1
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Sung S, Kim E, Niida H, Kim C, Lee J. Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells. Nucleic Acids Res 2023; 51:9122-9143. [PMID: 37496110 PMCID: PMC10516625 DOI: 10.1093/nar/gkad617] [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: 09/24/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
Telomere length must be maintained in actively dividing cells to avoid cellular arrest or death. In the absence of telomerase activity, activation of alternative lengthening of telomeres (ALT) allows the maintenance of telomeric length and prolongs the cellular lifespan. Our previous studies have established two types of ALT survivors from mouse embryonic stem cells. The key differences between these ALT survivors are telomere-constituting sequences: non-telomeric sequences and canonical telomeric repeats, with each type of ALT survivors being referred to as type I and type II, respectively. We explored how the characteristics of the two types of ALT lines reflect their fates using multi-omics approaches. The most notable gene expression signatures of type I and type II ALT cell lines were chromatin remodelling and DNA repair, respectively. Compared with type II cells, type I ALT cells accumulated more mutations and demonstrated persistent telomere instability. These findings indicate that cells of the same origin have separate routes for survival, thus providing insights into the plasticity of crisis-suffering cells and cancers.
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Affiliation(s)
- Sanghyun Sung
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
| | - Eunkyeong Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Chuna Kim
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
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2
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Yang C, Ma Z, Wang K, Dong X, Huang M, Li Y, Zhu X, Li J, Cheng Z, Bi C, Zhang X. HMGN1 enhances CRISPR-directed dual-function A-to-G and C-to-G base editing. Nat Commun 2023; 14:2430. [PMID: 37105976 PMCID: PMC10140177 DOI: 10.1038/s41467-023-38193-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
C-to-G base editors have been successfully constructed recently, but limited work has been done on concurrent C-to-G and A-to-G base editing. In addition, there is also limited data on how chromatin-associated factors affect the base editing. Here, we test a series of chromatin-associated factors, and chromosomal protein HMGN1 was found to enhance the efficiency of both C-to-G and A-to-G base editing. By fusing HMGN1, GBE and ABE to Cas9, we develop a CRISPR-based dual-function A-to-G and C-to-G base editor (GGBE) which is capable of converting simultaneous A and C to G conversion with substantial editing efficiency. Accordingly, the HMGN1 role shown in this work and the resulting GGBE tool further broaden the genome manipulation capacity of CRISPR-directed base editors.
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Affiliation(s)
- Chao Yang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhenzhen Ma
- College of Life Sciences, Nankai University, Tianjin, China
| | - Keshan Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingxiao Dong
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Meiyu Huang
- College of Life Sciences, Guangxi Normal University, Guilin, China
| | - Yaqiu Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiagu Zhu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ju Li
- College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Zhihui Cheng
- College of Life Sciences, Nankai University, Tianjin, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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3
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Weiss TJ, Crawford ER, Posada V, Rahman H, Liu T, Murphy BM, Arnold TE, Gray S, Hu Z, Hennessey RC, Yu L, D'Orazio JA, Burd CJ, Zippin JH, Grossman D, Burd CE. Cell-intrinsic melanin fails to protect melanocytes from ultraviolet-mutagenesis in the absence of epidermal melanin. Pigment Cell Melanoma Res 2023; 36:6-18. [PMID: 36148789 PMCID: PMC10092168 DOI: 10.1111/pcmr.13070] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/30/2022] [Accepted: 09/21/2022] [Indexed: 12/31/2022]
Abstract
Melanin is a free-radical scavenger, antioxidant, and broadband absorber of ultraviolet (UV) radiation which protects the skin from environmental carcinogenesis. However, melanin synthesis and UV-induced reactive melanin species are also implicated in melanocyte genotoxicity. Here, we attempted to reconcile these disparate functions of melanin using a UVB-sensitive, NRAS-mutant mouse model, TpN. We crossed TpN mice heterozygous for an inactivating mutation in Tyrosinase to produce albino and black littermates on a C57BL/6J background. These animals were then exposed to a single UVB dose on postnatal day three when keratinocytes in the skin have yet to be melanized. Approximately one-third (35%) of black mice were protected from UVB-accelerated tumor formation. However, melanoma growth rates, tumor mutational burdens, and gene expression profiles were similar in melanomas from black and albino mice. Skin from albino mice contained more cyclobutane pyrimidine dimer (CPD) positive cells than black mice 1-h post-irradiation. However, this trend gradually reversed over time with CPDs becoming more prominent in black than albino melanocytes at 48 h. These results show that in the absence of epidermal pigmentation, melanocytic melanin limits the tumorigenic effects of acute UV exposure but fails to protect melanocytes from UVB-induced mutagenesis.
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Affiliation(s)
- Tirzah J Weiss
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Emma R Crawford
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Valentina Posada
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Hafeez Rahman
- The University of Utah Huntsman Cancer Institute, Salt Lake City, Utah, USA.,Department of Dermatology, The University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, USA
| | - Tong Liu
- The University of Utah Huntsman Cancer Institute, Salt Lake City, Utah, USA.,Department of Dermatology, The University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, USA
| | - Brandon M Murphy
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Tiffany E Arnold
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Shannon Gray
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Zhexuan Hu
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Rebecca C Hennessey
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - John A D'Orazio
- Department of Pediatrics, University of Kentucky College of Medicine, Lexington, Kentucky, USA.,Markey Cancer Center, University of Kentucky, Lexington, Kentucky, USA
| | - Craig J Burd
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Jonathan H Zippin
- Department of Pharmacology, Joan and Sanford I. Weill Medical College of Cornell University, New York, New York, USA.,Department of Dermatology, Joan and Sanford I. Weill Medical College of Cornell University, New York, New York, USA.,Joan and Sanford I. Weill Medical College of Cornell University, Englander Institute for Precision Medicine, New York, New York, USA
| | - Douglas Grossman
- The University of Utah Huntsman Cancer Institute, Salt Lake City, Utah, USA.,Department of Dermatology, The University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, USA
| | - Christin E Burd
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
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4
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Wu Z, Huang Y, Yuan W, Wu X, Shi H, Lu M, Xu A. Expression, tumor immune infiltration, and prognostic impact of HMGs in gastric cancer. Front Oncol 2022; 12:1056917. [PMID: 36568211 PMCID: PMC9780705 DOI: 10.3389/fonc.2022.1056917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Background In the past decade, considerable research efforts on gastric cancer (GC) have been expended, however, little advancement has been made owing to the lack of effective biomarkers and treatment options. Herein, we aimed to examine the levels of expression, mutations, and clinical relevance of HMGs in GC to provide sufficient scientific evidence for clinical decision-making and risk management. Methods GC samples were obtained from The Cancer Genome Atlas (TCGA). University of California Santa Cruz (UCSC) XENA, Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier Plotter, cBioPortal, GeneMANIA, STRING, LinkedOmics, and DAVID databases were employed. The "ggplot2" package in the R software (×64 3.6.3) was used to thoroughly analyze the effects of HMGs. qRT-PCR was performed to assess HMG levels in GC cell lines. Results A total of 375 GC tissues and 32 paraneoplastic tissues were analyzed. The levels of HMGA1, HMGA2, HMGB1, HMGB2, HMGB3, HMGN1, HMGN2, and HMGN4 expression were increased in GC tissues relative to normal gastric tissues. HMGA1, HMGA2, HMGB1, HMGB2, and HMGB3 were highly expressed in GC cell lines. The OS was significantly different in the group showing low expressions of HMGA1, HMGA2, HMGB1, HMGB2, HMGB3, HMGN2, HMGN3, and HMGN5. There was a significant difference in RFS between the groups with low HMGA2, HMGB3, and high HMGN2 expression. The levels of HMGA2, HMGB3, and HMGN1 had a higher accuracy for prediction to distinguish GC from normal tissues (AUC value > 0.9). HMGs were tightly associated with immune infiltration and tumor immune escape and antitumor immunity most likely participates in HMG-mediated oncogenesis in GC. GO and KEGG enrichment analyses showed that HMGs played a vital role in the cell cycle pathway. Conclusions Our results strongly suggest a vital role of HMGs in GC. HMGA2 and HMGB3 could be potential markers for prognostic prediction and treatment targets for GC by interrupting the cell cycle pathway. Our findings might provide renewed perspectives for the selection of prognostic biomarkers among HMGs in GC and may contribute to the determination of the optimal strategy for the treatment of these patients.
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Affiliation(s)
- Zhiheng Wu
- Department of General Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China,Department of General Surgery, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Yang Huang
- Department of General Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China,Department of General Surgery, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Weiwei Yuan
- Department of General Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China,Department of General Surgery, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Xiong Wu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, PR China, State Key Laboratory of Optometry, Ophthalmology, and Visual Science, Wenzhou, Zhejiang, China
| | - Hui Shi
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Ming Lu
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Aman Xu
- Department of General Surgery, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China,Department of General Surgery, Anhui Public Health Clinical Center, Hefei, Anhui, China
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5
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Ihewulezi C, Saint-Jeannet JP. Function of chromatin modifier Hmgn1 during neural crest and craniofacial development. Genesis 2021; 59:e23447. [PMID: 34478234 DOI: 10.1002/dvg.23447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
The neural crest is a dynamic embryonic structure that plays a major role in the formation of the vertebrate craniofacial skeleton. Neural crest formation is regulated by a complex sequence of events directed by a network of transcription factors working in concert with chromatin modifiers. The high mobility group nucleosome binding protein 1 (Hmgn1) is a nonhistone chromatin architectural protein, associated with transcriptionally active chromatin. Here we report the expression and function of Hmgn1 during Xenopus neural crest and craniofacial development. Hmgn1 is broadly expressed at the gastrula and neurula stages, and is enriched in the head region at the tailbud stage, especially in the eyes and the pharyngeal arches. Hmgn1 knockdown affected the expression of several neural crest specifiers, including sox8, sox10, foxd3, and twist1, while other genes (sox9 and snai2) were only marginally affected. The specificity of this phenotype was confirmed by rescue, where injection of Hmgn1 mRNA was able to restore sox10 expression in morphant embryos. The reduction in neural crest gene expression at the neurula stage in Hmgn1 morphant embryos correlated with a decreased number of sox10- and twist1-positive cells in the pharyngeal arches at the tailbud stage, and hypoplastic craniofacial cartilages at the tadpole stage. These results point to a novel role for Hmgn1 in the control of gene expression essential for neural crest and craniofacial development. Future work will investigate the precise mode of action of Hmgn1 in this context.
