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Lin-Feng Chen

Profile picture for Lin-Feng Chen

Contact Information

Department of Biochemistry
University of Illinois
600 S Mathews Ave
Urbana, IL 61801

Professor of Biochemistry

Research Interests

Research Topics

Chromatin Structure, Host-Pathogen Interactions, Metabolic Regulation, Molecular Immunology, Regulation of Gene Expression, Signal Transduction

Disease Research Interests

Cancer, Infectious Diseases, Metabolic Disorders/Diabetes

Research Description

Epigenetic regulation of NF-κB in immunity and cancer; NF-κB signaling and H. pylori-mediated gastric disease; Role of Brd4 in innate immune response and diseases.

I. Epigenetic regulation of NF-κB in immunity and cancer

The eukaryotic transcription factor NF-κB regulates a wide range of host genes that govern the inflammatory and immune responses in mammals. The NF-κB signaling pathway controls multiple key cellular processes, including programmed cell death, cell proliferation, and differentiation. NF-κB is activated by a variety of chemokines, bacteria, viruses and their products via distinct signal transduction pathways mediated by different receptors, including TNF-α receptors, Toll-like receptors, and antigen-specific T- and B-cell receptors. The long-term goals of this laboratory are to determine how the NF-κB transcription factor complex is regulated at the molecular level and to elucidate the roles of NF-κB in inflammation, apoptosis, and tumorigenesis. In particular, we are interested in dissecting how different stimuli converge to activate NF-κB under normal and pathological conditions using a combination of biochemical, molecular, cellular, and genetic approaches.

Currently, we are interested in the role of post-translational modifications of NF-κB and histones in the regulation of NF-κB signaling pathway.

Post-translational modifications and NF-κB activation While it is clear that post-translational modifications, including phosphorylation and acetylation, play critical roles in shaping the nuclear function of NF-κB, many unanswered questions remain. For example, how do these modifications regulate NF-κB in vivo? Do they contribute significantly to the NF-κBs proinflammatory or anti-apoptotic functions? Is there a "transcription factor code" generated by acetylation, phosphorylation, and other modifications? If so, does it mediate the selection of specific target genes or control the strength and duration of the nuclear action of NF-κB? Answering these questions would advance our understanding of how NF-κB is regulated and could also provide exciting new therapeutic options for manipulating NF-κB action in cancer or inflammation.

Chromatin remodeling and NF-κB activationTo increase the accessibility of the cell’s transcription and replication machinery to promoters, chromatin remodeling must occur. For example, the conformation of chromatin is altered by chromatin remodeling complexes and the N-terminal tails of histones are modified by enzymes, including histone acetyltransferases and deacetylases, kinases, and methyl transferases. These enzymes play important roles in regulation of gene expression by modifying the histones and thus controlling the accessibility of chromatin by accessory regulator factors. Several of these enzymes interact with NF-κB and regulate NF-κB-dependent transactivation. However, it remains largely unknown whether and how chromatin remodeling mediates NF-κB target gene selection. How are these enzymes regulated in the NF-κB signaling pathway? Using different approaches including chromatin immunoprecipitation assays, we will identify the enzymes that are recruited to different NF-κB target genes in a stimulus-specific manner and determine how these recruitments are regulated.

II. NF-κB signaling and H. pylori-mediated gastric disease

Infection with Helicobacter pylori causes gastritis and peptic ulceration and is the strongest risk factor for the development of gastric cancer, the second leading cause of cancer-related death worldwide. The mechanisms involved in the bacterium’s ability to induce gastric cancer are believed to be linked to infection-associated chronic gastritis, which is characterized by increased expression of multiple inflammatory genes. Virulence factor CagA of H. pylori is critical for the infection-initiated inflammation. The transcription factor NF-κB plays a key role in regulating the immune and inflammatory response. Transcriptional activation of NF-κB relies on the proximal cytoplasmic events leading to the activation of IKKs and a series of nuclear events in which NF-κB is post-translationally modified. NF-κB is activated by H. pylori infection in a CagA-dependent manner and is responsible for H. pylori-associated gastritis. However, the mechanism by which H. pylori utilizes its CagA to activate NF-κB and to promote inflammation-associated gastritis and gastric cancer is not clear.

Recently, we demonstrate that CagA physically associates with TAK1 (TGF-β activated kinase 1) and enhances the activity of TAK1 and TAK1-induced NF-κB activation via the TRAF6-mediated K63-linked ubiquitination of TAK1. These findings reveal that polyubiquitination of TAK1 regulates the activation of NF-κB and is utilized by H. pylori CagA for the H. pylori-induced inflammatory response.

