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Kimura-Ishimaru C, Liang S, Matsuse K, Iwama R, Sato K, Watanabe N, Tezaki S, Horiuchi H, Fukuda R. Mar1, a high mobility group box protein, regulates n-alkane adsorption and cell morphology of the dimorphic yeast Yarrowia lipolytica. Appl Environ Microbiol 2024; 90:e0054624. [PMID: 39058021 PMCID: PMC11337826 DOI: 10.1128/aem.00546-24] [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: 03/22/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
The dimorphic yeast Yarrowia lipolytica possesses an excellent ability to utilize n-alkane as a sole carbon and energy source. Although there are detailed studies on the enzymes that catalyze the reactions in the metabolic processes of n-alkane in Y. lipolytica, the molecular mechanism underlying the incorporation of n-alkane into the cells remains to be elucidated. Because Y. lipolytica adsorbs n-alkane, we postulated that Y. lipolytica incorporates n-alkane through direct interaction with it. We isolated and characterized mutants defective in adsorption to n-hexadecane. One of the mutants harbored a nonsense mutation in MAR1 (Morphology and n-alkane Adsorption Regulator 1) encoding a protein containing a high mobility group box. The deletion mutant of MAR1 exhibited defects in adsorption to n-hexadecane and filamentous growth on solid media, whereas the strain that overexpressed MAR1 exhibited hyperfilamentous growth. Fluorescence microscopic observations suggested that Mar1 localizes in the nucleus. RNA-sequencing analysis revealed the alteration of the transcript levels of several genes, including those encoding transcription factors and cell surface proteins, by the deletion of MAR1. These findings suggest that MAR1 is involved in the transcriptional regulation of the genes required for n-alkane adsorption and cell morphology transition.IMPORTANCEYarrowia lipolytica, a dimorphic yeast capable of assimilating n-alkane as a carbon and energy source, has been extensively studied as a promising host for bioconversion of n-alkane into useful chemicals and bioremediation of soil and water contaminated by petroleum. While the metabolic pathway of n-alkane in this yeast and the enzymes involved in this pathway have been well characterized, the molecular mechanism to incorporate n-alkane into the cells is yet to be fully understood. Due to the ability of Y. lipolytica to adsorb n-alkane, it has been hypothesized that Y. lipolytica incorporates n-alkane through direct interaction with it. In this study, we identified a gene, MAR1, which plays a crucial role in the transcriptional regulation of the genes necessary for the adsorption to n-alkane and the transition of the cell morphology in Y. lipolytica. Our findings provide valuable insights that could lead to advanced applications of Y. lipolytica in n-alkane bioconversion and bioremediation.
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Affiliation(s)
| | - Simiao Liang
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Katsuro Matsuse
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenta Sato
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Natsuhito Watanabe
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Tezaki
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Chikhirzhina E, Tsimokha A, Tomilin AN, Polyanichko A. Structure and Functions of HMGB3 Protein. Int J Mol Sci 2024; 25:7656. [PMID: 39062899 PMCID: PMC11276821 DOI: 10.3390/ijms25147656] [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: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
HMGB3 protein belongs to the group of HMGB proteins from the superfamily of nuclear proteins with high electrophoretic mobility. HMGB proteins play an active part in almost all cellular processes associated with DNA-repair, replication, recombination, and transcription-and, additionally, can act as cytokines during infectious processes, inflammatory responses, and injuries. Although the structure and functions of HMGB1 and HMGB2 proteins have been intensively studied for decades, very little attention has been paid to HMGB3 until recently. In this review, we summarize the currently available data on the molecular structure, post-translational modifications, and biological functions of HMGB3, as well as the possible role of the ubiquitin-proteasome system-dependent HMGB3 degradation in tumor development.
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Affiliation(s)
- Elena Chikhirzhina
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Av. 4, 194064 St. Petersburg, Russia; (A.T.); (A.N.T.); (A.P.)
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Takahashi M, Chong HB, Zhang S, Yang TY, Lazarov MJ, Harry S, Maynard M, Hilbert B, White RD, Murrey HE, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali ASO, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher DE, Maheswaran S, Haber DA, Boland GM, Sade-Feldman M, Jenkins RW, Hata AN, Bardeesy NM, Suvà ML, Martin BR, Liau BB, Ott CJ, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell 2024; 187:2536-2556.e30. [PMID: 38653237 PMCID: PMC11143475 DOI: 10.1016/j.cell.2024.03.027] [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: 10/01/2023] [Revised: 01/15/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors for a wide range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed "DrugMap," an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NF-κB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NF-κB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription-factor activity.
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Affiliation(s)
- Mariko Takahashi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA.
| | - Harrison B Chong
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Siwen Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Tzu-Yi Yang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Matthew J Lazarov
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Stefan Harry
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Kira Vordermark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Jonathan Assaad
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Magdy Gohar
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Benedikt R Dürr
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Marianne Richter
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Himani Patel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | | | | | - Karla Rubio
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Antonio Villanueva
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Junbing Zhang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Maolin Ge
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farah Makram
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Hanna Griesshaber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Drew Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ann-Sophie Koglin
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Barbara Karakyriakou
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Alexander Healy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - George Popoola
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Inbal Rachmin
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Neha Khandelwal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | | | - Pei-Chieh Tien
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Nicholas Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Tobias Hosp
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sanne van den Ouweland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Toshiro Hara
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lillian Bussema
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lei Shi
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Martin Q Rasmussen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Ana Carolina Domingues
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Aleigha Lawless
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacy Fang
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Satoshi Yoda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Linh Phuong Nguyen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Marie Reeves
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Farrah Nicole Wakefield
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Adam Acker
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Sarah Elizabeth Clark
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Taronish Dubash
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - John Kastanos
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA
| | - Eugene Oh
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - David E Fisher
- Cutaneous Biology Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shyamala Maheswaran
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel A Haber
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Genevieve M Boland
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Surgery, Harvard Medical School, Boston, MA 02114, USA
| | - Moshe Sade-Feldman
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Russell W Jenkins
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Aaron N Hata
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Nabeel M Bardeesy
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Mario L Suvà
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Miguel N Rivera
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S Lawrence
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Harvard Medical School, Boston, MA 02114, USA.
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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Su H, Zou R, Su J, Chen X, Yang H, An N, Yang C, Tang J, Liu H, Yao C. Sterile inflammation of peritoneal membrane caused by peritoneal dialysis: focus on the communication between immune cells and peritoneal stroma. Front Immunol 2024; 15:1387292. [PMID: 38779674 PMCID: PMC11109381 DOI: 10.3389/fimmu.2024.1387292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Peritoneal dialysis is a widely used method for treating kidney failure. However, over time, the peritoneal structure and function can deteriorate, leading to the failure of this therapy. This deterioration is primarily caused by infectious and sterile inflammation. Sterile inflammation, which is inflammation without infection, is particularly concerning as it can be subtle and often goes unnoticed. The onset of sterile inflammation involves various pathological processes. Peritoneal cells detect signals that promote inflammation and release substances that attract immune cells from the bloodstream. These immune cells contribute to the initiation and escalation of the inflammatory response. The existing literature extensively covers the involvement of different cell types in the sterile inflammation, including mesothelial cells, fibroblasts, endothelial cells, and adipocytes, as well as immune cells such as macrophages, lymphocytes, and mast cells. These cells work together to promote the occurrence and progression of sterile inflammation, although the exact mechanisms are not fully understood. This review aims to provide a comprehensive overview of the signals from both stromal cells and components of immune system, as well as the reciprocal interactions between cellular components, during the initiation of sterile inflammation. By understanding the cellular and molecular mechanisms underlying sterile inflammation, we may potentially develop therapeutic interventions to counteract peritoneal membrane damage and restore normal function.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huafeng Liu
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Cuiwei Yao
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
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Tian Z, Zhu L, Xie Y, Hu H, Ren Q, Liu J, Wang Q. The mechanism of high mobility group box-1 protein and its bidirectional regulation in tumors. BIOMOLECULES & BIOMEDICINE 2024; 24:477-485. [PMID: 37897664 PMCID: PMC11088895 DOI: 10.17305/bb.2023.9760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023]
Abstract
High-mobility group box-1 protein (HMGB1) is a nonhistone chromatin-related protein widely found in eukaryotic cells. It is involved in the transcription, replication, and repair of DNA to maintain nuclear homeostasis. It participates in cell growth, differentiation, and signal transduction. Recent studies showed that HMGB1 has a bidirectional regulatory effect on tumors by regulating TLR4/MYD88/NF-κB and RAGE/AMPK/mTOR signaling pathways. On the one hand, it is highly expressed in a variety of tumors, promoting tumor proliferation and invasion, while on the other hand, it induces autophagy and apoptosis of tumor cells and stimulates tumor-infiltrating lymphocytes to produce an anti-tumor immune response. At present, HMGB1 could be used as a target to regulate the drug resistance and prognostication in cancer. Clinical applications of HMGB1 in cancer need further in-depth studies.
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Affiliation(s)
- Zhongjia Tian
- The Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Lin Zhu
- The Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Yutong Xie
- The Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Huan Hu
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Qunli Ren
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Jianguo Liu
- The Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
| | - Qian Wang
- The Affiliated Stomatological Hospital of Zunyi Medical University, Zunyi, China
- Oral Disease Research Key Laboratory of Guizhou Tertiary Institution, School of Stomatology, Zunyi Medical University, Zunyi, China
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Liao M, Cao J, Chen W, Wang M, Jin Z, Ye J, Ren Y, Wei Y, Xue Y, Chen D, Zhang Y, Chen S. HMGB1 prefers to interact with structural RNAs and regulates rRNA methylation modification and translation in HeLa cells. BMC Genomics 2024; 25:345. [PMID: 38580917 PMCID: PMC10996203 DOI: 10.1186/s12864-024-10204-6] [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: 05/30/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND High-mobility group B1 (HMGB1) is both a DNA binding nuclear factor modulating transcription and a crucial cytokine that mediates the response to both infectious and noninfectious inflammation such as autoimmunity, cancer, trauma, and ischemia reperfusion injury. HMGB1 has been proposed to control ribosome biogenesis, similar as the other members of a class of HMGB proteins. RESULTS Here, we report that HMGB1 selectively promotes transcription of genes involved in the regulation of transcription, osteoclast differentiation and apoptotic process. Improved RNA immunoprecipitation by UV cross-linking and deep sequencing (iRIP-seq) experiment revealed that HMGB1 selectively bound to mRNAs functioning not only in signal transduction and gene expression, but also in axon guidance, focal adhesion, and extracellular matrix organization. Importantly, HMGB1-bound reads were strongly enriched in specific structured RNAs, including the domain II of 28S rRNA, H/ACA box snoRNAs including snoRNA63 and scaRNAs. RTL-P experiment showed that overexpression of HMGB1 led to a decreased methylation modification of 28S rRNA at position Am2388, Cm2409, and Gm2411. We further showed that HMGB1 overexpression increased ribosome RNA expression levels and enhanced protein synthesis. CONCLUSION Taken together, our results support a model in which HMGB1 binds to multiple RNA species in human cancer cells, which could at least partially contribute to HMGB1-modulated rRNA modification, protein synthesis function of ribosomes, and differential gene expression including rRNA genes. These findings provide additional mechanistic clues to HMGB1 functions in cancers and cell differentiation.
