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Mathov Y, Nissim-Rafinia M, Leibson C, Galun N, Marques-Bonet T, Kandel A, Liebergal M, Meshorer E, Carmel L. Inferring DNA methylation in non-skeletal tissues of ancient specimens. Nat Ecol Evol 2025; 9:153-165. [PMID: 39567757 PMCID: PMC11726462 DOI: 10.1038/s41559-024-02571-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/01/2024] [Indexed: 11/22/2024]
Abstract
Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.
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Affiliation(s)
- Yoav Mathov
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chen Leibson
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Galun
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arye Kandel
- Orthopedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Meir Liebergal
- Orthopedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Lu H, Wang Y, Chaudhary S, Balaga V, Ke H, Shi F, Liu J, Huo Y, Romanienko PJ, Xia B, De S, Chan CS, Shen Z. Medulloblastomas Initiated by Homologous Recombination Defects in Mice. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:2007-2022. [PMID: 39168365 PMCID: PMC11816638 DOI: 10.1016/j.ajpath.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/08/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024]
Abstract
Germline mutations of homologous-recombination (HR) genes are among the top contributors to medulloblastomas. A significant portion of human medulloblastomas exhibit genomic signatures of HR defects. Whether ablation of Brca2 and Palb2, and their related Brca1 and Bccip genes, in the mouse brain can differentially initiate medulloblastomas was explored here. Conditional knockout mouse models of these HR genes and a conditional knockdown of Bccip (shBccip-KD) were established. Deletion of any of these genes led to microcephaly and neurologic defects, with Brca1- and Bccip- producing the worst defects. Trp53 co-deletion significantly rescued the microcephaly with Brca1, Palb2, and Brca2 deficiency but exhibited limited impact on Bccip- mice. For the first time, inactivation of either Brca1 or Palb2 with Trp53 was found to induce medulloblastomas. Despite shBccip-CKD being highly penetrative, Bccip/Trp53 deletions failed to induce medulloblastomas. The tumors displayed diverse immunohistochemical features and chromosome copy number variation. Although there were widespread up-regulations of cell proliferative pathways, most of the tumors expressed biomarkers of the sonic hedgehog subgroup. The medulloblastomas developed from Brca1-, Palb2-, and Brca2- mice were highly sensitive to a poly (ADP-ribose) polymerase inhibitor but not the ones from shBccip-CKD mice. These models recapitulate the spontaneous medulloblastoma development with high penetrance and a narrow time window, providing ideal platforms to test therapeutic agents with the ability to differentiate HR-defective and HR-proficient tumors.
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Affiliation(s)
- Huimei Lu
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Yuan Wang
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Shipra Chaudhary
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Varshita Balaga
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Hua Ke
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Fuqian Shi
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Jingmei Liu
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Yanying Huo
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | | | - Bing Xia
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Chang S Chan
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey; Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey.
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Gonçalves JIB, de Castro VR, Martins WA, Xavier FAC, Da Costa JC, Neto EP, Palmini A, Marinowic DR. Case Report: Molecular Analyses of Cell-Cycle-Related Genes in Cortical Brain Tissue of a Patient with Rasmussen Encephalitis. Int J Mol Sci 2024; 25:8487. [PMID: 39126055 PMCID: PMC11313535 DOI: 10.3390/ijms25158487] [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: 06/26/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Rasmussen's encephalitis (RE) stands as a rare neurological disorder marked by progressive cerebral hemiatrophy and epilepsy resistant to medical treatment. Despite extensive study, the primary cause of RE remains elusive, while its histopathological features encompass cortical inflammation, neuronal degeneration, and gliosis. The underlying molecular mechanisms driving disease progression remain largely unexplored. In this case study, we present a patient with RE who underwent hemispherotomy and has remained seizure-free for over six months, experiencing gradual motor improvement. Furthermore, we conducted molecular analysis on the excised brain tissue, unveiling a decrease in the expression of cell-cycle-associated genes coupled with elevated levels of BDNF and TNF-α proteins. These findings suggest the potential involvement of cell cycle regulators in the progression of RE.
