Articles of Interest

Articles of Interest to ISCC Investigators (290)

This is a list of publications that could be of interest to Investigators of Intestinal Stem Cell Research or related work. Authors names that are in bold represent past or present ISCC Investigators.
Stewart CJ, Estes MK, Ramani S. Establishing Human Intestinal Enteroid/Organoid Lines from Preterm Infant and Adult Tissue. Methods Mol Biol, 2020 Mar, 2121: 185-98.
Solorzano-Vargas RS, Bjerknes M, Wang J, Wu SV, Garcia-Careaga MG, Pisit D, Cheng H, German MS, Georgia S, Martin MG. Null mutations of NEUROG3 are associated with delayed onset diabetes mellitus. JCI Insight, 2019 Dec.

Zhang X, McGrath PS, Salomone J, Rahal M, McCauley HA, Schweitzer J, Kovall R, Gebelein B, Wells JM. a href="" target=”_blank”>A Comprehensive Structure-Function Study of Neurogenin3 Disease-Causing Alleles during Human Pancreas and Intestinal Organoid Development. Dev Cell, 2019 Aug, 50(3): 367-80 e7. PMCID: 7082840.

Dekaney CM, King S, Sheahan B, Cortes JE. Mist1 Expression Is Required for Paneth Cell Maturation. Cell Mol Gastroenterol Hepatol, 2019 Jul Epub, 8(4): 549-60. PMCID: 6889789.

Zwarycz B, Gracz AD, Rivera KR, Williamson IA, Samsa LA, Starmer J, Daniele MA, Salter-Cid L, Zhao Q, Magness ST. IL22 Inhibits Epithelial Stem Cell Expansion in an Ileal Organoid Model. Cell Mol Gastroenterol Hepatol, 2019 Jul, 7(1): 1-17. PMCID: 6199238.

Marchelletta R, Yu J, Moon C, Kim MM. Evaluation of Compound Activity in Primary Human Intestinal Organoids Using Gene Expression and Histology. Curr Protoc Pharmacol, 2019 Jun, 85(1): e54.

Ayyaz A, Kumar S, Sangiorgi B, Ghoshal B, Gosio J, Ouladan S, Fink M, Barutcu S, Trcka D, Shen J, Chan K, Wrana JL, Gregorieff A. Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell. Nature, 2019 May, 569(7754): 121-5.

Gonzalez LM, Stewart AS, Freund J, Kucera CR, Dekaney CM, Magness ST, Blikslager AT. Preservation of reserve intestinal epithelial stem cells following severe ischemic injury. Am J Physiol Gastrointest Liver Physiol, 2019 Apr, 316(4): G482-G94. PMCID: 6483022.

Jones JC, Brindley CD, Elder NH, Myers MG, Jr., Rajala MW, Dekaney CM, McNamee EN, Frey MR, Shroyer NF, Dempsey PJ. Cellular Plasticity of Defa4(Cre)-Expressing Paneth Cells in Response to Notch Activation and Intestinal Injury. Cell Mol Gastroenterol Hepatol, 2019 Apr, 7(3): 533-54. PMCID: 6402430.

Co JY, Margalef-Catala M, Li X, Mah AT, Kuo CJ, Monack DM, Amieva MR. Controlling Epithelial Polarity: A Human Enteroid Model for Host-Pathogen Interactions. Cell Rep, 2019 Feb, 26(9): 2509-20 e4. PMCID: 6391775.

Dubrovsky G, Huynh N, Thomas AL, Shekherdimian S, Dunn JC. Double plication for spring-mediated in-continuity intestinal lengthening in a porcine model. Surgery, 2019 Feb, 165(2): 389-92.

Jadhav U, Shivdasani RA. Dissecting Cell Lineages: From Microscope to Kaleidoscope. Cell, 2019 Feb, 176(5): 949-51.

Miller AJ, Dye BR, Ferrer-Torres D, Hill DR, Overeem AW, Shea LD, Spence JR. Generation of lung organoids from human pluripotent stem cells in vitro. Nat Protoc, 2019 Feb, 14(2): 518-40.

Dubrovsky G, Huynh N, Thomas AL, Shekherdimian S, Dunn JC. Intestinal lengthening via multiple in-continuity springs. J Pediatr Surg, 2019 Jan, 54(1): 39-43.

Gehart H, Clevers H. Tales from the crypt: new insights into intestinal stem cells. Nat Rev Gastroenterol Hepatol, 2019 Jan, 16(1): 19-34.

Zhao M, Tao F, Venkatraman A, Li Z, Smith SE, Unruh J, Chen S, Ward C, Qian P, Perry JM, Marshall H, Wang J, He XC, Li L. N-Cadherin-Expressing Bone and Marrow Stromal Progenitor Cells Maintain Reserve Hematopoietic Stem Cells. Cell Rep, 2019 Jan Epub, 26(3): 652-69 e6.
Gracz AD, Samsa LA, Fordham MJ, Trotier DC, Zwarycz B, Lo YH, Bao K, Starmer J, Raab JR, Shroyer NF, Reinhardt RL, Magness ST. Sox4 Promotes Atoh1-Independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates. Gastroenterology, 2018 Nov, 155(5): 1508-23 e10. PMCID: 6232678.

Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L. Author Correction: Suppression of m(6)A reader Ythdf2 promotes hematopoietic stem cell expansion. Cell Res, 2018 Oct, 28(10): 1042. PMCID: 6170484.