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Affiliation(s)
- Meimei Liao
- Department of Ultrasound Imaging, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Jiarui Cao
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Wen Chen
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Mengwei Wang
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Zhihui Jin
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Jia Ye
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Yijun Ren
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Yaqiang Xue
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2Nd Road, Hubei, Wuhan, 430075, China
| | - Sen Chen
- Department of Orthopedics, Renmin Hospital of Wuhan University, Hubei, Wuhan, People's Republic of China.
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Ye J, Gao S, Liu Z, Chen X, He J, Hu Z. The HMGB1-RAGE axis in nucleus accumbens facilitates cocaine-induced conditioned place preference via modulating microglial activation. Brain Behav 2024; 14:e3457. [PMID: 38450910 PMCID: PMC10918599 DOI: 10.1002/brb3.3457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/22/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
INTRODUCTION Repeated exposure to cocaine induces microglial activation. Cocaine exposure also induces a release of high mobility group box-1 (HMGB1) from neurons into the extracellular space in the nucleus accumbens (NAc). HMGB1 is an important late inflammatory mediator of microglial activation. However, whether the secretion of HMGB1 acts on microglia or contributes to cocaine addiction is largely unknown. METHODS Rats were trained by intraperitoneal cocaine administration and cocaine-induced conditioned place preference (CPP). Expression of HMGB1 was regulated by viral vectors. Activation of microglia was inhibited by minocycline. Interaction of HMGB1 and the receptor for advanced glycation end products (RAGE) was disrupted by peptide. RESULTS Cocaine injection facilitated HMGB1 signaling, together with the delayed activation of microglia concurrently in the NAc. Furthermore, the inhibition of HMGB1 or microglia activation attenuated cocaine-induced CPP. Box A, a specific antagonist to interrupt the interaction of HMGB1 and RAGE, abolished the expression of cocaine reward memory. Meanwhile, the inhibition of HMGB1-RAGE interaction suppressed cocaine-induced microglial activation, as well as the consolidation of cocaine-induced memory. CONCLUSION All above results suggest that the neural HMGB1 induces activation of microglia through RAGE, which contributes to the consolidation of cocaine reward memory. These findings offer HMGB1-RAGE axis as a new target for the treatment of drug addiction.
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Affiliation(s)
- Jian Ye
- Department of Pharmacology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Shuang‐Qi Gao
- Department of Pharmacology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Departments of NeurosurgeryThird Affiliated Hospital of Sun Yat‐Sen UniversityGuangzhouGuangdong ProvinceChina
| | - Zi‐Cun Liu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xi Chen
- Department of Pharmacology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Jin‐Gang He
- Department of Pharmacology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Zhuang‐Li Hu
- Department of Pharmacology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei ProvinceWuhanChina
- The Research Center for Depression, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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8
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Tan BG, Gustafsson CM, Falkenberg M. Mechanisms and regulation of human mitochondrial transcription. Nat Rev Mol Cell Biol 2024; 25:119-132. [PMID: 37783784 DOI: 10.1038/s41580-023-00661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2023] [Indexed: 10/04/2023]
Abstract
The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.
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Affiliation(s)
- Benedict G Tan
- Institute for Mitochondrial Diseases and Ageing, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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9
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Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genet 2024; 20:e1011107. [PMID: 38181050 PMCID: PMC10795994 DOI: 10.1371/journal.pgen.1011107] [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: 08/10/2023] [Revised: 01/18/2024] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are part of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-ΔHMG and lsd2-ΔC, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complex (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stress conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.
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Affiliation(s)
- Haoran Liu
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Bahjat Fadi Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David de la Cerda
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Brendan Matthew Lemezis
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jieyu Gao
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, Florida, United States of America
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Ke Zhang Reid
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
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10
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Liu XN, Cheng ZP. Expression of high-mobility group box-1 in eutopic/ectopic endometrium and correlations with inflammation-related factors in adenomyosis. Gynecol Endocrinol 2023; 39:2269265. [PMID: 37967572 DOI: 10.1080/09513590.2023.2269265] [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: 04/24/2023] [Accepted: 10/05/2023] [Indexed: 11/17/2023] Open
Abstract
OBJECTIVE To investigate the expression of HMGB1 and toll-like receptor 4 (TLR4) in adenomyosis eutopic/ectopic endometrium. METHODS Twenty patients with adenomyosis and 20 controls, all undergoing laparoscopy, were recruited from September 2015 to July 2016. Samples were collected from the endometrium without adenomyosis (CE), the eutopic endometrium with adenomyosis (EuE), and the ectopic endometrium with adenomyosis (EE). The mRNA and protein expression of HMGB1 and TLR4, and interleukin-6 (IL-6) and interleukin-8 (IL-8) RNA expression levels were measured. RESULTS The average age of the adenomyosis women was 43.4 ± 5.3 years; their BMI was 23.3 ± 2.3 kg/m2. The control group included women aged 38.8 ± 9.8 years, with BMI 22.2 ± 3.4 kg/m2. The mRNA expression levels of HMGB1, TLR4, IL-6, and IL-8 in the EE and EuE groups were higher than those in the CE group (p < .01), and those in the EE group were higher than those in the EuE group (p < .01). The protein expression levels of HMGB1 and TLR4 in the EE and EuE groups were higher than those in the CE group (p < .01); they were higher in the EE group than the ones in the EuE group (p < .01). HMGB1 mRNA was significantly positively correlated with TLR4 in EuE and EC patients (r = 0.538 and r = 0.916, p < .01), as well as with IL-6 (r = 0.470 and r = 0.976, p < .01) and IL-8 (r = 0.574 and r = 0.650, p < .01). CONCLUSIONS The overexpression of HMGB1 and TLR4 in EuE and EE is positively correlated with IL-6 and IL-8 expression. The HMGB1 signaling-mediated immune-inflammatory system might be involved in the development of adenomyosis.
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Affiliation(s)
- Xiu-Ni Liu
- Department of Gynecology and Obstetrics, Tenth People's Hospital, Tongji University, Shanghai, PR China
| | - Zhong-Ping Cheng
- Department of Gynecology and Obstetrics, Tenth People's Hospital, Tongji University, Shanghai, PR China
- Institute of Gynecological Minimal Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
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11
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Schrott S, Osman C. Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae. Nucleic Acids Res 2023; 51:11813-11835. [PMID: 37850632 PMCID: PMC10681731 DOI: 10.1093/nar/gkad849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals are critical for mtDNA maintenance and packaging and have been linked to mtDNA copy number control. Here, we discover the previously unrecognized mitochondrial HMG-box protein Cim1 (copy number influence on mtDNA) in Saccharomyces cerevisiae, which exhibits metabolic state dependent mtDNA association. Surprisingly, in contrast to Abf2's supportive role in mtDNA maintenance, Cim1 negatively regulates mtDNA copy number. Cells lacking Cim1 display increased mtDNA levels and enhanced mitochondrial function, while Cim1 overexpression results in mtDNA loss. Intriguingly, Cim1 deletion alleviates mtDNA maintenance defects associated with loss of Abf2, while defects caused by Cim1 overexpression are mitigated by simultaneous overexpression of Abf2. Moreover, we find that the conserved LON protease Pim1 is essential to maintain low Cim1 levels, thereby preventing its accumulation and concomitant repressive effects on mtDNA. We propose a model in which the protein ratio of antagonistically acting Cim1 and Abf2 determines mtDNA copy number.
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Affiliation(s)
- Simon Schrott
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, Planegg-Martinsried 82152, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, Planegg-Martinsried 82152, Germany
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12
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Chen X, Liu Q, Wu E, Ma Z, Tuo B, Terai S, Li T, Liu X. The role of HMGB1 in digestive cancer. Biomed Pharmacother 2023; 167:115575. [PMID: 37757495 DOI: 10.1016/j.biopha.2023.115575] [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: 08/08/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
High mobility group box protein B1 (HMGB1) belongs to the HMG family, is widely expressed in the nucleus of digestive mucosal epithelial cells, mesenchymal cells and immune cells, and binds to DNA to participate in genomic structural stability, mismatch repair and transcriptional regulation to maintain normal cellular activities. In the context of digestive inflammation and tumors, HMGB1 readily migrates into the extracellular matrix and binds to immune cell receptors to affect their function and differentiation, further promoting digestive tract tissue injury and tumor development. Notably, HMGB1 can also promote the antitumor immune response. Therefore, these seemingly opposing effects in tumors make targeted HMGB1 therapies important in digestive cancer. This review focuses on the role of HMGB1 in tumors and its effects on key pathways of digestive cancer and aims to provide new possibilities for targeted tumor therapy.
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Affiliation(s)
- Xiangqi Chen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Qian Liu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Enqing Wu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Zhiyuan Ma
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China
| | - Shuji Terai
- Division of Gastroenterology & Hepatology, Graduate School of Medical and Dental Sciences, Niigata University, Japan
| | - Taolang Li
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China.
| | - Xuemei Liu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, China.
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13
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Huang Y, Liangpunsakul S, Rudraiah S, Ma J, Keshipeddy SK, Wright D, Costa A, Burgess D, Zhang Y, Huda N, Wang L, Yang Z. HMGB2 is a potential diagnostic marker and therapeutic target for liver fibrosis and cirrhosis. Hepatol Commun 2023; 7:e0299. [PMID: 37930124 PMCID: PMC10629741 DOI: 10.1097/hc9.0000000000000299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/23/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND High mobility group proteins 1 and 2 (HMGB1 and HMGB2) are 80% conserved in amino acid sequence. The function of HMGB1 in inflammation and fibrosis has been extensively characterized. However, an unaddressed central question is the role of HMGB2 on liver fibrosis. In this study, we provided convincing evidence that the HMGB2 expression was significantly upregulated in human liver fibrosis and cirrhosis, as well as in several mouse liver fibrosis models. METHODS The carbon tetrachloride (CCl4) induced liver fibrosis mouse model was used. AAV8-Hmgb2 was utilized to overexpress Hmgb2 in the liver, while Hmgb2-/- mice were used for loss of function experiments. The HMGB2 inhibitor inflachromene and liposome-shHMGB2 (lipo-shHMGB2) were employed for therapeutic intervention. RESULTS The serum HMGB2 levels were also markedly elevated in patients with liver fibrosis and cirrhosis. Deletion of Hmgb2 in Hmgb2-/- mice or inhibition of HMGB2 in mice using a small molecule ICM slowed the progression of CCl4-induced liver fibrosis despite constant HMGB1 expression. In contrast, AAV8-mediated overexpression of Hmgb2 enchanced CCl4-incuded liver fibrosis. Primary hepatic stellate cells (HSCs) isolated from Hmgb2-/- mice showed significantly impaired transdifferentiation and diminished activation of α-SMA, despite a modest induction of HMGB1 protein. RNA-seq analysis revealed the induction of top 45 CCl4-activated genes in multiple signaling pathways including integrin signaling and inflammation. The activation of these genes by CCl4 were abolished in Hmgb2-/- mice or in ICM-treated mice. These included C-X3-C motif chemokine receptor 1 (Cx3cr1) associated with inflammation, cyclin B (Ccnb) associated with cell cycle, DNA topoisomerase 2-alpha (Top2a) associated with intracellular component, and fibrillin (Fbn) and fibromodulin (Fmod) associated with extracellular matrix. CONCLUSION We conclude that HMGB2 is indispensable for stellate cell activation. Therefore, HMGB2 may serve as a potential therapeutic target to prevent HSC activation during chronic liver injury. The blood HMGB2 level may also serve as a potential diagnostic marker to detect early stage of liver fibrosis and cirrhosis in humans.
