Current Lab Members:

Robert Holt
Eric Yung
Lisa Dreolini
Kyla Cochrane
Craig Rive
Sophie Sneddon
Govinda Sharma
Scott Brown
Chris May
Jelena Sihvonen
Payal Sipahimalani
Kirsten San Juan
Vanessa Zhu

View Past Lab Members

Robert Holt


Affiliations:
  • Head of Sequencing, Michael Smith Genome Sciences Centre, BC Cancer Agency
  • Distinguished Scientist, BC Cancer Agency
  • Professor, Molecular Biology & Biochemistry, Simon Fraser University
  • Professor, Department of Medical Genetics, University of British Columbia

Education:

  • Ph.D. - Pharmacology, University of Alberta, 1998
  • B.Sc. - Biology, University of British Columbia, 1992

Eric Yung

Lab Manager / Staff Scientist


Affiliations:

Education:

  • Post Doc - Leukemia/Gene Therapy, Terry Fox Laboratories/BC Cancer Agency, 2014
  • Post Doc - Gene Therapy/Virology, Children's Hospital/Harvard University, 2004
  • Ph.D. - Molecular Genetics/Virology, Albert Einstein College of Medicine, 2003
  • B.Sc. - Biochemistry, University of British Columbia, 1993

Research:

Advances in Adoptive Cell Therapy (ACT) - which involves isolation of natural tumor infiltrating T cells (TILs), ex vivo activation and expansion, and then re-delivery to the patient – has proven successful for some patients. While the antigens mediating TIL reactivity remain largely unknown, examples of T cells that respond to single amino acid changes originating from somatic tumor mutations have been described. These types of neoantigens, when originating from common recurrent tumor mutations, could be broadly useful ACT targets. KRAS codon 12 mutations are the most common recurrent point mutations in human cancers and account for more than 90% of all pancreatic ductal adenocarcinomas (PDACs). Given the predominance of these KRAS mutations, and their potential immunogenicity from previous studies, we carried out an analysis of The Cancer Genome Atlas (TCGA) data to explore the frequency of predicted immunogenic mutant KRAS epitopes and their HLA restriction patterns. We identified HLA allele A*02:01 as the most common restricted allele for the predominant KRAS aa 5-14 epitopes. Previous studies have tested MHC presentation of synthetic mutant KRAS peptides, however there has been no demonstration of the natural presentation of mutant KRAS peptides. To model KRAS mutant epitope presentation, we used PANC-1 cells, which are hemizygous for the KRAS G12D mutation and are HLA-A*02:01 positive, were examined using weak acid elution and Mass Spectroscopy-Multiple Reaction Monitoring (MS-MRM). We identified approximately 1201 copies of the mutant G12D peptide (KLVVVGADGV) per cell, compared to 10839 copies of the wild-type peptide (KLVVVGAGGV).

We propose to activate and expand T cells from PDAC patient peripheral blood, and isolate mutation-reactive cytolytic T-cell clones for subsequent ACT, as a secondary therapy after primary treatment, to prevent recurrence. Our approach leverages the mutation specificity of PDACs and the convenience of peripheral blood as a source of diverse, viable and non-exhausted cytolytic T cells.

Lisa Dreolini

Genomics Technologist


Affiliations:

Education:

Other:

  • e-mail: ldreolini@bcgsc.ca

Kyla Cochrane

Postdoctoral Fellow


Affiliations:

Education:

Research:

A substantial portion of the cancer burden worldwide is attributable to infectious agents such as viruses or bacteria. Some of these can directly cause cancers, others can facilitate cancer development, and still others may have no causative role but their existence can indicate the presence of a cancer or risk of developing one. Recently, Fusobacterium nucleatum (Fn) has been found to be highly elevated in a subset of colorectal cancer. Fn is a well recognized benign resident of mucosal surfaces often present in the absence of pathogenicity. The reason why Fn may in some cases be pathogenic and at other times an apparently benign, commensal organism is not yet completely understood. So far we have only a rudimentary idea of Fn gene expression, especially during host infection. Therefore the overall goal of my work is to identify genes associated with Fn virulence, and to determine how expression levels of these genes are modulated during infection of the bacterium into host cells using RNA-Seq. I hypothesize that Fn virulence is directly linked to its invasive capacity, and that invasive Fn isolates require select sets of genes that endow these strains with this (and perhaps other) pathogenic properties, setting them apart from commensal isolates. An alternative hypothesis is that there is no difference in the virulence gene repertoires of commensal and invasive strains, but genes associated with pathogenicity are upregulated under certain circumstances to promote invasion and tumorigenesis. Successful identification of gene targets will allow for the subsequent development of neutralizing antibodies against identified virulence determinants in vaccination strategies. Targeted vaccination against specific virulence genes, as opposed to a general anti-Fn vaccine, will avoid the potential problem of vaccine inefficiency caused by tolerisation to commensal Fn.

Other:

  • e-mail: kcochrane@bcgsc.ca

Craig Rive

Postdoctoral Fellow


Affiliations:

Education:

  • Ph.D. - The Immunopathogenesis of Delayed Drug Hypersensitivity, Murdoch University, 2016
  • B.Sc. - Molecular Biology and Biomedical Science with First Class Honours in Molecular Biology, 2012
  • B.Forensics - Forensic Biology and Toxioclogy, 2011

Research:

Honours - The non-specific amplification and sequencing of RNA viral sequences in patient plasma, in order to remove the bias inherent in standard PCR based amplification methods and develop a bead based capture assay to capture and amplify HLA sequences to improve HLA typing using the next generation sequencing platforms.

