ISCC Publications

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Publications from ISCC Support (229)

This is a list of publications representing the work supported by funding from the ISCC program. The articles are ordered by year of publication. Authors names that are in bold represent past or present ISCC Investigators.

2020 (8)

Bahar Halpern K, Massalha H, Zwick RK, Moor AE, Castillo-Azofeifa D, Rozenberg M, Farack L, Egozi A, Miller DR, Averbukh I, Harnik Y, Weinberg-Corem N, de Sauvage FJ, Amit I, Klein OD, Shoshkes-Carmel M, Itzkovitz S. Lgr5+ telocytes are a signaling source at the intestinal villus tip. Nat Commun, 2020 Apr, 11(1): 1936. PMCID: 7176679.

Chen L, Vasoya RP, Toke NH, Parthasarathy A, Luo S, Chiles E, Flores J, Gao N, Bonder EM, Su X, Verzi MP. HNF4 Regulates Fatty Acid Oxidation and Is Required for Renewal of Intestinal Stem Cells in Mice. Gastroenterology, 2020 Mar, 158(4): 985-99 e9. PMCID: 7062567.

McCarthy N, Manieri E, Storm EE, Saadatpour A, Luoma AM, Kapoor VN, Madha S, Gaynor LT, Cox C, Keerthivasan S, Wucherpfennig K, Yuan GC, de Sauvage FJ, Turley SJ, Shivdasani RA. Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient. Cell Stem Cell, 2020 Feb Epub.

Murata K, Jadhav U, Madha S, van Es J, Dean J, Cavazza A, Wucherpfennig K, Michor F, Clevers H, Shivdasani RA. Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells. Cell Stem Cell, 2020 Feb.

Jadhav U, Manieri E, Nalapareddy K, Madha S, Chakrabarti S, Wucherpfennig K, Barefoot M, Shivdasani RA. Replicational Dilution of H3K27me3 in Mammalian Cells and the Role of Poised Promoters. Mol Cell, 2020 Jan.

Luca VC, Miao Y, Li X, Hollander MJ, Kuo CJ, Garcia KC. Surrogate R-spondins for tissue-specific potentiation of Wnt Signaling. PLoS One, 2020 Jan Epub, 15(1): e0226928. PMCID: 6949110 following competing interests: K.C.G. is a founder and scientific advisor of Surrozen, Inc. K.C.G. and V.C.L. are inventors on a patent (WO2018132572A1) applied for by Stanford University describing surrogate RSPOs. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Middelhoff M, Nienhuser H, Valenti G, Maurer HC, Hayakawa Y, Takahashi R, Kim W, Jiang Z, Malagola E, Cuti K, Tailor Y, Zamechek LB, Renz BW, Quante M, Yan KS, Wang TC. Prox1-positive cells monitor and sustain the murine intestinal epithelial cholinergic niche. Nat Commun, 2020 Jan, 11(1): 111. PMCID: 6949263.

Singh AP, Hung YH, Shanahan MT, Kanke M, Bonfini A, Dame MK, Biraud M, Peck BCE, Oyesola OO, Freund JM, Cubitt RL, Curry EG, Gonzalez LM, Bewick GA, Tait-Wojno ED, Kurpios NA, Ding S, Spence JR, Dekaney CM, Buchon N, Sethupathy P. Enteroendocrine Progenitor Cell-Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner. Cell Mol Gastroenterol Hepatol, 2020 Jan, 9(3): 447-64. PMCID: 7021555.

2019 (20)

Kolawole AO, Mirabelli C, Hill DR, Svoboda SA, Janowski AB, Passalacqua KD, Rodriguez BN, Dame MK, Freiden P, Berger RP, Vu DL, Hosmillo M, O'Riordan MXD, Schultz-Cherry S, Guix S, Spence JR, Wang D, Wobus CE. Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. PLoS Pathog, 2019 Nov Epub, 15(10): e1008057. PMCID: 6957189.

Chen L, Toke NH, Luo S, Vasoya RP, Aita R, Parthasarathy A, Tsai YH, Spence JR, Verzi MP. HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine. Development, 2019 Aug, 146(19). PMCID: 6803367.

Wosen JE, Ilstad-Minnihan A, Co JY, Jiang W, Mukhopadhyay D, Fernandez-Becker NQ, Kuo CJ, Amieva MR, Mellins ED. Human Intestinal Enteroids Model MHC-II in the Gut Epithelium. Front Immunol, 2019 Aug, 10: 1970. PMCID: 6710476.

Yoo JH, Donowitz M. Intestinal enteroids/organoids: A novel platform for drug discovery in inflammatory bowel diseases. World J Gastroenterol, 2019 Aug Review, 25(30): 4125-47. PMCID: 6700704.

Solorzano-Vargas RS, Bjerknes M, Wu SV, Wang J, Stelzner M, Dunn JCY, Dhawan S, Cheng H, Georgia S, , Martin MG. √. J Biol Chem, 2019 Jul.

Dang LT, Miao Y, Ha A, Yuki K, Park K, Janda CY, Jude KM, Mohan K, Ha N, Vallon M, Yuan J, Vilches-Moure JG, Kuo CJ, Garcia KC, Baker D. Receptor subtype discrimination using extensive shape complementary designed interfaces. Nat Struct Mol Biol, 2019 Jun, 26(6): 407-14. PMCID: 6582999.

Khalil HA, Hong SN, Rouch JD, Scott A, Cho Y, Wang J, Lewis MS, Martin MG, Dunn JCY, Stelzner MG. Intestinal epithelial replacement by transplantation of cultured murine and human cells into the small intestine. PLoS One, 2019 Jun Epub, 14(5): e0216326. PMCID: 6544206.

Meriwether D, Sulaiman D, Volpe C, Dorfman A, Grijalva V, Dorreh N, Solorzano-Vargas RS, Wang J, O'Connor E, Papesh J, Larauche M, Trost H, Palgunachari MN, Anantharamaiah GM, Herschman HR, , Martin MG, Fogelman AM, Reddy ST. Apolipoprotein A-I mimetics mitigate intestinal inflammation in COX2-dependent inflammatory bowel disease model. J Clin Invest, 2019 Jun, 130: 3670-85. PMCID: 6715371.

Chen L, Toke NH, Luo S, Vasoya RP, Fullem RL, Parthasarathy A, Perekatt AO, Verzi MP. A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity. Nat Genet, 2019 May, 51(5): 777-85.

Holloway EM, Capeling MM, Spence JR. Biologically inspired approaches to enhance human organoid complexity. Development, Review, 2019 Apr Epub, 146(8). PMCID: 6503984.

Chen MS, Lo YH, Chen X, Williams CS, Donnelly JM, Criss ZK, Patel S, Butkus JM, Dubrulle J, Finegold MJ, Shroyer NF. Growth Factor-Independent 1 Is a Tumor Suppressor Gene in Colorectal Cancer. Molecular Cancer Research, 2019 Mar, 17(3): 697-708.

Hayakawa Y, Tsuboi M, Asfaha S, Kinoshita H, Niikura R, Konishi M, Hata M, Oya Y, Kim W, Middelhoff M, Hikiba Y, Higashijima N, Ihara S, Ushiku T, Fukayama M, Tailor Y, Hirata Y, Guha C, Yan KS, Koike K, Wang TC. BHLHA15-Positive Secretory Precursor Cells Can Give Rise to Tumors in Intestine and Colon in Mice. Gastroenterology, 2019 Mar, 156(4): 1066-81 e16. PMCID: 6409180.

Jadhav U, Cavazza A, Banerjee KK, Xie H, O'Neill NK, Saenz-Vash V, Herbert Z, Madha S, Orkin SH, Zhai H, Shivdasani RA. Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA. Mol Cell, 2019 Mar [Epub ahead of print].

Kumar N, Tsai YH, Chen L, Zhou A, Banerjee KK, Saxena M, Huang S, Toke NH, Xing J, Shivdasani RA, Spence JR, Verzi MP. The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Development, 2019 Mar, 146(5). PMCID: 6432663.

Capeling MM, Czerwinski M, Huang S, Tsai YH, Wu A, Nagy MS, Juliar B, Sundaram N, Song Y, Han WM, Takayama S, Alsberg E, Garcia AJ, Helmrath M, Putnam AJ, Spence JR. Nonadhesive Alginate Hydrogels Support Growth of Pluripotent Stem Cell-Derived Intestinal Organoids. Stem Cell Reports, 2019 Feb, 12(2): 381-94.

