1
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Chen Z, Tang X, Li W, Li T, Huang J, Jiang Y, Qiu J, Huang Z, Tan R, Ji X, Lv L, Yang Z, Chen H. HIST1H2BK predicts neoadjuvant-chemotherapy response and mediates 5-fluorouracil resistance of gastric cancer cells. Transl Oncol 2024; 46:102017. [PMID: 38852277 DOI: 10.1016/j.tranon.2024.102017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/23/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Neoadjuvant chemotherapy (NACT) is routinely used to treat patients with advanced gastric cancer (AGC). However, the identification of reliable markers to determine which AGC patients would benefit from NACT remains challenging. METHODS A systematic screening of plasma proteins between NACT-sensitive and NACT-resistant AGC patients was performed by a mass spectrometer (n = 6). The effect of the most differential plasma protein was validated in two independent cohorts with AGC patients undergoing NACT (ELISA cohort: n = 155; Validated cohort: n = 203). The expression of this candidate was examined in a cohort of AGC tissues using immunohistochemistry (n = 34). The mechanism of this candidate on 5-Fluorouracil (5-FU) resistance was explored by cell-biology experiments in vitro and vivo. RESULTS A series of differential plasma proteins between NACT-sensitive and NACT-resistant AGC patients was identified. Among them, plasma HIST1H2BK was validated as a significant biomarker for predicting NACT response and prognosis. Moreover, HIST1H2BK was over-expression in NACT-resistant tissues compared to NACT-sensitive tissues in AGC. Mechanistically, HIST1H2BK inhibited 5-FU-induced apoptosis by upregulating A2M transcription and then activating LRP/PI3K/Akt pathway, thereby promoting 5-FU resistance in GC cells. Intriguingly, HIST1H2BK-overexpressing 5-FU-resistant GC cells propagated resistance to 5-FU-sensitive GC cells through the secretion of HIST1H2BK. CONCLUSION This study highlights significant differences in plasma protein profiles between NACT-resistant and NACT-sensitive AGC patients. Plasma HIST1H2BK emerged as an effective biomarker for achieving more accurate NACT in AGC. The mechanism of intracellular and secreted HIST1H2BK on 5-FU resistance provided a novel insight into chemoresistance in AGC.
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Affiliation(s)
- Zijian Chen
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Xiaocheng Tang
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Weiyao Li
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Tuoyang Li
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jintuan Huang
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Yingming Jiang
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Jun Qiu
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Zhenze Huang
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Rongchang Tan
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Xiang Ji
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Li Lv
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Zuli Yang
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China.
| | - Hao Chen
- Department of General Surgery (Department of Gastrointestinal Surgery section 2), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China.
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2
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Li W, Cao P, Xu P, Sun F, Wang C, Zhang J, Dong S, Wilson JR, Xu D, Fan H, Feng Z, Zhang X, Zhu Q, Fan Y, Brown N, Justin N, Gamblin SJ, Li H, Zhang Y, He J. Rapid reconstitution of ubiquitinated nucleosome using a non-denatured histone octamer ubiquitylation approach. Cell Biosci 2024; 14:81. [PMID: 38886783 PMCID: PMC11184750 DOI: 10.1186/s13578-024-01265-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Histone ubiquitination modification is emerging as a critical epigenetic mechanism involved in a range of biological processes. In vitro reconstitution of ubiquitinated nucleosomes is pivotal for elucidating the influence of histone ubiquitination on chromatin dynamics. RESULTS In this study, we introduce a Non-Denatured Histone Octamer Ubiquitylation (NDHOU) approach for generating ubiquitin or ubiquitin-like modified histone octamers. The method entails the co-expression and purification of histone octamers, followed by their chemical cross-linking to ubiquitin using 1,3-dibromoacetone. We demonstrate that nucleosomes reconstituted with these octamers display a high degree of homogeneity, rendering them highly compatible with in vitro biochemical assays. These ubiquitinated nucleosomes mimic physiological substrates in function and structure. Additionally, we have extended this method to cross-linking various histone octamers and three types of ubiquitin-like proteins. CONCLUSIONS Overall, our findings offer an efficient strategy for producing ubiquitinated nucleosomes, advancing biochemical and biophysical studies in the field of chromatin biology.
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Affiliation(s)
- Weijie Li
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Peirong Cao
- Department of Neuroscience, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, P.R. China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Pengqi Xu
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Fahui Sun
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Chi Wang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Jiale Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuqi Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jon R Wilson
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Difei Xu
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Hengxin Fan
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zhenhuan Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China
| | - Qingjun Zhu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yingzhi Fan
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Nick Brown
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Neil Justin
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | | | - He Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China
| | - Ying Zhang
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Jun He
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510799, China.
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3
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Phillips M, Malone KL, Boyle BW, Montgomery C, Kressy IA, Joseph FM, Bright KM, Boyson SP, Chang S, Nix JC, Young NL, Jeffers V, Frietze S, Glass KC. Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains. J Med Chem 2024; 67:8186-8200. [PMID: 38733345 PMCID: PMC11149620 DOI: 10.1021/acs.jmedchem.4c00210] [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] [Indexed: 05/13/2024]
Abstract
The ATPase family AAA+ domain containing 2 (ATAD2) protein and its paralog ATAD2B have a C-terminal bromodomain (BRD) that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2/B BRDs to select acetylated lysine among multiple histone post-translational modifications. The ATAD2B BRD can bind acetylated histone ligands that also contain adjacent methylation or phosphorylation marks, while the presence of these modifications significantly weakened the acetyllysine binding activity of the ATAD2 BRD. Our structural studies provide mechanistic insights into how ATAD2/B BRD-binding pocket residues coordinate the acetyllysine group in the context of adjacent post-translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands impact the recognition of an adjacent acetyllysine residue. Our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2/B BRDs, resulting in distinct binding modes.
