ABSTRACT: Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas (diagnostic/surgical samples)
Project description:Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas
Project description:Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas (excision/x-ray samples)
Project description:Gene expression is widely used for the characterization of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilization due to sample x-ray and of diagnostic core-cutting. Twenty-three and 56 sample pairs, respectively, were suitable for analysis. In general, there is a good correlation in gene expression between pairs of core-cuts except where genes have a narrow dynamic range. Increases in the expression of several stress/early-response genes (e.g., FOS, FOSB, JUN) were found in both studies. Substantial changes in expression of early response genes occur within an hour after surgery and in IL6, IGFB2 and MYC as a result of diagnostic core-cut biopsy. Similar correlation coefficients to the average gene expression profiles of intrinsic subtype, particularly LumA and LumB, can lead to discordances between assigned subtypes.
Project description:Gene expression is widely used for the characterization of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilization due to sample x-ray and of diagnostic core-cutting. Twenty-three and 56 sample pairs, respectively, were suitable for analysis. In general, there is a good correlation in gene expression between pairs of core-cuts except where genes have a narrow dynamic range. Increases in the expression of several stress/early-response genes (e.g., FOS, FOSB, JUN) were found in both studies. Substantial changes in expression of early response genes occur within an hour after surgery and in IL6, IGFB2 and MYC as a result of diagnostic core-cut biopsy. Similar correlation coefficients to the average gene expression profiles of intrinsic subtype, particularly LumA and LumB, can lead to discordances between assigned subtypes.
Project description:Gene expression profiling of CMS4 colon cancer treated with Imatinib in the ImPACCT study. Fresh-frozen biopsies were taken during diagnostic colonoscopy for CMS4 identification. Five patients gave informed consent for two week of neoadjuvant Imatinib therapy prior to removal of the primary tumor. Fresh-frozen samples were taken from surgically resected colon cancer specimens.
Project description:Trihydroxyphenolic compounds, such as Epigallocatechin Gallate (EGCG), cause fibroblast-specific TGFb1 receptor kinase and lysyl oxidase like 2 (LOXL2) inhibition, reducing fibroblast activation and collagen cross-linking in fibrotic mice lungs and in cultured human precision cut lung slices (PCLS) derived from Interstitial Lung Disease (ILD) / Idiopathic Pulmonary Fibrosis (IPF) patients. When taken for two weeks, EGCG reduced protein markers of pro-fibrotic signaling in spare tissue from diagnostic surgical biopsies from ILD patients. Here, we report the result of single-cell RNA sequencing on lung tissue from ILD patients who took EGCG (600mg by mouth daily) for two weeks prior to diagnostic surgical biopsy and donated spare tissue and from control/untreated biopsy samples, including comparison to normal donor and end-stage ILD explant lung tissues.
Project description:Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. This study aims to compare genome-scale DNA methylation between core biopsies (in this GEO accession) and surgical specimens (previously published in GSE66313; see Overall Design below). Within-subject variability in DNA methylation was significantly lower than between-subject variability (all P < 2.20E-16). In 641 CpGs whose methylation was related with increased hazard of invasive breast cancer, lower within-subject than between-subject variability was observed in 92.3% of the study participants (P < 0.05). Between patient-matched core biopsy and surgical specimens, < 0.6% of CpGs measured had changes in median DNA methylation > 15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making.
Project description:Samples were taken from either surgically resected specimens or during surveillance colonoscopic examination. The expression profiles were determined using Affymetrix Human Genome U133 Plus 2.0 arrays. Comparison between the sample groups allow to identify a set of discriminating genes that can be used for molecular markers for predicting development of cancer and/or dysplasia in ulcerative colitis, and to characterize potential diagnostic markers in UC-associated neoplasm. Keywords: repeat
Project description:We have employed single cell sequencing data to study the tumor microenvironment in patients with soft tissue sarcoma. This includes longitudinal biopsy and surgical specimens during a phase 1 clinical trial (NCT04420975) testing pre-operative hypofractionated radiation therapy with BO-112 (Highlight Therapeutics). As a comparison, we included surgical specimens from a cohort of patients undergoing pre-operative hypofractionated radiation therapy alone (NCT02701153).
