Alenghat Lab
Publications

Publications

Eshleman, EM; Rice, T; Potter, C; Waddell, A; Hashimoto-Hill, S; Woo, V; Field, S; Engleman, L; Lim, H-W; Schumacher, MA; Frey, MR; Denson, LA; Finkelman, FD; Alenghat, T. Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity. Immunity. 2024; 57(2):319-332.e6.

Eshleman, EM; Shao, T-Y; Woo, V; Rice, T; Engleman, L; Didriksen, BJ; Whitt, J; Haslam, DB; Way, SS; Alenghat, T. Intestinal epithelial HDAC3 and MHC class II coordinate microbiota-specific immunity. Journal of Clinical Investigation. 2023; 133(4).

Woo, V; Eshleman, EM; Hashimoto-Hill, S; Whitt, J; Wu, S-E; Engleman, L; Rice, T; Karns, R; Qualls, JE; Haslam, DB; Vallance, BA; Alenghat, T. Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. Cell Host and Microbe. 2021; 29(12):1744-1756.e5.

Wu, S-E; Hashimoto-Hill, S; Woo, V; Eshleman, EM; Whitt, J; Engleman, L; Karns, R; Denson, LA; Haslam, DB; Alenghat, T. Microbiota-derived metabolite promotes HDAC3 activity in the gut. Nature. 2020; 586(7827):108-112.

Oherle, K; Acker, E; Bonfield, M; Wang, T; Gray, J; Lang, I; Bridges, J; Lewkowich, I; Xu, Y; Ahlfeld, S; Zacharias, W; Alenghat, T; Deshmukh, H. Insulin-like Growth Factor 1 Supports a Pulmonary Niche that Promotes Type 3 Innate Lymphoid Cell Development in Newborn Lungs. Immunity. 2020; 52(2):275-294.e9.

Kelly, D; Kotliar, M; Woo, V; Jagannathan, S; Whitt, J; Moncivaiz, J; Aronow, BJ; Dubinsky, MC; Hyams, JS; Markowitz, JF; Karns, R; Barski, A; Denson, LA; Alenghat, T. Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. JCI Insight. 2018; 3(18).

Whitt, J; Woo, V; Lee, P; Moncivaiz, J; Haberman, Y; Denson, L; Tso, P; Alenghat, T. Disruption of Epithelial HDAC3 in Intestine Prevents Diet-Induced Obesity in Mice. Gastroenterology. 2018; 155(2):501-513.

Jiang, TT; Shao, T-Y; Ang, WXG; Kinder, JM; Turner, LH; Pham, G; Whitt, J; Alenghat, T; Way, SS. Commensal Fungi Recapitulate the Protective Benefits of Intestinal Bacteria. Cell Host and Microbe. 2017; 22(6):809-816.e4.

Whitsett, JA; Alenghat, T. Respiratory epithelial cells orchestrate pulmonary innate immunity. Nature Immunology. 2015; 16(1):27-35.

Alenghat, T; Osborne, LC; Saenz, SA; Kobuley, D; Ziegler, CGK; Mullican, SE; Choi, I; Grunberg, S; Sinha, R; Wynosky-Dolfi, M; Bushman, FD; Won, K-J; Lazar, MA; Artis, D. Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis. Nature. 2013; 504(7478):153-157.

Caminero, A; Tropini, C; Valles-Colomer, M; Shung, DL; Gibbons, SM; Surette, MG; Sokol, H; Tomeo, NJ; Tarr, PI; Verdu, EF. Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI. Nature Reviews Gastroenterology and Hepatology. 2025; 22(11):788-803.

Stevens, J; Culberson, E; Kinder, J; Ramiriqui, A; Gray, J; Bonfield, M; Shao, T-Y; Al Gharaibeh, F; Peterson, L; Steinmeyer, S; Sengupta, S; Alenghat, T; Way, SS; Deshmukh, H. Microbiota-derived inosine programs protective CD8+ T cell responses against influenza in newborns. Cell. 2025; 188(16):4239-4256.e19.

Hari Gopal, S; Alenghat, T; Pammi, M. Early life epigenetics and childhood outcomes: a scoping review. Pediatric Research. 2025; 97(4):1305-1314.

Didriksen, BJ; Eshleman, EM; Alenghat, T. Epithelial regulation of microbiota-immune cell dynamics. Mucosal Immunology. 2024; 17(2):303-313.

Eshleman, EM; Rice, T; Potter, C; Waddell, A; Hashimoto-Hill, S; Woo, V; Field, S; Engleman, L; Lim, H-W; Schumacher, MA; Frey, MR; Denson, LA; Finkelman, FD; Alenghat, T. Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity. Immunity. 2024; 57(2):319-332.e6.

Eshleman, EM; Alenghat, T. Cleaving an epithelial path to food tolerance. Cell Research. 2023; 33(12):896-897.

Velez Lopez, A; Waddell, A; Antonacci, S; Castillo, D; Santucci, N; Ollberding, NJ; Eshleman, EM; Denson, LA; Alenghat, T. Microbiota-derived butyrate dampens linaclotide stimulation of the guanylate cyclase C pathway in patient-derived colonoids. Neurogastroenterology and Motility. 2023; 35(12):e14681.

