ABSTRACT: RNA sequencing of tissue samples taken from pediatric cancer patients of varying disease type. Patients represented those with terminal disease with samples taken from resection or autopsy.
Project description:We profiled genome-wide gene expression in non-tumorous human lung tissues. The overall goal of this project is to improve our molecular understanding of various lung diseases including lung cancer and chronic obstructive pulmonary disease (COPD). The samples from the University of British Columbia (UBC) were derived from a long-standing tissue bank started by Drs. James C. Hogg and Peter D. Paré (Ding L, Quinlan KB, Elliott WM, Hamodat M, Paré PD, Hogg JC, Hayashi S. A Lung Tissue Bank for Gene Expression Studies in Chronic Obstructive Pulmonary Disease. COPD: Journal of Chronic Obstructive Pulmonary Disease 2004;1:191-204 (PMID 17136987)). Lung specimens were obtained from patients undergoing lung surgery. Primarily this was for resection of benign or malignant lesions. Some were the diseased lungs from transplant recipients. Patients are approached prior to surgery and asked if they would like to donate a portion of the lung tissue that is to be removed for research. It is explained that this would be done after the appropriate diagnostic specimens are taken and that only portions of lung that would be otherwise discarded will be used for research. A small number of lung samples were obtained at the time of autopsy. Immediately after resection, the lobes or lungs were inflated using a 50% mixture of Cryomatrix and saline. The specimens were then frozen in liquid nitrogen fumes and stored at -80C for later RNA extraction. RNAs were extracted and then hybridized to a single custom-made whole-genome human Affymetrix array.
Project description:In this exploratory study, we used laser microdissection to extract dopaminergic neurons from 10 human SNpc samples obtained at autopsy in Parkinson’s disease patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nano-LC-MS/MS, respectively, and the differential expression between Parkinson’s disease and control group was assessed.
Project description:High grade serous ovarian cancer (HGSC) is frequently characterized by homologous recombination (HR) DNA repair deficiency, and while most such tumors are sensitive to initial treatment, acquired resistance is common. We undertook a multi-omics approach to interrogate the molecular diversity in end-stage disease, using multiple autopsy samples collected from 15 women with HR-deficient HGSC. Patients had polyclonal disease, and several resistance mechanisms were identified within most patients, including reversion mutations and HR restoration by other means. We also observed frequent whole genome duplication, and global changes in immune composition with evidence of immune escape. This analysis highlights diverse evolutionary changes within HGSC that conspire to evade therapy and ultimately overwhelm individual patients. Methylation profiling was done on 29 end stage high grade serous ovarian cancer samples. 38 primary tumours, 6 autopsy tumours and 7 fallopian tube normals from GSE65820 were also used as part of the cohort.
Project description:An immunopurification strategy was used to isolate intact LE, Lys from frozen human autopsy brain samples. LE, Lys isolated from BA9 samples of JNCL patients were compared with age matched unaffected controls and Niemann Pick Type C (NPC) disease patients. The protein content of LE, Lys was analyzed using shotgun proteomics.
Project description:This study focuses on inflammatory bowel disease gene expression profiling. Surgical specimens from 134 patients undergoing bowel resection for inflammatory bowel disease (IBD) and non IBD controls at Mount Sinai Medical Center were collected as the source of tissue. Control samples (CLs) were harvested from normal non inflamed bowel located more than 10 cm away from the tumor from patients undergoing bowel resection for sporadic colon cancer. Ulcerative colitis (UC) and Crohn’s (CD) patient samples were all isolated from areas containing moderate to severe inflammation. The diagnostic pathology report for each specimen was provided by the Mount Sinai Hospital Pathology Department. Patients with UC and patients with CD shared common medications including corticosteroids, infliximab, azathioprine, and mesalamine.
Project description:In this study, we performed the first genome-wide expression profiling of post-mortem brains of a cohort of patients deceased from SVD and compared them to age-matched normal controls. Normal-appearing frontal temporal and occipital cortical and subcortical brain samples were dissected at autopsy from 5 patients diagnosed with pure SVD and 5 control patients without neurological disease and immediately frozen.
Project description:We obtained snap-frozen tissue samples from 20 colorectal cancer (CRC) patients with stage III disease who had undergone curative resection. The expression profiles were determined using Affymetrix Human Genome U133Plus 2.0 arrays. We used microarrays to identify potential gene deregulation correlated with the outcomes of colon cancer patients.
Project description:Rheumatoid arthritis (RA) is a complex and clinically heterogeneous autoimmune disease. Microarray analysis of 83 synovial samples provides insight into the expression-level differences between patients at the site of disease activity. Synovial samples from Rheumatoid Arthritis patients were obtained during joint resection and profiled using microarrays.
Project description:We performed scATAC-seq on primary glioblastoma tissue samples taken at time of initial resection to map the global chromatin profiles of glioblastoma cells and associated non-neoplastic cells