Barker N, van Es JH, Kuipers J, Kujala P, van den Born M, Cozijnsen M, et al. Identification of stem cells in small gut and colon by marker gene Lgr5. Nature. 2007;449:1003–7.
Bankaitis ED, Ha A, Kuo CJ, Magness ST. Reserve stem cells in intestinal homeostasis and damage. Gastroenterology. 2018;155:1348–61.
Beumer J, Clevers H. Regulation and plasticity of intestinal stem cells throughout homeostasis and regeneration. Improvement. 2016;143:3639–49.
Vega PN, Lau KS, Goldenring JR. Not all insults are created equal for awakening dormant stem cell talents. Cell Mol Gastroenterol Hepatol. 2019;7:619–21.
Ayyaz A, Kumar S, Sangiorgi B, Ghoshal B, Gosio J, Ouladan S, et al. Single-cell transcriptomes of the regenerating gut reveal a revival stem cell. Nature. 2019;569:121–5.
Davidson LA, Goldsby JS, Callaway ES, Shah MS, Barker N, Chapkin RS. Alteration of colonic stem cell gene signatures throughout the regenerative response to damage. Biochim Biophys Acta. 2012;1822:1600–7.
Yan KS, Chia LA, Li X, Ootani A, Su J, Lee JY, et al. The intestinal stem cell markers Bmi1 and Lgr5 establish two functionally distinct populations. Proc Natl Acad Sci USA. 2012;109:466–71.
Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, et al. Intestinal enteroendocrine lineage cells possess homeostatic and injury-inducible stem cell exercise. Cell Stem Cell. 2017;21:78–90.e6.
Tetteh PW, Basak O, Farin HF, Wiebrands Ok, Kretzschmar Ok, Begthel H, et al. Alternative of misplaced Lgr5-positive stem cells by plasticity of their enterocyte-lineage daughters. Cell Stem Cell. 2016;18:203–13.
Calabi F, Cilli V. CBFA2T1, a gene rearranged in human leukemia, is a member of a multigene household. Genomics. 1998;52:332–41.
Rossetti S, Hoogeveen AT, Sacchi N. The MTG proteins: chromatin repression gamers with a ardour for networking. Genomics. 2004;84:1–9.
Calabi F, Pannell R, Pavloska G. Gene concentrating on reveals a vital position for MTG8 within the intestine. Mol Cell Biol. 2001;21:5658–66.
McDonough EM, Barrett CW, Parang B, Mittal MK, Smith JJ, Bradley AM, et al. MTG16 is a tumor suppressor in colitis-associated carcinoma. JCI Perception. 2017;2:e78210.
Amann JM, Chyla BJ, Ellis TC, Martinez A, Moore AC, Franklin JL, et al. Mtgr1 is a transcriptional corepressor that’s required for upkeep of the secretory cell lineage within the small gut. Mol Cell Biol. 2005;25:9576–85.
Baulies A, Angelis N, Foglizzo V, Danielsen ET, Patel H, Novellasdemunt L, et al. The transcription co-repressors MTG8 and MTG16 regulate exit of intestinal stem cells from their area of interest and differentiation into enterocyte vs secretory lineages. Gastroenterology. 2020;159:1328–41.e3.
Martinez JA, Williams CS, Amann JM, Ellis TC, Moreno-Miralles I, Washington MK, et al. Deletion of Mtgr1 sensitizes the colonic epithelium to dextran sodium sulfate-induced colitis. Gastroenterology. 2006;131:579–88.
Parang B, Rosenblatt D, Williams AD, Washington MK, Revetta F, Brief SP, et al. The transcriptional corepressor MTGR1 regulates intestinal secretory lineage allocation. FASEB J. 2015;29:786–95.
Moore AC, Amann JM, Williams CS, Tahinci E, Farmer TE, Martinez JA, et al. Myeloid translocation gene members of the family affiliate with T-cell components (TCFs) and affect TCF-dependent transcription. Mol Cell Biol. 2008;28:977–87.