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Affiliation(s)
- Yi Huang
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Suthat Liangpunsakul
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University, Indianapolis, Indiana, USA
- Medicine Service, Roudebush Veterans Administration Medical Center, Indianapolis, Indiana, USA
| | - Swetha Rudraiah
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA
| | - Jing Ma
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University, Indianapolis, Indiana, USA
| | - Santosh K. Keshipeddy
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Dennis Wright
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Antonio Costa
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Diane Burgess
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Yuxia Zhang
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nazmul Huda
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University, Indianapolis, Indiana, USA
| | - Li Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Zhihong Yang
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University, Indianapolis, Indiana, USA
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14
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Takahashi M, Chong HB, Zhang S, Lazarov MJ, Harry S, Maynard M, White R, Murrey HE, Hilbert B, Neil JR, Gohar M, Ge M, Zhang J, Durr BR, Kryukov G, Tsou CC, Brooijmans N, Alghali ASO, Rubio K, Vilanueva A, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Assaad J, Makram F, Rachman I, Khandelwal N, Tien PC, Popoola G, Chen N, Vordermark K, Richter M, Patel H, Yang TY, Griesshaber H, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Fisher DE, Maheswaran S, Haber DA, Boland G, Sade-Feldman M, Jenkins R, Hata A, Bardeesy N, Suva ML, Martin B, Liau B, Ott C, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563287. [PMID: 37961514 PMCID: PMC10634688 DOI: 10.1101/2023.10.20.563287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cysteine-focused chemical proteomic platforms have accelerated the clinical development of covalent inhibitors of a wide-range of targets in cancer. However, how different oncogenic contexts influence cysteine targeting remains unknown. To address this question, we have developed DrugMap , an atlas of cysteine ligandability compiled across 416 cancer cell lines. We unexpectedly find that cysteine ligandability varies across cancer cell lines, and we attribute this to differences in cellular redox states, protein conformational changes, and genetic mutations. Leveraging these findings, we identify actionable cysteines in NFκB1 and SOX10 and develop corresponding covalent ligands that block the activity of these transcription factors. We demonstrate that the NFκB1 probe blocks DNA binding, whereas the SOX10 ligand increases SOX10-SOX10 interactions and disrupts melanoma transcriptional signaling. Our findings reveal heterogeneity in cysteine ligandability across cancers, pinpoint cell-intrinsic features driving cysteine targeting, and illustrate the use of covalent probes to disrupt oncogenic transcription factor activity.
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15
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Wang Y, Wang F, Lu H, Lin R, Liu J, Liu Y, Xu J, Wu Y, Wang Z, Zhou M, Mo X, Wu Z, Shou H, Zheng S, Mao C. Rice chromatin protein OsHMGB1 is involved in phosphate homeostasis and plant growth by affecting chromatin accessibility. THE NEW PHYTOLOGIST 2023; 240:727-743. [PMID: 37553956 DOI: 10.1111/nph.19189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Although phosphorus is one of the most important essential elements for plant growth and development, the epigenetic regulation of inorganic phosphate (Pi) signaling is poorly understood. In this study, we investigated the biological function and mode of action of the high-mobility-group box 1 protein OsHMGB1 in rice (Oryza sativa), using molecular and genetic approaches. We determined that OsHMGB1 expression is induced by Pi starvation and encodes a nucleus-localized protein. Phenotypic analysis of Oshmgb1 mutant and OsHMGB1 overexpression transgenic plants showed that OsHMGB1 positively regulates Pi homeostasis and plant growth. Transcriptome deep sequencing and chromatin immunoprecipitation followed by sequencing indicated that OsHMGB1 regulates the expression of a series of phosphate starvation-responsive (PSR) genes by binding to their promoters. Furthermore, an assay for transposase-accessible chromatin followed by sequencing revealed that OsHMGB1 is involved in maintaining chromatin accessibility. Indeed, OsHMGB1 occupancy positively correlated with genome-wide chromatin accessibility and gene expression levels. Our results demonstrate that OsHMGB1 is a transcriptional facilitator that regulates the expression of a set of PSR genes to maintain Pi homeostasis in rice by increasing the chromatin accessibility, revealing a key epigenetic mechanism that fine-tune plant acclimation responses to Pi-limited environments.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong Lu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rongbin Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiaming Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yu Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yunrong Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ming Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhongchang Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuanzao Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Yazhou Bay Science and Technology City, Zhejiang University, Yazhou District, Sanya, Hainan, 572024, China
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16
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Wang X, Chen S, Wen F, Zeng Y, Zhang Y. RNA helicase DHX33 regulates HMGB family genes in human cancer cells. Cell Signal 2023; 110:110832. [PMID: 37543097 DOI: 10.1016/j.cellsig.2023.110832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/07/2023]
Abstract
RNA helicase DHX33 has been shown to be aberrantly expressed in various human cancers, however, its role in tumorigenesis remains incompletely understood. In this report, we uncovered that a family of DNA architecture proteins, HMGBs, can be regulated by DHX33 in cancer cells but not in normal cells. Specifically, DHX33 knockdown caused the downregulation of HMGBs at the levels of both gene transcription and protein expression. Notably, in RAS driven lung tumorigenesis, nuclear HMGBs proteins can be induced via DHX33. When DHX33 was knocked out, HMGBs overexpression was debilitated. Mechanistically, DHX33 was found to bind to the promoters of HMGB family genes and regulated their transcription through demethylation on gene promoters. Our study reveals a novel mechanism for DHX33 to promote tumorigenesis and highlights its therapeutic value in human cancers.
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Affiliation(s)
- Xingshun Wang
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653199, China
| | - Shiyun Chen
- Shenzhen KeYe Life Technologies, Co., Ltd, Shenzhen, Guangdong 518122, China; Southern University of Science and Technology, Shenzhen, China
| | - Fuyu Wen
- Shenzhen KeYe Life Technologies, Co., Ltd, Shenzhen, Guangdong 518122, China
| | - Yong Zeng
- The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, Yunnan 653199, China.
| | - Yandong Zhang
- Shenzhen KeYe Life Technologies, Co., Ltd, Shenzhen, Guangdong 518122, China.
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17
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Mollah MMI. Spätzle processing enzyme is required to activate dorsal switch protein 1 induced Toll immune signalling pathway in Tenebrio molitor. PLoS One 2023; 18:e0291976. [PMID: 37733725 PMCID: PMC10513244 DOI: 10.1371/journal.pone.0291976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Dorsal switch protein 1 (DSP1) acts as a damage-associated molecular pattern (DAMP) molecule to activate immune responses in Tenebrio molitor. From a previous study in Spodoptera exigua, we found that DSP1 activates Toll immune signalling pathway to induce immune responses by melanisation, PLA2 activity and AMP synthesis. However, the target site of DSP1 in this pathway remains unknown. The objective of this study was to determine the role of spätzle processing enzyme in the DSP1 induced toll immune signalling pathway. To address this, we analyzed spätzle processing enzyme (Tm-SPE) of the three-step serine protease cascade of T. molitor Toll pathway. Tm-SPE expressed in all developmental stages and larval tissues. Upon immune challenge, its expression levels were upregulated but significantly reduced after RNA interference (RNAi). In addition, the induction of immune responses upon immune challenge or recombinant DSP1 injection was significantly increased. Loss of function using RNA interference revealed that the Tm-SPE is involved in connecting DSP1 induced immune responses like hemocyte nodule formation, phenoloxidase (PO) activity, phospholipase A2 (PLA2) activity and antimicrobial peptide (AMP) synthesis. These suggest that Tm-SPE controls the DSP1 induced activation of Toll immune signalling pathway required for both cellular and humoral immune responses. However, to confirm the target molecule of DSP1 in three-step proteolytic cascade, we have to check other upstream serine proteases like Spatzle activating enzyme (SAE) or modular serine protease (MSP).
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Affiliation(s)
- Md. Mahi Imam Mollah
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, Republic of Korea
- Department of Entomology, Faculty of Agriculture, Patuakhali Science and Technology University, Patuakhali, Bangladesh
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18
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Lidman J, Sallova Y, Matečko-Burmann I, Burmann BM. Structure and dynamics of the mitochondrial DNA-compaction factor Abf2 from S. cerevisiae. J Struct Biol 2023; 215:108008. [PMID: 37543301 DOI: 10.1016/j.jsb.2023.108008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
Mitochondria are essential organelles that produce most of the energy via the oxidative phosphorylation (OXPHOS) system in all eukaryotic cells. Several essential subunits of the OXPHOS system are encoded by the mitochondrial genome (mtDNA) despite its small size. Defects in mtDNA maintenance and expression can lead to severe OXPHOS deficiencies and are amongst the most common causes of mitochondrial disease. The mtDNA is packaged as nucleoprotein structures, referred to as nucleoids. The conserved mitochondrial proteins, ARS-binding factor 2 (Abf2) in the budding yeast Saccharomyces cerevisiae (S. cerevisiae) and mitochondrial transcription factor A (TFAM) in mammals, are nucleoid associated proteins (NAPs) acting as condensing factors needed for packaging and maintenance of the mtDNA. Interestingly, gene knockout of Abf2 leads, in yeast, to the loss of mtDNA and respiratory growth, providing evidence for its crucial role. On a structural level, the condensing factors usually contain two DNA binding domains called high-mobility group boxes (HMG boxes). The co-operating mechanical activities of these domains are crucial in establishing the nucleoid architecture by bending the DNA strands. Here we used advanced solution NMR spectroscopy methods to characterize the dynamical properties of Abf2 together with its interaction with DNA. We find that the two HMG-domains react notably different to external cues like temperature and salt, indicating distinct functional properties. Biophysical characterizations show the pronounced difference of these domains upon DNA-binding, suggesting a refined picture of the Abf2 functional cycle.
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Affiliation(s)
- Jens Lidman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Ylber Sallova
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Irena Matečko-Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden; Department of Psychiatry and Neurochemistry, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden.
