Human Oncology & Pathogenesis Program

The Joe Chan Lab

Research

Joe Chan, MD, PhD

Assistant Professor

Assistant Professor

The Joe Chan Lab combines machine learning with disruptive single-cell sequencing and multiplex spatial imaging to study lineage plasticity in cancer, with a particular focus on histological transformation, as a mechanism of acquired resistance, immune escape, and metastasis. The lab has a special interest in quantifying plasticity across space, time, and cancer types.

View Lab Overview

Publications Highlights

Chan JM*, Zaidi S, Love JR, Setty M, Wadosky KM, Gopalan A, Choo Z, Persad S, Choi J, LaClair J, Lawrence K, Chaudhary O, Xu T, Masilionis I, Linkov I, Wang S, Lee C, Barlas A, Morris MJ, Mazutis L, Chaligne R, Chen Y, Goodrich DW, Karthaus WR, Pe’er D, Sawyers CL. Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Science, Aug 2022; 377(6611): 1180-1191. PMID: PMC9653178.

Chan JM*, Quintanal-Villalonga A, Gao VR, Xie Y, Allaj V, Chaudhary O, Masilionis I, Egger J, Chow A, Walle T, Mattar M, Yarlagadda D, Wang JL, Uddin F, Offin M, Ciampricotti M, Qeriqi M, Bahr A, de Stanchina E, Bhanot UK, Lai WV, Bott MJ, Jones DR, Ruiz A, Baine MK, Li Y, Rekhtman N, Poirier JT, Nawy T, Sen T, Mazutis L, Hollmann TJ, Pe’er D, Rudin CM. Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Cancer Cell, 2021 Nov 8;39(11):1479-1496.e18. PMCID: PMC8628860.

Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Manoj P, Donoghue M, Won HH, Chan JM, Ciampricotti M, Chow A, Offin M, Chang JC, Ray-Kirton J, Tischfield SE, Egger J, Bhanot UK, I Linkov, Asher M, Sinha S, Silber J, Iacobuzio-Donahue CA, Roehrl MH, Hollmann TJ, Yu HA, Qiu J, de Stanchina E, Baine MK, Rekhtman N, Poirier JT, Loomis B, Koche RP, Rudin CM, Sen T. Multi-omic analysis of lung tumors defines pathways activated in neuroendocrine transformation. Cancer Discovery, 2021. 11(12):3028-3047. doi: 10.1158/2159-8290.CD-20-1863. PMCID: PMC9437746.

Quintanal-Villalonga A, Taniguchi H, Zhan YA, Hasan MM, Chavan SS, Meng F, Uddin F, Allaj V, Manoj P, Shah NS, Chan JM, Ciampricotti M, Chow A, Offin M, Ray-Kirton J, Egger JD, Bhanot UK, Linkov I, Asher M, Roehrl MH, Ventura K, Qiu J, de Stanchina E, Chang JC, Rekhtman N, Houck-Loomis B, Koche RP, Yu HA, Sen T, Rudin CM. Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation. J Hematol Oncol, 2021. 14(1):170. doi: 10.1186/s13045-021-01186-z. PMCID: PMC8520275.

Quintanal-Villalonga A, Chan JM*, Yu HA, Pe’er D, Sawyers CL, Sen T, Rudin CM. Lineage plasticity in cancer: a shared pathway of therapeutic resistance. Nature Reviews: Clinical Oncology, 03/2020. 17(6):360-371. doi: 10.1038/s41571-020-0340-z. PMCID: PMC7397755.

View All Publications

People

Joe Chan, MD, PhD

Assistant Professor

Assistant Professor

MD, PhD, Columbia University Physicians & Surgeons

[email protected]: Email Address

Members

Christina Marciante

Administrative Assistant

Swanand Rakhade

Medical Student

Sahil Sahni

Graduate Student

Hrishikesh Somayaji

Postdoctoral Scholar

Emmanuel Spanos

Graduate Student

Eric Sun

MD/PhD Graduate Student

Samuel Taylor

MD/PhD Fellow

Mamie Wang

Bioinformatics Software Engineer III

Forest Yang

Postdoctoral Scholar

Britney Forsyth

Bioinformatics Software Engineer

Lena Morrill Gavarró

Postdoctoral Fellow

Morgan Lallo

Bioinformatics Intern

Riazat Ryan

Postdoctoral Fellow

Xinjun Wang

Assistant Attending

Zhanyu Wang

Graduate Research Assistant

Achievements

Clinical Investigator Award, K08CA259161, National Cancer Institute (2021-Current)
Young Investigator Award, American Society of Clinical Oncology & Conquer Cancer Foundation (2021-Current)
Lung Cancer Research Fellowship, American Association for Cancer Research (2021)
Harborside Endowed Merit Award, American Society of Clinical Oncology & Conquer Cancer Foundation (2021)
World Conference on Lung Cancer Early Career Award, International Association for the Study of Lung Cancer (2021)

Gerry Fellowship, Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center (2020-2021)
Distinguished Young Investigator Award, EGFR Resisters (2020)

Open Positions

To learn more about available postdoctoral opportunities, please visit our Career Center

To learn more about compensation and benefits for postdoctoral researchers at MSK, please visit Resources for Postdocs

Career Opportunities

The laboratory has funding for multiple positions, including graduate students, postdocs, and bioinformatics engineers. Experience in programming is strongly preferred.

Apply now

Get in Touch

[email protected]

Lab Head Email

Disclosures

Members of the MSK Community 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. These activities outside of MSK further our mission, provide productive collaborations, and promote the practical application of scientific discoveries.

MSK requires doctors, faculty members, and leaders 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. Not all disclosed interests and relationships present conflicts of interest. MSK reviews all disclosed interests and relationships to assess whether a conflict of interest exists and whether formal COI management is needed.

Joe Chan discloses the following relationships and financial interests:

No disclosures meeting criteria for time period

The information published here is a complement to other publicly reported data and 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, 2024 through disclosure submission in spring 2025). 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].

View all disclosures