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Affiliation(s)
| | - Vinicius Rosa de Castro
- Graduate Program in Medicine and Health Sciences, Medical School, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil;
- Epilepsy Surgery Program, Saint Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-001, Brazil; (W.A.M.); (E.P.N.); (A.P.)
| | - William Alves Martins
- Epilepsy Surgery Program, Saint Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-001, Brazil; (W.A.M.); (E.P.N.); (A.P.)
| | | | - Jaderson Costa Da Costa
- Brain Institute of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (J.I.B.G.); (F.A.C.X.); (J.C.D.C.)
- Graduate Program in Medicine and Health Sciences, Medical School, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil;
| | - Eliseu Paglioli Neto
- Epilepsy Surgery Program, Saint Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-001, Brazil; (W.A.M.); (E.P.N.); (A.P.)
| | - André Palmini
- Epilepsy Surgery Program, Saint Lucas Hospital, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90610-001, Brazil; (W.A.M.); (E.P.N.); (A.P.)
| | - Daniel Rodrigo Marinowic
- Brain Institute of Rio Grande do Sul, Porto Alegre 90610-000, Brazil; (J.I.B.G.); (F.A.C.X.); (J.C.D.C.)
- Graduate Program in Medicine and Health Sciences, Medical School, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre 90619-900, Brazil;
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Lu Q, Zhou Y, Qian Q, Chen Z, Tan Q, Chen H, Yin F, Wang Y, Liu Z, Tian P, Sun D. Whole-exome sequencing identifies high-confidence genes for tic disorders in a Chinese Han population. Clin Chim Acta 2024; 561:119759. [PMID: 38880274 DOI: 10.1016/j.cca.2024.119759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/23/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Tic disorder (TD) is a polygenic neurodevelopmental disorder with high susceptibility. However, identifying high-confidence risk genes has been challenging due to poor replication across multiple studies. METHODS Whole-exome sequencing was performed on 390 TD patients and 372 unaffected individuals in a Chinese Han population. Analysis of variance, burden analysis and in silico prediction were used to identify candidate genes for TD. To facilitate data analysis and to focus on high-confidence genes, we defined a panel of 160 genes as known causal or candidate TD genes from previous studies. Gene enrichment and protein-protein interaction analysis were utilized to detect potential novel TD risk genes. RESULTS Totally, 14 variants across 12 known TD candidate genes were considered potential susceptibility variants. Ten variants across 10 known TD candidate genes were identified as potential disease-causing variants. Burden analysis identified variants of 28 known genes were significantly excess in TD patients. In addition, 354 previously unproven TD genes are over-represented in patients. Genes enriched in the PI3K-Akt signaling, sphingolipid metabolism and serotonergic synaptic pathways, as well as those interacting with FN1, were considered potential new candidate genes for TD. CONCLUSIONS This is the largest WES study focusing on TD patients in a Chinese Han population. Several variants recurring in our cohort were identified as high-confidence risk loci for TD. Moreover, we provided potential new risk genes that may be prioritized for further investigation.
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Affiliation(s)
- Qing Lu
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yong Zhou
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Qiaoqiao Qian
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhigang Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China
| | - Qianqian Tan
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Haiyun Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Fan Yin
- Puluo (Wuhan) Medical Biotechnology Co., LTD, Wuhan 430070, China; Department of Marketing, Wuhan Kindstar Clinical Diagnostic Institute Co., Ltd., Wuhan 430000, China
| | - Yue Wang
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Peichao Tian
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Dan Sun
- Department of Neurology, Wuhan Children's Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
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5
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He J, Kou SH, Li J, Ding X, Wang SM. Pathogenic variants in human DNA damage repair genes mostly arose after the latest human out-of-Africa migration. Front Genet 2024; 15:1408952. [PMID: 38948361 PMCID: PMC11211533 DOI: 10.3389/fgene.2024.1408952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction The DNA damage repair (DDR) system in human genome is pivotal in maintaining genomic integrity. Pathogenic variation (PV) in DDR genes impairs their function, leading to genome instability and increased susceptibility to diseases, especially cancer. Understanding the evolution origin and arising time of DDR PV is crucial for comprehending disease susceptibility in modern humans. Methods We used big data approach to identify the PVs in DDR genes in modern humans. We mined multiple genomic databases derived from 251,214 modern humans of African and non-Africans. We compared the DDR PVs between African and non-African. We also mined the DDR PVs in the genomic data derived from 5,031 ancient humans. We used the DDR PVs from ancient humans as the intermediate to further the DDR PVs between African and non-African. Results and discussion We