Developmental Biology Program

The Danwei Huangfu Lab

Research

Pictured: Danwei Huangfu
Danwei Huangfu, PhD
We apply both precision gene editing and large-scale CRISPR screening in human pluripotent stem cells (hPSCs) to explore mechanisms underlying human development. Specifically, we are interrogating the protein-coding regulators of pancreatic development and β cell function. The pathways that regulate these processes can be exploited for therapeutics to prevent and reverse diseases such as type 1 and type 2 diabetes. In a second, closely related area, we are developing approaches to discover developmental enhancers, and to understand the epigenetic regulation of noncoding regulatory elements with a focus on DNA methylation.

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The MSK MorPhiC project

Huangfu lab 2023

Publications Highlights

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA. Nat Genet. 2023 Aug;55(8):1336-1346. doi: 10.1038/s41588-023-01450-7. Epub 2023 Jul 24. [PMID: 37488417]

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction. Yang D, Cho H, Tayyebi Z, Shukla A, Luo R, Dixon G, Ursu V, Stransky S, Tremmel DM, Sackett SD, Koche R, Kaplan SJ, Li QV, Park J, Zhu Z, Rosen BP, Pulecio J, Shi ZD, Bram Y, Schwartz RE, Odorico JS, Sidoli S, Wright CV, Leslie CS, Huangfu D. Nat Cell Biol. 2022 Jul;24(7):1064-1076. doi: 10.1038/s41556-022-00946-4. Epub 2022 Jul 4. [PMID: 35787684]

QSER1 protects DNA methylation valleys from de novo methylation. Dixon G, Pan H, Yang D, Rosen BP, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, Torregroza I, He C, Sidoli S, Evans T, Elemento O, Huangfu D. Science. 2021 Apr 9;372(6538):eabd0875. doi: 10.1126/science.abd0875. [PMID: 33833093]

Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D. Nat Genet. 2019 Jun;51(6):999-1010. doi: 10.1038/s41588-019-0408-9. Epub 2019 May 20. [PMID: 31110351]

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells. Verma N, Pan H, Doré LC, Shukla A, Li QV, Pelham-Webb B, Teijeiro V, González F, Krivtsov A, Chang CJ, Papapetrou EP, He C, Elemento O, Huangfu D. Nat Genet. 2018 Jan;50(1):83-95. doi: 10.1038/s41588-017-0002-y. Epub 2017 Dec 4.

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People

Pictured: Danwei Huangfu

Danwei Huangfu, PhD

  • The Huangfu laboratory uses human pluripotent stem cells (hPSCs) as a powerful genetic model to interrogate the transcriptional and epigenetic mechanisms underlying cell fate decisions in development and disease.
  • PhD, Cornell University, Weill Graduate School of Medical Sciences
  • BS, Fudan University
[email protected]
Email Address
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Members

Inbal   Caspi
Inbal Caspi

Graduate Research Assistant

Julian Pulecio

Sr. Research Scientist

Dapeng Yang
Dapeng Yang

Sr. Research Scientist

Xian Zhang
Xian Zhang

Sr. Research Scientist

Adonis C. John
Adonis C. John

Lead, Research Administrative Assistant

Sharon Adeniyi
Sharon Adeniyi

Research Technician

Tamara Casteels
Tamara Casteels

Research Fellow - NYSTEM Training Award at the CSCB

Hyein Cho
Hyein Cho

Sr. Computational Biologist

Tingfeng Guo
Tingfeng Guo

Research Fellow

Nan Hu
Nan Hu

Bioinformatics Software Engineer

Hanuman Kale
Hanuman Kale

Research Scholar

Sricharan Kannan

Research Technician

Samuel Kaplan
Samuel Kaplan

Graduate Research Assistant

GSK Student
Dingyu Liu

Graduate Research Assistant

Pallavi Mohapatra
Pallavi Mohapatra

Research Fellow

Arushi Rana
Arushi Rana

Research Technician

Xianming Wang
Xianming Wang

Research Fellow

Breanna Williams
Breanna Williams

Research Technician

Jielin Yan
Jielin Yan

Graduate Research Assistant

Nan Zhang
Nan Zhang

Research Fellow

Lab Alumni
Gary Dixon
Gary Dixon

Graduate Research Assistant

Kihyun Lee
Kihyun Lee

Graduate Research Assistant

Tracey Leonardo

Research Technician

Qing Li, BS
Qing Li

Graduate Research Assistant

Renhe Luo
Renhe Luo

Scientist, Spark, New York, NY

Robert Rickert
Robert Rickert

Research Technician

Bess Rosen
Bess Rosen

Graduate Research Assistant

Abhijit Shukla

Research Fellow

Chew-Li Soh, PhD
Chew-Li Soh

Research Fellow

Virginia Teijeiro

Graduate Research Assistant

Nipun Verma
Nipun Verma

Graduate Research Assistant

Daniela C. Georgieva
Daniela C. Georgieva

Research Technician

Federico Gonzalez-Grassi
Federico Gonzalez-Grassi

Research Fellow

Katherine Lelli, PhD
Katherine Lelli

Research Fellow

Zhong-Dong Shi
Zhong-Dong Shi

Research Fellow

Zengrong Zhu, PhD
Zengrong Zhu

Research Associate

Georgina Berrozpe
Georgina Berrozpe

Senior Research Scientist

Jeyaram (Jey) Ravichandran Damodaran
Jeyaram Ravichandran Damodaran

Sr. Research Technician

Laura Pereira

Scientific Research Lead

Lab Affiliations

Achievements

  • Basil O’Connor Scholar, March of Dimes Birth Defects Foundation (2012-2014)
  • Louis V. Gerstner, Jr. Young Investigators Award, Memorial Sloan Kettering Cancer Center (2011-2014)
  • Award from Harvard Catalyst & InnoCentive for the Ideation Challenge on “What Do We Not Know to Cure Type 1 Diabetes” (2010)
  • Helen Hay Whitney Postdoctoral Fellowship (2006-2009)

Lab News & Events

Accolades

Team Recognitions

  • Renhe Luo's paper on endoderm enhancer discovery is out in Nature Genetics (2023)
  • Jeyaram (Jey) Ravichandran Damodaran is joining the Weill Cornell BCMB program (2023)
  • Julian Pulecio is selected as a member of the 2023 cohort of MERIT Emerging Leaders
  • Dingyu Liu receives the Bruce Charles Forbes Fellowship (2023)
  • Tamara Casteels receives the NYSTEM Training Award at the CSCB (2022)
  • Tamara Casteels receives the Award of Excellence for her PhD thesis with Stefan Kubicek in CeMM (2022)
  • Nan Zhang receives CDMRP PRMRP Discovery Award (2022)
  • Dapeng Yang's paper on HHEX and pancreas specification is out in Nature Cell Biology (2022)

Open Positions

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Disclosures

Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.

MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.

Danwei Huangfu discloses the following relationships and financial interests:

  • Gene and Genome Editing
    Professional Services and Activities (Uncompensated)
  • Stem Cell Reports
    Professional Services and Activities (Uncompensated)
  • The Jackson Laboratory
    Professional Services and Activities

The information published here is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.


This page and data include information for a specific MSK annual disclosure period (January 1, 2022 through disclosure submission in spring 2023). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at [email protected].


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