Archive for August 2020

Rheumatologist
Assistant professor in the Rheumatology department of the Medicine and Health Sciences Faculty of the University of Sherbrooke since 2006.
Associate professor in the Rheumatology department of the Medicine and Health Sciences Faculty of the University of Sherbrooke since 2014.

Training

Graduation and residency at the University of Sao Paulo, Brazil

Academic interests:

Continuous medical training targeted at the first line. Close collaborator with the Continuing Education Centre of FMSS in multiple rheumatology educational activities.

Research interests:

Scleroderma; close collaborator with the Canadian Scleroderma Research Group. The main research objectives relate to the treatment of problems common in scleroderma, such as malabsorption syndrome, faecal incontinence and digital ulcers.

Pulmonologist
Junior Scientist, RI-MUHC , Montreal General Hospital
Translational Research in Respiratory Diseases Program
Centre for Innovative Medicine
Assistant Professor, Department of Medicine, Faculty of Medicine, McGill University
Department of Medicine, Division of Respiratory Medicine, MUHC

My research focuses on interstitial lung diseases (ILD), a group of progressive, devastating lung diseases characterized by inflammation and scarring (fibrosis) of the lung tissue. The burden of disease is heavy: idiopathic pulmonary fibrosis, the most devastating form of ILD, has a median survival of only three to five years. The incidence and societal burden of ILD are increasing over time. Unfortunately, the right diagnosis is often initially missed or delayed, which will affect long term prognosis. Certain medications have been shown to slow the decline in lung function, but differences in treatment initiation can occur for reasons that remain largely unknown. My research program aims to identify discrepancies and delays in the care of patients with ILD from diagnosis to management, identify the risk factors for those delays, predict disease progression and explore the use of certain medications in understudied populations.

Selected Publications

Click on  to see my current publications list

Eighth Quarter Report – May 2019

This Project is a hypothesis-generating study for the control of lung damage in patients with idiopathic pulmonary fibrosis (IPF) and both lung and skin damage in systemic scleroderma (SSc) patients either with or without interstitial lung disease (ILD). Enrolment of SSc patients with and without ILD to provide blood and skin tissue samples was completed during the first quarter at the end of August 2017 with samples stored in The Scleroderma Biobank at St. Paul’s Hospital in Vancouver.  Enrolment of patients with IPF and normal controls was completed by mid-November 2017.   Skin-fibroblast extraction and growth from skin samples (from all but the IPF patients from whom no skin samples were taken due to ethical reasons as their skin is not affected) were completed and stored in the Biobank before the Christmas 2017 break.  With some extra efforts by laboratory staff, extraction of miRNA from all five tissue types was completed by mid-April 2018 but miRNA extraction was not sufficient in the fifth tissue for whole genome sequencing (WGS) without additional processing by the laboratory and so this was placed on indefinite hold due to cost. A sixth tissue remains stored in the Biobank because its miRNA can be amplified for miRNA WGS but at additional cost.

After receiving frozen tissue-samples from the laboratory at St. Paul’s Hospital on 16 May 2018, the British Columbia Genome Sciences Centre (BCGSC) provided miRNA sequencing data on 92 samples on 26 July 2018, another 92 samples on 7 Aug 2018, and the last 92 samples on 2 Jan 2019.  All 276 samples comprise 3 tissue-types, with some duplicates, from 11 limited SSc-ILD patients, 12 diffuse SSc-ILD patients, 9 patients with limited SSc only, 5 patients with diffuse SSc only, 19 patients with IPF, and 16 control participants. Quality control assessments on the last 92 samples were completed on 17 Feb 2019, at which point the Project was eight months behind schedule.  As of 21 May 2019, the list of novel miRNA’s in the 3 tissue-types has yet to be received from BCGSC so the Project is eleven months behind schedule and counting.  Nevertheless, March 2019 saw the start, in earnest, of comprehensive statistical analysis of the miRNA WGS data inclusive of seeking to generate hypotheses for the role of known miRNA’s in lung and skin damage (and in particular, calcium deposits in the skin). While the details of the results cannot be presented until completion of independent review by other scientists, the results have been judged so successful by the scientific research team that recruitment of a second cohort of patients and controls has already begun in order to verify the results that have been found thus far.  We look forward to seeing how the novel miRNA’s fit into the picture and are eager to receive this data.  Results will be made available the SABC membership and general public as soon as they emerge from the scientific-review process.