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19
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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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20
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Liu W, Ming S, Zhao X, Zhu X, Gong Y. Developmental expression of high-mobility group box 1 (HMGB1) in the mouse cochlea. Eur J Histochem 2023; 67:3704. [PMID: 37667832 PMCID: PMC10518653 DOI: 10.4081/ejh.2023.3704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023] Open
Abstract
The expression changes of high-mobility group box 1 (HMGB1) in the mouse cochlea have recently been implicated in noise-induced hearing loss, suggesting that HMGB1 participates in regulating cochlear function. However, the precise role of HMGB1 in the auditory system remains largely unclear. This study aimed to investigate its function in the developing mouse cochlea by examining the expression pattern of HMGB1 in the mouse cochlea from embryonic day (E) 18.5 to postnatal day (P) 28 using double immunofluorescence on frozen sections. Our findings revealed that HMGB1 was extensively expressed in the cell nucleus across various regions of the mouse cochlea, including the organ of Corti. Furthermore, its expression underwent developmental regulation during mouse cochlear development. Specifically, HMGB1 was found to be localized in the tympanic border cells at each developmental stage, coinciding with the gradual anatomical in this region during development. In addition, HMGB1 was expressed in the greater epithelial ridge (GER) and supporting cells of the organ of Corti, as validated by the supporting cell marker Sox2 at P1 and P8. However, at P14, the expression of HMGB1 disappeared from the GER, coinciding with the degeneration of the GER into the inner sulcus cells. Moreover, we observed that HMGB1 co-localized with Ki-67-positive proliferating cells in several cochlear regions during late embryonic and early postnatal stages, including the GER, the tympanic border cells, cochlear lateral wall, and cochlear nerves. Furthermore, by dual-staining Ki-67 with neuronal marker TUJ1 and glial marker Sox10, we determined the expression of Ki-67 in the neonatal glial cells. Our spatial-temporal analysis demonstrated that HMGB1 exhibited distinct expression patterns during mouse cochlear development. The co-localization of HMGB1 with Ki-67-positive proliferating cells suggested that HMGB1 may play a role in cochlear development.
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Affiliation(s)
- Wenjing Liu
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongda Hospital, Southeast University, Nanjing.
| | - Shanshan Ming
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongda Hospital, Southeast University, Nanjing.
| | - Xiaobing Zhao
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongda Hospital, Southeast University, Nanjing.
| | - Xin Zhu
- Department of Otorhinolaryngology-Head and Neck Surgery, Zhongda Hospital, Southeast University, Nanjing.
| | - Yuxiang Gong
- Department of Nephrology, Zhongda Hospital, Southeast University, Nanjing.
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21
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Maor-Landaw K, Avidor I, Rostowsky N, Salti B, Smirnov M, Ofek-Lalzar M, Levin L, Brekhman V, Lotan T. The Molecular Mechanisms Employed by the Parasite Myxobolus bejeranoi (Cnidaria: Myxozoa) from Invasion through Sporulation for Successful Proliferation in Its Fish Host. Int J Mol Sci 2023; 24:12824. [PMID: 37629003 PMCID: PMC10454682 DOI: 10.3390/ijms241612824] [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: 07/22/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Myxozoa is a unique group of obligate endoparasites in the phylum Cnidaria that can cause emerging diseases in wild and cultured fish populations. Recently, we identified a new myxozoan species, Myxobolus bejeranoi, which infects the gills of cultured tilapia while suppressing host immunity. To uncover the molecular mechanisms underlying this successful parasitic strategy, we conducted transcriptomics analysis of M. bejeranoi throughout the infection. Our results show that histones, which are essential for accelerated cell division, are highly expressed even one day after invasion. As the infection progressed, conserved parasitic genes that are known to modulate the host immune reaction in different parasitic taxa were upregulated. These genes included energy-related glycolytic enzymes, as well as calreticulin, proteases, and miRNA biogenesis proteins. Interestingly, myxozoan calreticulin formed a distinct phylogenetic clade apart from other cnidarians, suggesting a possible function in parasite pathogenesis. Sporogenesis was in its final stages 20 days post-exposure, as spore-specific markers were highly expressed. Lastly, we provide the first catalog of transcription factors in a Myxozoa species, which is minimized compared to free-living cnidarians and is dominated by homeodomain types. Overall, these molecular insights into myxozoan infection support the concept that parasitic strategies are a result of convergent evolution.
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Affiliation(s)
- Keren Maor-Landaw
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3103301, Israel; (K.M.-L.); (I.A.); (N.R.); (B.S.); (V.B.)
| | - Itamar Avidor
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3103301, Israel; (K.M.-L.); (I.A.); (N.R.); (B.S.); (V.B.)
| | - Nadav Rostowsky
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3103301, Israel; (K.M.-L.); (I.A.); (N.R.); (B.S.); (V.B.)
| | - Barbara Salti
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3103301, Israel; (K.M.-L.); (I.A.); (N.R.); (B.S.); (V.B.)
| | - Margarita Smirnov
- Central Fish Health Laboratory, Department of Fisheries and Aquaculture, Ministry of Agriculture and Rural Development, Nir David 1080300, Israel;
| | - Maya Ofek-Lalzar
- Bioinformatic Unit, University of Haifa, Mt. Carmel, Haifa 3498838, Israel;
| | - Liron Levin
- Bioinformatics Core Facility, llse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
| | - Vera Brekhman
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3103301, Israel; (K.M.-L.); (I.A.); (N.R.); (B.S.); (V.B.)
| | - Tamar Lotan
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa 3103301, Israel; (K.M.-L.); (I.A.); (N.R.); (B.S.); (V.B.)
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22
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Ma Y, Feng Q, Han B, Yu R, Jin Z. Elevated HMGB1 promotes the malignant progression and contributes to cisplatin resistance of non-small cell lung cancer. Hereditas 2023; 160:33. [PMID: 37518006 PMCID: PMC10388484 DOI: 10.1186/s41065-023-00294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND HMGB1 (high mobility group box B-1) exhibits crucial role in tumor genesis and development, including lung cancer. Whereas, more HMGB1-related details in non-small cell lung cancer (NSCLC) are still largely unclear. METHODS The HMGB1 and inflammatory factors in malignant (MPE) and non-malignant pleural effusion (BPE) were determined by ELISA. Additionally, qRT-PCR, western blot, or immunohistochemistry were used to determine HMGB1, drug-resistant and apoptotic proteins' expressions in NSCLC A549, A549-DDP cell lines, and xenograft model. Cell viability, migration/ invasion, and apoptosis were analyzed using MTT, Transwell, and flow cytometry assays, respectively. RESULTS Inflammatory factors and HMGB1 expressions in MPE were significantly higher than BPE of NSCLC. Compared with preoperative and adjacent tissues, significantly higher HMGB1, drug-resistant protein, and anti-apoptotic protein expressions were observed in recurrent tissues. Overexpressed HMGB1 induced NSCLC cells to exhibit stronger aggressive, proliferative, and drug-resistant features. The related abilities were reversed when HMGB1 was interfered. Overexpressed HMGB1 showed a similar co-localization with drug resistant protein P-gp in cytoplasm in xenograft model, while low HMGB1 expression localized in cell nucleus. CONCLUSIONS HMGB1 overexpression significantly promoted the malignant progression and cisplatin resistance of NSCLC in vitro and in vivo.
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Affiliation(s)
- Ying Ma
- Department of Thoracic Surgery, Affiliated People's Hospital of Inner Mongolia Medical University, No.1 Tong Dao Bei Road, Hohhot, 010059, China
| | - Qin Feng
- Inner Mongolia Cancer Hospital and Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, 010020, China
| | - Bateer Han
- Inner Mongolia Cancer Hospital and Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, 010020, China
| | - Rong Yu
- Inner Mongolia Cancer Hospital and Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot, 010020, China
| | - Zhiyong Jin
- Department of Thoracic Surgery, Affiliated People's Hospital of Inner Mongolia Medical University, No.1 Tong Dao Bei Road, Hohhot, 010059, China.
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23
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Tarrés-Solé A, Battistini F, Gerhold JM, Piétrement O, Martínez-García B, Ruiz-López E, Lyonnais S, Bernadó P, Roca J, Orozco M, Le Cam E, Sedman J, Solà M. Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism. Nucleic Acids Res 2023; 51:5864-5882. [PMID: 37207342 PMCID: PMC10287934 DOI: 10.1093/nar/gkad397] [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: 07/19/2022] [Revised: 04/01/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.