Sinagoga KL, McCauley HA, Munera JO, Reynolds NA, Enriquez JR, Watson C, Yang HC, Helmrath MA, Wells JM. Deriving functional human enteroendocrine cells from pluripotent stem cells. Development, 2018 Oct, 145(19). PMCID: 6198470.

Trisno SL, Philo KED, McCracken KW, Cata EM, Ruiz-Torres S, Rankin SA, Han L, Nasr T, Chaturvedi P, Rothenberg ME, Mandegar MA, Wells SI, Zorn AM, Wells JM. Esophageal Organoids from Human Pluripotent Stem Cells Delineate Sox2 Functions during Esophageal Specification. Cell Stem Cell, 2018 Oct.

Chao X, Wang S, Zhao K, Li Y, Williams JA, Li T, Chavan H, Krishnamurthy P, He XC, Li L, Ballabio A, Ni HM, Ding WX. Impaired TFEB-Mediated Lysosome Biogenesis and Autophagy Promote Chronic Ethanol-Induced Liver Injury and Steatosis in Mice. Gastroenterology, 2018 Sep, 155(3): 865-79 e12. PMCID: 6120772.

Li Z, Qian P, Shao W, Shi H, He XC, Gogol M, Yu Z, Wang Y, Qi M, Zhu Y, Perry JM, Zhang K, Tao F, Zhou K, Hu D, Han Y, Zhao C, Alexander R, Xu H, Chen S, Peak A, Hall K, Peterson M, Perera A, Haug JS, Parmely T, Li H, Shen B, Zeitlinger J, He C, Li L. Suppression of m(6)A reader Ythdf2 promotes hematopoietic stem cell expansion. Cell Res, 2018 Sep, 28(9): 904-17. PMCID: 6123498.

Chatterji P, Hamilton KE, Liang S, Andres SF, Wijeratne HRS, Mizuno R, Simon LA, Hicks PD, Foley SW, Pitarresi JR, Klein-Szanto AJ, Mah AT, Van Landeghem L, Gregory BD, Lengner CJ, Madison BB, Shah P, Rustgi AK. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. Genes Dev, 2018 Aug, 32(15-16): 1020-34. PMCID: 6075153.

Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, Chen YC, Troyanskaya O, Spence JR, Kretzler M, Cebrian C. Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. Development, 2018 Aug Epub, 145(16). PMCID: 6124540.

Shivdasani RA. Limited gut cell repertoire for multiple hormones. Nat Cell Biol, 2018 Aug, 20(8): 865-7.

Castillo-Azofeifa D, Seidel K, Gross L, Golden EJ, Jacquez B, Klein OD, Barlow LA. SOX2 regulation by hedgehog signaling controls adult lingual epithelium homeostasis. Development, 2018 Jul, 145(14). PMCID: 6078335.

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, 2018 Jul: 1-18.

Huynh N, Dubrovsky G, Rouch JD, Scott A, Chiang E, Nguyen T, Wu BM, Shekherdimian S, Krummel TM, Dunn JCY. Three-dimensionally printed surface features to anchor endoluminal spring for distraction enterogenesis. PLoS One, 2018 Jul Epub, 13(7): e0200529. PMCID: 6042758 in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

Marchix J, Goddard G, Helmrath MA. Host-Gut Microbiota Crosstalk in Intestinal Adaptation. Cell Mol Gastroenterol Hepatol, 2018 Jul, 6(2): 149-62. PMCID: 6047313.

Giroux V, Stephan J, Chatterji P, Rhoades B, Wileyto EP, Klein-Szanto AJ, Lengner CJ, Hamilton KE, Rustgi AK. Mouse Intestinal Krt15+ Crypt Cells Are Radio-Resistant and Tumor Initiating. Stem Cell Reports, 2018 Jun, 10(6): 1947-58. PMCID: 5993649.

Zwarycz B, Gracz AD, Magness ST. Organoid Cultures for Assessing Intestinal Epithelial Differentiation and Function in Response to Type-2 Inflammation. Methods Mol Biol, 2018 Jun Epub, 1799: 397-417.

Shoshkes-Carmel M, Wang YJ, Wangensteen KJ, Toth B, Kondo A, Massassa EE, Itzkovitz S, Kaestner KH: Subepithelial telocytes are an important source of Wnts that supports intestinal crypts Nature 2018 May.

Sheahan B, Dekaney CM. Decrypting the Crypt: Novel Monoclonal Antibodies to Identify Intestinal Stem Cell Populations. Cell Mol Gastroenterol Hepatol, 2018 May, 6(1): 121-2. PMCID: 6007819.

Greicius G, Kabiri Z, Sigmundsson K, Liang C, Bunte R, Singh MK, Virshup DM: PDGFRalpha(+) pericryptal stromal cells are the critical source of Wnts and RSPO3 for murine intestinal stem cells in vivo. Proc Natl Acad SciU S A 2018 Apr, 115(14):E3173-E3181.

van der Hee B, Loonen LMP, Taverne N, Taverne-Thiele JJ, Smidt H, Wells JM. Optimized procedures for generating an enhanced, near physiological 2D culture system from porcine intestinal organoids. Stem Cell Res, 2018 Apr, 28: 165-71.

Leibowitz BJ, Yang L, Wei L, Buchanan ME, Rachid M, Parise RA, Beumer JH, Eiseman JL, Schoen RE, Zhang L, Yu J. Targeting p53-dependent stem cell loss for intestinal chemoprotection. Sci Transl Med, 2018 Feb, 10(427). PMCID: 5827930.

