Seventh Quarter Report – February 2019
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.