Ph.D. - Completed Ph.D. at the Institute for Immunology and Infectious Diseases, Murdoch University, Perth Western Australia. Focusing on delayed T cell mediated drug-induced hypersensitivity reactions (HSR's).

Post Ph.D. - Worked as a Research Assistant for the Tumour Immunology Group and the National Centre for Asbestos Related Disease, helping to investigate Lung Cancer and mesothelioma Neo-Antigen T-cell responses.

Currently - Working for the Holtlab as a Post Doctoral Fellow for the BC Cancer Agency in research and development. The primacy goal is to work on the current chimeric antigen receptor (CAR) T cell project and work on a number of development projects which may assist in this.

Sophie Sneddon

Postdoctoral Fellow


Affiliations:

Education:

Research:

The ability to identify a range of potential tumour-specific mutated neo-antigens that can be targeted by clinical immunotherapy approaches is a recent and exciting development made possible, in part, by advances in high-throughput next generation sequencing and computational biological approaches. My research team has recently identified a novel neo-antigen in a murine model of malignant mesothelioma (MM), an asbestos-induced cancer affecting the mesothelial cells of the pleural and peritoneal cavities that is associated with exposure to asbestos. As treatment of MM is limited and survival is 9-12 months post-diagnosis, the identification of a human neo-antigen is important and may form the basis of functional studies that could lead to personalized treatment options for the disease.

My project aims to utilize next generation sequencing technologies to identify MM tumour-specific somatic mutations that could lead to mutated neo-antigens in a cohort of thirty human and fifteen murine samples. Specifically, I will utilize the expertise of the Holt Lab at the GSC in order to analyse RNA sequence data produced for the human cohort in order to identify potential neo-antigens, examine expression of genes of interest, including immune-associated genes, TCR and HLA expression as well as gene fusion events.

Other:

Govinda Sharma

PhD Candidate


Affiliations:

Education:

Research:

Infiltration of cytotoxic T-lymphocytes (CTL) into solid tumor masses is a sign of a developed immune response to cancer, with higher numbers of tumor-infiltrating lymphocytes (TIL) correlating significantly with enhanced patient survival outcomes. In response to this phenomenon, expansion ex vivo of tumoricidal TIL and subsequent re-administration of expanded cells into patients has formed a promising new branch of cancer therapeutics, called adoptive immunotherapy. However, one of largest remaining hurdles in the field of cancer immunotherapy is the lack of knowledge regarding the identity of tumor antigens eliciting CTL responses in cancer patients and, therefore, the inability to appropriately isolate and deploy specific tumor-reactive CTL cell lines.

Existing methods in use for T-cell antigen identification are limited in scalability and reliability and, therefore, require the biased selection of small candidate antigen panels to systematically pan for positive hits. I am developing a novel methodology for identification of T-cell antigens capable of interrogating orders of magnitude more potential antigens than conventional methods. My approach involves providing a population of target antigen-presenting cells with a FRET-based granzyme-B (GzmB)-cleavable reporter gene linked to a library of short peptide-encoding sequences to be screened. Transfected target cells which receive a dose of GzmB from co-cultured CTL lines of interest can be detected and isolated from the population-at-large by FACS. The identity of recovered epitopes is then determined using deep sequencing.

I am currently in the process of benchmarking this approach in the context of well-studied model antigen systems as well as patient-derived test systems. My aim is to recapitulate the antigens found by conventional methods in prior studies in these patient samples while using the expanded candidate antigen screening space afforded by my novel method to find new epitopes that were previously undiscovered in those studies.

Other:

Scott Brown

PhD Candidate


Affiliations:

Education:

Research:

Cancer is a disease of the genome, arising from spontaneous changes in the DNA of a single cell. These are mutations, and can be detected by the immune system, allowing specialized white blood cells called T cells to seek out and destroy the mutated cells. Tumours can form when these mutations are not visible to the T cells. Over the past few years there has been a flurry of research on helping the body’s immune system detect these mutated cancer cells in a strategy known as cancer immunotherapy and, in 2013, Science magazine named cancer immunotherapy as the Breakthrough of the Year. Despite some great successes, these therapies are not yet effective in all patients.

My project will use large, public, cancer genome datasets to predict, computationally, the interaction between a tumour and the immune system on a patient by patient level. There is a large but finite set of characteristics that a patient’s immune system can have, which defines the interaction between T cell and tumour. This is one reason why tumours found in different patients will be comprised of dramatically different sets of mutations. Any immunotherapy that will target these unique mutations will need to be personalized for each patient. By extracting the immune characteristics from patient genomes, I will perform computational predictions to determine which mutations are most likely to be detected by that patient’s immune system, indicating the best targets for immunotherapies.

By obtaining a better understanding of the unique interaction between tumours and T cells for any given patient, researchers will be better able to design effective immunotherapies. This could have immediate clinical consequences; improving treatment for the hundreds of thousands of people living with cancer in Canada by reducing the chance of recurrence. It would mark a leap forward in cancer immunotherapy and cancer treatment in general.

Other:

  • Tel: 604-675-8000 x 7501
  • e-mail: sbrown@bcgsc.ca

Chris May

Masters Student


Affiliations:

Education:

Other:

  • Tel: 604-675-8000 x 7500
  • e-mail: cmay@bcgsc.ca

Jelena Sihvonen

Directed Studies Student
Prev: Co-op, UBC 2015


Affiliations:

Education:

Christina Tran

Directed Studies Student


Affiliations:

Education:

Payal Sipahimalani

Projects Manager


Affiliations:

Education:

Other:

  • Tel: 604-707-5900 x 67-5432
  • e-mail: payals@bcgsc.ca

Kirsten San Juan

Admin Assistant

Vanessa Zhu

Admin Assistant

View Past Lab Members