Rajan A, Vela L, Zeng XL, Yu X, Shroyer N, Blutt SE, Poole NM, Carlin LG, Nataro JP, Estes MK, Okhuysen PC, Maresso AW. Novel Segment- and Host-Specific Patterns of Enteroaggregative Escherichia coli Adherence to Human Intestinal Enteroids. MBio, 2018 Feb, 9(1). PMCID: 5821088.

Wei L, Leibowitz BJ, Epperly M, Bi C, Li A, Steinman J, Wipf P, Li S, Zhang L, Greenberger J, Yu J. The GS-nitroxide JP4-039 improves intestinal barrier and stem cell recovery in irradiated mice. Sci Rep, 2018 Feb Epub, 8(1): 2072. PMCID: 5794877.

Miller AJ, Hill DR, Nagy MS, Aoki Y, Dye BR, Chin AM, Huang S, Zhu F, White ES, Lama V, Spence JR: In Vitro Induction and In Vivo Engraftment of Lung Bud Tip Progenitor Cells Derived from Human Pluripotent Stem Cells. Stem Cell Reports 2018 Jan, 10(1):101-119.
Hill DR, Huang S, Tsai YH, Spence JR, Young VB: Real-time Measurement of Epithelial Barrier Permeability in Human Intestinal Organoids. J Vis Exp 2017 Dec(130).

Sarwer DB, Dilks RJ, Spitzer JC, Berkowitz RI, Wadden TA, Moore RH, Chittams JL, Brandt ML, Chen MK, Courcoulas AP, Harmon CM, Helmrath MA, Michalsky MP, Xanthakos SA, Zeller MH, Jenkins TM, Inge TH: Changes in Dietary Intake and Eating Behavior in Adolescents After Bariatric Surgery: an Ancillary Study to the Teen-LABS Consortium. Obes Surg 2017 Dec, 27(12):3082-3091.

Smith AR, Kuo CJ. Organoids lead the cancer attack. Nat Med, 2017 Dec, 23(12): 1399-400.

Chen Y, Zhou W, Roh T, Estes MK, Kaplan DL. In vitro enteroid-derived three-dimensional tissue model of human small intestinal epithelium with innate immune responses. PLoS One, 2017 Nov, 12(11): e0187880. PMCID: 5706668

Xue X, Bredell BX, Anderson ER, Martin A, Mays C, Nagao-Kitamoto H, Huang S, Gyorffy B, Greenson JK, Hardiman K, Spence JR, Kamada N, Shah YM: Quantitative proteomics identifies STEAP4 as a critical regulator of mitochondrial dysfunction linking inflammation and colon cancer. Proc Natl Acad Sci U S A 2017 Nov, 114(45):E9608-E9617.

Joosten SPJ, Zeilstra J, van Andel H, Mijnals RC, Zaunbrecher J, Duivenvoorden AAM, van de Wetering M, Clevers H, Spaargaren M, Pals ST. MET Signaling Mediates Intestinal Crypt-Villus Development, Regeneration, and Adenoma Formation and Is Promoted by Stem Cell CD44 Isoforms. Gastroenterology, 2017 Oct, 153(4): 1040-53 e4.

Laucirica DR, Triantis V, Schoemaker R, Estes MK, Ramani S: Milk Oligosaccharides Inhibit Human Rotavirus Infectivity in MA104 Cells. J Nutr 2017 Sep, 147(9):1709-1714.

Schlieve CR, Fowler KL, Thornton M, Huang S, Hajjali I, Hou X, Grubbs B, Spence JR, Grikscheit TC: Neural Crest Cell Implantation Restores Enteric Nervous System Function and Alters the Gastrointestinal Transcriptome in Human Tissue-Engineered Small Intestine. Stem Cell Reports 2017 Sep, 9(3):883-896.

Tadesse S, Corner G, Dhima E, Houston M, Guha C, Augenlicht L, Velcich A: MUC2 mucin deficiency alters inflammatory and metabolic pathways in the mouse intestinal mucosa. Oncotarget 2017 Sep, 8(42):71456-71470.

Laczko D, Wang F, Johnson FB, Jhala N, Rosztoczy A, Ginsberg GG, Falk GW, Rustgi AK, Lynch JP: Modeling Esophagitis Using Human Three-Dimensional Organotypic Culture System. Am J Pathol 2017 Aug, 187(8):1787-1799.

Xu L, Cheng D, Huang Z, Ding S, Zhang W, Tan H, Shi H, Chen R, Zou Y, Wang TC, Yang X, Ge J: Histamine promotes the differentiation of macrophages from CD11b+ myeloid cells and formation of foam cells through a Stat6-dependent pathway. Atherosclerosis 2017 Aug, 263:42-52.

Hu JK, Du W, Shelton SJ, Oldham MC, DiPersio CM, Klein OD : An FAK-YAP-mTOR Signaling Axis Regulates Stem Cell-Based Tissue Renewal in Mice. Cell Stem Cell 2017 Jul, 21(1):91-106 e106.

Lo YH, Noah TK, Chen MS, Zou W, Borras E, Vilar E, Shroyer NF. SPDEF Induces Quiescence of Colorectal Cancer Cells by Changing the Transcriptional Targets of beta-catenin. Gastroenterology, 2017 Jul, 153(1): 205-18 e8.

