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Xiang Y, Liu S, Wan S, Chen Q, Song Y, Feng G, Zhang X, Bai L, Zhu Y. Interleukin-1 increases SERPINE1 expression in human granulosa-lutein cell via P50/P52 signaling pathways. Mol Cell Endocrinol 2024; 591:112274. [PMID: 38777211 DOI: 10.1016/j.mce.2024.112274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
It has been reported that immune factors are associated with the occurrence of polycystic ovary syndrome (PCOS). Interleukin-1 (IL-1) is a member of the interleukin family that widely participates in the regulation of the inflammatory response in the immune system. In addition, it has been reported that aberrant IL-1 accumulation in serum is associated with the occurrence of PCOS. However, little is known about how IL-1 participates in the pathogenesis of PCOS. In the present study, we demonstrated that the immune microenvironment was altered in follicular fluid from PCOS patients and that the expression levels of two IL-1 cytokines, IL-1α and IL-1β were increased. Transcriptome analysis revealed that IL-1α and IL-1β treatment induced primary human granulosa-lutein (hGL) cell inflammatory response and increased the expression of serpin family E member 1 (SERPINE1). Mechanistically, we demonstrated that IL-1α and IL-1β upregulated SERPINE1 expression through IL-1R1-mediated activation of downstream P50 and P52 signaling pathways in human granulosa cells. Our study highlighted the role of immune state changes in the occurrence of PCOS and provided new insight into the treatment of patients with IL-1-induced ovarian function disorders.
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Affiliation(s)
- Yu Xiang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Shuangying Liu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Shan Wan
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Qingqing Chen
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Yang Song
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Guofang Feng
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Xinyue Zhang
- Center for Reproductive Medicine, The First Hospital of Jilin University, Changchun, Jilin, 130015, China
| | - Long Bai
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China.
| | - Yimin Zhu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Zhejiang Key Laboratory of Maternal and Infant Health, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China.
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Li RZ, Han CZ, Glass CK. TIANA: transcription factors cooperativity inference analysis with neural attention. BMC Bioinformatics 2024; 25:274. [PMID: 39174927 PMCID: PMC11342676 DOI: 10.1186/s12859-024-05852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 07/01/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Growing evidence suggests that distal regulatory elements are essential for cellular function and states. The sequences within these distal elements, especially motifs for transcription factor binding, provide critical information about the underlying regulatory programs. However, cooperativities between transcription factors that recognize these motifs are nonlinear and multiplexed, rendering traditional modeling methods insufficient to capture the underlying mechanisms. Recent development of attention mechanism, which exhibit superior performance in capturing dependencies across input sequences, makes them well-suited to uncover and decipher intricate dependencies between regulatory elements. RESULT We present Transcription factors cooperativity Inference Analysis with Neural Attention (TIANA), a deep learning framework that focuses on interpretability. In this study, we demonstrated that TIANA could discover biologically relevant insights into co-occurring pairs of transcription factor motifs. Compared with existing tools, TIANA showed superior interpretability and robust performance in identifying putative transcription factor cooperativities from co-occurring motifs. CONCLUSION Our results suggest that TIANA can be an effective tool to decipher transcription factor cooperativities from distal sequence data. TIANA can be accessed through: https://github.com/rzzli/TIANA .
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Affiliation(s)
- Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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3
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An W, Lakhina S, Leong J, Rawat K, Husain M. Host Innate Antiviral Response to Influenza A Virus Infection: From Viral Sensing to Antagonism and Escape. Pathogens 2024; 13:561. [PMID: 39057788 PMCID: PMC11280125 DOI: 10.3390/pathogens13070561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Influenza virus possesses an RNA genome of single-stranded, negative-sensed, and segmented configuration. Influenza virus causes an acute respiratory disease, commonly known as the "flu" in humans. In some individuals, flu can lead to pneumonia and acute respiratory distress syndrome. Influenza A virus (IAV) is the most significant because it causes recurring seasonal epidemics, occasional pandemics, and zoonotic outbreaks in human populations, globally. The host innate immune response to IAV infection plays a critical role in sensing, preventing, and clearing the infection as well as in flu disease pathology. Host cells sense IAV infection through multiple receptors and mechanisms, which culminate in the induction of a concerted innate antiviral response and the creation of an antiviral state, which inhibits and clears the infection from host cells. However, IAV antagonizes and escapes many steps of the innate antiviral response by different mechanisms. Herein, we review those host and viral mechanisms. This review covers most aspects of the host innate immune response, i.e., (1) the sensing of incoming virus particles, (2) the activation of downstream innate antiviral signaling pathways, (3) the expression of interferon-stimulated genes, (4) and viral antagonism and escape.
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Affiliation(s)
| | | | | | | | - Matloob Husain
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.A.); (S.L.); (J.L.); (K.R.)
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4
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Wu W, Arunagiri V, Do-Umehara HC, Chen C, Gu S, Biswas I, Ridge KM, Budinger GRS, Liu S, Liu J. Miz1 represses type I interferon production and limits viral clearance during influenza A virus infection. Sci Signal 2024; 17:eadg7867. [PMID: 38593156 PMCID: PMC11182629 DOI: 10.1126/scisignal.adg7867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Type I interferons (IFNs) are critical for the antiviral immune response, and fine-tuning type I IFN production is critical to effectively clearing viruses without causing harmful immunopathology. We showed that the transcription factor Miz1 epigenetically repressed the expression of genes encoding type I IFNs in mouse lung epithelial cells by recruiting histone deacetylase 1 (HDAC1) to the promoters of Ifna and Ifnb. Loss of function of Miz1 resulted in augmented production of these type I IFNs during influenza A virus (IAV) infection, leading to improved viral clearance in vitro and in vivo. IAV infection induced Miz1 accumulation by promoting the cullin-4B (CUL4B)-mediated ubiquitylation and degradation of the E3 ubiquitin ligase Mule (Mcl-1 ubiquitin ligase E3; also known as Huwe1 or Arf-BP1), which targets Miz1 for degradation. As a result, Miz1 accumulation limited type I IFN production and favored viral replication. This study reveals a previously unrecognized function of Miz1 in regulating antiviral defense and a potential mechanism for influenza viruses to evade host immune defense.
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Affiliation(s)
- Wenjiao Wu
- Department of Surgery, College of Medicine; Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Pharmacy, Guangdong Second Provincial General Hospital, 466 Middle Xingang Road, Guangzhou, 510317, Guangdong, China
| | - Vinothini Arunagiri
- Department of Surgery, College of Medicine; Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hanh Chi Do-Umehara
- Department of Surgery, College of Medicine; Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Cong Chen
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shuyin Gu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Indrani Biswas
- Department of Surgery, College of Medicine; Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Karen M. Ridge
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - G. R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Jing Liu
- Department of Surgery, College of Medicine; Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
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5
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Wiggins DA, Maxwell JN, Nelson DE. Exploring the role of CITED transcriptional regulators in the control of macrophage polarization. Front Immunol 2024; 15:1365718. [PMID: 38646545 PMCID: PMC11032013 DOI: 10.3389/fimmu.2024.1365718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Macrophages are tissue resident innate phagocytic cells that take on contrasting phenotypes, or polarization states, in response to the changing combination of microbial and cytokine signals at sites of infection. During the opening stages of an infection, macrophages adopt the proinflammatory, highly antimicrobial M1 state, later shifting to an anti-inflammatory, pro-tissue repair M2 state as the infection resolves. The changes in gene expression underlying these transitions are primarily governed by nuclear factor kappaB (NF-κB), Janus kinase (JAK)/signal transducer and activation of transcription (STAT), and hypoxia-inducible factor 1 (HIF1) transcription factors, the activity of which must be carefully controlled to ensure an effective yet spatially and temporally restricted inflammatory response. While much of this control is provided by pathway-specific feedback loops, recent work has shown that the transcriptional co-regulators of the CBP/p300-interacting transactivator with glutamic acid/aspartic acid-rich carboxy-terminal domain (CITED) family serve as common controllers for these pathways. In this review, we describe how CITED proteins regulate polarization-associated gene expression changes by controlling the ability of transcription factors to form chromatin complexes with the histone acetyltransferase, CBP/p300. We will also cover how differences in the interactions between CITED1 and 2 with CBP/p300 drive their contrasting effects on pro-inflammatory gene expression.
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Affiliation(s)
| | | | - David E. Nelson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
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6
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Che B, Sun D, Zhang C, Hou J, Zhao W, Jing G, Mu Y, Cao Y, Dai L, Zhang C. Gradient Nanoconfinement Facilitates Binding of Transcriptional Factor NF-κB to Histone- and Protamine-DNA Complexes. NANO LETTERS 2023; 23:2388-2396. [PMID: 36857512 DOI: 10.1021/acs.nanolett.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Mechanically induced chromosome reorganization plays important roles in transcriptional regulation. However, the interplay between chromosome reorganization and transcription activities is complicated, such that it is difficult to decipher the regulatory effects of intranuclear geometrical cues. Here, we simplify the system by introducing DNA, packaging proteins (i.e., histone and protamine), and transcription factor NF-κB into a well-defined fluidic chip with changing spatical confinement ranging from 100 to 500 nm. It is uncovered that strong nanoconfinement suppresses higher-order folding of histone- and protamine-DNA complexes, the fracture of which exposes buried DNA segments and causes increased quantities of NF-κB binding to the DNA chain. Overall, these results reveal a pathway of how intranuclear geometrical cues alter the open/closed state of a DNA-protein complex and therefore affect transcription activities: i.e., NF-κB binding.
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Affiliation(s)
- Bingchen Che
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
- School of Physics, Northwest University, Xi'an 710069, People's Republic of China
| | - Dan Sun
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Chen Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Jiaqing Hou
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Wei Zhao
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
| | - Guangyin Jing
- School of Physics, Northwest University, Xi'an 710069, People's Republic of China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore 639798, Singapore
| | - Yaoyu Cao
- Institute of Photonics Technology, Jinan University, 510632, Guangzhou, People's Republic of China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, People's Republic of China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, People's Republic of China
| | - Ce Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, People's Republic of China
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7
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Wan S, Chen Q, Xiang Y, Sang Y, Tang M, Song Y, Feng G, Ye B, Bai L, Zhu Y. Interleukin-1 increases cyclooxygenase-2 expression and prostaglandin E2 production in human granulosa-lutein cell via nuclear factor kappa B/P65 and extracellular signal-regulated kinase 1/2 signaling pathways. Mol Cell Endocrinol 2023; 566-567:111891. [PMID: 36801432 DOI: 10.1016/j.mce.2023.111891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/03/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
A multitude of cytokines have been reported to participate in the folliculogenesis process in female. Interleukin-1 (IL-1), belonging to interleukin family, is originally identified as an important immune factor involved in inflammation response. Besides the immunity system, IL-1 is also expressed in reproductive system. However, the role of IL-1 in regulating ovarian follicle function remains to be elucidated. In the current study, using the primary human granulosa-lutein (hGL) and immortalized human granulosa-like tumor cell line (KGN) models, we demonstrated that both IL-1α and IL-1β increased prostaglandin E2 (PGE2) production via upregulating its cyclooxygenase (COX) enzyme COX-2 expression in human granulosa cells. Mechanistically, IL-1α and IL-1β treatment activated nuclear factor kappa B (NF-κB) signaling pathway. Using the specific siRNA to knock down endogenous gene expression, we found that the inhibition of p65 expression abolished IL-1α and IL-1β-induced upregulation of COX-2 expression whereas knockdown of p50 and p52 had no effect. Moreover, our results also showed that IL-1α and IL-1β promoted the nuclear translocation of p65. ChIP assay demonstrated the transcriptional regulation of p65 on COX-2 expression. Additionally, we also found that IL-1α and IL-1β could activate the extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway. The inhibition of ERK1/2 signaling pathway activation reversed IL-1α and IL-1β-induced upregulation of COX-2 expression. Our findings shed light on the cellular and molecular mechanisms by which IL-1 modulates the COX-2 expression through NF-κB/P65 and ERK1/2 signaling pathways in human granulosa cells.