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Affiliation(s)
- Chibuike Ihewulezi
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, USA
| | - Jean-Pierre Saint-Jeannet
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, USA
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6
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Jing Y, Tian G, Qin X, Liu Z, Li XD. Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2-nucleosome association. RSC Chem Biol 2021; 2:1257-1262. [PMID: 34458839 PMCID: PMC8341127 DOI: 10.1039/d1cb00070e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 02/01/2023] Open
Abstract
Lysine succinylation (Ksucc) is a novel posttranslational modification that frequently occurs on chromatin proteins including histones and non-histone proteins. Histone Ksucc affects nucleosome dynamics by increasing the DNA unwrapping rate and accessibility. However, very little is known about the regulation and functions of Ksucc located on non-histone chromosomal proteins. Here, we site-specifically installed a succinyl lysine analogue (Kcsucc) onto the non-histone chromosomal protein HMG-17 (HMGN2) to mimic the natural succinylated protein. We found that the incorporation of Kcsucc into HMGN2 at the K30 site (HMGN2Kc30succ), which is located within the nucleosome-binding domain (NBD), leads to significantly decreased HMGN2 binding to the mononucleosome. HMGN2Kc30succ also increased the nucleosomal DNA accessibility by promoting nucleosomal DNA unwrapping in the entry/exit region. This study reveals a novel mechanism of non-histone protein succinylation on altering chromatin recruitment, which can further affect nucleosome and chromatin dynamics. Succinylated HMGN2, prepared by a ‘thiol–ene reaction’, disrupted the association of HMGN2 with the nucleosome and increased nucleosomal DNA accessibility.![]()
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Affiliation(s)
- Yihang Jing
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Gaofei Tian
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Xiaoyu Qin
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Zheng Liu
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong Pokfulam Road Hong Kong China
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7
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Obulisamy PK, Mehariya S. Polyhydroxyalkanoates from extremophiles: A review. BIORESOURCE TECHNOLOGY 2021; 325:124653. [PMID: 33465644 DOI: 10.1016/j.biortech.2020.124653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.
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Affiliation(s)
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania "Luigi Vanvitelli", Real Casa dell'Annunziata, Italy
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8
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Tiwari V, Baptiste BA, Okur MN, Bohr VA. Current and emerging roles of Cockayne syndrome group B (CSB) protein. Nucleic Acids Res 2021; 49:2418-2434. [PMID: 33590097 DOI: 10.1093/nar/gkab085] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cockayne syndrome (CS) is a segmental premature aging syndrome caused primarily by defects in the CSA or CSB genes. In addition to premature aging, CS patients typically exhibit microcephaly, progressive mental and sensorial retardation and cutaneous photosensitivity. Defects in the CSB gene were initially thought to primarily impair transcription-coupled nucleotide excision repair (TC-NER), predicting a relatively consistent phenotype among CS patients. In contrast, the phenotypes of CS patients are pleiotropic and variable. The latter is consistent with recent work that implicates CSB in multiple cellular systems and pathways, including DNA base excision repair, interstrand cross-link repair, transcription, chromatin remodeling, RNAPII processing, nucleolin regulation, rDNA transcription, redox homeostasis, and mitochondrial function. The discovery of additional functions for CSB could potentially explain the many clinical phenotypes of CSB patients. This review focuses on the diverse roles played by CSB in cellular pathways that enhance genome stability, providing insight into the molecular features of this complex premature aging disease.
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Affiliation(s)
- Vinod Tiwari
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Mustafa N Okur
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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9
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Shin E, Lee S, Kang H, Kim J, Kim K, Youn H, Jin YW, Seo S, Youn B. Organ-Specific Effects of Low Dose Radiation Exposure: A Comprehensive Review. Front Genet 2020; 11:566244. [PMID: 33133150 PMCID: PMC7565684 DOI: 10.3389/fgene.2020.566244] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
Ionizing radiation (IR) is a high-energy radiation whose biological effects depend on the irradiation doses. Low-dose radiation (LDR) is delivered during medical diagnoses or by an exposure to radioactive elements and has been linked to the occurrence of chronic diseases, such as leukemia and cardiovascular diseases. Though epidemiological research is indispensable for predicting and dealing with LDR-induced abnormalities in individuals exposed to LDR, little is known about epidemiological markers of LDR exposure. Moreover, difference in the LDR-induced molecular events in each organ has been an obstacle to a thorough investigation of the LDR effects and a validation of the experimental results in in vivo models. In this review, we summarized the recent reports on LDR-induced risk of organ-specifically arranged the alterations for a comprehensive understanding of the biological effects of LDR. We suggested that LDR basically caused the accumulation of DNA damages, controlled systemic immune systems, induced oxidative damages on peripheral organs, and even benefited the viability in some organs. Furthermore, we concluded that understanding of organ-specific responses and the biological markers involved in the responses is needed to investigate the precise biological effects of LDR.
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Affiliation(s)
- Eunguk Shin
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Sungmin Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Hyunkoo Kang
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Jeongha Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Kyeongmin Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - Young Woo Jin
- Laboratory of Low Dose Risk Assessment, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Sciences, Seoul, South Korea
| | - Songwon Seo
- Laboratory of Low Dose Risk Assessment, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Sciences, Seoul, South Korea
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea.,Department of Biological Sciences, Pusan National University, Busan, South Korea
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10
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Human HMGN1 and HMGN2 are not required for transcription-coupled DNA repair. Sci Rep 2020; 10:4332. [PMID: 32152397 PMCID: PMC7062826 DOI: 10.1038/s41598-020-61243-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription-coupled repair (TCR) removes DNA lesions from the transcribed strand of active genes. Stalling of RNA polymerase II (RNAPII) at DNA lesions initiates TCR through the recruitment of the CSB and CSA proteins. The full repertoire of proteins required for human TCR – particularly in a chromatin context - remains to be determined. Studies in mice have revealed that the nucleosome-binding protein HMGN1 is required to enhance the repair of UV-induced lesions in transcribed genes. However, whether HMGN1 is required for human TCR remains unaddressed. Here, we show that knockout or knockdown of HMGN1, either alone or in combination with HMGN2, does not render human cells sensitive to UV light or Illudin S-induced transcription-blocking DNA lesions. Moreover, transcription restart after UV irradiation was not impaired in HMGN-deficient cells. In contrast, TCR-deficient cells were highly sensitive to DNA damage and failed to restart transcription. Furthermore, GFP-tagged HMGN1 was not recruited to sites of UV-induced DNA damage under conditions where GFP-CSB readily accumulated. In line with this, HMGN1 did not associate with the TCR complex, nor did TCR proteins require HMGN1 to associate with DNA damage-stalled RNAPII. Together, our findings suggest that HMGN1 and HMGN2 are not required for human TCR.
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11
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Biological Functions of HMGN Chromosomal Proteins. Int J Mol Sci 2020; 21:ijms21020449. [PMID: 31936777 PMCID: PMC7013550 DOI: 10.3390/ijms21020449] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Chromatin plays a key role in regulating gene expression programs necessary for the orderly progress of development and for preventing changes in cell identity that can lead to disease. The high mobility group N (HMGN) is a family of nucleosome binding proteins that preferentially binds to chromatin regulatory sites including enhancers and promoters. HMGN proteins are ubiquitously expressed in all vertebrate cells potentially affecting chromatin function and epigenetic regulation in multiple cell types. Here, we review studies aimed at elucidating the biological function of HMGN proteins, focusing on their possible role in vertebrate development and the etiology of disease. The data indicate that changes in HMGN levels lead to cell type-specific phenotypes, suggesting that HMGN optimize epigenetic processes necessary for maintaining cell identity and for proper execution of specific cellular functions. This manuscript contains tables that can be used as a comprehensive resource for all the English written manuscripts describing research aimed at elucidating the biological function of the HMGN protein family.
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12
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Liu EY, Russ J, Lee EB. Neuronal Transcriptome from C9orf72 Repeat Expanded Human Tissue is Associated with Loss of C9orf72 Function. FREE NEUROPATHOLOGY 2020; 1:23. [PMID: 32905541 PMCID: PMC7470232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A hexanucleotide G4C2 repeat expansion in C9orf72 is the most common genetic cause of familial and sporadic cases of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). The mutation is associated with a reduction of C9orf72 protein and accumulation of toxic RNA and dipeptide repeat aggregates. The accumulation of toxic RNA has been proposed to sequester RNA binding proteins thereby altering RNA processing, consistent with previous transcriptome studies that have shown that the C9orf72 repeat expansion is linked to abundant splicing alterations and transcriptome changes. Here, we used a subcellular fractionation method and FACS to enrich for neuronal nuclei from C9orf72 repeat expanded post-mortem human ALS/FTD brains, and to remove neuronal nuclei with TDP-43 pathology which are observed in nearly all symptomatic C9orf72 repeat expanded cases. We show that the C9orf72 expansion is associated with relatively mild gene expression changes. Dysregulated genes were enriched for vesicle transport pathways, which is consistent with the known functions of C9orf72 protein. Further analysis suggests that the C9orf72 transcriptome is not driven by toxic RNA but is rather shaped by the depletion of pathologic TDP-43 nuclei and the loss of C9orf72 expression. These findings argue against RNA binding protein sequestration in neurons as a major contributor to C9orf72 mediated toxicity.
