Surface expression of antitoxin on engineered bacteria neutralises genotoxic colibactin in the gut. S Yang, Z Wang, C Fang, M Yang, S Khawaled, S Bonanno, N Joshi, Y Wei, K Zhang, VM Pellegrin, M Guan, S Zhang, AC Bader, N Ye, AE Haley, MK Dame, JR Spence, X He, JG Fox, O Yilmaz, YM Shah, R Romee, J Li. Nature Microbiology. Jan2026. PMID: 41361522

RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells. RI Cabrera-Silva, ZS Wilson, J Miranda, S Fan, M Dame, S Bishu, JR Spence, JC Brazil, J Colacino, A Nusrat, CA Parkos. bioRxiv [Preprint]. Nov2025. PMID: 41332536

A scalable long-term in vitro model of human colonic epithelium with continuous barrier function. AJ Cuttitta, SR Meyer, T Frum, B Gunuguntla, A Wu, S Huang, J Morgan, MK Dame, JZ Sexton, JR Spence. bioRxiv [Preprint]. Sep2025. PMID: 41040326

Lysophosphatidic acid and sphingosine-1-phosphate are apical polarity cues in multiple organoid systems. AM Tidball, J Luo, JC Walker, CY Yang, K Lee, RC Spencer, C Matthews, G Feng, PP Hsu, Y Lee, J Morgan, CJ Childs, MK Eiken, KD Walton, JR Spence. Cell Reports. Jun2025. PMID: 40503936

Fibroblast lipid metabolism through ACSL4 regulates epithelial sensitivity to ferroptosis in IBD. W Huang , Y Zhang , N Das , S Solanki , C Jain , M El-Derany , I Koo , H Bell , N Aabed , R Singhal , C Castillo , K Buscher , Y Ying , J Dimitroff , A Sharma , J Shi , S Hogan , M Dame , P Higgins , J Colacino , TG Oh , J Spence , A Patterson , A Greenberg , J Greenson , A Nusrat, Y Shah. Nat Metabolism. June 2025. PMID: 40571769

Targeting enteroendocrine cell differentiation in colorectal cancer. CA Ladaika. Doctoral Dissertation, Department of Biology, Indiana University. May 2025

TRAIL-inducing imipridones ONC201, ONC206, and ONC212 demonstrate anti-neoplastic effects in colonic adenoma-derived organoids. AJ Lannigan, J Chan, L Zhou, VV Prabhu, M Dame, D Brenner, J Spence, WS El-Deiry, AG Raufi. Cancer Research. 15Apr2025. Volume 85 Issue 8 Supplement 1.

TRAIL-inducing imipridone ONC201/TIC10 demonstrates anti-neoplastic effects in colonic adenoma-derived organoids. AJ Lannigan, J Chan, M Schwermann, L Zhou, VV Prabhu, M Dame, D Brenner, J Spence, WS El-Deiry, AG Raufi. Cancer Research. 22Mar2025. Volume 84 Issue 6 Supplement 6.

WNT signaling contributes to the extrahepatic bile duct proliferative response to obstruction in mice. AN Calder, MQ Peter, JW Tobias, NH Mohamad Zaki, TM Keeley, TL Frankel, LC Samuelson, and N Razumilava. JCI Insight. 05Dec2024. PMID: 39636699

Bivalent norovirus mRNA vaccine elicits cellular and humoral responses protecting human enteroids from GII.4 infection. EN Atochina-Vasserman, LC Lindesmith, C Mirabelli, NA Ona, EK Reagan, PD Brewer-Jensen, X Mercado-Lopez, H Shahnawaz, JA Meshanni, I Baboo, ML Mallory, MR Zweigart, SR May, BL Mui, YK Tam, CE Wobus, RS Baric, D Weissman. Nature NPJ Vaccines. 01Oct2024. PMID: 39353926

Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth. KL Donahue, HR Watkoske, P Kadiyala, W Du, K Brown, MK Scales, AM Elhossiny, CE Espinoza, EL Lasse-Opsahl, BD Griffith, Y Wen, L Sun, A Velez-Delgado, NM Renollet, J Morales, NM Nedzesky, RK Baliira, RE Menjivar, PI Medina-Cabrera, A Rao, B Allen, J Shi, TL Frankel, ES Carpenter, F Bednar, Y Zhang, MP di Magliano. Cancer Discovery. 2024. PMID: 38958646