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Affiliation(s)
- Margaret Phillips
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446, United States
| | - Kiera L Malone
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Brian W Boyle
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Cameron Montgomery
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446, United States
| | - Isabelle A Kressy
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
| | - Faith M Joseph
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kathleen M Bright
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Samuel P Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446, United States
| | - Sunsik Chang
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446, United States
| | - Jay C Nix
- Molecular Biology Consortium, Advanced Light Source, Berkeley, California 94720, United States
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Victoria Jeffers
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Karen C Glass
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, Vermont 05405, United States
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont 05446, United States
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4
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Brown AL, Meiborg AB, Franz-Wachtel M, Macek B, Gordon S, Rog O, Weadick CJ, Werner MS. Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2. Genetics 2024; 227:iyae041. [PMID: 38513719 DOI: 10.1093/genetics/iyae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation-or lack thereof-of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with Caenorhabditis elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity and has revealed the first loss of PRC2 in a multicellular organism.
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Affiliation(s)
- Audrey L Brown
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adriaan B Meiborg
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for joint PhD degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, 72074 Tübingen, Germany
| | - Spencer Gordon
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael S Werner
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
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5
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Tod NP, Vogelauer M, Cheng C, Karimian A, Schmollinger S, Camacho D, Kurdistani SK. The role of histone H3 leucine 126 in fine-tuning the copper reductase activity of nucleosomes. J Biol Chem 2024; 300:107314. [PMID: 38657861 PMCID: PMC11134540 DOI: 10.1016/j.jbc.2024.107314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The copper reductase activity of histone H3 suggests undiscovered characteristics within the protein. Here, we investigated the function of leucine 126 (H3L126), which occupies an axial position relative to the copper binding. Typically found as methionine or leucine in copper-binding proteins, the axial ligand influences the reduction potential of the bound ion, modulating its tendency to accept or yield electrons. We found that mutation of H3L126 to methionine (H3L126M) enhanced the enzymatic activity of native yeast nucleosomes in vitro and increased intracellular levels of Cu1+, leading to improved copper-dependent activities including mitochondrial respiration and growth in oxidative media with low copper. Conversely, H3L126 to histidine (H3L126H) mutation decreased nucleosome's enzymatic activity and adversely affected copper-dependent activities in vivo. Our findings demonstrate that H3L126 fine-tunes the copper reductase activity of nucleosomes and highlights the utility of nucleosome enzymatic activity as a novel paradigm to uncover previously unnoticed features of histones.
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Affiliation(s)
- Nataliya P Tod
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Maria Vogelauer
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Chen Cheng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Ansar Karimian
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Stefan Schmollinger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Dimitrios Camacho
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
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6
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Selvam K, Wyrick JJ, Parra MA. DNA Repair in Nucleosomes: Insights from Histone Modifications and Mutants. Int J Mol Sci 2024; 25:4393. [PMID: 38673978 PMCID: PMC11050016 DOI: 10.3390/ijms25084393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
DNA repair pathways play a critical role in genome stability, but in eukaryotic cells, they must operate to repair DNA lesions in the compact and tangled environment of chromatin. Previous studies have shown that the packaging of DNA into nucleosomes, which form the basic building block of chromatin, has a profound impact on DNA repair. In this review, we discuss the principles and mechanisms governing DNA repair in chromatin. We focus on the role of histone post-translational modifications (PTMs) in repair, as well as the molecular mechanisms by which histone mutants affect cellular sensitivity to DNA damage agents and repair activity in chromatin. Importantly, these mechanisms are thought to significantly impact somatic mutation rates in human cancers and potentially contribute to carcinogenesis and other human diseases. For example, a number of the histone mutants studied primarily in yeast have been identified as candidate oncohistone mutations in different cancers. This review highlights these connections and discusses the potential importance of DNA repair in chromatin to human health.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Michael A. Parra
- Department of Chemistry, Susquehanna University, Selinsgrove, PA 17870, USA
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7
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Buckenmeyer MJ, Brooks EA, Taylor MS, Yang L, Holewinski RJ, Meyer TJ, Galloux M, Garmendia-Cedillos M, Pohida TJ, Andresson T, St Croix B, Wolf MT. Engineering Tumor Stroma Morphogenesis Using Dynamic Cell-Matrix Spheroid Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585805. [PMID: 38903106 PMCID: PMC11188064 DOI: 10.1101/2024.03.19.585805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The tumor microenvironment consists of resident tumor cells organized within a compositionally diverse, three-dimensional (3D) extracellular matrix (ECM) network that cannot be replicated in vitro using bottom-up synthesis. We report a new self-assembly system to engineer ECM-rich 3D MatriSpheres wherein tumor cells actively organize and concentrate microgram quantities of decellularized ECM dispersions which modulate cell phenotype. 3D colorectal cancer (CRC) MatriSpheres were created using decellularized small intestine submucosa (SIS) as an orthotopic ECM source that had greater proteomic homology to CRC tumor ECM than traditional ECM formulations such as Matrigel. SIS ECM was rapidly concentrated from its environment and assembled into ECM-rich 3D stroma-like regions by mouse and human CRC cell lines within 4-5 days via a mechanism that was rheologically distinct from bulk hydrogel formation. Both ECM organization and transcriptional regulation by 3D ECM cues affected programs of malignancy, lipid metabolism, and immunoregulation that corresponded with an in vivo MC38 tumor cell subpopulation identified via single cell RNA sequencing. This 3D modeling approach stimulates tumor specific tissue morphogenesis that incorporates the complexities of both cancer cell and ECM compartments in a scalable, spontaneous assembly process that may further facilitate precision medicine.