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Affiliation(s)
- Shan Wan
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Qingqing Chen
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Yu Xiang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Yimiao Sang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Minyue Tang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Yang Song
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Guofang Feng
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Bingru Ye
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China
| | - Long Bai
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China.
| | - Yimin Zhu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310002, China; Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310002, China.
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8
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Pan W, Meshcheryakov VA, Li T, Wang Y, Ghosh G, Wang VYF. Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation. eLife 2023; 12:e86258. [PMID: 36779700 PMCID: PMC9991059 DOI: 10.7554/elife.86258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/07/2023] [Indexed: 02/14/2023] Open
Abstract
The mammalian NF-κB p52:p52 homodimer together with its cofactor Bcl3 activates transcription of κB sites with a central G/C base pair (bp), while it is inactive toward κB sites with a central A/T bp. To understand the molecular basis for this unique property of p52, we have determined the crystal structures of recombinant human p52 protein in complex with a P-selectin(PSel)-κB DNA (5'-GGGGTGACCCC-3') (central bp is underlined) and variants changing the central bp to A/T or swapping the flanking bp. The structures reveal a nearly two-fold widened minor groove in the central region of the DNA as compared to all other currently available NF-κB-DNA complex structures, which have a central A/T bp. Microsecond molecular dynamics (MD) simulations of free DNAs and p52 bound complexes reveal that free DNAs exhibit distinct preferred conformations, and p52:p52 homodimer induces the least amount of DNA conformational changes when bound to the more transcriptionally active natural G/C-centric PSel-κB, but adopts closed conformation when bound to the mutant A/T and swap DNAs due to their narrowed minor grooves. Our binding assays further demonstrate that the fast kinetics favored by entropy is correlated with higher transcriptional activity. Overall, our studies have revealed a novel conformation for κB DNA in complex with NF-κB and pinpoint the importance of binding kinetics, dictated by DNA conformational and dynamic states, in controlling transcriptional activation for NF-κB.
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Affiliation(s)
- Wenfei Pan
- Faculty of Health Sciences, University of MacauTaipaChina
| | | | - Tianjie Li
- Department of Physics, Chinese University of Hong KongShatinHong Kong
| | - Yi Wang
- Department of Physics, Chinese University of Hong KongShatinHong Kong
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of MacauTaipaChina
- MoE Frontiers Science Center for Precision Oncology, University of MacauTaipaMacao
- Cancer Centre, Faculty of Health Sciences, University of MacauTaipaChina
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9
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Li W, Yuan J. Targeting RIPK1 kinase for modulating inflammation in human diseases. Front Immunol 2023; 14:1159743. [PMID: 36969188 PMCID: PMC10030951 DOI: 10.3389/fimmu.2023.1159743] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023] Open
Abstract
Receptor-Interacting Serine/Threonine-Protein Kinase 1 (RIPK1) is a master regulator of TNFR1 signaling in controlling cell death and survival. While the scaffold of RIPK1 participates in the canonical NF-κB pathway, the activation of RIPK1 kinase promotes not only necroptosis and apoptosis, but also inflammation by mediating the transcriptional induction of inflammatory cytokines. The nuclear translocation of activated RIPK1 has been shown to interact BAF-complex to promote chromatin remodeling and transcription. This review will highlight the proinflammatory role of RIPK1 kinase with focus on human neurodegenerative diseases. We will discuss the possibility of targeting RIPK1 kinase for the treatment of inflammatory pathology in human diseases.
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Affiliation(s)
- Wanjin Li
- *Correspondence: Wanjin Li, ; Junying Yuan,
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10
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An Expanded Interplay Network between NF-κB p65 (RelA) and E2F1 Transcription Factors: Roles in Physiology and Pathology. Cancers (Basel) 2022; 14:cancers14205047. [PMID: 36291831 PMCID: PMC9600032 DOI: 10.3390/cancers14205047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription Factors (TFs) are the main regulators of gene expression, controlling among others cell homeostasis, identity, and fate. TFs may either act synergistically or antagonistically on nearby regulatory elements and their interplay may activate or repress gene expression. The family of NF-κB TFs is among the most important TFs in the regulation of inflammation, immunity, and stress-like responses, while they also control cell growth and survival, and are involved in inflammatory diseases and cancer. The family of E2F TFs are major regulators of cell cycle progression in most cell types. Several studies have suggested the interplay between these two TFs in the regulation of numerous genes controlling several biological processes. In the present study, we compared the genomic binding landscape of NF-κB RelA/p65 subunit and E2F1 TFs, based on high throughput ChIP-seq and RNA-seq data in different cell types. We confirmed that RelA/p65 has a binding profile with a high preference for distal enhancers bearing active chromatin marks which is distinct to that of E2F1, which mostly generates promoter-specific binding. Moreover, the RelA/p65 subunit and E2F1 cistromes have limited overlap and tend to bind chromatin that is in an active state even prior to immunogenic stimulation. Finally, we found that a fraction of the E2F1 cistrome is recruited by NF-κΒ near pro-inflammatory genes following LPS stimulation in immune cell types.
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Mansouri S, Heylmann D, Stiewe T, Kracht M, Savai R. Cancer genome and tumor microenvironment: Reciprocal crosstalk shapes lung cancer plasticity. eLife 2022; 11:79895. [PMID: 36074553 PMCID: PMC9457687 DOI: 10.7554/elife.79895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
Lung cancer classification and treatment has been revolutionized by improving our understanding of driver mutations and the introduction of tumor microenvironment (TME)-associated immune checkpoint inhibitors. Despite the significant improvement of lung cancer patient survival in response to either oncogene-targeted therapy or anticancer immunotherapy, many patients show initial or acquired resistance to these new therapies. Recent advances in genome sequencing reveal that specific driver mutations favor the development of an immunosuppressive TME phenotype, which may result in unfavorable outcomes in lung cancer patients receiving immunotherapies. Clinical studies with follow-up after immunotherapy, assessing oncogenic driver mutations and the TME immune profile, not only reveal the underlying potential molecular mechanisms in the resistant lung cancer patients but also hold the key to better treatment choices and the future of personalized medicine. In this review, we discuss the crosstalk between cancer cell genomic features and the TME to reveal the impact of genetic alterations on the TME phenotype. We also provide insights into the regulatory role of cellular TME components in defining the genetic landscape of cancer cells during tumor development.
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Affiliation(s)
- Siavash Mansouri
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Daniel Heylmann
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, Giessen, Germany
| | - Thorsten Stiewe
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany.,Institute of Molecular Oncology, Marburg, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Member of the Cardio-Pulmonary Institute (CPI), Frankfurt, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany.,Member of the German Center for Lung Research (DZL), Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.,Member of the Cardio-Pulmonary Institute (CPI), Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University Frankfurt, Frankfurt, Germany
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12
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Baughman HER, Narang D, Chen W, Villagrán Suárez AC, Lee J, Bachochin MJ, Gunther TR, Wolynes PG, Komives EA. An intrinsically disordered transcription activation domain increases the DNA binding affinity and reduces the specificity of NFκB p50/RelA. J Biol Chem 2022; 298:102349. [PMID: 35934050 PMCID: PMC9440430 DOI: 10.1016/j.jbc.2022.102349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/03/2022] Open
Abstract
Many transcription factors contain intrinsically disordered transcription activation domains (TADs), which mediate interactions with coactivators to activate transcription. Historically, DNA-binding domains and TADs have been considered as modular units, but recent studies have shown that TADs can influence DNA binding. Whether these results can be generalized to more TADs is not clear. Here, we biophysically characterized the NFκB p50/RelA heterodimer including the RelA TAD and investigated the TAD's influence on NFκB-DNA interactions. In solution, we show the RelA TAD is disordered but compact, with helical tendency in two regions that interact with coactivators. We determined that the presence of the TAD increased the stoichiometry of NFκB-DNA complexes containing promoter DNA sequences with tandem κB recognition motifs by promoting the binding of NFκB dimers in excess of the number of κB sites. In addition, we measured the binding affinity of p50/RelA for DNA containing tandem κB sites and single κB sites. While the presence of the TAD enhanced the binding affinity of p50/RelA for all κB sequences tested, it also increased the affinity for nonspecific DNA sequences by over 10-fold, leading to an overall decrease in specificity for κB DNA sequences. In contrast, previous studies have generally reported that TADs decrease DNA-binding affinity and increase sequence specificity. Our results reveal a novel function of the RelA TAD in promoting binding to nonconsensus DNA, which sheds light on previous observations of extensive nonconsensus DNA binding by NFκB in vivo in response to strong inflammatory signals.
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Affiliation(s)
- Hannah E R Baughman
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Dominic Narang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Wei Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Amalia C Villagrán Suárez
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Joan Lee
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Maxwell J Bachochin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Tristan R Gunther
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
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13
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Zhu Q, Wu Y, Mai J, Guo G, Meng J, Fang X, Chen X, Liu C, Zhong S. Comprehensive Metabolic Profiling of Inflammation Indicated Key Roles of Glycerophospholipid and Arginine Metabolism in Coronary Artery Disease. Front Immunol 2022; 13:829425. [PMID: 35371012 PMCID: PMC8965586 DOI: 10.3389/fimmu.2022.829425] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Background Systemic immune inflammation is a key mediator in the progression of coronary artery disease (CAD), concerning various metabolic and lipid changes. In this study, the relationship between the inflammatory index and metabolic profile in patients with CAD was investigated to provide deep insights into metabolic disturbances related to inflammation. Methods Widely targeted plasma metabolomic and lipidomic profiling was performed in 1,234 patients with CAD. Laboratory circulating inflammatory markers were mainly used to define general systemic immune and low-grade inflammatory states. Multivariable-adjusted linear regression was adopted to assess the associations between 860 metabolites and 7 inflammatory markers. Least absolute shrinkage and selection operator (LASSO) logistic-based classifiers and multivariable logistic regression were applied to identify biomarkers of inflammatory states and develop models for discriminating an advanced inflammatory state. Results Multiple metabolites and lipid species were linearly associated with the seven inflammatory markers [false discovery rate (FDR) <0.05]. LASSO and multivariable-adjusted logistic regression analysis identified significant associations between 45 metabolites and systemic immune-inflammation index, 46 metabolites and neutrophil-lymphocyte ratio states, 32 metabolites and low-grade inflammation score, and 26 metabolites and high-sensitivity C-reactive protein states (P < 0.05). Glycerophospholipid metabolism and arginine and proline metabolism were determined as key altered metabolic pathways for systemic immune and low-grade inflammatory states. Predictive models based solely on metabolite combinations showed feasibility (area under the curve: 0.81 to 0.88) for discriminating the four parameters that represent inflammatory states and were successfully validated using a validation cohort. The inflammation-associated metabolite, namely, β-pseudouridine, was related to carotid and coronary arteriosclerosis indicators (P < 0.05). Conclusions This study provides further information on the relationship between plasma metabolite profiles and inflammatory states represented by various inflammatory markers in CAD. These metabolic markers provide potential insights into pathological changes during CAD progression and may aid in the development of therapeutic targets.