Interferon-gamma signaling drives epithelial TNF-alpha receptor-2 expression during colonic tissue repair. Watson S, Cabrera-Silva RI, Parkos CA, Nusrat A, Quiros M. The FASEB Journal. 2024. PMID: 39139033

Bile salt hydrolase catalyses formation of amine-conjugated bile acids. Rimal B, Collins SL, Tanes CE, Rocha ER, Granda MA, Solanki S, Hoque NJ, Gentry EC, Koo I, Reilly ER, Hao F, Paudel D, Singh V, Yan T, Kim MS, Bittinger K, Zackular JP, Krausz KW, Desai D, Amin S, Coleman JP, Shah YM, Bisanz JE, Gonzalez FJ, Vanden Heuvel JP, Wu GD, Zemel BS, Dorrestein PC, Weinert EE, Patterson AD. Nature. 2024. PMID: 38326609.

In Vitro Porcine (Explant) Colon Culture. In: Baratta, M. (eds) Epithelial Cell Culture. de Oliveira Costa M, Dame MK. Methods in Molecular Biology, vol 2749. 2024. PMID: 38133777

Near-Infrared In Vivo Imaging of Claudin-1 Expression by Orthotopically Implanted Patient-Derived Colonic Adenoma Organoids. Jaiswal S, Wang F, Wu X, Chang T-S, Shirazi A, Lee M, Dame MK, Spence JR, Wang TD. Diagnostics. 2024. PMID: 38337789

Single-cell multi-omics reveals insights into differentiation of rare cell types in mucinous colorectal cancer. Ladaika CA, Ghobashi AH, Boulton WC, Miller SA, O’Hagan HM. bioRxiv. 2024. PMID: 38370733

Near-infrared imaging of colonic adenomas in vivo using orthotopic human organoids for early cancer detection. Wu X, Chen C-W, Jaiswal S, Chang T-S, Zhang R, Dame MK, Duan Y, Jiang H, Spence JR, Hsieh S-Y* and Wang TD. Cancers. 2023. PMID: 37835489

Region-specific Wnt signaling responses promote gastric polyp formation in familial adenomatous polyposis patients. McGowan KP, Delgado E, Keeley TM, Hibdon ES , Turgeon DK , Stoffel EM , Samuelson LC. JCI Insight. 2023. PMID: 37943618

KRT17High/CXCL8+ tumor cells display both classical and basal features and regulate myeloid infiltration in the pancreatic cancer microenvironment. Carpenter ES, Kadiyala P, Elhossiny AM, Pasca Di Magliano M, et al. Clin Cancer Res. 2023, PMID: 37851080

Transferrin receptor-mediated iron uptake promotes colon tumorigenesis. Kim H, Villareal LB, Liu Z, Haneef M, Falcon DM, Martin DR, Lee HA, Dame MK, Attili D, Chen Y, Varani J, Spence JR, Kovbasnjuk O, Colacino JA, Lyssiotis CA, Shah YM, Lin HC, Xue X. Advanced Science. 2023. PMID: 36703617

Iron promotes glycolysis to drive colon tumorigenesis. Liu Z, Villareal L, Goodla L, Kim H, Falcon DM, Haneef M, Martin DR, Zhang L, Lee H-J, Kremer D, Lyssiotis CA, Shah YM, Lin HC, Lin H-K, Xue X. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. 2023. PMID: 37579983

A multi-mineral intervention to counter pro-inflammatory activity and to improve the barrier in human colon organoids. Varani J, McClintock SD, Nadeem DM, Harber ZD, Aslam MN. Frontiers in Cell and Developmental Biology. 2023. PMID: 37476158

A Pilot Study: Transcriptional Profiling, Functional Analysis, and Organoid Modeling of Intestinal Mucosa in Hirschsprung’s Disease. Lotakis DM, Dheer R, Dame MK, Cuttitta AJ, Tigani DJ, Spence JR, Young VB, Ralls M. Journal of Pediatric Surgery. 2023 Feb. PMID: 36922279

