Dr. Federico Gaiti
Dr. Federico Gaiti
Dr. Federico Gaiti
Early-Career Investigator

Email: federico.gaiti@uhnresearch.ca

Twitter: @fgaiti

Early-Career Investigator
  • The focus of our group is to dissect the mechanisms that drive and facilitate cancer evolution
  • Our work includes novel computational frameworks and single-cell multi-omics methodologies to decipher the interactions between genome, epigenome, and phenotype in human cancers
  • Our goal is to discover fundamental principles in evolutionary biology of cancer to inform the future design and application of novel therapeutic options to address tumour evolution

Dr. Gaiti’s research focuses on providing novel insights into a central aspect of human biology – the somatic evolution of cancer cells. Cancer progression, relapse, and resistance to therapy are the result of an evolutionary optimization process in which genetic alterations generate diversity. This genetic diversity provides the critical substrate for malignant cells to evolve and adapt to the selective pressures provided by therapy. However, in addition to genetic diversity, there is a whole host of regulatory factors, like epigenetic regulation, that fuel cancer evolution. Thus, the study of cancer requires the integration of multiple dimensions at the resolution of the single cell — the fundamental unit of somatic evolution.

The goal of Dr. Gaiti’s research program is to develop and apply computational and experimental genomics and epigenomics approaches for the study of cancer evolution and analysis of single-cell multi-omics data, empowering us to simultaneously interrogate the multi-faceted axes of diversity that drive tumour evolution.

Current efforts in the lab focus on understanding:

  1. Role of non-genetic/epigenetic alterations (DNA methylation or chromatin factors) in dictating malignant cell states.
  2. The phenotypic plasticity of malignant cell states.
  3. The impact of cell extrinsic factors (such as tumour microenvironment) on malignant cell states.
Experience & Education

PhD, University of Queensland, Brisbane, Australia

Postdoctoral Fellow, Weill Cornell Medical College, New York, NY, U.S.

Current Affiliations

Early-Career Investigator, Ontario Institute for Cancer Research

Scientist, Princess Margaret Cancer Centre

Assistant Professor, Department of Medical Biophysics, University of Toronto

Select Publications
  • Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F, Landau DA. Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. Cell Stem Cell. 2023 Sep 7;30(9):1262-1281.e8. doi: 10.1016/j.stem.2023.07.012. Epub 2023 Aug 14. | PubMed PMID: 37582363; PubMed Central PMCID: PMC10528176.
  • Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes. 2023 September; 14(10):1856.
  • Chaligne R*, Gaiti F*, Silverbush D*, Schiffman JS*, Weisman HR, Kluegel L, Gritsch S, Deochand SD, Gonzalez Castro LN, Richman AR, Klughammer J, Biancalani T, Muus C, Sheridan C, Alonso A, Izzo F, Park J, Rozenblatt-Rosen O, Regev A, Suvà ML, Landau DA. Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states. Nat Genet. 2021 Oct;53(10):1469-1479. doi: 10.1038/s41588-021-00927-7. Epub 2021 Sep 30. PubMed PMID: 34594037. *Co-first authors
  • Gaiti F*, Chaligne R*, Gu H*, Brand RM, Kothen-Hill S, Schulman RC, Grigorev K, Risso D, Kim KT, Pastore A, Huang KY, Alonso A, Sheridan C, Omans ND, Biederstedt E, Clement K, Wang L, Felsenfeld JA, Bhavsar EB, Aryee MJ, Allan JN, Furman R, Gnirke A, Wu CJ, Meissner A, Landau DA. Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia. 2019 May;569(7757):576-580. doi: 10.1038/s41586-019-1198-z.Epub 2019 May 15. PubMed PMID: 31092926; PubMed Central PMCID: PMC6533116. *Co-first authors
  • Pastore A*, Gaiti F*, Lu SX, Brand RM, Kulm S, Chaligne R, Gu H, Huang KY, Stamenova EK, Béguelin W, Jiang Y, Schulman RC, Kim KT, Alonso A, Allan JN, Furman RR, Gnirke A, Wu CJ, Melnick AM, Meissner A, Bernstein BE, Abdel-Wahab O, Landau DA. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat Commun. 2019 Apr 23;10(1):1874. doi: 10.1038/s41467-019-09645-5. PubMed PMID: 31015400; PubMed Central PMCID: PMC6478836. *Co-first authors
  • Gu H*, Raman AT*, Wang X, Gaiti F, Chaligne R, Mohammad AW, Arczewska A, Smith ZD, Landau DA, Aryee MJ, Meissner A, Gnirke A. Smart-RRBS for single-cell methylome and transcriptome analysis. Nat Protoc. 2021 Jul 9;. doi: 10.1038/s41596-021-00571-9. [Epub ahead of print] Review. PubMed PMID: 34244697. *Co-first authors

PubMed search link for all publications: https://www.ncbi.nlm.nih.gov/myncbi/1dkybb-Qg9YQB/bibliography/public/

Research Areas
Cancer Origins Informatics Prevention
  • Gilead Research Scholar
  • NIH Pathway to Independence Award (K99/R00)
  • American Society of Hematology Scholar Award
  • Bruce D. Cheson, MD Postdoctoral Fellowship grantee – Lymphoma Research Foundation
  • Emerging Leaders in Computational Oncology Symposium Award
  • Leukemia & Lymphoma Society Award
Opportunities to Collaborate

If you’re interested in collaborating with Dr. Gaiti, please contact him directly.

Visit OICR’s Collaborative Research Resources directory for more opportunities to collaborate with OICR researchers.