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Overview

Signals are transmitted to chromatin to facilitate rapid, robust, and selective gene expression within the three billion base-pair genome in response to environmental cues, such as pathogen sensing. The goal of our ongoing research is to reveal mechanisms allowing for this scope and selectivity, and to understand them in the context of dynamic and fluid chromatin and all of its constituents (as a multi-molecular assembly or “biomolecular condensate”). Our recent studies of pathways that transmit extracellular signals to selectively induce gene expression establish the cooperative function of epigenetic mechanisms (histone modifications) and transcription factor activation and their coordinated regulation by chromatin-associated kinases. We are finding that these signaling-to-chromatin pathways are potent in regulation of enhancer activation and higher order chromatin architecture, both during the inflammatory process and in cancer. In ongoing and future work we extend these studies to understand how epigenetic processes provide an “evolutionary toolbox” for adaptations driven by spatiotemporal changes in gene expression. These studies have potential to synthesize an understanding of the extensive cooption of immune genes for non-immune processes (ex. thermogenesis, neuronal development), reveal novel mechanisms of adaptation, and explain inflammation- and age-associated pathologies.

Highlights

  1. 1
    Nature · 2020
    PMID: 32699416PMCID: PMC7517595DOISenior author135 citations
  2. 2
    Cell · 2023
    CPChristopher ParkhurstCWClaire WingertLPLucinda PaddockMBMichael Bale+18 more →SZSteven Zvi Josefowicz
    PMID: 37597510PMCID: PMC10638861DOISenior author257 citations
  3. 3
    The Journal of experimental medicine · 2021
    PMID: 34297037PMCID: PMC8313408DOISenior author19 citations

Publications

50 publications

Active

14 grants
  • PI
    Global Variation in Human Stem and Progenitor Cells: Shaping the Immune System
    NIAID · 2026–2031 · via NIH RePORTER
    P01AI189645-01A1
  • MPI
    Hematopoietic stem cell encoded anti-tumor immunity: mechanisms and function
    National Cancer Institute · 2026–2031 · via Memorial Sloan Kettering Cancer Center
    R01CA303125-01A1
  • Sub-PI
    Trained immunity signatures of reduced vaccine responses in older adults
    National Institute of Allergy and Infectious Diseases · 2026–2031 · via The Jackson Laboratory for Genomic Medicine
    R01AI198970-01
  • PI
    Histone Variant H3.3 as a Transcription Rheostat in the Immune System
    National Institute of Allergy and Infectious Diseases · 2019–2030· 4 renewals
    R01AI148416-07
  • MPI
    Structure, Function, and Dynamics of Macro-molecular Complexes that Execute and Regulate Genome Function."
    National Institute of General Medical Sciences · 2021–2030 · via Cornell University - Ithaca· 3 renewals
    RM1GM139738-06
  • MPI
    Negative Regulation of Osteoclastogenesis
    National Inst of Arthritis & Musculoskeletal & Skin Diseases · 2024–2029 · via Hospital for Special Surgery
    R01AR084248-02
  • KP
    Mythili Ketavarapu - Awarded NSF GRFP prior to matriculating at WCGS
    National Science Foundation · 2025–2028Fellowship
    NSF 231744-01
  • Co-I
    Impact of SARS-CoV-2 infection on respiratory viral immune responses in children with and without asthma
    National Institute of Allergy and Infectious Diseases · 2023–2028
    R01AI173504-01
  • Sub-PI
    Hematopoietic epigenetic memory as a driver of inflammaging
    Hevolution Foundation · 2024–2028 · via Jackson Laboratory
    HF-GRO-23-1199240-4
  • Co-I
    Regulatory T Cell Dysfunction as a Biomarker for Personalized Therapeutic Target Identification in SLE
    National Institute of Allergy and Infectious Diseases · 2026–2027
    R56AI195877-01A1
  • Sub-PI
    HSS RESEARCH COLLABORATION AGREEMENT With Funding
    Scleroderma Foundation · 2026–2027 · via Hospital for Special SurgeryContract
    HSS 265500-01
  • PI
    Epigenetic regulation of immunity: molecular mechanisms of inflammatory priming and altered hematopoiesis
    Burroughs Wellcome Fund · 2022–2027
    BWF 221853-05
  • PI
    Central Innate Immune Memory in BCG induced tumor immunity: Mechanisms and predictors of patient response
    American Society of Hematology Inc · 2025–2026
    ASH 251896-01
  • KP
    Epigenetic basis and therapeutic targeting of the unique lymphoma immunological niche
    National Cancer Institute · 2024–2026
    P01CA272295-02
Completed grants (16)
  • Sub-PI
    Quantitative mapping of dynamic epigenetic states in rare and stimulated immune cells
    National Institute of Allergy and Infectious Diseases · 2022–2025 · via EpiCypher, Inc.
    R44AI167215-03
  • PI
    Mechanisms of dynamic chromatin reorganization regulating B-cell differentiation and Lymphomagenesis
    Starr Cancer Consortium · 2023–2024
    I16-068
  • MPI
    ASH award
    American Society of Hematology Inc · 2022–2024
    ASH 226321-01
  • Sub-PI
    Leveraging functional genomics to create an epigenetic toolbox for inflammation research and drug discovery
    National Institute of Allergy and Infectious Diseases · 2021–2024 · via EpiCypher, Inc.
    R44AI162386-03
  • Co-I
    Immune Cells and Secretory Pathways Leading to Human Systemic Autoimmunity
    National Institute of Allergy and Infectious Diseases · 2019–2024· 2 renewals
    U19AI144301-03S1
  • KP
    Describing the Epigenetic Mechanisms in Control of Hematopoietic Development and Rapid Inflammatory Responses
    National Heart, Lung, and Blood Institute · 2021–2024Fellowship
    F31HL152706-01A1
  • Co-I
    The Mark Foundation ASPIRE Phase II Proposal
    The Mark Foundation for Cancer Research · 2020–2023
    MFCR 201610-01
  • PI
    Addgene 704323
    Addgene, Inc. · 2022–2023
    Addgene 704323
  • PI
    Mechanisms of dynamic chromatin reorganization regulating B-cell maturation and lymphomagenesis
    Starr Cancer Consortium · 2021–2022
    I14-0020
  • KP
    Signaling to Chromatin Pathways in Regulation of Germinal Center B Cell Differentiation and Lymphoma
    Lymphoma Research Foundation · 2020–2022
    LRF 200713-01
  • Co-I
    The molecular mechanism of tumor suppression by PTEN via repression of satellite DNA (Cornell Seed Grant_Track 2)
    Cornell University · 2021–2021
    CU 211704-01
  • PI
    Center of Excellence for Genomic Studies
    Weill Cornell Medical College · 2019–2021
    CU 212636-01
  • PI
    Signaling to chromatin pathways in macrophage response to pathogens
    American Association of Immunologists · 2020–2021Fellowship
    AAI 202397-01
  • PI
    Regulation of Chromatin by Histone Phosphorylation
    National Institute of General Medical Sciences · 2017–2020
    R00GM113019-05
  • PI
    Regulation of Chromatin by Histone Phosphorylation
    NIGMS · 2015–2017 · via NIH RePORTER
    K99GM113019-02
  • PI
    Writing and Interpreting the Chromatin Enhancer Code in Myeloid Cells
    NIGMS · 2012–2015 · via NIH RePORTER
    F32GM100616-03