University researchers involved in this project are Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of British Columbia and Dr. Kevin Keen of both The University of British Columbia and The University of Northern British Columbia. Rounding out the Leadership Team are Ms. Rosanne Queen and Mr. Robert Buzza for the Scleroderma Association of BC.

Seventh Quarter Report – February 2019

This Project is a hypothesis-generating study for the control of lung damage in patients with idiopathic pulmonary fibrosis (IPF) and both lung and skin damage in systemic scleroderma (SSc) patients either with or without interstitial lung disease (ILD). Enrolment of SSc patients with and without ILD to provide blood and skin tissue samples was completed during the first quarter at the end of August 2017 with samples stored in The Scleroderma Biobank at St. Paul’s Hospital in Vancouver. Enrolment of patients with IPF and normal controls was completed by mid-November 2017. Skin-fibroblast extraction and growth from skin samples (from all but the IPF patients from whom no skin samples were taken due to ethical reasons as their skin is not affected) were completed and stored in the Biobank before the Christmas 2017 break. With some extra efforts by laboratory staff, extraction of miRNA from all five tissue types was completed by mid-April 2018 but miRNA extraction was not sufficient in the fifth tissue for whole genome sequencing (WGS) without additional processing by the laboratory and so this was placed on indefinite hold due to cost. A sixth tissue remains stored in the Biobank because its miRNA can be amplified for miRNA WGS but at additional cost. 

After receiving frozen tissue-samples from the laboratory at St. Paul’s Hospital, on May 16 2018, the British Columbia Genome Sciences Centre (BCGSC) provided miRNA sequencing data on 92 samples on July 26 2018, another 92 samples on August 7 2018, and the last 92 samples on January 2 2019. Quality control assessments on the last 92 samples were completed on February 17 2019, at which point the Project was eight months behind schedule. All 276 samples comprise three tissue-types, with some duplicates, from 11 limited SSc-ILD patients, 12 diffuse SSc-ILD patients, 9 patients with limited SSc only, 5 patients with diffuse SSc only, 19 patients with IPF, and 16 control participants. A limited experiment with 4 samples and 2 different tissues to examine a new procedure for amplifying miRNA for WGS was initiated in December 2018 with promising results in late February 2019, inclusive of a cross-comparison with the expression of 750 miRNA’s as measured on the NanoString platform in October 2018 for 3 different tissue types. The third tissue type examined on the NanoString platform in October was blood serum for the purpose of verifying 3 different methods for preparing serum. The least expensive method for blood serum was deemed the best for NanoString.

March 2019 will see the start, in earnest by researchers, of comprehensive statistical analysis of the miRNA WGS data inclusive of seeking to understand the role of miRNA’s in skin damage and calcinosis.

University researchers involved in this project are Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of British Columbia and Dr. Kevin Keen of both The University of British Columbia and The University of Northern British Columbia. Rounding out the Leadership Team are Ms. Rosanne Queen and Mr. Robert Buzza for the Scleroderma Association of B.C.