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8
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Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
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Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
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9
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de Groen PC. A new, all-encompassing aetiology of type 1 diabetes. Immunology 2024; 171:77-91. [PMID: 37772700 DOI: 10.1111/imm.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
The aetiology of type 1 diabetes (T1D) is considered multifactorial with the contribution of the MHC on chromosome 6 being most important. Multiple factors also contribute to the aetiology of colorectal neoplasia, but the final event causing the change from normal mucosa to polyp and from polyp to cancer is due to a single somatic mutation event. Repeated formation of colorectal neoplasia within an at-risk population results in a predictable, tapering, exponential neoplasia distribution. Critical mutations driving colorectal neoplasia formation occur in mutation-prone DNA. These observations led to three hypotheses related to T1D. First, a single somatic mutation within the MHC of antigen presenting cells results in a change in phenotype from normal to T1D. Second, the distribution of additional autoimmune diseases (AAIDs) among persons with T1D adheres to a predictable, tapering, exponential distribution. And third, critical mutations driving development of T1D occur in mutation-prone DNA. To address the hypotheses in an orderly fashion, a new analytical method called genome-wide aetiology analysis (GWEA) consisting of nine steps is presented. All data required for GWEA of T1D are obtained from peer-reviewed publications or publicly available genome and proteome databases. Critical GWEA steps include AAID distribution among persons with T1D, analysis of at-risk HLA loci for mutation-prone DNA, determination of the role of non-MHC genes on GWAS, and verification of human data by cell culture or animal experiments. GWEA results show that distribution of AAID among persons with T1D adheres to a predictable, tapering, exponential distribution. A single, critical, somatic mutation within the epitope-binding groove of at-risk HLA loci alters HLA-insulin-peptide-T-cell-receptor (TCR) complex binding affinity and creates a new pathway that leads to loss of self-tolerance. The at-risk HLA loci, in particular binding pockets P1, P4 and P9, are encoded by mutation-prone DNA: GC-rich DNA sequence and somatic hypermutation hotspots. All other genes on GWAS can but do not have to amplify the new autoimmune pathway by facilitating DNA mutations, changing peptide binding affinity, reducing signal inhibition or augmenting signal intensity. Animal experiments agree with human studies. In conclusion, T1D is caused by a somatic mutation within the epitope-binding groove of an at-risk HLA gene that affects HLA-insulin-peptide-TCR complex binding affinity and initiates an autoimmune pathway. The nature of the peptide that binds to a mutated epitope-binding groove of an at-risk HLA gene determines the type of autoimmune disease that develops, that is, one at-risk HLA locus, multiple autoimmune diseases. Thus, T1D and AAIDs, and therefore common autoimmune diseases, share a similar somatic mutation-based aetiology.
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Affiliation(s)
- Piet C de Groen
- Division of Gastroenterology, Hepatology & Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
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10
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Matamá T, Costa C, Fernandes B, Araújo R, Cruz CF, Tortosa F, Sheeba CJ, Becker JD, Gomes A, Cavaco-Paulo A. Changing human hair fibre colour and shape from the follicle. J Adv Res 2023:S2090-1232(23)00350-8. [PMID: 37967812 DOI: 10.1016/j.jare.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 09/21/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023] Open
Abstract
INTRODUCTION Natural hair curvature and colour are genetically determined human traits, that we intentionally change by applying thermal and chemical treatments to the fibre. Presently, those cosmetic methodologies act externally and their recurrent use is quite detrimental to hair fibre quality and even to our health. OBJECTIVES This work represents a disruptive concept to modify natural hair colour and curvature. We aim to model the fibre phenotype as it is actively produced in the follicle through the topical delivery of specific bioactive molecules to the scalp. METHODS Transcriptome differences between curly and straight hairs were identified by microarray. In scalp samples, the most variable transcripts were mapped by in situ hybridization. Then, by using appropriate cellular models, we screened a chemical library of 1200 generic drugs, searching for molecules that could lead to changes in either fibre colour or curvature. A pilot-scale, single-centre, investigator-initiated, prospective, blind, bilateral (split-scalp) placebo-controlled clinical study with the intervention of cosmetics was conducted to obtain a proof of concept (RNEC n.92938). RESULTS We found 85 genes transcribed significantly different between curly and straight hair, not previously associated with this human trait. Next, we mapped some of the most variable genes to the inner root sheath of follicles, reinforcing the role of this cell layer in fibre shape moulding. From the drug library screening, we selected 3 and 4 hits as modulators of melanin synthesis and gene transcription, respectively, to be further tested in 33 volunteers. The intentional specific hair change occurred: 8 of 14 volunteers exhibited colour changes, and 16 of 19 volunteers presented curvature modifications, by the end of the study. CONCLUSION The promising results obtained are the first step towards future cosmetics, complementary or alternative to current methodologies, taking hair styling to a new level: changing hair from the inside out.
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Affiliation(s)
- Teresa Matamá
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, 4710-057 Braga, Portugal.
| | - Cristiana Costa
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Bruno Fernandes
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Rita Araújo
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal; CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Célia F Cruz
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Francisco Tortosa
- Serviço de Anatomia Patológica, CHLN - Hospital de Santa Maria / Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Unidade de Anatomia Patológica, Hospital CUF Descobertas, Rua Mário Botas (Parque das Nações), 1998-018, Lisboa, Portugal
| | - Caroline J Sheeba
- ICVS - Life and Health Sciences Research Institute, University of Minho, 4710-057 Braga, Portugal; NIHR Central Commissioning Facility (CCF), Grange House, 15 Church Street, Twickenham, TW1 3NL, UK
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras, 2780-156, Portugal; Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Andreia Gomes
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Artur Cavaco-Paulo
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, 4710-057 Braga, Portugal; Solfarcos - Pharmaceutical and Cosmetic Solutions Ltd, Avenida Imaculada Conceição n. 589, 4700-034 Braga, Portugal.