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Affiliation(s)
- Elaine Y. Liu
- Translational Neuropathology Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Jenny Russ
- Translational Neuropathology Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward B. Lee
- Translational Neuropathology Research Laboratory, University of Pennsylvania, Philadelphia, PA, USA
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13
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Garza-Manero S, Sindi AAA, Mohan G, Rehbini O, Jeantet VHM, Bailo M, Latif FA, West MP, Gurden R, Finlayson L, Svambaryte S, West AG, West KL. Maintenance of active chromatin states by HMGN2 is required for stem cell identity in a pluripotent stem cell model. Epigenetics Chromatin 2019; 12:73. [PMID: 31831052 PMCID: PMC6907237 DOI: 10.1186/s13072-019-0320-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
Background Members of the HMGN protein family modulate chromatin structure and influence epigenetic modifications. HMGN1 and HMGN2 are highly expressed during early development and in the neural stem/progenitor cells of the developing and adult brain. Here, we investigate whether HMGN proteins contribute to the chromatin plasticity and epigenetic regulation that is essential for maintaining pluripotency in stem cells. Results We show that loss of Hmgn1 or Hmgn2 in pluripotent embryonal carcinoma cells leads to increased levels of spontaneous neuronal differentiation. This is accompanied by the loss of pluripotency markers Nanog and Ssea1, and increased expression of the pro-neural transcription factors Neurog1 and Ascl1. Neural stem cells derived from these Hmgn-knockout lines also show increased spontaneous neuronal differentiation and Neurog1 expression. The loss of HMGN2 leads to a global reduction in H3K9 acetylation, and disrupts the profile of H3K4me3, H3K9ac, H3K27ac and H3K122ac at the Nanog and Oct4 loci. At endodermal/mesodermal genes, Hmgn2-knockout cells show a switch from a bivalent to a repressive chromatin configuration. However, at neuronal lineage genes whose expression is increased, no epigenetic changes are observed and their bivalent states are retained following the loss of HMGN2. Conclusions We conclude that HMGN1 and HMGN2 maintain the identity of pluripotent embryonal carcinoma cells by optimising the pluripotency transcription factor network and protecting the cells from precocious differentiation. Our evidence suggests that HMGN2 regulates active and bivalent genes by promoting an epigenetic landscape of active histone modifications at promoters and enhancers.
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Affiliation(s)
- Sylvia Garza-Manero
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Abdulmajeed Abdulghani A Sindi
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.,Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Albaha University, Albaha-Alaqiq, Saudi Arabia
| | - Gokula Mohan
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.,Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Ohoud Rehbini
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Valentine H M Jeantet
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Mariarca Bailo
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Faeezah Abdul Latif
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Maureen P West
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Ross Gurden
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Lauren Finlayson
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Silvija Svambaryte
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Adam G West
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Katherine L West
- Institute of Cancer Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK. .,School of Life Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK.
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14
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Mowery CT, Reyes JM, Cabal-Hierro L, Higby KJ, Karlin KL, Wang JH, Kimmerling RJ, Cejas P, Lim K, Li H, Furusawa T, Long HW, Pellman D, Chapuy B, Bustin M, Manalis SR, Westbrook TF, Lin CY, Lane AA. Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression. Cell Rep 2019; 25:1898-1911.e5. [PMID: 30428356 PMCID: PMC6321629 DOI: 10.1016/j.celrep.2018.10.061] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/21/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute normalization unmasks global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulates transcriptional changes seen with triplication of a Down syndrome critical region on distal chromosome 21, and HMGN1 is necessary for B cell phenotypes in DS models. Absolute exogenous-normalized chromatin immunoprecipitation sequencing (ChIP-Rx) also reveals a global increase in histone H3K27 acetylation caused by HMGN1. Transcriptional amplification downstream of HMGN1 is enriched for stage-specific programs of B cells and B cell acute lymphoblastic leukemia, dependent on the developmental cellular context. These data offer a mechanistic explanation for DS transcriptional patterns and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted. How trisomy 21 contributes to Down syndrome phenotypes, including increased leukemia risk, is not well understood. Mowery et al. use per-cell normalization approaches to reveal global transcriptional amplification in Down syndrome models. HMGN1 overexpression is sufficient to induce these alterations and promotes lineage-associated transcriptional programs, signaling, and B cell progenitor phenotypes.
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Affiliation(s)
- Cody T Mowery
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jaime M Reyes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lucia Cabal-Hierro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kelly J Higby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kristen L Karlin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Jarey H Wang
- Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Robert J Kimmerling
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hubo Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Takashi Furusawa
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Department of Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, USA
| | - Scott R Manalis
- Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas F Westbrook
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Charles Y Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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15
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Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer. Genes (Basel) 2019; 10:genes10100794. [PMID: 31614829 PMCID: PMC6826716 DOI: 10.3390/genes10100794] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022] Open
Abstract
Development requires the careful orchestration of several biological events in order to create any structure and, eventually, to build an entire organism. On the other hand, the fate transformation of terminally differentiated cells is a consequence of erroneous development, and ultimately leads to cancer. In this review, we elaborate how development and cancer share several biological processes, including molecular controls. Transcription factors (TF) are at the helm of both these processes, among many others, and are evolutionarily conserved, ranging from yeast to humans. Here, we discuss four families of TFs that play a pivotal role and have been studied extensively in both embryonic development and cancer—high mobility group box (HMG), GATA, paired box (PAX) and basic helix-loop-helix (bHLH) in the context of their role in development, cancer, and their conservation across several species. Finally, we review TFs as possible therapeutic targets for cancer and reflect on the importance of natural resistance against cancer in certain organisms, yielding knowledge regarding TF function and cancer biology.
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16
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Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019; 19:e1800438. [PMID: 30901150 DOI: 10.1002/pmic.201800438] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/24/2019] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
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17
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18
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Yang D, Han Z, Alam MM, Oppenheim JJ. High-mobility group nucleosome binding domain 1 (HMGN1) functions as a Th1-polarizing alarmin. Semin Immunol 2018; 38:49-53. [PMID: 29503123 DOI: 10.1016/j.smim.2018.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/26/2018] [Indexed: 12/16/2022]
Abstract
High-mobility group (HMG) nucleosome binding domain 1 (HMGN1), which previously was thought to function only as a nucleosome-binding protein that regulates chromatin structure, histone modifications, and gene expression, was recently discovered to be an alarmin that contributes extracellularly to the generation of innate and adaptive immune responses. HMGN1 promotes DC recruitment through interacting with a Gαi protein-coupled receptor (GiPCR) and activates DCs predominantly through triggering TLR4. HMGN1 preferentially promotes Th1-type immunity, which makes it relevant for the fields of vaccinology, autoimmunity, and oncoimmunology. Here, we discuss the alarmin properties of HMGN1 and update recent advances on its roles in immunity and potential applications for immunotherapy of tumors.
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Affiliation(s)
- De Yang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA.
| | - Zhen Han
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA
| | - Md Masud Alam
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA
| | - Joost J Oppenheim
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institute of Health, USA.
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19
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Arts RJW, Huang PK, Yang D, Joosten LAB, van der Meer JWM, Oppenheim JJ, Netea MG, Cheng SC. High-Mobility Group Nucleosome-Binding Protein 1 as Endogenous Ligand Induces Innate Immune Tolerance in a TLR4-Sirtuin-1 Dependent Manner in Human Blood Peripheral Mononuclear Cells. Front Immunol 2018; 9:526. [PMID: 29593748 PMCID: PMC5861144 DOI: 10.3389/fimmu.2018.00526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/28/2018] [Indexed: 11/13/2022] Open
Abstract
High-mobility group nucleosome-binding protein 1 (HMGN1) functions as a non-histone chromatin-binding protein in the cell nucleus. However, extracellular HMGN1 acts as an endogenous danger-associated inflammatory mediator (also called alarmin). We demonstrated that HMGN1 not only directly stimulated cytokine production but also had the capacity to induce immune tolerance by a TLR4-dependent pathway, similar to lipopolysaccharide (LPS)-induced tolerance. HMGN1-induced tolerance was accompanied by a metabolic shift associated with the inhibition of the induction of Warburg effect (aerobic glycolysis) and histone deacetylation via Sirtuin-1. In addition, HMGN1 pre-challenge of mice also downregulated TNF production similar to LPS-induced tolerance in vivo. In conclusion, HMGN1 is an endogenous TLR4 ligand that can induce both acute stimulation of cytokine production and long-term tolerance, and thus it might play a modulatory role in sterile inflammatory processes such as those induced by infection, trauma, or ischemia.
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Affiliation(s)
- Rob J W Arts
- Department of Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Po-Kai Huang
- College of Life Science, Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
| | - De Yang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institue at Frederick, Frederick, MD, United States
| | - Leo A B Joosten
- Department of Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jos W M van der Meer
- Department of Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Joost J Oppenheim
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institue at Frederick, Frederick, MD, United States
| | - Mihai G Netea
- Department of Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Shih-Chin Cheng
- College of Life Science, Institute of Molecular Medicine, National Tsing Hua University, Hsinchu City, Taiwan
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20
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Murphy KJ, Cutter AR, Fang H, Postnikov YV, Bustin M, Hayes JJ. HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic Acids Res 2017; 45:9917-9930. [PMID: 28973435 PMCID: PMC5622319 DOI: 10.1093/nar/gkx579] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/28/2017] [Indexed: 01/23/2023] Open
Abstract
The structure of the nucleosome, the basic building block of the chromatin fiber, plays a key role in epigenetic regulatory processes that affect DNA-dependent processes in the context of chromatin. Members of the HMGN family of proteins bind specifically to nucleosomes and affect chromatin structure and function, including transcription and DNA repair. To better understand the mechanisms by which HMGN 1 and 2 alter chromatin, we analyzed their effect on the organization of histone tails and linker histone H1 in nucleosomes. We find that HMGNs counteract linker histone (H1)-dependent stabilization of higher order ‘tertiary’ chromatin structures but do not alter the intrinsic ability of nucleosome arrays to undergo salt-induced compaction and self-association. Surprisingly, HMGNs do not displace H1s from nucleosomes; rather these proteins bind nucleosomes simultaneously with H1s without disturbing specific contacts between the H1 globular domain and nucleosomal DNA. However, HMGNs do alter the nucleosome-dependent condensation of the linker histone C-terminal domain, which is critical for stabilizing higher-order chromatin structures. Moreover, HMGNs affect the interactions of the core histone tail domains with nucleosomal DNA, redirecting the tails to more interior positions within the nucleosome. Our studies provide new insights into the molecular mechanisms whereby HMGNs affect chromatin structure.