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Affiliation(s)
- Aleix Tarrés-Solé
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Joachim M Gerhold
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Olivier Piétrement
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | | | - Elena Ruiz-López
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Sébastien Lyonnais
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Inserm, CNRS and Université de Montpellier, France, Sébastien Lyonnais, UAR 3725 CNRS, Université de Montpellier, 34000 Montpellier, France
| | - Joaquim Roca
- Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
- Department of Biochemistry, University of Barcelona, Barcelona 08028, Spain
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy Campus, 114 rue Edouard Vaillant 94805VillejuifCedex, France
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Maria Solà
- Structural MitoLab, Molecular Biology Institute Barcelona (IBMB-CSIC), Barcelona Science Park, Barcelona 08028, Spain
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24
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Ozden B, Boopathi R, Barlas AB, Lone IN, Bednar J, Petosa C, Kale S, Hamiche A, Angelov D, Dimitrov S, Karaca E. Molecular Mechanism of Nucleosome Recognition by the Pioneer Transcription Factor Sox. J Chem Inf Model 2023. [PMID: 37307148 DOI: 10.1021/acs.jcim.2c01520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pioneer transcription factors (PTFs) have the remarkable ability to directly bind to chromatin to stimulate vital cellular processes. In this work, we dissect the universal binding mode of Sox PTF by combining extensive molecular simulations and physiochemistry approaches, along with DNA footprinting techniques. As a result, we show that when Sox consensus DNA is located at the solvent-facing DNA strand, Sox binds to the compact nucleosome without imposing any significant conformational changes. We also reveal that the base-specific Sox:DNA interactions (base reading) and Sox-induced DNA changes (shape reading) are concurrently required for sequence-specific nucleosomal DNA recognition. Among three different nucleosome positions located on the positive DNA arm, a sequence-specific reading mechanism is solely satisfied at the superhelical location 2 (SHL2). While SHL2 acts transparently for solvent-facing Sox binding, among the other two positions, SHL4 permits only shape reading. The final position, SHL0 (dyad), on the other hand, allows no reading mechanism. These findings demonstrate that Sox-based nucleosome recognition is essentially guided by intrinsic nucleosome properties, permitting varying degrees of DNA recognition.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Ramachandran Boopathi
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble 38000, France
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
- Laboratoire de Biologie et de Modélisation de la Cellule (LBMC), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, 46 Allée d'Italie, Lyon 69007, France
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Imtiaz N Lone
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
| | - Jan Bednar
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble 38000, France
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC)/Université de Strasbourg/CNRS/INSERM, Illkirch Cedex 67404, France
| | - Dimitar Angelov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Laboratoire de Biologie et de Modélisation de la Cellule (LBMC), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, 46 Allée d'Italie, Lyon 69007, France
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Institut for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université Grenoble Alpes, Grenoble 38000, France
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir 35340, Turkey
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25
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Wang X, Bigman LS, Greenblatt HM, Yu B, Levy Y, Iwahara J. Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic Acids Res 2023; 51:4701-4712. [PMID: 36774964 PMCID: PMC10250230 DOI: 10.1093/nar/gkad045] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 02/14/2023] Open
Abstract
In eukaryotes, many DNA/RNA-binding proteins possess intrinsically disordered regions (IDRs) with large negative charge, some of which involve a consecutive sequence of aspartate (D) or glutamate (E) residues. We refer to them as D/E repeats. The functional role of D/E repeats is not well understood, though some of them are known to cause autoinhibition through intramolecular electrostatic interaction with functional domains. In this work, we investigated the impacts of D/E repeats on the target DNA search kinetics for the high-mobility group box 1 (HMGB1) protein and the artificial protein constructs of the Antp homeodomain fused with D/E repeats of varied lengths. Our experimental data showed that D/E repeats of particular lengths can accelerate the target association in the overwhelming presence of non-functional high-affinity ligands ('decoys'). Our coarse-grained molecular dynamics (CGMD) simulations showed that the autoinhibited proteins can bind to DNA and transition into the uninhibited complex with DNA through an electrostatically driven induced-fit process. In conjunction with the CGMD simulations, our kinetic model can explain how D/E repeats can accelerate the target association process in the presence of decoys. This study illuminates an unprecedented role of the negatively charged IDRs in the target search process.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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26
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Zhou J, Toh SHM, Tan TK, Balan K, Lim JQ, Tan TZ, Xiong S, Jia Y, Ng SB, Peng Y, Jeyasekharan AD, Fan S, Lim ST, Ong CAJ, Ong CK, Sanda T, Chng WJ. Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma. Mol Cancer 2023; 22:69. [PMID: 37032358 PMCID: PMC10084643 DOI: 10.1186/s12943-023-01767-1] [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: 05/23/2022] [Accepted: 03/24/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Extranodal natural killer/T-cell lymphoma (NKTL) is an aggressive type of non-Hodgkin lymphoma with dismal outcome. A better understanding of disease biology and key oncogenic process is necessary for the development of targeted therapy. Super-enhancers (SEs) have been shown to drive pivotal oncogenes in various malignancies. However, the landscape of SEs and SE-associated oncogenes remain elusive in NKTL. METHODS We used Nano-ChIP-seq of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs NKTL primary tumor samples. Integrative analysis of RNA-seq and survival data further pinned down high value, novel SE oncogenes. We utilized shRNA knockdown, CRISPR-dCas9, luciferase reporter assay, ChIP-PCR to investigate the regulation of transcription factor (TF) on SE oncogenes. Multi-color immunofluorescence (mIF) staining was performed on an independent cohort of clinical samples. Various function experiments were performed to evaluate the effects of TOX2 on the malignancy of NKTL in vitro and in vivo. RESULTS SE landscape was substantially different in NKTL samples in comparison with normal tonsils. Several SEs at key transcriptional factor (TF) genes, including TOX2, TBX21(T-bet), EOMES, RUNX2, and ID2, were identified. We confirmed that TOX2 was aberrantly overexpressed in NKTL relative to normal NK cells and high expression of TOX2 was associated with worse survival. Modulation of TOX2 expression by shRNA, CRISPR-dCas9 interference of SE function impacted on cell proliferation, survival and colony formation ability of NKTL cells. Mechanistically, we found that RUNX3 regulates TOX2 transcription by binding to the active elements of its SE. Silencing TOX2 also impaired tumor formation of NKTL cells in vivo. Metastasis-associated phosphatase PRL-3 has been identified and validated as a key downstream effector of TOX2-mediated oncogenesis. CONCLUSIONS Our integrative SE profiling strategy revealed the landscape of SEs, novel targets and insights into molecular pathogenesis of NKTL. The RUNX3-TOX2-SE-TOX2-PRL-3 regulatory pathway may represent a hallmark of NKTL biology. Targeting TOX2 could be a valuable therapeutic intervene for NKTL patients and warrants further study in clinic.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Sabrina Hui-Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Tuan Zea Tan
- Genomics and Data Analytics Core (GeDaC), Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Yunlu Jia
- Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
| | - Soon Thye Lim
- Director's office, National Cancer Centre, Singapore, 168583, Singapore
- Office of Education, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre, Singapore, 168583, Singapore
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Singapore, 168583, Singapore
- Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre, Singapore, 168583, Singapore
- SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- SingHealth Duke-NUS Surgery Academic Clinical Program, Duke-NUS Medical School, Singapore, 169857, Singapore
- Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, 138673, Singapore
| | - Choon Kiat Ong
- Division of Cellular and Molecular Research, Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore.
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- NUS Centre for Cancer Research (N2CR), 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Singapore.
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27
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Luan Y, Tang Z, He Y, Xie Z. Intra-Domain Residue Coevolution in Transcription Factors Contributes to DNA Binding Specificity. Microbiol Spectr 2023; 11:e0365122. [PMID: 36943132 PMCID: PMC10100741 DOI: 10.1128/spectrum.03651-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Understanding the basis of the DNA-binding specificity of transcription factors (TFs) has been of long-standing interest. Despite extensive efforts to map millions of putative TF binding sequences, identifying the critical determinants for DNA binding specificity remains a major challenge. The coevolution of residues in proteins occurs due to a shared evolutionary history. However, it is unclear how coevolving residues in TFs contribute to DNA binding specificity. Here, we systematically collected publicly available data sets from multiple large-scale high-throughput TF-DNA interaction screening experiments for the major TF families with large numbers of TF members. These families included the Homeobox, HLH, bZIP_1, Ets, HMG_box, ZF-C4, and Zn_clus TFs. We detected TF subclass-determining sites (TSDSs) and showed that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs, particularly for the Homeobox, HLH, Ets, bZIP_1, and HMG_box TF families. By in silico modeling, we showed that mutation of the highly coevolving residues could significantly reduce the stability of the TF-DNA complex. The distant residues from the DNA interface also contributed to TF-DNA binding activity. Overall, our study gave evidence that coevolved residues relate to transcriptional regulation and provided insights into the potential application of engineered DNA-binding domains and proteins. IMPORTANCE While unraveling DNA-binding specificity of TFs is the key to understanding the basis and molecular mechanism of gene expression regulation, identifying the critical determinants that contribute to DNA binding specificity remains a major challenge. In this study, we provided evidence showing that coevolving residues in TF domains contributed to DNA binding specificity. We demonstrated that the TSDSs were more likely to coevolve with other TSDSs than with non-TSDSs. Mutation of the coevolving residue pairs (CRPs) could significantly reduce the stability of THE TF-DNA complex, and even the distant residues from the DNA interface contribute to TF-DNA binding activity. Collectively, our study expands our knowledge of the interactions among coevolved residues in TFs, tertiary contacting, and functional importance in refined transcriptional regulation. Understanding the impact of coevolving residues in TFs will help understand the details of transcription of gene regulation and advance the application of engineered DNA-binding domains and protein.
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Affiliation(s)
- Yizhao Luan
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zehua Tang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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28
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Yuan Y, Sun M, Jin Z, Zheng C, Ye H, Weng H. Dapagliflozin ameliorates diabetic renal injury through suppressing the self-perpetuating cycle of inflammation mediated by HMGB1 feedback signaling in the kidney. Eur J Pharmacol 2023; 943:175560. [PMID: 36736941 DOI: 10.1016/j.ejphar.2023.175560] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023]
Abstract
Dapagliflozin, the Sodium-glucose cotransporter 2 (SGLT2) inhibitor class of glucose-lowering agents, has shown the significantly nephroprotective effects to reduce the risk of kidney failure in diabetes. However, the underlying mechanisms are incompletely understood to explain the beneficial effects of dapagliflozin on kidney function. Here, we demonstrated that the administered of dapagliflozin for 12 weeks improved the proteinuria, histomorphology damage, oxidative stress, and macrophage infiltrations in the kidney of streptozotocin (STZ)-induced diabetic mice. Meanwhile, dapagliflozin attenuated the renal inflammation and fibrosis by reducing the pro-inflammatory factors interleukin-6 (IL-6), IL-1β, and tumor necrosis factor α (TNF-α) and anti-fiber factor fibronectin (FN) and elevating the anti-inflammatory factor IL-10. Our data revealed that dapagliflozin exerted anti-inflammatory effects by inhibiting the activation of high mobility group box 1 (HMGB1)/TLR2/4/NF-κB signaling pathway. Consistently, we found that dapagliflozin suppressed the expression of HMGB1 and downstream TLR2/4/NF-κB signaling proteins in the human proximal tubular (HK-2) stimulated by high glucose and lipids or HMGB1 and RAW264.7 cells stimulated by IL-1β, respectively. Further experiments were performed in the indirect co-culture model of RAW264.7 and HK-2 cells induced by high glucose and lipids. The results again confirmed the effects of dapagliflozin on alleviating inflammatory response and regulating the proportions of M1/M2 macrophage. It is indicated that the feedback signaling of HMGB1 between the tubules and macrophage involves in the persistence of the inflammation. These data demonstrate that dapagliflozin suppress the self-perpetuating inflammation by blocking the feedback loop of HMGB1 in the kidney, which contribute to ameliorate the renal injury in diabetes.
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Affiliation(s)
- Yan Yuan
- School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Mengyao Sun
- School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Zijie Jin
- School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Chen Zheng
- School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Huijing Ye
- School of Pharmacy, Fudan University, 201203, Shanghai, China
| | - Hongbo Weng
- School of Pharmacy, Fudan University, 201203, Shanghai, China.
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29
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Zhou L, Ou S, Liang T, Li M, Xiao P, Cheng J, Zhou J, Yuan L. MAEL facilitates metabolic reprogramming and breast cancer progression by promoting the degradation of citrate synthase and fumarate hydratase via chaperone-mediated autophagy. FEBS J 2023. [PMID: 36866961 DOI: 10.1111/febs.16768] [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: 10/17/2022] [Revised: 01/15/2023] [Accepted: 01/30/2023] [Indexed: 03/04/2023]
Abstract
Metabolic reprogramming is a hallmark of cancer. Several studies have shown that inactivation of Krebs cycle enzymes, such as citrate synthase (CS) and fumarate hydratase (FH), facilitates aerobic glycolysis and cancer progression. MAEL has been shown to play an oncogenic role in bladder, liver, colon, and gastric cancers, but its role in breast cancer and metabolism is still unknown. Here, we demonstrated that MAEL promoted malignant behaviours and aerobic glycolysis in breast cancer cells. Mechanistically, MAEL interacted with CS/FH and HSAP8 via its MAEL domain and HMG domain, respectively, and then enhanced the binding affinity of CS/FH with HSPA8, facilitating the transport of CS/FH to the lysosome for degradation. MAEL-induced degradation of CS and FH could be suppressed by the lysosome inhibitors leupeptin and NH4 Cl, but not by the macroautophagy inhibitor 3-MA or the proteasome inhibitor MG132. These results suggested that MAEL promoted the degradation of CS and FH via chaperone-mediated autophagy (CMA). Further studies showed that the expression of MAEL was significantly and negatively correlated with CS and FH in breast cancer. Moreover, overexpression of CS or/and FH could reverse the oncogenic effects of MAEL. Taken together, MAEL promotes a metabolic shift from oxidative phosphorylation to glycolysis by inducing CMA-dependent degradation of CS and FH, thereby promoting breast cancer progression. These findings have elucidated a novel molecular mechanism of MAEL in cancer.
