Troutman Lab Publications

1.

Weinhaus, B., Homan, S., Kincaid, M., Tadwalkar, A., Gu, X., Kumar, S., Slaughter, A., Zhang, J., Wu, Q., Kofron, J. M., Troutman, T. D., DeFalco, T. & Lucas, D. Differential regulation of fetal bone marrow and liver hematopoiesis by yolk-sac-derived myeloid cells. Nat Commun 16, 4427 (2025).

2.

Felton, J. M., Edsall, L. E., Troutman, T. D., Mack, L., Kotliar, M., Morgenstern, N. B.-B., Psaila, A. M., Rochman, M., Klingler, A. M., Osswald, G. A., Zhang, S., Dunn, J. L. M., Wronowski, B., Shoda, T., Caldwell, J. M., Herro, R., Barski, A., Quinlan, K. G. R., Weirauch, M. T. & Rothenberg, M. E. Epigenetic and transcriptional programming of murine eosinophils in the esophagus. Nature Communications 16, (2025).

3.

Proper, S. P., Dwyer, A. T., Appiagyei, A., Felton, J. M., Ben-Baruch Morgenstern, N., Marlman, J. M., Kotliar, M., Barski, A., Troutman, T. D., Rothenberg, M. E., Mersha, T. B. & Azouz, N. P. Aryl hydrocarbon receptor and IL-13 signaling crosstalk in human keratinocytes and atopic dermatitis. Front Allergy 5, 1323405 (2024).

4.

Ganguly, S., Rosenthal, S. B., Ishizuka, K., Troutman, T. D., Rohm, T. V., Khader, N., Aleman-Muench, G., Sano, Y., Archilei, S., Soroosh, P., Olefsky, J. M., Feldstein, A. E., Kisseleva, T., Loomba, R., Glass, C. K., Brenner, D. A. & Dhar, D. Lipid-associated macrophages’ promotion of fibrosis resolution during MASH regression requires TREM2. Proc Natl Acad Sci U S A 121, e2405746121 (2024).

5.

Dunn, J. L. M., Szep, A., Gonzalez Galan, E., Zhang, S., Marlman, J., Caldwell, J., Troutman, T. D. & Rothenberg, M. E. Eosinophil specialization is regulated by exposure to the esophageal epithelial microenvironment. J Leukoc Biol https://doi.org/10.1093/jleuko/qiae102 (2024) doi:10.1093/jleuko/qiae102.

6.

Abe, Y., Kofman, E. R., Ouyang, Z., Cruz-Becerra, G., Spann, N. J., Seidman, J. S., Troutman, T. D., Stender, J. D., Taylor, H., Fan, W., Link, V. M., Shen, Z., Sakai, J., Downes, M., Evans, R. M., Kadonaga, J. T., Rosenfeld, M. G. & Glass, C. K. A TLR4/TRAF6-dependent signaling pathway mediates NCoR coactivator complex formation for inflammatory gene activation. Proc Natl Acad Sci U S A 121, e2316104121 (2024).

7.

Underwood, B., Troutman, T. D. & Schwartz, J. T. Breaking down the complex pathophysiology of eosinophilic esophagitis. Ann Allergy Asthma Immunol 130, 28–39 (2023).

8.

Shao, T. Y., Jiang, T. T., Stevens, J., Russi, A. E., Troutman, T. D., Bernieh, A., Pham, G., Erickson, J. J., Eshleman, E. M., Alenghat, T., Jameson, S. C., Hogquist, K. A., Weaver, C. T., Haslam, D. B., Deshmukh, H. & Way, S. S. Kruppel-like factor 2+ CD4 t cells avert microbiota-induced intestinal inflammation. Cell Rep 42, 113323 (2023).

9.

Proper, S. P., Dwyer, A. T., Appiagyei, A., Felton, J. M., Morgenstern, N. B.-B., Marlman, J. M., Kotliar, M., Barski, A., Troutman, T. D., Rothenberg, M. E., Mersha, T. B. & Azouz, N. P. Aryl hydrocarbon receptor (AHR) and IL-13 signaling crosstalk in human keratinocytes and atopic dermatitis. bioRxiv https://doi.org/10.1101/2023.06.17.545291 (2023) doi:10.1101/2023.06.17.545291.

10.

Bennett, H., Troutman, T. D., Zhou, E., Spann, N. J., Link, V. M., Seidman, J. S., Nickl, C. K., Abe, Y., Sakai, M., Pasillas, M. P., Marlman, J. M., Guzman, C., Hosseini, M., Schnabl, B. & Glass, C. K. Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on kupffer cell epigenomes and transcriptomes. Nat Immunol 24, 1825–1838 (2023).