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11
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Maugeri S, Sibbitts J, Privitera A, Cardaci V, Di Pietro L, Leggio L, Iraci N, Lunte SM, Caruso G. The Anti-Cancer Activity of the Naturally Occurring Dipeptide Carnosine: Potential for Breast Cancer. Cells 2023; 12:2592. [PMID: 37998326 PMCID: PMC10670273 DOI: 10.3390/cells12222592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Carnosine is an endogenous dipeptide composed of β-alanine and L-histidine, possessing a multimodal pharmacodynamic profile that includes anti-inflammatory and anti-oxidant activities. Carnosine has also shown its ability to modulate cell proliferation, cell cycle arrest, apoptosis, and even glycolytic energy metabolism, all processes playing a key role in the context of cancer. Cancer is one of the most dreaded diseases of the 20th and 21st centuries. Among the different types of cancer, breast cancer represents the most common non-skin cancer among women, accounting for an estimated 15% of all cancer-related deaths in women. The main aim of the present review was to provide an overview of studies on the anti-cancer activity of carnosine, and in particular its activity against breast cancer. We also highlighted the possible advantages and limitations involved in the use of this dipeptide. The first part of the review entailed a brief description of carnosine's biological activities and the pathophysiology of cancer, with a focus on breast cancer. The second part of the review described the anti-tumoral activity of carnosine, for which numerous studies have been carried out, especially at the preclinical level, showing promising results. However, only a few studies have investigated the therapeutic potential of this dipeptide for breast cancer prevention or treatment. In this context, carnosine has shown to be able to decrease the size of cancer cells and their viability. It also reduces the levels of vascular endothelial growth factor (VEGF), cyclin D1, NAD+, and ATP, as well as cytochrome c oxidase activity in vitro. When tested in mice with induced breast cancer, carnosine proved to be non-toxic to healthy cells and exhibited chemopreventive activity by reducing tumor growth. Some evidence has also been reported at the clinical level. A randomized phase III prospective placebo-controlled trial showed the ability of Zn-carnosine to prevent dysphagia in breast cancer patients undergoing adjuvant radiotherapy. Despite this evidence, more preclinical and clinical studies are needed to better understand carnosine's anti-tumoral activity, especially in the context of breast cancer.
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Affiliation(s)
- Salvatore Maugeri
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
| | - Jay Sibbitts
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Anna Privitera
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Vincenzo Cardaci
- Scuola Superiore di Catania, University of Catania, 95123 Catania, Italy
- Vita-Salute San Raffaele University, 20132 Milano, Italy
| | - Lucia Di Pietro
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Scuola Superiore di Catania, University of Catania, 95123 Catania, Italy
| | - Loredana Leggio
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Nunzio Iraci
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Susan M. Lunte
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Department of Chemistry, University of Kansas, Lawrence, KS 66047, USA
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Giuseppe Caruso
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Unit of Neuropharmacology and Translational Neurosciences, Oasi Research Institute-IRCCS, 94018 Troina, Italy
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12
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Salomoni P, Flanagan AM, Cottone L. (B)On(e)-cohistones and the epigenetic alterations at the root of bone cancer. Cell Death Differ 2023:10.1038/s41418-023-01227-9. [PMID: 37828086 DOI: 10.1038/s41418-023-01227-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of mutations in histones in a number of human neoplasms and developmental syndromes represents the most compelling evidence to date for a causal role of epigenetic perturbations in human disease. In most cases, these mutations have gain of function properties that cause deviation from normal developmental processes leading to embryo defects and/or neoplastic transformation. These exciting discoveries represent a step-change in our understanding of the role of chromatin (dys)regulation in development and disease. However, the mechanisms of action of oncogenic histone mutations (oncohistones) remain only partially understood. Here, we critically assess existing literature on oncohistones focussing mainly on bone neoplasms. We show how it is possible to draw parallels with some of the cell-autonomous mechanisms of action described in paediatric brain cancer, although the functions of oncohistones in bone tumours remain under-investigated. In this respect, it is becoming clear that histone mutations targeting the same residues display, at least in part, tissue-specific oncogenic mechanisms. Furthermore, it is emerging that cancer cells carrying oncohistones can modify the surrounding microenvironment to support growth and/or alter differentiation trajectories. A better understanding of oncohistone function in different neoplasms provide potential for identification of signalling that could be targeted therapeutically. Finally, we discuss some of the main concepts and future directions in this research area, while also drawing possible connections and parallels with other cancer epigenetic mechanisms.
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Affiliation(s)
- Paolo Salomoni
- Nuclear Function Group, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany.
| | - Adrienne M Flanagan
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, Middlesex, HA7 4LP, UK
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Lucia Cottone
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
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13
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Romhányi D, Szabó K, Kemény L, Groma G. Histone and Histone Acetylation-Related Alterations of Gene Expression in Uninvolved Psoriatic Skin and Their Effects on Cell Proliferation, Differentiation, and Immune Responses. Int J Mol Sci 2023; 24:14551. [PMID: 37833997 PMCID: PMC10572426 DOI: 10.3390/ijms241914551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Psoriasis is a chronic immune-mediated skin disease in which the symptom-free, uninvolved skin carries alterations in gene expression, serving as a basis for lesion formation. Histones and histone acetylation-related processes are key regulators of gene expression, controlling cell proliferation and immune responses. Dysregulation of these processes is likely to play an important role in the pathogenesis of psoriasis. To gain a complete overview of these potential alterations, we performed a meta-analysis of a psoriatic uninvolved skin dataset containing differentially expressed transcripts from nearly 300 individuals and screened for histones and histone acetylation-related molecules. We identified altered expression of the replication-dependent histones HIST2H2AA3 and HIST2H4A and the replication-independent histones H2AFY, H2AFZ, and H3F3A/B. Eight histone chaperones were also identified. Among the histone acetyltransferases, ELP3 and KAT5 and members of the ATAC, NSL, and SAGA acetyltransferase complexes are affected in uninvolved skin. Histone deacetylation-related alterations were found to affect eight HDACs and members of the NCOR/SMRT, NURD, SIN3, and SHIP HDAC complexes. In this article, we discuss how histone and histone acetylation-related expression changes may affect proliferation and differentiation, as well as innate, macrophage-mediated, and T cell-mediated pro- and anti-inflammatory responses, which are known to play a central role in the development of psoriasis.
