Dr. Mathieu Lupien

Investigator II

Dr. Mathieu Lupien is a scientist at the Princess Margaret Cancer Centre and holds a cross-appointment with OICR.

Lupien’s research highlights the need to characterize and understand the role of noncoding regulatory elements as targets of genetic and epigenetic changes in oncogenesis. This can inform of new therapeutic targets and serve as a source of biomarkers for patient stratification.

Lupien is recognized for three seminal discoveries:

  1. Epigenetic modifications on histones can discriminate cell-type-specific-noncoding gene regulatory elements in normal and cancer cells.
  2. Epigenetic alterations at gene regulatory elements underlie cancer initiation and progression.
  3. Noncoding genetic alterations promoting cancer development preferentially target gene regulatory elements.

Lupien’s research is centered on identifying the changes in cancer cells and to reveal their underlying molecular biology. The ultimate goal is to develop new and improved strategies to hinder cancer development.

Current affiliations

  • Investigator II, OICR;
  • Associate Professor, Department of Medical Biophysics, University of Toronto;
  • Senior scientist, Princess Margaret Cancer Centre.

Research interests

  • Epigenomics;
  • Chromatin architecture;
  • Genetics of cancer;
  • Bioinformatics;
  • Computational science;
  • Transcriptional regulation;
  • Breast cancer;
  • Prostate cancer;
  • Cancer stem cells.

Select publications

Bailey SD, Desai K, Kron KJ, Mazrooei P, Sinnott-Armstrong NA, Treloar AE, Dowar M, Thu KL, Cescon DW, Silvester J, Yang SY, Wu X, Pezo RC, Haibe-Kains B, Mak TW, Bedard PL, Pugh TJ, Sallari RC, Lupien M
Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.
Nat Genet. 2016 Oct;48(10):1260-6. doi: 10.1038/ng.3650. Epub 2016 Aug 29.
PMID: 27571262

Gallo M, Coutinho FJ, Vanner RJ, Gayden T, Mack SC, Murison A, Remke M, Li R, Takayama N, Desai K, Lee L, Lan X, Park NI, Barsyte-Lovejoy D, Smil D, Sturm D, Kushida MM, Head R, Cusimano MD, Bernstein M, Clarke ID, Dick JE, Pfister SM, Rich JN, Arrowsmith CH, Taylor MD, Jabado N, Bazett-Jones DP, Lupien M, Dirks PB
MLL5 Orchestrates a Cancer Self-Renewal State by Repressing the Histone Variant H3.3 and Globally Reorganizing Chromatin.
Cancer Cell. 2015 Dec 14;28(6):715-29. doi: 10.1016/j.ccell.2015.10.005. Epub 2015 Nov 25.

Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M
ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.
Nat Commun. 2015 Feb 3;2:6186. doi: 10.1038/ncomms7186.

Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD
Epigenomic alterations define lethal CIMP-positive ependymomas of infancy.
Nature. 2014 Feb 27;506(7489):445-50. doi: 10.1038/nature13108. Epub 2014 Feb 19

Cowper-Sal lari R, Zhang X, Wright JB, Bailey SD, Cole MD, Eeckhoute J, Moore JH, Lupien M.
Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression.
Nat Genet. 2012 Nov;44(11):1191-8. doi: 10.1038/ng.2416. Epub 2012 Sep 23



  • 2014 Rising Star in Prostate Cancer Research Award;
  • 2014 CIHR New Investigator Salary Award;
  • 2012 Till and McCulloch Discovery of the Year (Basic) Award;
  • 2012 OICR Investigator Level I Award.

Previous experience

  • Scientist, The Princess Margaret Cancer Centre;
  • Assistant Professor, Department of Medical Biophysics, University of Toronto;
  • Director, Quantitative Epigenomics Laboratory, Institute for Quantitative Biomedical Sciences, Dartmouth Medical School;
  • Assistant Professor, Department of Genetics, Dartmouth Medical School, Norris Cotton Cancer Center;
  • Postdoctoral Fellow, Molecular Pathology, Harvard Medical School, Dana-Farber Cancer Institute.

Opportunities to collaborate

Inquire directly with Dr. Lupien for opportunities to collaborate.

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