Publications

2024

Shumway AJ, Shanahan MT, Hollville E, Chen K, Beasley C, Villanueva JW, Albert S, Lian G, Cure MR, Schaner M, Zhu LC, Bantumilli S, Deshmukh M, Furey TS, Sheikh SZ, Sethupathy P. Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn’s disease. JCI Insight. 2024 Feb 22;9(4):e168800. doi: 10.1172/jci.insight.168800. PMID: 38385744; PMCID: PMC10967384.

Levic DS, Niedzwiecki D, Kandakatla A, Karlovich NS, Juneja A, Park J, Stolarchuk C, Adams S, Willer JR, Schaner MR, Lian G, Beasley C, Marjoram L, Flynn AD, Valentine JF, Onken JE, Sheikh SZ, Davis EE, Evason KJ, Garman KS, Bagnat M. TNF promoter hypomethylation is associated with mucosal inflammation in IBD and anti-TNF response. medRxiv [Preprint]. 2024 Feb 6:2024.02.05.24302343. doi: 10.1101/2024.02.05.24302343. PMID: 38370739; PMCID: PMC10871362.

Chen KA, Nishiyama NC, Kennedy Ng MM, Shumway A, Joisa CU, Schaner MR, Lian G, Beasley C, Zhu LC, Bantumilli S, Kapadia MR, Gomez SM, Furey TS, Sheikh SZ. Linking gene expression to clinical outcomes in pediatric Crohn’s disease using machine learning. Sci Rep. 2024 Feb 1;14(1):2667. doi: 10.1038/s41598-024-52678-0. PMID: 38302662; PMCID: PMC10834600.

2023

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.

2022

Sazonovs A, Stevens CR, Venkataraman GR, Yuan K, Avila B, Abreu MT, Ahmad T, Allez M, Ananthakrishnan AN, Atzmon G, Baras A, Barrett JC, Barzilai N, Beaugerie L, Beecham A, Bernstein CN, Bitton A, Bokemeyer B, Chan A, Chung D, Cleynen I, Cosnes J, Cutler DJ, Daly A, Damas OM, Datta LW, Dawany N, Devoto M, Dodge S, Ellinghaus E, Fachal L, Farkkila M, Faubion W, Ferreira M, Franchimont D, Gabriel SB, Ge T, Georges M, Gettler K, Giri M, Glaser B, Goerg S, Goyette P, Graham D, Hämäläinen E, Haritunians T, Heap GA, Hiltunen M, Hoeppner M, Horowitz JE, Irving P, Iyer V, Jalas C, Kelsen J, Khalili H, Kirschner BS, Kontula K, Koskela JT, Kugathasan S, Kupcinskas J, Lamb CA, Laudes M, Lévesque C, Levine AP, Lewis JD, Liefferinckx C, Loescher BS, Louis E, Mansfield J, May S, McCauley JL, Mengesha E, Mni M, Moayyedi P, Moran CJ, Newberry RD, O’Charoen S, Okou DT, Oldenburg B, Ostrer H, Palotie A, Paquette J, Pekow J, Peter I, Pierik MJ, Ponsioen CY, Pontikos N, Prescott N, Pulver AE, Rahmouni S, Rice DL, Saavalainen P, Sands B, Sartor RB, Schiff ER, Schreiber S, Schumm LP, Segal AW, Seksik P, Shawky R, Sheikh SZ, Silverberg MS, Simmons A, Skeiceviciene J, Sokol H, Solomonson M, Somineni H, Sun D, Targan S, Turner D, Uhlig HH, van der Meulen AE, Vermeire S, Verstockt S, Voskuil MD, Winter HS, Young J; Belgium IBD Consortium; Cedars-Sinai IBD; International IBD Genetics Consortium; NIDDK IBD Genetics Consortium; NIHR IBD BioResource; Regeneron Genetics Center; SHARE Consortium; SPARC IBD Network; UK IBD Genetics Consortium, Duerr RH, Franke A, Brant SR, Cho J, Weersma RK, Parkes M, Xavier RJ, Rivas MA, Rioux JD, McGovern DPB, Huang H, Anderson CA, Daly MJ. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility. Nat Genet. 2022 Sep;54(9):1275-1283. doi: 10.1038/s41588-022-01156-2. Epub 2022 Aug 29. PMID: 36038634.

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.

Kanke M, Kennedy Ng MM, Connelly S, Singh M, Schaner M, Shanahan MT, Wolber EA, Beasley C, Lian G, Jain A, Long MD, Barnes EL, Herfarth HH, Isaacs KL, Hansen JJ, Kapadia M, Guillem JG, Feschotte C, Furey TS, Sheikh SZ, Sethupathy P. Single-Cell Analysis Reveals Unexpected Cellular Changes and Transposon Expression Signatures in the Colonic Epithelium of Treatment-Naïve Adult Crohn’s Disease Patients. Cell Mol Gastroenterol Hepatol. 2022;13(6):1717-1740. doi: 10.1016/j.jcmgh.2022.02.005. Epub 2022 Feb 12. PMID: 35158099; PMCID: PMC9046244.