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Affiliation(s)
- Dóra Romhányi
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
| | - Kornélia Szabó
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- Hungarian Centre of Excellence for Molecular Medicine-University of Szeged Skin Research Group (HCEMM-USZ Skin Research Group), H-6720 Szeged, Hungary
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Lajos Kemény
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- Hungarian Centre of Excellence for Molecular Medicine-University of Szeged Skin Research Group (HCEMM-USZ Skin Research Group), H-6720 Szeged, Hungary
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
| | - Gergely Groma
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary; (D.R.); (K.S.); (L.K.)
- HUN-REN-SZTE Dermatological Research Group, H-6720 Szeged, Hungary
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14
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Cohen LRZ, Meshorer E. H3K36 methylation is a reprogramming barrier. Nat Cell Biol 2023; 25:1077-1078. [PMID: 37460696 DOI: 10.1038/s41556-023-01147-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Affiliation(s)
- Lea Rachel Zehava Cohen
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eran Meshorer
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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15
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Involvement of the H3.3 Histone Variant in the Epigenetic Regulation of Gene Expression in the Nervous System, in Both Physiological and Pathological Conditions. Int J Mol Sci 2023; 24:11028. [PMID: 37446205 DOI: 10.3390/ijms241311028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
All the cells of an organism contain the same genome. However, each cell expresses only a minor fraction of its potential and, in particular, the genes encoding the proteins necessary for basal metabolism and the proteins responsible for its specific phenotype. The ability to use only the right and necessary genes involved in specific functions depends on the structural organization of the nuclear chromatin, which in turn depends on the epigenetic history of each cell, which is stored in the form of a collection of DNA and protein modifications. Among these modifications, DNA methylation and many kinds of post-translational modifications of histones play a key role in organizing the complex indexing of usable genes. In addition, non-canonical histone proteins (also known as histone variants), the synthesis of which is not directly linked with DNA replication, are used to mark specific regions of the genome. Here, we will discuss the role of the H3.3 histone variant, with particular attention to its loading into chromatin in the mammalian nervous system, both in physiological and pathological conditions. Indeed, chromatin modifications that mark cell memory seem to be of special importance for the cells involved in the complex processes of learning and memory.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
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16
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Ostroverkhova D, Espiritu D, Aristizabal MJ, Panchenko AR. Leveraging Gene Redundancy to Find New Histone Drivers in Cancer. Cancers (Basel) 2023; 15:3437. [PMID: 37444547 DOI: 10.3390/cancers15133437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Histones play a critical role in chromatin function but are susceptible to mutagenesis. In fact, numerous mutations have been observed in several cancer types, and a few of them have been associated with carcinogenesis. Histones are peculiar, as they are encoded by a large number of genes, and the majority of them are clustered in three regions of the human genome. In addition, their replication and expression are tightly regulated in a cell. Understanding the etiology of cancer mutations in histone genes is impeded by their functional and sequence redundancy, their unusual genomic organization, and the necessity to be rapidly produced during cell division. Here, we collected a large data set of histone gene mutations in cancer and used it to investigate their distribution over 96 human histone genes and 68 different cancer types. This analysis allowed us to delineate the factors influencing the probability of mutation accumulation in histone genes and to detect new histone gene drivers. Although no significant difference in observed mutation rates between different histone types was detected for the majority of cancer types, several cancers demonstrated an excess or depletion of mutations in histone genes. As a consequence, we identified seven new histone genes as potential cancer-specific drivers. Interestingly, mutations were found to be distributed unevenly in several histone genes encoding the same protein, pointing to different factors at play, which are specific to histone function and genomic organization. Our study also elucidated mutational processes operating in genomic regions harboring histone genes, highlighting POLE as a factor of potential interest.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Daniel Espiritu
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
| | | | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON K7L 3N6, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
- School of Computing, Queen's University, Kingston, ON K7L 3N6, Canada
- Ontario Institute of Cancer Research, Toronto, ON M5G 0A3, Canada
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17
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Methylation analysis of histone 4-related gene HIST1H4F and its effect on gene expression in bladder cancer. Gene 2023; 866:147352. [PMID: 36898511 DOI: 10.1016/j.gene.2023.147352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Recently, aberrant DNA methylation of the HIST1H4F gene (encodes Histone 4 protein) has been shown in many types of cancer, which may serve as a promising biomarker for early cancer diagnosis. However, the correlation between DNA methylation of the HIST1H4F gene and its role in gene expression is unclear in bladder cancer. Therefore, the first objective of this study is to explore the DNA methylation pattern of the HIST1H4F gene and then further elucidate its effects on HIST1H4F mRNA expression in bladder cancer. To this end, the methylation pattern of the HIST1H4F gene was analyzed by pyrosequencing and the effects of the methylation profiles of this gene on HIST1H4F mRNA expression in bladder cancer were examined by qRT-PCR. Sequencing analysis revealed significantly higher methylation frequencies of the HIST1H4F gene in bladder tumor samples compared to normal samples (p < 0,0001). However, when we evaluated the correlations between hypermethylation of HIST1H4F and the clinicopathological parameters (tumor stage, tumor grade, lymph node metastasis, muscle-invasion), no significant difference was found between the groups (p > 0.05). In addition, we examined the role of hypermethylation of the HIST1H4F gene on HIST1H4F mRNA expression. We found that hypermethylation of HIST1H4F in the exon have no effect HIST1H4F mRNA expression in bladder cancer (p > 0.05). We also confirmed our finding in cultured T24 cell line which HIST1H4F gene is hypermethylated. Our results suggest that hypermethylation of the HIST1H4F seems to be a promising early diagnostic biomarker in bladder cancer patients. However, further studies are needed to determine the role of HIST1H4F hypermethylation in tumorigenesis.