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Affiliation(s)
- Kevin J Murphy
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Amber R Cutter
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - He Fang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
| | - Yuri V Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
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21
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Deng T, Postnikov Y, Zhang S, Garrett L, Becker L, Rácz I, Hölter SM, Wurst W, Fuchs H, Gailus-Durner V, de Angelis MH, Bustin M. Interplay between H1 and HMGN epigenetically regulates OLIG1&2 expression and oligodendrocyte differentiation. Nucleic Acids Res 2017; 45:3031-3045. [PMID: 27923998 PMCID: PMC5389484 DOI: 10.1093/nar/gkw1222] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/22/2016] [Indexed: 01/22/2023] Open
Abstract
An interplay between the nucleosome binding proteins H1 and HMGN is known to affect chromatin dynamics, but the biological significance of this interplay is still not clear. We find that during embryonic stem cell differentiation loss of HMGNs leads to down regulation of genes involved in neural differentiation, and that the transcription factor OLIG2 is a central node in the affected pathway. Loss of HMGNs affects the expression of OLIG2 as well as that of OLIG1, two transcription factors that are crucial for oligodendrocyte lineage specification and nerve myelination. Loss of HMGNs increases the chromatin binding of histone H1, thereby recruiting the histone methyltransferase EZH2 and elevating H3K27me3 levels, thus conferring a repressive epigenetic signature at Olig1&2 sites. Embryonic stem cells lacking HMGNs show reduced ability to differentiate towards the oligodendrocyte lineage, and mice lacking HMGNs show reduced oligodendrocyte count and decreased spinal cord myelination, and display related neurological phenotypes. Thus, the presence of HMGN proteins is required for proper expression of neural differentiation genes during embryonic stem cell differentiation. Specifically, we demonstrate that the dynamic interplay between HMGNs and H1 in chromatin epigenetically regulates the expression of OLIG1&2, thereby affecting oligodendrocyte development and myelination, and mouse behavior.
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Affiliation(s)
- Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lillian Garrett
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ildikó Rácz
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Molecular Psychiatry, University of Bonn, 53125 Bonn, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Technische Universität München-Weihenstephan, Chair of Developmental Genetics c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE) Site Munich, Munich Germany.,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336 Munich, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum, München, German Research Center for Environmental Health, 85764 Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, 85354 Freising, Germany.,German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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22
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Kugler J, Postnikov YV, Furusawa T, Kimura S, Bustin M. Elevated HMGN4 expression potentiates thyroid tumorigenesis. Carcinogenesis 2017; 38:391-401. [PMID: 28186538 DOI: 10.1093/carcin/bgx015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/07/2017] [Indexed: 12/19/2022] Open
Abstract
Thyroid cancer originates from genetic and epigenetic changes that alter gene expression and cellular signaling pathways. Here, we report that altered expression of the nucleosome-binding protein HMGN4 potentiates thyroid tumorigenesis. Bioinformatics analyses reveal increased HMGN4 expression in thyroid cancer. We find that upregulation of HMGN4 expression in mouse and human cells, and in the thyroid of transgenic mice, alters the cellular transcription profile, downregulates the expression of the tumor suppressors Atm, Atrx and Brca2, and elevates the levels of the DNA damage marker γH2AX. Mouse and human cells overexpressing HMGN4 show increased tumorigenicity as measured by colony formation, by tumor generation in nude mice, and by the formation of preneoplastic lesions in the thyroid of transgenic mice. Our study identifies a novel epigenetic factor that potentiates thyroid oncogenesis and raises the possibility that HMGN4 may serve as an additional diagnostic marker, or therapeutic target in certain thyroid cancers.
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Affiliation(s)
- Jamie Kugler
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
| | - Yuri V Postnikov
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
| | - Takashi Furusawa
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
| | - Shioko Kimura
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda MD 20892, USA
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23
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Canel NG, Bevacqua RJ, Hiriart MI, Rabelo NC, de Almeida Camargo LS, Romanato M, de Calvo LP, Salamone DF. Sperm pretreatment with heparin and l-glutathione, sex-sorting, and double cryopreservation to improve intracytoplasmic sperm injection in bovine. Theriogenology 2017; 93:62-70. [DOI: 10.1016/j.theriogenology.2016.12.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
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24
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Stratigi K, Chatzidoukaki O, Garinis GA. DNA damage-induced inflammation and nuclear architecture. Mech Ageing Dev 2016; 165:17-26. [PMID: 27702596 DOI: 10.1016/j.mad.2016.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 12/12/2022]
Abstract
Nuclear architecture and the chromatin state affect most-if not all- DNA-dependent transactions, including the ability of cells to sense DNA lesions and restore damaged DNA back to its native form. Recent evidence points to functional links between DNA damage sensors, DNA repair mechanisms and the innate immune responses. The latter raises the question of how such seemingly disparate processes operate within the intrinsically complex nuclear landscape and the chromatin environment. Here, we discuss how DNA damage-induced immune responses operate within chromatin and the distinct sub-nuclear compartments highlighting their relevance to chronic inflammation.
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Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Ourania Chatzidoukaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR71409, Heraklion, Crete, Greece.
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Abstract
PURPOSE Alarmins are constitutively present endogenous molecules that essentially act as early warning signals for the immune system. We provide a brief overview of major alarmins and highlight their roles in tumor immunity. METHODS We searched PubMed up to January 10, 2016, using alarmins and/or damage-associated molecular patterns (DAMPs), as key words. We selected and reviewed articles that focused on the discovery and functions of alarmin and their roles in tumor immunity. FINDINGS Alarmins are essentially endogenous immunostimulatory DAMP molecules that are exposed in response to danger (eg, infection or tissue injury) as a result of degranulation, cell death, or induction. They are sensed by chemotactic receptors and pattern recognition receptors to induce immune responses by promoting the recruitment and activation of leukocytes, particularly antigen-presenting cells. IMPLICATIONS Accumulating data suggest that certain alarmins, High-mobility group nucleosome-binding protein 1 (HMGN1) in particular, contribute to the generation of antitumor immunity. Some alarmins can also be used as cancer biomarkers. Therefore, alarmins can potentially be applied for our fight against cancers.
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Affiliation(s)
- Yingjie Nie
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland; Guizhou Provincial Peoples' Hospital, Guiyang, Guizhou Province, China
| | - De Yang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland; Basic Research Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Joost J Oppenheim
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
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26
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Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M. HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells. Nucleic Acids Res 2016; 44:7144-58. [PMID: 27112571 PMCID: PMC5009722 DOI: 10.1093/nar/gkw323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/14/2016] [Indexed: 12/18/2022] Open
Abstract
The activation of naïve B lymphocyte involves rapid and major changes in chromatin organization and gene expression; however, the complete repertoire of nuclear factors affecting these genomic changes is not known. We report that HMGN proteins, which bind to nucleosomes and affect chromatin structure and function, co-localize with, and maintain the intensity of DNase I hypersensitive sites genome wide, in resting but not in activated B cells. Transcription analyses of resting and activated B cells from wild-type and Hmgn−/− mice, show that loss of HMGNs dampens the magnitude of the transcriptional response and alters the pattern of gene expression during the course of B-cell activation; defense response genes are most affected at the onset of activation. Our study provides insights into the biological function of the ubiquitous HMGN chromatin binding proteins and into epigenetic processes that affect the fidelity of the transcriptional response during the activation of B cell lymphocytes.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Remy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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27
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28
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Yang D, Bustin M, Oppenheim JJ. Harnessing the alarmin HMGN1 for anticancer therapy. Immunotherapy 2015; 7:1129-31. [PMID: 26567750 DOI: 10.2217/imt.15.76] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- De Yang
- Laboratory of Molecular Immunoregulation, Cancer & Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute at Bethesda, Bethesda, MD 20892, USA
| | - Joost J Oppenheim
- Laboratory of Molecular Immunoregulation, Cancer & Inflammation Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
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29
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Reeves R. High mobility group (HMG) proteins: Modulators of chromatin structure and DNA repair in mammalian cells. DNA Repair (Amst) 2015; 36:122-136. [PMID: 26411874 DOI: 10.1016/j.dnarep.2015.09.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It has been almost a decade since the last review appeared comparing and contrasting the influences that the different families of High Mobility Group proteins (HMGA, HMGB and HMGN) have on the various DNA repair pathways in mammalian cells. During that time considerable progress has been made in our understanding of how these non-histone proteins modulate the efficiency of DNA repair by all of the major cellular pathways: nucleotide excision repair, base excision repair, double-stand break repair and mismatch repair. Although there are often similar and over-lapping biological activities shared by all HMG proteins, members of each of the different families appear to have a somewhat 'individualistic' impact on various DNA repair pathways. This review will focus on what is currently known about the roles that different HMG proteins play in DNA repair processes and discuss possible future research areas in this rapidly evolving field.
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Affiliation(s)
- Raymond Reeves
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-4660, USA.