Castillo-Azofeifa D, Fazio EN, Nattiv R, Good HJ, Wald T, Pest MA, de Sauvage FJ, Klein OD, Asfaha S.Atoh1(+) secretory progenitors possess renewal capacity independent of Lgr5(+) cells during colonic regeneration. EMBO J, 2019 Feb, 38(4). PMCID: 6376326.

Han X, Lee A, Huang S, Gao J, Spence JR, Owyang C. Lactobacillus rhamnosus GG prevents epithelial barrier dysfunction induced by interferon-gamma and fecal supernatants from irritable bowel syndrome patients in human intestinal enteroids and colonoids. Gut Microbes, 2019 Jan, 10(1): 59-76. PMCID: 6363076.

Hu D, Yan H, He XC, Li L. Recent advances in understanding intestinal stem cell regulation. F1000Res, 2019 Jan Epub, 8. PMCID: 6343229.

Jones KB, Furukawa S, Marangoni P, Ma H, Pinkard H, D'Urso R, Zilionis R, Klein AM, Klein OD. Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells. Cell Stem Cell, 2019 Jan, 24(1): 183-92 e8. PMCID: 6320295.

Schoenborn AA, von Furstenberg RJ, Valsaraj S, Hussain FS, Stein M, Shanahan MT, Henning SJ, Gulati AS. The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells. Gut Microbes, 2019 Jan, 10(1): 45-58. PMCID: 6363071.

2018 (37)

Neal JT, Li X, Zhu J, Giangarra V, Grzeskowiak CL, Ju J, Liu IH, Chiou SH, Salahudeen AA, Smith AR, Deutsch BC, Liao L, Zemek AJ, Zhao F, Karlsson K, Schultz LM, Metzner TJ, Nadauld LD, Tseng YY, Alkhairy S, Oh C, Keskula P, Mendoza-Villanueva D, De La Vega FM, Kunz PL, Liao JC, Leppert JT, Sunwoo JB, Sabatti C, Boehm JS, Hahn WC, Zheng GXY, Davis MM, Kuo CJ. Organoid Modeling of the Tumor Immune Microenvironment. Cell, 2018 Dec, 175(7): 1972-88 e16.

Banerjee KK, Saxena M, Kumar N, Chen L, Cavazza A, Toke NH, O'Neill NK, Madha S, Jadhav U, Verzi MP, Shivdasani RA. Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development. Genes Dev, 2018 Nov, 32(21-22): 1430-42. PMCID: 6217732.

Rankin CR, Theodorou E, Man Law IK, Rowe L, Kokkotou E, Pekow J, Wang J, Martin MG, Pothoulakis C, Padua D. Identification of novel mRNAs and lncRNAs associated with mouse experimental colitis and human inflammatory bowel disease. Am J Physiol Gastrointest Liver Physiol, 2018 Nov, 315(5): G722-G33.

Cortez AR, Poling HM, Brown NE, Singh A, Mahe MM, Helmrath MA. Transplantation of human intestinal organoids into the mouse mesentery: A more physiologic and anatomic engraftment site. Surgery, 2018 Oct, 164(4): 643-50.

Lee KK, McCauley HA, Broda TR, Kofron MJ, Wells JM, Hong CI. Human stomach-on-a-chip with luminal flow and peristaltic-like motility. Lab Chip, 2018 Oct, 18(20): 3079-85.

Lueschow SR, Stumphy J, Gong H, Kern SL, Elgin TG, Underwood MA, Kalanetra KM, Mills DA, Wong MH, Meyerholz DK, Good M, McElroy SJ. Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis. PLoS One, 2018 Oct Epub, 13(10): e0204967. PMCID: 6166990

Vallon M, Yuki K, Nguyen TD, Chang J, Yuan J, Siepe D, Miao Y, Essler M, Noda M, Garcia KC, Kuo CJ. A RECK-WNT7 Receptor-Ligand Interaction Enables Isoform-Specific Regulation of Wnt Bioavailability. Cell Rep, 2018 Oct Epub, 25(2): 339-49 e9. PMCID: 6338448.

Weichselbaum L, Klein OD . The intestinal epithelial response to damage. Sci China Life Sci, Review, 2018 Oct, 61(10): 1205-11.

Cruz-Acuna R, Quiros M, Huang S, Siuda D, Spence JR, Nusrat A, Garcia AJ. PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery. Nat Protoc, 2018 Sep, 13(9): 2102-19. Publisher Correction: PEG-4MAL hydrogels for human organoid generation, culture, and in vivo delivery. Nat Protoc, 2018 Oct.

Samsa LA, Williamson IA, Magness ST. Quantitative Analysis of Intestinal Stem Cell Dynamics Using Microfabricated Cell Culture Arrays. Methods Mol Biol, 2018 Sep, 1842: 139-66.

Santos AJM, Lo YH, Mah AT, Kuo CJ. The Intestinal Stem Cell Niche: Homeostasis and Adaptations. Trends Cell Biol, 2018 Dec, 28(12): 1062-78. PMCID: 6338454.

Bankaitis ED, Ha A, Kuo CJ, Magness ST . Reserve Stem Cells in Intestinal Homeostasis and Injury. Gastroenterology, Review, 2018 Aug.

Pont AR, Yan KS. Intestinal Crypts Assume the Fetal Position in Response to Injury. Cell Stem Cell, 2018 Aug, 23(2): 158-9.

Nusse YM, Savage AK, Marangoni P, Rosendahl-Huber AKM, Landman TA, de Sauvage FJ, Locksley RM, Klein OD: Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche. Nature 2018 Jul, 559(7712):109-113. PMCID: 6042247.

Srivillibhuthur M, Warder BN, Toke NH, Shah PP, Feng Q, Gao N, Bonder EM, Verzi MP: TFAM is required for maturation of the fetal and adult intestinal epithelium. Dev Biol 2018 Jul, 439(2):92-101. PMCID: 5978755.

Dubrovsky G, Dunn JCY . Mechanisms for intestinal regeneration. Curr Opin Pediatr, Review, 2018 Jun, 30(3): 424-9.

McKinley KL, Stuurman N, Royer LA, Schartner C, Castillo-Azofeifa D, Delling M, Klein OD, Vale RD: Cellular aspect ratio and cell division mechanics underlie the patterning of cell progeny in diverse mammalian epithelia. Elife 2018 Jun Epub, 7. PMCID: 6023609.

Poling HM, Wu D, Brown N, Baker M, Hausfeld TA, Huynh N, Chaffron S, Dunn JCY, Hogan SP, Wells JM, Helmrath MA, Mahe MM. Mechanically induced development and maturation of human intestinal organoids in vivo. Nat Biomed Eng, 2018 Jun, 2(6): 429-42. PMCID: 6108544.

Smith NR, Swain JR, Davies PS, Gallagher AC, Parappilly MS, Beach CZ, Streeter PR, Williamson IA, Magness ST, Wong MH. Monoclonal Antibodies Reveal Dynamic Plasticity Between Lgr5- and Bmi1-Expressing Intestinal Cell Populations. Cell Mol Gastroenterol Hepatol, 2018 Jun, 6(1): 79-96. PMCID: 6008251.

Takebe T, Wells JM, Helmrath MA, Zorn AM. Organoid Center Strategies for Accelerating Clinical Translation. Cell Stem Cell, 2018 Jun, 22(6): 806-9.

Thiagarajah JR, Kamin DS, Acra S, Goldsmith JD, Roland JT, Lencer WI, Muise AM, Goldenring JR, Avitzur Y, Martin MG, Pedi CC: Advances in Evaluation of Chronic Diarrhea in Infants. Gastroenterology 2018 Jun, 154(8):2045-2059 e2046. PMCID: 6044208.

Chatterji P, Rustgi AK . RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. Trends Mol Med, Review, 2018 May, 24(5): 490-506. PMCID: 5927824.

Knickelbein K, Tong J, Chen D, Wang YJ, Misale S, Bardelli A, Yu J, Zhang L: Restoring PUMA induction overcomes KRAS-mediated resistance to anti-EGFR antibodies in colorectal cancer. Oncogene 2018 Aug, 37(33): 4599-610. PMCID: 6195818.

Tsai YH, Czerwinski M, Wu A, Dame MK, Attili D, Hill E, Colacino JA, Nowacki LM, Shroyer NF, Higgins PDR, Kao JY, Spence JR. A Method for Cryogenic Preservation of Human Biopsy Specimens and Subsequent Organoid Culture. Cell Mol Gastroenterol Hepatol, 2018 May 6(2): 218-22 e7. PMCID: 6085494.