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Affiliation(s)
- Lin Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China.,College of Clinical Laboratory, Changsha Medical University, China
| | - Shuobo Ou
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China
| | - Ting Liang
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China
| | - Meiling Li
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China
| | - Pei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China
| | - Jiaxin Cheng
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China
| | - Jianlin Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish & Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, China
| | - Liqin Yuan
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
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30
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Torp MK, Vaage J, Stensløkken KO. Mitochondria-derived damage-associated molecular patterns and inflammation in the ischemic-reperfused heart. Acta Physiol (Oxf) 2023; 237:e13920. [PMID: 36617670 DOI: 10.1111/apha.13920] [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: 07/08/2022] [Revised: 10/01/2022] [Accepted: 01/02/2023] [Indexed: 01/10/2023]
Abstract
Cardiac cell death after myocardial infarction release endogenous structures termed damage-associated molecular patterns (DAMPs) that trigger the innate immune system and initiate a sterile inflammation in the myocardium. Cardiomyocytes are energy demanding cells and 30% of their volume are mitochondria. Mitochondria are evolutionary endosymbionts originating from bacteria containing molecular patterns similar to bacteria, termed mitochondrial DAMPs (mDAMPs). Consequently, mitochondrial debris may be particularly immunogenic and damaging. However, the role of mDAMPs in myocardial infarction is not clarified. Identifying the most harmful mDAMPs and inhibiting their early inflammatory signaling may reduce infarct size and the risk of developing post-infarct heart failure. The focus of this review is the role of mDAMPs in the immediate pro-inflammatory phase after myocardial infarction before arrival of immune cells in the myocardium. We discuss different mDAMPs, their role in physiology and present knowledge regarding their role in the inflammatory response of acute myocardial infarction.
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Affiliation(s)
- May-Kristin Torp
- Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jarle Vaage
- Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital, Oslo, Norway
| | - Kåre-Olav Stensløkken
- Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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31
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The involvement of an HMG-box gene in germ cell genesis in Pyropia haitanensis. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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32
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Wang X, Mayorga-Flores M, Bien KG, Bailey AO, Iwahara J. DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein. J Biol Chem 2022; 298:102577. [DOI: 10.1016/j.jbc.2022.102577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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33
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Belmadani S, Matrougui K. Role of High Mobility Group Box 1 in Cardiovascular Diseases. Inflammation 2022; 45:1864-1874. [PMID: 35386038 PMCID: PMC11145736 DOI: 10.1007/s10753-022-01668-3] [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: 10/13/2021] [Revised: 02/27/2022] [Accepted: 03/28/2022] [Indexed: 11/05/2022]
Abstract
High Mobility Group Box 1 (HMGB1) is a ubiquitous, highly conserved nuclear and cytosolic protein that has diverse biological roles depending on its cellular location and posttranslational modifications. The HMGB1 is localized in the nucleus but can be translocated to the cytoplasm to modulate the intracellular signaling and eventually secreted outside the cells. It is widely established that HMGB1 plays a key role in inflammation; however, the role of HMGB1 in the cardiovascular diseases is not well understood. In this review, we will discuss the latest reports on the pathophysiological link between HMGB1 and cardiovascular complications, with special emphasis on the inflammation. Thus, the understanding of the role of HMGB1 may provide new insights into developing new HMGB1-based therapies.
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Affiliation(s)
- Souad Belmadani
- Department of Physiological Sciences, EVMS, Norfolk, Virginia, 23501, USA
| | - Khalid Matrougui
- Department of Physiological Sciences, EVMS, Norfolk, Virginia, 23501, USA.
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34
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Li R, Meng S, Ji M, Rong X, You Z, Cai C, Guo X, Lu C, Liang G, Cao G, Li B, Yang Y. HMG20A Inhibit Adipogenesis by Transcriptional and Epigenetic Regulation of MEF2C Expression. Int J Mol Sci 2022; 23:ijms231810559. [PMID: 36142473 PMCID: PMC9505946 DOI: 10.3390/ijms231810559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/29/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022] Open
Abstract
Obesity and its associated metabolic disease do serious harm to human health. The transcriptional cascade network with transcription factors as the core is the focus of current research on adipogenesis and its mechanism. Previous studies have found that HMG domain protein 20A (HMG20A) is highly expressed in the early stage of adipogenic differentiation of porcine intramuscular fat (IMF), which may be involved in regulating adipogenesis. In this study, HMG20A was found to play a key negative regulatory role in adipogenesis. Gain- and loss-of-function studies revealed that HMG20A inhibited the differentiation of SVF cells and C3H10T1/2 cells into mature adipocytes. RNA-seq was used to screen differentially expressed genes after HMG20A knockdown. qRT-PCR and ChIP-PCR confirmed that MEF2C was the real target of HMG20A, and HMG20A played a negative regulatory role through MEF2C. HMG20A binding protein LSD1 was found to alleviate the inhibitory effect of HMG20A on adipogenesis. Further studies showed that HMG20A could cooperate with LSD1 to increase the H3K4me2 of the MEF2C promoter and then increase the expression of MEF2C. Collectively, these findings highlight a role for HMG20A-dependent transcriptional and epigenetic regulation in adipogenesis.
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35
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Bosire R, Fadel L, Mocsár G, Nánási P, Sen P, Sharma AK, Naseem MU, Kovács A, Kugel J, Kroemer G, Vámosi G, Szabó G. Doxorubicin impacts chromatin binding of HMGB1, Histone H1 and retinoic acid receptor. Sci Rep 2022; 12:8087. [PMID: 35577872 PMCID: PMC9110345 DOI: 10.1038/s41598-022-11994-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Doxorubicin (Dox), a widely used anticancer DNA-binding drug, affects chromatin in multiple ways, and these effects contribute to both its efficacy and its dose-limiting side effects, especially cardiotoxicity. Here, we studied the effects of Dox on the chromatin binding of the architectural proteins high mobility group B1 (HMGB1) and the linker histone H1, and the transcription factor retinoic acid receptor (RARα) by fluorescence recovery after photobleaching (FRAP) and fluorescence correlation spectroscopy (FCS) in live cells. At lower doses, Dox increased the binding of HMGB1 to DNA while decreasing the binding of the linker histone H1. At higher doses that correspond to the peak plasma concentrations achieved during chemotherapy, Dox reduced the binding of HMGB1 as well. This biphasic effect is interpreted in terms of a hierarchy of competition between the ligands involved and Dox-induced local conformational changes of nucleosome-free DNA. Combined, FRAP and FCS mobility data suggest that Dox decreases the overall binding of RARα to DNA, an effect that was only partially overcome by agonist binding. The intertwined interactions described are likely to contribute to both the effects and side effects of Dox.
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Affiliation(s)
- Rosevalentine Bosire
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Lina Fadel
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Mocsár
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Pialy Sen
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Anshu Kumar Sharma
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Muhammad Umair Naseem
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,Doctoral School of Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Kovács
- Department of Radiation Therapy, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jennifer Kugel
- Department of Biochemistry, University of Colorado, Boulder, USA
| | - Guido Kroemer
- Centre de Recherche Des Cordeliers, Equipe Labellisée Par La Ligue Contre Le Cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - György Vámosi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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36
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Michl-Holzinger P, Obermeyer S, Markusch H, Pfab A, Ettner A, Bruckmann A, Babl S, Längst G, Schwartz U, Tvardovskiy A, Jensen ON, Osakabe A, Berger F, Grasser KD. Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in Arabidopsis. Nucleic Acids Res 2022; 50:5014-5028. [PMID: 35489065 PMCID: PMC9122599 DOI: 10.1093/nar/gkac293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/15/2022] Open
Abstract
The heterodimeric histone chaperone FACT, consisting of SSRP1 and SPT16, contributes to dynamic nucleosome rearrangements during various DNA-dependent processes including transcription. In search of post-translational modifications that may regulate the activity of FACT, SSRP1 and SPT16 were isolated from Arabidopsis cells and analysed by mass spectrometry. Four acetylated lysine residues could be mapped within the basic C-terminal region of SSRP1, while three phosphorylated serine/threonine residues were identified in the acidic C-terminal region of SPT16. Mutational analysis of the SSRP1 acetylation sites revealed only mild effects. However, phosphorylation of SPT16 that is catalysed by protein kinase CK2, modulates histone interactions. A non-phosphorylatable version of SPT16 displayed reduced histone binding and proved inactive in complementing the growth and developmental phenotypes of spt16 mutant plants. In plants expressing the non-phosphorylatable SPT16 version we detected at a subset of genes enrichment of histone H3 directly upstream of RNA polymerase II transcriptional start sites (TSSs) in a region that usually is nucleosome-depleted. This suggests that some genes require phosphorylation of the SPT16 acidic region for establishing the correct nucleosome occupancy at the TSS of active genes.
