A cancer rainbow mouse for visualizing the functional genomics of oncogenic clonal expansion
NATURE COMMUNICATIONS
Authors: Boone, Peter G.; Rochelle, Lauren K.; Ginzel, Joshua D.; Lubkov, Veronica; Roberts, Wendy L.; Nicholls, P. J.; Bock, Cheryl; Flowers, Mei Lang; von Furstenberg, Richard J.; Stripp, Barry R.; Agarwal, Pankaj; Borowsky, Alexander D.; Cardiff, Robert D.; Barak, Larry S.; Caron, Marc G.; Lyerly, H. Kim; Snyder, Joshua C.
Abstract
Field cancerization is a premalignant process marked by clones of oncogenic mutations spreading through the epithelium. The timescales of intestinal field cancerization can be variable and the mechanisms driving the rapid spread of oncogenic clones are unknown. Here we use a Cancer rainbow (Crainbow) modelling system for fluorescently barcoding somatic mutations and directly visualizing the clonal expansion and spread of oncogenes. Crainbow shows that mutations of beta-catenin (Ctnnb1) within the intestinal stem cell results in wide-spread expansion of oncogenes during perinatal development but not in adults. In contrast, mutations that extrinsically disrupt the stem cell microenvironment can spread in adult intestine without delay. We observe the rapid spread of premalignant clones in Crainbow mice expressing oncogenic Rspondin-3 (RSPO3), which occurs by increasing crypt fission and inhibiting crypt fixation. Crainbow modelling provides insight into how somatic mutations rapidly spread and a plausible mechanism for predetermining the intratumor heterogeneity found in colon cancers.
Identification and functional validation of genetic variants in potential miRNA target sites of established BMI genes
INTERNATIONAL JOURNAL OF OBESITY
Authors: Kumar, Pankaj; Traurig, Michael; Baier, Leslie J.
Abstract
Objective MicroRNAs (miRNAs) play an important role in posttranscriptional regulation by binding to target sites in the 3 ' UTR of protein-coding genes. Genetic variation within target sites may potentially disrupt the binding activity of miRNAs, thereby impacting this regulation. In the current study, we investigated whether any established BMI-associated genetic variants potentially function by altering a miRNA target site. Methods The genomic positions of all predicted miRNA target site seed regions were identified, and these positions were queried in the T2D Knowledge Portal for variants that associated with BMI in the GIANT UK Biobank. This in silico analysis identified ten target site variants that associated with BMI with a P value <= 5 x 10(-8). These ten variants mapped to nine genes, FAIM2, CCDC171, ADPGK, ZNF654, MLXIP, NT5C2, SHISA4, SLC25A22, and CTNNB1. Results In vitro functional analyses showed that five of these target site variants, rs7132908 (FAIM2), rs4963153 (SLC25A22), rs9460 (ADPGK), rs11191548 (NT5C2), and rs3008747 (CCDC171), disrupted the binding activity of miRNAs to their target in an allele-specific manner. Conclusion In conclusion, our study suggests that some established variants for BMI may function by altering miRNA binding to a 3 ' UTR target site.