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Trainee Publications

2023

  • Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora K, Tang CY, Zheng A, Magness ST, Burclaff J. An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal stem cells. bioRxiv [Preprint]. 2023 Oct 10:2023.10.09.561410. doi: 10.1101/2023.10.09.561410. PMID: 37873351; PMCID: PMC10592697.
  • Darlington KC, Peery AF, Keku TO, Woosley JT, Sandler RS. CYP2C19 Genotype Is Not Associated With the Risk of Microscopic Colitis. Gastro Hep Adv. 2023;2(2):242-243. doi: 10.1016/j.gastha.2022.09.013. Epub 2022 Oct 3. PMID: 37398925; PMCID: PMC10312123.
  • Awoniyi M, Wang J, Ngo B, Meadows V, Tam J, Viswanathan A, Lai Y, Montgomery S, Farmer M, Kummen M, Thingholm L, Schramm C, Bang C, Franke A, Lu K, Zhou H, Bajaj JS, Hylemon PB, Ting J, Popov YV, Hov JR, Francis HL, Sartor RB. Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC. Gut. 2023 Apr;72(4):671-685. doi: 10.1136/gutjnl-2021-326500. Epub 2022 Jun 15. PMID: 35705368; PMCID: PMC9751228.
  • Steinbach EC, Smeekens JM, Roy S, Toyonaga T, Cornaby C, Perini LB, Berglind AE, Kulis MD, Kim EH, Ferris MT, Furey TS, Burks AW, Sheikh SZ. Intestinal epithelial cell barrier dysfunction and elevated Angiopoietin-like 4 identified in orally susceptible peanut allergy model. Clin Exp Allergy. 2023 Feb;53(2):210-215. doi: 10.1111/cea.14248. Epub 2022 Nov 6. PMID: 36336910; PMCID: PMC9976618.