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Affiliation(s)
- Philipp Michl-Holzinger
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Simon Obermeyer
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Hanna Markusch
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Alexander Pfab
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Andreas Ettner
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute for Biochemistry I, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Sabrina Babl
- Institute for Biochemistry III, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Gernot Längst
- Institute for Biochemistry III, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Centre, Biology and Pre-Clinical Medicine, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Akihisa Osakabe
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Centre for Biochemistry, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
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37
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Yang W, Wu W, Liang H, Chen J, Dong X. TOX3 regulates the proliferation and apoptosis of colorectal cancer by downregulating RhoB via the activation of MAPK pathway. Cell Biol Int 2022; 46:1074-1088. [PMID: 35347804 DOI: 10.1002/cbin.11802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/30/2022] [Accepted: 02/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Wei Yang
- Department of General Surgery, The first affiliated hospital of Soochow UniversitySuzhou215006P.R.China
| | - Wei Wu
- Department of General Surgery, The affiliated hospital of Yangzhou UniversityYangzhou225000P.R.China
| | - Hailiang Liang
- Department of General Surgery, The affiliated hospital of Yangzhou UniversityYangzhou225000P.R.China
| | - Jiejing Chen
- Department of General Surgery, The affiliated hospital of Yangzhou UniversityYangzhou225000P.R.China
| | - Xiaoqiang Dong
- Department of General Surgery, The first affiliated hospital of Soochow UniversitySuzhou215006P.R.China
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38
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Koenig A, Buskiewicz-Koenig IA. Redox Activation of Mitochondrial DAMPs and the Metabolic Consequences for Development of Autoimmunity. Antioxid Redox Signal 2022; 36:441-461. [PMID: 35352943 PMCID: PMC8982130 DOI: 10.1089/ars.2021.0073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Reactive oxygen species (ROS) are well known to promote innate immune responses during and in the absence of microbial infections. However, excessive or prolonged exposure to ROS provokes innate immune signaling dysfunction and contributes to the pathogenesis of many autoimmune diseases. The relatively high basal expression of pattern recognition receptors (PRRs) in innate immune cells renders them prone to activation in response to minor intrinsic or extrinsic ROS misbalances in the absence of pathogens. Critical Issues: A prominent source of ROS are mitochondria, which are also major inter-organelle hubs for innate immunity activation, since most PRRs and downstream receptor molecules are directly located either at mitochondria or at mitochondria-associated membranes. Due to their ancestral bacterial origin, mitochondria can also act as quasi-intrinsic self-microbes that mimic a pathogen invasion and become a source of danger-associated molecular patterns (DAMPs) that triggers innate immunity from within. Recent Advances: The release of mitochondrial DAMPs correlates with mitochondrial metabolism changes and increased generation of ROS, which can lead to the oxidative modification of DAMPs. Recent studies suggest that ROS-modified mitochondrial DAMPs possess increased, persistent immunogenicity. Future Directions: Herein, we discuss how mitochondrial DAMP release and oxidation activates PRRs, changes cellular metabolism, and causes innate immune response dysfunction by promoting systemic inflammation, thereby contributing to the onset or progression of autoimmune diseases. The future goal is to understand what the tipping point for DAMPs is to become oxidized, and whether this is a road without return. Antioxid. Redox Signal. 36, 441-461.
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Affiliation(s)
- Andreas Koenig
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
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The acidic domain of Hmga2 and the domain’s linker region are critical for driving self-renewal of hematopoietic stem cell. Int J Hematol 2022; 115:553-562. [DOI: 10.1007/s12185-021-03274-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022]
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Choi WS, Garcia-Diaz M. A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM). Nucleic Acids Res 2021; 50:322-332. [PMID: 34928349 PMCID: PMC8754647 DOI: 10.1093/nar/gkab1230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 11/13/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.
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Affiliation(s)
- Woo Suk Choi
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
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Zhang Z, Niu J, Li Q, Huang Y, Jiang B, Wu Y, Huang Y, Jian J. HMG20A from Nile tilapia (Oreochromis niloticus) involved in the immune response to bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2021; 119:499-507. [PMID: 34687883 DOI: 10.1016/j.fsi.2021.10.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
High-mobility group 20 A (HMG20A) has important biological functions, such as inhibiting the differentiation of red blood cells and nerve cells, promoting the proliferation and metastasis of cancer cells, and regulating inflammatory reaction. However, the role of HMG20A in the response to bacterial infection in the economic fish Nile tilapia (Oreochromis niloticus) remains unclear. In this study, a HMG20A homolog was successfully identified and characterized from Nile tilapia (On-HMG20A), and its expression model and biological effects on bacterial infection were analyzed. The open reading frame (ORF) of On-HMG20A was 876 bp in length, which encoded 291 amino acids and possessed a HMG domain (High mobility group domains) and coiled coil region. Results of the expression model showed that On-HMG20A was widely distributed in immune-related tissues of healthy tilapia and upregulated in a time-dependent manner after being challenged by Streptococcus agalactiae. Meanwhile, knocking down the expression of On-HMG20A can reduce the inflammatory response of tilapia and the degree of tissue damage caused by S. agalactiae. Moreover, knocking down the expression of On-HMG20A can reduce the bacterial load of tilapia tissues after being challenged by S. agalactiae and improve the survival rate. Collectively, these results showed that On-HMG20A may be related to the immune response of Nile tilapia against bacterial infection.
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Affiliation(s)
- Zhiqiang Zhang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Jinzhong Niu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Qi Li
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Yongxiong Huang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Baijian Jiang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Yiqin Wu
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China
| | - Yu Huang
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China.
| | - Jichang Jian
- College of Fishery, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animal, Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institutes, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen, China
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Tang Y, Kong J, Zhou B, Wang X, Liu X, Wang Y, Zhu S. Mesenteric Lymph Duct Ligation Alleviates Acute Lung Injury Caused by Severe Acute Pancreatitis Through Inhibition of High Mobility Group Box 1-Induced Inflammation in Rats. Dig Dis Sci 2021; 66:4344-4353. [PMID: 33433807 PMCID: PMC8589802 DOI: 10.1007/s10620-020-06801-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acute lung injury (ALI) is the most common complication and one of the leading causes of mortality of severe acute pancreatitis (SAP). Nevertheless, no effective therapeutic schemes are presently available. AIMS To investigate the effect and potential mechanism of mesenteric lymph duct ligation (MLDL) on experimental SAP-induced ALI. METHODS Immediately following MLDL, rats were subjected to SAP by retrograde injection of 5% sodium taurocholate into the biliopancreatic duct. At 24 h after modeling, tissues were collected for morphological examination. The levels of TNF-α, IL-6, intercellular adhesion molecule-1 (ICAM1), diamine oxidase (DAO), and D-lactic acid (D-LA) in serum, and the myeloperoxidase (MPO) activity in lung tissues were determined. Moreover, the expressions of high mobility group box 1 (HMGB1), receptor of advanced glycation endproducts (RAGE), and NF-κB p65 at the mRNA and protein levels in lung tissues, and the expressions of HMGB1, RAGE, and TNF-α at the mRNA level in intestinal lymphoid tissues were evaluated. RESULTS MLDL significantly attenuated the histological injury of the pancreas and lung and reduced the production of TNF-α, IL-6, and ICAM1. Besides, MLDL repressed the activity of MPO in the lung. However, the levels of serum DAO and D-LA were decreased without obvious morphological improvement in intestinal injury. Moreover, MLDL apparently reduced the up-regulation of HMGB1, RAGE, and NF-κB p65 in lung tissues, as well as the expressions of HMGB1, RAGE, and TNF-α in intestinal lymphoid tissues. CONCLUSIONS Mesenteric lymph was a source of harmful factors leading to SAP-ALI. MLDL could alleviate SAP-ALI probably by inhibiting HMGB1-induced production of inflammation factors.
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Affiliation(s)
- Yishuang Tang
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Kong
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bingduo Zhou
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Xiaosu Wang
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaowen Liu
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Wang
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shengliang Zhu
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Liang H, Huang Y, Gao Q. Role of non-canonical pyroptosis in sepsis and other inflammatory diseases. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:1276-1284. [PMID: 34911863 PMCID: PMC10929856 DOI: 10.11817/j.issn.1672-7347.2021.210174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 11/03/2022]
Abstract
As a form of new programmed cell death, pyroptosis is divided into a canonical pyroptosis pathway and a non-canonical pyroptosis pathway. In recent years, it is reported that non-canonical pyroptosis is closely related to inflammatory reactions, which directly affects the occurrence, development, and outcome of sepsis, inflammatory bowel disease, respiratory disease, nerve system inflammatory disease, and other inflammatory diseases. When the cells were infected with Gram-negative bacteria or lipopolysaccharide (LPS), it can induce the activation of cysteinyl aspartate specific proteinase(caspase)-4/5/11 and directly bind to the cells to cleave gasdermin D (GSDM-D) into the active amino-terminus of GSDM-D. The amino-terminus of GSDM-D with membrane punching activity migrates to the cell membrane, triggering the rupture of the cell membrane, and the cell contents discharge, leading to the occurrence of non-canonical pyroptosis. After activation of caspase-11, it also promotes the canonical pyroptosis, activates and releases interleukin-1β and interleukin-18, which aggravated inflammation. Caspase-4/5/11, GSDM-D, Toll-like receptor 4 and high mobility group protein B1 are the key molecules of the non-canonical pyroptosis. Exploring the mechanisms of non-canonical pyroptosis and the related research progresses in inflammatory diseases intensively is of great significance for clinical prevention and treatment of the relevant diseases.
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Affiliation(s)
- Huan Liang
- Department of Physiology, Bengbu Medical College, Bengbu Anhui 233000.
- Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu Medical College, Bengbu Anhui 233000, China.
| | - Yuhui Huang
- Department of Physiology, Bengbu Medical College, Bengbu Anhui 233000
- Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu Medical College, Bengbu Anhui 233000, China
| | - Qin Gao
- Department of Physiology, Bengbu Medical College, Bengbu Anhui 233000.
- Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Bengbu Medical College, Bengbu Anhui 233000, China.
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Bou-Rouphael J, Durand BC. T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development. Front Cell Dev Biol 2021; 9:784998. [PMID: 34901027 PMCID: PMC8651982 DOI: 10.3389/fcell.2021.784998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Since its first discovery in the late 90s, Wnt canonical signaling has been demonstrated to affect a large variety of neural developmental processes, including, but not limited to, embryonic axis formation, neural proliferation, fate determination, and maintenance of neural stem cells. For decades, studies have focused on the mechanisms controlling the activity of β-catenin, the sole mediator of Wnt transcriptional response. More recently, the spotlight of research is directed towards the last cascade component, the T-cell factor (TCF)/Lymphoid-Enhancer binding Factor (LEF), and more specifically, the TCF/LEF-mediated switch from transcriptional activation to repression, which in both embryonic blastomeres and mouse embryonic stem cells pushes the balance from pluri/multipotency towards differentiation. It has been long known that Groucho/Transducin-Like Enhancer of split (Gro/TLE) is the main co-repressor partner of TCF/LEF. More recently, other TCF/LEF-interacting partners have been identified, including the pro-neural BarH-Like 2 (BARHL2), which belongs to the evolutionary highly conserved family of homeodomain-containing transcription factors. This review describes the activities and regulatory modes of TCF/LEF as transcriptional repressors, with a specific focus on the functions of Barhl2 in vertebrate brain development. Specific attention is given to the transcriptional events leading to formation of the Organizer, as well as the roles and regulations of Wnt/β-catenin pathway in growth of the caudal forebrain. We present TCF/LEF activities in both embryonic and neural stem cells and discuss how alterations of this pathway could lead to tumors.
