflammation. Immune signaling abnormalities in the small intestine can trigger chronic type 2 inflammation. Applicants analyzed 58,067 immune cells from the mouse small intestine by single-cell RNA-seq at steady state and after induction of a type 2 inflammatory reaction to ovalbumin. Cell type composition and cell programs shifted in response to inflammation, especially in ILC2s. A key transcript in the inflammation-induced program in intestinal KLRG1+ILC2s was exon 5 of Calca, encoding the alpha-calcitonin gene-related peptide (a-CGRP). a-CGRP antagonized IL-25-induced activation of intestinal ILC2s and reduced their frequency in an ovalbumin reaction model. ?-CGRP activated a cAMP response, which suppressed ILC2 proliferation.Type: ApplicationFiled: March 13, 2020Publication date: May 12, 2022Inventors: Aviv Regev, Heping Xu, Jiarui Ding, Ramnik Xavier
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Patent number: 11285144Abstract: A method for treating inflammation and/or autoimmune diseases comprises administering to a subject in need thereof, a composition comprising a CDK8 inhibitor. In another aspect, a method for increasing IL-10 production comprises administering to a subject in need thereof a CDK8 inhibitor. In another aspect, a method for enhancing Treg cell differentiation, comprising administering a composition comprising a CDK8 inhibitor. In certain example embodiments, the subject suffers from an inflammatory bowel disease. In certain other example embodiments, the subject requires immunosuppression to prevent rejection following a transplantation procedure.Type: GrantFiled: August 3, 2017Date of Patent: March 29, 2022Assignees: The Broad Institute, Inc., The General Hospital Corporation, Dana-Farber Cancer Institute, Inc., President and Fellows of Harvard CollegeInventors: Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, Liv Johannessen, Nathanael Gray, Bernard Khor, Jose Perez
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Patent number: 11241435Abstract: The present disclosure provides methods of treating and/or preventing osteoporosis using salt-inducible kinase (SIK) inhibitors. Also provided are methods of using SIK inhibitors for increasing the function of osteocytes, increasing the number of osteoblasts, increasing the activity of osteoblasts, inhibiting the resorption of a bone, decreasing the number of osteoclasts, inhibiting the activity of osteoclasts, increasing the mass of a bone, down-regulating the expression of the gene SOST, and/or inhibiting the activity of sclerostin. The SIK inhibitors may be combined with Src inhibitors or CSF I R inhibitors. Exemplary SIK inhibitors include the compounds of the formula: (I), (II), (III), (IV), (V) or (VI).Type: GrantFiled: September 16, 2017Date of Patent: February 8, 2022Assignees: The General Hospital Corporation, The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc.Inventors: Marc Wein, Henry Kronenberg, Thomas Sundberg, Ramnik Xavier, Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Alykhan Shamji
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Publication number: 20210325387Abstract: The present invention provides for a human cell atlas of the colon from healthy and diseased subjects. The atlas was obtained by single sequencing of about 117,000 cells. The present invention discloses novel markers for cell types. Moreover, genes associated with disease are identified in the colon and colon specific cell types. The invention provides for diagnostic assays based on gene markers and cell composition, as well as target cell types that express genes associated with disease. Finally, disclosed are novel cell types and methods of quantitating, detecting and isolating the cell types.Type: ApplicationFiled: July 17, 2018Publication date: October 21, 2021Inventors: Alexander K. Shalek, Christopher Smillie, Rebecca H. Herbst, Moshe Biton, Aviv Regev, Jose Ordovas-Montanes, Ramnik Xavier
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Publication number: 20210147425Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind C protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.Type: ApplicationFiled: November 20, 2020Publication date: May 20, 2021Applicants: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc., The General Hospital CorporationInventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