Reddy VK, Brief SP, Barrett CW, Mittal MK, Keating CE, Thompson JJ, et al. BVES regulates intestinal stem cell packages and intestinal crypt viability after radiation. Stem Cells. 2016;34:1626–36.
Thompson JJ, Brief SP, Parang B, Brown RE, Li C, Ng VH, et al. Blood vessel epicardial substance (BVES) reduces LRP6 receptor and cytoplasmic -catenin ranges to modulate Wnt signaling and intestinal homeostasis. Carcinogenesis. 2019;40:1086–98.
Brown RE, Jacobse J, Anant SA, Blunt KM, Chen B, Vega PN, et al. MTG16 regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription components. JCI Perception. 2022;7:e153045.
Thompson JJ, Brief SP, Parang B, Brown RE, Li C, Ng VH, et al. Blood vessel epicardial substance reduces LRP6 receptor and cytoplasmic beta-catenin ranges to modulate Wnt signaling and intestinal homeostasis. Carcinogenesis. 2019;40:1086–98.
Chinowsky CR, Pinette JA, Meenderink LM, Lau KS, Tyska MJ. Nonmuscle myosin-2 contractility-dependent actin turnover limits the size of epithelial microvilli. Mol Biol Cell. 2020;31:2803–15.
Postema MM, Grega-Larson NE, Meenderink LM, Tyska MJ. PACSIN2-dependent apical endocytosis regulates the morphology of epithelial microvilli. Mol Biol Cell. 2019;30:2515–26.
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon offers quick and bias-aware quantification of transcript expression. Nat Strategies. 2017;14:417–9.
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019;47:D766–73.
Love MI, Anders S, Kim V, Huber W. RNA-Seq workflow: gene-level exploratory evaluation and differential expression. F1000Res. 2015;4:1070.
Love MI, Soneson C, Hickey PF, Johnson LK, Pierce NT, Shepherd L, et al. Tximeta: reference sequence checksums for provenance identification in RNA-seq. PLoS Comput Biol. 2020;16:e1007664.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq information with DESeq2. Genome Biol. 2014;15:550.
Pagès H, Carlson, M, Falcon S, Li N. AnnotationDbi: manipulation of SQLite-based annotations in Bioconductor. R bundle model 1.54.1. 2021.
Banerjee A, Herring CA, Chen B, Kim H, Simmons AJ, Southard-Smith AN, et al. Succinate produced by intestinal microbes promotes specification of tuft cells to suppress ileal irritation. Gastroenterology. 2020;159:2101–15.e5.
Simmons AJ, Lau KS. Dissociation and inDrops microfluidic encapsulation of human intestine tissues for single-cell atlasing research. STAR Protoc. 2022;3:101570.
Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, et al. Droplet barcoding for single-cell transcriptomics utilized to embryonic stem cells. Cell. 2015;161:1187–201.
Arceneaux D, Chen Z, Simmons AJ, Heiser CN, Southard-Smith AN, Brenan MJ, et al. A contamination targeted strategy for optimizing the single-cell RNA-seq experiment. iScience. 2023;26:107242.
Southard-Smith AN, Simmons AJ, Chen B, Jones AL, Ramirez Solano MA, Vega PN, et al. Twin listed library design permits compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. BMC Genomics. 2020;21:456.
Vega PN, Nilsson A, Kumar MP, Niitsu H, Simmons AJ, Ro J, et al. Most cancers-associated fibroblasts and squamous epithelial cells represent a novel microenvironment in a mouse mannequin of inflammation-induced colon most cancers. Entrance Oncol. 2022;12:878920.
Heiser CN, Wang VM, Chen B, Hughey JJ, Lau KS. Automated high quality management and cell identification of droplet-based single-cell information utilizing dropkick. Genome Res. 2021;31:1742–52.
Chen B, Ramirez-Solano MA, Heiser CN, Liu Q, Lau KS. Processing single-cell RNA-seq information for dimension reduction-based analyses utilizing open-source instruments. STAR Protoc. 2021;2:100450.
Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression information evaluation. Genome Biol. 2018;19:15.
