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Du T, Li G, Zong Q, Luo H, Pan Y, Ma K. Nuclear alpha-synuclein accelerates cell senescence and neurodegeneration. Immun Ageing 2024; 21:47. [PMID: 38997709 PMCID: PMC11242018 DOI: 10.1186/s12979-024-00429-0] [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: 01/21/2024] [Accepted: 04/16/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND The progression of Parkinson's disease (PD) is related to ageing. The accumulation of nuclear alpha-synuclein (α-syn) may accelerate the occurrence of neurodegenerative diseases, but its role in PD remains poorly understood. METHODS In the present study, α-syn expression was specifically targeted to the nucleus by constructing an adeno-associated virus (AAV) vector in which a nuclear localization sequence (NLS) was added to the α-syn coding sequence. Virus-mediated gene transfer, behavioural tests, RNA-Seq, immunohistochemistry, western blotting, and quantitative real-time PCR were then performed. RESULTS In vivo experiments using a mouse model showed that nuclear α-syn increased the severity of the PD-like phenotype, including the loss of dopaminergic neurons concomitant with motor impairment and the formation of α-syn inclusions. These nuclear inclusions contained α-syn species of high molecular weights and induced strong transcriptional dysregulation, especially induced high expression of p21 and senescence-associated secretory phenotype (SASP)-related genes. In addition, the transcriptional alterations induced by nuclear α-syn were associated with gliosis, inflammation, oxidative and DNA damage, and lysosomal dysfunction, and they eventually accelerated neuronal loss and neurodegeneration. CONCLUSIONS Our results suggest that nuclear α-syn plays a crucial role in PD pathogenesis.
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Affiliation(s)
- Tingfu Du
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Guoxiang Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Qinglan Zong
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Haiyu Luo
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China
| | - Kaili Ma
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650118, China.
- Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Diseases, Kunming, 650118, China.
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2
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Wang Y, Tsukioka D, Oda S, Suzuki MG, Suzuki Y, Mitani H, Aoki F. Involvement of H2A variants in DNA damage response of zygotes. Cell Death Discov 2024; 10:231. [PMID: 38744857 PMCID: PMC11094039 DOI: 10.1038/s41420-024-01999-0] [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: 02/15/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Phosphorylated H2AX, known as γH2AX, forms in response to genotoxic insults in somatic cells. Despite the high abundance of H2AX in zygotes, the level of irradiation-induced γH2AX is low at this stage. Another H2A variant, TH2A, is present at a high level in zygotes and can also be phosphorylated at its carboxyl end. We constructed H2AX- or TH2A-deleted mice using CRISPR Cas9 and investigated the role of these H2A variants in the DNA damage response (DDR) of zygotes exposed to γ-ray irradiation at the G2 phase. Our results showed that compared to irradiated wild-type zygotes, irradiation significantly reduced the developmental rates to the blastocyst stage in H2AX-deleted zygotes but not in TH2A-deleted ones. Furthermore, live cell imaging revealed that the G2 checkpoint was activated in H2AX-deleted zygotes, but the duration of arrest was significantly shorter than in wild-type and TH2A-deleted zygotes. The number of micronuclei was significantly higher in H2AX-deleted embryos after the first cleavage, possibly due to the shortened cell cycle arrest of damaged embryos and, consequently, the insufficient time for DNA repair. Notably, FRAP analysis suggested the involvement of H2AX in chromatin relaxation. Moreover, phosphorylated CHK2 foci were found in irradiated wild-type zygotes but not in H2AX-deleted ones, suggesting a critical role of these foci in maintaining cell cycle arrest for DNA repair. In conclusion, H2AX, but not TH2A, is involved in the DDR of zygotes, likely by creating a relaxed chromatin structure with enhanced accessibility for DNA repair proteins and by facilitating the formation of pCHK2 foci to prevent premature cleavage.
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Affiliation(s)
- Yuan Wang
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
| | - Dai Tsukioka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Shoji Oda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hiroshi Mitani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Fugaku Aoki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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3
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Cheng C, Yao H, Li H, Liu J, Liu Z, Wu Y, Zhu L, Hu H, Fang Z, Wu L. Blockade of the deubiquitinating enzyme USP48 degrades oncogenic HMGA2 and inhibits colorectal cancer invasion and metastasis. Acta Pharm Sin B 2024; 14:1624-1643. [PMID: 38572092 PMCID: PMC10985028 DOI: 10.1016/j.apsb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 04/05/2024] Open
Abstract
HMGA2, a pivotal transcription factor, functions as a versatile regulator implicated in the progression of diverse aggressive malignancies. In this study, mass spectrometry was employed to identify ubiquitin-specific proteases that potentially interact with HMGA2, and USP48 was identified as a deubiquitinating enzyme of HMGA2. The enforced expression of USP48 significantly increased HMGA2 protein levels by inhibiting its degradation, while the deprivation of USP48 promoted HMGA2 degradation, thereby suppressing tumor invasion and metastasis. We discovered that USP48 undergoes SUMOylation at lysine 258, which enhances its binding affinity to HMGA2. Through subsequent phenotypic screening of small molecules, we identified DUB-IN-2 as a remarkably potent pharmacological inhibitor of USP48. Interestingly, the small-molecule inhibitor targeting USP48 induces destabilization of HMGA2. Clinically, upregulation of USP48 or HMGA2 in cancerous tissues is indicative of poor prognosis for patients with colorectal cancer (CRC). Collectively, our study not only elucidates the regulatory mechanism of DUBs involved in HMGA2 stability and validates USP48 as a potential therapeutic target for CRC, but also identifies DUB-IN-2 as a potent inhibitor of USP48 and a promising candidate for CRC treatment.
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Affiliation(s)
- Can Cheng
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hanhui Yao
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Heng Li
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Comprehensive Surgery, Anhui Provincial Cancer Hospital, West District of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Jingwen Liu
- Anhui Provincial Hospital Health Management Center, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Zhengyi Liu
- Department of Breast Surgery, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou 450003, China
| | - Yang Wu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Liang Zhu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Hejie Hu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Zhengdong Fang
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Liang Wu
- Department of General Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
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Hidmi O, Oster S, Monin J, Aqeilan RI. TOP1 and R-loops facilitate transcriptional DSBs at hypertranscribed cancer driver genes. iScience 2024; 27:109082. [PMID: 38375218 PMCID: PMC10875566 DOI: 10.1016/j.isci.2024.109082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/26/2023] [Accepted: 01/28/2024] [Indexed: 02/21/2024] Open
Abstract
DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employ several techniques to map DSBs, R-loops, and topoisomerase 1 cleavage complex (TOP1cc) to comprehensively investigate the interplay between transcription, DSBs, topoisomerase 1 (TOP1), and R-loops. Our findings reveal the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops. Remarkably, transcription-associated DSBs at these loci are significantly reduced upon depletion of R-loops and TOP1, uncovering the pivotal roles of TOP1 and R-loops in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development, highlighting the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations.