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Publication number: 20210128642Abstract: Microbes expressing cholesterol oxidoreductase (COR) proteins, methods of engineering the microbes expressing COR proteins, compositions and methods of using the microbes are provided.Type: ApplicationFiled: September 18, 2020Publication date: May 6, 2021Inventors: Douglas KENNY, Hera VLAMAKIS, Ramnik XAVIER, Emily BALSKUS, Damian PLICHTA
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Patent number: 10954242Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.Type: GrantFiled: July 5, 2017Date of Patent: March 23, 2021Assignees: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc., The General Hospital CorporationInventors: Nathanael S. Gray, Yanke Liang, Hwan Geun Choi, Thomas Sundberg, Alykhan Shamji, Ramnik Xavier, David E. Fisher, Nisma Mujahid
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Publication number: 20210071255Abstract: The present invention is generally directed to using a single cell atlas for identifying genes and gene programs that are associated with a phenotype (e.g., disease phenotypes or traits). The present invention is also generally directed to identifying interacting genetic variants using a single cell atlas as a prior for selecting variants for testing. The single cell atlas is used for constructing gene modules. Interactions are tested within and between modules. Applicants identified genetic variants that can be used to identify pathways and cell types important for IBD risk. Moreover, genetic variants were identified that can be used as therapeutic targets.Type: ApplicationFiled: September 8, 2020Publication date: March 11, 2021Inventors: Aviv Regev, Karthik Jagadeesh, Ramnik Xavier, Christopher Smillie
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Publication number: 20210040442Abstract: 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 epithelial cell sub-types are also found in the trachea. Accordingly, disclosed are methods of modulating epithelial cell differentiation, maintenance and/or function, related methods for the treatment of disease, including IBD and asthma. Also disclosed are methods and kits for identifying cell types, their differentiation, homeostasis and activation.Type: ApplicationFiled: April 12, 2018Publication date: February 11, 2021Inventors: Jayaraj Rajagopal, Aviv Regev, Moshe Biton, Adam Haber, Daniel Montoro, Ramnik Xavier
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Publication number: 20200338087Abstract: The present disclosure provides methods of treating and/or preventing inflammatory bowel disease (IBD) and graft-versus-host disease (GVHD) using salt-inducible kinase (SIK) inhibitors, such as macrocyclic SIK inhibitors of Formula (I), imidazolyl SIK inhibitors of Formula (II), and urea and carbamate SIK inhibitors of Formula (III-A) (e.g., urea and carbamate STK inhibitors of Formula (III)).Type: ApplicationFiled: April 19, 2019Publication date: October 29, 2020Applicants: Dana-Farber Cancer Institute, Inc., The Broad Institute, Inc., President and Fellows of Harvard College, The General Hospital Corporation d/b/a Massachusetts General HospitalInventors: Alykhan Shamji, Thomas Sundberg, Nathanael S. Gray, Ramnik Xavier, Stuart L. Schreiber, Hwan Geun Choi, Yanke Liang
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Publication number: 20200317675Abstract: The present disclosure provides compounds of Formula (I), (II), and (III). The provided compounds are able to bind protein kinases (e.g., SIK) and may be useful in modulating (e.g., inhibiting) the activity of a protein kinase (e.g., SIK, (e.g., SIK1, SIK2, or SIK3)) in a subject or cell. The provided compounds may be useful in treating or preventing a disease (e.g., proliferative disease, musculoskeletal disease, genetic disease, hematological disease, neurological disease, painful condition, psychiatric disorder, or metabolic disorder) in a subject in need thereof. Also provided are pharmaceutical compositions, kits, methods, and uses that include or involve a compound described herein.Type: ApplicationFiled: July 5, 2017Publication date: October 8, 2020Applicants: The Broad Institute, Inc., Dana-Farber Cancer Institute, Inc., The General Hospital CorporationInventors: Nathanael S. GRAY, Yanke LIANG, Hwan Geun CHOI, Thomas SUNDBERG, Alykhan SHAMJI, Ramnik XAVIER, David E. FISHER, Nisma MUJAHID