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Affiliation(s)
- Qian Zhu
- School of Medicine, South China University of Technology, Guangzhou, China.,Department of Pharmacy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yonglin Wu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jinxia Mai
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Gongjie Guo
- School of Medicine, South China University of Technology, Guangzhou, China.,Department of Pharmacy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jinxiu Meng
- Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xianhong Fang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Chen Liu
- Department of Cardiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shilong Zhong
- School of Medicine, South China University of Technology, Guangzhou, China.,Department of Pharmacy, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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14
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Li H, Chen W, Gou M, Li W, Tong J, Zhou Y, Xie T, Yu T, Feng W, Li Y, Chen S, Tian B, Tan S, Wang Z, Pan S, Li N, Luo X, Zhang P, Huang J, Tian L, Li CSR, Tan Y. The relationship between TLR4/NF-κB/IL-1β signaling, cognitive impairment, and white-matter integrity in patients with stable chronic schizophrenia. Front Psychiatry 2022; 13:966657. [PMID: 36051545 PMCID: PMC9424630 DOI: 10.3389/fpsyt.2022.966657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/22/2022] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Previous studies have implicated intricate interactions between innate immunity and the brain in schizophrenia. Monocytic Toll-like receptor (TLR) 4 signaling, a crucial "sensor" of innate immunity, was reported to be over-activated in link with cognitive impairment in schizophrenia. As TLR4 is predominantly expressed on gliocytes prior to expression in neurons, we hypothesized that higher TLR4 levels may contribute to cognitive deterioration by affecting white matter microstructure. METHODS Forty-four patients with stable chronic schizophrenia (SCS) and 59 healthy controls (HCs) were recruited in this study. The monocytic function was detected with lipopolysaccharide (LPS) stimulation to simulate bacterial infection. Basal and LPS- stimulated levels of TLR4, nuclear factor-kappa B (NF-κB), and interleukin (IL)-1β were quantified with flow cytometry. Cognitive function was assessed by the MATRICS Consensus Cognitive Battery (MCCB) and psychopathological symptoms were evaluated by the Positive and Negative Syndrome Scale (PANSS). We employed diffusion tensor imaging with a 3-T scanner and evaluated white-matter integrity with fractional anisotropy (FA). Subcortical volume and cortical thickness were also assessed. RESULTS The TLR4/NF-κB/IL-1β signaling pathway was activated in patients with SCS, but responded sluggishly to LPS stimulation when compared with HCs. Furthermore, monocytic TLR4 expressions were inversely correlated with cognitive function and white matter FA, but not with cortical thickness or subcortical gray matter volume in schizophrenia. CONCLUSION Our findings support altered TLR4 signaling pathway activity in association with deficits in cognition and white matter integrity in schizophrenia.
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Affiliation(s)
- Hongna Li
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Wenjin Chen
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Mengzhuang Gou
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Wei Li
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Jinghui Tong
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Yanfang Zhou
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Ting Xie
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Ting Yu
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Wei Feng
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Yanli Li
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Song Chen
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Baopeng Tian
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Shuping Tan
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Zhiren Wang
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Shujuan Pan
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Na Li
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - Ping Zhang
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Junchao Huang
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
| | - Li Tian
- Department of Physiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Chiang-Shan R Li
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - Yunlong Tan
- Peking University HuiLongGuan Clinical Medical School, Beijing Huilongguan Hospital, Beijing, China
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15
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Dosch AR, Singh S, Nagathihalli NS, Datta J, Merchant NB. Interleukin-1 signaling in solid organ malignancies. Biochim Biophys Acta Rev Cancer 2021; 1877:188670. [PMID: 34923027 DOI: 10.1016/j.bbcan.2021.188670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
As inflammation plays a critical role in the development and progression of cancer, therapeutic targeting of cytokine pathways involved in both tumorigenesis and dictating response to clinical treatments are of significant interest. Recent evidence has highlighted the importance of the pro-inflammatory cytokine interleukin-1 (IL-1) as a key mediator of tumor growth, metastatic disease spread, immunosuppression, and drug resistance in cancer. IL-1 promotes tumorigenesis through diverse mechanisms, including the activation of oncogenic signaling pathways directly in tumor cells and via orchestrating crosstalk between the cellular constituents of the tumor microenvironment (TME), thereby driving cancer growth. This review will provide an overview of IL-1 signaling and physiology and summarize the disparate mechanisms involving IL-1 in tumorigenesis and cancer progression. Additionally, clinical studies targeting IL-1 signaling in the management of solid organ tumors will be summarized herein.
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Affiliation(s)
- Austin R Dosch
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States of America
| | - Samara Singh
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States of America
| | - Nagaraj S Nagathihalli
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States of America
| | - Jashodeep Datta
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States of America
| | - Nipun B Merchant
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States of America; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States of America.
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16
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Liu S, He L, Wu J, Wu X, Xie L, Dai W, Chen L, Xie F, Liu Z. DHX9 contributes to the malignant phenotypes of colorectal cancer via activating NF-κB signaling pathway. Cell Mol Life Sci 2021; 78:8261-8281. [PMID: 34773477 PMCID: PMC11072136 DOI: 10.1007/s00018-021-04013-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/27/2021] [Accepted: 10/24/2021] [Indexed: 12/25/2022]
Abstract
Colorectal cancer (CRC) is the leading cause of cancer-related mortality worldwide, which makes it urgent to identify novel therapeutic targets for CRC treatment. In this study, DHX9 was filtered out as the prominent proliferation promoters of CRC by siRNA screening. Moreover, DHX9 was overexpressed in CRC cell lines, clinical CRC tissues and colitis-associated colorectal cancer (CAC) mouse model. The upregulation of DHX9 was positively correlated with poor prognosis in patients with CRC. Through gain- and loss-of function experiments, we found that DHX9 promoted CRC cell proliferation, colony formation, apoptosis resistance, migration and invasion in vitro. Furthermore, a xenograft mouse model and a hepatic metastasis mouse model were utilized to confirm that forced overexpression of DHX9 enhanced CRC outgrowth and metastasis in vivo, while DHX9 ablation produced the opposite effect. Mechanistically, from one aspect, DHX9 enhances p65 phosphorylation, promotes p65 nuclear translocation to facilitate NF-κB-mediated transcriptional activity. From another aspect, DHX9 interacts with p65 and RNA polymerase II (RNA Pol II) to enhance the downstream targets of NF-κB (e.g., Survivin, Snail) expression to potentiate the malignant phenotypes of CRC. Together, our results suggest that DHX9 may be a potential therapeutic target for prevention and treatment of CRC patients.
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Affiliation(s)
- Shenglan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Liangmei He
- Department of Gastroenterology, The First Affiliated Hospital, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junhong Wu
- Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xinqiang Wu
- Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lu Xie
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Wei Dai
- College of Pharmacy, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Lingxia Chen
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Fuhua Xie
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
| | - Zhiping Liu
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
- Center for Immunology, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, Jiangxi, China.
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17
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Meier-Soelch J, Mayr-Buro C, Juli J, Leib L, Linne U, Dreute J, Papantonis A, Schmitz ML, Kracht M. Monitoring the Levels of Cellular NF-κB Activation States. Cancers (Basel) 2021; 13:5351. [PMID: 34771516 PMCID: PMC8582385 DOI: 10.3390/cancers13215351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The NF-κB signaling system plays an important regulatory role in the control of many biological processes. The activities of NF-κB signaling networks and the expression of their target genes are frequently elevated in pathophysiological situations including inflammation, infection, and cancer. In these conditions, the outcome of NF-κB activity can vary according to (i) differential activation states, (ii) the pattern of genomic recruitment of the NF-κB subunits, and (iii) cellular heterogeneity. Additionally, the cytosolic NF-κB activation steps leading to the liberation of DNA-binding dimers need to be distinguished from the less understood nuclear pathways that are ultimately responsible for NF-κB target gene specificity. This raises the need to more precisely determine the NF-κB activation status not only for the purpose of basic research, but also in (future) clinical applications. Here we review a compendium of different methods that have been developed to assess the NF-κB activation status in vitro and in vivo. We also discuss recent advances that allow the assessment of several NF-κB features simultaneously at the single cell level.
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Affiliation(s)
- Johanna Meier-Soelch
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Christin Mayr-Buro
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Jana Juli
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Lisa Leib
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps University, 35032 Marburg, Germany;
| | - Jan Dreute
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany;
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, Justus Liebig University, 35392 Giessen, Germany; (J.M.-S.); (C.M.-B.); (J.J.); (L.L.)
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18
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Shen Z, Hoeksema MA, Ouyang Z, Benner C, Glass CK. MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. Bioinformatics 2021; 36:i84-i92. [PMID: 32657363 PMCID: PMC7355228 DOI: 10.1093/bioinformatics/btaa476] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MOTIVATION Genetic variation in regulatory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity of the regulatory elements. However, it is unclear which motifs are prone to impact transcriptional regulation if mutated. Current motif analysis tools either prioritize TFs based on motif enrichment without linking to a function or are limited in their applications due to the assumption of linearity between motifs and their functional effects. RESULTS We present MAGGIE (Motif Alteration Genome-wide to Globally Investigate Elements), a novel method for identifying motifs mediating TF binding and function. By leveraging measurements from diverse genotypes, MAGGIE uses a statistical approach to link mutations of a motif to changes of an epigenomic feature without assuming a linear relationship. We benchmark MAGGIE across various applications using both simulated and biological datasets and demonstrate its improvement in sensitivity and specificity compared with the state-of-the-art motif analysis approaches. We use MAGGIE to gain novel insights into the divergent functions of distinct NF-κB factors in pro-inflammatory macrophages, revealing the association of p65-p50 co-binding with transcriptional activation and the association of p50 binding lacking p65 with transcriptional repression. AVAILABILITY AND IMPLEMENTATION The Python package for MAGGIE is freely available at https://github.com/zeyang-shen/maggie. The accession number for the NF-κB ChIP-seq data generated for this study is Gene Expression Omnibus: GSE144070. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zeyang Shen
- Department of Cellular and Molecular Medicine, School of Medicine.,Department of Bioengineering, Jacobs School of Engineering
| | | | - Zhengyu Ouyang
- Department of Cellular and Molecular Medicine, School of Medicine
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California, San Diego, CA 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, School of Medicine.,Department of Medicine, School of Medicine, University of California, San Diego, CA 92093, USA
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19
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Francis M, Gopinathan G, Salapatas A, Nares S, Gonzalez M, Diekwisch T, Luan X. SETD1 and NF-κB Regulate Periodontal Inflammation through H3K4 Trimethylation. J Dent Res 2020; 99:1486-1493. [PMID: 32762504 PMCID: PMC7684838 DOI: 10.1177/0022034520939029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The inflammatory response to periodontal pathogens is dynamically controlled by the chromatin state on inflammatory gene promoters. In the present study, we have focused on the effect of the methyltransferase SETD1B on histone H3 lysine K4 (H3K4) histone trimethylation on inflammatory gene promoters. Experiments were based on 3 model systems: 1) an in vitro periodontal ligament (PDL) cell culture model for the study of SETD1 function as it relates to histone methylation and inflammatory gene expression using Porphyromonas gingivalis lipopolysaccharide (LPS) as a pathogen, 2) a subcutaneous implantation model to determine the relationship between SETD1 and nuclear factor κB (NF-κB) through its activation inhibitor BOT-64, and 3) a mouse periodontitis model to test whether the NF-κB activation inhibitor BOT-64 reverses the inflammatory tissue destruction associated with periodontal disease. In our PDL progenitor cell culture model, P. gingivalis LPS increased H3K4me3 histone methylation on IL-1β, IL-6, and MMP2 gene promoters, while SETD1B inhibition decreased H3K4me3 enrichment and inflammatory gene expression in LPS-treated PDL cells. LPS also increased SETD1 nuclear localization in a p65-dependent fashion and the nuclear translocation of p65 as mediated through SETD1, suggestive of a synergistic effect between SETD1 and p65 in the modulation of inflammation. Confirming the role of SETD1 in p65-mediated periodontal inflammation, BOT-64 reduced the number of SETD1-positive cells in inflamed periodontal tissues, restored periodontal tissue integrity, and enhanced osteogenesis in a periodontal inflammation model in vivo. Together, these results have established the histone lysine methyltransferase SETD1 as a key factor in the opening of the chromatin on inflammatory gene promoters through histone H3K4 trimethylation. Our studies also confirmed the role of BOT-64 as a potent molecular therapeutic for the restoration of periodontal health through the inhibition of NF-κB activity and the amelioration of SETD1-induced chromatin relaxation.