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30
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Nagao M, Lanjakornsiripan D, Itoh Y, Kishi Y, Ogata T, Gotoh Y. High mobility group nucleosome-binding family proteins promote astrocyte differentiation of neural precursor cells. Stem Cells 2015; 32:2983-97. [PMID: 25069414 DOI: 10.1002/stem.1787] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/17/2014] [Accepted: 06/23/2014] [Indexed: 11/07/2022]
Abstract
Astrocytes are the most abundant cell type in the mammalian brain and are important for the functions of the central nervous system. Although previous studies have shown that the STAT signaling pathway or its regulators promote the generation of astrocytes from multipotent neural precursor cells (NPCs) in the developing mammalian brain, the molecular mechanisms that regulate the astrocytic fate decision have still remained largely unclear. Here, we show that the high mobility group nucleosome-binding (HMGN) family proteins, HMGN1, 2, and 3, promote astrocyte differentiation of NPCs during brain development. HMGN proteins were expressed in NPCs, Sox9(+) glial progenitors, and GFAP(+) astrocytes in perinatal and adult brains. Forced expression of either HMGN1, 2, or 3 in NPCs in cultures or in the late embryonic neocortex increased the generation of astrocytes at the expense of neurons. Conversely, knockdown of either HMGN1, 2, or 3 in NPCs suppressed astrocyte differentiation and promoted neuronal differentiation. Importantly, overexpression of HMGN proteins did not induce the phosphorylation of STAT3 or activate STAT reporter genes. In addition, HMGN family proteins did not enhance DNA demethylation and acetylation of histone H3 around the STAT-binding site of the gfap promoter. Moreover, knockdown of HMGN family proteins significantly reduced astrocyte differentiation induced by gliogenic signal ciliary neurotrophic factor, which activates the JAK-STAT pathway. Therefore, we propose that HMGN family proteins are novel chromatin regulatory factors that control astrocyte fate decision/differentiation in parallel with or downstream of the JAK-STAT pathway through modulation of the responsiveness to gliogenic signals.
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Affiliation(s)
- Motoshi Nagao
- Department of Rehabilitation for the Movement Functions, Research Institute, National Rehabilitation Center for Persons with Disabilities, Saitama, Japan
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31
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Deng T, Zhu ZI, Zhang S, Postnikov Y, Huang D, Horsch M, Furusawa T, Beckers J, Rozman J, Klingenspor M, Amarie O, Graw J, Rathkolb B, Wolf E, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, van der Velde A, Tessarollo L, Ovcherenko I, Landsman D, Bustin M. Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers. Genome Res 2015; 25:1295-308. [PMID: 26156321 PMCID: PMC4561489 DOI: 10.1101/gr.192229.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/07/2015] [Indexed: 12/29/2022]
Abstract
DNase I hypersensitive sites (DHSs) are a hallmark of chromatin regions containing regulatory DNA such as enhancers and promoters; however, the factors affecting the establishment and maintenance of these sites are not fully understood. We now show that HMGN1 and HMGN2, nucleosome-binding proteins that are ubiquitously expressed in vertebrate cells, maintain the DHS landscape of mouse embryonic fibroblasts (MEFs) synergistically. Loss of one of these HMGN variants led to a compensatory increase of binding of the remaining variant. Genome-wide mapping of the DHSs in Hmgn1(-/-), Hmgn2(-/-), and Hmgn1(-/-)n2(-/-) MEFs reveals that loss of both, but not a single HMGN variant, leads to significant remodeling of the DHS landscape, especially at enhancer regions marked by H3K4me1 and H3K27ac. Loss of HMGN variants affects the induced expression of stress-responsive genes in MEFs, the transcription profiles of several mouse tissues, and leads to altered phenotypes that are not seen in mice lacking only one variant. We conclude that the compensatory binding of HMGN variants to chromatin maintains the DHS landscape, and the transcription fidelity and is necessary to retain wild-type phenotypes. Our study provides insight into mechanisms that maintain regulatory sites in chromatin and into functional compensation among nucleosome binding architectural proteins.
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Affiliation(s)
- Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Z Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Martin Klingenspor
- Molecular Nutritional Medicine, Technische Universität München, 85350 Freising, Germany; Center for Nutrition and Food Sciences, Technische Universität München, 85350 Freising, Germany
| | - Oana Amarie
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Developmental Genetics (IDG), 85764 Neuherberg, Germany
| | - Jochen Graw
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Developmental Genetics (IDG), 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, 81377 Munich, Germany
| | - Eckhard Wolf
- Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, 81377 Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, 81675 Munich, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Arjan van der Velde
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Ivan Ovcherenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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32
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Wei F, Yang F, Jiang X, Yu W, Ren X. High-mobility group nucleosome-binding protein 1 is a novel clinical biomarker in non-small cell lung cancer. Tumour Biol 2015; 36:9405-10. [PMID: 26113410 DOI: 10.1007/s13277-015-3693-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/18/2015] [Indexed: 01/13/2023] Open
Abstract
The involvement of alarmin high-mobility group nucleosome-binding protein 1 (HMGN1) in non-small cell lung cancer (NSCLC) is unknown. To address the presence of HMGN1 in the serum of different stages of NSCLC patients and healthy controls, we enrolled a consecutive sample of adult serum at diagnosis and correlated it with clinicopathologic outcomes. A total of 100 NSCLC patients and 23 healthy volunteers were enrolled from January 2012 through December 2013. Serum HMGN1 levels were determined by enzyme-linked immunosorbent assay (ELISA). Additionally, HMGN1 levels in 50 NSCLC patients with early-stage disease who received curative pneumonectomy were correlated with survivals. Kaplan-Meier plots were used to analyze the data. The patients with NSCLC were characterized by significantly higher serum levels of HMGN1 (0.4585 ± 0.0640 ng/ml) compared to those in healthy controls (0.3578 ± 0.0304 ng/ml). The serum HMGN1 levels were 0.4027 ± 0.0271 ng/ml, 0.4604 ± 0.0328 ng/ml, 0.5408 ± 0.0459 ng/ml, and 0.4213 ± 0.0341 ng/ml in patients with TNM stages I, II, IV, and IV, respectively (p < 0.001). There were significant differences among four groups (p < 0.001). Additionally, a positive correlation between serum HMGN1 and tumor stage was found in local disease, while serum HMGN1 level in metastatic NSCLC patients was significantly decreased. The Kaplan-Meier plots showed that patients with high serum HMGN1 had a poorer overall survival (OS) after curative pneumonectomy than those with low serum HMGN1 (p = 0.019). Inflammation triggered by alarmins plays a role in NSCLC pathogenesis. HMGN1 can serve as a useful clinical parameter for evaluating disease progression and predicting the outcomes for early-stage patients with NSCLC undergoing pneumonectomy.
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Affiliation(s)
- Feng Wei
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin; Key Laboratory of Cancer Prevention and Therapy, Tianjin, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China
| | - Fan Yang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin; Key Laboratory of Cancer Prevention and Therapy, Tianjin, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China.,Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China
| | - Xiangli Jiang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin; Key Laboratory of Cancer Prevention and Therapy, Tianjin, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin; Key Laboratory of Cancer Prevention and Therapy, Tianjin, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China
| | - Xiubao Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; National Clinical Research Center for Cancer; Key Laboratory of Cancer Immunology and Biotherapy, Tianjin; Key Laboratory of Cancer Prevention and Therapy, Tianjin, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China. .,Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, 300060, People's Republic of China.
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Human C6orf211 encodes Armt1, a protein carboxyl methyltransferase that targets PCNA and is linked to the DNA damage response. Cell Rep 2015; 10:1288-96. [PMID: 25732820 DOI: 10.1016/j.celrep.2015.01.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 12/08/2014] [Accepted: 01/24/2015] [Indexed: 11/20/2022] Open
Abstract
Recent evidence supports the presence of an L-glutamyl methyltransferase(s) in eukaryotic cells, but this enzyme class has been defined only in certain prokaryotic species. Here, we characterize the human C6orf211 gene product as "acidic residue methyltransferase-1" (Armt1), an enzyme that specifically targets proliferating cell nuclear antigen (PCNA) in breast cancer cells, predominately methylating glutamate side chains. Armt1 homologs share structural similarities with the SAM-dependent methyltransferases, and negative regulation of activity by automethylation indicates a means for cellular control. Notably, shRNA-based knockdown of Armt1 expression in two breast cancer cell lines altered survival in response to genotoxic stress. Increased sensitivity to UV, adriamycin, and MMS was observed in SK-Br-3 cells, while in contrast, increased resistance to these agents was observed in MCF7 cells. Together, these results lay the foundation for defining the mechanism by which this post-translational modification operates in the DNA damage response (DDR).