III. Regulation and function of Brd4 in cancer and immunity

Brd4 has emerged as an important factor in regulating many biological processes, including cell cycle, inflammatory response, metabolism and tumorigenesis. We have recently identified bromodomain-containing factor Brd4 as a key regulator of NF-κB-mediated inflammatory response and cancer development. We have also demonstrated that small molecules inhibiting Brd4 possess strong anti-tumor and anti-inflammatory activities in cultured cells and in mouse models (Zou et al, Oncogene, 2014;Chen et al, J. Immunology, 2016). However, the regulation of Brd4 and its pathophysiological functions remain largely unknown. We are investigating on how Brd4 is regulated in cancer cells and how Brd4 regulates the innate immune response using Brd4 knockout animals. These studies will provide insights into the regulation of Brd4 and whether Brd4 represents a novel therapeutic target for the treatment of cancer and inflammtory diseases.


B.S. 1987 Xiamen University, China
M.S. 1990 Peking Union Medical University
Ph.D. 1999 Kyoto University, Japan
Postdoc. 1999-2003 Gladstone Institute of Immunology and Virology, University of California, San Francisco

Additional Campus Affiliations

Highlighted Publications

Representative Publications

Modi N, Chen YH, DongXC, Hu XM, Lau GW, Wilson KT, Peek RM and Chen LF,2023. BRD4 regulates glycolysis-dependent Nos2 expression in macrophages upon H. pylori infection. Cellular and Molecular Gastroenterology and Hepatology.[in press]

Dong XC and Chen LF, 2021. Protocol for measuring NLRC4 inflammasome activation and pyroptosis in murine bone-marrow-derived macrophages. STAR Protocols. [Abstract]

Hu XM, Dong XC, Li G, Chen J, He X, Sun H, Kim DH, Kemper JK, Chen LF. 2021. Brd4 modulates diet-induced obesity via PPARγ-dependent Gdf3 expression in adipose tissue macrophages. JCI Insight .6:e143379. [Abstract]

Dong XC, Hu XM, Bao Y, Li G, Yang XD, Slauch JM and Chen LF, 2021. Brd4 regulates NLRC4 inflammasome activation by facilitating IRF8-mediated transcription of Naips. JCB. 220:e202005148 [Abstract]

Jung H, Chen J, Hu X, Sun H, Wu S, Chiang C, Kemper B, Chen LF * and Kemper, JK*. 2020. BRD4 inhibition and FXR activation, individually beneficial in cholestasis, are antagonistic in combination. JCI Insight 6:e141640 [Abstract] (*corresponding author)

Chen YH, Sheppard D, Dong XC, Hu XM, Chen MH, Chen RC, Chakrabarti J, Zavros Y, Peek RM, and Chen LF. 2020. H. pylori infection confers resistance to apoptosis via Brd4-dependent BIRC3 eRNA synthesis. Cell Death & Disease 11:667 [Abstract]

Yang XD, Li WG, Zhang S, Wu D, Jiang XL, Tan R, Niu XY, Wang Q, Wu XF, Liu ZD, Chen LF, Qin J, Su B. 2019. PLK4 deubiquitination by Spata2-CYLD suppresses NEK7-mediated NLRP3 inflammasome activation at the centrosome. EMBO J. 39:e102201 [Abstract]

Dong XC, Hu XM, Chen J, Hu D and Chen LF. 2018. BRD4 regulates cellular senescence in gastric cancer cells via E2F/miR-106b/p21 axis. Cell Death & Disease 9:203

Xiong MH, Bao Y,, Xu X, Wang H, Han Z, Wang Z, Liu YY, Huang SY, Song ZY, Chen J, Peek RM, Yin LC,Chen LF*, and Cheng JJ*. 2017. Selective killing of Helicobacter pylori with pH-responsive helix–coil conformation transitionable antimicrobial polypeptides Proc. Natl. Acad. Sci. U.S.A. 114:12675-12680 (*corresponding author)

Hu XM, Dong SH, Chen J, Zhou XZ, Chen R, Lu KP, Chen LF. 2017. Prolyl isomerase Pin1 regulates the stability, transcriptional activity and oncogenic potential of Brd4. Oncogene 36:5177-5188

Bao Y, Wu XW, Chen JJ, Hu XM, Zeng FX, Cheng JJ, Jin H, Lin X and Chen LF. 2017. Brd4 modulates the innate immune response through Mnk2-eIF4E pathway-dependent translational control of IκBα. Proc. Natl. Acad. Sci. U.S.A. 114:E3993-E4001