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Affiliation(s)
- M. Francis
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
| | - G. Gopinathan
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - A. Salapatas
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
| | - S. Nares
- Department of Periodontics, UIC College of Dentistry, Chicago, IL, USA
| | - M. Gonzalez
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - T.G.H. Diekwisch
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
| | - X. Luan
- Department of Oral Biology, UIC College of Dentistry, Chicago, IL, USA
- Department of Periodontics and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX, USA
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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21
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Han R, Wang J, Chen H, Luo X, Li A, Dan X, Li Y. Grouper (Epinephelus coioides) IRAK-4 regulates activation of NF-κB and expression of inflammatory cytokines in grouper spleen cells. FISH & SHELLFISH IMMUNOLOGY 2020; 106:938-947. [PMID: 32919054 DOI: 10.1016/j.fsi.2020.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/30/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
IRAK-4 is a serine/threonine kinase that can bind to interleukin-1 receptor induced by interleukin-1. It plays a key role in the Toll-like receptor signaling pathway and is involved in innate and adaptive immune responses. In this study, piscine IRAK-4 significantly activated nuclear factor (NF)-κB signaling in grouper spleen cells. Grouper (Epinephelus coioides) IRAK-4 (EcIRAK-4) co-localized with EcMyD88 and did not impair EcMyD88-dependent NF-κB activation. Different doses of EcIRAK-4 caused different degrees of nuclear translocation of the transcription factor NF-κB p65 subunit, and it induced transcription of multiple pro-inflammatory cytokines. Using expression vectors of deletion domains or mutations at important sites of EcIRAK-4, we found that the EcIRAK-4 kinase domain is necessary for its signal transduction function. The conserved amino acid sites performed functions similar to those in mammals, and grouper-specific amino acids such as E339 also played important roles. These findings provide information about the functional characteristics of IRAK-4 in lower vertebrates.
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Affiliation(s)
- Rui Han
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China
| | - Jiule Wang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China
| | - Hongping Chen
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China
| | - Xiaochun Luo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
| | - Anxing Li
- State Key Laboratory of Biocontrol/Guangdong Provincial key Lab for Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong Province, PR China
| | - Xueming Dan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China.
| | - Yanwei Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, Agricultural University, Guangzhou, 510642, China.
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Bellet MM, Pieroni S, Castelli M, Piobbico D, Fallarino F, Romani L, Della-Fazia MA, Servillo G. HOPS/Tmub1 involvement in the NF-kB-mediated inflammatory response through the modulation of TRAF6. Cell Death Dis 2020; 11:865. [PMID: 33060567 PMCID: PMC7567074 DOI: 10.1038/s41419-020-03086-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/23/2022]
Abstract
HOPS/Tmub1 is a ubiquitously expressed transmembrane ubiquitin-like protein that shuttles between nucleus and cytoplasm during cell cycle progression. HOPS causes cell cycle arrest in G0/G1 phase, an event associated to stabilization of p19Arf, an important tumor suppressor protein. Moreover, HOPS plays an important role in driving centrosomal assembly and maintenance, mitotic spindle proper organization, and ultimately a correct cell division. Recently, HOPS has been described as an important regulator of p53, which acts as modifier, stabilizing p53 half-life and playing a key role in p53 mediating apoptosis after DNA damage. NF-κB is a transcription factor with a central role in many cellular events, including inflammation and apoptosis. Our experiments demonstrate that the transcriptional activity of the p65/RelA NF-κB subunit is regulated by HOPS. Importantly, Hops−/− cells have remarkable alterations of pro-inflammatory responses. Specifically, we found that HOPS enhances NF-κB activation leading to increase transcription of inflammatory mediators, through the reduction of IκBα stability. Notably, this effect is mediated by a direct HOPS binding to the E3 ubiquitin ligase TRAF6, which lessens TRAF6 stability ultimately leading increased IKK complex activation. These findings uncover a previously unidentified function of HOPS/Tmub1 as a novel modulator of TRAF6, regulating inflammatory responses driven by activation of the NF-κB signaling pathway. The comprehension on how HOPS/Tmub1 takes part to the inflammatory processes in vivo and whether this function is important in the control of proliferation and tumorigenesis could establish the basis for the development of novel pharmacological strategies.
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Affiliation(s)
- Marina Maria Bellet
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Stefania Pieroni
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Marilena Castelli
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Danilo Piobbico
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Francesca Fallarino
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | - Luigina Romani
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy
| | | | - Giuseppe Servillo
- Department of Experimental Medicine, University of Perugia, 06132, Perugia, Italy.
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23
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Kunkl M, Amormino C, Frascolla S, Sambucci M, De Bardi M, Caristi S, Arcieri S, Battistini L, Tuosto L. CD28 Autonomous Signaling Orchestrates IL-22 Expression and IL-22-Regulated Epithelial Barrier Functions in Human T Lymphocytes. Front Immunol 2020; 11:590964. [PMID: 33178223 PMCID: PMC7592429 DOI: 10.3389/fimmu.2020.590964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022] Open
Abstract
IL-22 is a member of the IL-10 cytokine family involved in host protection against extracellular pathogens, by promoting epithelial cell regeneration and barrier functions. Dysregulation of IL-22 production has also frequently been observed in acute respiratory distress syndrome (ARDS) and several chronic inflammatory and autoimmune diseases. We have previously described that human CD28, a crucial co-stimulatory receptor necessary for full T cell activation, is also able to act as a TCR independent signaling receptor and to induce the expression of IL-17A and inflammatory cytokines related to Th17 cells, which together with Th22 cells represent the main cellular source of IL-22. Here we characterized the role of CD28 autonomous signaling in regulating IL-22 expression in human CD4+ T cells. We show that CD28 stimulation in the absence of TCR strongly up-regulates IL-22 gene expression and secretion. As recently observed for IL-17A, we also found that CD28-mediated regulation of IL-22 transcription requires the cooperative activities of both IL-6-activated STAT3 and RelA/NF-κB transcription factors. CD28-mediated IL-22 production also promotes the barrier functions of epithelial cells by inducing mucin and metalloproteases expression. Finally, by using specific inhibitory drugs, we also identified CD28-associated class 1A phosphatidylinositol 3-kinase (PI3K) as a pivotal mediator of CD28-mediated IL-22 expression and IL-22-dependent epithelial cell barrier functions.
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Affiliation(s)
- Martina Kunkl
- Department of Biology and Biotechnology Charles Darwin, Sapienza University, Rome, Italy
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
| | - Carola Amormino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University, Rome, Italy
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
| | - Simone Frascolla
- Department of Biology and Biotechnology Charles Darwin, Sapienza University, Rome, Italy
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
| | - Manolo Sambucci
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Silvana Caristi
- Department of Biology and Biotechnology Charles Darwin, Sapienza University, Rome, Italy
| | - Stefano Arcieri
- Department of Surgical Sciences, Sapienza University of Rome, Rome, Italy
| | - Luca Battistini
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Loretta Tuosto
- Department of Biology and Biotechnology Charles Darwin, Sapienza University, Rome, Italy
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, Rome, Italy
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tBHQ Induces a Hormetic Response That Protects L6 Myoblasts against the Toxic Effect of Palmitate. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3123268. [PMID: 32509140 PMCID: PMC7246405 DOI: 10.1155/2020/3123268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/20/2020] [Indexed: 12/27/2022]
Abstract
Nutritional status, in particular overweight and obesity, as well as sedentarism and high-fat diet consumption, are important risk factors to develop chronic diseases, which have a higher impact on the elderly's health. Therefore, these nutritional problems have become a concern to human healthspan and longevity. The fatty acids obtained thru the diet or due to fatty acid synthesis during obesity accumulate within the body generating toxicity and cell death. Fat is not only stored in adipose tissue, but it can also be stored in skeletal muscle. Palmitic acid (PA) has been reported as one of the most important saturated free fatty acids; it is associated to chronic oxidative stress and increased mitochondrial ROS production causing cell death by apoptosis. In skeletal muscle, palmitate has been associated with various pathophysiological consequences, which lead to muscle deterioration during aging and obesity. Since molecules that modify redox state have been proven to prevent cellular damage by inducing a hormetic response, the aim of this study was to evaluate if tert-butylhydroquinone (tBHQ) could activate an antioxidant hormetic response that would be able to protect L6 myoblasts from palmitate toxic effect. Our results provide evidence that tBHQ is able to protect L6 myoblasts against the toxicity induced by sodium palmitate due to a synergistic activation of different signaling pathways such as Nrf2 and NF-κB.
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25
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Li D, Gao C, Zhao L, Zhang Y. Inflammatory response is modulated by lincRNACox2 via the NF‑κB pathway in macrophages infected by Mycobacterium tuberculosis. Mol Med Rep 2020; 21:2513-2521. [PMID: 32323851 PMCID: PMC7185307 DOI: 10.3892/mmr.2020.11053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/26/2020] [Indexed: 01/20/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are long non-coding transcripts from the intergenic regions of annotated protein-coding genes. lincRNA cyclooxygenase 2 (Cox2) is an early-primary response gene regulated by the NF-κB signaling pathway in macrophages. It was found that lincRNACox2 was significantly increased in patients with the Mycobacterium tuberculosis (M. tuberculosis) H37Ra strain infection and macrophages, using reverse transcription-quantitative PCR (RT-qPCR). ELISA, western blotting and RT-qPCR results indicated that the inflammatory response factors tumor necrosis factor-α, interferon-γ, interleukin-6, Cox2 and inducible nitric oxide synthase were significantly increased in H37Ra infected macrophages. In addition, the inflammatory regulating proteins NF-κB and Stat3 were significantly increased in H37Ra infected macrophages but decreased in lincRNACox2 knockdown macrophages infected with H37Ra. Moreover, the knockdown of lincRNACox2 increased the apoptotic rate of H37Ra infected macrophages and facilitated the proliferation of H37Ra. Collectively, the present results suggested that lincRNACox2 may be required for the activation of NF-κB and Stat3, in order to regulate inflammatory responses involved in resistance to M. tuberculosis infection.
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Affiliation(s)
- Danye Li
- Department of Pulmonary and Critical Care Medicine, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Caiyan Gao
- Department of Respiration, Hongda Hospital of Jiamusi University, Jiamusi, Heilongjiang 154004, P.R. China
| | - Ling Zhao
- Department of Pathology, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Yongming Zhang
- Department of Pulmonary and Critical Care Medicine, China‑Japan Friendship Hospital, Beijing 100029, P.R. China
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26
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Liu W, Cheng L, Li Q, Jing J. TRIP6 regulates the proliferation, migration, invasion and apoptosis of osteosarcoma cells by activating the NF-κB signaling pathway. Exp Ther Med 2020; 19:2317-2325. [PMID: 32104300 PMCID: PMC7027267 DOI: 10.3892/etm.2020.8466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/18/2019] [Indexed: 11/06/2022] Open
Abstract
Thyroid hormone receptor-interacting protein 6 (TRIP6), a member of the zyxin family of Lin-Isl-Mec (LIM) proteins, is an adaptor protein primarily expressed in epithelial cells. TRIP6 can regulate a variety of cellular responses, such as actin cytoskeletal reorganization and cell adhesion. However, to the best of our knowledge, the role of TRIP6 in osteosarcoma (Os) has not been previously reported. Therefore, the present study investigated the role of TRIP6 in the occurrence and development of Os, and the potential of utilizing TRIP6 as a therapeutic target in Os. The present results suggested that the expression levels of TRIP6 were significantly increased in Os cells and clinical tissue specimens compared with normal osteoblasts and adjacent non-tumor tissue. Moreover, the present results suggested that overexpressing TRIP6 significantly increased proliferation, migration and invasion, while inhibiting apoptosis in Os cells. However, silencing TRIP6 decreased proliferation, migration and invasion, while activating apoptosis in Os cells. The present results suggested that overexpression of TRIP6 increased NF-κB activation by decreasing the protein expression levels of inhibitor of κBα, and increasing total and phosphorylated P65 levels. The present results indicated that TRIP6 silencing decreased NF-κB activation. Collectively, the present results suggested that TRIP6 may play a role in promoting Os cell proliferation, migration and invasion, while inhibiting cell apoptosis. Furthermore, TRIP6 may be utilized as a novel prognostic biomarker and therapeutic target in Os.