Gifford GB, Demitrack ES, Keeley TM, Tam A, La Cunza N, Dedhia PH, Spence JR, Simeone DM, Saotome I, Louvi A, Siebel CW, Samuelson LC: Notch1 and Notch2 receptors regulate mouse and human gastric antral epithelial cell homoeostasis. Gut 2017 Jun, 66(6):1001-1011.

Greer SU, Nadauld LD, Lau BT, Chen J, Wood-Bouwens C, Ford JM, Kuo CJ, Ji HP: Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases. Genome Med 2017 Jun, 9(1):57.

Jin G, Sakitani K, Wang H, Jin Y, Dubeykovskiy A, Worthley DL, Tailor Y, Wang TC: The G-protein coupled receptor 56, expressed in colonic stem and cancer cells, binds progastrin to promote proliferation and carcinogenesis. Oncotarget 2017 Jun, 8(25):40606-40619.

Lal DR, Gadepalli SK, Downard CD, Ostlie DJ, Minneci PC, Swedler RM, Chelius TH, Cassidy L, Rapp CT, Billmire D, Bruch S, Burns RC, Deans KJ, Fallat ME, Fraser JD, Grabowski J, Hebel F, Helmrath MA, Hirschl RB, Kabre R, Kohler J, Landman MP, Leys CM, Mak GZ, Raque J, Rymeski B, Saito JM, St Peter SD, von Allmen D, Warner BW, Sato TT, Midwest Pediatric Surgery C: Challenging surgical dogma in the management of proximal esophageal atresia with distal tracheoesophageal fistula: Outcomes from the Midwest Pediatric Surgery Consortium. J Pediatr Surg 2017 Jun.

Marcinkowski EF, Ottesen R, Niland J, Vito C. Acceptance of adjuvant chemotherapy recommendations in early-stage hormone-positive breast cancer. J Surg Res, 2017 Jun, 214: 79-85.

Prochazkova M, Hakkinen TJ, Prochazka J, Spoutil F, Jheon AH, Ahn Y, Krumlauf R, Jernvall J, Klein OD. FGF signaling refines Wnt gradients to regulate the patterning of taste papillae. Development, 2017 Jun, 144(12): 2212-21. PMCID: 5482992.

Shanker S, Hu L, Ramani S, Atmar RL, Estes MK, Venkataram Prasad BV: Structural features of glycan recognition among viral pathogens. Curr Opin Struct Biol 2017 Jun, 44:211-218.

Wang Y, Gunasekara DB, Reed MI, DiSalvo M, Bultman SJ, Sims CE, Magness ST, Allbritton NL. A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. Biomaterials, 2017 Jun, 128: 44-55. PMCID: 5392043.
Xu B, Li H, Perry JM, Singh VP, Unruh J, Yu Z, Zakari M, McDowell W, Li L, Gerton JL: Ribosomal DNA copy number loss and sequence variation in cancer. J PLoS Genet 2017 Jun, 13(6):e1006771.

Zheng X, Goodwin AF, Tian H, Jheon AH, Klein OD: Ras Signaling Regulates Stem Cells and Amelogenesis in the Mouse Incisor. J Dent Res 2017 Jun:22034517717255.

Almohazey D, Lo YH, Vossler CV, Simmons AJ, Hsieh JJ, Bucar EB, Schumacher MA, Hamilton KE, Lau KS, Shroyer NF, Frey MR. The ErbB3 receptor tyrosine kinase negatively regulates Paneth cells by PI3K-dependent suppression of Atoh1. Cell Death Differ, 2017 May, 24(5): 855-65. PMCID: 5423110.

Miller AJ, Spence JR: In Vitro Models to Study Human Lung Development, Disease and Homeostasis. Physiology (Bethesda) 2017 May, 32(3):246-260.

Oxburgh L, Carroll TJ, Cleaver O, Gossett DR, Hoshizaki DK, Hubbell JA, Humphreys BD, Jain S, Jensen J, Kaplan DL, Kesselman C, Ketchum CJ, Little MH, McMahon AP, Shankland SJ, Spence JR, Valerius MT, Wertheim JA, Wessely O, Zheng Y, Drummond IA: (Re)Building a Kidney. J Am Soc Nephrol 2017 May, 28(5):1370-1378.

Seidel K, Marangoni P, Tang C, Houshmand B, Du W, Maas RL, Murray S, Oldham MC, Klein OD. Resolving stem and progenitor cells in the adult mouse incisor through gene co-expression analysis. Elife, 2017 May Epub, 6. PMCID: 5419740.

Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I: Challenges and emerging directions in single-cell analysis. Genome Biol 2017 May, 18(1):84.

Shao Y, Taniguchi K, Gurdziel K, Townshend RF, Xue X, Yong KMA, Sang J, Spence JR, Gumucio DL, Fu J: Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche. Nat Mater 2017 Apr, 16(4):419-425.

Arora N, Imran Alsous J, Guggenheim JW, Mak M, Munera J, Wells JM, Kamm RD, Asada HH, Shvartsman SY, Griffith LG: A process engineering approach to increase organoid yield. Development 2017 Mar, 144(6):1128-1136.

Carr JS, King S, Dekaney CM. Depletion of enteric bacteria diminishes leukocyte infiltration following doxorubicin-induced small intestinal damage in mice. PLoS One, 2017 Mar, 12(3): e0173429. PMCID: 5336284.

Fendler W, Malachowska B, Meghani K, Konstantinopoulos PA, Guha C, Singh VK, Chowdhury D: Evolutionarily conserved serum microRNAs predict radiation-induced fatality in nonhuman primates. Sci Transl Med 2017 Mar, 9(379).