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Affiliation(s)
- Osama Hidmi
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sara Oster
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Monin
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rami I. Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Cyprus Cancer Research Institute (CCRI), Nicosia, Cyprus
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5
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Zhou Z, Wang T, Hu T, Xu H, Cui L, Xue B, Zhao X, Pan X, Yu S, Li H, Qin Y, Zhang J, Ma L, Liang R, Tan C. Synergistic Interaction between Metal Single-Atoms and Defective WO 3- x Nanosheets for Enhanced Sonodynamic Cancer Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2311002. [PMID: 38408758 DOI: 10.1002/adma.202311002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/03/2024] [Indexed: 02/28/2024]
Abstract
Although metal single-atom (SA)-based nanomaterials are explored as sonosensitizers for sonodynamic therapy (SDT), they normally exhibit poor activities and need to combine with other therapeutic strategies. Herein, the deposition of metal SAs on oxygen vacancy (OV)-rich WO3- x nanosheets to generate a synergistic effect for efficient SDT is reported. Crystalline WO3 and OV-rich WO3- x nanosheets are first prepared by simple calcination of the WO3 ·H2 O nanosheets under an air and N2 atmosphere, respectively. Pt, Cu, Fe, Co, and Ni metal SAs are then deposited on WO3- x nanosheets to obtain metal SA-decorated WO3- x nanocomposites (M-WO3- x ). Importantly, the Cu-WO3- x sonosensitizer exhibits a much higher activity for ultrasound (US)-induced production of reactive oxygen species than that of the WO3- x and Cu SA-decorated WO3 , which is also higher than other M-WO3- x nanosheets. Both the experimental and theoretical results suggest that the excellent SDT performance of the Cu-WO3- x nanosheets should be attributed to the synergistic effect between Cu SAs and WO3- x OVs. Therefore, after polyethylene glycol modification, the Cu-WO3- x can quickly kill cancer cells in vitro and effectively eradicate tumors in vivo under US irradiation. Transcriptome sequencing analysis and further molecular validation suggest that the Cu-WO3- x -mediated SDT-activated apoptosis and TNF signaling pathways are potential drivers of tumor apoptosis induction.
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Affiliation(s)
- Zhan Zhou
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, P. R. China
| | - Tao Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Tingting Hu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077, P. R. China
| | - Hao Xu
- Interdisciplinary Research Center of Biology & Catalysis, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Lin Cui
- Interdisciplinary Research Center of Biology & Catalysis, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Baoli Xue
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, P. R. China
| | - Xinshuo Zhao
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, P. R. China
| | - Xiangrong Pan
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, P. R. China
| | - Shilong Yu
- Institute of Advanced Materials (IAM) and Key Laboratory of Flexible Electronics (KLoFE), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Hai Li
- Institute of Advanced Materials (IAM) and Key Laboratory of Flexible Electronics (KLoFE), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Yong Qin
- Interdisciplinary Research Center of Biology & Catalysis, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
- State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, 030001, P. R. China
| | - Jiankang Zhang
- Interdisciplinary Research Center of Biology & Catalysis, School of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Lufang Ma
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, P. R. China
| | - Ruizheng Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
- Quzhou Institute for Innovation in Resource Chemical Engineering, Quzhou, 324000, P. R. China
| | - Chaoliang Tan
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, 999077, P. R. China
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6
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Vivek Hari Sundar G, Madhu A, Archana A, Shivaprasad PV. Plant histone variants at the nexus of chromatin readouts, stress and development. Biochim Biophys Acta Gen Subj 2024; 1868:130539. [PMID: 38072208 DOI: 10.1016/j.bbagen.2023.130539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/21/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Histones are crucial proteins that are involved in packaging the DNA as condensed chromatin inside the eukaryotic cell nucleus. Rather than being static packaging units, these molecules undergo drastic variations spatially and temporally to facilitate accessibility of DNA to replication, transcription as well as wide range of gene regulatory machineries. In addition, incorporation of paralogous variants of canonical histones in the chromatin is ascribed to specific functions. Given the peculiar requirement of plants to rapidly modulate gene expression levels on account of their sessile nature, histones and their variants serve as additional layers of gene regulation. This review summarizes the mechanisms and implications of distribution, modifications and differential incorporation of histones and their variants across plant genomes, and outlines emerging themes.
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Affiliation(s)
- G Vivek Hari Sundar
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
| | - Aravind Madhu
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - A Archana
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India.
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7
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Gavito-Covarrubias D, Ramírez-Díaz I, Guzmán-Linares J, Limón ID, Manuel-Sánchez DM, Molina-Herrera A, Coral-García MÁ, Anastasio E, Anaya-Hernández A, López-Salazar P, Juárez-Díaz G, Martínez-Juárez J, Torres-Jácome J, Albarado-Ibáñez A, Martínez-Laguna Y, Morán C, Rubio K. Epigenetic mechanisms of particulate matter exposure: air pollution and hazards on human health. Front Genet 2024; 14:1306600. [PMID: 38299096 PMCID: PMC10829887 DOI: 10.3389/fgene.2023.1306600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 02/02/2024] Open
Abstract
Environmental pollution nowadays has not only a direct correlation with human health changes but a direct social impact. Epidemiological studies have evidenced the increased damage to human health on a daily basis because of damage to the ecological niche. Rapid urban growth and industrialized societies importantly compromise air quality, which can be assessed by a notable accumulation of air pollutants in both the gas and the particle phases. Of them, particulate matter (PM) represents a highly complex mixture of organic and inorganic compounds of the most variable size, composition, and origin. PM being one of the most complex environmental pollutants, its accumulation also varies in a temporal and spatial manner, which challenges current analytical techniques used to investigate PM interactions. Nevertheless, the characterization of the chemical composition of PM is a reliable indicator of the composition of the atmosphere, the quality of breathed air in urbanized societies, industrial zones and consequently gives support for pertinent measures to avoid serious health damage. Epigenomic damage is one of the most promising biological mechanisms of air pollution-derived carcinogenesis. Therefore, this review aims to highlight the implication of PM exposure in diverse molecular mechanisms driving human diseases by altered epigenetic regulation. The presented findings in the context of pan-organic cancer, fibrosis, neurodegeneration and metabolic diseases may provide valuable insights into the toxicity effects of PM components at the epigenomic level and may serve as biomarkers of early detection for novel targeted therapies.