Shao, T-Y; Jiang, TT; Stevens, J; Russi, AE; Troutman, TD; Bernieh, A; Pham, G; Erickson, JJ; Eshleman, EM; Alenghat, T; Weaver, CT; Haslam, DB; Deshmukh, H; Way, SS. Kruppel-like factor 2+ CD4 T cells avert microbiota-induced intestinal inflammation. Cell reports. 2023; 42(11):113323.

Overcast, GR; Meibers, HE; Eshleman, EM; Saha, I; Waggoner, L; Patel, KN; Jain, VG; Haslam, DB; Alenghat, T; Vandussen, KL; Pasare, C. IEC-intrinsic IL-1R signaling holds dual roles in regulating intestinal homeostasis and inflammation. Journal of Experimental Medicine (JEM). 2023; 220(6).

Jensen, SN; Teng, F; Alenghat, T; Lazar, MA; Sonnenberg, GF. Microbiota engage a HDAC3 rheostat to shape ILC3 metabolism and function in the gut. Journal of Immunology. 2023; 210(Supplement_1):228.04-228.04.

Eshleman, EM; Rice, T; Potter, C; Woo, V; Field, S; Hashimoto-Hill, S; Waddell, A; Engelman, L; Finkelman, FD; Alenghat, T. Microbiota dampen type 2 immunity by epigenetically restricting tuft cell differentiation. Journal of Immunology. 2023; 210(Supplement_1):150.08-150.08.

Eshleman, EM; Shao, T-Y; Woo, V; Rice, T; Engleman, L; Didriksen, BJ; Whitt, J; Haslam, DB; Way, SS; Alenghat, T. Intestinal epithelial HDAC3 and MHC class II coordinate microbiota-specific immunity. Journal of Clinical Investigation. 2023; 133(4).

Kharofa, J; Apewokin, S; Alenghat, T; Ollberding, NJ. Metagenomic analysis of the fecal microbiome in colorectal cancer patients compared to healthy controls as a function of age. Cancer Medicine. 2023; 12(3):2945-2957.

Grasset, EK; Alenghat, T. Good intentions gone wrong: The B cell block to epithelial repair. Immunity. 2022; 55(12):2222-2224.

Fawad, JA; Luzader, DH; Hanson, GF; Moutinho, TJ; Mckinney, CA; Mitchell, PG; Brown-Steinke, K; Kumar, A; Park, M; Lee, S; Alenghat, T; Hong, CI; Papin, JA; Moore, SR. Histone Deacetylase Inhibition by Gut Microbe-Generated Short-Chain Fatty Acids Entrains Intestinal Epithelial Circadian Rhythms. Gastroenterology. 2022; 163(5):1377-1390.e11.

Eshleman, EM; Shao, T-Y; Woo, V; Rice, T; Whitt, J; Engleman, L; Way, SS; Alenghat, T. Epithelial MHC class II directs microbiota-specific intestinal immune homeostasis. Journal of Immunology. 2022; 208(Supplement_1):115.03-115.03.

Eshleman, EM; Shao, T-Y; Woo, V; Rice, T; Whitt, J; Engleman, L; Way, SS; Alenghat, T. Intestinal epithelial MHC class II regulation by HDAC3 instructs microbiota-specific CD4+ T cells. bioRxiv. 2022; 2022.01.01.473735.

Negi, S; Hashimoto-Hill, S; Alenghat, T. Neonatal microbiota-epithelial interactions that impact infection. Frontiers in Microbiology. 2022; 13:955051.

Hashimoto-Hill, S; Colapietro, L; Woo, V; Antonacci, S; Whitt, J; Engleman, L; Alenghat, T. Dietary phytate primes epithelial antibacterial immunity in the intestine. Frontiers in Immunology. 2022; 13:952994.

Woo, V; Alenghat, T. Epigenetic regulation by gut microbiota. Gut Microbes. 2022; 14(1):2022407.

Woo, V; Eshleman, EM; Hashimoto-Hill, S; Whitt, J; Wu, S-E; Engleman, L; Rice, T; Karns, R; Qualls, JE; Haslam, DB; Vallance, BA; Alenghat, T. Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. Cell Host and Microbe. 2021; 29(12):1744-1756.e5.

Eshleman, EM; Alenghat, T. Epithelial sensing of microbiota-derived signals. Genes and Immunity. 2021; 22(5-6):237-246.

Woo, V; Eshleman, EM; Whitt, J; Hashimoto-Hill, S; Wu, S-E; Engleman, L; Rice, T; Karns, R; Vallance, BA; Alenghat, T. Commensal bacterial-derived retinoic acid primes host defense to intestinal infection. bioRxiv. 2021; 2021.01.27.428280.

Hashimoto-Hill, S; Alenghat, T. Inflammation-Associated Microbiota Composition Across Domestic Animals. Frontiers in Genetics. 2021; 12:649599.

Hashimoto-Hill, S; Kelly, DR; Alenghat, T. Chapter 12 Epigenomics of intestinal disease. In: Medical Epigenetics. Elsevier; 2021:213-230.

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