Wang Q, Wang K, Solorzano-Vargas RS, Lin PY, Walthers CM, Thomas AL, Martin MG, Dunn JCY: Bioengineered intestinal muscularis complexes with long-term spontaneous and periodic contractions. PLoS One 2018 May Epub, 13(5):e0195315. PMCID: 5931477.

Wells JM, Watt FM. Diverse mechanisms for endogenous regeneration and repair in mammalian organs. Nature, 2018 May, 557(7705): 322-8.

Chen D, Tong J, Yang L, Wei L, Stolz DB, Yu J, Zhang J, Zhang L: PUMA amplifies necroptosis signaling by activating cytosolic DNA sensors. Proc Natl Acad Sci USA 2018 Apr, 115(15):3930-3935. PMCID: 5899441.

Fletcher R, Wang YJ, Schoen RE, Finn OJ, Yu J, Zhang L: Colorectal cancer prevention: Immune modulation taking the stage. Biochim Biophys Acta 2018 Apr, 1869(2):138-148. PMCID: 5955808.

Kuo CJ, Curtis C. Organoids reveal cancer dynamics. Nature, 2018 Apr, 556(7702): 441-2.

Ramani S, Crawford SE, Blutt SE, Estes MK. Human organoid cultures: transformative new tools for human virus studies. Curr Opin Virol, Review, 2018 Apr, 29: 79-86. PMCID: 5944856.

Spence JR: Taming the Wild West of Organoids, Enteroids, and Mini-Guts. Cell Mol Gastroenterol Hepatol 2018 Apr, 5(2):159-160. PMCID: 5904044.

Blutt SE, Crawford SE, Ramani S, Zou WY, Estes MK: Engineered Human Gastrointestinal Cultures to Study the Microbiome and Infectious Diseases. Cell Mol Gastroenterol Hepatol 2018 Mar Epub, 5(3): 241-51. PMCID: 5904028.

Dame MK, Attili D, McClintock SD, Dedhia PH, Ouillette P, Hardt O, Chin AM, Xue X, Laliberte J, Katz EL, Newsome GM, Hill DR, Miller AJ, Tsai YH, Agorku D, Altheim CH, Bosio A, Simon B, Samuelson LC, Stoerker JA, Appelman HD, Varani J, Wicha MS, Brenner DE, Shah YM, Spence JR, Colacino JA. Identification, isolation, and characterization of human LGR5-positive colon adenoma cells. Development, 2018 Feb, 145(6). PMCID: 5897593.

Rankin SA, McCracken KW, Luedeke DM, Han L, Wells JM, Shannon JM, Zorn AM: Timing is everything: Reiterative Wnt, BMP and RA signaling regulate developmental competence during endoderm organogenesis. Dev Biol 2018 Feb, 434(1):121-132. PMCID: 5785443.

Wang B, Rong X, Palladino END, Wang J, Fogelman AM, Wang B, Rong X, Palladino END, Wang J, Fogelman AM, Martin MG, Alrefai WA, Ford DA, Tontonoz P: Phospholipid Remodeling and Cholesterol Availability Regulate Intestinal Stemness and Tumorigenesis. Cell Stem Cell 2018 Feb Epub, 22(2):206-220 e4. PMCID: 5807072.

Goretsky T, Bradford EM, Ye Q, Lamping OF, Vanagunas T, Moyer MP, Keller PC, Sinh P, Llovet JM, Gao T, She QB, Li L, Barrett TA. Beta-catenin cleavage enhances transcriptional activation. Sci Rep, 2018 Jan, 8(1): 671. PMCID: 5766502.

Zou WY, Blutt SE, Zeng XL, Chen MS, Lo YH, Castillo-Azofeifa D, Klein OD , Shroyer NF , Donowitz M , Estes MK: Epithelial WNT Ligands Are Essential Drivers of Intestinal Stem Cell Activation. Cell Rep 2018 Jan, 22(4):1003-1015. PMCID: 5798462.

2017 (37)

Mochel JP, Jergens AE, Kingsbury D, Kim HJ, Martin MG, Allenspach K: Intestinal Stem Cells to Advance Drug Development, Precision, and Regenerative Medicine: A Paradigm Shift in Translational Research. AAPS J 2017 Dec, 20(1):17.

Tong K, Pellon-Cardenas O, Sirihorachai VR, Warder BN, Kothari OA, Perekatt AO, Fokas EE, Fullem RL, Zhou A, Thackray JK, Tran H, Zhang L, Xing J, Verzi MP: Degree of Tissue Differentiation Dictates Susceptibility to BRAF-Driven Colorectal Cancer. Cell Rep 2017 Dec, 21(13):3833-3845.

Cruz-Acuna R, Quiros M, Farkas AE, Dedhia PH, Huang S, Siuda D, Garcia-Hernandez V, Miller AJ, Spence JR, Nusrat A, Garcia AJ: Synthetic hydrogels for human intestinal organoid generation and colonic wound repair. Nat Cell Biol 2017 Nov, 19(11):1326-1335.

Hill DR, Huang S, Nagy MS, Yadagiri VK, Fields C, Mukherjee D, Bons B, Dedhia PH, Chin AM, Tsai YH, Thodla S, Schmidt TM, Walk S, Young VB, Spence JR: Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. Elife 2017 Nov, 6.

Blutt SE, Broughman JR, Zou W, Zeng XL, Karandikar UC, In J, Zachos NC, Kovbasnjuk O, Donowitz M, Estes MK . Gastrointestinal microphysiological systems. Exp Biol Med (Maywood), Review, 2017 Oct, 242(16): 1633-42. PMCID: 5661769.

Yousefi M, Li L, Lengner CJ: Hierarchy and Plasticity in the Intestinal Stem Cell Compartment. Trends Cell Biol 2017 Oct, 27(10):753-764.

Quiros M, Nishio H, Neumann PA, Siuda D, Brazil JC, Azcutia V, Hilgarth R, O'Leary MN, Garcia-Hernandez V, Leoni G, Feng M, Bernal G, Williams H, Dedhia PH, Gerner-Smidt C, Spence J, Parkos CA, Denning TL, Nusrat A: Macrophage-derived IL-10 mediates mucosal repair by epithelial WISP-1 signaling.J Clin Invest 2017 Sep, 127(9):3510-3520.

Tong J, Tan S, Nikolovska-Coleska Z, Yu J, Zou F, Zhang L : FBW7-Dependent Mcl-1 Degradation Mediates the Anticancer Effect of Hsp90 Inhibitors. Mol Cancer Ther 2017 Sep, 16(9):1979-1988.

Moorefield EC, Andres SF, Blue RE, Van Landeghem L, Mah AT, Santoro MA, Ding S: Aging effects on intestinal homeostasis associated with expansion and dysfunction of intestinal epithelial stem cells. Aging (Albany NY) 2017 Aug, 9(8):1898-1915.

Jadhav U, Saxena M, O'Neill NK, Saadatpour A, Yuan GC, Herbert Z, Murata K, Shivdasani RA : Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell 2017 Jul, 21(1):65-77 e65.

Middelhoff M, Westphalen CB, Hayakawa Y, Yan KS, Gershon MD, Wang TC , Quante M: Dclk1-expressing tuft cells: Critical modulators of the intestinal niche?. Am J Physiol Gastrointest Liver Physiol 2017 Jul:ajpgi 00073 02017.

Munera JO, Sundaram N, Rankin SA, Hill D, Watson C, Mahe M, Vallance JE, Shroyer NF, Sinagoga KL, Zarzoso-Lacoste A, Hudson JR, Howell JC, Chatuvedi P, Spence JR, Shannon JM, Zorn AM, Helmrath MA, Wells JM: Differentiation of Human Pluripotent Stem Cells into Colonic Organoids via Transient Activation of BMP Signaling. Cell Stem Cell 2017 Jul, 21(1):51-64 e56. Erratum Published : Differentiation of Human Pluripotent Stem Cells into Colonic Organoids via Transient Activation of BMP Signaling. Cell Stem Cell, 2019 May, 24(5): 829. PMCID: 6530774.

Spechler SJ, Merchant JL, Wang TC, Chandrasoma P, Fox JG, Genta RM, Goldenring JR, Hayakawa Y, Kuipers EJ, Lund PK, McKeon F, Mills JC, Odze RD, Peek RM, Jr., Pham T, Que J, Rustgi AK, Shaheen NJ, Shivdasani RA, Souza RF, Storz P, Todisco A, Wang DH, Wright NA: A Summary of the 2016 James W. Freston Conference of the American Gastroenterological Association: Intestinal Metaplasia in the Esophagus and Stomach: Origins, Differences, Similarities and Significance. Gastroenterology 2017 Jul, 153(1):e6-e13.