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Affiliation(s)
- Dulcemaría Gavito-Covarrubias
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
- Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla, Mexico
| | - Josué Guzmán-Linares
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
| | - Ilhuicamina Daniel Limón
- Laboratory of Neuropharmacology, Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Dulce María Manuel-Sánchez
- Laboratory of Neuropharmacology, Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
| | - Estela Anastasio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
| | - Arely Anaya-Hernández
- Centro de Investigación en Genética y Ambiente, Universidad Autónoma de Tlaxcala, Tlaxcala, Mexico
| | - Primavera López-Salazar
- Centro de Investigaciones en Dispositivos Semiconductores (CIDS), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Gabriel Juárez-Díaz
- Centro de Investigaciones en Dispositivos Semiconductores (CIDS), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Javier Martínez-Juárez
- Centro de Investigaciones en Dispositivos Semiconductores (CIDS), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Julián Torres-Jácome
- Laboratorio de Fisiopatología Cardiovascular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Alondra Albarado-Ibáñez
- Laboratorio de Fisiopatología Cardiovascular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Ygnacio Martínez-Laguna
- Vicerrectoría de Investigación y Estudios de Posgrado, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Carolina Morán
- Centro de Investigación en Fisicoquímica de Materiales, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Mexico
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla, Puebla, Mexico
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Fragkos M, Choleza M, Papadopoulou P. The Role of γH2AX in Replication Stress-induced Carcinogenesis: Possible Links and Recent Developments. CANCER DIAGNOSIS & PROGNOSIS 2023; 3:639-648. [PMID: 37927801 PMCID: PMC10619570 DOI: 10.21873/cdp.10266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Cancer is a condition characterized by genomic instability and gross chromosomal aberrations. The inability of the cell to timely and efficiently complete its replication cycle before entering mitosis is one of the most common causes of DNA damage and carcinogenesis. Phosphorylation of histone 2AX (H2AX) on S139 (γH2AX) is an indispensable step in the response to DNA damage, as it is required for the assembly of repair factors at the sites of damage. γH2AX is also a marker of DNA replication stress, mainly due to fork collapse that often follows prolonged replication stalling or repair of arrested forks, which involves the generation of DNA breaks. Although the role of γH2AX in the repair of DNA breaks has been well defined, the function of γH2AX in replicative stress remains unclear. In this review, we present the recent advances in the field of replication stress, and highlight a novel function for γH2AX that is independent of its role in the response to DNA damage. We discuss studies that support a role for γΗ2ΑΧ early in the response to replicative stress, which does not involve the repair of DNA breaks. We also highlight recent data proposing that γH2AX acts as a chromatin remodeling component, implicated in the efficient resolution of stalled replication forks. Understanding the mechanism by which γH2AX enables cellular recovery after replication stress will allow identification of novel cancer biomarkers, as well as new targets for cancer therapies.
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Affiliation(s)
- Michalis Fragkos
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| | - Maria Choleza
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
| | - Paraskevi Papadopoulou
- Department of Science and Mathematics, Deree-The American College of Greece, Athens, Greece
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9
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Kuwayama N, Kujirai T, Kishi Y, Hirano R, Echigoya K, Fang L, Watanabe S, Nakao M, Suzuki Y, Ishiguro KI, Kurumizaka H, Gotoh Y. HMGA2 directly mediates chromatin condensation in association with neuronal fate regulation. Nat Commun 2023; 14:6420. [PMID: 37828010 PMCID: PMC10570362 DOI: 10.1038/s41467-023-42094-9] [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: 01/09/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Identification of factors that regulate chromatin condensation is important for understanding of gene regulation. High-mobility group AT-hook (HMGA) proteins 1 and 2 are abundant nonhistone chromatin proteins that play a role in many biological processes including tissue stem-progenitor cell regulation, but the nature of their protein function remains unclear. Here we show that HMGA2 mediates direct condensation of polynucleosomes and forms droplets with nucleosomes. Consistently, most endogenous HMGA2 localized to transposase 5- and DNase I-inaccessible chromatin regions, and its binding was mostly associated with gene repression, in mouse embryonic neocortical cells. The AT-hook 1 domain was necessary for chromatin condensation by HMGA2 in vitro and in cellulo, and an HMGA2 mutant lacking this domain was defective in the ability to maintain neuronal progenitors in vivo. Intrinsically disordered regions of other proteins could substitute for the AT-hook 1 domain in promoting this biological function of HMGA2. Taken together, HMGA2 may regulate neural cell fate by its chromatin condensation activity.
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Grants
- This research was supported by AMED-CREST and AMED-PRIME of the Japan Agency for Medical Research and Development (JP22gm1310004, JP22gm6110021), SECOM Science and Technology Foundation SECOM Science and Technology Foundation (for Y.K.), Platform Project for Supporting Drug Discovery and Life Science Research from AMED JP21am0101076 and (for H.K.), Research Support Project for Life Science and Drug Discovery from AMED JP22ama121009 (for H.K.), Japan Science and Technology Agency ERATO JPMJER1901 (for H.K.) and by KAKENHI grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan and the Japan Society for the Promotion of Science (JP21J14115 for N.K.; JP22K15033 for T.K.;16H06279, 20H03179, 21H00242 and 22H04687 for Y.K.; 20K07589 for S.W.; JP20H00449, JP18H05534 for H.K.; JP22H00431, JP16H06279 and JP22H04925 for Y.G.)
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Affiliation(s)
- Naohiro Kuwayama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Kishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rina Hirano
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Kenta Echigoya
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Lingyan Fang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Sugiko Watanabe
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Mitsuyoshi Nakao
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Kei-Ichiro Ishiguro
- Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, 113-0033, Japan.
