Systemic circulating microRNA landscape in Lynch syndrome

Abstract

Circulating microRNAs (c-miRs) are small noncoding RNA molecules that migrate throughout the body and regulate gene expression. Global c-miR expression patterns (c-miRnomes) change with sporadic carcinogenesis and have predictive potential in early detection of cancers. However, there are no studies that have assessed whether c-miRnomes display similar potential in carriers of inherited pathogenic mismatch-repair gene variants (path_MMR), known as Lynch syndrome (LS), who are predisposed to highly increased cancer risk. Using high-throughput sequencing and bioinformatic approaches, we conducted an exploratory analysis to characterize systemic c-miRnomes of path_MMR carriers, sporadic rectal cancer patients and non-LS controls. We showed for the first time that cancer-free path_MMR carriers have a systemic c-miRnome of 40 differentially expressed c-miRs that can distinguish them from non-LS controls. The systemic c-miRnome of cancer-free path_MMR carriers also resembles the systemic c-miRnomes of cancer patients with or without path_MMR. Our pathway analysis linked the found differentially expressed c-miRs to carcinogenesis. A total of 508 putative target genes were identified for 32 out of 40 differentially expressed c-miRs, and 238 of them were enriched in cancer-related pathways. The most enriched c-miR-target genes include well-known oncogenes and tumor suppressor genes such as BCL2, AKT3, PIK3CA, KRAS, NRAS, CDKN1A and PIK3R1. Taken together, our findings suggest that LS and sporadic carcinogenesis share common biological pathways and alterations in these pathways can produce a c-miR signature which can track potential oncogenic stress in cancer-free path_MMR carriers. Therefore, c-miRs hold potential in monitoring the LS risk stratification patterns during clinical surveillance or cancer management.

Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study

“…To separate serum, the whole blood samples were allowed to clot for 30 minutes at room temperature, centrifuged at 1,800 × g for 10 minutes and aliquoted. Methods of sample collection, preanalytic preparation, c-miR extraction, library preparation, and sequencing have been described previously in detail ( 18 ).…”

“…High-throughput c-miR expression data of cancer-free LS carriers ( n = 86) as well as of healthy non-carrier control samples ( n = 37) were generated as described earlier ( 18 ). Briefly, c-miRs were extracted using affinity column-based approach (miRNeasy Serum/Plasma advanced kit, Qiagen), ligated to sequencing adapters from both 5′ and 3′ end, reverse transcribed into cDNA using unique molecular identifier (UMI)-assigning primers, and purified with magnetic beads (Qiaseq miRNA Library preparation kit, Qiagen).…”

“…Quality controls throughout the RNA isolation, library preparation, and sequencing protocols were conducted with qRT-PCR (Bio-Rad), TapeStation 4200 (Agilent) and Qubit fluorometer (Invitrogen), respectively. To increase the cohort size, we performed small RNA sequencing (RNA-seq) experiment on additional 24 LS carriers using the same analysis pipeline as described ( 18 ). Thus, the current study composed of 110 cancer-free LS carriers who are registered in the LSRFi and 37 healthy non-carrier control samples.…”

“…We were first to report that the c-miR signature of cancer-free LS carriers is associated with carcinogenesis by displaying aberrant expression compared with healthy population but similar expression when compared with patients with sporadic rectal cancer ( 18 ). To build on that, the primary aim of this study was to investigate whether c-miRs can be used in LS cancer risk prediction during a 4-year prospective surveillance period.…”

The Clinical Significance of MicroRNAs in Colorectal Cancer Signaling Pathways: A Review

“…73 Nevertheless, certain microRNAs have recently emerged as significant regulators of genes associated with MMR, including MLH1, MSH2, MSH6, and PMS2. 74 Valeri et al identified that mir-155 compromises MMR mission by targeting the 3′UTR of MLH1, MSH2, and MSH6. 75 Overexpression of this molecule correlated with a hypermutated phenotype and MSI in CRC cell lines.…”