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34
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Zhang J, Li C, Tang X, Lu Q, Sa R, Zhang H. Proteome changes in the small intestinal mucosa of broilers (Gallus gallus) induced by high concentrations of atmospheric ammonia. Proteome Sci 2015; 13:9. [PMID: 25741220 PMCID: PMC4347970 DOI: 10.1186/s12953-015-0067-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/11/2015] [Indexed: 01/15/2023] Open
Abstract
Background Ammonia is a well-known toxicant both existing in atmospheric and aquatic system. So far, most studies of ammonia toxicity focused on mammals or aquatic animals. With the development of poultry industry, ammonia as a main source of contaminant in the air is causing more and more problems on broiler production, especially lower growth rate. The molecular mechanisms that underlie the negative effects of ammonia on the growth and intestine of broilers are yet unclear. We investigated the growth, gut morphology, and mucosal proteome of Arbor Acres broilers (Gallus gallus) exposed to high concentrations of atmospheric ammonia by performing a proteomics approach integrated with traditional methods. Results Exposure to ammonia interfered with the development of immune organ and gut villi. Meanwhile, it greatly reduced daily weight gain and feed intake, and enhanced feed conversion ratio. A total of 43 intestinal mucosal proteins were found to be differentially abundant. Up-regulated proteins are related to oxidative phosphorylation and apoptosis. Down-regulated proteins are related to cell structure and growth, transcriptional and translational regulation, immune response, oxidative stress and nutrient metabolism. These results indicated that exposure to ammonia triggered oxidative stress, and interfered with nutrient absorption and immune function in the small intestinal mucosa of broilers. Conclusions These findings have important implications for understanding the toxic mechanisms of ammonia on intestine of broilers, which provides new information that can be used for intervention using nutritional strategies in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0067-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jize Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Cong Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Qingping Lu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Renna Sa
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 People's Republic of China
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Furusawa T, Rochman M, Taher L, Dimitriadis EK, Nagashima K, Anderson S, Bustin M. Chromatin decompaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness. Nat Commun 2015; 6:6138. [PMID: 25609380 PMCID: PMC4304400 DOI: 10.1038/ncomms7138] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/15/2014] [Indexed: 12/19/2022] Open
Abstract
In most metazoan nuclei, heterochromatin is located at the nuclear periphery in contact with the nuclear lamina, which provides mechanical stability to the nucleus. We show that in cultured cells, chromatin de-compaction by the nucleosome binding protein HMGN5 decreases the sturdiness, elasticity, and rigidity of the nucleus. Mice overexpressing HMGN5, either globally or only in the heart, are normal at birth but develop hypertrophic heart with large cardiomyoctyes, deformed nuclei and disrupted lamina, and die of cardiac malfunction. Chromatin de-compaction is seen in cardiomyocytes of newborn mice but misshaped nuclei with disrupted lamina are seen only in adult cardiomyocytes, suggesting that loss of heterochromatin diminishes the ability of the nucleus to withstand the mechanical forces of the contracting heart. Thus, heterochromatin enhances the ability of the nuclear lamina to maintain the sturdiness and shape of the eukaryotic nucleus; a structural role for chromatin that is distinct from its genetic functions.
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Affiliation(s)
- Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Leila Taher
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock 18057, Germany
| | - Emilios K Dimitriadis
- Biomedical Engineering and Physical Science Shared Resource Program, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kunio Nagashima
- Electron microscopy laboratory, Leidos Biomedical Research Inc., SAIC-Frederick Inc.,Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, USA
| | - Stasia Anderson
- Animal Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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36
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Su B, Shi B, Tang Y, Guo Z, Yu X, He X, Li X, Gao X, Zhou L. HMGN5 knockdown sensitizes prostate cancer cells to ionizing radiation. Prostate 2015; 75:33-44. [PMID: 25307178 DOI: 10.1002/pros.22888] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/05/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND High Mobility Group N (HMGN) proteins are a family of chromatin structural proteins that specifically bind to nucleosome core particles. HMGN5 is a novel and characteristic member of the HMGN protein family. We have previously found that HMGN5 is upregulated in prostate cancer and its downregulation had been demonstrated to induce apoptosis and G2-M cell cycle arrest. METHODS The radiosensitization effect of HMGN5 knockdown on PC3 and DU145 cells was assessed using clonogenic assay, flow cytometry, and comet assay. The DNA double-strand break (DSB) repair kinetics of HMGN5 knockdown and control cells after radiation exposure was evaluated using immunocytofluorescence. The mitochondrial reactive oxygen species (ROS) levels were estimated using Dihydrorhodamine 123 (DHR 123) probes. Expression of mitochondrial antioxidant MnSOD was measured by real-time PCR and Western blot. The expression of antiapoptotic proteins Bcl-2 and Bcl-xL as well as cleavage of caspase-3, caspase-9, and PARP were also measured using Western blot. RESULTS HMGN5 knockdown cells exhibit decreased clonogenic survival and increased apoptosis rate in response to 2-8 Gy ionizing radiation (IR). Loss of HMGN5 does not affect the DSB repair kinetics after radiation exposure. HMGN5 knockdown cells demonstrated increased mitochondrial ROS level and suppressed induction of MnSOD upon radiation compared with control cells upon radiation. Further, MnSOD knockdown resulted in inhibited cell viability as well as increased mitochondrial ROS level and apoptosis upon radiation in PC3 and DU145 cells. Finally, HMGN5 knockdown cells showed significantly decreased levels of antiapoptotic proteins Bcl-2 and Bcl-xL as well as increased cleavage of caspase-3, caspase-9, and PARP compared with control cells after radiation. CONCLUSIONS HMGN5 knockdown sensitizes prostate cancer cells to ionizing radiation, and the radiosensitization effect may be partially mediated through suppressed induction of MnSOD and enhanced activation of apoptosis pathway in response to IR.
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Affiliation(s)
- Boxing Su
- Department of Urology, Peking University First Hospital and the Institute of Urology, Peking University, Beijing, China; National Urological Cancer Center, Beijing, China
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Kang R, Chen R, Zhang Q, Hou W, Wu S, Cao L, Huang J, Yu Y, Fan XG, Yan Z, Sun X, Wang H, Wang Q, Tsung A, Billiar TR, Zeh HJ, Lotze MT, Tang D. HMGB1 in health and disease. Mol Aspects Med 2014; 40:1-116. [PMID: 25010388 PMCID: PMC4254084 DOI: 10.1016/j.mam.2014.05.001] [Citation(s) in RCA: 678] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/05/2014] [Indexed: 12/22/2022]
Abstract
Complex genetic and physiological variations as well as environmental factors that drive emergence of chromosomal instability, development of unscheduled cell death, skewed differentiation, and altered metabolism are central to the pathogenesis of human diseases and disorders. Understanding the molecular bases for these processes is important for the development of new diagnostic biomarkers, and for identifying new therapeutic targets. In 1973, a group of non-histone nuclear proteins with high electrophoretic mobility was discovered and termed high-mobility group (HMG) proteins. The HMG proteins include three superfamilies termed HMGB, HMGN, and HMGA. High-mobility group box 1 (HMGB1), the most abundant and well-studied HMG protein, senses and coordinates the cellular stress response and plays a critical role not only inside of the cell as a DNA chaperone, chromosome guardian, autophagy sustainer, and protector from apoptotic cell death, but also outside the cell as the prototypic damage associated molecular pattern molecule (DAMP). This DAMP, in conjunction with other factors, thus has cytokine, chemokine, and growth factor activity, orchestrating the inflammatory and immune response. All of these characteristics make HMGB1 a critical molecular target in multiple human diseases including infectious diseases, ischemia, immune disorders, neurodegenerative diseases, metabolic disorders, and cancer. Indeed, a number of emergent strategies have been used to inhibit HMGB1 expression, release, and activity in vitro and in vivo. These include antibodies, peptide inhibitors, RNAi, anti-coagulants, endogenous hormones, various chemical compounds, HMGB1-receptor and signaling pathway inhibition, artificial DNAs, physical strategies including vagus nerve stimulation and other surgical approaches. Future work further investigating the details of HMGB1 localization, structure, post-translational modification, and identification of additional partners will undoubtedly uncover additional secrets regarding HMGB1's multiple functions.
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Affiliation(s)
- Rui Kang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
| | - Ruochan Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Qiuhong Zhang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Wen Hou
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Sha Wu
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Lizhi Cao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jin Huang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yan Yu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xue-Gong Fan
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhengwen Yan
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA; Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510510, China
| | - Haichao Wang
- Laboratory of Emergency Medicine, The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Qingde Wang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Allan Tsung
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Herbert J Zeh
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Daolin Tang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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38
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Wei F, Yang D, Tewary P, Li Y, Li S, Chen X, Howard OMZ, Bustin M, Oppenheim JJ. The Alarmin HMGN1 contributes to antitumor immunity and is a potent immunoadjuvant. Cancer Res 2014; 74:5989-98. [PMID: 25205103 PMCID: PMC6309998 DOI: 10.1158/0008-5472.can-13-2042] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alarmins are endogenous mediators that are elicited rapidly in response to danger signals, enhancing innate and adaptive immune responses by promoting the recruitment and maturation of antigen-presenting cells (APC). The nucleosome-binding protein HMGN1 is a potent alarmin that binds TLR4 and induces antigen-specific Th1 immune responses, but its contributions to antitumor immunity have not been explored. We found that ovalbumin (OVA)-expressing EG7 mouse thymoma cells grew much faster in Hmgn1-deficient mice than littermate-matched controls. Tumor-bearing Hmgn1(-/-) mice generated fewer OVA-specific CD8 cells in the spleen than EG7-bearing Hmgn1(+/+) mice, suggesting that HMGN1 supported T cell-mediated antitumor immunity. In addition, EG7 tumors expressing HMGN1 grew more slowly than control EG7 tumors, suggesting greater resistance to HMGN1-expressing tumors. This resistance relied on T cell-mediated immunity because it was abolished by in vivo depletion of CD4(+) and CD8(+) T cells. Moreover, mice vaccinated with a DNA vector expressing an HMGN1-gp100 fusion protein manifested gp100-specific, Th1-polarized immune responses, acquiring resistance to challenge with mouse B16F1 melanoma. Overall, our findings show that HMGN1 contributes to antitumor immunity and it may offer an effective adjuvant to heighten responses to cancer vaccines.