identified 1,060 single-base DDR PVs across 77 DDR genes in modern humans of African and non-African. Direct comparison of the DDR PVs between African and non-African showed that 82.1% of the non-African PVs were not present in African. We further identified 397 single-base DDR PVs in 56 DDR genes in the 5,031 ancient humans dated between 45,045 and 100 years before present (BP) lived in Eurasian continent therefore the descendants of the latest out-of-Africa human migrants occurred 50,000-60,000 years ago. By referring to the ancient DDR PVs, we observed that 276 of the 397 (70.3%) ancient DDR PVs were exclusive in non-African, 106 (26.7%) were shared between non-African and African, and only 15 (3.8%) were exclusive in African. We further validated the distribution pattern by testing the PVs in BRCA and TP53, two of the important genes in genome stability maintenance, in African, non-African, and Ancient humans. Our study revealed that DDR PVs in modern humans mostly emerged after the latest out-of-Africa migration. The data provides a foundation to understand the evolutionary basis of disease susceptibility, in particular cancer, in modern humans.
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Affiliation(s)
| | | | | | | | - San Ming Wang
- Department of Public Health and Medical Administration, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, University of Macau, Taipa, China
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6
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Gupta A, Lechpammer M, Brossier NM. Germline BRCA2 pathogenic variants in pediatric ganglioglioma: Case report and review of the literature. Childs Nerv Syst 2024; 40:1609-1612. [PMID: 38168858 DOI: 10.1007/s00381-023-06267-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND BRCA1 and BRCA2 are tumor suppressor genes associated with increased risk of breast and ovarian cancer in adulthood. Patients with germline pathogenic variants in these genes have also been reported to develop brain tumors, although it is unclear whether these syndromes are associated with significant increased risk of brain tumor formation. RESULTS Here, we report a case of a child with germline BRCA2 pathogenic variant presenting with a symptomatic ganglioglioma. To our knowledge, this is the first such patient to be reported. We discuss prior cases of brain tumors in BRCA1/2 patients and evidence for a potential role for BRCA1/2 pathogenic variants in brain tumor formation. CONCLUSION BRCA2 germline variants may increase the risk of developing some types of pediatric brain tumors, but further study is needed to determine its effect on low-grade glioma formation.
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Affiliation(s)
- Anya Gupta
- Departments of Pediatrics, Washington University School of Medicine, Box 8208, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | | | - Nicole M Brossier
- Departments of Pediatrics, Washington University School of Medicine, Box 8208, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.
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Zhao B, Li J, Sinha S, Qin Z, Kou SH, Xiao F, Lei H, Chen T, Cao W, Ding X, Wang SM. Pathogenic variants in human DNA damage repair genes mostly arose in recent human history. BMC Cancer 2024; 24:415. [PMID: 38575974 PMCID: PMC10993466 DOI: 10.1186/s12885-024-12160-6] [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: 09/21/2023] [Accepted: 03/21/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Genome stability is maintained by the DNA damage repair (DDR) system composed of multiple DNA repair pathways of hundreds of genes. Germline pathogenic variation (PV) in DDR genes damages function of the affected DDR genes, leading to genome instability and high risk of diseases, in particular, cancer. Knowing evolutionary origin of the PVs in human DDR genes is essential to understand the etiology of human diseases. However, answer to the issue remains largely elusive. In this study, we analyzed evolutionary origin for the PVs in human DDR genes. METHODS We identified 169 DDR genes by referring to various databases and identified PVs in the DDR genes of modern humans from ClinVar database. We performed a phylogenetic analysis to analyze the conservation of human DDR PVs in 100 vertebrates through cross-species genomic data comparison using the phyloFit program of the PHAST package and visualized the results using the GraphPad Prism software and the ggplot module. We identified DDR PVs from over 5000 ancient humans developed a database to host the DDR PVs ( https://genemutation.fhs.um.edu.mo/dbDDR-AncientHumans ). Using the PV data, we performed a molecular archeological analysis to compare the DDR PVs between modern humans and ancient humans. We analyzed evolution selection of DDR genes across 20 vertebrates using the CodeML in PAML for phylogenetic analysis. RESULTS Our phylogenic analysis ruled out cross-species conservation as the origin of human DDR PVs. Our archeological approach identified rich DDR PVs shared between modern and ancient humans, which were mostly dated within the last 5000 years. We also observed similar pattern of quantitative PV distribution between modern and ancient humans. We further detected a set of ATM, BRCA2 and CHEK2 PVs shared between human and Neanderthals. CONCLUSIONS Our study reveals that human DDR PVs mostly arose in recent human history. We propose that human high cancer risk caused by DDR PVs can be a by-product of human evolution.
