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Scleroderma Association of B.C. Research

SABC Genome Research Project

The aim of the SABC Genome Research Project is to identify biomarkers specific to people who have pulmonary fibrosis caused by systemic sclerosis (scleroderma). Being able to distinguish between pulmonary fibrosis that is idiopathic (of various or unknown origin) or the result of scleroderma will allow medical professionals to provide patients with an accurate diagnosis. Identifying reliable biomarkers also provides an opportunity to develop a functional cure; an ongoing treatment that corrects and prevents the disease from continuing to damage the affected organs (in this case, lungs).

SABC funds and co-leads a research study that began recruiting scleroderma patients with and without interstitial lung disease (ILD) in July 2017. Blood samples have also been taken from patients with idiopathic pulmonary fibrosis (IPF) only and both blood and skin samples have been taken from control participants. This research program is creating a firm foundation for intensive research to control lung and skin damage in patients with scleroderma and lung damage in patients with IPF, with the expectation of receiving future support from donations and, hopefully, research funding agencies.

Researcher profiles

Dr. Pearce Wilcox

Dr. Wilcox is a respirologist at St. Paul’s Hospital and Professor of Medicine at The University of British Columbia (UBC). He graduated from Medical School at Queen’s University, Kingston, Ontario in 1980, did his Internal Medicine Residency at the University of Western Ontario from 1980-83 and his Fellowship in Respirology at UBC in 1983-86. He is also certified by the American Board of Internal Medicine.

Dr. Wilcox is the Medical Director of the Providence Health Care Pulmonary Function Laboratory at St. Paul’s Hospital and a Co-Director of the Scleroderma Respiratory Clinic. He is the Medical Director for the UBC Adult Cystic Fibrosis Program based at St. Paul’s Hospital.

He is associated with The James Hogg Research Centre at St. Paul’s Hospital and the UBC Institute of Heart and Lung Health and is a member of the Canadian Thoracic Society Executive Committee, currently Past President. Dr. Wilcox’s research interests include clinical research in cystic fibrosis as well as pulmonary manifestations of connective tissue disorders.

Dr. Chris Ryerson

Dr. Chris Ryerson completed his core clinical training at the University of British Columbia and an interstitial lung disease (ILD) fellowship and Masters degree in clinical research at the University of California San Francisco before joining UBC faculty in 2011.

He is an Associate Professor at UBC, director of the St. Paul’s Hospital ILD clinical and research program, and Head of the Division of Respiratory Medicine at Providence Health Care. His research focuses on management and prognostication of ILD.

Dr. Ryerson is also involved in several national and international clinical practice guidelines on the diagnosis and management of fibrotic ILD.

Dr. Kevin J. Keen

Kevin J. Keen, Ph.D., is a Professor in the Department of Mathematics and Statistics at The University of Northern British Columbia and a Visiting Professor in the Department of Medicine at The University of British Columbia. He has held visiting appointments with the Netherlands Institute for Health Sciences (Erasmus University, Rotterdam) and the Faculty of Medicine at Leiden University.

Dr. Keen has published more than thirty peer-reviewed articles in journals, two book chapters, and two editions of a textbook on statistical graphics. His research involves the development of novel statistical techniques and cutting-edge computer software for the analysis of multivariate data in the study of complex diseases. He is the co-author of articles on lung and skin involvement in scleroderma.

Dr. Keen is accredited as a Professional Statistician (P.Stat.) by both the Statistical Society of Canada and the American Statistical Association (ASA) and is a Fellow of the Royal Statistical Society.

Dr. James V. Dunne

James V. Dunne, MB, FRCP(C), is currently on staff at St. Paul’s Hospital and Vancouver General Hospital in British Columbia, Canada. He is a Clinical Assistant Professor for the University of British Columbia’s Department of Medicine, and specializes in rheumatology.

Scleroderma and fibromyalgia are also among Dr. Dunne’s clinical interests; he is a contributor to the book The Fibromyalgia Syndrome: A Clinical Case Definition for Practitioners. He has also been published in the journal Arthritis & Rheumatology, and other peer-reviewed journals.

Dr. Dunne has the unique distinction of studying in four countries: Ireland, England, the United States (fellowship), and Canada.

Research Study Progress

2021

March 2021

In February 2021, Dr. Keen completed the biostatistical analysis of the biomarker laboratory results obtained before the holiday break in December 2020. The second biomarker laboratory work and biostatistical analysis are planned for early in the second quarter of 2021. Preparation of the samples for the confirmatory miRNA analysis were completed before the end of March 2021. These will be processed by the BC Genome Sciences Centre hopefully in April 2021 so that the bioinformatic and biostatistical analyses can be completed, or at least preliminary results, by the end of June 2021.

2020

December 2020

Work continued for continuation of human-participant approval by UBC/Providence and UNBC Research Ethics Boards for the Program and the Scleroderma Biobank at St. Paul’s Hospital in Vancouver. Laboratory prepwork begun for two new biomarker analyses using banked blood samples.