2021

Roy S, Sheikh SZ, Furey TS. A machine learning approach identifies 5-ASA and ulcerative colitis as being linked with higher COVID-19 mortality in patients with IBD. Sci Rep. 2021 Aug 13;11(1):16522. doi: 10.1038/s41598-021-95919-2. PMID: 34389789; PMCID: PMC8363640.

2020

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 M, Gaston Guillem J, Koruda MJ, Rahbar R, Sadiq T, Gulati AS, Sethupathy P, Furey TS, Ehre C, Sheikh SZ. “Increased Colonic Expression of ACE2 Associates with Poor Prognosis in Crohn’s disease.” bioRxiv [Preprint]. 2020 Nov 24:2020.11.24.396382. doi: 10.1101/2020.11.24.396382. PMID: 33269348

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 Jun 16:S2352-345X(20)30094-1. doi: 10.1016/j.jcmgh.2020.06.005. Online ahead of print. PMID: 32561494

Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. “Crohn’s Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria”
Inflamm Bowel Dis. 2020 May 29:izaa103. doi: 10.1093/ibd/izaa103. Online ahead of print. PMID: 32469069

2019

Furey TS, Sethupathy P, Sheikh SZ. “Redefining the IBDs using genome-scale molecular phenotyping.”
Nat Rev Gastroenterol Hepatol. 2019 May;16(5):296-311. doi: 10.1038/s41575-019-0118-x. PMID: 30787446

2018

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. “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. [Epub ahead of print] PMID: 30282822

2017

Lickwar CR, Camp JG, Weiser M, Cocchiaro JL, Kingsley DM, Furey TS, Sheikh SZ, Rawls JF. “Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.”
PLoS Biol. 2017 Aug 29;15(8):e2002054. doi: 10.1371/journal.pbio.2002054. PMID: 28850571

2016

Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR,
Schaner MS, Herfarth HH, Sartor RB, McGovern DP, Rahbar R, Sadiq TS, Koruda MJ,
Furey TS, Sheikh SZ. “Molecular classification of Crohn’s disease reveals two
clinically relevant subtypes.”
Gut. 2016 Oct 14. PMID: 27742763.

Abdalla M, Sheikh SZ. “Harnessing the Power of Posttranscriptional Gene Silencing in Crohn’s Disease.”
Clin Transl Gastroenterol. 2016 Mar 31;7:e160. PubMed PMID: 27030950.

2015

Peck BC, Weiser M, Lee SE, Gipson GR, Iyer VB, Sartor RB, Herfarth HH, Long MD, Hansen JJ, Isaacs KL, Trembath DG, Rahbar R, Sadiq TS, Furey TS, Sethupathy P, Sheikh SZ. “MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn’s Disease and May Have Prognostic Utility.”
Inflamm Bowel Dis. 2015 Sep;21(9):2178-87. PubMed PMID: 26164662.

Steinbach EC, Gipson GR, Sheikh SZ. “Induction of Murine Intestinal Inflammation by Adoptive Transfer of Effector CD4+ CD45RB high T Cells into Immunodeficient Mice.”
J Vis Exp. 2015 Apr 21;(98). doi: 10.3791/52533. PubMed PMID: 25938395.

Lynch VJ, Nnamani MC, Kapusta A, Brayer K, Plaza SL, Mazur EC, Emera D, Sheikh SZ, Grützner F, Bauersachs S, Graf A, Young SL, Lieb JD, DeMayo FJ, Feschotte C, Wagner GP. “Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy.”
Cell Rep. 2015 Feb 3;10(4):551-61. doi: 10.1016/j.celrep.2014.12.052. Epub 2015 Jan 29. PubMed PMID: 25640180; PubMed Central PMCID: PMC4447085

2014

Hughes JT, Herfarth HH, Isaacs K, Plevy S, Sartor RS, Sheikh SZ, Hansen JJ, Long MD. “Infliximab Retreatment in Inflammatory Bowel Disease: A Single Center Routine Clinical Experience”
Clin Gastroenterol Hepatol. 2014 May 14. PMID: 24835819

Steinbach EC , Kobayashi  T, Russo S, Sheikh SZ, Gipson G, Uno J, Mishima Y, Bo Liu B, Herfarth H, Ting J, Sartor R, Plevy SE. “Innate PI3K p110δ regulates Th1/Th17 development and microbiota-dependent colitis.”
J Immunol. 2014 Apr 15. PubMed PMID: 24634494

Kobayashi T, Steinbach EC, Russo SM, Matsuoka KM, Nochi T, Maharshak N, Borst L, Hostager B, Garcia-Martinez JV, Rothman PB, Kashiwada MK, Sheikh SZ, Murray PJ, Plevy SE. “NFIL3 deficient mice develop microbiota dependent, IL-12/23 driven spontaneous colitis.”
J Immunol. 2014 Jan 17. PubMed PMID: 24442434.