Spence JR: Clocking the Pace of Organoid Research. Cell Mol Gastroenterol Hepatol 2017 Jul, 4(1):203-204.

Yan KS, Gevaert O, Zheng GXY, Anchang B, Probert CS, Larkin KA, Davies PS, Cheng ZF, Kaddis JS, Han A, Roelf K, Calderon RI, Cynn E, Hu X, Mandleywala K, Wilhelmy J, Grimes SM, Corney DC, Boutet SC, Terry JM, Belgrader P, Ziraldo SB, Mikkelsen TS, Wang F, von Furstenberg RJ, Smith NR, Chandrakesan P, May R, Chrissy MAS, Jain R, Cartwright CA, Niland JC, Hong YK, Carrington J, Breault DT, Epstein J, Houchen CW, Lynch JP, Martin MG, Plevritis SK, Curtis C, Ji HP, Li L, Henning SJ, Wong MH, Kuo CJ: Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity. Cell Stem Cell 2017 Jul, 21(1):78-90 e76.

Chin AM, Hill DR, Aurora M, Spence JR : Morphogenesis and maturation of the embryonic and postnatal intestine. Semin Cell Dev Biol 2017 Jun, 66:81-93.

Kim GA, Spence JR , Takayama S. Bioengineering for intestinal organoid cultures. Curr Opin Biotechnol, Review, 2017 Jun, 47: 51-8.

McCracken KW, Wells JM : Mechanisms of embryonic stomach development. Semin Cell Dev Biol 2017 Jun, 66:36-42.

Janda CY, Dang LT, You C, Chang J, de Lau W, Zhong ZA, Yan KS, Marecic O, Siepe D, Li X, Moody JD, Williams BO, Clevers H, Piehler J, Baker D, Kuo CJ, Garcia KC: Surrogate Wnt agonists that phenocopy canonical Wnt and beta-catenin signalling. Nature 2017 May, 545(7653):234-237.

Smith NR, Davies PS, Levin TG, Gallagher AC, Keene DR, Sengupta SK, Wieghard N, El Rassi E, Wong MH : Cell Adhesion Molecule CD166/ALCAM Functions Within the Crypt to Orchestrate Murine Intestinal Stem Cell Homeostasis. Cell Mol Gastroenterol Hepatol 2017 May, 3(3):389-409.

Tong J, Wang P, Tan S, Chen D, Nikolovska-Coleska Z, Zou F, Yu J, Zhang L : Mcl-1 Degradation Is Required for Targeted Therapeutics to Eradicate Colon Cancer Cells. Cancer Res 2017 May, 77(9):2512-2521.

Yan KS, Janda CY, Chang J, Zheng GXY, Larkin KA, Luca VC, Chia LA, Mah AT, Han A, Terry JM, Ootani A, Roelf K, Lee M, Yuan J, Li X, Bolen CR, Wilhelmy J, Davies PS, Ueno H, von Furstenberg RJ, Belgrader P, Ziraldo SB, Ordonez H, Henning SJ, Wong MH, Snyder MP, Weissman IL, Hsueh AJ, Mikkelsen TS, Garcia KC, Kuo CJ: Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal. Nature 2017 May, 545(7653):238-242.

Chang J, Mancuso MR, Maier C, Liang X, Yuki K, Yang L, Kwong JW, Wang J, Rao V, Vallon M, Kosinski C, Zhang JJ, Mah AT, Xu L, Li L, Gholamin S, Reyes TF, Li R, Kuhnert F, Han X, Yuan J, Chiou SH, Brettman AD, Daly L, Corney DC, Cheshier SH, Shortliffe LD, Wu X, Snyder M, Chan P, Giffard RG, Chang HY, Andreasson K, Kuo CJ: Gpr124 is essential for blood-brain barrier integrity in central nervous system disease. Nat Med 2017 Apr, 23(4):450-460.

Mahe MM, Brown NE, Poling HM, Helmrath MA : In Vivo Model of Small Intestine. Methods Mol Biol 2017 Apr, 1597:229-245. Erratum to: In Vivo Model of Small Intestine. Methods Mol Biol, 2017 Jul Epub, 1597: E1.

Munera JO, Wells JM : Generation of Gastrointestinal Organoids from Human Pluripotent Stem Cells. Methods Mol Biol 2017 Apr, 1597:167-177.

Hill DR, Spence JR : Gastrointestinal Organoids: Understanding the Molecular Basis of the Host-Microbe Interface. Cell Mol Gastroenterol Hepatol 2017 Mar, 3(2):138-149.

McCauley HA, Wells JM : Pluripotent stem cell-derived organoids: using principles of developmental biology to grow human tissues in a dish. Development 2017 Mar, 144(6):958-962.

Rouch JD, Dunn JC : New insights and interventions for short bowel syndrome. Curr Pediatr Rep 2017 Mar, 5(1):1-5.

Tsai YH, Nattiv R, Dedhia PH, Nagy MS, Chin AM, Thomson M, Klein OD , Spence JR : In vitro patterning of pluripotent stem cell-derived intestine recapitulates in vivo human development. Development 2017 Mar, 144(6):1045-1055.

Chandrakesan P, Yao J, Qu D, May R, Weygant N, Ge Y, Ali N, Sureban SM, Gude M, Vega K, Bannerman-Menson E, Xia L, Bronze M, An G, Houchen CW: Dclk1, a tumor stem cell marker, regulates pro-survival signaling and self-renewal of intestinal tumor cells. Mol Cancer 2017 Feb, 16(1):30.

Hong SN, Dunn JC, Stelzner M, Martin MG : Concise Review: The Potential Use of Intestinal Stem Cells to Treat Patients with Intestinal Failure. Stem Cells Transl Med 2017 Feb, 6(2):666-676.

Tong J, Tan S, Zou F, Yu J, Zhang L : FBW7 mutations mediate resistance of colorectal cancer to targeted therapies by blocking Mcl-1 degradation. Oncogene 2017 Feb, 36(6):787-796.

Yu H, Hasan NM, In JG, Estes MK, Kovbasnjuk O, Zachos NC, Donowitz M : The Contributions of Human Mini-Intestines to the Study of Intestinal Physiology and Pathophysiology. Annu Rev Physiol 2017 Feb, 79:291-312.

Czerwinski M, Spence JR: Hacking the Matrix. Cell Stem Cell 2017 Jan, 20(1):9-10.

Hayakawa Y, Sakitani K, Konishi M, Asfaha S, Niikura R, Tomita H, Renz BW, Tailor Y, Macchini M, Middelhoff M, Jiang Z, Tanaka T, Dubeykovskaya ZA, Kim W, Chen X, Urbanska AM, Nagar K, Westphalen CB, Quante M, Lin CS, Gershon MD, Hara A, Zhao CM, Chen D, Worthley DL, Koike K, Wang TC: Nerve Growth Factor Promotes Gastric Tumorigenesis through Aberrant Cholinergic Signaling. Cancer Cell 2017 Jan, 31(1):21-34.

Lo YH, Chung E, Li Z, Wan YW, Mahe MM, Chen MS, Noah TK, Bell KN, Yalamanchili HK, Klisch TJ, Liu Z, Park JS, Shroyer NF: Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine. Cell Mol Gastroenterol Hepatol 2017 Jan, 3(1):51-71.

Workman MJ, Mahe MM, Trisno S, Poling HM, Watson CL, Sundaram N, Chang CF, Schiesser J, Aubert P, Stanley EG, Elefanty AG, Miyaoka Y, Mandegar MA, Conklin BR, Neunlist M, Brugmann SA, Helmrath MA, Wells JM: Engineered human pluripotent-stem-cell-derived intestinal tissues with a functional enteric nervous system. Nat Med 2017 Jan, 23(1):49-59.

2016 (31)

Aurora M, Spence JR : hPSC-derived lung and intestinal organoids as models of human fetal tissue. Dev Biol 2016 Dec, 420(2):230-238.

Kulkarni S, Wang TC, Guha C : Stromal Progenitor Cells in Mitigation of Non-Hematopoietic Radiation Injuries. Curr Pathobiol Rep 2016 Dec, 4(4):221-230.

Chandrakesan P, May R, Weygant N, Qu D, Berry WL, Sureban SM, Ali N, Rao C, Huycke M, Bronze MS, Houchen CW: Intestinal tuft cells regulate the ATM mediated DNA Damage response via Dclk1 dependent mechanism for crypt restitution following radiation injury. Sci Rep 2016 Nov, 6:37667.

