Sixth Quarter Report – November 2018
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.