Maresin-2 promotes mucosal repair and has therapeutic potential when encapsulated in thermostable nanoparticles. Miranda J, Brazil JC, Morris AH, Parkos CA, Quiros M, Nusrat A. Proc Natl Acad Sci U S A. 2023 Jan. PMID: 36669099

Dysregulated amino acid sensing drives colorectal cancer growth and metabolic reprogramming leading to chemoresistance. Solanki S, Sanchez K, Ponnusamy V, Kota V, Bell HN, Cho CS, Kowalsky AH, Green M, Lee JH, Shah YM. Gastroenterology. 2022 Nov. PMID: 36410445.

Intestinal epithelial BLT1 promotes mucosal repair. Hayashi S, Muraleedharan CK, Oku M, Tomar S, Hogan SP, Quiros M, Parkos CA, Nusrat A. JCI Insight. 2022 Oct 27. PMID: 36301666.

Mapping the adult human esophagus in vivo and in vitro. Ferrer-Torres D, Wu JH, Zhang CJ, Hammer MA, Dame MK, Wu A, Holloway EM, Karpoff K, McCarthy CL, Bohm MS, Cuttitta AJ, Tigani DJ, Huang S, Tsai YH, Miller AJ, Walker T, Bayer DE, Hogan SP, Turgeon DK, Lin J, Higgins PDR, Sexton J, Spence JR. Development. 2022 Oct 15. PMID: 36278875.

Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H,  McCarthy C, Hoostal M, Rosevelt A, Muraleedharan CK, Gillilland 3rd MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, and Kamada N. Cell Reports. 2022 PMID: 35858565.

Rapid establishment of human colonic organoid knockout lines. Gu W, Colarusso JL, Dame MK, Spence JR, Zhou Q. Star Protocols. 2022. PMCID: PMC9026586

R-SPONDIN2+ Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development. Hein RFC, Wu JH, Tsai H, Wu A, Miller AJ, Holloway EM, Frum T, Conchola AS, Szenker-Ravi E, Reversade B, Yan KS, Kuo CJ, Spence JR. Dev Cell. 2022. PMID: 35679862

Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells. Schwartz AJ, Goyert JW, Solanki S, Kerk SA, Chen B, Castillo C, Hsu PP, Do BT, Singhal R, Dame MK, Lee H-J, Spence JR, Lakhal-Littleton S, Vander Heiden MG, Lyssiotis CA, Xue X, Shah YM. Nat Metab. 2021. PMID: 34155415

SATB2 preserves colon stem cell identity and mediates ileum-colon conversion via enhancer remodeling. Gu W, Wang H, Huang X, Kraiczy J, Singh PNP, Ng C, Dagdeviren S, Houghton S, Pellon-Cardenas O, Lan Y, Nie Y, Zhang J, Banerjee KK, Onufer EJ, Warner BW, Spence J, Scherl E, Rafii S, Lee RT, Verzi MP, Redmond D, Longman R, Helin K, Shivdasani RA, Zhou Q. Cell Stem Cell. 2021. PMID: 34582804.

Membrane bound Peroxiredoxin-1 serves as a biomarker for in vivo detection of sessile serrated adenomas. Jaiswal S, Joshi B, Chen J, Wang F, Dame MK, Spence JR, Newsome GM, Katz EL, Shah YM, Ramakrishnan SK, Li G, Lee M, Appelman HD, Kuick R, Wang TD. Antioxid Redox Signal. 2021. PMID: 34409853

UBCH5 family members differentially impact stabilization of mutant p53 via RNF128 Iso1 during Barrett’s progression to esophageal adenocarcinoma. Ray P*, Nancarrow DJ*, Ferrer-Torres D*, Wang Z, Martinho MS, Hinton T, Wu J, Wu A, Turgeon DK, Hammer M, Dame M, Lawrence TS, O’Brien PJ, Spence J, Beer DJ+, Ray D+. Cell Mol Gastroenterol Hepatol. 2021. PMID: 34416429