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Affiliation(s)
- Feng Wei
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300060, China
| | - De Yang
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital; Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin 300060, China
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, MD 21702, USA
| | - Poonam Tewary
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, MD 21702, USA
| | - Yana Li
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Sandra Li
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Xin Chen
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
- Basic Research Program, Leidos Biomedical Research, Inc., Frederick National Lab, Frederick, MD 21702, USA
| | - O. M. Zack Howard
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joost J. Oppenheim
- Laboratory of Molecular Immunoregulation, Cancer and Inflammation Program, Center for Cancer Research, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
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Weng M, Song F, Chen J, Wu J, Qin J, Jin T, Xu J. The high-mobility group nucleosome-binding domain 5 is highly expressed in breast cancer and promotes the proliferation and invasion of breast cancer cells. Tumour Biol 2014; 36:959-66. [PMID: 25315189 DOI: 10.1007/s13277-014-2715-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/05/2014] [Indexed: 11/27/2022] Open
Abstract
The high-mobility group nucleosome-binding domain 5 (HMGN5) is a member of the high-mobility group proteins family. Previous study found that HMGN5 is required for tumorigenesis in vitro, and aberrations in the expression of HMGN5 were found in human osteosarcoma, prostate cancer, and squamous cell carcinoma. Nevertheless, the role of HMGN5 in breast cancer remains unclear. This study aimed to investigate the expression and clinical significance of HMGN5 in human breast cancer, confirm the oncogenic role of HMGN5, and explore the mechanism by which HMGN5 contributes to invasion and metastasis. HMGN5 expression was detected in breast cancer tissues and corresponding adjacent non-cancerous tissues from 43 patients by immunohistochemistry, and the clinicopathologic characteristics of all patients were also analyzed. Next, knockdown of HMGN5 protein in MDA-MB-231 cells was performed through a small interfering RNA (siRNA) technique, and cell viability, apoptosis, and invasion were detected by cell vitality test, flow cytometry, and transwell assay, respectively. Immunohistostaining showed that HMGN5 were highly expressed in the nucleus in all breast cancer tissues as compared with the adjacent non-cancerous tissues (ANCT;(73.5 ± 11 vs. 31.0 ± 5 %, P < 0.01). HMGN5 expression level was associated with the poorly differentiated tumor cells, lymph node involvement tumor, and T4 staging tumor. Knockdown of HMGN5 inhibited cell growth, suppressed invasion, and increased cell apoptosis in human breast cancer MDA-MB-231 cells. Western blot analysis demonstrated that the expressions of PCNA, connective tissue growth factor (CTGF), and MMP-9 were decreased in human breast MDA-MB-231 cells depleted of HMGN5. In addition, the apoptotic markers (cleaved PARP and cleaved caspase-3) were significantly increased by HMGN5 knockdown, but microtubule-associated protein 1 light chain 3-II/I (LC3-II/I) did not alter. HMGN5 plays an oncogenic role in human breast cancer by inhibiting cell proliferation and invasion, and activating apoptosis, which could be exploited as a target for therapy in human breast cancer.
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Affiliation(s)
- Mingzhe Weng
- Department of General Surgery of Shanghai First People's Hospital, Shanghai Jiaotong University, No. 100 Haining Road, 200080, Shanghai, People's Republic of China,
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40
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Kong XD, Liu N, Xu XJ. Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome. ACTA ACUST UNITED AC 2014; 47:834-41. [PMID: 25118625 PMCID: PMC4181218 DOI: 10.1590/1414-431x20143792] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/07/2014] [Indexed: 01/15/2023]
Abstract
In this study, biomarkers and transcriptional factor motifs were identified in order
to investigate the etiology and phenotypic severity of Down syndrome. GSE 1281, GSE
1611, and GSE 5390 were downloaded from the gene expression ominibus (GEO). A robust
multiarray analysis (RMA) algorithm was applied to detect differentially expressed
genes (DEGs). In order to screen for biological pathways and to interrogate the Kyoto
Encyclopedia of Genes and Genomes (KEGG) pathway database, the database for
annotation, visualization, and integrated discovery (DAVID) was used to carry out a
gene ontology (GO) function enrichment for DEGs. Finally, a transcriptional
regulatory network was constructed, and a hypergeometric distribution test was
applied to select for significantly enriched transcriptional factor motifs.
CBR1, DYRK1A, HMGN1,
ITSN1, RCAN1, SON,
TMEM50B, and TTC3 were each up-regulated
two-fold in Down syndrome samples compared to normal samples; of these,
SON and TTC3 were newly reported.
CBR1, DYRK1A, HMGN1,
ITSN1, RCAN1, SON,
TMEM50B, and TTC3 were located on human
chromosome 21 (mouse chromosome 16). The DEGs were significantly enriched in
macromolecular complex subunit organization and focal adhesion pathways. Eleven
significantly enriched transcription factor motifs (PAX5,
EGR1, XBP1, SREBP1,
OLF1, MZF1, NFY,
NFKAPPAB, MYCMAX, NFE2, and
RP58) were identified. The DEGs and transcription factor motifs
identified in our study provide biomarkers for the understanding of Down syndrome
pathogenesis and progression.
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Affiliation(s)
- X D Kong
- Prenatal Diagnosis Center, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - N Liu
- Prenatal Diagnosis Center, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - X J Xu
- Prenatal Diagnosis Center, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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Lane AA, Chapuy B, Lin CY, Tivey T, Li H, Townsend EC, van Bodegom D, Day TA, Wu SC, Liu H, Yoda A, Alexe G, Schinzel AC, Sullivan TJ, Malinge S, Taylor JE, Stegmaier K, Jaffe JD, Bustin M, te Kronnie G, Izraeli S, Harris MH, Stevenson KE, Neuberg D, Silverman LB, Sallan SE, Bradner JE, Hahn WC, Crispino JD, Pellman D, Weinstock DM. Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation. Nat Genet 2014; 46:618-23. [PMID: 24747640 PMCID: PMC4040006 DOI: 10.1038/ng.2949] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/13/2014] [Indexed: 12/14/2022]
Abstract
Down syndrome confers a 20-fold increased risk of B cell acute lymphoblastic leukemia (B-ALL)1 and polysomy 21 is the most frequent somatic aneuploidy amongst all B-ALLs2. Yet, the mechanistic links between chr.21 triplication and B-ALL remain undefined. Here we show that germline triplication of only 31 genes orthologous to human chr.21q22 confers murine progenitor B cell self-renewal in vitro, maturation defects in vivo, and B-ALL with either BCR-ABL or CRLF2 with activated JAK2. Chr.21q22 triplication suppresses H3K27me3 in progenitor B cells and B-ALLs, and “bivalent” genes with both H3K27me3 and H3K4me3 at their promoters in wild-type progenitor B cells are preferentially overexpressed in triplicated cells. Strikingly, human B-ALLs with polysomy 21 are distinguished by their overexpression of genes marked with H3K27me3 in multiple cell types. Finally, overexpression of HMGN1, a nucleosome remodeling protein encoded on chr.21q223–5, suppresses H3K27me3 and promotes both B cell proliferation in vitro and B-ALL in vivo.
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Affiliation(s)
- Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Bjoern Chapuy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Trevor Tivey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Hubo Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth C Townsend
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Diederik van Bodegom
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Tovah A Day
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shuo-Chieh Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Huiyun Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Akinori Yoda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Anna C Schinzel
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - Timothy J Sullivan
- Microarray Core, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Sébastien Malinge
- Institut National de la Santé et de la Recherche Médicale (INSERM) U985, Institut Gustave Roussy, Villejuif, France
| | | | - Kimberly Stegmaier
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | | | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Shai Izraeli
- 1] Department of Pediatric Hemato-Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel. [2] Department of Human Molecular Genetics and Biochemsitry, Tel Aviv University, Tel Aviv, Israel
| | - Marian H Harris
- Department of Pathology, Children's Hospital Boston, Boston, Massachusetts, USA
| | - Kristen E Stevenson
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Donna Neuberg
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - William C Hahn
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois, USA
| | - David Pellman
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - David M Weinstock
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute, Cambridge, Massachusetts, USA
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Zucchi FCR, Yao Y, Ilnytskyy Y, Robbins JC, Soltanpour N, Kovalchuk I, Kovalchuk O, Metz GAS. Lifetime stress cumulatively programs brain transcriptome and impedes stroke recovery: benefit of sensory stimulation. PLoS One 2014; 9:e92130. [PMID: 24651125 PMCID: PMC3961295 DOI: 10.1371/journal.pone.0092130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/18/2014] [Indexed: 12/24/2022] Open
Abstract
Prenatal stress (PS) represents a critical variable affecting lifetime health trajectories, metabolic and vascular functions. Beneficial experiences may attenuate the effects of PS and its programming of health outcomes in later life. Here we investigated in a rat model (1) if PS modulates recovery following cortical ischemia in adulthood; (2) if a second hit by adult stress (AS) exaggerates stress responses and ischemic damage; and (3) if tactile stimulation (TS) attenuates the cumulative effects of PS and AS. Prenatally stressed and non-stressed adult male rats underwent focal ischemic motor cortex lesion and were tested in skilled reaching and skilled walking tasks. Two groups of rats experienced recurrent restraint stress in adulthood and one of these groups also underwent daily TS therapy. Animals that experienced both PS and AS displayed the most severe motor disabilities after lesion. By contrast, TS promoted recovery from ischemic lesion and reduced hypothalamic-pituitary-adrenal axis activity. The data also showed that cumulative effects of adverse and beneficial lifespan experiences interact with disease outcomes and brain plasticity through the modulation of gene expression. Microarray analysis of the lesion motor cortex revealed that cumulative PS and AS interact with genes related to growth factors and transcription factors, which were not affected by PS or lesion alone. TS in PS+AS animals reverted these changes, suggesting a critical role for these factors in activity-dependent motor cortical reorganization after ischemic lesion. These findings suggest that beneficial experience later in life can moderate adverse consequences of early programming to improve cerebrovascular health.