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2022

  • Heppert JK, Lickwar CR, Tillman MC, Davis BR, Davison JM, Lu HY, Chen W, Busch-Nentwich EM, Corcoran DL, Rawls JF. Conserved roles for Hnf4 family transcription factors in zebrafish development and intestinal function. Genetics. 2022 Nov 30;222(4):iyac133. doi: 10.1093/genetics/iyac133. PMID: 36218393; PMCID: PMC9713462.
  • Barnes EL, Darlington K, Herfarth HH. Disease Monitoring of the Ileoanal Pouch: How to Utilize Biomarkers, Imaging, and Pouchoscopy. Curr Gastroenterol Rep. 2022 Nov;24(11):127-136. doi: 10.1007/s11894-022-00850-9. Epub 2022 Oct 18. PMID: 36255602
  • Lee VH, Gulati AS. Implications of Paneth cell dysfunction on gastrointestinal health and disease. Curr Opin Gastroenterol. 2022 Nov 1;38(6):535-540. doi: 10.1097/MOG.0000000000000887. Epub 2022 Sep 24. PMID: 36165037; PMCID: PMC9561020.
  • Pang MJ, Burclaff JR, Jin R, Adkins-Threats M, Osaki LH, Han Y, Mills JC, Miao ZF, Wang ZN. Gastric Organoids: Progress and Remaining Challenges. Cell Mol Gastroenterol Hepatol. 2022;13(1):19-33. doi: 10.1016/j.jcmgh.2021.09.005. Epub 2021 Sep 20. PMID: 34547535; PMCID: PMC8600088.
  • Blakeley-Ruiz JA, McClintock CS, Shrestha HK, Poudel S, Yang ZK, Giannone RJ, Choo JJ, Podar M, Baghdoyan HA, Lydic R, Hettich RL. Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice. ISME Communications 2022;2:66.
  • Orenduff MC, Coleman MF, Glenny EM, Huffman KM, Rezeli ET, Bareja A, Pieper CF, Kraus VB, Hursting SD. Differential effects of calorie restriction and rapamycin on age-related molecular and functional changes in skeletal muscle. Exp Gerontol. 2022 May 24:111841. doi: 10.1016/j.exger.2022.111841. Epub ahead of print. PMID: 35623538
  • Bowers LW, Glenny EM, Punjala A, Lanman NA, Goldbaum A, Himbert C, Montgomery SA, Yang P, Roper J, Ulrich CM, Dannenberg AJ, Coleman MF, Hursting SD. Weight Loss and/or Sulindac Mitigate Obesity-associated Transcriptome, Microbiome, and Protumor Effects in a Murine Model of Colon Cancer. Cancer Prev Res (Phila). 2022 Aug 1;15(8):481-495. doi: 10.1158/1940-6207.CAPR-21-0531. PMID: 35653548; PMCID: PMC9357192.
  • Breau KA, Ok MT, Gomez-Martinez I, Burclaff J, Kohn NP, Magness ST. Efficient transgenesis and homology-directed gene targeting in monolayers of primary human small intestinal and colonic epithelial stem cells. Stem Cell Reports. 2022 Apr 25:S2213-6711(22)00194-1. doi: 10.1016/j.stemcr.2022.04.005. Epub ahead of print. PMID: 35523179.
  • Hoffner O’Connor M, Berglind A, Kennedy Ng MM, Keith BP, Lynch ZJ, Schaner MR, Steinbach EC, Herzog J, Trad OK, Jeck WR, Arthur JC, Simon JM, Sartor RB, Furey TS, Sheikh SZ. BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis. Front Immunol. 2022 Mar 24;13:856966. doi: 10.3389/fimmu.2022.856966. PMID: 35401533; PMCID: PMC8988134.
  • Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST. A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. Cell Mol Gastroenterol Hepatol. 2022 Feb 15:S2352-345X(22)00034-0. doi: 10.1016/j.jcmgh.2022.02.007. Epub ahead of print. PMID: 35176508.
  • Blakeley-Ruiz JA, Kleiner M. Considerations for constructing a protein sequence database for metaproteomics. Comput Struct Biotechnol J. 2022 Jan 21;20:937-952. doi: 10.1016/j.csbj.2022.01.018. PMID: 35242286; PMCID: PMC8861567.
  • Fouladi F, Bulik-Sullivan EC, Glenny EM, Thornton LM, Reed KK, Thomas S, Kleiman S, Watters A, Oakes J, Huh EY, Tang Q, Liu J, Djukic Z, Harper L, Trillo-Ordoñez Y, Sun S, Blakely I, Mehler PS, Fodor AA, Tarantino LM, Bulik CM, Carroll IM. Reproducible changes in the anorexia nervosa gut microbiota following inpatient therapy remain distinct from non-eating disorder controls. Gut Microbes. 2022 Jan-Dec;14(1):2143217. doi: 10.1080/19490976.2022.2143217. PMID: 36398862; PMCID: PMC9678007.

