Francisco J. Sánchez-Rivera

Francisco J. Sánchez-Rivera

Assistant Professor of Biology; Intramural Faculty, Koch Institute

Francisco J. Sánchez-Rivera aims to understand how genetic variation shapes normal physiology and disease, with a focus on cancer.






Koch Institute for Integrative Cancer Research


Jamie Rothman



  • PhD, 2016, Biology, MIT
  • BS, 2008, Microbiology, University of Puerto Rico at Mayagüez

Research Summary

The overarching goal of the Sánchez-Rivera laboratory is to elucidate the cellular and molecular mechanisms by which genetic variation shapes normal physiology and disease, particularly in the context of cancer. To do so, we develop and apply genome engineering technologies, genetically-engineered mouse models (GEMMs), and single cell lineage tracing and omics approaches to obtain comprehensive biological pictures of disease evolution at single cell resolution. By doing so, we hope to produce actionable discoveries that could pave the way for better therapeutic strategies to treat cancer and other diseases.


  • V Foundation Award, 2022
  • Hanna H. Gray Fellowship, Howard Hughes Medical Institute, 2018-2026
  • GMTEC Postdoctoral Researcher Innovation Grant, Memorial Sloan Kettering Cancer Center, 2020-2022
  • 100 inspiring Hispanic/Latinx scientists in America, Cell Mentor/Cell Press, 2020

Key Publications

  1. High-throughput evaluation of genetic variants with prime editing sensor libraries. Gould, SI, Wuest, AN, Dong, K, Johnson, GA, Hsu, A, Narendra, VK, Atwa, O, Levine, SS, Liu, DR, Sánchez Rivera, FJ et al.. 2024. Nat Biotechnol , .
    doi: 10.1038/s41587-024-02172-9PMID:38472508
  2. A prime editor mouse to model a broad spectrum of somatic mutations in vivo. Ely, ZA, Mathey-Andrews, N, Naranjo, S, Gould, SI, Mercer, KL, Newby, GA, Cabana, CM, Rideout, WM 3rd, Jaramillo, GC, Khirallah, JM et al.. 2024. Nat Biotechnol 42, 424-436.
    doi: 10.1038/s41587-023-01783-yPMID:37169967
  3. Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Sánchez-Rivera, FJ, Diaz, BJ, Kastenhuber, ER, Schmidt, H, Katti, A, Kennedy, M, Tem, V, Ho, YJ, Leibold, J, Paffenholz, SV et al.. 2022. Nat Biotechnol 40, 862-873.
    doi: 10.1038/s41587-021-01172-3PMID:35165384
  4. Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1. Romero, R, Sánchez-Rivera, FJ, Westcott, PMK, Mercer, KL, Bhutkar, A, Muir, A, González Robles, TJ, Lamboy Rodríguez, S, Liao, LZ, Ng, SR et al.. 2020. Nat Cancer 1, 589-602.
    doi: 10.1038/s43018-020-0071-1PMID:34414377
  5. Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Sánchez-Rivera, FJ, Papagiannakopoulos, T, Romero, R, Tammela, T, Bauer, MR, Bhutkar, A, Joshi, NS, Subbaraj, L, Bronson, RT, Xue, W et al.. 2014. Nature 516, 428-31.
    doi: 10.1038/nature13906PMID:25337879

Recent Publications

  1. Author Correction: Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma. Mazur, PK, Herner, A, Mello, SS, Wirth, M, Hausmann, S, Sánchez-Rivera, FJ, Lofgren, SM, Kuschma, T, Hahn, SA, Vangala, D et al.. 2024. Nat Med , .
    doi: 10.1038/s41591-024-03054-yPMID:38816611
  2. Deconstructing cancer with precision genome editing. Johnson, GA, Gould, SI, Sánchez-Rivera, FJ. 2024. Biochem Soc Trans 52, 803-819.
    doi: 10.1042/BST20230984PMID:38629716
  3. High-throughput evaluation of genetic variants with prime editing sensor libraries. Gould, SI, Wuest, AN, Dong, K, Johnson, GA, Hsu, A, Narendra, VK, Atwa, O, Levine, SS, Liu, DR, Sánchez Rivera, FJ et al.. 2024. Nat Biotechnol , .
    doi: 10.1038/s41587-024-02172-9PMID:38472508
  4. Solid tumor growth depends on an intricate equilibrium of malignant cell states. Torborg, SR, Grbovic-Huezo, O, Singhal, A, Holm, M, Wu, K, Han, X, Ho, YJ, Haglund, C, Mitchell, MJ, Lowe, SW et al.. 2023. bioRxiv , .
    doi: 10.1101/2023.12.30.573100PMID:38234855
  5. Somatic mouse models of gastric cancer reveal genotype-specific features of metastatic disease. Leibold, J, Tsanov, KM, Amor, C, Ho, YJ, Sánchez-Rivera, FJ, Feucht, J, Baslan, T, Chen, HA, Tian, S, Simon, J et al.. 2024. Nat Cancer 5, 315-329.
    doi: 10.1038/s43018-023-00686-wPMID:38177458
  6. Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. Karagiannis, D, Wu, W, Li, A, Hayashi, M, Chen, X, Yip, M, Mangipudy, V, Xu, X, Sánchez-Rivera, FJ, Soto-Feliciano, YM et al.. 2024. Cell Rep 43, 113629.
    doi: 10.1016/j.celrep.2023.113629PMID:38165806
  7. Aberrant gene activation in synovial sarcoma relies on SSX specificity and increased PRC1.1 stability. Benabdallah, NS, Dalal, V, Scott, RW, Marcous, F, Sotiriou, A, Kommoss, FKF, Pejkovska, A, Gaspar, L, Wagner, L, Sánchez-Rivera, FJ et al.. 2023. Nat Struct Mol Biol 30, 1640-1652.
    doi: 10.1038/s41594-023-01096-3PMID:37735617
  8. Generation of precision preclinical cancer models using regulated in vivo base editing. Katti, A, Vega-Pérez, A, Foronda, M, Zimmerman, J, Zafra, MP, Granowsky, E, Goswami, S, Gardner, EE, Diaz, BJ, Simon, JM et al.. 2024. Nat Biotechnol 42, 437-447.
    doi: 10.1038/s41587-023-01900-xPMID:37563300
  9. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Sánchez Rivera, FJ, Dow, LE. 2024. Cold Spring Harb Perspect Med 14, .
    doi: 10.1101/cshperspect.a041384PMID:37487630
  10. Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma. Chen, X, Li, Y, Zhu, F, Xu, X, Estrella, B, Pazos, MA 2nd, McGuire, JT, Karagiannis, D, Sahu, V, Mustafokulov, M et al.. 2023. Nat Commun 14, 4259.
    doi: 10.1038/s41467-023-39990-5PMID:37460547
More Publications




Photo credit: Adam Lerner