Colorectal cancer cells utilize autophagy to maintain mitochondrial metabolism for cell proliferation under nutrient stress. Samantha N Devenport, Rashi Singhal, Megan D Radyk, Joseph G Taranto, Samuel A Kerk, Brandon Chen, Joshua W Goyert, Chesta Jain, Nupur K Das, Katherine Oravecz-Wilson, Li Zhang, Joel K Greenson, Y Eugene Chen, Scott A Soleimanpour, Pavan Reddy, Costas A Lyssiotis, Yatrik M Shah. JCI insight. 2021. PMID: 34138755

Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model. Hung, Y.-H., Huang S., Dame M. K., Yu Q., Yu Q.C., Zeng Y. A., Camp J. G., Spence J. R. and Sethupathy P. Nucleic Acids Res. 2021. PMID: 33406262

Low-level Mouse DNA in Conditioned Medium Generates False Positive Cross-species Contamination Results in Human Organoid Cultures. Bohm MS, Dame MK, Boyd J, Su K, Wu A, Attili D, Colacino JA, Spence JR. Front. Cell Dev. Biol. 2020. PMID: 33240885

Ulcerative Colitis-Derived Colonoid Culture: A multi-mineral-approach to improve barrier protein expression. Aslam MN, Mcclintock SD, Attili D, Pandya S, Rehman H, Nadeem DM, Jawad-Makki MAH, Rizvi AH, Berner MM, Dame MK, Turgeon DK, Varani J. Front. Cell Dev. Biol. 2020. PMID: 33330453

Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. Palikuqi B, Nguyen D-HT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY and Rafii S. Nature. 2020. PMID: 32908310

Identification and Isolation of Human LGR5+ Cells Using an Antibody-Based Strategy. Dame MK, Huang S, Attili D, Spence JR, Colacino JA. Methods Mol Biol. 2020. PMID: 32705632

Histone H3K9 methylation regulates chronic stress and IL-6-induced colon epithelial permeability and visceral pain. Wiley JW, Zong Y, Zheng G, Zhu S, Hong S. Neurogastroenterol Motil. 2020. PMID: 32743845

Infectious Norovirus Is Chronically Shed by Immunocompromised Pediatric Hosts. Davis A, Cortez V, Grodzki M, Dallas R, Ferrolino J, Freiden P, Maron G, Hakim H, Hayden RT, Tang L, Huys A, Kolawole AO, Wobus C.E, Jones MK, Karst SM, Schultz-Cherry S. Viruses. 2020. PMID: 32516960

Targeting epithelial expressed Sialyl Lewis glycans improves colonic mucosal wound healing and protects against colitis. Kelm M, Quiros M, Azcutia V, Boerner K, Cummings RD, Nusrat A, *Brazil JC, *Parkos CA. JCI Insights. 2020. PMID: 32427587

Erythroid differentiation regulator-1 induced by microbiota in early life drives intestinal stem cell proliferation and regeneration. Abo H, Chassaing B, Harusato A, Quiros M, Brazil JC, Ngo VL, Viennois E, Merlin D, Gewirtz AT, Nusrat A, and Denning TL. Nat Commun. Jan 2020;11(1):513. PMCID: PMC6981263

Differentiation of human colon tissue in culture: Effects of calcium on trans-epithelial electrical resistance and tissue cohesive properties. McClintock SD, Dame MK, Richter A, Attili D, Silvestri SS, Berner MM, Bohm MS, Karpoff K, McCarthy C, Spence JR, Varani J, Aslam MN. PLoS One. Mar 2020 PMID: 32134920

Regulation of neutrophil function by selective targeting of glycan epitopes expressed on the integrin CD11b/CD18. Kelm M, Lehoux S, Azcutia V, Cummings RD, Nusrat A, Parkos CA, Brazil JC. FASEB. 23 December 2019. PMID: 31907993

Enteroendocrine Progenitor Cell-Enriched miR-7 Regulates Intestinal Epithelial Proliferation in an Xiap-Dependent Manner. Singh AP, Hung Y, Shanahan MT, Kanke M, Bonfini A, Dame MK, Biraud M, Peck BC, 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. Cell Mol Gastroenterol Hepatol. 2019. PMID: 31756561 