Nalapareddy K, Nattamai KJ, Kumar RS, Karns R, Wikenheiser-Brokamp KA, Sampson LL, Mahe MM, Sundaram N, Yacyshyn MB, Yacyshyn B, Helmrath MA, Zheng Y, Geiger H: Canonical Wnt Signaling Ameliorates Aging of Intestinal Stem Cells. Cell Rep 2017 Mar, 18(11):2608-2621.

Noel G, Baetz NW, Staab JF, Donowitz M, Kovbasnjuk O, Pasetti MF, Zachos NC: A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions. Sci Rep 2017 Mar, 7:45270.

Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes MK, Himmelfarb J, Truskey G, Wikswo JP, Taylor DL: Corrigendum: Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci Rep 2017 Mar, 7:44517.

von Burstin J, Bachhuber F, Paul M, Schmid RM, Rustgi AK: The TALE homeodomain transcription factor MEIS1 activates the pro-metastatic melanoma cell adhesion molecule Mcam to promote migration of pancreatic cancer cells. Mol Carcinog 2017 Mar, 56(3):936-944.

Yang TB, Chen Q, Deng JT, Jagannathan G, Tobias JW, Schultz DC, Wang S, Lengner CJ, Rustgi AK, Lynch JP, Johnson FB. Mutual reinforcement between telomere capping and canonical Wnt signalling in the intestinal stem cell niche. Nat Commun, 2017 Mar Epub, 8: 14766. PMCID: 5357864.

Zhang LQ, Van Haandel L, Xiong M, Huang P, Heruth DP, Bi C, Gaedigk R, Jiang X, Li DY, Wyckoff G, Grigoryev DN, Gao L, Li L, Wu M, Leeder JS, Ye SQ. Metabolic and molecular insights into an essential role of nicotinamide phosphoribosyltransferase. Cell Death Dis, 2017 Mar, 8(3): e2705. PMCID: 5386535.

Zou WY, Blutt SE, Crawford SE, Ettayebi K, Zeng XL, Saxena K, Ramani S, Karandikar UC, Zachos NC, Estes MK: Human Intestinal Enteroids: New Models to Study Gastrointestinal Virus Infections. Methods Mol Biol 2017 Mar.

Peck BC, Mah AT, Pitman WA, Ding S, Lund PK, Sethupathy P: Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status. J Biol Chem 2017 Feb, 292(7):2586-2600.

Brodin NP, Velcich A, Guha C, Tome WA: A Model for Precise and Uniform Pelvic- and Limb-Sparing Abdominal Irradiation to Study the Radiation-Induced Gastrointestinal Syndrome in Mice Using Small Animal Irradiation Systems. Dose Response 2017 Jan, 15(1):1559325816685798.

McCracken KW, Aihara E, Martin B, Crawford CM, Broda T, Treguier J, Zhang X, Shannon JM, Montrose MH, Wells JM: Wnt/beta-catenin promotes gastric fundus specification in mice and humans. Nature 2017 Jan, 541(7636):182-187.

Sakamoto N, Feng Y, Stolfi C, Kurosu Y, Green M, Lin J, Green ME, Sentani K, Yasui W, McMahon M, Hardiman KM, Spence JR, Horita N, Greenson JK, Kuick R, Cho KR, Fearon ER: BRAF(V600E) cooperates with CDX2 inactivation to promote serrated colorectal tumorigenesis. Elife 2017 Jan, 6.

Saxena K, Simon LM, Zeng XL, Blutt SE, Crawford SE, Sastri NP, Karandikar UC, Ajami NJ, Zachos NC, Kovbasnjuk O, Donowitz M, Conner ME, Shaw CA, Estes MK: A paradox of transcriptional and functional innate interferon responses of human intestinal enteroids to enteric virus infection. Proc Natl Acad Sci U S A 2017 Jan, 114(4):E570-E579.

Schellnegger R, Quante A, Rospleszcz S, Schernhammer M, Hohl B, Tobiasch M, Pastula A, Brandtner A, Abrams JA, Strauch K, Schmid RM, Vieth M, Wang TC, Quante M. Goblet Cell Ratio in Combination with Differentiation and Stem Cell Markers in Barrett Esophagus Allow Distinction of Patients with and without Esophageal Adenocarcinoma. Cancer Prev Res (Phila), 2017 Jan, 10(1): 55-66. PMCID: 5219855.

Stzepourginski I, Nigro G, Jacob JM, Dulauroy S, Sansonetti PJ, Eberl G, Peduto L: CD34+ mesenchymal cells are a major component of the intestinal stem cells niche at homeostasis and after injury. Proc Natl Acad Sci USA 2017 Jan, 114(4):E506-E513.

Saxena M, Roman AKS, O'Neill NK, Sulahian R, Jadhav U, Shivdasani RA. Transcription factor-dependent 'anti-repressive' mammalian enhancers exclude H3K27me3 from extended genomic domains. Genes Dev, 2017 Dec 1, 31(23-24): 2391-404. PMCID: 5795785.
Hayakawa Y, Chang W, Jin G, Wang TC: Gastrin and upper GI cancers. Curr Opin Pharmacol 2016 Dec, 31:31-37.

Jadhav U, Shivdasani RA : Natural Selection, Crypt Fitness, and Pol III Dependency in the Intestine. Cell Mol Gastroenterol Hepatol 2016 Nov, 2(6):714-715.