Chen JJ, Wang Z, Hu, XM, Chen R, Romero-Gallo J, Perk RM. and Chen LF. 2016. BET inhibition Attenuates H. pylori-induced Inflammatory Response by Suppressing Inflammatory Gene Transcription and Enhancer Activation. J. Immunology 196:4132-42

Zou ZH, Huang B, Wu XW, Zhang HJ, Qi J, Bradner J, Nair S and Chen LF. 2014. Brd4 maintains constitutively active NF-κB in cancer cells by binding to acetylated RelA. Oncogene. 33:2395-404

Tsang YH, Lamb A, Romero-Gallo J, Huang B, Ito K, Peek RM, Ito Y and Chen LF. 2010. Helicobacter pylori CagA targets gastric tumor suppressor RUNX3 for proteasome-mediated degradation. Oncogene 29:5643-50

Yang XD, Tajkhorshid E., Chen LF. 2010. "Functional interplay between acetylation and methylation of the RelA subunit of NF-κB." Mol. Cell. Biol. 30:2170-2180 [Abstract]

Lamb A, Yang XD, Tsang YH, Li JD, Higashi H, Hatakeyama M, Peek RM, Blanke SR, Chen LF. 2009. "Helicobacter pylori CagA activates NF-κB by inducing TRAF6-mediated K63-ubiquitination of TAK1." EMBO Report 10:1242-1249 [Abstract]

Yang XD, Huang B, Li MX, Lamb A, Kelleher NL, Chen LF. 2009. "Negative regulation of NF-κB action by Set9-mediated lysine methylation of RelA subunit." EMBO J. 28:1055-1066 [Abstract]

Huang B, Yang XD, Zhou MM, Ozato K, Chen LF. 2009. "Brd4 coactivates transcriptional activation of NF-κB via specific binding to acetylated RelA." Mol. Cell. Biol. 29(5):1375-87 [Abstract]

Ishinaga H., Jono H., Lim J.H., Kweon S.M., Xu H., Ha U.H., Xu H., Koga T., Yan C., Feng X.H., Chen LF.*, Li J.D.*. 2007. "TGF-β induces p65 acetylation to enhance bacteria-induced NF-κB activation." EMBO J. 26:1150-1162 (*corresponding author). [Abstract]

Chen L.F.*, Williams S., Mu Y., Nakano H., Duerr J.M., Buckbinder L., and Greene W.C.*. 2005. "RelA phosphorylation regulates RelA acetylation." Mol. Cell. Biol. 25:7966-7975 (*corresponding author) [Abstract]

Chen, L.-F. and Greene, W.C. (2004) "Shaping the nuclear action of NF-κB," Nat. Rev. Mol. Cell. Biol. 5:302–401. [Abstract]

Chen, L.-F., Mu, Y., and Greene, W.C. (2002) "Acetylation of RelA at discrete sites regulates distinct nuclear functions of NF-κB," EMBO J. 21:6539–6548. [Abstract]

Chen, L.-F., Fischle, W., Verdin, E., and Greene, W.C. (2001) "Duration of nuclear NF-κB action regulated by reversible acetylation," Science 293:1653–1657. [Abstract]

Recent Publications

Modi, N., Chen, Y., Dong, X., Hu, X., Lau, G. W., Wilson, K. T., Peek, R. M., & Chen, L. F. (2024). BRD4 Regulates Glycolysis-Dependent Nos2 Expression in Macrophages Upon H pylori Infection. CMGH, 17(2), 292-308.e1.

Zhao, X., Lin, S., Ren, H., Sun, S., Zheng, L., Chen, L. F., & Wang, Z. (2024). The histone methyltransferase ASH1L protects against bone loss by inhibiting osteoclastogenesis. Cell Death and Differentiation, 31(5), 605-617.

Toska, A., Modi, N., & Chen, L.-F. (2023). RUNX3 Meets the Ubiquitin-Proteasome System in Cancer. Cells, 12(5), Article 717.

Chen, L.-F., Cheng, J., Xiong, M., & Bao, Y. (2022). Conformation switchable antimicrobial peptides and methods of using the same. (U.S. Patent No. 11225507).

Zhou, K., Zhuang, S., Liu, F., Chen, Y., Li, Y., Wang, S., Li, Y., Wen, H., Lin, X., Wang, J., Huang, Y., He, C., Xu, N., Li, Z., Xu, L., Zhang, Z., Chen, L. F., Chen, R., & Liu, M. (2022). Disrupting the Cdk9/Cyclin T1 heterodimer of 7SK snRNP for the Brd4 and AFF1/4 guided reconstitution of active P-TEFb. Nucleic acids research, 50(2), 750-762.

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