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18
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Chang W, Zhao Y, Rayêe D, Xie Q, Suzuki M, Zheng D, Cvekl A. Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation. Epigenetics Chromatin 2023; 16:4. [PMID: 36698218 PMCID: PMC9875507 DOI: 10.1186/s13072-023-00478-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Cellular differentiation is marked by temporally and spatially coordinated gene expression regulated at multiple levels. DNA methylation represents a universal mechanism to control chromatin organization and its accessibility. Cytosine methylation of CpG dinucleotides regulates binding of methylation-sensitive DNA-binding transcription factors within regulatory regions of transcription, including promoters and distal enhancers. Ocular lens differentiation represents an advantageous model system to examine these processes as lens comprises only two cell types, the proliferating lens epithelium and postmitotic lens fiber cells all originating from the epithelium. RESULTS Using whole genome bisulfite sequencing (WGBS) and microdissected lenses, we investigated dynamics of DNA methylation and chromatin changes during mouse lens fiber and epithelium differentiation between embryos (E14.5) and newborns (P0.5). Histone H3.3 variant chromatin landscapes were also generated for both P0.5 lens epithelium and fibers by chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Tissue-specific features of DNA methylation patterns are demonstrated via comparative studies with embryonic stem (ES) cells and neural progenitor cells (NPCs) at Nanog, Pou5f1, Sox2, Pax6 and Six3 loci. Comparisons with ATAC-seq and RNA-seq data demonstrate that reduced methylation is associated with increased expression of fiber cell abundant genes, including crystallins, intermediate filament (Bfsp1 and Bfsp2) and gap junction proteins (Gja3 and Gja8), marked by high levels of histone H3.3 within their transcribed regions. Interestingly, Pax6-binding sites exhibited predominantly DNA hypomethylation in lens chromatin. In vitro binding of Pax6 proteins showed Pax6's ability to interact with sites containing one or two methylated CpG dinucleotides. CONCLUSIONS Our study has generated the first data on methylation changes between two different stages of mammalian lens development and linked these data with chromatin accessibility maps, presence of histone H3.3 and gene expression. Reduced DNA methylation correlates with expression of important genes involved in lens morphogenesis and lens fiber cell differentiation.
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Affiliation(s)
- William Chang
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Yilin Zhao
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Danielle Rayêe
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Qing Xie
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Masako Suzuki
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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19
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The Role of Epigenetics in Brain and Spinal Cord Tumors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1394:119-136. [PMID: 36587385 DOI: 10.1007/978-3-031-14732-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identification of distinct genetic and epigenetic profiles in various neuroepithelial tumors has improved the classification and uncovered novel diagnostic, prognostic, and predictive molecular biomarkers for improved prediction of treatment response and outcome. Especially, in pediatric high-grade brain tumors, such as diffuse midline glioma, H3K27M-altered and posterior fossa group A-ependymoma, epigenetic changes predominate, along with changes in expression of known oncogenes and tumor suppressor genes induced by histone modifications and DNA methylation. The precise role of epigenetic abnormalities is important for understanding tumorigenesis and the establishment of brain tumor treatment strategies. Using powerful epigenetic-based therapies for cancer cells, the aberrantly regulated epigenome can be restored to a more normal state through epigenetic reprogramming. Combinations of agents targeting DNA methylation and/or other epigenetic modifications may be a promising cancer treatment. Therefore, the integration of multi-omics data including epigenomics is now important for classifying primary brain tumors and predicting their biological behavior. Recent advances in molecular genetics and epigenetic integrated diagnostics of brain tumors influence new strategies for targeted therapy.
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Corcoran ET, Jacob Y. Direct assessment of histone function using histone replacement. Trends Biochem Sci 2023; 48:53-70. [PMID: 35853806 PMCID: PMC9789166 DOI: 10.1016/j.tibs.2022.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 02/09/2023]
Abstract
Histones serve many purposes in eukaryotic cells in the regulation of diverse genomic processes, including transcription, replication, DNA repair, and chromatin organization. As such, experimental systems to assess histone function are fundamental resources toward elucidating the regulation of activities occurring on chromatin. One set of important tools for investigating histone function are histone replacement systems, in which endogenous histone expression can be partially or completely replaced with a mutant histone. Histone replacement systems allow systematic screens of histone regulatory functions and the direct assessment of functions for histone residues. In this review, we describe existing histone replacement systems in model organisms, the benefits and limitations of these systems, and opportunities for future research with histone replacement strategies.
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Affiliation(s)
- Emma Tung Corcoran
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CT 06511, USA.