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Affiliation(s)
- Wei Liu
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Li Cheng
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Qingning Li
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Juehua Jing
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
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27
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Banach-Orłowska M, Wyszyńska R, Pyrzyńska B, Maksymowicz M, Gołąb J, Miączyńska M. Cholesterol restricts lymphotoxin β receptor-triggered NF-κB signaling. Cell Commun Signal 2019; 17:171. [PMID: 31878945 PMCID: PMC6933913 DOI: 10.1186/s12964-019-0460-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lymphotoxin β receptor (LTβR) plays important roles in the development of the immune system and immune response. At the cellular level, ligand-bound LTβR activates the pro-inflammatory NF-κB pathway but the detailed mechanisms regulating its signaling remain unknown. Understanding them is of high importance since LTβR and its ligands are promising therapeutic targets. Here, we studied the consequences of perturbed cellular cholesterol content on LTβR-induced NF-κB signaling. METHODS To modulate cholesterol availability and/or level in lung carcinoma A549 and H2228, and endothelial HUVEC cells different treatment regimens with filipin, methyl-β-cyclodextrin and simvastatin were applied. LTβR localization was studied by confocal microscopy. The activity of LTβR-induced NF-κB pathway was assessed by measuring the levels of NF-κB pathway inhibitor IκBα and phosphorylation of RelA transcription factor by Western blotting. The NF-κB transcriptional response, production of chemokines and adhesion molecules were examined by qRT-PCR, ELISA, and Western blotting, respectively. Adherence of different types of primary immune cells to epithelial A549 cells and endothelial HUVECs was measured fluorometrically. Interactions of LTβR with its protein partners were investigated by immunoprecipitation. RESULTS We showed that filipin-mediated sequestration of cholesterol or its depletion from the plasma membrane with methyl-β-cyclodextrin impaired LTβR internalization and potentiated LTβR-dependent activation of the canonical branch of the NF-κB pathway. The latter was manifested by enhanced degradation of IκBα inhibitor, elevated RelA phosphorylation, substantial increase in the expression of NF-κB target genes encoding, among others, cytokines and adhesion molecules known to play important roles in immune response. It was followed by robust secretion of CXCL8 and upregulation of ICAM1, that favored the adhesion of immune cells (NK and T cells, neutrophils) to A549 cells and HUVECs. Mechanistically, we showed that cholesterol depletion stabilized interactions of ligand-stimulated LTβR with modified forms of TRAF2 and NEMO proteins. CONCLUSIONS Our results showed that the reduction of the plasma membrane content of cholesterol or its sequestration strongly potentiated signaling outcome initiated by LTβR. Thus, drugs modulating cholesterol levels could potentially improve efficacy of LTβR-based therapies. Video abstract.
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Affiliation(s)
- Magdalena Banach-Orłowska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland.
| | - Renata Wyszyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Beata Pyrzyńska
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Maksymowicz
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Marta Miączyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, 02-109, Warsaw, Poland
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28
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Khan SZ, Gasperino S, Zeichner SL. Nuclear Transit and HIV LTR Binding of NF-κB Subunits Held by IκB Proteins: Implications for HIV-1 Activation. Viruses 2019; 11:v11121162. [PMID: 31888181 PMCID: PMC6949894 DOI: 10.3390/v11121162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
No effective therapy to eliminate the HIV latently infected cell reservoir has been developed. One approach, “shock and kill”, employs agents that activate HIV, subsequently killing the activated infected cells and/or virus. Shock and kill requires agents that safely and effectively activate HIV. One class of activation agents works through classical NF-κB pathways, but global NF-κB activators are non-specific and toxic. There exist two major IκBs: IκBα, and IκBε, which hold activating NF-κB subunits in the cytoplasm, releasing them for nuclear transit upon cell stimulation. IκBα was considered the main IκB responsible for gene expression regulation, including HIV activation. IκBε is expressed in cells constituting much of the latent HIV reservoir, and IκBε knockout mice have a minimal phenotype, suggesting that IκBε could be a valuable target for HIV activation and reservoir depletion. We previously showed that targeting IκBε yields substantial increases in HIV expression. Here, we show that IκBε holds c-Rel and p65 activating NF-κB subunits in the cytoplasm, and that targeting IκBε with siRNA produces a strong increase in HIV expression associated with enhanced c-Rel and p65 transit to the nucleus and binding to the HIV LTR of the activating NF-κBs, demonstrating a mechanism through which targeting IκBε increases HIV expression. The findings suggest that it may be helpful to develop HIV activation approaches, acting specifically to target IκBε and its interactions with the NF-κBs.
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Affiliation(s)
- Sohrab Z. Khan
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
| | - Sofia Gasperino
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
| | - Steven L. Zeichner
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
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29
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Mulero MC, Wang VYF, Huxford T, Ghosh G. Genome reading by the NF-κB transcription factors. Nucleic Acids Res 2019; 47:9967-9989. [PMID: 31501881 PMCID: PMC6821244 DOI: 10.1093/nar/gkz739] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/05/2019] [Accepted: 08/21/2019] [Indexed: 12/25/2022] Open
Abstract
The NF-κB family of dimeric transcription factors regulates transcription by selectively binding to DNA response elements present within promoters or enhancers of target genes. The DNA response elements, collectively known as κB sites or κB DNA, share the consensus 5'-GGGRNNNYCC-3' (where R, Y and N are purine, pyrimidine and any nucleotide base, respectively). In addition, several DNA sequences that deviate significantly from the consensus have been shown to accommodate binding by NF-κB dimers. X-ray crystal structures of NF-κB in complex with diverse κB DNA have helped elucidate the chemical principles that underlie target selection in vitro. However, NF-κB dimers encounter additional impediments to selective DNA binding in vivo. Work carried out during the past decades has identified some of the barriers to sequence selective DNA target binding within the context of chromatin and suggests possible mechanisms by which NF-κB might overcome these obstacles. In this review, we first highlight structural features of NF-κB:DNA complexes and how distinctive features of NF-κB proteins and DNA sequences contribute to specific complex formation. We then discuss how native NF-κB dimers identify DNA binding targets in the nucleus with support from additional factors and how post-translational modifications enable NF-κB to selectively bind κB sites in vivo.
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Affiliation(s)
- Maria Carmen Mulero
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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30
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Comoglio F, Simonatto M, Polletti S, Liu X, Smale ST, Barozzi I, Natoli G. Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells. Genes Dev 2019; 33:1159-1174. [PMID: 31371436 PMCID: PMC6719622 DOI: 10.1101/gad.326348.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/03/2019] [Indexed: 12/22/2022]
Abstract
Accessibility of the genomic regulatory information is largely controlled by the nucleosome-organizing activity of transcription factors (TFs). While stimulus-induced TFs bind to genomic regions that are maintained accessible by lineage-determining TFs, they also increase accessibility of thousands of cis-regulatory elements. Nucleosome remodeling events underlying such changes and their interplay with basal positioning are unknown. Here, we devised a novel quantitative framework discriminating different types of nucleosome remodeling events in micrococcal nuclease ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) data sets and used it to analyze nucleosome dynamics at stimulus-regulated cis-regulatory elements. At enhancers, remodeling preferentially affected poorly positioned nucleosomes while sparing well-positioned nucleosomes flanking the enhancer core, indicating that inducible TFs do not suffice to overrule basal nucleosomal organization maintained by lineage-determining TFs. Remodeling events appeared to be combinatorially driven by multiple TFs, with distinct TFs showing, however, different remodeling efficiencies. Overall, these data provide a systematic view of the impact of stimulation on nucleosome organization and genome accessibility in mammalian cells.
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Affiliation(s)
- Federico Comoglio
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
- Department of Hematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Marta Simonatto
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
| | - Sara Polletti
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
| | - Xin Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, California 90095, USA
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London W12 00N, United Kingdom
| | - Gioacchino Natoli
- Humanitas University (Hunimed), Pieve Emanuele, Milano 20090, Italy
- Humanitas Istituto di Ricovero e Cura a Carattere Scientifico, Rozzano, Milano 20089, Italy
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31
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Xu G, Xia Z, Deng F, Liu L, Wang Q, Yu Y, Wang F, Zhu C, Liu W, Cheng Z, Zhu Y, Zhou L, Zhang Y, Lu M, Liu S. Inducible LGALS3BP/90K activates antiviral innate immune responses by targeting TRAF6 and TRAF3 complex. PLoS Pathog 2019; 15:e1008002. [PMID: 31404116 PMCID: PMC6705879 DOI: 10.1371/journal.ppat.1008002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/22/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022] Open
Abstract
The galectin 3 binding protein (LGALS3BP, also known as 90K) is a ubiquitous multifunctional secreted glycoprotein originally identified in cancer progression. It remains unclear how 90K functions in innate immunity during viral infections. In this study, we found that viral infections resulted in elevated levels of 90K. Further studies demonstrated that 90K expression suppressed virus replication by inducing IFN and pro-inflammatory cytokine production. Upon investigating the mechanisms behind this event, we found that 90K functions as a scaffold/adaptor protein to interact with TRAF6, TRAF3, TAK1 and TBK1. Furthermore, 90K enhanced TRAF6 and TRAF3 ubiquitination and served as a specific ubiquitination substrate of TRAF6, leading to transcription factor NF-κB, IRF3 and IRF7 translocation from the cytoplasm to the nucleus. Conclusions: 90K is a virus-induced protein capable of binding with the TRAF6 and TRAF3 complex, leading to IFN and pro-inflammatory production. The innate immune system detects the presence of viruses through germline-encoded pattern-recognition receptors (PRRs) and leads to the production of proinflammatory cytokines and interferons (IFNs) as the first line of defense against viral infections. Here, we identified a host protein, LGALS3BP, as a positive regulator of PRR-mediated signal transduction pathways by interacting with TRAF6-TAK1 and TRAF3-TBK1 axes, enhancing their recruitment and promoting the ubiquitination of TRAF6 and TRAF3. LGALS3BP exhibited antiviral activity toward a broad range of viral infections. LGALS3BP-/- mice are highly susceptible to lethal influenza A virus infection with increasing pulmonary viral load, morbidity and mortality. Thus, our study highlight the importance of LGALS3BP in host antiviral innate immune responses.