Sixth Quarter Report – November 2018

This Project is a hypothesis-generating study for the control of lung damage in patients with idiopathic pulmonary fibrosis (IPF) and lung and skin damage in systemic scleroderma (SSc) patients with or without interstitial lung disease (ILD). Enrolment of SSc patients with and without ILD to provide blood and skin tissue samples was completed during the first quarter at the end of August 2017 with samples stored in The Scleroderma Biobank at St. Paul’s Hospital in Vancouver. Enrolment of patients with IPF and normal controls was completed by mid-November 2017.  Skin-fibroblast extraction and growth from skin samples (from all but the IPF patients from whom no skin samples were taken due to ethical reasons as their skin is not affected) were completed and stored in the Biobank before the Christmas 2017 break. With some extra efforts by laboratory staff to harvest sufficient miRNA for two of the tissues, extraction of miRNA from all five tissue types was completed by mid-April 2018 but miRNA extraction was not sufficient in the fifth tissue for whole genome sequencing (WGS) without additional processing by the laboratory and so this was placed on indefinite hold due to cost. A sixth tissue remains stored in the Biobank because its miRNA cannot be amplified for miRNA WGS, also for cost reasons, but will be analyzed by NanoString miRNA expression chemistry.

After receiving frozen tissue-samples from the laboratory at St. Paul’s Hospital on May 16 2018, the British Columbia Genome Sciences Centre (BCGSC) provided miRNA sequencing data on 92 samples on July 26 2018 and another 92 samples on August 7 2018. After completing quality control checks for miRNA sequencing for these 184 samples in mid-November and combining a few samples, a further 13 tissue- samples were shipped on November 27 2018 to BCGSC to complete the third set. All 276 samples comprise 3 tissue-types, with some duplicates, from 11 limited SSc-ILD patients, 12 diffuse SSc-ILD patients, 9 patients with limited SSc only, 5 patients with diffuse SSc only, 19 patients with IPF, and 16 control participants. Progress has been affected by vacations understandably taken by laboratory staff during August and November. All will be taking vacations in December. It is expected to receive the miRNA sequences for the last 92 samples and to complete all quality control checks by the end of January 2019.

After training of laboratory staff, two cartridges were processed as a developmental test of the NanoString platform for miRNA expression analysis in October. The first cartridge failed due to a manufacturing defect and a second replacement cartridge plus reagents were provided by NanoString at no extra cost but the samples on the first cartridge were unfortunately lost. The NanoString technology was successfully validated on 3 tissue types in samples from 3 participants, inclusive of verifying 3 different methods for preparing samples of blood serum. Ironically, the least expensive method for blood serum was deemed the best for NanoString.

University researchers involved in this project are Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of British Columbia and Dr. Kevin Keen of both The University of British Columbia and The University of Northern British Columbia. Rounding out the Leadership Team are Ms. Rosanne Queen and Mr. Robert Buzza for the Scleroderma Association of B.C.

Fifth Quarter Report – August 2018

This Project is a hypothesis-generating study for the control of lung damage in patients with idiopathic pulmonary fibrosis (IPF) and lung and skin damage in systemic scleroderma (SSc) patients both with and without interstitial lung disease (ILD). Enrolment of SSc patients with and without ILD to provide blood and skin tissue samples closed ahead of schedule during the first quarter by the end of August 2017 with samples stored in The Scleroderma Biobank at St. Paul’s Hospital in Vancouver. Enrolment of patients with idiopathic pulmonary fibrosis (IPF) and normal controls was completed by the middle of November. Skin fibroblast extraction and growth from skin samples (from all but the IPF patients from whom no skin samples were taken due to ethical reasons as their skin is not affected) were completed by the laboratory at St. Paul’s and stored in the Biobank before the Christmas 2017 break. Extra efforts were required by laboratory staff to harvest sufficient miRNA for two of the tissues, which doubled the time required for extraction but not for much-added cost in terms of purchasing reagents and other consumables. Extraction of miRNA from all five tissue types was completed by mid-April 2018 but miRNA extraction was not sufficient in the fifth tissue for whole genome sequencing (WGS) without additional processing by the laboratory and so this was placed on indefinite hold due to cost. A sixth tissue remains stored in the Biobank because its miRNA cannot be amplified for miRNA WGS, also for cost reasons, but will be analyzed by Nanostring miRNA expression chemistry.