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10
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Rubio K, Müller JM, Mehta A, Watermann I, Olchers T, Koch I, Wessels S, Schneider MA, Araujo-Ramos T, Singh I, Kugler C, Stoleriu MG, Kriegsmann M, Eichhorn M, Muley T, Merkel OM, Braun T, Ammerpohl O, Reck M, Tresch A, Barreto G. Preliminary results from the EMoLung clinical study showing early lung cancer detection by the LC score. Discov Oncol 2023; 14:181. [PMID: 37787775 PMCID: PMC10547665 DOI: 10.1007/s12672-023-00799-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 09/22/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Lung cancer (LC) causes more deaths worldwide than any other cancer type. Despite advances in therapeutic strategies, the fatality rate of LC cases remains high (95%) since the majority of patients are diagnosed at late stages when patient prognosis is poor. Analysis of the International Association for the Study of Lung Cancer (IASLC) database indicates that early diagnosis is significantly associated with favorable outcome. However, since symptoms of LC at early stages are unspecific and resemble those of benign pathologies, current diagnostic approaches are mostly initiated at advanced LC stages. METHODS We developed a LC diagnosis test based on the analysis of distinct RNA isoforms expressed from the GATA6 and NKX2-1 gene loci, which are detected in exhaled breath condensates (EBCs). Levels of these transcript isoforms in EBCs were combined to calculate a diagnostic score (the LC score). In the present study, we aimed to confirm the applicability of the LC score for the diagnosis of early stage LC under clinical settings. Thus, we evaluated EBCs from patients with early stage, resectable non-small cell lung cancer (NSCLC), who were prospectively enrolled in the EMoLung study at three sites in Germany. RESULTS LC score-based classification of EBCs confirmed its performance under clinical conditions, achieving a sensitivity of 95.7%, 91.3% and 84.6% for LC detection at stages I, II and III, respectively. CONCLUSIONS The LC score is an accurate and non-invasive option for early LC diagnosis and a valuable complement to LC screening procedures based on computed tomography.
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Affiliation(s)
- Karla Rubio
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, 54000, Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, EcoCampus, Benemérita Universidad Autónoma de Puebla, 72570, Puebla, Mexico
| | - Jason M Müller
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Aditi Mehta
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Pharmaceutical Technology and Biopharmaceutics, Department of Pharmacy, Ludwig-Maximilians-University (LMU) Munich, 81377, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Munich, Germany
| | - Iris Watermann
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- LungenClinic Grosshansdorf (GHD), Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927, Großhansdorf, Germany
| | - Till Olchers
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- LungenClinic Grosshansdorf (GHD), Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927, Großhansdorf, Germany
| | - Ina Koch
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Munich, Germany
- Asklepios Biobank für Lungenerkrankungen, Asklepios Klinik Gauting GmbH, 82131, Gauting, Germany
| | - Sabine Wessels
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), 69120, Heidelberg, Germany
| | - Marc A Schneider
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), 69120, Heidelberg, Germany
| | - Tania Araujo-Ramos
- German Cancer Research Center (DKFZ) Heidelberg, Division Chronic Inflammation and Cancer, Emmy Noether Research Group Epigenetic Machineries and Cancer, 69120, Heidelberg, Germany
| | - Indrabahadur Singh
- German Cancer Research Center (DKFZ) Heidelberg, Division Chronic Inflammation and Cancer, Emmy Noether Research Group Epigenetic Machineries and Cancer, 69120, Heidelberg, Germany
| | - Christian Kugler
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- LungenClinic Grosshansdorf (GHD), Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927, Großhansdorf, Germany
| | - Mircea Gabriel Stoleriu
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Munich, Germany
- Asklepios Biobank für Lungenerkrankungen, Asklepios Klinik Gauting GmbH, 82131, Gauting, Germany
| | - Mark Kriegsmann
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Translational Lung Research Center Heidelberg (TLRC), 69120, Heidelberg, Germany
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Eichhorn
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Translational Lung Research Center Heidelberg (TLRC), 69120, Heidelberg, Germany
- Department of Thoracic Surgery, University of Heidelberg, 69120, Heidelberg, Germany
| | - Thomas Muley
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, 69126, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), 69120, Heidelberg, Germany
| | - Olivia M Merkel
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Pharmaceutical Technology and Biopharmaceutics, Department of Pharmacy, Ludwig-Maximilians-University (LMU) Munich, 81377, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Munich, Germany
| | - Thomas Braun
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Ole Ammerpohl
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- Institute of Human Genetics, University Medical Center Ulm, 89081, Ulm, Germany
| | - Martin Reck
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany
- LungenClinic Grosshansdorf (GHD), Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927, Großhansdorf, Germany
| | - Achim Tresch
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany.
- Center for Data and Simulation Science, University of Cologne, Cologne, Germany.
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, 54000, Nancy, France.
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany.
- German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL), Gießen, Germany.
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11
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Rubio K, Molina-Herrera A, Pérez-González A, Hernández-Galdámez HV, Piña-Vázquez C, Araujo-Ramos T, Singh I. EP300 as a Molecular Integrator of Fibrotic Transcriptional Programs. Int J Mol Sci 2023; 24:12302. [PMID: 37569677 PMCID: PMC10418647 DOI: 10.3390/ijms241512302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Fibrosis is a condition characterized by the excessive accumulation of extracellular matrix proteins in tissues, leading to organ dysfunction and failure. Recent studies have identified EP300, a histone acetyltransferase, as a crucial regulator of the epigenetic changes that contribute to fibrosis. In fact, EP300-mediated acetylation of histones alters global chromatin structure and gene expression, promoting the development and progression of fibrosis. Here, we review the role of EP300-mediated epigenetic regulation in multi-organ fibrosis and its potential as a therapeutic target. We discuss the preclinical evidence that suggests that EP300 inhibition can attenuate fibrosis-related molecular processes, including extracellular matrix deposition, inflammation, and epithelial-to-mesenchymal transition. We also highlight the contributions of small molecule inhibitors and gene therapy approaches targeting EP300 as novel therapies against fibrosis.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus Valsequillo, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus Valsequillo, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus Valsequillo, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
| | - Hury Viridiana Hernández-Galdámez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07360, Mexico
| | - Carolina Piña-Vázquez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07360, Mexico
| | - Tania Araujo-Ramos
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Indrabahadur Singh
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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12
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Das R, Dey A, Uppal S. A method for in situ visualization of Protein-Nascent RNA interactions in single cell using Proximity Ligation Assay (IPNR-PLA) in mammalian cells. Transcription 2023; 14:146-157. [PMID: 36927323 PMCID: PMC10807467 DOI: 10.1080/21541264.2023.2190296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
Proximity ligation assay (PLA) is an immunofluorescence assay, which determines in situ interaction of two biomolecules present within 40 nm close proximity. Here, we describe a modification of PLA for visual detection of in situ protein interactions with nascent RNA in a single cell (IPNR-PLA). In IPNR-PLA, nascent RNA is labeled by incorporating 5-fluorouridine (FU), a uridine nucleotide analogue, followed by covalent cross-linking of the interacting partners in proximity to newly synthesized RNA. By using combination of anti-BrdU antibody, which specifically binds to FU, and primary antibody against a protein of interest, the IPNR reaction results in fluorescent puncta as a positive signal, only if the candidate proteins are in proximity to nascent RNA. We have validated this method by demonstrating known CDK9 and elongating RNA pol II interaction with nascent RNA. Finally, we used this method to test for the presence of DNA double strand breaks as well as Poly (ADP-ribose) polymerase 1 (PARP1), an RNA binding protein, in the vicinity of nascent RNA in cancer cells. The capability of performing parallel IF labeling and quantifiable multiparameter measurements within heterogeneous cell populations makes IPNR-PLA very attractive for use in biological studies. Overall, we have developed the IPNR-PLA method for analysis of protein association with nascent RNA with single-cell resolution, which is highly sensitive, quantitative, efficient, and requires little starting experimental material.