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Affiliation(s)
- Gang Xu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhangchuan Xia
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Feiyan Deng
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lin Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiming Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Yi Yu
- The Key Laboratory of Biosystems Homeostasis and Protection of the Ministry of Education and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Weiyong Liu
- Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhikui Cheng
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Zhou
- Animal Biosafety Level III Laboratory at the Center for Animal Experiment, School of Medicine, Wuhan University, Wuhan, China
| | - Yi Zhang
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Food and Pharmaceutical Engineering, Hubei University of Technology, Wuhan, China
| | - Mengji Lu
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Shi Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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Komegae EN, Fonseca MT, da Silveira Cruz-Machado S, Turato WM, Filgueiras LR, Markus RP, Steiner AA. Site-Specific Reprogramming of Macrophage Responsiveness to Bacterial Lipopolysaccharide in Obesity. Front Immunol 2019; 10:1496. [PMID: 31316525 PMCID: PMC6611339 DOI: 10.3389/fimmu.2019.01496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/14/2019] [Indexed: 12/14/2022] Open
Abstract
The mechanisms by which obesity may alter immune responses to pathogens are poorly understood. The present study assessed whether the intrinsic responsiveness of resident macrophages to bacterial lipopolysaccharide (LPS) is reprogrammed in high-fat diet (HFD)-induced obesity. Macrophages from adipose tissue, lung alveoli, and the peritoneal cavity were extracted from obese rats on a HFD or from their lean counterparts, and subsequently studied in culture under identical conditions. CD45+/CD68+ cells (macrophages) were abundant in all cultures, and became the main producers of TNF-α upon LPS stimulation. But although all macrophage subpopulations responded to LPS with an M1-like profile of cytokine secretion, the TNF-α/IL-10 ratio was the lowest in adipose tissue macrophages, the highest in alveolar macrophages, and intermediary in peritoneal macrophages. What is more, diet exerted qualitatively distinct effects on the cytokine responses to LPS, with obesity switching adipose tissue macrophages to a more pro-inflammatory program and peritoneal macrophages to a less pro-inflammatory program, while not affecting alveolar macrophages. Such reprogramming was not associated with changes in the inflammasome-dependent secretion of IL-1β. The study further shows that the effects of diet on TNF-α/IL-10 ratios were linked to distinct patterns of NF-κB accumulation in the nucleus: while RelA was the NF-κB subunit most impacted by obesity in adipose tissue macrophages, cRel was the subunit affected in peritoneal macrophages. It is concluded that obesity causes dissimilar, site-specific changes in the responsiveness of resident macrophages to bacterial LPS. Such plasticity opens new avenues of investigation into the mechanisms linking obesity to pathogen-induced immune responses.
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Affiliation(s)
- Evilin N Komegae
- Neuroimmunology of Sepsis Laboratory, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Monique T Fonseca
- Neuroimmunology of Sepsis Laboratory, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Walter M Turato
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Luciano R Filgueiras
- Neuroimmunology of Sepsis Laboratory, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Regina P Markus
- Laboratory of Chronopharmacology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre A Steiner
- Neuroimmunology of Sepsis Laboratory, Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Mai HN, Chung YH, Shin EJ, Jeong JH, Jung TW, Sharma N, Lei XG, Nah SY, Jang CG, Kim DJ, Yang BK, Kim HC. Overexpression of glutathione peroxidase-1 attenuates cocaine-induced reproductive dysfunction in male mice by inhibiting nuclear factor κB. Chem Biol Interact 2019; 307:136-146. [PMID: 31059705 DOI: 10.1016/j.cbi.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
Since reproductive toxicity is associated with oxidative stress, nuclear factor κB (NFκB), a redox-sensitive transcription factor, may be involved in the reproductive dysfunction induced by the abusive drug, such as cocaine. In the present study, we investigated whether NFκB mediates cocaine-induced reproductive dysfunction in male mice, and whether glutathione peroxidase (GPx)-1, a well-known enzymatic antioxidant, modulates NFκB activity to affect this reproductive dysfunction. Cocaine treatment significantly increased nuclear translocation of NFκB and its DNA binding activity in the testis of mice. Treatment with cocaine resulted in a significant increase in sperm abnormality, and in significant decreases in the sperm viability and sperm level. Furthermore, cocaine significantly reduced hypothalamic gonadotropin-releasing-hormone expression and plasma testosterone level. These alterations were more pronounced in the GPx-1 knockout (GPx-1 KO) than wild type (WT) mice, and they were less pronounced in GPx-1 overexpressing transgenic (GPx-1 TG) than in non-transgenic (non-TG) mice. Pyrrolidine dithiocarbamate (PDTC), an NFκB inhibitor, was more effective in attenuating cocaine-induced reproductive toxicity in GPx-1 KO than in WT mice. Although PDTC treatment was also significantly protective against the reproductive toxicity in non-TG mice, PDTC did not show additional positive effects against the protective potential mediated by GPx-1 overexpression in mice. Therefore, our results suggest that GPx-1 gene is a protective factor in response to reproductive dysfunction induced by cocaine in male mice, and that NFκB is a critical mediator of protective activity of GPx-1 gene in our experimental conditions.
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Affiliation(s)
- Huynh Nhu Mai
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chunchon, 24341, Republic of Korea
| | - Yoon Hee Chung
- Department of Anatomy, College of Medicine, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Eun-Joo Shin
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chunchon, 24341, Republic of Korea
| | - Ji Hoon Jeong
- Department of Pharmacology, College of Medicine, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Tae Woo Jung
- Department of Pharmacology, College of Medicine, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Naveen Sharma
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chunchon, 24341, Republic of Korea
| | - Xin Gen Lei
- Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA
| | - Seung-Yeol Nah
- Ginsentology Research Laboratory and Department of Physiology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Choon-Gon Jang
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Dae-Joong Kim
- Department of Anatomy and Cell Biology, Medical School, Kangwon National University, Chunchon, 24341, Republic of Korea
| | - Boo-Keun Yang
- Department of Animal Resource Science, College of Animal Life Science, Kangwon National University, Chunchon, 24341, Republic of Korea
| | - Hyoung-Chun Kim
- Neuropsychopharmacology and Toxicology Program, College of Pharmacy, Kangwon National University, Chunchon, 24341, Republic of Korea.
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Nikopoulou C, Parekh S, Tessarz P. Ageing and sources of transcriptional heterogeneity. Biol Chem 2019; 400:867-878. [DOI: 10.1515/hsz-2018-0449] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
Abstract
Abstract
Cellular heterogeneity is an important contributor to biological function and is employed by cells, tissues and organisms to adapt, compensate, respond, defend and/or regulate specific processes. Research over the last decades has revealed that transcriptional noise is a major driver for cell-to-cell variability. In this review we will discuss sources of transcriptional variability, in particular bursting of gene expression and how it could contribute to cellular states and fate decisions. We will highlight recent developments in single cell sequencing technologies that make it possible to address cellular heterogeneity in unprecedented detail. Finally, we will review recent literature, in which these new technologies are harnessed to address pressing questions in the field of ageing research, such as transcriptional noise and cellular heterogeneity in the course of ageing.
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Affiliation(s)
- Chrysa Nikopoulou
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
- Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) , University of Cologne , Joseph-Stelzmann-Str. 26 , D-50931 Cologne , Germany
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35
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Brignall R, Moody AT, Mathew S, Gaudet S. Considering Abundance, Affinity, and Binding Site Availability in the NF-κB Target Selection Puzzle. Front Immunol 2019; 10:609. [PMID: 30984185 PMCID: PMC6450194 DOI: 10.3389/fimmu.2019.00609] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/07/2019] [Indexed: 12/21/2022] Open
Abstract
The NF-κB transcription regulation system governs a diverse set of responses to various cytokine stimuli. With tools from in vitro biochemical characterizations, to omics-based whole genome investigations, great strides have been made in understanding how NF-κB transcription factors control the expression of specific sets of genes. Nonetheless, these efforts have also revealed a very large number of potential binding sites for NF-κB in the human genome, and a puzzle emerges when trying to explain how NF-κB selects from these many binding sites to direct cell-type- and stimulus-specific gene expression patterns. In this review, we surmise that target gene transcription can broadly be thought of as a function of the nuclear abundance of the various NF-κB dimers, the affinity of NF-κB dimers for the regulatory sequence and the availability of this regulatory site. We use this framework to place quantitative information that has been gathered about the NF-κB transcription regulation system into context and thus consider questions it answers, and questions it raises. We end with a brief discussion of some of the future prospects that new approaches could bring to our understanding of how NF-κB transcription factors orchestrate diverse responses in different biological contexts.
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Affiliation(s)
- Ruth Brignall
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Amy T Moody
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States.,Laboratory for Systems Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, United States.,Department of Microbiology, Tufts University School of Medicine, Boston, MA, United States
| | - Shibin Mathew
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
| | - Suzanne Gaudet
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston, MA, United States
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36
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Mai HN, Chung YH, Shin EJ, Kim DJ, Sharma N, Lee YJ, Jeong JH, Nah SY, Jang CG, Kim HC. Glutathione peroxidase-1 overexpressing transgenic mice are protected from cocaine-induced drug dependence. Neurochem Int 2019; 124:264-273. [DOI: 10.1016/j.neuint.2019.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/13/2019] [Accepted: 01/22/2019] [Indexed: 11/29/2022]
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37
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Riedlinger T, Liefke R, Meier-Soelch J, Jurida L, Nist A, Stiewe T, Kracht M, Schmitz ML. NF-κB p65 dimerization and DNA-binding is important for inflammatory gene expression. FASEB J 2018; 33:4188-4202. [PMID: 30526044 PMCID: PMC6404571 DOI: 10.1096/fj.201801638r] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Increasing evidence shows that many transcription factors execute important biologic functions independent from their DNA-binding capacity. The NF-κB p65 (RELA) subunit is a central regulator of innate immunity. Here, we investigated the relative functional contribution of p65 DNA-binding and dimerization in p65-deficient human and murine cells reconstituted with single amino acid mutants preventing either DNA-binding (p65 E/I) or dimerization (p65 FL/DD). DNA-binding of p65 was required for RelB-dependent stabilization of the NF-κB p100 protein. The antiapoptotic function of p65 and expression of the majority of TNF-α–induced genes were dependent on p65’s ability to bind DNA and to dimerize. Chromatin immunoprecipitation with massively parallel DNA sequencing experiments revealed that impaired DNA-binding and dimerization strongly diminish the chromatin association of p65. However, there were also p65-independent TNF-α–inducible genes and a subgroup of p65 binding sites still allowed some residual chromatin association of the mutants. These sites were enriched in activator protein 1 (AP-1) binding motifs and showed increased chromatin accessibility and basal transcription. This suggests a mechanism of assisted p65 chromatin association that can be in part facilitated by chromatin priming and cooperativity with other transcription factors such as AP-1.—Riedlinger, T., Liefke, R., Meier-Soelch, J., Jurida, L., Nist, A., Stiewe, T., Kracht, M., Schmitz, M. L. NF-κB p65 dimerization and DNA-binding is important for inflammatory gene expression.
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Affiliation(s)
- Tabea Riedlinger
- Institute of Biochemistry, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
| | - Robert Liefke
- Institute of Biochemistry, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany.,Institute of Molecular Biology and Tumor Research (IMT), Philipps University Marburg, Marburg, Germany
| | - Johanna Meier-Soelch
- Rudolf-Buchheim-Institute of Pharmacology, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany; and
| | - Liane Jurida
- Rudolf-Buchheim-Institute of Pharmacology, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany; and
| | - Andrea Nist
- Genomics Core Facility-Institute of Molecular Oncology, Philipps University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility-Institute of Molecular Oncology, Philipps University Marburg, Marburg, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany; and
| | - M Lienhard Schmitz
- Institute of Biochemistry, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
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38
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Miraghazadeh B, Cook MC. Nuclear Factor-kappaB in Autoimmunity: Man and Mouse. Front Immunol 2018; 9:613. [PMID: 29686669 PMCID: PMC5900062 DOI: 10.3389/fimmu.2018.00613] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
NF-κB (nuclear factor-kappa B) is a transcription complex crucial for host defense mediated by innate and adaptive immunity, where canonical NF-κB signaling, mediated by nuclear translocation of RelA, c-Rel, and p50, is important for immune cell activation, differentiation, and survival. Non-canonical signaling mediated by nuclear translocation of p52 and RelB contributes to lymphocyte maturation and survival and is also crucial for lymphoid organogenesis. We outline NF-κB signaling and regulation, then summarize important molecular contributions of NF-κB to mechanisms of self-tolerance. We relate these mechanisms to autoimmune phenotypes described in what is now a substantial catalog of immune defects conferred by mutations in NF-κB pathways in mouse models. Finally, we describe Mendelian autoimmune syndromes arising from human NF-κB mutations, and speculate on implications for understanding sporadic autoimmune disease.