Kulkarni S, Koller A, Mani KM, Wen R, Alfieri A, Saha S, Wang J, Patel P, Bandeira N, Guha C, Chen EI: Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow. Int J Radiat Oncol Biol Phys 2016 Nov, 96(3):566-577.

Meyer LA, Cronin AM, Sun CC, Bixel K, Bookman MA, Cristea MC, Griggs JJ, Levenback CF, Burger RA, Mantia-Smaldone G, Matulonis UA, Niland JC, O'Malley DM, Wright AA. Use and Effectiveness of Neoadjuvant Chemotherapy for Treatment of Ovarian Cancer. J Clin Oncol, 2016 Nov, 34(32): 3854-63. PMCID: 5477982.

Allen JI, Wang TC, Cohen WS, Shah VH: How to Succeed in Academic Gastroenterology. Gastroenterology 2016 Oct, 151(4):578-581 e576.

Larsen BM, Marty-Santos L, Newman M, Lukacs DT, Spence JR, Wellik DM: Hox6 genes modulate in vitro differentiation of mESCs to insulin-producing cells. In Vitro Cell Dev Biol Anim 2016 Oct, 52(9):974-982.

Dye BR, Dedhia PH, Miller AJ, Nagy MS, White ES, Shea LD, Spence JR: A bioengineered niche promotes in vivo engraftment and maturation of pluripotent stem cell derived human lung organoids. Elife 2016 Sep, 5.

Ettayebi K, Crawford SE, Murakami K, Broughman JR, Karandikar U, Tenge VR, Neill FH, Blutt SE, Zeng XL, Qu L, Kou B, Opekun AR, Burrin D, Graham DY, Ramani S, Atmar RL, Estes MK. Replication of human noroviruses in stem cell-derived human enteroids. Science, 2016 Sep, 353(6306): 1387-93. PMCID: 5305121.

Karandikar UC, Crawford SE, Ajami NJ, Murakami K, Kou B, Ettayebi K, Papanicolaou GA, Jongwutiwes U, Perales MA, Shia J, Mercer D, Finegold MJ, Vinje J, Atmar RL, Estes MK. Detection of human norovirus in intestinal biopsies from immunocompromised transplant patients. J Gen Virol, 2016 Sep, 97(9): 2291-300. PMCID: 5756488.

Koledova Z, Zhang X, Streuli C, Clarke RB, Klein OD, Werb Z, Lu P: SPRY1 regulates mammary epithelial morphogenesis by modulating EGFR-dependent stromal paracrine signaling and ECM remodeling. Proc Natl Acad Sci U S A 2016 Sep, 113(39):E5731-5740.

Qian P, Li L. Single-cell RNA-seq technology lends a hand into HSC ontogeny. Sci China Life Sci, 2016 Sep, 59(9): 977-8.

Rigby RJ, Carr J, Orgel K, King SL, Lund PK, Dekaney CM. Intestinal bacteria are necessary for doxorubicin-induced intestinal damage but not for doxorubicin-induced apoptosis. Gut Microbes, 2016 Sep, 7(5): 414-23. PMCID: 5046166.

Sharir A, Klein OD : Watching a deep dive: Live imaging provides lessons about tooth invagination. J Cell Biol 2016 Sep, 214(6):645-647.

Lloyd RE, Estes MK : Editorial overview: Viruses and cell metabolism. Curr Opin Virol 2016 Aug, 19: vii-viii.

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Pierzchalska M, Grabacka M, Michalik M, Zyla K, Pierzchalski P. Prostaglandin E2 supports growth of chicken embryo intestinal organoids in Matrigel matrix. Biotechniques. May 2012;52(5):307-315. [PubMed Abstract]

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Stringer EJ, Duluc I, Saandi T, Davidson I, Bialecka M, Sato T, Barker N, Clevers H, Pritchard CA, Winton DJ, Wright NA, Freund JN, Deschamps J, Beck F. Cdx2 determines the fate of postnatal intestinal endoderm. Development 2012;139(3):465-74. [PubMed Abstract]

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VanDussen KL, Carulli AJ, Keeley TM, Patel SR, Puthoff BJ, Magness ST, Tran IT, Maillard I, Siebel C, Kolterud A, Grosse AS, Gumucio DL, Ernst SA, Tsai YH, Dempsey PJ, Samuelson LC. Notch signaling modulates proliferation and differentiation of intestinal crypt base columnar stem cells. Development 2012;139(3):488-97. [PubMed Abstract]

Van Landeghem L, Santoro MA, Krebs AE, Mah AT, Dehmer JJ, Gracz AD, Scull BP, McNaughton K, Magness ST, Lund PK. Activation of two distinct Sox9-EGFP expressing intestinal stem cell populations during crypt regeneration after irradiation. Am J Physiol Gastrointest Liver Physiol 2012. [PubMed Abstract]

Wong VW, Stange DE, Page ME, Buczacki S, Wabik A, Itami S, van de Wetering M, Poulsom R, Wright NA, Trotter MW, Watt FM, Winton DJ, Clevers H, Jensen KB. Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling. Nat Cell Biol 2012;14(4):401-8. [PubMed Abstract]

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Yui S, Nakamura T, Sato T, Nemoto Y, Mizutani T, Zheng X, Ichinose S, Nagaishi T, Okamoto R, Tsuchiya K, Clevers H, Watanabe M. Functional engraftment of colon epithelium expanded in vitro from a single adult Lgr5(+) stem cell. Nat Med 2012;18(4):618-23. [PubMed Abstract]