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Affiliation(s)
- Rituparna Das
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Anusree Dey
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Sheetal Uppal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay,Mumbai, India
- Life Sciences, Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
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13
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Lim B, Djekidel MN, Matsui Y, Jung S, Yuan ZF, Wang X, Yang X, Pilehroud AS, Pan H, Wang F, Pruett-Miller S, Kavdia K, Pagala V, Fan Y, Peng J, Xu B, Peng JC. Phosphorylation of 53BP1 by ATM enforce neurodevelopmental programs in cortical organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539457. [PMID: 37205560 PMCID: PMC10187281 DOI: 10.1101/2023.05.04.539457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
53BP1 is a well-established DNA damage repair factor recently shown to regulate gene expression and critically influence tumor suppression and neural development. For gene regulation, how 53BP1 is regulated remains unclear. Here, we showed that 53BP1-serine 25 phosphorylation by ATM is required for neural progenitor cell proliferation and neuronal differentiation in cortical organoids. 53BP1-serine 25 phosphorylation dynamics controls 53BP1 target genes for neuronal differentiation and function, cellular response to stress, and apoptosis. Beyond 53BP1, ATM is required for phosphorylation of factors in neuronal differentiation, cytoskeleton, p53 regulation, and ATM, BNDF, and WNT signaling pathways for cortical organoid differentiation. Overall, our data suggest that 53BP1 and ATM control key genetic programs required for human cortical development.
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14
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Rubio K, Romero-Olmedo AJ, Sarvari P, Swaminathan G, Ranvir VP, Rogel-Ayala DG, Cordero J, Günther S, Mehta A, Bassaly B, Braubach P, Wygrecka M, Gattenlöhner S, Tresch A, Braun T, Dobreva G, Rivera MN, Singh I, Graumann J, Barreto G. Non-canonical integrin signaling activates EGFR and RAS-MAPK-ERK signaling in small cell lung cancer. Theranostics 2023; 13:2384-2407. [PMID: 37215577 PMCID: PMC10196829 DOI: 10.7150/thno.79493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/25/2023] [Indexed: 05/24/2023] Open
Abstract
Background: Small cell lung cancer (SCLC) is an extremely aggressive cancer type with a patient median survival of 6-12 months. Epidermal growth factor (EGF) signaling plays an important role in triggering SCLC. In addition, growth factor-dependent signals and alpha-, beta-integrin (ITGA, ITGB) heterodimer receptors functionally cooperate and integrate their signaling pathways. However, the precise role of integrins in EGF receptor (EGFR) activation in SCLC remains elusive. Methods: We analyzed human precision-cut lung slices (hPCLS), retrospectively collected human lung tissue samples and cell lines by classical methods of molecular biology and biochemistry. In addition, we performed RNA-sequencing-based transcriptomic analysis in human lung cancer cells and human lung tissue samples, as well as high-resolution mass spectrometric analysis of the protein cargo from extracellular vesicles (EVs) that were isolated from human lung cancer cells. Results: Our results demonstrate that non-canonical ITGB2 signaling activates EGFR and RAS/MAPK/ERK signaling in SCLC. Further, we identified a novel SCLC gene expression signature consisting of 93 transcripts that were induced by ITGB2, which may be used for stratification of SCLC patients and prognosis prediction of LC patients. We also found a cell-cell communication mechanism based on EVs containing ITGB2, which were secreted by SCLC cells and induced in control human lung tissue RAS/MAPK/ERK signaling and SCLC markers. Conclusions: We uncovered a mechanism of ITGB2-mediated EGFR activation in SCLC that explains EGFR-inhibitor resistance independently of EGFR mutations, suggesting the development of therapies targeting ITGB2 for patients with this extremely aggressive lung cancer type.