Chin AM, Tsai YH, Finkbeiner SR, Nagy MS, Walker EM, Ethen NJ, Williams BO, Battle MA, Spence JR : A Dynamic WNT/beta-CATENIN Signaling Environment Leads to WNT-Independent and WNT-Dependent Proliferation of Embryonic Intestinal Progenitor Cells. Stem Cell Reports 2016 Nov, 7(5):826-839.

In JG, Foulke-Abel J, Estes MK, Zachos NC, Kovbasnjuk O, Donowitz M : Human mini-guts: new insights into intestinal physiology and host-pathogen interactions. Nat Rev Gastroenterol Hepatol 2016 Nov, 13(11):633-642.

Wei L, Leibowitz BJ, Wang X, Epperly M, Greenberger J, Zhang L, Yu J : Inhibition of CDK4/6 protects against radiation-induced intestinal injury in mice. J Clin Invest 2016 Nov, 126(11):4076-4087.

Saha S, Aranda E, Hayakawa Y, Bhanja P, Atay S, Brodin NP, Li J, Asfaha S, Liu L, Tailor Y, Zhang J, Godwin AK, Tome WA, Wang TC, Guha C, Pollard JW: Macrophage-derived extracellular vesicle-packaged WNTs rescue intestinal stem cells and enhance survival after radiation injury. Nat Commun 2016 Oct, 7:13096.

Westphalen CB, Middelhoff M, Quante M, Wang TC : Epithelial Dclk1+ cells are not neural crest derived. Stem Cell Investig 2016 Oct, 3:60.

Henning SJ, von Furstenberg RJ. GI stem cells - new insights into roles in physiology and pathophysiology. J Physiol, 2016 Sep, 594(17): 4769-79. PMCID: 4847377.

Mah AT, Yan KS, Kuo CJ : Wnt pathway regulation of intestinal stem cells. J Physiol 2016 Sep, 594(17):4837-4847.

Sailaja BS, He XC, Li L : The regulatory niche of intestinal stem cells. J Physiol 2016 Sep, 594(17):4827-4836.

Smith NR, Gallagher AC, Wong MH: Defining a stem cell hierarchy in the intestine: markers, caveats and controversies. J Physiol 2016 Sep, 594(17):4781-4790.

Soffers JH, Hansen D, Sinagoga KL, Li B, Martin MG, Wells J, Grompe M, Li L : Stem Cells and Regeneration in the Digestive System: Keystone Meeting. Gastroenterology 2016 Sep, 151(3):e6-9.

Tsai YH, Hill DR, Kumar N, Huang S, Chin AM, Dye BR, Nagy MS, Verzi MP , Spence JR : LGR4 and LGR5 Function Redundantly During Human Endoderm Differentiation. Cell Mol Gastroenterol Hepatol 2016 Sep, 2(5):648-662 e648.

Kim TH, Saadatpour A, Guo G, Saxena M, Cavazza A, Desai N, Jadhav U, Jiang L, Rivera MN, Orkin SH, Yuan GC, Shivdasani RA: Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5(+) Intestinal Stem Cells. Cell Rep 2016 Aug, 16(8):2053-2060.

Lund PK, Verzi MP. Singling Out Intestinal Epithelial Stem Cells. Gastroenterology, 2016 Aug, 151(2): 228-31.

Wang Y, Wang X, Flores ER, Yu J, Chang S: Dysfunctional telomeres induce p53-dependent and independent apoptosis to compromise cellular proliferation and inhibit tumor formation. Aging Cell 2016 Aug, 15(4):646-660.

Belinson H, Savage AK, Fadrosh D, Kuo YM, Lin D, Valladares R, Nusse Y, Wynshaw-Boris A, Lynch SV, Locksley RM, Klein OD: Dual epithelial and immune cell function of Dvl1 regulates gut microbiota composition and intestinal homeostasis. JCI Insight 2016 Jul, 1(10).

Khalil HA, Lei NY, Brinkley G, Scott A, Wang J, Kar UK, Jabaji ZB, Lewis M, Martin MG, Dunn JC, Stelzner MG: A novel culture system for adult porcine intestinal crypts. Cell Tissue Res 2016 Jul, 365(1):123-134.

Jadhav U, Nalapareddy K, Saxena M, O'Neill NK, Pinello L, Yuan GC, Orkin SH, Shivdasani RA : Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells. Cell 2016 Jun, 165(6):1389-1400.

Li X, Ootani A, Kuo C: An Air-Liquid Interface Culture System for 3D Organoid Culture of Diverse Primary Gastrointestinal Tissues. Methods Mol Biol 2016 Jun, 1422:33-40.

Scott A, Rouch JD, Jabaji Z, Khalil HA, Solorzano S, Lewis M, Martin MG, Stelzner MG, Dunn JC : Long-term renewable human intestinal epithelial stem cells as monolayers: A potential for clinical use. J Pediatr Surg 2016 Jun, 51(6):995-1000.

Dedhia PH, Bertaux-Skeirik N, Zavros Y, Spence JR : Organoid Models of Human Gastrointestinal Development and Disease. Gastroenterology 2016 May, 150(5):1098-1112.

Neal JT, Kuo CJ : Organoids as Models for Neoplastic Transformation. Annu Rev Pathol 2016 May, 11:199-220.

Chandrakesan P, Panneerselvam J, Qu D, Weygant N, May R, Bronze MS, Houchen CW : Regulatory Roles of Dclk1 in Epithelial Mesenchymal Transition and Cancer Stem Cells. J Carcinog Mutagen 2016 Apr, 7(2).

Chen D, Yu J, Zhang L : Necroptosis: an alternative cell death program defending against cancer. Biochim Biophys Acta 2016 Apr, 1865(2):228-236.

Mah AT, Kuo CJ : Home Sweet Home: a Foxl1+ Mesenchymal Niche for Intestinal Stem Cells. Cell Mol Gastroenterol Hepatol 2016 Mar, 2(2):116-117.

Kim TH, Shivdasani RA . Stomach development, stem cells and disease. Development, Review, 2016 Feb, 143(4): 554-65. PMCID: 4760317.

Wells JM : Regenerative medicine in 2015: Generating and regenerating the digestive system. Nat Rev Gastroenterol Hepatol 2016 Feb, 13(2):65-66.

Zachos NC, Kovbasnjuk O, Foulke-Abel J, In J, Blutt SE, de Jonge HR, Estes MK, Donowitz M. Human Enteroids/Colonoids and Intestinal Organoids Functionally Recapitulate Normal Intestinal Physiology and Pathophysiology. J Biol Chem, 2016 Feb, 291(8): 3759-66. PMCID: 4759158.

Rouch JD, Scott A, Lei NY, Solorzano-Vargas RS, Wang J, Hanson EM, Kobayashi M, Lewis M, Stelzner MG, Dunn JC, Eckmann L, Martin MG: Development of Functional Microfold (M) Cells from Intestinal Stem Cells in Primary Human Enteroids. PLoS One 2016 Jan, 11(1):e0148216.

2015 (29)

Asfaha S : Intestinal stem cells and inflammation. Curr Opin Pharmacol 2015 Dec, 25:62-66.

Sailaja BS, He XC, Li L : Stem Cells Matter in Response to Fasting. Cell Rep 2015 Dec, 13(11):2325-2326.

Zhao M, Li L . Regulation of hematopoietic stem cells in the niche. Sci China Life Sci, Review, 2015 Dec, 58(12): 1209-15.

Hamilton KE, Chatterji P, Lundsmith ET, Andres SF, Giroux V, Hicks PD, Noubissi FK, Spiegelman VS, Rustgi AK: Loss of Stromal IMP1 Promotes a Tumorigenic Microenvironment in the Colon. Mol Cancer Res 2015 Nov, 13(11):1478-1486.

Chandrakesan P, May R, Qu D, Weygant N, Taylor VE, Li JD, Ali N, Sureban SM, Qante M, Wang TC, Bronze MS, Houchen CW: Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal. Oncotarget 2015 Oct, 6(31):30876-30886.

DiMarco RL, Dewi RE, Bernal G, Kuo C, Heilshorn SC: Protein-engineered scaffolds for in vitro 3D culture of primary adult intestinal organoids. Biomater Sci 2015 Oct, 3(10):1376-1385.

Finkbeiner SR, Freeman JJ, Wieck MM, El-Nachef W, Altheim CH, Tsai YH, Huang S, Dyal R, White ES, Grikscheit TC, Teitelbaum DH, Spence JR: Generation of tissue-engineered small intestine using embryonic stem cell-derived human intestinal organoids. Biol Open 2015 Oct, 4(11):1462-1472.