11.

Arimoto, K. I., Miyauchi, S., Troutman, T. D., Zhang, Y., Liu, M., Stoner, S. A., Davis, A. G., Fan, J. B., Huang, Y. J., Yan, M., Glass, C. K. & Zhang, D. E. Expansion of interferon inducible gene pool via USP18 inhibition promotes cancer cell pyroptosis. Nat Commun 14, 251 (2023).

12.

Gene-by-environment regulation of kupffer cell transcriptomes and epigenomes. Nat Immunol 24, 1797–1798 (2023).

13.

Bennett, H., Troutman, T. D., Zhou, E., Spann, N. J., Link, V. M., Seidman, J. S., Nickl, C. K., Abe, Y., Sakai, M., Pasillas, M. P., Marlman, J. M., Guzman, C., Hosseini, M., Schnabl, B. & Glass, C. K. Systematic analysis of transcriptional and epigenetic effects of genetic variation in kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms. bioRxiv 2022.09.22.509046 (2022) doi:10.1101/2022.09.22.509046.

14.

Troutman, T. D., Kofman, E. & Glass, C. K. Exploiting dynamic enhancer landscapes to decode macrophage and microglia phenotypes in health and disease. Mol Cell 81, 3888–3903 (2021).

15.

Troutman, T. D., Bennett, H., Sakai, M., Seidman, J. S., Heinz, S. & Glass, C. K. Purification of mouse hepatic non-parenchymal cells or nuclei for use in ChIP-seq and other next-generation sequencing approaches. STAR Protoc 2, 100363 (2021).

16.

Texari, L., Spann, N. J., Troutman, T. D., Sakai, M., Seidman, J. S. & Heinz, S. An optimized protocol for rapid, sensitive and robust on-bead ChIP-seq from primary cells. STAR Protoc 2, 100358 (2021).

17.

Rosenthal, S. B., Liu, X., Ganguly, S., Dhar, D., Pasillas, M. P., Ricciardelli, E., Li, R. Z., Troutman, T. D., Kisseleva, T., Glass, C. K. & Brenner, D. A. Heterogeneity of HSCs in a mouse model of NASH. Hepatology 74, 667–685 (2021).

18.

Sun, X., Seidman, J. S., Zhao, P., Troutman, T. D., Spann, N. J., Que, X., Zhou, F., Liao, Z., Pasillas, M., Yang, X., Magida, J. A., Kisseleva, T., Brenner, D. A., Downes, M., Evans, R. M., Saltiel, A. R., Tsimikas, S., Glass, C. K. & Witztum, J. L. Neutralization of oxidized phospholipids ameliorates non-alcoholic steatohepatitis. Cell Metab 31, 189–206 e8 (2020).

19.

Seidman, J. S., Troutman, T. D., Sakai, M., Gola, A., Spann, N. J., Bennett, H., Bruni, C. M., Ouyang, Z., Li, R. Z., Sun, X., Vu, B. T., Pasillas, M. P., Ego, K. M., Gosselin, D., Link, V. M., Chong, L. W., Evans, R. M., Thompson, B. M., McDonald, J. G., Hosseini, M., Witztum, J. L., Germain, R. N. & Glass, C. K. Niche-specific reprogramming of epigenetic landscapes drives myeloid cell diversity in nonalcoholic steatohepatitis. Immunity 52, 1057–1074 e7 (2020).

20.

Irizarry-Caro, R. A., McDaniel, M. M., Overcast, G. R., Jain, V. G., Troutman, T. D. & Pasare, C. TLR signaling adapter BCAP regulates inflammatory to reparatory macrophage transition by promoting histone lactylation. Proc Natl Acad Sci U S A 117, 30628–30638 (2020).

21.

Bennett, H., Troutman, T. D., Sakai, M. & Glass, C. K. Epigenetic regulation of kupffer cell function in health and disease. Front Immunol 11, 609618 (2020).

22.

Sakai, M., Troutman, T. D., Seidman, J. S., Ouyang, Z., Spann, N. J., Abe, Y., Ego, K. M., Bruni, C. M., Deng, Z., Schlachetzki, J. C. M., Nott, A., Bennett, H., Chang, J., Vu, B. T., Pasillas, M. P., Link, V. M., Texari, L., Heinz, S., Thompson, B. M., McDonald, J. G., Geissmann, F. & Glass, C. K. Liver-derived signals sequentially reprogram myeloid enhancers to initiate and maintain kupffer cell identity. Immunity 51, 655–670 e8 (2019).

23.