2021

  • Glenny EM, Fouladi F, Thomas SA, Bulik-Sullivan EC, Tang Q, Djukic Z, Trillo-Ordonez YS, A Fodor A, Tarantino LM, M Bulik C, M Carroll I. Gut microbial communities from patients with anorexia nervosa do not influence body weight in recipient germ-free mice. Gut Microbes. 2021 Jan-Dec;13(1):1-15. doi: 10.1080/19490976.2021.1897216. PMID: 33769200; PMCID: PMC8007138.
  • Fletcher JR, Pike CM, Parsons RJ, Rivera AJ, Foley MH, McLaren MR, Montgomery SA, Theriot CM. Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota. Nat Commun. 2021 Jan 19;12(1):462. doi: 10.1038/s41467-020-20746-4. PMID: 33469019; PMCID: PMC7815924.
  • Smeekens JM, Johnson-Weaver BT, Hinton AL, Azcarate-Peril MA, Moran TP, Immormino RM, Kesselring JR, Steinbach EC, Orgel KA, Staats HF, Burks AW, Mucha PJ, Ferris MT, Kulis MD. Fecal IgA, Antigen Absorption, and Gut Microbiome Composition Are Associated With Food Antigen Sensitization in Genetically Susceptible Mice. Front Immunol. 2021 Jan 19;11:599637. doi: 10.3389/fimmu.2020.599637. PMID: 33542716; PMCID: PMC7850988.
  • Awoniyi M, Wang J, Ngo B, Meadows V, Tam J, Viswanathan A, Lai Y, Montgomery SA, Farmer M, Kummen M, Thingholm LB, Schramm C, Bang C, Franke A, Lu K, Ting JPY, Popov YV, Hov JR, r Francis H, Sartor RB. Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in PSC. Gut Submitted, Nov. 2021. Submitted to bioRxiv 11/1/2021 (https://biorxiv.org/cgi/content/short/2021.10.31.466701v1)
  • Foley MH, O’Flaherty S, Allen G, Rivera AJ, Stewart AK, Barrangou R, Theriot CM. Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2017709118. doi: 10.1073/pnas.2017709118. PMID: 33526676; PMCID: PMC8017965.
  • Toyonaga T, Araba KC, Kennedy MM, Keith BP, Wolber EA, Beasley C, Steinbach EC, Schaner MR, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Kapadia MR, Guillem JG, Gulati AS, Sethupathy P, Furey TS, Ehre C, Sheikh SZ. Increased colonic expression of ACE2 associates with poor prognosis in Crohn’s disease. Sci Rep. 2021 Jun 29;11(1):13533. doi: 10.1038/s41598-021-92979-2. PMID: 34188154; PMCID: PMC8241995.
  • Pang MJ, Burclaff JR, Jin R, Adkins-Threats M, Osaki LH, Han Y, Mills JC, Miao ZF, Wang ZN. Gastric Organoids: Progress and Remaining Challenges. Cell Mol Gastroenterol Hepatol. 2022;13(1):19-33. doi: 10.1016/j.jcmgh.2021.09.005. Epub 2021 Sep 20. PMID: 34547535; PMCID: PMC8600088.
  • Glenny EM, Coleman MF, Giles ED, Wellberg EA, Hursting SD. Designing Relevant Preclinical Rodent Models for Studying Links Between Nutrition, Obesity, Metabolism, and Cancer. Annu Rev Nutr. 2021 Oct 11;41:253-282. doi: 10.1146/annurev-nutr-120420-032437. Epub 2021 Aug 6. PMID: 34357792.
  • Toyonaga T, Araba KC, Kennedy MM, Keith BP, Wolber EA, Beasley C, Steinbach EC, Schaner MR, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Kapadia MR, Guillem JG, Gulati AS, Sethupathy P, Furey TS, Ehre C, Sheikh SZ. Increased colonic expression of ACE2 associates with poor prognosis in Crohn’s disease. Sci Rep. 2021 Jun 29;11(1):13533. doi: 10.1038/s41598-021-92979-2. PMID: 34188154; PMCID: PMC8241995.

     

  2020

  • Heppert, J.K., and Davison, J.M., Kelly C., Padilla Mercado G., Lickwar, C.R., Rawls, J.F. Transcriptional programs underlying cellular identity and environmental sensitivity in the intestinal epithelium.– Nature Reviews Gastroenterology and Hepatology. (In-press)
  • Bhatt AP, Pellock SJ, Biernat KA, Walton WG, Wallace BD, Creekmore BC, Letertre MM, Swann JR, Wilson ID, Roques JR, Darr DB, Bailey ST, Montgomery SA, Roach JM, Azcarate-Peril MA, Sartor RB, Gharaibeh RZ, Bultman SJ, and Redinbo MR. 2020 Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy. Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7374-7381. doi: 10.1073/pnas.1918095117. Epub 2020 Mar 13. PMID: 32170007PMCID: PMC7132129
  • Selle K., Fletcher J.R., H. Tuson, D.S. Schmitt, L. McMillan, G.S. Vridhambal, A.J. Rivera, S.A. Montgomery, L.-C. Fortier, R. Barrangou, C.M. Theriot, D.G. Ousterout. 2020   In vivo targeting of Clostridioides difficile using phage-delivered CRISPR-Cas3 antimicrobials. mBio. 2020 Mar 10;11(2). pii: e00019-20. doi: 10.1128/mBio.00019-20.
  • Jariwala PB, Pellock SJ, Goldfarb D, Cloer EW, Artola M, Simpson JB, Bhatt AP, Walton WG, Roberts LR, Major MB, Davies GJ, Overkleeft HS, Redinbo MR. 2020  Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling. ACS Chem Biol. 2020 Jan 17;15(1):217-225. doi: 10.1021/acschembio.9b00788. Epub 2019 Dec 12. PMID: 31774274
  • Toyonaga T, Steinbach EC, Keith BP, Barrow JB, Schaner MR, Wolber EA, Beasley C, Huling J, Wang Y, Allbritton NL, Chaumont N, Sadiq TS, Koruda MJ, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Shanahan MT, Rahbar R, Furey TS, Sethupathy P, Sheikh SZ. Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn’s Disease. Cell Mol Gastroenterol Hepatol. 2020;10(4):779-796. doi: 10.1016/j.jcmgh.2020.06.005. Epub 2020 Jun 16. PMID: 32561494; PMCID: PMC7502566.