Huang JY, Sweeney EG, Sigal M, Zhang HC, Remington SJ, Cantrell MA, Kuo CJ , Guillemin K, Amieva MR: Chemodetection and Destruction of Host Urea Allows Helicobacter pylori to Locate the Epithelium. Cell Host Microbe 2015 Aug, 18(2):147-156.

Qu D, Weygant N, May R, Chandrakesan P, Madhoun M, Ali N, Sureban SM, An G, Schlosser MJ, Houchen CW : Ablation of Doublecortin-Like Kinase 1 in the Colonic Epithelium Exacerbates Dextran Sulfate Sodium-Induced Colitis. PLoS One 2015 Aug, 10(8):e0134212.

Seiler KM, Schenhals EL, von Furstenberg RJ, Allena BK, Smith BJ, Scaria D, Bresler MN, Dekaney CM, Henning SJ: Tissue underlying the intestinal epithelium elicits proliferation of intestinal stem cells following cytotoxic damage. Cell Tissue Res 2015 Aug, 361(2):427-438.

Sureban SM, May R, Qu D, Chandrakesan P, Weygant N, Ali N, Lightfoot SA, Ding K, Umar S, Schlosser MJ, Houchen CW: Dietary Pectin Increases Intestinal Crypt Stem Cell Survival following Radiation Injury. PLoS One 2015 Aug, 10(8):e0135561.

Asfaha S, Hayakawa Y, Muley A, Stokes S, Graham TA, Ericksen RE, Westphalen CB, von Burstin J, Mastracci TL, Worthley DL, Guha C, Quante M, Rustgi AK, Wang TC: Krt19(+)/Lgr5(-) Cells Are Radioresistant Cancer-Initiating Stem Cells in the Colon and Intestine. Cell Stem Cell 2015 Jun, 16(6):627-638.

Finkbeiner SR, Hill DR, Altheim CH, Dedhia PH, Taylor MJ, Tsai YH, Chin AM, Mahe MM, Watson CL, Freeman JJ, Nattiv R, Thomson M, Klein OD, Shroyer NF, Helmrath MA, Teitelbaum DH, Dempsey PJ, Spence JR: Transcriptome-wide Analysis Reveals Hallmarks of Human Intestine Development and Maturation In Vitro and In Vivo. Stem Cell Reports 2015 Jun.

Canani RB, Castaldo G, Bacchetta R, Martin MG, Goulet O: Congenital diarrhoeal disorders: advances in this evolving web of inherited enteropathies. Nat Rev Gastroenterol Hepatol 2015 May, 12(5):293-302.

Goodell MA, Nguyen H, Shroyer N: Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments. Nat Rev Mol Cell Biol 2015 May, 16(5):299-309.

Khalil HA, Lei NY, Nie W, Lewis MS, Stelzner MG, Martin MG, Dunn JC , Yoo J: Primary Myofibroblasts Maintain Short-Term Viability following Submucosal Injection in Syngeneic, Immune-Competent Mice Utilizing Murine Colonoscopy. PLoS One 2015 May, 10(5):e0127258.

Sinagoga KL, Wells JM : Generating human intestinal tissues from pluripotent stem cells to study development and disease. EMBO J 2015 May, 34(9):1149-1163.

Hamilton KE, Crissey MA, Lynch JP, Rustgi AK: Culturing adult stem cells from mouse small intestinal crypts. Cold Spring Harb Protoc 2015 Apr, 2015(4):354-358.

Tian H, Biehs B, Chiu C, Siebel CW, Wu Y, Costa M, de Sauvage FJ, Klein OD : Opposing activities of Notch and Wnt signaling regulate intestinal stem cells and gut homeostasis. Cell Rep 2015 Apr, 11(1):33-42.

Wang X, Wei L, Cramer JM, Leibowitz BJ, Judge C, Epperly M, Greenberger J, Wang F, Li L, Stelzner MG, Dunn JC, Martin MG, Lagasse E, Zhang L, Yu J: Pharmacologically blocking p53-dependent apoptosis protects intestinal stem cells and mice from radiation. < i>Sci Rep 2015 Apr, 5:8566.

Cantrell MA, Kuo CJ : Organoid modeling for cancer precision medicine. Genome Med 2015 Mar, 7(1):32.

Gracz AD, Williamson IA, Roche KC, Johnston MJ, Wang F, Wang Y, Attayek PJ, Balowski J, Liu XF, Laurenza RJ, Gaynor LT, Sims CE, Galanko JA, Li L, Allbritton NL, Magness ST: A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis. Nat Cell Biol 2015 Mar, 17(3):340-349.

Mahe MM, Sundaram N, Watson CL, Shroyer NF, Helmrath MA : Establishment of human epithelial enteroids and colonoids from whole tissue and biopsy. J Vis Exp 2015 Mar, (97).

McGrath PS, Wells JM : SnapShot: GI tract development. Cell 2015 Mar, 161(1):176-176 e171.

Salahudeen AA, Kuo CJ : Toward recreating colon cancer in human organoids. Nat Med 2015 Mar, 21(3):215-216.

Wells JM : Developmental biology. Regional identity of gut stem cells--one gene to rule them all. Nat Rev Gastroenterol Hepatol 2015 Mar, 12(3):125-126.

Nakagawa H, Whelan K, Lynch JP: Mechanisms of Barrett's oesophagus: intestinal differentiation, stem cells, and tissue models. Best Pract Res Clin Gastroenterol 2015 Feb, 29(1):3-16.

Yan KS, Kuo CJ : Ascl2 reinforces intestinal stem cell identity. Cell Stem Cell 2015 Feb, 16(2):105-106.

Chan CK, Seo EY, Chen JY, Lo D, McArdle A, Sinha R, Tevlin R, Seita J, Vincent-Tompkins J, Wearda T, Lu WJ, Senarath-Yapa K, Chung MT, Marecic O, Tran M, Yan KS, Upton R, Walmsley GG, Lee AS, Sahoo D, Kuo CJ, Weissman IL, Longaker MT: Identification and specification of the mouse skeletal stem cell. Cell 2015 Jan, 160(1-2):285-298.

2014 (22)

McCracken KW, Cata EM, Crawford CM, Sinagoga KL, Schumacher M, Rockich BE, Tsai YH, Mayhew CN, Spence JR, Zavros Y, Wells JM: Modelling human development and disease in pluripotent stem-cell-derived gastric organoids. Nature 2014 Dec, 516(7531):400-404.

Leibowitz B, Qiu W, Buchanan ME, Zou F, Vernon P, Moyer MP, Yin XM, Schoen RE, Yu J , Zhang L : BID mediates selective killing of APC-deficient cells in intestinal tumor suppression by nonsteroidal antiinflammatory drugs. Proc Natl Acad Sci U S A 2014 Nov, 111(46):16520-16525.

Watson CL, Mahe MM, Munera J, Howell JC, Sundaram N, Poling HM, Schweitzer JI, Vallance JE, Mayhew CN, Sun Y, Grabowski G, Finkbeiner SR, Spence JR, Shroyer NF, Wells JM, Helmrath MA: An in vivo model of human small intestine using pluripotent stem cells. Nat Med 2014 Nov, 20(11):1310-1314.

Chandrakesan P, Weygant N, May R, Qu D, Chinthalapally HR, Sureban SM, Ali N, Lightfoot SA, Umar S, Houchen CW : DCLK1 facilitates intestinal tumor growth via enhancing pluripotency and epithelial mesenchymal transition. Oncotarget 2014 Oct, 5(19):9269-9280.

Keene DR, Tufa SF, Wong MH, Smith NR, Sakai LY, Horton WA: Correlation of the same fields imaged in the TEM, confocal, LM, and microCT by image registration: from specimen preparation to displaying a final composite image. Methods Cell Biol 2014 Oct, 124:391-417.

Foulke-Abel J, In J, Kovbasnjuk O, Zachos NC, Ettayebi K, Blutt SE, Hyser JM, Zeng XL, Crawford SE, Broughman JR, Estes MK, Donowitz M . Human enteroids as an ex-vivo model of host-pathogen interactions in the gastrointestinal tract. Exp Biol Med (Maywood), Review, 2014 Sep, 239(9): 1124-34. PMCID: 4380516.

Hartman KG, Bortner JD, Jr., Falk GW, Ginsberg GG, Jhala N, Yu J , Martin MG , Rustgi AK, Lynch JP : Modeling human gastrointestinal inflammatory diseases using microphysiological culture systems. Exp Biol Med (Maywood) 2014 Sep, 239(9):1108-1123.