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Affiliation(s)
| | - Béatrice C. Durand
- Sorbonne Université, CNRS UMR7622, IBPS Developmental Biology Laboratory, Campus Pierre et Marie Curie, Paris, France
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Bhakat KK, Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair (Amst) 2021; 109:103246. [PMID: 34847380 DOI: 10.1016/j.dnarep.2021.103246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Genomic DNA in the nucleus is wrapped around nucleosomes, a repeating unit of chromatin. The nucleosome, consisting of octamer of core histones, is a barrier for several cellular processes that require access to the naked DNA. The FAcilitates Chromatin Transcription (FACT), a histone chaperone complex, is involved in nucleosome remodeling via eviction or assembly of histones during transcription, replication, and DNA repair. Increasing evidence suggests that FACT plays an important role in multiple DNA repair pathways including transcription-coupled nucleotide excision repair (TC-NER) of UV-induced damage, DNA single- and double-strand breaks (DSBs) repair, and base excision repair (BER) of oxidized or alkylated damaged bases. Further, studies have shown overexpression of FACT in multiple types of cancer and its association with drug resistance and patients' poor prognosis. In this review, we discuss how FACT is accumulated at the damage site and what functions it performs. We describe the known mechanisms by which FACT facilitates repair of different types of DNA damage. Further, we highlight the recent advances in a class of FACT inhibitors, called curaxins, which show promise as a new adjuvant therapy to sensitize multiple types of cancer to chemotherapy and radiation.
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Affiliation(s)
- Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198.
| | - Sutapa Ray
- Department of Pediatric, Division of Hematology/oncology, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198
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Mutua V, Gershwin LJ. A Review of Neutrophil Extracellular Traps (NETs) in Disease: Potential Anti-NETs Therapeutics. Clin Rev Allergy Immunol 2021; 61:194-211. [PMID: 32740860 PMCID: PMC7395212 DOI: 10.1007/s12016-020-08804-7] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Activated neutrophils release neutrophil extracellular traps (NETs) in response to a variety of stimuli. NETosis is driven by protein-arginine deiminase type 4, with the release of intracellular granule components that function by capturing and destroying microbes, including viral, fungal, bacterial, and protozoal pathogens. The positive effects of pathogen control are countered by pro-inflammatory effects as demonstrated in a variety of diseases. Components of NETS are non-specific, and other than controlling microbes, they cause injury to surrounding tissue by themselves or by increasing the pro-inflammatory response. NETs can play a role in enhancement of the inflammation seen in autoimmune diseases including psoriasis, rheumatoid arthritis, and systemic lupus erythematosis. In addition, autoinflammatory diseases such as gout have been associated with NETosis. Inhibition of NETs may decrease the severity of many diseases improving survival. Herein, we describe NETosis in different diseases focusing on the detrimental effect of NETs and outline possible therapeutics that can be used to mitigate netosis. There is a need for more studies and clinical trials on these and other compounds that could prevent or destroy NETs, thereby decreasing damage to patients.
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Affiliation(s)
- Victoria Mutua
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, 1 Shields Ave, Davis, CA, USA.
| | - Laurel J Gershwin
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, 1 Shields Ave, Davis, CA, USA
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Ramazan ZK, Sarı İ, Yıldırım BG, Güntürk İ, Küçük E, Erşan S, Seydel GŞ. The Evaluation of oxidative stress, 3-nitrotyrosine, and HMGB-1 levels in patients with Wet Type Age-Related Macular Degeneration. J Med Biochem 2021; 41:275-281. [PMID: 36042902 PMCID: PMC9375537 DOI: 10.5937/jomb0-32189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/19/2021] [Indexed: 11/04/2022] Open
Abstract
Background This study aims to compare serum HMGB-1, 3-nitrotyrosine (3-NT), TAS, TOS, and OSI levels in Wettype Age-Related Macular Degeneration (wAMD) patients and healthy controls to determine the correlation of these parameters with each other. Methods Thirty patients with Wet-type Age-Related Macular Degeneration (wAMD) and 27 healthy adults, as controls were enrolled in the study. We determined the TAS and TOS levels in serum samples of both groups using commercial kits on a microplate reader. Serum HMGB-1 and 3-NT levels were measured with the enzyme-linked immunosorbent assay method. Results HMGB-1 levels were significantly higher in the patient group (137.51 pg/mL, p=0.001), while there was no difference between the two groups in serum 3-NT levels (p=0.428). A statistically significant difference found in the levels of TOS and OSI (p=0.001 and p=0.045, respectively) between the patients and controls, however, no significant difference was observed between the groups in terms of TAS levels (p=0.228). Conclusions Oxidative stress and HMGB-1 levels were increased in wAMD patients and enhanced oxidative stress may be associated with increased tissue necrosis and inflammation. Thus administration of antioxidant treatment in addition to routine therapy should be considered in wAMD.
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Affiliation(s)
- Zor Kürşad Ramazan
- Niğde Ömer Halisdemir University School of Medicine Department of Ophthalmology, Bor Yolu, Niğde, Turkey
| | - İsmail Sarı
- Niğde Ömer Halisdemir University School of Medicine Department of Biochemistry, Bor Yolu, Niğde, Turkey
| | - Biçer Gamze Yıldırım
- Niğde Ömer Halisdemir University School of Medicine Department of Ophthalmology, Bor Yolu, Niğde, Turkey
| | - İnayet Güntürk
- Niğde Ömer Halisdemir University, Healthcare Services, Zübeyde Hanım Health Services Vocational High School, Bor Yolu, Niğde, Turkey
| | - Erkut Küçük
- Niğde Ömer Halisdemir University School of Medicine Department of Ophthalmology, Bor Yolu, Niğde, Turkey
| | - Serpil Erşan
- Niğde Ömer Halisdemir University School of Medicine Department of Biochemistry, Bor Yolu, Niğde, Turkey
| | - Gönül Şeyda Seydel
- Niğde Ömer Halisdemir University School of Medicine Department of Medical Biochemistry, Bor Yolu, Niğde, Turkey
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Sun L, Wang R, Hu G, Liu H, Lv K, Duan Y, Shen N, Wu J, Hu J, Liu Y, Jin Q, Zhang F, Xu X. Single cell RNA sequencing (scRNA-Seq) deciphering pathological alterations in streptozotocin-induced diabetic retinas. Exp Eye Res 2021; 210:108718. [PMID: 34364890 DOI: 10.1016/j.exer.2021.108718] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 11/28/2022]
Abstract
Diabetic retinopathy (DR) is an irreversible and progressive diabetic complication leading to visual impairment, even blindness. Due to the delicate and complicated structure of the retina, the pathology of DR has not been completely elucidated yet. We constructed a transcriptome atlas of >14,000 single cells from healthy and streptozotocin (STZ)-induced diabetic murine retinas to decipher pathological alterations of DR. We found four stress-inducible genes Cirbp, Rmb3, Mt1 and Mt2 commonly induced in most types of retinal cells. Bipolar cells were little affected on both number and gene expression. Diabetes increased expression of inflammatory factor genes in retinal microglia, and stimulated expression of immediate early genes (IEGs) in retinal astrocytes. A large number of genes were deregulated in diabetic vascular endothelial cells (ECs), and the differentially expressed genes were paired to the pathways functioning in metabolism, shear stress and vascular permeability. These pathways were mapped by more deregulated genes in a subpopulation of ECs specifically presented in diabetic retinas (diabetic retinal ECs, DRECs). Moreover, several inflammation pathways were activated in DRECs, and the most significant one is the IL-17 signaling pathway. According to the EC markers, DRECs were mainly capillary ECs, confirmed by immunofluorescent staining of S100a9, a target gene of the IL-17 signaling pathway. This study deciphered pathological alterations of DR, and provided clues for potential targets for DR therapy.
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Affiliation(s)
- Licheng Sun
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Ruonan Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Guangyi Hu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Huazhen Liu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Kangjia Lv
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Yi Duan
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Ning Shen
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Jiali Wu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Jing Hu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Yujuan Liu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China
| | - Qihuang Jin
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China.
| | - Fang Zhang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China.
| | - Xun Xu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, 200080, Shanghai, China; National Clinical Research Center for Eye Diseases, 200080, Shanghai, China; Shanghai Key Laboratory of Fundus Diseases, 200080, Shanghai, China; Shanghai Engineering Center for Visual Science and Photomedicine, 200080, Shanghai, China; Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 200080, Shanghai, China.
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Malar C M, Roux C, Corradi N. Regulation of mating genes during arbuscular mycorrhizal isolate co-existence-where is the evidence? THE ISME JOURNAL 2021; 15:2173-2179. [PMID: 33654264 PMCID: PMC8319156 DOI: 10.1038/s41396-021-00924-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
A recent study published by Mateus et al. [1] claimed that 18 "mating-related" genes are differentially expressed in the model arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis when genetically distinct fungal strains co-colonize a host plant. To clarify the level of evidence for this interesting conclusion, we first aimed to validate the functional annotation of these 18 R. irregularis genes using orthology predictions. These analyses revealed that, although sequence relationship exists, only 2 of the claimed 18 R. irregularis mating genes are potential orthologues to validated fungal mating genes. We also investigated the RNA-seq data from Mateus et al. [1] using classical RNA-seq methods and statistics. This analysis found that the over-expression during strain co-existence was not significant at the typical cut-off of the R. irregularis strains DAOM197198 and B1 in plants. Overall, we do not find convincing evidence that the genes involved have functions in mating, or that they are reproducibly up or down regulated during co-existence in plants.
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Affiliation(s)
- Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Castanet-Tolosan, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada.
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Mollah MMI, Kim Y. HMGB1-like dorsal switch protein 1 of the mealworm, Tenebrio molitor, acts as a damage-associated molecular pattern. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 107:e21795. [PMID: 33973266 DOI: 10.1002/arch.21795] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
High-mobility group box 1 (HMGB1) is a nuclear protein highly conserved in eukaryotes and ubiquitously expressed to regulate transcription and chromatin remodeling. Dorsal switch protein 1 (DSP1) is its insect homolog. A lepidopteran DSP1 acts as a damage-associated molecular pattern (DAMP) in response to immune challenge. The objective of this study was to determine the role of DAMP in the mealworm beetle, Tenebrio molitor, a coleopteran insect. DSP1 of T. molitor (Tm-DSP1) encodes 536 amino acids and shares sequence similarities with Homo sapiens HMGB1 (56.3%) and Spodoptera exigua DSP1 (59.2%). An antisera raised against S. exigua DSP1 was cross-reactive to Tm-DSP1. Like other insect DSPs, Tm-DSP1 has a relatively long N-terminal extension in addition to two conserved HMG box domains. It was expressed in all developmental stages of T. molitor and different larval tissues. Upon immune challenge, its expression level was upregulated. Its RNA interference (RNAi) treatment resulted in a significant reduction in immune responses measured by hemocyte nodule formation against bacterial infection. In addition, the induction of some antimicrobial peptide genes to the immune challenge was suppressed by its RNAi treatment. Interestingly, phospholipase A2 associated with eicosanoid biosynthesis was significantly suppressed in its catalytic activity by the RNAi treatment specific to Tm-DSP1 expression. Without any pathogen infection, injection of a lepidopteran DSP1 induced both cellular and humoral immune responses. These results suggest that Tm-DSP1 in T. molitor can act as a DAMP molecule and mediate immune responses upon immune challenge.
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Affiliation(s)
- Md Mahi Imam Mollah
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, Korea
| | - Yonggyun Kim
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, Korea
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