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21
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Zob DL, Augustin I, Caba L, Panzaru MC, Popa S, Popa AD, Florea L, Gorduza EV. Genomics and Epigenomics in the Molecular Biology of Melanoma-A Prerequisite for Biomarkers Studies. Int J Mol Sci 2022; 24:ijms24010716. [PMID: 36614156 PMCID: PMC9821083 DOI: 10.3390/ijms24010716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Melanoma is a common and aggressive tumor originating from melanocytes. The increasing incidence of cutaneous melanoma in recent last decades highlights the need for predictive biomarkers studies. Melanoma development is a complex process, involving the interplay of genetic, epigenetic, and environmental factors. Genetic aberrations include BRAF, NRAS, NF1, MAP2K1/MAP2K2, KIT, GNAQ, GNA11, CDKN2A, TERT mutations, and translocations of kinases. Epigenetic alterations involve microRNAs, non-coding RNAs, histones modifications, and abnormal DNA methylations. Genetic aberrations and epigenetic marks are important as biomarkers for the diagnosis, prognosis, and prediction of disease recurrence, and for therapeutic targets. This review summarizes our current knowledge of the genomic and epigenetic changes in melanoma and discusses the latest scientific information.
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Affiliation(s)
- Daniela Luminita Zob
- Department of Medical Oncology, AI. Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
| | - Iolanda Augustin
- Department of Medical Oncology, AI. Trestioreanu Institute of Oncology, 022328 Bucharest, Romania
- Correspondence: (I.A.); (L.C.)
| | - Lavinia Caba
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
- Correspondence: (I.A.); (L.C.)
| | - Monica-Cristina Panzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
| | - Setalia Popa
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
| | - Alina Delia Popa
- Nursing Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
| | - Laura Florea
- Department of Nephrology-Internal Medicine, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania
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22
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Ishida H, Kono H. Free Energy Landscape of H2A-H2B Displacement From Nucleosome. J Mol Biol 2022; 434:167707. [PMID: 35777463 DOI: 10.1016/j.jmb.2022.167707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/11/2022] [Accepted: 06/23/2022] [Indexed: 12/14/2022]
Abstract
Nucleosome reconstitution plays an important role in many cellular functions. As an initial step, H2A-H2B dimer displacement, which is accompanied by disruption of many of the interactions within the nucleosome, should occur. To understand how H2A-H2B dimer displacement occurs, an adaptively biased molecular dynamics (ABMD) simulation was carried out to generate a variety of displacements of the H2A-H2B dimer from the fully wrapped to partially unwrapped nucleosome structures. With regards to these structures, the free energy landscape of the dimer displacement was investigated using umbrella sampling simulations. We found that the main contributors to the free energy were the docking domain of H2A and the C-terminal of H4. There were various paths for the dimer displacement which were dependent on the extent of nucleosomal DNA wrapping, suggesting that modulation of the intra-nucleosomal interaction by external factors such as histone chaperons could control the path for the H2A-H2B dimer displacement. Key residues which contributed to the free energy have also been reported to be involved in the mutations and posttranslational modifications (PTMs) which are important for assembling and/or reassembling the nucleosome at the molecular level and are found in cancer cells at the phenotypic level. Our results give insight into how the H2A-H2B dimer displacement proceeds along various paths according to different interactions within the nucleosome.
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Affiliation(s)
- Hisashi Ishida
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 619-0215 Kizugawa, Kyoto, Japan.
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 619-0215 Kizugawa, Kyoto, Japan
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23
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Mizugaki A, Wada T, Tsuchida T, Gando S. Association of Histones With Coagulofibrinolytic Responses and Organ Dysfunction in Adult Post-cardiac Arrest Syndrome. Front Cardiovasc Med 2022; 9:885406. [PMID: 35837604 PMCID: PMC9273886 DOI: 10.3389/fcvm.2022.885406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/03/2022] [Indexed: 11/23/2022] Open
Abstract
Background Patients successfully resuscitated from cardiac arrest often develop organ dysfunction caused by systemic inflammation and increased coagulation, leading to disseminated intravascular coagulation (DIC). The involvement of histones in DIC and organ dysfunction in patients with sepsis and trauma has been previously reported, raising the probability that histones may also be associated with pathophysiology in patients after cardiac arrest and resuscitation. This study evaluated the relationship between histones and organ dysfunction related to coagulofibrinolytic changes in patients with post-cardiac arrest syndrome (PCAS). Methods This prospective single-center observational study assessed 35 adult patients with PCAS who were divided into two groups, i.e., 15 patients with multiple organ dysfunction syndrome (MODS) and 20 patients without MODS. MODS was defined as a sequential organ failure assessment score of ≥12. The plasma levels of histones and coagulofibrinolytic markers, including soluble fibrin, tissue-type plasminogen activator, plasminogen activator inhibitor-1, plasmin-alpha 2-plasmin inhibitor complex (PIC), and soluble thrombomodulin, were measured in patients with PCAS immediately after admission to the emergency department, and 3 and 24 h after arriving at the hospital. Results PCAS patients with MODS had higher DIC scores [4 (3.0–5.0) vs. 1 (0.0–3.0), p = 0.012] and higher mortality rates (66.7% vs. 20.0%, p = 0.013) than those without MODS. Moreover, patients with MODS exhibited higher histone levels than those without MODS during the early phase of the post-resuscitation period. Severe endothelial injury and higher thrombin and plasmin generation were observed in the MODS group. Plasma levels of histones were positively correlated with those of soluble fibrin immediately after resuscitation (rho = 0.367, p = 0.030) and PIC 3 h after arriving at the hospital (rho = 0.480, p = 0.005). This correlation was prominent in the patient population with MODS (soluble fibrin: rho = 0.681, p = 0.005, PIC: rho = 0.742, p = 0.002). Conclusions This study demonstrated that elevated histone levels were associated with increased levels of thrombin, and subsequent plasmin generation in PCAS patients, especially those with MODS. Further studies are required to elucidate the causal relationship between histones and organ dysfunction related to DIC in PCAS.
