Scleroderma Association of BC Research Project    

September 2018 Update

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. 

Research Study Progress

Nov 2017 Collection of blood and skin tissue samples completed and stored in The Scleroderma Biobank at St. Paul’s Hospital in Vancouver

Dec 2017  Skin tissue growth completed

Apr 2018   Extraction of micro-RNA (miRNA) from tissue types

May 2018  Frozen tissue samples transferred to the BC Genome Sciences Centre for sequencing

Jul 2018    miRNA sequence data downloaded for one-third of the samples and quality control (QC) checks started by the scientific team members

Nov 2018  Anticipated completion of QC assessment for first third of the samples

 

This proof-of-concept study is to discover miRNA sequences and their differential expression amongst six different types of cells.  This study is important for the approximately 0.09% of adults in Canada with scleroderma and the approximately 0.04% of adults in Canada with IPF. 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 five years, contributing over $240,000 in donations to date. Your donations do make a difference in contributing to research that otherwise would not even be considered for funding for these two orphan diseases.

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.

 

Scleroderma Association of BC Research Project

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 16 May 2018, where these were entered in the queue for WGS analysis. On 26 Jul 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 7 Aug 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. Rounding out the Leadership Team are Ms. Rosanne Queen and Mr. Robert Buzza for the Scleroderma Association of BC.

 

Scleroderma Association of BC Research Project

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 on 16 May 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 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 BC.

 

Scleroderma Association of BC Research Project
Second Quarter Report     November 2017


Enrolment of Scleroderma (SSc) patients with and without interstitial lung disease (ILD) to provide blood and skin tissue samples closed ahead of schedule during the first quarter (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 completed was completed by the end of October and the middle of November, respectively. The delay in recruitment of controls was due to a report received in June 2017 from an international review panel for the project that requested that normal controls additionally provide skin biopsies so recruitment did not commence until midsummer. It was necessary to call back normal controls who already had given micro ribonucleic acid (miRNA) blood samples but not skin samples. Understanding the flow of idiopathic pulmonary fibrosis (IPF patients) through the Lung Clinic at St. Paul`s Hospital was a learning situation and it made sense to stretch out recruitment from among these patients.


Skin fibroblast extraction and growth from skin samples (from all but the IPF patients) are expected to be completed by the laboratory at St. Paul’s and stored in the Biobank before the shutdown over the Christmas break. The extraction of miRNA from all tissues for all patients is to begin after the Christmas break in preparation for next generation sequencing at Canada’s Michael Smith Genome Sciences Centre in Vancouver. New reagents were released to the market in November for amplifying low concentrations of miRNA. The laboratory will be running some tests for the Project with these new reagents.


With the additional collection of skin tissue from normal controls added to the design of the study on the authority of the international review panel, the Project has been enhanced by the addition of a second goal: to better understand the impact of known and miRNA sequences in regulating molecular pathways in skin damage in SSc. Because the skin is not affected in IPF patients, it is not ethical to ask them to undergo a skin biopsy. They have normal skin and the only source of normal skin for the Project need be from normal controls. With Rodnan skin scores for the patients with the limited and diffuse forms of scleroderma as well as skin tissues from them and the controls, it will be possible to search for regulating impacts of miRNA sequences in skin and relate this to miRNA sequences in circulating blood components in a quest for a biomarker for skin damage detectable in a simple blood test. The Project in its latest evolution has been restated as a hypothesis-generating study for the control of both lung damage in IPF and SSc-ILD patients and skin damage in SSc patients.


University researchers involved in this project are Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of Northern 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 BC.

 

 

Scleroderma Association of BC Research Project

First Quarter Report   -   August 2017

Enrolment of Scleroderma (SSc) patients with and without interstitial lung disease (ILD) to provide blood and skin tissue samples has closed ahead of schedule. This is an important milestone in the project. Another important milestone was the establishment of ``The Scleroderma Biobank” at St. Paul`s hospital in Vancouver ostensibly to store the collected samples and any derived products to be used in the course of this Project by Drs. James Dunne, Chris Ryerson, and Pearce Wilcox of The University of British Columbia and Dr. Kevin J. Keen of The University of Northern British Columbia.  A deliberate decision was taken in selecting the name of the Biobank to avoid a regional identification so to allow for growth of the storage of biological tissues for future use by any researchers using samples collected from anywhere in the globe.

 Enrolment of patients with idiopathic pulmonary fibrosis (IPF) and normal controls is continuing with the time to completion of this task extended for another month until the end of September 2017.  IPF is the form of ILD when it occurs in patients unassociated as a secondary disorder due to another disease.  By comparing SSc-ILD tissues with IPF tissues essentially the IPF tissues are acting as a second control group in this scientific study. The delay in recruitment of the normal controls is due to a report received in June 2017 from an international review panel for the project that requested that normal controls additionally provide skin biopsies. With the weight of this opinion from an international group of peers, it was possible to revise the study design accordingly.  A skin biopsy on the forearm results in minor discomfort and a small scar with the risk of a treatable infection.  It was therefore necessary to call back normal controls who already had given blood samples.  In addition to extra time requested of voluntary controls for the procedure, additional clinician time and clinical space for the minor surgical procedure of a forearm skin biopsy had to be added to the initial study plan.  Understanding the flow of IPF patients through the Lung Clinic at St. Paul`s Hospital was another learning situation and it made sense to stretch out recruitment from among these patients.

 The initially stated goal of the Project is to better understand the impact of known and novel micro ribonucleic acid (miRNA) sequences in regulating molecular pathways in IPF and SSc-ILD.  With the additional collection of skin tissue from normal controls added to the design of the study on the authority of the international review panel, the Project has been enhanced by the addition of a second goal:  to better understand the impact of known and miRNA sequences in regulating molecular pathways in skin damage in SSc.  Because the skin is not affected in IPF patients, it is not ethical to ask them to undergo a skin biopsy.  They have normal skin and the only source of normal skin for the Project need be from normal controls.  With Rodnan skin scores for the patients with the limited and diffuse forms of scleroderma as well as skin tissues from them and the controls, it will be possible to search for regulating impacts of miRNA sequences in skin and relate this to miRNA sequences in circulating blood components in a quest for a biomarker for skin damage detectable in a simple blood test.  The Project in its latest evolution can be restated as a hypothesis-generating study for the control of both lung damage in IPF and SSc-ILD patients and skin damage in SSc patients.