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Hamilton KE, Simmons JG, Ding S, Van Landeghem L, Lund PK. Cytokine-Induction of Tumor Necrosis Factor Receptor 2 (TNFR2) is Mediated by STAT3 in Colon Cancer Cells. Mol Cancer Res 2011. [PubMed Abstract]

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Kunii J, Takahashi K, Kasakura K, Tsuda M, Nakano K, Hosono A, Kaminogawa S. Commensal bacteria promote migration of mast cells into the intestine. Immunobiology 2011;216(6):692-7. [PubMed Abstract]

Merlos-Suarez A, Barriga FM, Jung P, Iglesias M, Cespedes MV, Rossell D, Sevillano M, Hernando-Momblona X, da Silva-Diz V, Munoz P, Clevers H, Sancho E, Mangues R, Batlle E. The Intestinal Stem Cell SignatureIdentifies Colorectal Cancer Stem Cells and Predicts Disease Relapse. Cell Stem Cell 2011. [PubMed Abstract]

Mongroo, P. S.; Noubissi, F. K.; Cuatrecasas, M.; Kalabis, J.; King, C. E.; Johnstone, C. N.; Bowser, M. J.; Castells, A.; Spiegelman, V. S.; Rustgi, A. K. IMP-1 displays cross-talk with K-Ras and modulates colon cancer cell survival through the novel proapoptotic protein CYFIP2. Cancer Res 71(6):2172-2182; 2011 [PubMed Abstract]

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Perry JM, He XC, Sugimura R, Grindley JC, Haug JS, Ding S, Li L. Cooperation between both Wnt/{beta}-catenin and PTEN/PI3K/Akt signaling promotes primitive hematopoietic stem cell self-renewal and expansion. Genes Dev 2011;25(18):1928-42. [PubMed Abstract]

Mustata RC, Van Loy T, Lefort A, Libert F, Strollo S, Vassart G, Garcia MI. Lgr4 is required for Paneth cell differentiation and maintenance of intestinal stem cells ex vivo. EMBO Rep 2011;12(6):558-64. [PubMed Abstract]

Powell AE, Anderson EC, Davies PS, Silk AD, Pelz C, Impey S, Wong MH. Fusion between Intestinal epithelial cells and macrophages in a cancer context results in nuclear reprogramming. Cancer Res 2011;71(4):1497-505. [PubMed Abstract]

Powell DW, Pinchuk IV, Saada JI, Chen X, Mifflin RC. Mesenchymal cells of the intestinal lamina propria. Annu Rev Physiol 2011;73:213-37. [PubMed Abstract]

Qin HH, Dunn JC. Small Intestinal Submucosa Seeded with Intestinal Smooth Muscle Cells in a Rodent Jejunal Interposition Model. J Surg Res 2011. [PubMed Abstract]

Ramalingam S, Daughtridge GW, Johnston MJ, Gracz AD, Magness ST. Distinct Levels of Sox9 Expression Mark Colon Epithelial Stem Cells that Form Colonoids in Culture. Am J Physiol Gastrointest Liver Physiol 2011. [PubMed Abstract]

Reizel Y, Chapal-Ilani N, Adar R, Itzkovitz S, Elbaz J, Maruvka YE, Segev E, Shlush LI, Dekel N, Shapiro E. Colon stem cell and crypt dynamics exposed by cell lineage reconstruction. J PLoS Genet 2011;7(7):e1002192. [PubMed Abstract]

Sainathan SK, Bishnupuri KS, Aden K, Luo Q, Houchen CW, Anant S, Dieckgraefe BK. Toll-like receptor-7 ligand imiquimod induces type I interferon and antimicrobial peptides to ameliorate dextran sodium sulfate-induced acute colitis. Inflamm Bowel Dis 2011. [PubMed Abstract]

Sakthianandeswaren A, Christie M, D'Andreti C, Tsui C, Jorissen RN, Li S, Fleming NI, Gibbs P, Lipton L, Malaterre J, Ramsay RG, Phesse TJ, Ernst M, Jeffery RE, Poulsom R, Leedham SJ, Segditsas S, Tomlinson IP, Bernhard OK, Simpson RJ, Walker F, Faux MC, Church N, Catimel B, Flanagan DJ, Vincan E, Sieber OM. PHLDA1 expression marks the putative epithelial stem cells and contributes to intestinal tumorigenesis. Cancer Res 2011;71(10):3709-19. [PubMed Abstract]

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Spence JR, Mayhew CN, Rankin SA, Kuhar MF, Vallance JE, Tolle K, Hoskins EE, Kalinichenko VV, Wells SI, Zorn AM, Shroyer NF, Wells JM. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 2011;470(7332):105-9. [PubMed Abstract]

Speck KE, Garrison AP, Rigby RJ, von Allmen DC, Lund PK, Helmrath MA. Inflammation enhances resection-induced intestinal adaptive growth in IL-10 null mice. J Surg Res 2011;168(1):62-9. [PubMed Abstract]

Stark R, Zupekan T, Bondada S, Dunn JC. Restoration of mechanically lengthened jejunum into intestinal continuity in rats. J Pediatr Surg 2011;46(12):2321-6. [PubMed Abstract]

Sureban SM, May R, Lightfoot S, Hoskins AB, Lerner MR, Brackett DJ, Postier RG, Ramanujam R, Mohammed A, Rao CV, Wyche JH, Anant S, Houchen CW. DCAMKL-1 regulates epithelial-mesenchymal transition in human pancreatic cells through a miR-200a-dependent mechanism. Cancer Res 2011. [PubMed Abstract]