Epithelial CD47 is critical for mucosal repair in the murine intestine in vivo. Reed M, Luissint AC, Azcutia V, Fan S, O'Leary MN, Quiros M, Brazil J, Nusrat A and CA Parkos. Nat Commun. Nov 2019;10(1):5004. PMCID: PMC6825175

Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape. Kolawole AO, Mirabelli C, Hill DR, Svoboda SA, Janowski AB, Passalacqua KD, Rodriguez BN, Dame MK, Freiden P, Berger RP, Vu D, Hosmillo M, O’Riordan MXD, Schultz-Cherry S, Guix S, Spence JR, Wang D, Wobus CE. PLoS Pathogens. Oct 2019. PMID: 31671153

Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD. Golob, J. L., M. M. DeMeules, T. Loeffelholz, Z. Z. Quinn, M. K. Dame, S. S. Silvestri, M. C. Wu, T. M. Schmidt, T. L. Fiedler, M. J. Hoostal, M. Mielcarek, J. Spence, S. A. Pergam and D. N. Fredricks. Blood Advances. 2019;3(19):2866. PMCID: PMC6784520

Calcium-induced differentiation in normal human colonoid cultures: Cell-cell / cell-matrix adhesion, barrier formation and tissue integrity. Attili D, McClintock SD, Rizvi AH, Pandya S, Rehman H, Nadeem DM, Richter A, Thomas D, Dame MK, Turgeon DK, Varani J, Aslam MN. PLoS One, April 2019 PMCID: PMC6469792

Role of JAM-A tyrosine phosphorylation in epithelial barrier dysfunction during intestinal inflammation. Fan, S., Weight, C.M., Luissint, A.C., Hilgarth, R.S., Brazil, J.C., Ettel, M., Nusrat, A., and Parkos, C.A. Mol Biol Cell. 2019. PMID: 30625033

Calcium-induced differentiation of human colon adenomas in colonoid culture: calcium alone versus calcium with additional trace elements. McClintock SD, Colacino JA, Attili D, Dame MK, Richter A, Reddy AR, Basrur V, Rizvi AH, Turgeon DK, Varani J, and Aslam MN.  Cancer Prev Res (Phila). 2018 Jul;11(7):413-428. 2018 Apr 10. PMCID: PMC6030430

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. Han X, Lee A, Huang S, Gao J, Spence JR, Owyang C. Gut Microbes. 2018 Jul 24:1-18. PMID: 30040527

A method for cryogenic preservation of human biopsies and subsequent organoid culture. Tsai YH, Czerwinski M, Wu A, Dame MK, Attili D, Hill E, Colacino JA, Nowacki LM, Shroyer NF, Higgins PDR, Kao JY, and Spence JR.  Cell Mol Gastroenterol Hepatol. 2018 May 30;6(2):218-222.e7. PMCID: PMC6085494

Identification, isolation, and characterization of human LGR5-positive colon adenoma cells.  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, 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. Development. 2018 Mar 14;145(6). PMCID: PMC5897593

In Vitro Porcine Colon Culture. Costa MO, Hill JE, Dame MK, Harding JCS. In: Baratta M. (eds) Epithelial Cell Culture. Methods in Molecular Biology, Humana Press, New York, NY. 2018;1817:185-195.

Real-time measurement of epithelial barrier permeability in human intestinal organoids. Hill DR, Huang S, Tsai YH, Spence JR, Young VB. J Vis Exp. 2017 Dec 18;(130). PMCID: PMC5755602

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. 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. Elife. 2017 Nov 7;6. PMCID: PMC5711377

Quantitative proteomics identifies STEAP4 as a critical regulator of mitochondrial dysfunction linking inflammation and colon cancer. Xue X, Bredell BX, Anderson ER, Martin A, Mays C, Nagao-Kitamoto H, Huang S, Győrffy B, Greenson JK, Hardiman K, Spence JR, Kamada N, Shah YM. Proc Natl Acad Sci USA. 2017 Nov 7;114(45):E9608-E9617. Epub 2017 Oct 23. PMCID: PMC5692584

BRAFV600E cooperates with CDX2 inactivation to promote serrated colorectal tumorigenesis. 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. Elife. 2017 Jan 10;6. PMCID: PMC5268782