The laboratory at St. Paul’s Hospital transferred 275 frozen tissue samples to the British Columbia Genome Sciences Centre (BCGSC) on May 16 2018, where these were entered in the queue for WGS analysis. On July 26 2018, processed miRNA sequence data from 92 duplicate samples of whole blood comprising 11 patients with both limited SSc and ILD, 19 patients with IPF, and 16 control participants was downloaded from BCGSC and quality control checks were commenced by the Project team. Raw miRNA sequence data for these samples were downloaded from BCGSC on August 7 2018 with quality control checking continuing until mid-August and then suspended due to vacations.

The original design called for miRNA WGS analysis on three tissue types and Nanostring miRNA expression analysis on four tissue types. This experimental design had to be altered because two more tissues were added and miRNA WGS analysis can only be done on three of the four original tissue types. Nanostring analysis requires one-tenth the amount of miRNA. There is ample miRNA for Nanostring analysis for five tissue types. In June, there was to be a developmental run using Nanostring for one tissue type from each of four patients with SSc-ILD, four patients with IPF, and four controls but this and WGS miRNA for the remaining 184 duplicate samples has been delayed until October pending completion of the quality control assessments.

University researchers involved in this project are Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of British Columbia and Dr. Kevin Keen of The University of Northern British Columbia.

Fourth Quarter Report – May 2018

This Project is a hypothesis-generating study for the control of lung damage in patients with idiopathic pulmonary fibrosis (IPF) and lung and skin damage in systemic scleroderma (SSc) patients both with and without interstitial lung disease (ILD). Enrolment of SSc patients with and without ILD to provide blood and skin tissue samples closed ahead of schedule during the first quarter by the end of August 2017 with samples stored in The Scleroderma Biobank at St. Paul`s hospital in Vancouver. Enrolment of patients with idiopathic pulmonary fibrosis (IPF) and normal controls was completed by the end of October and the middle of November, respectively, 2017.

Skin fibroblast extraction and growth from skin samples (from all but the IPF patients from whom no skin samples were taken due to ethical reasons as their skin is not affected) were completed by the laboratory at St. Paul’s and stored in the Biobank before the shutdown over the Christmas 2017 break. At the end of February 2018, extraction of micro ribonucleic acid (miRNA) was completed for four tissue types from all participants. Extra efforts were required by laboratory staff to harvest sufficient miRNA for two of the tissues, which doubled the time required for extraction but not for much-added cost in terms of purchasing reagents and other consumables. Extraction of miRNA from the fifth tissue was completed by mid-April but miRNA extraction was not sufficient for whole genome sequencing (WGS) without additional processing by the laboratory and so this was placed on indefinite hold due to cost. A sixth tissue remains stored in the Biobank because its miRNA cannot be amplified for miRNA WGS, also for cost reasons, but will be analyzed by Nanostring miRNA expression chemistry. The laboratory at St. Paul’s Hospital transferred 275 frozen tissue samples to the British Columbia Genome Sciences Centre 16 May 16 2018, where these were entered in the queue for WGS analysis.

The original design called for miRNA WGS analysis on three tissue types and Nanostring miRNA expression analysis on four tissue types. This experimental design had to be altered because two more tissues were added and miRNA WGS analysis can only be done on three of the four original tissue types. Nanostring analysis requires one-tenth the amount of miRNA. There is ample miRNA for Nanostring analysis for five tissue types. In June, there will be a developmental run using Nanostring for one tissue type from each of four patients with SSc-ILD, four patients with IPF, and four controls.

University researchers involved in this project are Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of British Columbia and Dr. Kevin Keen of The University of Northern British Columbia. Rounding out the Leadership Team are Ms. Rosanne Queen and Mr. Robert Buzza for the Scleroderma Association of B.C.

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.

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