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Affiliation(s)
- Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
- Translational Research Unit, Canberra Hospital, Acton, ACT, Australia
| | - Matthew C. Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
- Translational Research Unit, Canberra Hospital, Acton, ACT, Australia
- Department of Immunology, Canberra Hospital, Acton, ACT, Australia
- *Correspondence: Matthew C. Cook,
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39
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Tilborghs S, Corthouts J, Verhoeven Y, Arias D, Rolfo C, Trinh XB, van Dam PA. The role of Nuclear Factor-kappa B signaling in human cervical cancer. Crit Rev Oncol Hematol 2017; 120:141-150. [PMID: 29198328 DOI: 10.1016/j.critrevonc.2017.11.001] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/01/2017] [Indexed: 12/27/2022] Open
Abstract
Background The Nuclear Factor kappaB (NF-kB) family consists of transcription factors that play a complex and essential role in the regulation of immune responses and inflammation. NF-kB has recently generated considerable interest as it has been implicated in human cancer initiation, progression and resistance to treatment. In the present comprehensive review the different aspects of NF-kB signaling in the carcinogenesis of cancer of the uterine cervix are discussed. NF-kB functions as part of a network, which determines the pattern of its effects on the expression of several other genes (such as crosstalks with reactive oxygen species, p53, STAT3 and miRNAS) and thus its function. Activation of NF-kB triggered by a HPV infection is playing an important role in the innate and adaptive immune response of the host. The virus induces down regulation of NF-kB to liquidate the inhibitory activity for its replication triggered by the immune system leading a status of persistant HPV infection. During the progression to high grade intraepithelial neoplasia and cervical cancer NF-KB becomes constitutionally activated again. Mutations in NF-kB genes are rare in solid tumors but mutations of upstream signaling molecules such as RAS, EGFR, PGF, HER2 have been implicated in elevated NF-kB signaling. NF-kB can stimulate transcription of proliferation regulating genes (eg. cyclin D1 and c-myc), genes involved in metastasis, VEGF dependent angiogenesis and cell immortality by telomerase. NF-kB activation can also induce the expression of activation-induced cytodine deaminase (AID) and the APOBEC proteins, providing a mechanistic link between the NF-kB pathway and mutagenic characteristic of cervical cancer. Inhibition of NF-kB has the potential to be used to reverse resistance to radiotherapy and systemic anti-cancer medication, but currently no clinicaly active NF-kB targeting strategies are available.
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Affiliation(s)
- Sam Tilborghs
- Multidisciplinary Oncologic Centre Antwerp (MOCA) Antwerp University Hospital, Edegem, Belgium
| | - Jerome Corthouts
- Multidisciplinary Oncologic Centre Antwerp (MOCA) Antwerp University Hospital, Edegem, Belgium
| | - Yannick Verhoeven
- Multidisciplinary Oncologic Centre Antwerp (MOCA) Antwerp University Hospital, Edegem, Belgium
| | - David Arias
- Phase I - Early Clinical Trials Unit & Center for Oncological Research (CORE), Antwerp University, Belgium
| | - Christian Rolfo
- Multidisciplinary Oncologic Centre Antwerp (MOCA) Antwerp University Hospital, Edegem, Belgium; Phase I - Early Clinical Trials Unit & Center for Oncological Research (CORE), Antwerp University, Belgium
| | - Xuan Bich Trinh
- Multidisciplinary Oncologic Centre Antwerp (MOCA) Antwerp University Hospital, Edegem, Belgium; Gynecologic Oncology Unit, Antwerp University Hospital & Centre of Oncologic Research (CORE), Antwerp University, Belgium
| | - Peter A van Dam
- Multidisciplinary Oncologic Centre Antwerp (MOCA) Antwerp University Hospital, Edegem, Belgium; Gynecologic Oncology Unit, Antwerp University Hospital & Centre of Oncologic Research (CORE), Antwerp University, Belgium.
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40
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Hong R, Wang K, Shi H. Astrocyte elevated gene-1 promotes inflammation and invasion of fibroblast-like synoviocytes in rheumatoid arthritis. Tissue Cell 2017; 49:672-679. [PMID: 28927747 DOI: 10.1016/j.tice.2017.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/30/2017] [Accepted: 09/12/2017] [Indexed: 11/30/2022]
Abstract
Astrocyte elevated gene-1 (AEG-1) was initially induced by HIV-1 infection and involved in tumor progression, migration and invasion as a nuclear factor-κB (NF-κB)-dependent gene. The present study we intended to investigate the protein expression of AEG-1 significantly associated with rheumatoid arthritis. Western blot analysis and immunohistochemistry demonstrated that AEG-1 was upregulated in synovial tissue of RA patients compared with the controls. Double immunofluorescent staining suggested that AEG-1 was expressed in fibroblast-like synoviocytes (FLS) of RA patients. Furthermore, the expression of AEG-1 in FLS was increased in time-dependent manner by TNF-α stimulation. Upon TNF-α-treated FLS, AEG-1 transferred from the cytoplasm to nucleus where it interacted with the p65 subunit of NF-κB, as examined by immunoprecipitation and immunofluorescent staining assay. Moreover, the inhibition of AEG-1 by RNA interference significantly suppressed TNF-α-induced IL-6 and MMP-3 expression, leading to attenuation of FLS migration and invasion and markedly decreased the phosphorylation of P65 and IκBα, as well as AKT in FLS. Collectively, Our findings provided evidence that AEG-1 contributed to the production of inflammatory cytokines, migration and invasion of RA FLS, and underscored the importance of AEG-1 in the inflammation process of RA.
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Affiliation(s)
- Ruilong Hong
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, PR China
| | - Kun Wang
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, PR China
| | - Hongguang Shi
- Department of Orthopaedics, Affiliated Hospital of Nantong University, Nantong University, Nantong 226001, PR China.
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41
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Shin SY, Kim HW, Jang HH, Hwang YJ, Choe JS, Lim Y, Kim JB, Lee YH. γ-Oryzanol-Rich Black Rice Bran Extract Enhances the Innate Immune Response. J Med Food 2017; 20:855-863. [PMID: 28686509 DOI: 10.1089/jmf.2017.3966] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The innate immune response is an important host primary defense system against pathogens. γ-Oryzanol is one of the nutritionally important phytoceutical components in rice bran oil. The goal of this study was to investigate the effect of γ-oryzanol-rich extract from black rice bran (γORE) on the activation of the innate immune system. In this study, we show that γORE increased the expression of CD14 and Toll-like receptor 4 and enhanced the phagocytic activity of RAW264.7 macrophages. Furthermore, γORE and its active ingredient γ-oryzanol promoted the secretion of innate cytokines, interleukin-8, and CCL2, which facilitate phagocytosis by RAW264.7 cells. These findings suggest that γ-oryzanol in the γORE enhances innate immune responses.
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Affiliation(s)
- Soon Young Shin
- 1 Department of Biological Sciences, Sanghuh College of Life Sciences, Konkuk University , Seoul, Korea.,2 Cancer and Metabolism Institute, Konkuk University , Seoul, Korea
| | - Heon-Woong Kim
- 3 Functional Food and Nutrition Division, National Institute of Agricultural Sciences , Rural Development Administration, Jeonju, Korea
| | - Hwan-Hee Jang
- 3 Functional Food and Nutrition Division, National Institute of Agricultural Sciences , Rural Development Administration, Jeonju, Korea
| | - Yu-Jin Hwang
- 3 Functional Food and Nutrition Division, National Institute of Agricultural Sciences , Rural Development Administration, Jeonju, Korea
| | - Jeong-Sook Choe
- 3 Functional Food and Nutrition Division, National Institute of Agricultural Sciences , Rural Development Administration, Jeonju, Korea
| | - Yoongho Lim
- 4 Division of Bioscience and Biotechnology, BMIC, Konkuk University , Seoul, Korea
| | - Jung-Bong Kim
- 3 Functional Food and Nutrition Division, National Institute of Agricultural Sciences , Rural Development Administration, Jeonju, Korea
| | - Young Han Lee
- 1 Department of Biological Sciences, Sanghuh College of Life Sciences, Konkuk University , Seoul, Korea.,2 Cancer and Metabolism Institute, Konkuk University , Seoul, Korea
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Mathy NW, Chen XM. Long non-coding RNAs (lncRNAs) and their transcriptional control of inflammatory responses. J Biol Chem 2017; 292:12375-12382. [PMID: 28615453 DOI: 10.1074/jbc.r116.760884] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as potential key regulators of the inflammatory response, particularly by modulating the transcriptional control of inflammatory genes. lncRNAs may act as an enhancer or suppressor to inflammatory transcription, function as scaffold molecules through interactions with RNA-binding proteins in chromatin remodeling complexes, and modulate dynamic and epigenetic control of inflammatory transcription in a gene-specific and time-dependent fashion. Here, we will review recent literature regarding the role of lncRNAs in transcriptional control of inflammatory responses. Better understanding of lncRNA regulation of inflammation will provide novel targets for the development of new therapeutic strategies.
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Affiliation(s)
- Nicholas W Mathy
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178.
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Worzfeld T, Pogge von Strandmann E, Huber M, Adhikary T, Wagner U, Reinartz S, Müller R. The Unique Molecular and Cellular Microenvironment of Ovarian Cancer. Front Oncol 2017; 7:24. [PMID: 28275576 PMCID: PMC5319992 DOI: 10.3389/fonc.2017.00024] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/07/2017] [Indexed: 12/13/2022] Open
Abstract
The reciprocal interplay of cancer cells and host cells is an indispensable prerequisite for tumor growth and progression. Cells of both the innate and adaptive immune system, in particular tumor-associated macrophages (TAMs) and T cells, as well as cancer-associated fibroblasts enter into a malicious liaison with tumor cells to create a tumor-promoting and immunosuppressive tumor microenvironment (TME). Ovarian cancer, the most lethal of all gynecological malignancies, is characterized by a unique TME that enables specific and efficient metastatic routes, impairs immune surveillance, and mediates therapy resistance. A characteristic feature of the ovarian cancer TME is the role of resident host cells, in particular activated mesothelial cells, which line the peritoneal cavity in huge numbers, as well as adipocytes of the omentum, the preferred site of metastatic lesions. Another crucial factor is the peritoneal fluid, which enables the transcoelomic spread of tumor cells to other pelvic and peritoneal organs, and occurs at more advanced stages as a malignancy-associated effusion. This ascites is rich in tumor-promoting soluble factors, extracellular vesicles and detached cancer cells as well as large numbers of T cells, TAMs, and other host cells, which cooperate with resident host cells to support tumor progression and immune evasion. In this review, we summarize and discuss our current knowledge of the cellular and molecular interactions that govern this interplay with a focus on signaling networks formed by cytokines, lipids, and extracellular vesicles; the pathophysiologial roles of TAMs and T cells; the mechanism of transcoelomic metastasis; and the cell type selective processing of signals from the TME.