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Affiliation(s)
- Karla Rubio
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365; F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School; Charlestown, MA, 02129, USA
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, EcoCampus, Benemérita Universidad Autónoma de Puebla; Puebla 72570, Mexico
| | - Addi J. Romero-Olmedo
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Department of Medicine, Philipps-University Marburg; Marburg, Germany
| | - Pouya Sarvari
- Independent Researcher, collaborator of International Laboratory EPIGEN-CONCYTEP
| | | | - Vikas P. Ranvir
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Diana G. Rogel-Ayala
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365; F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
| | - Julio Cordero
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK)
| | - Stefan Günther
- ECCPS Bioinformatics and Deep Sequencing Platform, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
| | - Aditi Mehta
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
- Pharmaceutical Technology and Biopharmaceutics, Department of Pharmacy, Ludwig-Maximilians-University of Munich; Munich, Germany
| | - Birgit Bassaly
- Institute for Pathology, Justus Liebig University; 35392 Gießen, Germany
| | - Peter Braubach
- Institute for Pathology, Hannover Medical School; Hanover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Research Network; Hanover, Germany
| | - Malgorzata Wygrecka
- Center for Infection and Genomics of the Lung (CIGL), Universities of Giessen and Marburg Lung Center; Giessen, Germany
- Institute of Lung Health, German Center for Lung Research (DZL); Giessen, Germany
| | | | - Achim Tresch
- CECAD, University of Cologne; Cologne, Germany
- Faculty of Medicine and University Hospital, University of Cologne; Cologne, Germany
- Center for Data and Simulation Science, University of Cologne; Cologne, Germany
| | - Thomas Braun
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
| | - Gergana Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK)
| | - Miguel N. Rivera
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School; Charlestown, MA, 02129, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School; Charlestown, MA, 02129, USA
| | - Indrabahadur Singh
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Johannes Graumann
- Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
- Institute of Translational Proteomics, Department of Medicine, Philipps-University Marburg; 35043 Marburg, Germany
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365; F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research; 61231 Bad Nauheim, Germany
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, EcoCampus, Benemérita Universidad Autónoma de Puebla; Puebla 72570, Mexico
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15
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Rubio K, Hernández-Cruz EY, Rogel-Ayala DG, Sarvari P, Isidoro C, Barreto G, Pedraza-Chaverri J. Nutriepigenomics in Environmental-Associated Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12030771. [PMID: 36979019 PMCID: PMC10045733 DOI: 10.3390/antiox12030771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Complex molecular mechanisms define our responses to environmental stimuli. Beyond the DNA sequence itself, epigenetic machinery orchestrates changes in gene expression induced by diet, physical activity, stress and pollution, among others. Importantly, nutrition has a strong impact on epigenetic players and, consequently, sustains a promising role in the regulation of cellular responses such as oxidative stress. As oxidative stress is a natural physiological process where the presence of reactive oxygen-derived species and nitrogen-derived species overcomes the uptake strategy of antioxidant defenses, it plays an essential role in epigenetic changes induced by environmental pollutants and culminates in signaling the disruption of redox control. In this review, we present an update on epigenetic mechanisms induced by environmental factors that lead to oxidative stress and potentially to pathogenesis and disease progression in humans. In addition, we introduce the microenvironment factors (physical contacts, nutrients, extracellular vesicle-mediated communication) that influence the epigenetic regulation of cellular responses. Understanding the mechanisms by which nutrients influence the epigenome, and thus global transcription, is crucial for future early diagnostic and therapeutic efforts in the field of environmental medicine.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Estefani Y Hernández-Cruz
- Postgraduate in Biological Sciences, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
| | - Diana G Rogel-Ayala
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | | | - Ciro Isidoro
- Department of Health Sciences, Università del Piemonte Orientale, Via Paolo Solaroli 17, 28100 Novara, Italy
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad de Mexico 04510, Mexico
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16
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Gaudreau-Lapierre A, Klonisch T, Nicolas H, Thanasupawat T, Trinkle-Mulcahy L, Hombach-Klonisch S. Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. Int J Mol Sci 2023; 24:ijms24044246. [PMID: 36835656 PMCID: PMC9966875 DOI: 10.3390/ijms24044246] [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: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
The non-histone chromatin binding protein High Mobility Group AT-hook protein 2 (HMGA2) has important functions in chromatin remodeling, and genome maintenance and protection. Expression of HMGA2 is highest in embryonic stem cells, declines during cell differentiation and cell aging, but it is re-expressed in some cancers, where high HMGA2 expression frequently coincides with a poor prognosis. The nuclear functions of HMGA2 cannot be explained by binding to chromatin alone but involve complex interactions with other proteins that are incompletely understood. The present study used biotin proximity labeling, followed by proteomic analysis, to identify the nuclear interaction partners of HMGA2. We tested two different biotin ligase HMGA2 constructs (BioID2 and miniTurbo) with similar results, and identified known and new HMGA2 interaction partners, with functionalities mainly in chromatin biology. These HMGA2 biotin ligase fusion constructs offer exciting new possibilities for interactome discovery research, enabling the monitoring of nuclear HMGA2 interactomes during drug treatments.
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Affiliation(s)
- Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Research Institute in Oncology and Hematology (RIOH), CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hannah Nicolas
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thatchawan Thanasupawat
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Correspondence: ; Tel.: +1-204-789-3982; Fax: +1-204-789-3920
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17
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Muciño-Hernández G, Acevo-Rodríguez PS, Cabrera-Benitez S, Guerrero AO, Merchant-Larios H, Castro-Obregón S. Nucleophagy contributes to genome stability through degradation of type II topoisomerases A and B and nucleolar components. J Cell Sci 2023; 136:286548. [PMID: 36633090 PMCID: PMC10112964 DOI: 10.1242/jcs.260563] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/24/2022] [Indexed: 01/13/2023] Open
Abstract
The nuclear architecture of mammalian cells can be altered as a consequence of anomalous accumulation of nuclear proteins or genomic alterations. Most of the knowledge about nuclear dynamics comes from studies on cancerous cells. How normal healthy cells maintain genome stability, avoiding accumulation of nuclear damaged material, is less understood. Here, we describe that primary mouse embryonic fibroblasts develop a basal level of nuclear buds and micronuclei, which increase after etoposide-induced DNA double-stranded breaks. Both basal and induced nuclear buds and micronuclei colocalize with the autophagic proteins BECN1 and LC3B (also known as MAP1LC3B) and with acidic vesicles, suggesting their clearance by nucleophagy. Some of the nuclear alterations also contain autophagic proteins and type II DNA topoisomerases (TOP2A and TOP2B), or the nucleolar protein fibrillarin, implying they are also targets of nucleophagy. We propose that basal nucleophagy contributes to genome and nuclear stability, as well as in response to DNA damage.
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Affiliation(s)
- Gabriel Muciño-Hernández
- Departamento de Neurodesarrollo y Fisiología, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
| | - Pilar Sarah Acevo-Rodríguez
- Departamento de Neurodesarrollo y Fisiología, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
| | - Sandra Cabrera-Benitez
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Mexico City, México
| | - Adán Oswaldo Guerrero
- Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Morelos, Mexico
| | - Horacio Merchant-Larios
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - Susana Castro-Obregón
- Departamento de Neurodesarrollo y Fisiología, División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico City, México
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18
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Li J, Wang R, Shi W, Chen X, Yi J, Yang X, Jin S. Epigenetic regulation in radiation-induced pulmonary fibrosis. Int J Radiat Biol 2022; 99:384-395. [PMID: 35895014 DOI: 10.1080/09553002.2022.2089365] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
PURPOSE Radiation-induced pulmonary fibrosis (RIPF) is a common and serious adverse effect of radiotherapy for thoracic tumors, which occurs in the irreversible stage of radiation-induced lung injury (RILI) >6 months after irradiation. It is characterized by progressive and irreversible destruction of lung tissue and deterioration of lung function, which may impair quality of life and lead to respiratory failure and death. We hope this will draw attention to the involvement of epigenetics in the regulation of RIPF. CONCLUSIONS This review summarizes research progress on the role and mechanism of DNA methylation, noncoding RNA and RNA methylation in RIPF or RILI, and the possible role and mechanism of histone modification in RIPF. We have noticed that in tissue fibrosis, the epigenetic regulation mechanisms inside and outside the nucleus can influence each other. We speculate that RIPF may be regulated by an epigenetic regulatory network during its development, and believe that TGF-β, SNAIL, PTEN and EZH2 are four targets worthy of in-depth study.