2019

  • Ziegler AL, Freeman CK, Fogle CA, Burke MJ, Davis JL, Cook VL, Southwood LL, Blikslager AT.  2019 Multicentre, blinded, randomised clinical trial comparing the use of flunixin meglumine with firocoxib in horses with small intestinal strangulating obstruction. Equine Vet J 3:329-335
  • Foley MH, O’Flaherty S, Barrangou R, Theriot CM. 2019  Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract. PLoS Pathog. 2019 Mar 7;15(3):e1007581. doi: 10.1371/journal.ppat.1007581. eCollection 2019 Mar. PMID:30845232
  • Biernat KA, Pellock SJ, Bhatt AP, Bivins MM, Walton WG, Tran BNT, Wei L, Snider MC, Cesmat AP, Tripathy A, Erie DA, Redinbo MR.  2019  Structure, function, and inhibition of drug reactivating human gut microbial β-glucuronidases. Sci Rep. 2019 Jan 29;9(1):825. doi: 10.1038/s41598-018-36069-w.  PMID: 30696850
  • Ervin SM, Hanley RP, Lim L, Walton WG, Pearce KH, Bhatt AP, James LI, Redinbo MR. 2019  Targeting Regorafenib-Induced Toxicity through Inhibition of Gut Microbial β-Glucuronidases. ACS Chem Biol. 2019 Dec 20;14(12):2737-2744. doi: 10.1021/acschembio.9b00663. Epub 2019 Nov 12.  PMID: 31663730
  • Bhatt AP, Grillo L, Redinbo MR. In Fimo: A Term Proposed for Excrement Examined Experimentally. Gastroenterology. 2019 Apr;156(5):1232. doi: 10.1053/j.gastro.2018.11.070. Epub 2018 Dec 13. PMID: 30553913; PMCID: PMC7256427.
  • Theriot CM, Fletcher JR. Human fecal metabolomic profiling could inform Clostridioides difficile infection diagnosis and treatment. J Clin Invest. 2019 Aug 12;129(9):3539-3541. doi: 10.1172/JCI130008. PMID: 31403467; PMCID: PMC6715351.
  • Oka A, Mishima Y, Liu B, Herzog JW, Steinbach EC, Kobayashi T, Plevy SE, Sartor RB. Phosphoinositide 3-Kinase P110δ-Signaling Is Critical for Microbiota-Activated IL-10 Production by B Cells that Regulate Intestinal Inflammation. Cells. 2019 Sep 21;8(10):1121. doi: 10.3390/cells8101121. PMID: 31546615; PMCID: PMC6829312.
  • Ziegler AL, Pridgen TA, Mills JK, Gonzalez LM, Van Landeghem L, Odle J, Blikslager AT. Correction: Epithelial restitution defect in neonatal jejunum is rescued by juvenile mucosal homogenate in a pig model of intestinal ischemic injury and repair. PLoS One. 2019 Feb 22;14(2):e0212962. doi: 10.1371/journal.pone.0212962. Erratum for: PLoS One. 2018 Aug 23;13(8):e0200674. PMID: 30794684; PMCID: PMC6386237.

