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Fourth Quarter Report – May 2018

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.