The laboratory and bioinformatic analyses for one of these two sub-projects was completed before the holiday break. Blood samples for the miRNA confirmatory cohort for PCR cross-validation were mostly completed but halted due to a global shortage of pipette tips needed for PCR analysis of he COVID-19 virus and its variants of concern.

September 2020

Preparation of blood samples for the miRNA confirmatory cohort continued as was preparation of samples for the PCR cross-validation. The results from the analysis of blood samples performed by the Mitogen Advanced Diagnostics Laboratory were accepted during the last week of September 2020. A decision was made to engage on a part-time basis, through existing research funding, a rheumatologist graduating from McGill University to serve as a postdoctoral fellow beginning in January 2021

August 2020

Biostatistical analysis was completed for cytokines for the first miRNA cohort. The remainder of the cytokine samples represents a historical cohort from approximately one decade ago and this required going back to archived electronic and paper records to confirm disease status.

Preparation of blood samples for PCR analysis for a second confirmatory batch of samples commenced.

July 2020

Blood samples from 337 participants were prepared and shipped to Eve Technologies for biomolecular analysis of circulating cytokines, which was received at month’s end. Available blood samples continued to be prepared for next next generation sequencing of miRNA molecules in the confirmation cohort.

June 2020

Decision to pursue peer review and publication in a biomedical journal regarding the diagnostic panel created with known micro-RNA (miRNA) molecules. Preparation and submission of an application to Providence Health Care Research Institute to resume tissue collection to complete the verification cohort.

Creation of a co-authorship partnership with Dr. Marvin Fritzler at the University of Calgary for biomolecular analyses of circulating cytokines and factors to be conducted at Mitogen Advanced Diagnostics Laboratory. Planning for resumption of biomolecular processing for the Project by the core research laboratory at St. Paul’s Hospital.

May 2020

Preparation and cost quote for next generation sequencing of miRNA molecules in the confirmation cohort.

April 2020

Identification of target biomolecular pathways for inflammation and calcinosis for miRNA’s in the diagnostic panel of known miRNA’s and plans for supporting laboratory analyses.

March 2020

Recruitment and sample preparation for verification cohort of miRNA-sequencing and PCR analyses has been placed on hold due to Covid-19. Biostatistical analysis of existing miRNA and clinical data, however, is continuing.

Feb 2020

Bioinformatic verification of PCR lab analysis.

Jan 2020

Polymerase chain reaction (PCR) lab analysis for biochemical pathway predicted by known-miRNA sequencing.

2019

Dec 2019

Approval from University-Industry Liaison Office to publish results for known miRNA’s in medical literature and encouragement to pursue patent protection for novel miRNA’s.

Oct 2019

Invention disclosure to UBC, UNBC, and PCH for known miRNA.

Aug 2019

Completion of differential expression analysis of known and unknown miRNA sequences in blood, skin, and cultured skin-fibroblasts.

Feb 2019

Completion of QC assessment for last third of the samples and QC examination for pilot study of fourth tissue.

2018

Nov 2018

Completion of QC assessment for first two-thirds of the samples.

July 2018

miRNA sequence data downloaded for one-third of the samples and quality control (QC) checks started by the scientific team members.

May 2018

Frozen tissue samples from three tissue types transferred to the BC Genome Sciences Centre for sequencing.

April 2018

Extraction of micro-RNA (miRNA) from tissue types.

2017

Dec 2017

Skin tissue growth completed.

Nov 2017

Collection of blood and skin tissue samples completed and stored in The Scleroderma Biobank at St. Paul’s Hospital in Vancouver.

July 2017

Commence collection of blood and skin tissues from study participants.

This proof-of-concept study is to discover miRNA sequences and their impact on biochemical processes at the cellular level with the goal of targeted therapeutic interventions to correct the disturbed cycle of regeneration in heart, lung, and skin tissues in scleroderma and lung tissue in IPF. This study is important for the approximately 15,604 Canadians with scleroderma and the approximately 7,045 Canadians with IPF (as confirmed by CT, biopsy, or bronchoscopy). Discovering which miRNA sequences are too low or too high and correcting these imbalances could lead to effective treatment of skin damage in patients with scleroderma and treatment of lung damage in patients with IPF only and in patients with both scleroderma and ILD.

SABC has been behind this project for the last four years. Your donations do make a difference in contributing to research of these two orphan diseases that otherwise would not even be considered by funding agencies.

Research Team

The research team brings together experts in respirology, rheumatology, bioinformatics, and genetical statistics to uniquely tackle this challenge. The team is led by SABC President Rosanne Queen, SABC past President Bob Buzza, Drs. James Dunne and Kevin Keen. Drs. Raewyn Broady, Robert Holt, Chris Ryerson and Pearce Wilcox round out the scientific research team.

Both Rosanne and Bob participate on the leadership team to keep us informed on the progress of this SABC-funded research program and to ensure the interests of patients and their families are at the forefront.

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