Moore, S. M., Seidman, J. S., Ellegood, J., Gao, R., Savchenko, A., Troutman, T. D., Abe, Y., Stender, J., Lee, D., Wang, S., Voytek, B., Lerch, J. P., Suh, H., Glass, C. K. & Muotri, A. R. Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice. Transl Psychiatry 9, 24 (2019).

24.

Allan, C. M., Heizer, P. J., Tu, Y., Sandoval, N. P., Jung, R. S., Morales, J. E., Sajti, E., Troutman, T. D., Saunders, T. L., Cusanovich, D. A., Beigneux, A. P., Romanoski, C. E., Fong, L. G. & Young, S. G. An upstream enhancer regulates Gpihbp1 expression in a tissue-specific manner. J Lipid Res 60, 869–879 (2019).

25.

Muse, E. D., Yu, S., Edillor, C. R., Tao, J., Spann, N. J., Troutman, T. D., Seidman, J. S., Henke, A., Roland, J. T., Ozeki, K. A., Thompson, B. M., McDonald, J. G., Bahadorani, J., Tsimikas, S., Grossman, T. R., Tremblay, M. S. & Glass, C. K. Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP in macrophages. Proc Natl Acad Sci U S A 115, E4680–E4689 (2018).

26.

Link, V. M., Duttke, S. H., Chun, H. B., Holtman, I. R., Westin, E., Hoeksema, M. A., Abe, Y., Skola, D., Romanoski, C. E., Tao, J., Fonseca, G. J., Troutman, T. D., Spann, N. J., Strid, T., Sakai, M., Yu, M., Hu, R., Fang, R., Metzler, D., Ren, B. & Glass, C. K. Analysis of genetically diverse macrophages reveals local and domain-wide mechanisms that control transcription factor binding and function. Cell 173, 1796–1809 e17 (2018).

27.

Deason, K., Troutman, T. D., Jain, A., Challa, D. K., Mandraju, R., Brewer, T., Ward, E. S. & Pasare, C. BCAP links IL-1R to the PI3K-mTOR pathway and regulates pathogenic Th17 cell differentiation. J Exp Med 215, 2413–2428 (2018).

28.

Eichenfield, D. Z., Troutman, T. D., Link, V. M., Lam, M. T., Cho, H., Gosselin, D., Spann, N. J., Lesch, H. P., Tao, J., Muto, J., Gallo, R. L., Evans, R. M. & Glass, C. K. Tissue damage drives co-localization of NF-kappaB, Smad3, and Nrf2 to direct rev-erb sensitive wound repair in mouse macrophages. Elife 5, (2016).

29.

Allison, K. A., Sajti, E., Collier, J. G., Gosselin, D., Troutman, T. D., Stone, E. L., Hedrick, S. M. & Glass, C. K. Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ t cells. Elife 5, (2016).

30.

Lin, K. M., Hu, W., Troutman, T. D., Jennings, M., Brewer, T., Li, X., Nanda, S., Cohen, P., Thomas, J. A. & Pasare, C. IRAK-1 bypasses priming and directly links TLRs to rapid NLRP3 inflammasome activation. Proc Natl Acad Sci U S A 111, 775–80 (2014).

31.

Furlan, S. N., Mandraju, R., Brewer, T., Roybal, K., Troutman, T. D., Hu, W., Palm, N. W., Unni, A. & Pasare, C. Enhancement of anti-tumor CD8 immunity by IgG1-mediated targeting of fc receptors. MAbs 6, 108–18 (2014).

32.

Troutman, T. D., Hu, W., Fulenchek, S., Yamazaki, T., Kurosaki, T., Bazan, J. F. & Pasare, C. Role for b-cell adapter for PI3K (BCAP) as a signaling adapter linking toll-like receptors (TLRs) to serine/threonine kinases PI3K/akt. Proc Natl Acad Sci U S A 109, 273–8 (2012).

33.

Troutman, T. D., Bazan, J. F. & Pasare, C. Toll-like receptors, signaling adapters and regulation of the pro-inflammatory response by PI3K. Cell Cycle 11, 3559–67 (2012).

34.

Murthy, A. K., Chaganty, B. K., Troutman, T., Guentzel, M. N., Yu, J. J., Ali, S. K., Lauriano, C. M., Chambers, J. P., Klose, K. E. & Arulanandam, B. P. Mannose-containing oligosaccharides of non-specific human secretory immunoglobulin a mediate inhibition of vibrio cholerae biofilm formation. PLoS One 6, e16847 (2011).

35.

Hu, W., Troutman, T. D., Edukulla, R. & Pasare, C. Priming microenvironments dictate cytokine requirements for t helper 17 cell lineage commitment. Immunity 35, 1010–22 (2011).