Publications

Mucosally sourced complement factor B modulates the host response to colitis

Thapa A, Nallapu A, Mougboh N, Nedunchezian S, Talati K, Yang B, Hyun J, Sanchez JM, Seet CS, Koon HW, Li Z, Ciorba MA, Michelsen K, Kulkarni HS, Kulkarni DH. Mucosally sourced complement factor B modulates the host response to colitis. bioRxiv [Preprint]. 2026 Jan 1:2025.12.31.697141. doi: 10.64898/2025.12.31.697141. PMID: 41509372; PMCID: PMC12776390.

Antigen Uptake in the Gut: An Underappreciated Piece to the Puzzle?

Kulkarni DH, Newberry RD. Antigen Uptake in the Gut: An Underappreciated Piece to the Puzzle? Annu Rev Immunol. 2025 Apr;43(1):571-588. doi: 10.1146/annurev-immunol-082523-090154. PMID: 40279313; PMCID: PMC12068241.

Local complement activation and modulation in mucosal immunity

Kulkarni DH, Starick M, Aponte Alburquerque R, Kulkarni HS. Local complement activation and modulation in mucosal immunity. Mucosal Immunol. 2024 Aug;17(4):739-751. doi: 10.1016/j.mucimm.2024.05.006. Epub 2024 Jun 4. PMID: 38838816; PMCID: PMC11929374.

Gut microbiota induces weight gain and inflammation in the gut and adipose tissue independent of manipulations in diet, genetics, and immune development

Kulkarni DH*, Rusconi B, Floyd AN, Joyce EL, Talati KB, Kousik H, Alleyne D, Harris DL, Garnica L, McDonough R, Bidani SS, Kulkarni HS, Newberry EP, McDonald KG, Newberry RD*. Gut microbiota induces weight gain and inflammation in the gut and adipose tissue independent of manipulations in diet, genetics, and immune development. Gut Microbes. 2023 Dec;15(2):2284240. doi: 10.1080/19490976.2023.2284240. Epub 2023 Nov 30. PMID: 38036944; PMCID: PMC10730159. (* Co-corresponding)

Vancomycin-induced gut microbial dysbiosis alters enteric neuron-macrophage interactions during a critical period of postnatal development

Schill EM, Joyce EL, Floyd AN, Udayan S, Rusconi B, Gaddipati S, Barrios BE, John V, Kaye ME, Kulkarni DH, Pauta JT, McDonald KG, Newberry RD. Vancomycin-induced gut microbial dysbiosis alters enteric neuron-macrophage interactions during a critical period of postnatal development. Front Immunol. 2023 Oct 12;14:1268909. doi: 10.3389/fimmu.2023.1268909. PMID: 37901245; PMCID: PMC10602895.

Role: Conducted data analysis for the study and scientific input.

Lung epithelial cell-derived C3 protects against pneumonia-induced lung injury

Sahu SK, Ozantürk AN, Kulkarni DH, Ma L, Barve RA, Dannull L, Lu A, Starick M, McPhatter J, Garnica L, Sanfillipo-Burchman M, Kunen J, Wu X, Gelman AE, Brody SL, Atkinson JP, Kulkarni HS. Lung epithelial cell-derived C3 protects against pneumonia-induced lung injury. Sci Immunol. 2023 Feb 3;8(80):eabp9547. doi: 10.1126/sciimmunol.abp9547. Epub 2023 Feb 3. PMID: 36735773; PMCID: PMC10023170.

Role: Conducted flow cytometric analysis for immune cells, assisted with study design and manuscript.

High-fat diet prevents the development of autoimmune diabetes in NOD mice

Clark AL, Yan Z, Chen SX, Shi V, Kulkarni DH, Diwan A, Remedi MS. High-fat diet prevents the development of autoimmune diabetes in NOD mice. Diabetes Obes Metab. 2021 Nov;23(11):2455-2465. doi: 10.1111/dom.14486. Epub 2021 Aug 2. PMID: 34212475; PMCID: PMC8490276.

Role: Conducted experiments critical for revision of the manuscript and also supported data analysis. Data generated and provided helped address reviewer concern.

Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens

Karvas RM, Khan SA, Verma S, Yin Y, Kulkarni D, Dong C, Park KM, Chew B, Sane E, Fischer LA, Kumar D, Ma L, Boon ACM, Dietmann S, Mysorekar IU, Theunissen TW. Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens. Cell Stem Cell. 2022 May 5;29(5):810-825.e8. doi: 10.1016/j.stem.2022.04.004. PMID: 35523141; PMCID: PMC9136997.

Role: Conducted data analysis for the study and scientific input.

Emerging roles of the complement system in host-pathogen interactions

Sahu SK, Kulkarni DH, Ozanturk AN, Ma L, Kulkarni HS. Emerging roles of the complement system in host-pathogen interactions. Trends Microbiol. 2022 Apr;30(4):390-402. doi: 10.1016/j.tim.2021.09.002. Epub 2021 Sep 29. PMID: 34600784; PMCID: PMC8930420.

Commensal Cryptosporidium colonization elicits a cDC1-dependent Th1 response that promotes intestinal homeostasis and limits other infections

Russler-Germain EV, Jung J, Miller AT, Young S, Yi J, Wehmeier A, Fox LE, Monte KJ, Chai JN, Kulkarni DH, Funkhouser-Jones LJ, Wilke G, Durai V, Zinselmeyer BH, Czepielewski RS, Greco S, Murphy KM, Newberry RD, Sibley LD, Hsieh CS. Commensal Cryptosporidium colonization elicits a cDC1-dependent Th1 response that promotes intestinal homeostasis and limits other infections. Immunity. 2021 Nov 9;54(11):2547-2564.e7. doi: 10.1016/j.immuni.2021.10.002. Epub 2021 Oct 28. PMID: 34715017; PMCID: PMC8716016.

Role: Conducted invivo experiments for histological assessment of gut epithelium.

Intestinal goblet cells sample and deliver lumenal antigens by regulated endocytic uptake and transcytosis

Gustafsson JK, Davis JE, Rappai T, McDonald KG, Kulkarni DH, Knoop KA, Hogan SP, Fitzpatrick JA, Lencer WI, Newberry RD. Intestinal goblet cells sample and deliver lumenal antigens by regulated endocytic uptake and transcytosis. Elife. 2021 Oct 22;10:e67292. doi: 10.7554/eLife.67292. PMID: 34677124; PMCID: PMC8594945.

Role: Conducted data analysis for the study, provided scientific input and feedback on manuscript.

A Novel Role of Circular RNA in Intestinal Epithelial Repair

Kulkarni DH, Newberry RD. A Novel Role of Circular RNA in Intestinal Epithelial Repair. Gastroenterology. 2021 Oct;161(4):1108-1110. doi: 10.1053/j.gastro.2021.07.031. Epub 2021 Jul 22. PMID: 34303659.

Goblet cell associated antigen passages support the induction and maintenance of oral tolerance

Kulkarni DH*, Gustafsson JK*, Knoop KA, McDonald KG, Bidani SS, Davis JE, Floyd AN, Hogan SP, Hsieh CS, Newberry RD. Goblet cell associated antigen passages support the induction and maintenance of oral tolerance. Mucosal Immunol. 2020 Mar;13(2):271-282. doi: 10.1038/s41385-019-0240-7. Epub 2019 Dec 9. PMID: 31819172; PMCID: PMC7044050.

In vivo labeling of epithelial cell-associated antigen passages in the murine intestine

Knoop KA, Kulkarni DH, McDonald KG, Gustafsson JK, Davis JE, Floyd AN, Newberry RD. In vivo labeling of epithelial cell-associated antigen passages in the murine intestine. Lab Anim (NY). 2020 Mar;49(3):79-88. doi: 10.1038/s41684-019-0438-z. Epub 2020 Feb 10. PMID: 32042160; PMCID: PMC8805201.

Regulatory T-cells Restraining Allergic Responses Develop Under Maternal Control

Knoop KA, McDonald KG, Coughlin PE, Kulkarni DH, Gustafsson JK, Ndao M, Beigelman A, Good M, Warner B, Elson C, Hsieh CS, Hogan SP, Tarr PI, Newberry RD. Regulatory T-cells Restraining Allergic Responses Develop Under Maternal Control. JCI Insight 2020;5(15):e137943

Role: Provided key scientific reagents and insight into the study design.