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Affiliation(s)
- Jiale Li
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Rui Wang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Wen Shi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiaoyi Chen
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Junxuan Yi
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Xiangshan Yang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Shunzi Jin
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
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19
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Vieujean S, Caron B, Haghnejad V, Jouzeau JY, Netter P, Heba AC, Ndiaye NC, Moulin D, Barreto G, Danese S, Peyrin-Biroulet L. Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models. Int J Mol Sci 2022; 23:7611. [PMID: 35886959 PMCID: PMC9321337 DOI: 10.3390/ijms23147611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn's disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, 4000 Liege, Belgium;
| | - Bénédicte Caron
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Vincent Haghnejad
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Jean-Yves Jouzeau
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Patrick Netter
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Anne-Charlotte Heba
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - Ndeye Coumba Ndiaye
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - David Moulin
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Guillermo Barreto
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Universidad de la Salud del Estado de Puebla, Puebla 72000, Mexico
| | - Silvio Danese
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and University Vita-Salute San Raffaele, 20132 Milan, Italy;
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
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20
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Foroozani M, Holder DH, Deal RB. Histone Variants in the Specialization of Plant Chromatin. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:149-172. [PMID: 35167758 PMCID: PMC9133179 DOI: 10.1146/annurev-arplant-070221-050044] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.
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Affiliation(s)
| | - Dylan H Holder
- Department of Biology, Emory University, Atlanta, Georgia, USA;
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia, USA;
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21
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Herchenröther A, Wunderlich TM, Lan J, Hake SB. Spotlight on histone H2A variants: From B to X to Z. Semin Cell Dev Biol 2022; 135:3-12. [PMID: 35365397 DOI: 10.1016/j.semcdb.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/30/2022]
Abstract
Chromatin, the functional organization of DNA with histone proteins in eukaryotic nuclei, is the tightly-regulated template for several biological processes, such as transcription, replication, DNA damage repair, chromosome stability and sister chromatid segregation. In order to achieve a reversible control of local chromatin structure and DNA accessibility, various interconnected mechanisms have evolved. One of such processes includes the deposition of functionally-diverse variants of histone proteins into nucleosomes, the building blocks of chromatin. Among core histones, the family of H2A histone variants exhibits the largest number of members and highest sequence-divergence. In this short review, we report and discuss recent discoveries concerning the biological functions of the animal histone variants H2A.B, H2A.X and H2A.Z and how dysregulation or mutation of the latter impacts the development of disease.
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Affiliation(s)
| | - Tim M Wunderlich
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany
| | - Jie Lan
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
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22
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Olmedo-Suárez MÁ, Ramírez-Díaz I, Pérez-González A, Molina-Herrera A, Coral-García MÁ, Lobato S, Sarvari P, Barreto G, Rubio K. Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs. Biomolecules 2022; 12:513. [PMID: 35454102 PMCID: PMC9032613 DOI: 10.3390/biom12040513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.
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Affiliation(s)
- Miguel Ángel Olmedo-Suárez
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Decanato de Ciencias de la Salud, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Sagrario Lobato
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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23
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Lee MO, Li J, Davis BW, Upadhyay S, Al Muhisen HM, Suva LJ, Clement TM, Andersson L. Hmga2 deficiency is associated with allometric growth retardation, infertility, and behavioral abnormalities in mice. G3 (BETHESDA, MD.) 2022; 12:6456304. [PMID: 34878116 PMCID: PMC9210324 DOI: 10.1093/g3journal/jkab417] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/13/2023]
Abstract
The high mobility group AT-hook 2 (HMGA2) protein works as an architectural regulator by binding AT-rich DNA sequences to induce conformational changes affecting transcription. Genomic deletions disrupting HMGA2 coding sequences and flanking noncoding sequences cause dwarfism in mice and rabbits. Here, CRISPR/Cas9 was used in mice to generate an Hmga2 null allele that specifically disrupts only the coding sequence. The loss of one or both alleles of Hmga2 resulted in reduced body size of 20% and 60%, respectively, compared to wild-type littermates as well as an allometric reduction in skull length in Hmga2-/- mice. Both male and female Hmga2-/- mice are infertile, whereas Hmga2+/- mice are fertile. Examination of reproductive tissues of Hmga2-/- males revealed a significantly reduced size of testis, epididymis, and seminal vesicle compared to controls, and 70% of knock-out males showed externalized penis, but no cryptorchidism was observed. Sperm analyses revealed severe oligospermia in mutant males and slightly decreased sperm viability, increased DNA damage but normal sperm chromatin compaction. Testis histology surprisingly revealed a normal seminiferous epithelium, despite the significant reduction in testis size. In addition, Hmga2-/- mice showed a significantly reduced exploratory behavior. In summary, the phenotypic effects in mouse using targeted mutagenesis confirmed that Hmga2 is affecting prenatal and postnatal growth regulation, male reproductive tissue development, and presents the first indication that Hmga2 function is required for normal mouse behavior. No specific effect, despite an allometric reduction, on craniofacial development was noted in contrast to previous reports of an altered craniofacial development in mice and rabbits carrying deletions of both coding and noncoding sequences at the 5' part of Hmga2.
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Affiliation(s)
- Mi Ok Lee
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Jingyi Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Srijana Upadhyay
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Hadil M Al Muhisen
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Larry J Suva
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
| | - Tracy M Clement
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Program in Toxicology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
- Corresponding author: Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Vet Med Research Bldg., 588 Raymond Stotzer Pw, TX 77843, USA.
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24
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Chen X, Li Y, Rubio K, Deng B, Li Y, Tang Q, Mao C, Liu S, Xiao D, Barreto G, Tao Y. Lymphoid-specific helicase in epigenetics, DNA repair and cancer. Br J Cancer 2022; 126:165-173. [PMID: 34493821 PMCID: PMC8770686 DOI: 10.1038/s41416-021-01543-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/26/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
Lymphoid-specific helicase (LSH) is a member of the SNF2 helicase family of chromatin-remodelling proteins. Dysfunctions or mutations in LSH causes an autosomal recessive disease known as immunodeficiency-centromeric instability-facial anomaly (ICF) syndrome. Interestingly, LSH participates in various aspects of epigenetic regulation, including nucleosome remodelling, DNA methylation, histone modifications and heterochromatin formation. Further, LSH plays a crucial role during DNA-damage repair, specifically during double-strand break (DSB) repair, since murine LSH was shown to be essential for non-homologous end joining (NHEJ) and homologous recombination (HR). Accordingly, overexpression of LSH drives tumorigenesis and malignancy. On the other hand, LSH homologs stabilise the genome. Thus, LSH might be implemented as a biomarker for various cancer types and potential target molecule to develop therapeutic strategies against them. In this review, we focus on the role of LSH in orchestrating chromatin rearrangements, such as DNA methylation and histone modifications, as well as in DNA-damage repair. Changes in chromatin structure may facilitate gene expression signatures that cause malignant transformation. We summarise recent findings of LSH in cancers and raise critical open questions for further studies.
