Academic Rank:
Professor, UBC
Medical Director, Centre for Clinical Genomics, Michael Smith Genome Sciences Centre, BC Cancer Agency
Medical Director, Cancer Genetics Laboratory, Pathology and Laboratory Medicine, BC Cancer Agency
Short Bio:

Titles and Affiliations

Aly Karsan is Professor of Pathology and Laboratory Medicine, University of British Columbia, and Medical Director of the Cancer Genetics Laboratory, and Centre for Clinical Genomics in the Genome Sciences Centre, at the British Columbia Cancer Agency. He received his MD from Queen’s University at Kingston, completed his residency in Hematological Pathology at the University of British Columbia, followed by a research fellowship at the University of Washington in Seattle. Dr. Karsan’s clinical focus is to bring new genomic technologies into the diagnostic arena. His research interests focus on functional genomics in myeloid malignancies with a particular interest in the myelodysplastic syndromes (MDS). Recent research has revolved around the role of microRNAs and innate immune signaling pathways in MDS.

Academic background

  • BA, Magna Cum Laude, Queen’s University, Kingston, ON, Life Sciences
  • University of St. Andrews, Scotland, Exchange scholarship (Queen’s University)
  • MD, Queen’s University, Faculty of Medicine, Medicine
  • Fellow of the Royal College of Physicians and Surgeons of Canada – Hematological Pathology


Primary Research Area
Blood Research
Secondary Research Area
Genetics, genomics proteomics and related approaches
Molecular Pathology & Cell Biology
Human Development & Aging

Research Interest

  • Myelodysplastic syndromes and myeloid malignancies
  • Innate immune signaling in vascular and hematopoietic function
  • Genomics for clinical diagnostics

My lab focuses on two major areas: (1) Understanding the molecular basis of myeloid malignancies, in particular the preleukemic bone marrow failure conditions called myelodysplastic syndromes (MDS); and (2) Determining the role of the endothelium in the development of the hematopoietic system. With respect to both areas we have been studying the role of two pathways: innate immune signaling as represented by the Toll-like receptor (TLR) pathways, and the Notch signaling pathway.

With respect to the myeloid malignancies, we have a major focus on understanding the relationship of non-coding RNAs and the regulation of the epigenome.  We have taken genomic approaches to study patient material followed by functional analyses of specific microRNAs. One example of translation of genomic studies to understanding biologic function is our discovery that microRNAs residing on the long arm of chromosome 5 act to independently regulate innate immune signaling DNA methylation. Deletion of chromosome arm 5q is the commonest structural anomaly seen in MDS, and current studies centre around establishing the function of these microRNAs, deregulated innate immune signaling and remodeling of the epigenome in the manifestations of MDS. We are using a variety of in vivo transplantation assays, in vitro cell biology and cell signaling studies as well as additional genomic approaches to answer these questions.

In separate work related to innate immune signaling, we have identified a novel protein, Sash1, by differential proteomic analysis that acts as a scaffold protein in the TLR signal transduction pathway. Expression analyses indicate that this molecule is highly expressed in the microvasculature. Molecular and cellular studies to elucidate the mechanisms of action of this protein are ongoing. As well we have generated a gene-targeted mouse model that demonstrates that loss of this protein results in perinatal death. Currently, we are generating a conditional gene-targeted mouse model to gain a better understanding of the physiologic role of Sash1.

Over the last few years my clinical interest has shifted to using genomics methodologies to deliver clinical diagnostic testing. We were the first accredited lab in Canada to use next-generation sequencing techniques to deliver clinical testing. We are currently developing various gene panels as well as genome-wide tests with the intention of taking these into the clinic.

Teaching Interest

I make use of both, my clinical and research expertise in teaching. I teach Pathology and Internal Medicine residents and students clinical aspects of Hematology/Hematopathology. As well I give resident (Hematology/ Hematopathology, Oncology) seminars on tumor angiogenesis.

I teach graduate student courses using my expertise derived from my research interests in endothelial biology, apoptosis, angiogenesis and tumor biology, and stem cell differentiation. Currently much of my teaching time is spent on grad students, undergrads and high school students who are rotate through my laboratory.