2013

*Onyiah, JC., *Sheikh, SZ., Maharshak, N., Russo, SM., Steinbach, EC., Kobayashi, T., Mackey, LC., Moeser, AJ., Rawls, JF., Borst, LB., Otterbein, LE., Plevy, SE. “Carbon monoxide and heme oxygenase-1 maintain intestinal homeostasis through augmented enteric bacterial clearance.”
Gastroenterology. 2013 Apr;144(4):789-98. 2012 Dec 22. PMID: 23266559. *Share first authorship 2013

2012

Kobayashi, T., Matsuoka, K., Sheikh, SZ., Russo, SM., Mishima, Y., deZoeten, E. F., Karp, C. L., Ting, J. P. Y. Sartor, R. B., Plevy, SE. “IL-10 regulates Il12b expression via histone deacetylation: Implications for intestinal macrophage homeostasis.”
J Immunol. 2012 Aug 15;189(4):1792-9. Epub 2012 Jul 11. PMID: 22786766

2011

Sheikh SZ, Hegazi RA, Kobayashi T, Onyiah JC, Russo SM, Matsuoka K, Sepulveda , AR, Li F, Otterbein LE, Plevy SE. “An Anti-Inflammatory Role for Carbon Monoxide and Heme Oxygenase-1 in Chronic Th2-Mediated Murine Colitis.”
J Immunol. 2011 May 1;186(9):5506-13. Epub 2011 Mar 28. PubMed PMID: 21444764.

Kobayashi T, Matsuoka K, Sheikh SZ, Elloumi HZ, Kamada N, Hisamatsu T, Hansen JJ, Doty KR, Pope SD, Smale ST, Hibi T, Rothman PB, Kashiwada M, Plevy SE. “NFIL3 Is a Regulator of IL-12 p40 in Macrophages and Mucosal Immunity.”
J Immunol. 2011 Apr 15;186(8):4649-55. Epub 2011 Mar 7. PubMed PMID: 21383239.

2010

Sheikh SZ, Kobayashi T, Matsuoka K, Onyiah JC, Plevy SE. “Characterization of an interferon-stimulated response element (ISRE) in the Il23a promoter.”
J Biol Chem. 2011 Jan 14;286(2):1174-80. Epub 2010 Nov 21. PMID: 21097874

Uno JK, Rao KN, Matsuoka K, Sheikh SZ, Kobayashi T, Li F, Steinbach EC, Sepulveda AR, Vanhaesebroeck B, Sartor RB, Plevy SE. “Altered Macrophage Function  Contributes to Colitis in Mice Defective in the Phosphoinositide-3 Kinase Subunit p110delta.”
Gastroenterology. 2010 Nov;139(5):1642-53, 1653.e1-6. PMID: 20637203.

Sheikh SZ, Matsuoka K, Kobayashi T, Li F, Rubinas T, Plevy SE. “Cutting edge: IFN-gamma is a negative regulator of IL-23 in murine macrophages and experimental colitis.”
J Immunol. 2010 Apr 15;184(8):4069-73. PMID: 20228197

Before 2010

Hakim W, Sheikh SZ, Inayat I, Bia M,  Caldwell C, Jain D, Smith D, Friedman A, Lorber M, Formica R, Mehal WZ. “HCV response in Patients with End Stage Renal Disease treated with Combination Pegylated Interferon & Ribavirin.”
J Clin Gastroenterol. 2009 May-Jun;43(5):477-81. PMID: 19142165.

Sheikh SZ, Matsuoka K, Uno JK, Plevy SE.  “Abnormal Mucosal Immune Response To Altered Bacterial Flora Following Restorative Proctocolectomy in Patients with Ulcerative Colitis.”
Clin Immunol. 2008 Jun;127(3):270-9. PMID: 18499066.

Qamar A, Sheikh SZ, Masud A, Jhandier MN, Inayat IB, Hakim W, Mehal WZ. “In vitro and in vivo protection of stellate cells from apoptosis by leptin.”
Dig Dis Sci. 2006 Oct;51(10):1697-705. PMID: 16957995.

Kuniyasu Y, Qamar A, Sheikh SZ, Jhandier MN, Hakim W, Mehal WZ. “Blocking intrahepatic deletion of activated CD8+ T cells by an altered peptide ligand.”
Cell Immunol. 2006 Jan;238(1):31-7. PMID: 16445896.

Mehal WZ, Sheikh SZ, Gorelik L, Flavell RA. “TGF-beta signaling regulates CD8+ T cell responses to high- and low-affinity TCR interactions.”
Int Immunol. 2005 May;17(5):531-8. Epub 2005 Apr 11. PMID: 15824070.

Kuniyasu Y, Marfani SM, Inayat IB, Sheikh SZ, Mehal WZ. “Kupffer cells required for high affinity peptide-induced deletion, not retention, of activated CD8+ T cells by mouse liver.”
Hepatology. 2004 Apr;39(4):1017-27. PMID:15057906.