Cryptic activation of an Irf8 enhancer governs cDC1 fate specification

Durai V, Bagadia P, Granja JM, Satpathy AT, Kulkarni DH, Davidson JT 4th, Wu R, Patel SJ, Iwata A, Liu TT, Huang X, Briseño CG, Grajales-Reyes GE, Wöhner M, Tagoh H, Kee BL, Newberry RD, Busslinger M, Chang HY, Murphy TL, Murphy KM. Cryptic activation of an Irf8 enhancer governs cDC1 fate specification. Nat Immunol. 2019 Sep;20(9):1161-1173. doi: 10.1038/s41590-019-0450-x. Epub 2019 Aug 12. PMID: 31406378; PMCID: PMC6707878.

Role: Conducted enteric infection experiments using animal model for this study.

Intestinal Macromolecular Transport Supporting Adaptive Immunity

Kulkarni DH, Newberry RD. Intestinal Macromolecular Transport Supporting Adaptive Immunity. Cell Mol Gastroenterol Hepatol. 2019;7(4):729-737. doi: 10.1016/j.jcmgh.2019.01.003. Epub 2019 Jan 30. PMID: 30710727; PMCID: PMC6463120.

Predicting Risk of Postoperative Disease Recurrence in Crohn's Disease: Patients With Indolent Crohn's Disease Have Distinct Whole Transcriptome Profiles at the Time of First Surgery

Cushing KC, Mclean R, McDonald KG, Gustafsson JK, Knoop KA, Kulkarni DH, Sartor RB, Newberry RD. Predicting Risk of Postoperative Disease Recurrence in Crohn’s Disease: Patients With Indolent Crohn’s Disease Have Distinct Whole Transcriptome Profiles at the Time of First Surgery. Inflamm Bowel Dis. 2019 Jan 1;25(1):180-193. doi: 10.1093/ibd/izy228. Erratum in: Inflamm Bowel Dis. 2019 Nov 14;25(12):e167. doi: 10.1093/ibd/izz145. PMID: 29982468; PMCID: PMC6354560.

Role: Conducted scientific input and assistance with data analysis.

Goblet cell associated antigen passages are inhibited during Salmonella typhimurium infection to prevent pathogen dissemination and limit responses to dietary antigens

Kulkarni DH, McDonald KG, Knoop KA, Gustafsson JK, Kozlowski KM, Hunstad DA, Miller MJ, Newberry RD. Goblet cell associated antigen passages are inhibited during Salmonella typhimurium infection to prevent pathogen dissemination and limit responses to dietary antigens. Mucosal Immunol. 2018 Jul;11(4):1103-1113. doi: 10.1038/s41385-018-0007-6. Epub 2018 Feb 14. PMID: 29445136; PMCID: PMC6037413.

Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria

Knoop KA, Gustafsson JK, McDonald KG, Kulkarni DH, Coughlin PE, McCrate S, Kim D, Hsieh CS, Hogan SP, Elson CO, Tarr PI, Newberry RD. Microbial antigen encounter during a preweaning interval is critical for tolerance to gut bacteria. Sci Immunol. 2017 Dec 15;2(18):eaao1314. doi: 10.1126/sciimmunol.aao1314. PMID: 29246946; PMCID: PMC5759965.

Role: Provided critical reagents for the study, data analysis and scientific input.

CCR6 promotes steady-state mononuclear phagocyte association with the intestinal epithelium, imprinting and immune surveillance

McDonald KG, Wheeler LW, McDole JR, Joerger S, Gustafsson JK, Kulkarni DH, Knoop KA, Williams IR, Miller MJ, Newberry RD. CCR6 promotes steady-state mononuclear phagocyte association with the intestinal epithelium, imprinting and immune surveillance. Immunology. 2017 Dec;152(4):613-627. doi: 10.1111/imm.12801. Epub 2017 Aug 30. PMID: 28746740; PMCID: PMC5680074.

Role: Conducted data analysis for the study and scientific input.