Jabaji Z, Brinkley GJ, Khalil HA, Sears CM, Lei NY, Lewis M, Martin MG, Dunn JC : Type I collagen as an extracellular matrix for the in vitro growth of human small intestinal epithelium. PLoS One 2014 Sep, 9(9):e107814.

Gracz AD, Magness ST . Defining hierarchies of stemness in the intestine: evidence from biomarkers and regulatory pathways. Am J Physiol Gastrointest Liver Physiol, Review, 2014 Aug, 307(3): G260-73. PMCID: 4121637.

Nadauld LD, Garcia S, Natsoulis G, Bell JM, Miotke L, Hopmans ES, Xu H, Pai RK, Palm C, Regan JF, Chen H, Flaherty P, Ootani A, Zhang NR, Ford JM, Kuo CJ, Ji HP: Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. Genome Biol 2014 Aug, 15(8):428.

Li X, Nadauld L, Ootani A, Corney DC, Pai RK, Gevaert O, Cantrell MA, Rack PG, Neal JT, Chan CW, Yeung T, Gong X, Yuan J, Wilhelmy J, Robine S, Attardi LD, Plevritis SK, Hung KE, Chen CZ, Ji HP, Kuo CJ: Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. Nat Med 2014 Jul, 20(7):769-777.

Shanahan MT, Carroll IM, Grossniklaus E, White A, von Furstenberg RJ, Barner R, Fodor AA, Henning SJ , Sartor RB, Gulati AS: Mouse Paneth cell antimicrobial function is independent of Nod2. Gut 2014 Jun, 63(6):903-910.

Chandrakesan P, Roy B, Jakkula LU, Ahmed I, Ramamoorthy P, Tawfik O, Papineni R, Houchen C, Anant S, Umar S: Utility of a bacterial infection model to study epithelial-mesenchymal transition, mesenchymal-epithelial transition or tumorigenesis. Oncogene 2014 May, 33(20):2639-2654.

Leibowitz BJ, Wei L, Zhang L , Ping X, Epperly M, Greenberger J , Cheng T , Yu J : Ionizing irradiation induces acute haematopoietic syndrome and gastrointestinal syndrome independently in mice. Nat Commun 2014 Mar, 5:3494.

May R, Qu D, Weygant N, Chandrakesan P, Ali N, Lightfoot SA, Li L, Sureban SM, Houchen CW : Brief report: Dclk1 deletion in tuft cells results in impaired epithelial repair after radiation injury. Stem Cells 2014 Mar, 32(3):822-827.

Qu D, May R, Sureban SM, Weygant N, Chandrakesan P, Ali N, Li L, Barrett T, Houchen CW : Inhibition of Notch signaling reduces the number of surviving Dclk1+ reserve crypt epithelial stem cells following radiation injury. Am J Physiol Gastrointest Liver Physiol 2014 Mar, 306(5):G404-411.

von Furstenberg RJ, Buczacki SJ, Smith BJ, Seiler KM, Winton DJ, Henning SJ : Side population sorting separates subfractions of cycling and non-cycling intestinal stem cells. Stem Cell Res 2014 Mar, 12(2):364-375.

DiMarco RL, Su J, Yan KS, Dewi R, Kuo CJ, Heilshorn SC: Engineering of three-dimensional microenvironments to promote contractile behavior in primary intestinal organoids. Integr Biol (Camb) 2014 Feb, 6(2):127-142.

Shivdasani RA. Radiation redux: reserve intestinal stem cells miss the call to duty. Cell Stem Cell, 2014 Feb, 14(2): 135-6. PMCID: 3955177.

Wells JM, Spence JR . How to make an intestine. Development, Review, 2014 Feb, 141(4): 752-60. PMCID: 3912826.

Lei NY, Jabaji Z, Wang J, Joshi VS, Brinkley GJ, Khalil H, Wang F, Jaroszewicz A, Pellegrini M, Li L, Lewis M, Stelzner M, Dunn JC, Martin MG: Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells. PLoS One 2014 Jan, 9(1):e84651.

Yucel G, Van Arnam J, Means PC, Huntzicker E, Altindag B, Lara MF, Yuan J, Kuo C, Oro AE: Partial proteasome inhibitors induce hair follicle growth by stabilizing beta-catenin. Stem Cells 2014 Jan, 32(1):85-92.

2013 (13)

Jabaji Z, Sears CM, Brinkley GJ, Lei NY, Joshi VS, Wang J, Lewis M, Stelzner M, Martin MG , Dunn JC : Use of collagen gel as an alternative extracellular matrix for the in vitro and in vivo growth of murine small intestinal epithelium. Tissue Eng Part C Methods 2013 Dec, 19(12):961-969.

Zhang L , Yu J : Role of apoptosis in colon cancer biology, therapy, and prevention. Curr Colorectal Cancer Rep 2013 Dec, 9(4).

Hartman KG, Bortner JD, Falk GW, Yu J, Martin MG, Rustgi AK, Lynch JP : Modeling inflammation and oxidative stress in gastrointestinal disease development using novel organotypic culture systems. Stem Cell Res Ther 2013 Dec, 4 Suppl 1:S5.

Lim X, Tan SH, Koh WL, Chau RM, Yan KS, Kuo CJ , van Amerongen R, Klein AM, Nusse R: Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. Science 2013 Dec, 342(6163):1226-1230.

Fuller MK, Faulk DM, Sundaram N, Mahe MM, Stout KM, von Furstenberg RJ, Smith BJ, McNaughton KK, Shroyer NF, Helmrath MA, Henning SJ: Intestinal stem cells remain viable after prolonged tissue storage. Cell Tissue Res 2013 Nov, 354(2):441-450.

Yu J : Intestinal stem cell injury and protection during cancer therapy. Transl Cancer Res 2013 Oct, 2(5):384-396.

Magness ST, Puthoff BJ, Crissey MA, Dunn J, Henning SJ, Houchen C, Kaddis JS, Kuo CJ, Li L, Lynch J, Martin MG, May R, Niland JC, Olack B, Qian D, Stelzner M, Swain JR, Wang F, Wang J, Wang X, Yan K, Yu J, Wong MH: A multicenter study to standardize reporting and analyses of fluorescence-activated cell-sorted murine intestinal epithelial cells. Am J Physiol Gastrointest Liver Physiol 2013 Oct, 305(8):G542-551.

Gracz AD, Fuller MK, Wang F, Li L, Stelzner M, Dunn JC , Martin MG , Magness ST : Brief report: CD24 and CD44 mark human intestinal epithelial cell populations with characteristics of active and facultative stem cells. Stem Cells 2013 Sep, 31(9):2024-2030.

Wang F, Scoville D, He XC, Mahe MM, Box A, Perry JM, Smith NR, Lei NY, Davies PS, Fuller MK, Haug JS, McClain M, Gracz AD, Ding S, Stelzner M, Dunn JC, Magness ST, Wong MH, Martin MG, Helmrath M, Li L: Isolation and characterization of intestinal stem cells based on surface marker combinations and colony-formation assay. Gastroenterology 2013 Aug, 145(2):383-395 e381-321.

Cheng Y, Kawamura K, Takae S, Deguchi M, Yang Q, Kuo C, Hsueh AJ: Oocyte-derived R-spondin2 promotes ovarian follicle development. FASEB J 2013 Jun, 27(6):2175-2184.

Qiu W, Liu H, Sebastini A, Sun Q, Wang H, Zhang L , Yu J : An apoptosis-independent role of SMAC in tumor suppression. Oncogene 2013 May, 32(19):2380-2389.

Qiu W, Wang X, Buchanan M, He K, Sharma R, Zhang L , Wang Q, Yu J : ADAR1 is essential for intestinal homeostasis and stem cell maintenance. Cell Death Dis 2013 Apr, 4:e599.

Barry ER, Morikawa T, Butler BL, Shrestha K, de la Rosa R, Yan KS, Fuchs CS, Magness ST, Smits R, Ogino S, Kuo CJ, Camargo FD: Restriction of intestinal stem cell expansion and the regenerative response by YAP. < i>Nature 2013 Jan, 493(7430):106-110.

2012 (10)

Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov JP, Beroukhim R, Kuo CJ, Goessling W, Hahn WC: beta-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Cell 2012 Dec, 151(7):1457-1473. Erratum in: Cell. 2013 Mar 28;153(1):267-70. PMID:23245941

Van Landeghem L, Blue RE, Dehmer JJ, Henning SJ , Helmrath MA, Lund PK : Localized intestinal radiation and liquid diet enhance survival and permit evaluation of long-term intestinal responses to high dose radiation in mice. PLoS One 2012 Dec, 7(12):e51310.