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Affiliation(s)
- Asumi Mizugaki
- Division of Acute and Critical Care Medicine, Department of Anesthesiology and Critical Care Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Takeshi Wada
- Division of Acute and Critical Care Medicine, Department of Anesthesiology and Critical Care Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
- *Correspondence: Takeshi Wada
| | - Takumi Tsuchida
- Division of Acute and Critical Care Medicine, Department of Anesthesiology and Critical Care Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Satoshi Gando
- Division of Acute and Critical Care Medicine, Department of Anesthesiology and Critical Care Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Department of Acute and Critical Care Center, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
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24
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Kreienbaum C, Paasche LW, Hake SB. H2A.Z's 'social' network: functional partners of an enigmatic histone variant. Trends Biochem Sci 2022; 47:909-920. [PMID: 35606214 DOI: 10.1016/j.tibs.2022.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein-protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes.
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Affiliation(s)
| | - Lena W Paasche
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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25
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Furth N, Shema E. It’s all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues. Int J Mol Sci 2022; 23:ijms23031103. [PMID: 35163027 PMCID: PMC8834906 DOI: 10.3390/ijms23031103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer cells accumulate epigenomic aberrations that contribute to cancer initiation and progression by altering both the genomic stability and the expression of genes. The awareness of such alterations could improve our understanding of cancer dynamics and the identification of new therapeutic strategies and biomarkers to refine tumor classification and treatment. Formalin fixation and paraffin embedding (FFPE) is the gold standard to preserve both tissue integrity and organization, and, in the last decades, a huge number of biological samples have been archived all over the world following this procedure. Recently, new chromatin immunoprecipitation (ChIP) techniques have been developed to allow the analysis of histone post-translational modifications (PTMs) and transcription factor (TF) distribution in FFPE tissues. The application of ChIP to genome-wide chromatin studies using real archival samples represents an unprecedented opportunity to conduct retrospective clinical studies thanks to the possibility of accessing large cohorts of samples and their associated diagnostic records. However, although recent attempts to standardize have been made, fixation and storage conditions of clinical specimens are still extremely variable and can affect the success of chromatin studies. The procedures introduced in the last few years dealt with this problem proponing successful strategies to obtain high-resolution ChIP profiles from FFPE archival samples. In this review, we compare the different FFPE-ChIP techniques, highlighting their strengths, limitations, common features, and peculiarities, as well as pitfalls and caveats related to ChIP studies in FFPE samples, in order to facilitate their application.
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27
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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28
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Espinosa L, Marruecos L. NF-κB-Dependent and -Independent (Moonlighting) IκBα Functions in Differentiation and Cancer. Biomedicines 2021; 9:1278. [PMID: 34572464 PMCID: PMC8468488 DOI: 10.3390/biomedicines9091278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 12/23/2022] Open
Abstract
IκBα is considered to play an almost exclusive role as inhibitor of the NF-κB signaling pathway. However, previous results have demonstrated that SUMOylation imposes a distinct subcellular distribution, regulation, NF-κB-binding affinity and function to the IκBα protein. In this review we discuss the main alterations of IκBα found in cancer and whether they are (most likely) associated with NF-κB-dependent or NF-κB-independent (moonlighting) activities of the protein.
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Affiliation(s)
- Lluís Espinosa
- Cancer Research Program, Institut Mar d’Investigacions Mèdiques, CIBERONC, Hospital del Mar, Doctor Aiguader 88, 08003 Barcelona, Spain;
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29
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Hsu CJ, Meers O, Buschbeck M, Heidel FH. The Role of MacroH2A Histone Variants in Cancer. Cancers (Basel) 2021; 13:cancers13123003. [PMID: 34203934 PMCID: PMC8232725 DOI: 10.3390/cancers13123003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The structural unit of chromatin is the nucleosome that is composed of DNA wrapped around a core of eight histone proteins. Histone variants can replace ‘standard’ histones at specific sites of the genome. Thus, histone variants modulate all functions in the context of chromatin, such as gene expression. Here, we provide a concise review on a group of histone variants termed macroH2A. They contain two additional domains that contribute to their increased size. We discuss how these domains mediate molecular functions in normal cells and the role of macroH2As in gene expression and cancer. Abstract The epigenome regulates gene expression and provides a molecular memory of cellular events. A growing body of evidence has highlighted the importance of epigenetic regulation in physiological tissue homeostasis and malignant transformation. Among epigenetic mechanisms, the replacement of replication-coupled histones with histone variants is the least understood. Due to differences in protein sequence and genomic distribution, histone variants contribute to the plasticity of the epigenome. Here, we focus on the family of macroH2A histone variants that are particular in having a tripartite structure consisting of a histone fold, an intrinsically disordered linker and a globular macrodomain. We discuss how these domains mediate different molecular functions related to chromatin architecture, transcription and DNA repair. Dysregulated expression of macroH2A histone variants has been observed in different subtypes of cancer and has variable prognostic impact, depending on cellular context and molecular background. We aim to provide a concise review regarding the context- and isoform-dependent contributions of macroH2A histone variants to cancer development and progression.
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Affiliation(s)
- Chen-Jen Hsu
- Internal Medicine C, Greifswald University Medicine, 17475 Greifswald, Germany;
| | - Oliver Meers
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain;
| | - Marcus Buschbeck
- Cancer and Leukaemia Epigenetics and Biology Program, Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain;
- Program for Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Correspondence: (M.B.); (F.H.H.); Tel.: +34-935-572-800 (M.B.); +49-383-486-6698 (F.H.H.); Fax: +49-383-486-6713 (F.H.H.)
| | - Florian H. Heidel
- Internal Medicine C, Greifswald University Medicine, 17475 Greifswald, Germany;
- Leibniz Institute on Aging, Fritz-Lipmann Institute, 07745 Jena, Germany
- Correspondence: (M.B.); (F.H.H.); Tel.: +34-935-572-800 (M.B.); +49-383-486-6698 (F.H.H.); Fax: +49-383-486-6713 (F.H.H.)
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