@article{48e99404614243099124607ff376790c,
title = "The transcriptomic landscape of mismatch repair-deficient intestinal stem cells",
abstract = "Lynch syndrome is the most common cause of hereditary colorectal cancer and is secondary to germline alterations in one of four DNA mismatch repair (MMR) genes. Here we aimed to provide novel insights into the initiation of MMR-deficient (MMRd) colorectal carcinogenesis by characterizing the expression profile of MMRd intestinal stem cells (ISC). A tissue-specific MMRd mouse model (Villin-Cre;Msh2LoxP/LoxP) was crossed with a reporter mouse (Lgr5-EGFP-IRES-creERT2) to trace and isolate ISCs (Lgr5{\th}) using flow cytometry. Three different ISC genotypes (Msh2-KO, Msh2-HET, and Msh2-WT) were isolated and processed for mRNA-seq and mass spectrometry, followed by bioinformatic analyses to identify expression signatures of complete MMRd and haplo-insufficiency. These findings were validated using qRT-PCR, IHC, and whole transcriptomic sequencing in mouse tissues, organoids, and a cohort of human samples, including normal colorectal mucosa, premalignant lesions, and early-stage colorectal cancers from patients with Lynch syndrome and patients with familial adenomatous polyposis (FAP) as controls. Msh2-KO ISCs clustered together with differentiated intestinal epithelial cells from all genotypes. Gene-set enrichment analysis indicated inhibition of replication, cell-cycle progression, and the Wnt pathway and activation of epithelial signaling and immune reaction. An expression signature derived from MMRd ISCs successfully distinguished MMRd neoplastic lesions of patients with Lynch syndrome from FAP controls. SPP1 was specifically upregulated in MMRd ISCs and colocalized with LGR5 in Lynch syndrome colorectal premalignant lesions and tumors. These results show that expression signatures of MMRd ISC recapitulate the initial steps of Lynch syndrome carcinogenesis and have the potential to unveil novel biomarkers of early cancer initiation. Significance: The transcriptomic and proteomic profile of MMR-deficient intestinal stem cells displays a unique set of genes with potential roles as biomarkers of cancer initiation and early progression.",
author = "Bommi, {Prashant V.} and Bowen, {Charles M.} and Laura Reyes-Uribe and Wenhui Wu and Hiroyuki Katayama and Pedro Rocha and Parra, {Edwin R.} and Alejandro Francisco-Cruz and Zuhal Ozcan and Elena Tosti and Willis, {Jason A.} and Hong Wu and Taggart, {Melissa W.} and Burks, {Jared K.} and Lynch, {Patrick M.} and Winfried Edelmann and Scheet, {Paul A.} and Wistuba, {Ignacio I.} and Sinha, {Krishna M.} and Hanash, {Samir M.} and Eduardo Vilar",
note = "Funding Information: We thank the patients and their families for their participation. We thank the staff of the Advanced Technology Genomics, and the Flow Cytometry and Cellular Imaging Core Facilities at UTMDACC for their assistance with RNA sequencing, FACS sorting of samples, and imaging acquisition of immunofluorescence, respectively. This work was supported by grant R01 CA219463 (NIH/NCI; to E. Vilar) and a Funding Information: M.W. Taggart reports grants from NCI during the conduct of the study. I.I. Wistuba reports grants and personal fees from Genentech/Roche, Bayer, Astra Zeneca/Medimmune, Pfizer, HTG Molecular, Merck, Guardant Health; personal fees from Bristol-Myers Squibb, Asuragen, GlaxoSmithKline, Oncocyte, Flame, MSD, Platform Health; and grants from DerpArray, Adaptive, Adaptimmune, EMD Serono, Takeda, Amgen, Karus, Johnson & Johnson, Iovance, 4D, Novartis, and Akoya outside the submitted work. S.M. Hanash reports a patent for IP filed pending. E. Vilar reports grants and personal fees from Janssen Research and Development and personal fees from Recursion Pharma outside the submitted work; in addition, E. Vilar, P.V. Bommi, W. Wu, H. Katayama, and S.M. Hanash report a U.S. Provisional Patent Application No. 63/152,751 pending. No disclosures were reported by the other authors. Funding Information: We thank the patients and their families for their participation. We thank the staff of the Advanced Technology Genomics, and the Flow Cytometry and Cellular Imaging Core Facilities at UTMDACC for their assistance with RNA sequencing, FACS sorting of samples, and imaging acquisition of immunofluorescence, respectively. This work was supported by grant R01 CA219463 (NIH/NCI; to E. Vilar) and a gift from the Feinberg Family Foundation (to W. Edelmann and E. Vilar); by the Multi-Investigator Research Award grant RP160668 (Cancer Prevention and Research Institute of Texas, to I.I. Wistuba), and the MD Anderson Lung Cancer Moon Shot Program (to I.W. Wistuba) and the Translational Molecular Pathology Immune-profiling Laboratory; by the NCI Research Specialist R50 CA243707-01A1 (to J.K. Burks); and P30 CA13330 and CA016672 (NIH/NCI) to the Albert Einstein Cancer Center and The University of Texas MD Anderson Cancer Center Core Support Grant, respectively. Funding Information: gift from the Feinberg Family Foundation (to W. Edelmann and E. Vilar); by the Multi-Investigator Research Award grant RP160668 (Cancer Prevention and Research Institute of Texas, to I.I. Wistuba), and the MD Anderson Lung Cancer Moon Shot Program (to I.W. Wistuba) and the Translational Molecular Pathology Immune-profiling Laboratory; by the NCI Research Specialist R50 CA243707-01A1 (to J.K. Burks); and P30 CA13330 and CA016672 (NIH/NCI) to the Albert Einstein Cancer Center and The University of Texas MD Anderson Cancer Center Core Support Grant, respectively. Publisher Copyright: {\textcopyright} 2021 American Association for Cancer Research.",
year = "2021",
month = may,
doi = "10.1158/0008-5472.CAN-20-2896",
language = "English (US)",
volume = "81",
pages = "2760--2773",
journal = "Cancer Research",
issn = "0008-5472",
number = "10",
}