Honors & distinctions

1 honor
  • PECASE (Presidential Early Career Award) · U.S. Government (PECASE)

Clinical research

1 study
Completed & closed trials (1)
  • PI
    Epigenomic signatures of COVID-19: Insights into pathogenesis, prognosis, and long-term consequences
    Weill Medical College of Cornell University · IRB STUDY CLOSURE (as of 2024)

Available technologies

News mentions

  • Three Institutional Scientists Receive Presidential Award
    January 16, 2025

    Drs. Steven Josefowicz, Ekta Khurana and Kristen Pleil were among 400 early-career scientists and engineers to receive the Presidential Early Career Award for Scientists and Engineers.

  • NIH Grant Will Support Lymphoma Research
    August 15, 2024

    Weill Cornell Medicine has received a five-year, $12.4 million grant from the National Cancer Institute, part of the National Institutes of Health, for an extensive program of basic and translational research on the biology of diffuse large B-cell lymphoma (DLBCL), the most common form of lymphoma.

  • Gut Fungi's Lasting Impact on Severe COVID-19 Immune Response
    October 23, 2023

    Certain gut-dwelling fungi flourish in severe cases of COVID-19, amplifying the excessive inflammation that drives this disease while also causing long-lasting changes in the immune system, according to a new study led by investigators at Weill Cornell Medicine and NewYork-Presbyterian.

  • Severe COVID-19 Can Alter Long-term Immune System Response
    August 18, 2023

    Severe COVID-19 infection triggers changes that affect gene expression in immune system stem cells, causing long-lasting alterations in the body’s immune response, according to a new study by Weill Cornell Medicine and Jackson Laboratory investigators.

  • Scientists Pitch Medical Innovations at 2023 Biomedical Business Plan Challenge
    June 16, 2023

    Six teams pitched their innovations at the 2023 Biomedical Business Plan Challenge Final Pitch Day competition for $100,000 in prize money, which can be used to help build their company, with the goal of ushering in the next generation of life science innovation and patient care.

Show 5 more mentions
5 PhD students · 1 MD-PhD student · 5 Postdocs

PhD · 5

MD-PhD · 1

Postdoc · 5

External relationships

Professional Services

Epistemyx Inc.

Other

Epistemyx Inc.