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Dudgeon C, Wang P, Sun X, Peng R, Sun Q, Yu J, Zhang L. PUMA induction by FoxO3a mediates the anticancer activities of the broad-range kinase inhibitor UCN-01. Mol Cancer Ther 2010;9(11):2893-902. [PubMed Abstract]

Gracz AD, Ramalingam S, Magness ST. Sox9 expression marks a subset of CD24-expressing small intestine epithelial stem cells that form organoids in vitro. Am J Physiol Gastrointest Liver Physiol. May 2010;298(5):G590-600. [PubMed Abstract]

Lan SY, Yu T, Xia ZS, Yuan YH, Shi L, Lin Y, Huang KH, Chen QK. Musashi 1-positive cells derived from mouse embryonic stem cells can differentiate into neural and intestinal epithelial-like cells in vivo. Cell Biol Int 2010;34(12):1171-80. [PubMed Abstract]

Leen JL, Izzo A, Upadhyay C, Rowland KJ, Dube PE, Gu S, Heximer SP, Rhodes CJ, Storm DR, Lund PK, Brubaker PL. Mechanism of Action of Glucagon-Like Peptide-2 to Increase IGF-I mRNA in Intestinal Subepithelial Fibroblasts. Endocrinology 2010. [PubMed Abstract]

Montgomery RK, Carlone DL, Richmond CA, Farilla L, Kranendonk ME, Henderson DE, Baffour-Awuah NY, Ambruzs DM, Fogli LK, Algra S, Breault DT. Mouse telomerase reverse transcriptase (mTert) expression marks slowly cycling intestinal stem cells. Proc Natl Acad Sci U S A 2010. [PubMed Abstract]

Pinchuk IV, Mifflin RC, Saada JI, Powell DW. Intestinal mesenchymal cells. Curr Gastroenterol Rep 2010;12(5):310-8. [PubMed Abstract]

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Runck LA, Kramer M, Ciraolo G, Lewis AG, Guasch G. Identification of epithelial label-retaining cells at the transition between the anal canal and the rectum in mice. Cell Cycle 2010;9(15):3039-45. [PubMed Abstract]

Schrader S, Notara M, Tuft SJ, Beaconsfield M, Geerling G, Daniels JT. Simulation of an in vitro niche environment that preserves conjunctival progenitor cells. Regen Med 2010;5(6):877-89. [PubMed Abstract]

Stairs DB, Kong J, Lynch JP. Cdx genes, inflammation, and the pathogenesis of intestinal metaplasia. Prog Mol Biol Transl Sci 2010;96:231-70. [PubMed Abstract]

Sugimura R, Li L. Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases. Birth Defects Res C Embryo Today 2010;90(4):243-56. [PubMed Abstract]

Sun G, Hasebe T, Fujimoto K, Lu R, Fu L, Matsuda H, Kajita M, Ishizuya-Oka A, Shi YB. Spatio-temporal expression profile of stem cell-associated gene LGR5 in the intestine during thyroid hormone-dependent metamorphosis in Xenopus laevis. PLoS One 2010;5(10):e13605. [PubMed Abstract]

Spence JR, Mayhew CN, Rankin SA, Kuhar MF, Vallance JE, Tolle K, Hoskins EE, Kalinichenko VV, Wells SI, Zorn AM, Shroyer NF, Wells JM. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 2010. [PubMed Abstract]

Sun G, Hasebe T, Fujimoto K, Lu R, Fu L, Matsuda H, Kajita M, Ishizuya-Oka A, Shi YB. Spatio-temporal expression profile of stem cell-associated gene LGR5 in the intestine during thyroid hormone-dependent metamorphosis in Xenopus laevis. PLoS One 2010;5(10):e13605. [PubMed Abstract]

VanDussen KL, Samuelson LC. Mouse atonal homolog 1 directs intestinal progenitors to secretory cell rather than absorptive cell fate. Dev Biol 2010;346(2):215-23. [PubMed Abstract]

Wang, Z.; Matsudaira, P.; Gong, Z. STORM: a general model to determine the number and adaptive changes of epithelial stem cells in teleost, murine and human intestinal tracts. PLoS One 5(11):e14063; 2010. [PubMed Abstract]

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Davies PS, Powell AE, Swain JR, Wong MH. Inflammation and proliferation act together to mediate intestinal cell fusion. PLoS One. 2009 Aug 6;4(8):e6530. [PubMed Abstract]

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Davies PS, Dismuke AD, Powell AE, Carroll KH, Wong MH. Wnt-reporter expression pattern in the mouse intestine during homeostasis. BMC Gastroenterol. 2008 Dec 2;8:57. [PubMed Abstract]

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Rizvi AZ, Swain JR, Bailey AS, Decker AD, Willenbring H, Grompe M, Fleming WH, Wong MH. Bone marrow-derived cells fuse with normal and transformed intestinal stem cells. PNAS. 2006 April 18;103(6):6321-6325. [PubMed Abstract]

Yaylaoglu MB, Agbemafle BM, Oesterreicher TJ, Finegold MJ, Thaller C, Henning SJ. Diverse patterns of cell-specific gene expression in response to glucocorticoid in the developing small intestine. AM J Physiol Gastrointest Liver Physiol. 2006 Dec;291(6):G1041-50. [PubMed Abstract]