    2018

  • Ziegler AL, Pridgen TA, Mills JK, Gonzalez LM, Van Landeghem L, Odle J, Blikslager AT. 2018  Epithelial restitution defect in neonatal jejunum is rescued by juvenile mucosal homogenate in a pig model of intestinal ischemic injury and repair. PLoS One. 13(8)
  • Keith BP*, Barrow JB*, Toyonaga T, Kazgan N, O’Connor MH, Shah ND, Schaner MS, Wolber EA, Trad OK, Gipson GR, Pitman WA, Kanke M, Saxena SJ, Chaumont N, Sadiq TS, Koruda MJ, Cotney PA, Allbritton N, Trembath DG, Sylvester F, Furey TS, Sethupathy P, Sheikh SZ. 2018.  Colonic epithelial miR-31 associates with the development of Crohn’s phenotypes. JCI Insight. 2018 Oct 4;3(19). pii: 122788. doi: 10.1172/jci.insight.122788.
  • Bhatt AP, Gunasekara DB, Speer J, Reed MI, Peña AN, Midkiff BR, Magness ST, Bultman SJ, Allbritton NL, Redinbo MR. 2018, Nonsteroidal Anti-Inflammatory Drug-Induced Leaky Gut Modeled Using Polarized Monolayers of Primary Human Intestinal Epithelial Cells. ACS Infect Dis. 2018 Jan 12;4(1):46-52. doi: 10.1021/acsinfecdis.7b00139.
  • Yauw STK, Arron M, Lomme RMLM, van den Broek P, Greupink R, Bhatt AP, Redinbo MR, van Goor H. 2018 Microbial Glucuronidase Inhibition Reduces Severity of Diclofenac-Induced Anastomotic Leak in Rats. Surg Infect (Larchmt). 2018 May/Jun;19(4):417-423. doi: 10.1089/sur.2017.245. Epub 2018 Apr 6. PMID: 29624485
  • Fletcher JR, Erwin S, Lanzas C, Theriot CM 2018. Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model.  mSphere. 2018 Mar 28;3(2). pii: e00089-18. doi: 10.1128/mSphere.00089-18. eCollection 2018 Mar-Apr.
  • 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):1508-1523.e10. doi: 10.1053/j.gastro.2018.07.023. Epub 2018 Jul 25. PMID: 30055169; PMCID: PMC6232678.
  • Wang JR, Holt J, McMillan L, Jones CD. FMLRC: Hybrid long read error correction using an FM-index. BMC Bioinformatics. 2018 Feb 9;19(1):50. doi: 10.1186/s12859-018-2051-3. PMID: 29426289; PMCID: PMC5807796.

2017

  • Ziegler AL, Blikslager AT. 2017 Impaired intestinal barrier function and relapsing digestive disease: Lessons from a porcine model of early life stress. Neurogastroenterol Motil. Nov;29(11):1-4
  • Pollet RM, D’Agostino EH, Walton WG, Xu Y, Little MS, Biernat KA, Pellock SJ, Patterson LM, Creekmore BC, Isenberg HN, Bahethi RR, Bhatt AP, Liu J, Gharaibeh RZ, Redinbo MR. 2017 An Atlas of β-Glucuronidases in the Human Intestinal Microbiome. Structure. 2017 Jul 5;25(7):967-977.e5. doi: 10.1016/j.str.2017.05.003
  • Bhatt AP, Redinbo MR, Bultman SJ. The role of the microbiome in cancer development and therapy. CA Cancer J Clin. 2017 Jul 8;67(4):326-344. doi: 10.3322/caac.21398. Epub 2017 May 8. PMID: 28481406; PMCID: PMC5530583.
  • Wang JR, Quach B, Furey TS. Correcting nucleotide-specific biases in high-throughput sequencing data. BMC Bioinformatics. 2017 Aug 1;18(1):357. doi: 10.1186/s12859-017-1766-x. PMID: 28764645; PMCID: PMC5540620.

2016