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Affiliation(s)
- Fabíola C. R. Zucchi
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
- Departments of Medicine and Biological Sciences, University of Mato Grosso State, Cáceres, MT, Brazil
| | - Youli Yao
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Jerrah C. Robbins
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Nasrin Soltanpour
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Gerlinde A. S. Metz
- Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
- * E-mail:
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43
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Postnikov YV, Furusawa T, Haines DC, Factor VM, Bustin M. Loss of the nucleosome-binding protein HMGN1 affects the rate of N-nitrosodiethylamine-induced hepatocarcinogenesis in mice. Mol Cancer Res 2014; 12:82-90. [PMID: 24296759 PMCID: PMC3905959 DOI: 10.1158/1541-7786.mcr-13-0392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
UNLABELLED We report that HMGN1, a nucleosome-binding protein that affects chromatin structure and function, affects the growth of N-nitrosodiethylamine (DEN)-induced liver tumors. Following a single DEN injection at 2 weeks of age, Hmgn1(tm1/tm1) mice, lacking the nucleosome-binding domain of HMGN1, had earlier signs of liver tumorigenesis than their Hmgn1(+/+) littermates. Detailed gene expression profiling revealed significant differences between DEN-injected and control saline-injected mice, but only minor differences between the injected Hmgn1(tm1/tm1) mice and their Hmgn1(+/+) littermates. Pathway analysis revealed that the most significant process affected by loss of HMGN1 involves the lipid/sterol metabolic pathway. Our study indicates that in mice, loss of HMGN1 leads to transcription changes that accelerate the progression of DEN-induced hepatocarcinogenesis, without affecting the type of tumors or the final total tumor burden of these mice. IMPLICATIONS Loss of HMGN1 leads to accelerated progression of DEN-induced hepatocarcinogenesis in mice.
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44
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Abstract
Transcriptional arrest caused by DNA damage is detrimental for cells and organisms as it impinges on gene expression and thereby on cell growth and survival. To alleviate transcriptional arrest, cells trigger a transcription-dependent genome surveillance pathway, termed transcription-coupled nucleotide excision repair (TC-NER) that ensures rapid removal of such transcription-impeding DNA lesions and prevents persistent stalling of transcription. Defective TC-NER is causatively linked to Cockayne syndrome, a rare severe genetic disorder with multisystem abnormalities that results in patients' death in early adulthood. Here we review recent data on how damage-arrested transcription is actively coupled to TC-NER in mammals and discuss new emerging models concerning the role of TC-NER-specific factors in this process.
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Affiliation(s)
- Wim Vermeulen
- Department of Genetics and Netherlands Proteomics Centre, Centre for Biomedical Genetics, Erasmus Medical Centre, 3015 GE Rotterdam, The Netherlands
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45
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HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells. Mol Cell Biol 2013; 33:3377-89. [PMID: 23775126 PMCID: PMC3753902 DOI: 10.1128/mcb.00435-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Chromatin structure plays a key role in regulating gene expression and embryonic differentiation; however, the factors that determine the organization of chromatin around regulatory sites are not fully known. Here we show that HMGN1, a nucleosome-binding protein ubiquitously expressed in vertebrate cells, preferentially binds to CpG island-containing promoters and affects the organization of nucleosomes, DNase I hypersensitivity, and the transcriptional profile of mouse embryonic stem cells and neural progenitors. Loss of HMGN1 alters the organization of an unstable nucleosome at transcription start sites, reduces the number of DNase I-hypersensitive sites genome wide, and decreases the number of nestin-positive neural progenitors in the subventricular zone (SVZ) region of mouse brain. Thus, architectural chromatin-binding proteins affect the transcription profile and chromatin structure during embryonic stem cell differentiation.
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46
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Kugler JE, Horsch M, Huang D, Furusawa T, Rochman M, Garrett L, Becker L, Bohla A, Hölter SM, Prehn C, Rathkolb B, Racz I, Aguilar-Pimentel JA, Adler T, Adamski J, Beckers J, Busch DH, Eickelberg O, Klopstock T, Ollert M, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Garfinkel B, Orly J, Ovcharenko I, Bustin M. High mobility group N proteins modulate the fidelity of the cellular transcriptional profile in a tissue- and variant-specific manner. J Biol Chem 2013; 288:16690-16703. [PMID: 23620591 DOI: 10.1074/jbc.m113.463315] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nuclei of most vertebrate cells contain members of the high mobility group N (HMGN) protein family, which bind specifically to nucleosome core particles and affect chromatin structure and function, including transcription. Here, we study the biological role of this protein family by systematic analysis of phenotypes and tissue transcription profiles in mice lacking functional HMGN variants. Phenotypic analysis of Hmgn1(tm1/tm1), Hmgn3(tm1/tm1), and Hmgn5(tm1/tm1) mice and their wild type littermates with a battery of standardized tests uncovered variant-specific abnormalities. Gene expression analysis of four different tissues in each of the Hmgn(tm1/tm1) lines reveals very little overlap between genes affected by specific variants in different tissues. Pathway analysis reveals that loss of an HMGN variant subtly affects expression of numerous genes in specific biological processes. We conclude that within the biological framework of an entire organism, HMGNs modulate the fidelity of the cellular transcriptional profile in a tissue- and HMGN variant-specific manner.
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Affiliation(s)
- Jamie E Kugler
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Di Huang
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Lillian Garrett
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alexander Bohla
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Prehn
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ildikó Racz
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Juan Antonio Aguilar-Pimentel
- Center of Allergy and Environment, Technische Universität München, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Jerzy Adamski
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Dirk H Busch
- Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Oliver Eickelberg
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany
| | - Markus Ollert
- Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Tobias Stöger
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany; Max Planck Institute of Psychiatry, Munich, Germany; Developmental Genetics, Technische Universität München c/o Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ali Önder Yildirim
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Andreas Zimmer
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Benny Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ivan Ovcharenko
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.
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Gaillard H, Aguilera A. Transcription coupled repair at the interface between transcription elongation and mRNP biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:141-50. [PMID: 23046879 DOI: 10.1016/j.bbagrm.2012.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/19/2012] [Accepted: 09/22/2012] [Indexed: 01/13/2023]
Abstract
During transcription, the nascent pre-mRNA associates with mRNA-binding proteins and undergoes a series of processing steps, resulting in export competent mRNA ribonucleoprotein complexes (mRNPs) that are transported into the cytoplasm. Throughout transcription elongation, RNA polymerases frequently deal with a number of obstacles that need to be removed for transcription resumption. One important type of hindrance consists of helix-distorting DNA lesions. Transcription-coupled repair (TC-NER), a specific sub-pathway of nucleotide excision repair, ensures a fast repair of such transcription-blocking lesions. While the nucleotide excision repair reaction is fairly well understood, its regulation and the way it deals with DNA transcription remains largely unknown. In this review, we update our current understanding of the factors involved in TC-NER and discuss their functional interplay with the processes of transcription elongation and mRNP biogenesis. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Kamileri I, Karakasilioti I, Garinis GA. Nucleotide excision repair: new tricks with old bricks. Trends Genet 2012; 28:566-73. [PMID: 22824526 DOI: 10.1016/j.tig.2012.06.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 06/05/2012] [Accepted: 06/19/2012] [Indexed: 12/22/2022]
Abstract
Nucleotide excision repair (NER) is a major DNA repair pathway that ensures that the genome remains functionally intact and is faithfully transmitted to progeny. However, defects in NER lead, in addition to cancer and aging, to developmental abnormalities whose clinical heterogeneity and varying severity cannot be fully explained by the DNA repair deficiencies. Recent work has revealed that proteins in NER play distinct roles, including some that go well beyond DNA repair. NER factors are components of protein complexes known to be involved in nucleosome remodeling, histone ubiquitination, and transcriptional activation of genes involved in nuclear receptor signaling, stem cell reprogramming, and postnatal mammalian growth. Together, these findings add new pieces to the puzzle for understanding NER and the relevance of NER defects in development and disease.
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Affiliation(s)
- Irene Kamileri
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
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Masaoka A, Gassman NR, Kedar PS, Prasad R, Hou EW, Horton JK, Bustin M, Wilson SH. HMGN1 protein regulates poly(ADP-ribose) polymerase-1 (PARP-1) self-PARylation in mouse fibroblasts. J Biol Chem 2012; 287:27648-58. [PMID: 22736760 DOI: 10.1074/jbc.m112.370759] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In mammalian cells, the nucleosome-binding protein HMGN1 (high mobility group N1) affects the structure and function of chromatin and plays a role in repair of damaged DNA. HMGN1 affects the interaction of DNA repair factors with chromatin and their access to damaged DNA; however, not all of the repair factors affected have been identified. Here, we report that HMGN1 affects the self-poly(ADP-ribosyl)ation (i.e., PARylation) of poly(ADP-ribose) polymerase-1 (PARP-1), a multifunctional and abundant nuclear enzyme known to recognize DNA lesions and promote chromatin remodeling, DNA repair, and other nucleic acid transactions. The catalytic activity of PARP-1 is activated by DNA with a strand break, and this results in self-PARylation and PARylation of other chromatin proteins. Using cells obtained from Hmgn1(-/-) and Hmgn1(+/+) littermate mice, we find that in untreated cells, loss of HMGN1 protein reduces PARP-1 self-PARylation. A similar result was obtained after MMS treatment of these cells. In imaging experiments after low energy laser-induced DNA damage, less PARylation at lesion sites was observed in Hmgn1(-/-) than in Hmgn1(+/+) cells. The HMGN1 regulation of PARP-1 activity could be mediated by direct protein-protein interaction as HMGN1 and PARP-1 were found to interact in binding assays. Purified HMGN1 was able to stimulate self-PARylation of purified PARP-1, and in experiments with cell extracts, self-PARylation was greater in Hmgn1(+/+) than in Hmgn1(-/-) extract. The results suggest a regulatory role for HMGN1 in PARP-1 activation.
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Affiliation(s)
- Aya Masaoka
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
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50
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Thompson LH. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. Mutat Res 2012; 751:158-246. [PMID: 22743550 DOI: 10.1016/j.mrrev.2012.06.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/09/2012] [Accepted: 06/16/2012] [Indexed: 12/15/2022]
Abstract
The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.
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Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
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