McKinney W. Knowledge buildings for statistical computing in Python. Proceedings of the ninth Python in Science Convention. Austin Texas: SciPy; 2010. p. 56–61.
Harris, Millman CR, van der Walt KJ, Gommers R SJ, Virtanen P, Cournapeau D, et al. Array programming with NumPy. Nature. 2020;585:357–62.
Gracz AD, Puthoff BJ, Magness ST. Identification, isolation, and tradition of intestinal epithelial stem cells from murine gut. Strategies Mol Biol. 2012;879:89–107.
Herring CA, Banerjee A, McKinley ET, Simmons AJ, Ping J, Roland JT, et al. Unsupervised trajectory evaluation of single-cell RNA-Seq and imaging information reveals different tuft cell origins within the intestine. Cell Syst. 2018;6:37–51.e9.
Karlsson M, Zhang C, Mear L, Zhong W, Digre A, Katona B, et al. A single-cell kind transcriptomics map of human tissues. Sci Adv. 2021;7:eabh2169.
Wang Y, Track W, Wang J, Wang T, Xiong X, Qi Z, et al. Single-cell transcriptome evaluation reveals differential nutrient absorption capabilities in human gut. J Exp Med. 2020;217:e20191130.
Farmer TE, Williams CS, Washington MK, Hiebert SW. Inactivation of the p19(ARF) tumor suppressor impacts intestinal epithelial cell proliferation and integrity. J Cell Biochem. 2008;104:2228–40.
Yan KS, Kuo CJ. Ascl2 reinforces intestinal stem cell id. Cell Stem Cell. 2015;16:105–6.
van der Flier LG, Haegebarth A, Stange DE, van de Wetering M, Clevers H. OLFM4 is a strong marker for stem cells in human gut and marks a subset of colorectal most cancers cells. Gastroenterology. 2009;137:15–7.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment evaluation: a knowledge-based strategy for decoding genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102:15545–50.
Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. PGC-1alpha-responsive genes concerned in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267–73.
Slee EA, Zhu H, Chow SC, MacFarlane M, Nicholson DW, Cohen GM. Benzyloxycarbonyl-Val-Ala-Asp (OMe) fluoromethylketone (Z-VAD.FMK) inhibits apoptosis by blocking the processing of CPP32. Biochem J. 1996;315:21–4.
Gunther C, Martini E, Wittkopf N, Amann Ok, Weigmann B, Neumann H, et al. Caspase-8 regulates TNF-alpha-induced epithelial necroptosis and terminal ileitis. Nature. 2011;477:335–9.
Welz PS, Wullaert A, Vlantis Ok, Kondylis V, Fernandez-Majada V, Ermolaeva M, et al. FADD prevents RIP3-mediated epithelial cell necrosis and power intestinal irritation. Nature. 2011;477:330–4.
Werts AD, Fulton WB, Ladd MR, Saad-Eldin A, Chen YX, Kovler ML, et al. A novel position for necroptosis within the pathogenesis of necrotizing enterocolitis. Cell Mol Gastroenterol Hepatol. 2020;9:403–23.
Komarov PG, Komarova EA, Kondratov RV, Christov-Tselkov Ok, Coon JS, Chernov MV, et al. A chemical inhibitor of p53 that protects mice from the negative effects of most cancers remedy. Science. 1999;285:1733–7.
Barker N. Grownup intestinal stem cells: important drivers of epithelial homeostasis and regeneration. Nat Rev Mol Cell Biol. 2014;15:19–33.
Creamer B, Shorter RG, Bamforth J. The turnover and shedding of epithelial cells. I. The turnover within the gastro-intestinal tract. Intestine. 1961;2:110–8.
Khurana S, George SP. Regulation of cell construction and performance by actin-binding proteins: villin’s perspective. FEBS Lett. 2008;582:2128–39.
Bretscher A, Weber Ok. Villin: the key microfilament-associated protein of the intestinal microvillus. Proc Natl Acad Sci USA. 1979;76:2321–5.