Fuller MK, Faulk DM, Sundaram N, Shroyer NF, Henning SJ, Helmrath MA : Intestinal crypts reproducibly expand in culture. J Surg Res 2012 Nov, 178(1):48-54.

King JB, von Furstenberg RJ, Smith BJ, McNaughton KK, Galanko JA, Henning SJ : CD24 can be used to isolate Lgr5+ putative colonic epithelial stem cells in mice. Am J Physiol Gastrointest Liver Physiol 2012 Aug, 303(4):G443-452.

Stelzner M,Helmrath M, Dunn JC, Henning SJ, Houchen CW, Kuo C, Lynch J, Li L, Magness ST, Martin MG, Wong MH, Yu J, Consortium NIHISC: A nomenclature for intestinal in vitro cultures. Am J Physiol Gastrointest Liver Physiol 2012 Jun, 302(12):G1359-1363.

Vega KJ, May R, Sureban SM, Lightfoot SA, Qu D, Reed A, Weygant N, Ramanujam R, Souza R, Madhoun M, Whorton J, Anant S, Meltzer SJ, Houchen CW: Identification of the putative intestinal stem cell marker doublecortin and CaM kinase-like-1 in Barrett's esophagus and esophageal adenocarcinoma. J Gastroenterol Hepatol 2012 Apr, 27(4):773-780.

Fan X, Krieg S, Hwang JY, Dhal S, Kuo CJ, Lasley BL, Brenner RM, Nayak NR: Dynamic regulation of Wnt7a expression in the primate endometrium: implications for postmenstrual regeneration and secretory transformation. Endocrinology 2012 Mar, 153(3):1063-1069.

Rankin EB, Wu C, Khatri R, Wilson TL, Andersen R, Araldi E, Rankin AL, Yuan J, Kuo CJ, Schipani E, Giaccia AJ: The HIF signaling pathway in osteoblasts directly modulates erythropoiesis through the production of EPO. Cell 2012 Mar, 149(1):63-74.

Gulati AS, Shanahan MT, Arthur JC, Grossniklaus E, von Furstenberg RJ, Kreuk L, Henning SJ , Jobin C, Sartor RB: Mouse background strain profoundly influences Paneth cell function and intestinal microbial composition. PLoS One 2012 Feb, 7(2):e32403.

Yan KS, Chia LA, Li X, Ootani A, Su J, Lee JY, Su N, Luo Y, Heilshorn SC, Amieva MR, Sangiorgi E, Capecchi MR, Kuo CJ: The intestinal stem cell markers Bmi1 and Lgr5 identify two functionally distinct populations. Proc Natl Acad Sci U S A 2012 Jan, 109(2):466-471.

2011 (14)

Ali N, Allam H, May R, Sureban SM, Bronze MS, Bader T, Umar S, Anant S, Houchen CW : Hepatitis C virus-induced cancer stem cell-like signatures in cell culture and murine tumor xenografts. J Virol 2011 Dec, 85(23):12292-12303.

Shkreli M, Sarin KY, Pech MF, Papeta N, Chang W, Brockman SA, Cheung P, Lee E, Kuhnert F, Olson JL, Kuo CJ, Gharavi AG, D'Agati VD, Artandi SE: Reversible cell-cycle entry in adult kidney podocytes through regulated control of telomerase and Wnt signaling. Nat Med 2011 Dec, 18(1):111-

Mustata G, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS , Yu J , Bahar I: Development of small-molecule PUMA inhibitors for mitigating radiation-induced cell death Curr Top Med Chem 2011 Nov, 11(3):281-290.

Lahar N, Lei NY, Wang J, Jabaji Z, Tung SC, Joshi V, Lewis M, Stelzner M, Martin MG , Dunn JC :Intestinal subepithelial myofibroblasts support in vitro and in vivo growth of human small intestinal epithelium. PLoS One 2011 Nov, 6(11):e26898.

Dehmer JJ, Garrison AP, Speck KE, Dekaney CM M, Van Landeghem L, Sun X, Henning SJ, Helmrath MA : Expansion of intestinal epithelial stem cells during murine development. PLoS One 2011 Nov, 6(11):e27070.

Qiu W, Wang X, Leibowitz B, Yang W, Zhang L, Yu J : PUMA-mediated apoptosis drives chemical hepatocarcinogenesis in mice. Hepatology 2011 Oct, 54(4):1249-1258.

King CE, Wang L, Winograd R, Madison BB, Mongroo PS, Johnstone CN, Rustgi AK: LIN28B fosters colon cancer migration, invasion and transformation through let-7-dependent and -independent mechanisms. Oncogene 2011 Oct, 30(40):4185-4193.

Li H, Wang P, Yu J, Zhang L : Cleaving Beclin 1 to suppress autophagy in chemotherapy-induced apoptosis. Autophagy 2011 Oct, 7(10):1239-1241.

Sureban SM, May R, Mondalek FG, Qu D, Ponnurangam S, Pantazis P, Anant S, Ramanujam RP, Houchen CW : Nanoparticle-based delivery of siDCAMKL-1 increases microRNA-144 and inhibits colorectal cancer tumor growth via a Notch-1 dependent mechanism. J Nanobiotechnology 2011 Sep, 9:40.

Yeung TM, Chia LA, Kosinski CM, Kuo CJ : Regulation of self-renewal and differentiation by the intestinal stem cell niche. Cell Mol Life Sci 2011 Aug, 68(15):2513-2523.

Leibowitz BJ, Qiu W, Liu H, Cheng T, Zhang L, Yu J : Uncoupling p53 functions in radiation-induced intestinal damage via PUMA and p21. Mol Cancer Res 2011 May, 9(5):616-625.

Li H, Wang P, Sun Q, Ding WX, Yin XM, Sobol RW, Stolz DB, Yu J, Zhang L : Following cytochrome c release, autophagy is inhibited during chemotherapy-induced apoptosis by caspase 8-mediated cleavage of Beclin 1. Cancer Res 2011 May, 71(10):3625-3634.

von Furstenberg RJ, Gulati AS, Baxi A, Doherty JM, Stappenbeck TS, Gracz AD, Magness ST , Henning SJ : Sorting mouse jejunal epithelial cells with CD24 yields a population with characteristics of intestinal stem cells. Am J Physiol Gastrointest Liver Physiol 2011 Mar, 300(3):G409-417.

Crissey MA, Guo RJ, Funakoshi S, Kong J, Liu J, Lynch JP : Cdx2 levels modulate intestinal epithelium maturity and Paneth cell development. Gastroenterology 2011 Feb, 140(2):517-528 e518.

2010 (8)

Levin TG, Powell AE, Davies PS, Silk AD, Dismuke AD, Anderson EC, Swain JR, Wong MH : Characterization of the intestinal cancer stem cell marker CD166 in the human and mouse gastrointestinal tract. Gastroenterology 2010 Dec, 139(6):2072-2082 e2075.

Qiu W, Wang X, Leibowitz B, Liu H, Barker N, Okada H, Oue N, Yasui W, Clevers H, Schoen RE, Yu J, Zhang L: Chemoprevention by nonsteroidal anti-inflammatory drugs eliminates oncogenic intestinal stem cells via SMAC-dependent apoptosis. Proc Natl Acad Sci U S A 2010 Nov, 107(46):20027-20032.

Chia LA, Kuo CJ : The intestinal stem cell. Prog Mol Biol Transl Sci 2010 Oct, 96:157-173.

Rankin EB, Fuh KC, Taylor TE, Krieg AJ, Musser M, Yuan J, Wei K, Kuo CJ, Longacre TA, Giaccia AJ: AXL is an essential factor and therapeutic target for metastatic ovarian cancer. Cancer Res 2010 Oct, 70(19):7570-7579.

Yu H, Shen H, Yuan Y, XuFeng R, Hu X, Garrison SP, Zhang L , Yu J , Zambetti GP, Cheng T : Deletion of Puma protects hematopoietic stem cells and confers long-term survival in response to high-dose gamma-irradiation. Blood 2010 Apr, 115(17):3472-3480.

Leibowitz B, Yu J : Mitochondrial signaling in cell death via the Bcl-2 family. Cancer Biol Ther 2010 Mar, 9(6):417-422.

Qiu W, Leibowitz B, Zhang L, Yu J : Growth factors protect intestinal stem cells from radiation-induced apoptosis by suppressing PUMA through the PI3K/AKT/p53 axis. Oncogene 2010 Mar, 29(11):1622-1632.

Li L, Clevers H: Coexistence of quiescent and active adult stem cells in mammals. Science 2010 Jan, 327(5965):542-545.