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Affiliation(s)
- Thomas Worzfeld
- Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), Philipps University, Marburg, Germany; Department of Pharmacology, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Elke Pogge von Strandmann
- Experimental Tumor Research, Clinic for Hematology, Oncology and Immunology, Center for Tumor Biology and Immunology, Philipps University , Marburg , Germany
| | - Magdalena Huber
- Institute of Medical Microbiology and Hygiene, Biomedical Research Center, Philipps University , Marburg , Germany
| | - Till Adhikary
- Institute of Molecular Biology and Tumor Research, Center for Tumor Biology and Immunology, Philipps University , Marburg , Germany
| | - Uwe Wagner
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, University Hospital of Giessen and Marburg (UKGM) , Marburg , Germany
| | - Silke Reinartz
- Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Center for Tumor Biology and Immunology (ZTI), Philipps University , Marburg , Germany
| | - Rolf Müller
- Institute of Molecular Biology and Tumor Research, Center for Tumor Biology and Immunology, Philipps University , Marburg , Germany
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Ma S, Ming Z, Gong AY, Wang Y, Chen X, Hu G, Zhou R, Shibata A, Swanson PC, Chen XM. A long noncoding RNA, lincRNA-Tnfaip3, acts as a coregulator of NF-κB to modulate inflammatory gene transcription in mouse macrophages. FASEB J 2016; 31:1215-1225. [PMID: 27979905 DOI: 10.1096/fj.201601056r] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/06/2016] [Indexed: 11/11/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (>200 nt) from the intergenic regions of annotated protein-coding genes. We report here that the lincRNA gene lincRNA-Tnfaip3, located at mouse chromosome 10 proximal to the tumor necrosis factor α-induced protein 3 (Tnfaip3) gene, is an early-primary response gene controlled by nuclear factor-κB (NF-κB) signaling in murine macrophages. Functionally, lincRNA- Tnfaip3 appears to mediate both the activation and repression of distinct classes of inflammatory genes in macrophages. Specifically, induction of lincRNA-Tnfaip3 is required for the transactivation of NF-κB-regulated inflammatory genes in response to bacterial LPSs stimulation. LincRNA-Tnfaip3 physically interacts with the high-mobility group box 1 (Hmgb1), assembling a NF-κB/Hmgb1/lincRNA-Tnfaip3 complex in macrophages after LPS stimulation. This resultant NF-κB/Hmgb1/lincRNA-Tnfaip3 complex can modulate Hmgb1-associated histone modifications and, ultimately, transactivation of inflammatory genes in mouse macrophages in response to microbial challenge. Therefore, our data indicate a new regulatory role of NF-κB-induced lincRNA-Tnfaip3 to act as a coactivator of NF-κB for the transcription of inflammatory genes in innate immune cells through modulation of epigenetic chromatin remodeling.-Ma, S., Ming, Z., Gong, A.-Y., Wang, Y., Chen, X., Hu, G., Zhou, R., Shibata, A., Swanson, P. C., Chen, X.-M. A long noncoding RNA, LincRNA-Tnfaip3, acts as a coregulator of NF-κB to modulate inflammatory gene transcription in mouse macrophages.
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Affiliation(s)
- Shibin Ma
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Zhenping Ming
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA.,Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Hubei, China; and
| | - Ai-Yu Gong
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Yang Wang
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Xiqiang Chen
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Guoku Hu
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Rui Zhou
- Department of Medical Parasitology, School of Basic Medical Sciences, Wuhan University, Hubei, China; and
| | - Annemarie Shibata
- Department of Biology, College of Arts and Sciences, Creighton University, Omaha, Nebraska, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, Nebraska, USA;
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Cheng J, Song J, He X, Zhang M, Hu S, Zhang S, Yu Q, Yang P, Xiong F, Wang DW, Zhou J, Ning Q, Chen Z, Eizirik DL, Zhou Z, Zhao C, Wang CY. Loss of Mbd2 Protects Mice Against High-Fat Diet-Induced Obesity and Insulin Resistance by Regulating the Homeostasis of Energy Storage and Expenditure. Diabetes 2016; 65:3384-3395. [PMID: 27554473 DOI: 10.2337/db16-0151] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022]
Abstract
Previous studies including ours demonstrated that methyl-CpG-binding domain 2 (MBD2) acts as a reader to decipher DNA methylome-encoded information. We thus in the current study used Mbd2-/- mice as a model to dissect the impact of high-fat diet (HFD) on DNA methylome relevant to the pathoetiology of obesity. It was interestingly noted that mice deficient in Mbd2 were protected from HFD-induced obesity and insulin resistance. Mechanistic study revealed that HFD rendered epididymal adipose tissues to undergo a DNA methylation turnover as evidenced by the changes of methylation levels and patterns. Specifically, HFD was noted with higher potency to induce DNA hypomethylation in genes relevant to energy storage than that in genes associated with energy expenditure. As a result, arrays of genes were subjected to expression changes, which led to an altered homeostasis for energy storage and expenditure in favor of obesity development. Loss of Mbd2 resulted in impaired implementation of above DNA methylation changes associated with altered energy homeostasis, which then protected mice from HFD-induced obesity and insulin resistance. Those data would provide novel insight into the understanding of the pathoetiology underlying obesity with potential for developing effective therapies against obesity in clinical settings.
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Affiliation(s)
- Jia Cheng
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Song
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu He
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Zhang
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuang Hu
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Zhang
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qilin Yu
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Yang
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Xiong
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dao Wen Wang
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Ning
- Department of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhishui Chen
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Decio L Eizirik
- Center for Diabetes Research, Universite Libre de Bruxelles, Brussels, Belgium
| | - Zhiguang Zhou
- Diabetes Center, Second Xiangya Hospital, Institute of Metabolism and Endocrinology, Central South University, Changsha, China
| | - Chunxia Zhao
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cong-Yi Wang
- The Center for Biomedical Research, Key Laboratory of Organ Transplantation, Ministry of Education, Tongji Medical College Union Hospital, Huazhong University of Science and Technology, Wuhan, China
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Pan L, Zhu B, Hao W, Zeng X, Vlahopoulos SA, Hazra TK, Hegde ML, Radak Z, Bacsi A, Brasier AR, Ba X, Boldogh I. Oxidized Guanine Base Lesions Function in 8-Oxoguanine DNA Glycosylase-1-mediated Epigenetic Regulation of Nuclear Factor κB-driven Gene Expression. J Biol Chem 2016; 291:25553-25566. [PMID: 27756845 DOI: 10.1074/jbc.m116.751453] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/14/2016] [Indexed: 11/06/2022] Open
Abstract
A large percentage of redox-responsive gene promoters contain evolutionarily conserved guanine-rich clusters; guanines are the bases most susceptible to oxidative modification(s). Consequently, 7,8-dihydro-8-oxoguanine (8-oxoG) is one of the most abundant base lesions in promoters and is primarily repaired via the 8-oxoguanine DNA glycosylase-1 (OOG1)-initiated base excision repair pathway. In view of a prompt cellular response to oxidative challenge, we hypothesized that the 8-oxoG lesion and the cognate repair protein OGG1 are utilized in transcriptional gene activation. Here, we document TNFα-induced enrichment of both 8-oxoG and OGG1 in promoters of pro-inflammatory genes, which precedes interaction of NF-κB with its DNA-binding motif. OGG1 bound to 8-oxoG upstream from the NF-κB motif increased its DNA occupancy by promoting an on-rate of both homodimeric and heterodimeric forms of NF-κB. OGG1 depletion decreased both NF-κB binding and gene expression, whereas Nei-like glycosylase-1 and -2 had a marginal effect. These results are the first to document a novel paradigm wherein the DNA repair protein OGG1 bound to its substrate is coupled to DNA occupancy of NF-κB and functions in epigenetic regulation of gene expression.
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Affiliation(s)
- Lang Pan
- From the Departments of Microbiology and Immunology and.,the Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China, and
| | - Bing Zhu
- From the Departments of Microbiology and Immunology and
| | - Wenjing Hao
- the Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China, and
| | - Xianlu Zeng
- the Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China, and
| | | | - Tapas K Hazra
- Medicine, and.,the Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555
| | - Muralidhar L Hegde
- the Department of Radiation Oncology and Neurology, Methodist Research Institute, Houston, Texas 77030
| | - Zsolt Radak
- From the Departments of Microbiology and Immunology and
| | - Attila Bacsi
- From the Departments of Microbiology and Immunology and
| | - Allan R Brasier
- Medicine, and.,the Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555
| | - Xueqing Ba
- From the Departments of Microbiology and Immunology and .,the Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China, and
| | - Istvan Boldogh
- From the Departments of Microbiology and Immunology and .,the Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555
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ASF1a enhances antiviral immune response by associating with CBP to mediate acetylation of H3K56 at the Ifnb promoter. Mol Immunol 2016; 78:57-64. [DOI: 10.1016/j.molimm.2016.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/15/2016] [Accepted: 08/13/2016] [Indexed: 01/01/2023]
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Sharma V, Monti P, Fronza G, Inga A. Human transcription factors in yeast: the fruitful examples of P53 and NF-кB. FEMS Yeast Res 2016; 16:fow083. [PMID: 27683095 DOI: 10.1093/femsyr/fow083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2016] [Indexed: 12/31/2022] Open
Abstract
The observation that human transcription factors (TFs) can function when expressed in yeast cells has stimulated the development of various functional assays to investigate (i) the role of binding site sequences (herein referred to as response elements, REs) in transactivation specificity, (ii) the impact of polymorphic nucleotide variants on transactivation potential, (iii) the functional consequences of mutations in TFs and (iv) the impact of cofactors or small molecules. These approaches have found applications in basic as well as applied research, including the identification and the characterisation of mutant TF alleles from clinical samples. The ease of genome editing of yeast cells and the availability of regulated systems for ectopic protein expression enabled the development of quantitative reporter systems, integrated at a chosen chromosomal locus in isogenic yeast strains that differ only at the level of a specific RE targeted by a TF or for the expression of distinct TF alleles. In many cases, these assays were proven predictive of results in higher eukaryotes. The potential to work in small volume formats and the availability of yeast strains with modified chemical uptake have enhanced the scalability of these approaches. Next to well-established one-, two-, three-hybrid assays, the functional assays with non-chimeric human TFs enrich the palette of opportunities for functional characterisation. We review ∼25 years of research on human sequence-specific TFs expressed in yeast, with an emphasis on the P53 and NF-кB family of proteins, highlighting outcomes, advantages, challenges and limitations of these heterologous assays.
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Affiliation(s)
- Vasundhara Sharma
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
| | - Paola Monti
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Gilberto Fronza
- U.O.C. Mutagenesi, IRCCS AOU San Martino-IST, Largo R. Benzi, 10, 16132, Genova, Italy
| | - Alberto Inga
- Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 9, 38123, Trento, Italy
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The PRKD1 promoter is a target of the KRas-NF-κB pathway in pancreatic cancer. Sci Rep 2016; 6:33758. [PMID: 27649783 PMCID: PMC5030668 DOI: 10.1038/srep33758] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/01/2016] [Indexed: 12/15/2022] Open
Abstract
Increased expression of PRKD1 and its gene product protein kinase D1 (PKD1) are linked to oncogenic signaling in pancreatic ductal adenocarcinoma, but a direct functional relationship to oncogenic KRas has not been established so far. We here describe the PRKD1 gene promoter as a target for oncogenic KRas signaling. We demonstrate that KRas-induced activation of the canonical NF-κB pathway is one mechanism of how PRKD1 expression is increased and identify the binding sites for NF-κB in the PRKD1 promoter. Altogether, these results describe a novel mechanism governing PRKD1 gene expression in PDA and provide a functional link between oncogenic KRas, NF-κB and expression of PRKD1.
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Inhibition of nuclear factor kappaB proteins-platinated DNA interactions correlates with cytotoxic effectiveness of the platinum complexes. Sci Rep 2016; 6:28474. [PMID: 27574114 PMCID: PMC5004165 DOI: 10.1038/srep28474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Nuclear DNA is the target responsible for anticancer activity of platinum anticancer drugs. Their activity is mediated by altered signals related to programmed cell death and the activation of various signaling pathways. An example is activation of nuclear factor kappaB (NF-κB). Binding of NF-κB proteins to their consensus sequences in DNA (κB sites) is the key biochemical activity responsible for the biological functions of NF-κB. Using gel-mobility-shift assays and surface plasmon resonance spectroscopy we examined the interactions of NF-κB proteins with oligodeoxyribonucleotide duplexes containing κB site damaged by DNA adducts of three platinum complexes. These complexes markedly differed in their toxic effects in tumor cells and comprised highly cytotoxic trinuclear platinum(II) complex BBR3464, less cytotoxic conventional cisplatin and ineffective transplatin. The results indicate that structurally different DNA adducts of these platinum complexes exhibit a different efficiency to affect the affinity of the platinated DNA (κB sites) to NF-κB proteins. Our results support the hypothesis that structural perturbations induced in DNA by platinum(II) complexes correlate with their higher efficiency to inhibit binding of NF-κB proteins to their κB sites and cytotoxicity as well. However, the full generalization of this hypothesis will require to evaluate a larger series of platinum(II) complexes.
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