Dudouet B, Robine S, Huet C, Sahuquillo-Merino C, Blair L, Coudrier E, et al. Adjustments in villin synthesis and subcellular distribution throughout intestinal differentiation of HT29-18 clones. J Cell Biol. 1987;105:359–69.
Maunoury R, Robine S, Pringault E, Leonard N, Gaillard JA, Louvard D. Developmental regulation of villin gene expression within the epithelial cell lineages of mouse digestive and urogenital tracts. Improvement. 1992;115:717–28.
Cray P, Sheahan BJ, Dekaney CM. Secretory sorcery: paneth cell management of intestinal restore and homeostasis. Cell Mol Gastroenterol Hepatol. 2021;12:1239–50.
Sato, van Es T, Snippert JH, Stange DE HJ, Vries RG, van den Born M, et al. Paneth cells represent the area of interest for Lgr5 stem cells in intestinal crypts. Nature. 2011;469:415–8.
Farin HF, Van Es JH, Clevers H. Redundant sources of Wnt regulate intestinal stem cells and promote formation of Paneth cells. Gastroenterology. 2012;143:1518–29.e7.
Durand A, Donahue B, Peignon G, Letourneur F, Cagnard N, Slomianny C, et al. Practical intestinal stem cells after Paneth cell ablation induced by the lack of transcription issue Math1 (Atoh1). Proc Natl Acad Sci USA. 2012;109:8965–70.
Boonekamp KE, Dayton TL, Clevers H. Intestinal organoids as instruments for enriching and finding out particular and uncommon cell sorts: advances and future instructions. J Mol Cell Biol. 2020;12:562–8.
Rath E, Moschetta A, Haller D. Mitochondrial perform – gatekeeper of intestinal epithelial cell homeostasis. Nat Rev Gastroenterol Hepatol. 2018;15:497–516.
Stringari C, Edwards RA, Pate KT, Waterman ML, Donovan PJ, Gratton E. Metabolic trajectory of mobile differentiation in small gut by Phasor Fluorescence Lifetime Microscopy of NADH. Sci Rep. 2012;2:568.
Yin X, Farin HF, van Es JH, Clevers H, Langer R, Karp JM. Area of interest-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny. Nat Strategies. 2014;11:106–12.
Poindexter SV, Reddy VK, Mittal MK, Williams AM, Washington MK, Harris E, et al. Transcriptional corepressor MTG16 regulates small intestinal crypt proliferation and crypt regeneration after radiation-induced damage. Am J Physiol Gastrointest Liver Physiol. 2015;308:G562–71.
Brief SP, Barrett CW, Stengel KR, Revetta FL, Choksi YA, Coburn LA, et al. Kaiso is required for MTG16-dependent results on colitis-associated carcinoma. Oncogene. 2019;38:5091–106.
Liu Y, Cheney MD, Gaudet JJ, Chruszcz M, Lukasik SM, Sugiyama D, et al. The tetramer construction of the Nervy homology two area, NHR2, is important for AML1/ETO’s exercise. Most cancers Cell. 2006;9:249–60.
Kitabayashi I, Ida Ok, Morohoshi F, Yokoyama A, Mitsuhashi N, Shimizu Ok, et al. The AML1-MTG8 leukemic fusion protein kinds a fancy with a novel member of the MTG8(ETO/CDR) household, MTGR1. Mol Cell Biol. 1998;18:846–58.
Valenta T, Degirmenci B, Moor AE, Herr P, Zimmerli D, Moor MB, et al. Wnt ligands secreted by subepithelial mesenchymal cells are important for the survival of intestinal stem cells and intestine homeostasis. Cell Rep. 2016;15:911–8.
Parang B, Bradley AM, Mittal MK, Brief SP, Thompson JJ, Barrett CW, et al. Myeloid translocation genes differentially regulate colorectal most cancers packages. Oncogene. 2016;35:6341–9.
Barrett CW, Fingleton B, Williams A, Ning W, Fischer MA, Washington MK, et al. MTGR1 is required for tumorigenesis within the murine AOM/DSS colitis-associated carcinoma mannequin. Most cancers Res. 2011;71:1302–12.