Yersinia pseudotuberculosis supports Th17 differentiation and limits de novo regulatory T cell induction by directly interfering with T cell receptor signaling

Pasztoi M, Bonifacius A, Pezoldt J, Kulkarni D, Niemz J, Yang J, Teich R, Hajek J, Pisano F, Rohde M, Dersch P, Huehn J. Yersinia pseudotuberculosis supports Th17 differentiation and limits de novo regulatory T cell induction by directly interfering with T cell receptor signaling. Cell Mol Life Sci. 2017 Aug;74(15):2839-2850. doi: 10.1007/s00018-017-2516-y. Epub 2017 Apr 4. PMID: 28378044; PMCID: PMC5491567.

Role: Conducted critical in vivo experiments in animal model of enteric infection. Data analysis and assisted with writing the manuscript.

Antibiotics promote the sampling of luminal antigens and bacteria via colonic goblet cell associated antigen passages

Knoop KA, Gustafsson JK, McDonald KG, Kulkarni DH, Kassel R, Newberry RD. Antibiotics promote the sampling of luminal antigens and bacteria via colonic goblet cell associated antigen passages. Gut Microbes. 2017 Jul 4;8(4):400-411. doi: 10.1080/19490976.2017.1299846. Epub 2017 Mar 7. Erratum for: Addendum to: KA Knoop, KG McDonald, DH Kulkarni, RD Newberry.. Antibiotics promote inflammation through the translocation of native commensal colonic bacteria. Gut 2016; 65:1100-9. PMID: 28267403; PMCID: PMC5570560.

Role: Conducted data analysis for the study and scientific input.

Antibiotics promote inflammation through the translocation of native commensal colonic bacteria

Knoop KA, McDonald KG, Kulkarni DH, Newberry RD. Antibiotics promote inflammation through the translocation of native commensal colonic bacteria. Gut. 2016 Jul;65(7):1100-9. doi: 10.1136/gutjnl-2014-309059. Epub 2015 Jun 4. PMID: 26045138; PMCID: PMC4670297.

Role: Performed data analysis and provided critical scientific inputs.

The intestinal micro-environment imprints stromal cells to promote efficient Treg induction in gut-draining lymph nodes

Cording S, Wahl B, Kulkarni D, Chopra H, Pezoldt J, Buettner M, Dummer A, Hadis U, Heimesaat M, Bereswill S, Falk C, Bode U, Hamann A, Fleissner D, Huehn J, Pabst O. The intestinal micro-environment imprints stromal cells to promote efficient Treg induction in gut-draining lymph nodes. Mucosal Immunol. 2014 Mar;7(2):359-68. doi: 10.1038/mi.2013.54. Epub 2013 Aug 14. PMID: 23945546.

Role: Conducted experiments with lymph node transplants to determine the role of dietary and microbial factors contributing to establishment of immune tolerance.

The cytotoxic necrotizing factor of Yersinia pseudotuberculosis (CNFY) enhances inflammation and Yop delivery during infection by activation of Rho GTPases

Schweer J, Kulkarni D, Kochut A, Pezoldt J, Pisano F, Pils MC, Genth H, Huehn J, Dersch P. The cytotoxic necrotizing factor of Yersinia pseudotuberculosis (CNFY) enhances inflammation and Yop delivery during infection by activation of Rho GTPases. PLoS Pathog. 2013;9(11):e1003746. doi: 10.1371/journal.ppat.1003746. Epub 2013 Nov 7. PMID: 24244167; PMCID: PMC3820761.

Effects of a germ-free environment on gut immune regulation and diabetes progression in non-obese diabetic (NOD) mice

Alam C, Bittoun E, Bhagwat D, Valkonen S, Saari A, Jaakkola U, Eerola E, Huovinen P, Hänninen A. Effects of a germ-free environment on gut immune regulation and diabetes progression in non-obese diabetic (NOD) mice. Diabetologia. 2011 Jun;54(6):1398-406. doi: 10.1007/s00125-011-2097-5. Epub 2011 Mar 5. PMID: 21380595.

Role: Conducted flow cytometry based analysis of intestinal immune cells from germ free mice on non-obese diabetic background.