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Affiliation(s)
- Xiangyu Chen
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yamei Li
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Karla Rubio
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, Nancy, France
- Univ Paris Est Creteil, Gly-CRRET, Brain and Lung Epigenetics (BLUE), Creteil, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- International Laboratory EPIGEN, Universidad de la Salud del Estado de Puebla, Puebla, Mexico
| | - Bi Deng
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yuyi Li
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Qinwei Tang
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Chao Mao
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China.
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China.
| | - Guillermo Barreto
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, Nancy, France.
- Univ Paris Est Creteil, Gly-CRRET, Brain and Lung Epigenetics (BLUE), Creteil, France.
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany.
- International Laboratory EPIGEN, Universidad de la Salud del Estado de Puebla, Puebla, Mexico.
| | - Yongguang Tao
- Department of Pathology, Xiangya Hospital, Central South University; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Hunan, China.
- NHC Key Laboratory of Carcinogenesis of Ministry of Health (Central South University); Cancer Research Institute, Central South University, Changsha, Hunan, China.
- Department of Thoracic Surgery, Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer and Second Xiangya Hospital, Central South University, Changsha, China.
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Mei Q, Liu Z, Zuo H, Yang Z, Qu J. Idiopathic Pulmonary Fibrosis: An Update on Pathogenesis. Front Pharmacol 2022; 12:797292. [PMID: 35126134 PMCID: PMC8807692 DOI: 10.3389/fphar.2021.797292] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, lethal fibrotic lung disease that occurs primarily in middle-aged and elderly adults. It is a major cause of morbidity and mortality. With an increase in life expectancy, the economic burden of IPF is expected to continuously rise in the near future. Although the exact pathophysiological mechanisms underlying IPF remain not known. Significant progress has been made in our understanding of the pathogenesis of this devastating disease in last decade. The current paradigm assumes that IPF results from sustained or repetitive lung epithelial injury and subsequent activation of fibroblasts and myofibroblast differentiation. Persistent myofibroblast phenotype contributes to excessive deposition of the extracellular matrix (ECM) and aberrant lung repair, leading to tissue scar formation, distortion of the alveolar structure, and irreversible loss of lung function. Treatments of patients with IPF by pirfenidone and nintedanib have shown significant reduction of lung function decline and slowing of disease progression in patients with IPF. However, these drugs do not cure the disease. In this review, we discuss recent advances on the pathogenesis of IPF and highlight the development of novel therapeutic strategies against the disease.
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Affiliation(s)
| | | | | | | | - Jing Qu
- *Correspondence: Zhenhua Yang, ; Jing Qu,
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26
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Beghè C, Gromak N. R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors. Methods Mol Biol 2022; 2528:215-237. [PMID: 35704194 DOI: 10.1007/978-1-0716-2477-7_14] [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] [Indexed: 06/15/2023]
Abstract
R-loops are non-B-DNA structures consisting of an RNA/DNA hybrid and a displaced single-stranded DNA. They arise during transcription and play important biological roles. However, perturbation of R-loop levels represents a source of DNA damage and genome instability resulting in human diseases, including cancer and neurodegeneration. In this chapter, we describe a protocol which allows detection of R-loop interactors using affinity purification with S9.6 antibody, specific for RNA/DNA hybrids, followed by Western blotting or mass spectrometry. Multiple specificity controls including addition of synthetic competitors and RNase H treatment are described to verify the specificity of identified R-loop-binding factors. The identification of new R-loop interacting factors and the characterization of their involvement in R-loop biology provides a powerful resource to study the role of these important structures in health and disease.
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Affiliation(s)
- Chiara Beghè
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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Liang B, Zhang XX, Li R, Gu N. Guanxin V protects against ventricular remodeling after acute myocardial infarction through the interaction of TGF-β1 and Vimentin. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 95:153866. [PMID: 34883417 DOI: 10.1016/j.phymed.2021.153866] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/08/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Our previous study demonstrated that Guanxin V (GXV), a traditional Chinese herbal medicine, has a significant therapeutic effect on ventricular remodeling. However, the mechanistic action of GXV in ventricular remodeling warrants clarification. PURPOSE Here, we aimed to explore the anti-ventricular remodeling contribution of GXV and to provide an experimental basis for clinical generalization. METHODS A ventricular remodeling model after acute myocardial infarction was constructed in Syrian hamsters. The echocardiography and biochemical indices of cardiac function and remodeling were evaluated in different groups. Moreover, we built a remodeling model in cardiomyocytes and further explored the mechanism. Transmission electron microscopy was used to observe the ultrastructure of cardiomyocytes. The vital markers involved in the signaling pathway were detected by RT-qPCR and immunoblotting. Transforming growth factor beta 1 (TGF-β1) was overexpressed with lentivirus to verify the necessity of TGF-β1 in GXV's anti-ventricular remodeling effect. Finally, co-immunoprecipitation was conducted to test the interaction of TGF-β1 and Vimentin. RESULTS In hamster cardiac remodeling induced by acute myocardial infarction, GXV alleviated apoptosis, cardiac hypertrophy, and cardiac remodeling, and even improved cardiac function. Mechanistically, GXV inhibited the remodeling process by directly targeting TGF-β1. Overexpression of TGF-β1 exacerbated the ventricular remodeling, whereas GXV reversed this dysregulation. GXV also decreased the up-regulated Vimentin level in pathological ventricular remodeling. Moreover, the interaction of Vimentin and TGF-β1 was confirmed by co-immunoprecipitation, and GXV impeded this interaction. CONCLUSION We showed that the interaction of Vimentin and TGF-β1 may be a novel target for ventricular remodeling and that GXV might be a new agent to fight against ventricular remodeling by targeting TGF-β1 and impeding its interaction with Vimentin.
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Affiliation(s)
- Bo Liang
- Nanjing University of Chinese Medicine, Nanjing, China
| | | | - Rui Li
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Ning Gu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.
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28
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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