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Affiliation(s)
- Bojin Zhao
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Jiaheng Li
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Zixin Qin
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Si Hoi Kou
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Fengxia Xiao
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - Huijun Lei
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Tianhui Chen
- Department of Cancer Prevention, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Wenming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Xiaofan Ding
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
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Drake DM, Afsharian K, Or B, Shapiro AM, Lai ML, Miller L, Wells PG. BRCA1 protein dose-dependent risk for embryonic oxidative DNA damage, embryopathies and neurodevelopmental disorders with and without ethanol exposure. Redox Biol 2024; 70:103070. [PMID: 38359745 PMCID: PMC10877410 DOI: 10.1016/j.redox.2024.103070] [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: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Although widely known as a tumor suppressor, the breast cancer 1 susceptibility protein (BRCA1) is also important in development, where it regulates fetal DNA repair pathways that protect against DNA damage caused by physiological and drug-enhanced levels of reactive oxygen species (ROS). We previously showed that conditional heterozygous (+/-) knockout (cKO) mouse embryos with a minor 28% BRCA1 deficiency developed normally in culture, but when exposed to the ROS-initiating drug, alcohol (ethanol, EtOH), exhibited embryopathies not evident in wild-type (+/+) littermates. Herein, we characterized a directBrca1 +/- knockout (KO) model with a 2-fold greater (58%) reduction in BRCA1 protein vs. the cKO model. We also characterized and compared learning & memory deficits in both the cKO and KO models. Even saline-exposed Brca1 +/- vs. +/+ KO progeny exhibited enhanced oxidative DNA damage and embryopathies in embryo culture and learning & memory deficits in females in vivo, which were not observed in the cKO model, revealing the potential pathogenicity of physiological ROS levels. The embryopathic EtOH concentration for cultured direct KO embryos was half that for cKO embryos, and EtOH affected Brca1 +/+ embryos only in the direct KO model. The spectrum and severity of EtOH embryopathies in culture were greater in both Brca1 +/- vs. +/+ embryos, and direct KO vs. cKO +/- embryos. Motor coordination deficits were evident in both male and female Brca1 +/- KO progeny exposed in utero to EtOH. The results in our direct KO model with a greater BRCA1 deficiency vs. cKO mice provide the first evidence for BRCA1 protein dose-dependent susceptibility to developmental disorders caused by physiological and drug-enhanced oxidative stress.
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Affiliation(s)
- Danielle M Drake
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Kian Afsharian
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Or
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aaron M Shapiro
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Michelle L Lai
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lutfiya Miller
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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9
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Huang LC, McKeown CR, He HY, Ta AC, Cline HT. BRCA1 and ELK-1 regulate neural progenitor cell fate in the optic tectum in response to visual experience in Xenopus laevis tadpoles. Proc Natl Acad Sci U S A 2024; 121:e2316542121. [PMID: 38198524 PMCID: PMC10801852 DOI: 10.1073/pnas.2316542121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
In developing Xenopus tadpoles, the optic tectum begins to receive patterned visual input while visuomotor circuits are still undergoing neurogenesis and circuit assembly. This visual input regulates neural progenitor cell fate decisions such that maintaining tadpoles in the dark increases proliferation, expanding the progenitor pool, while visual stimulation promotes neuronal differentiation. To identify regulators of activity-dependent neural progenitor cell fate, we profiled the transcriptomes of proliferating neural progenitor cells and newly differentiated neurons using RNA-Seq. We used advanced bioinformatic analysis of 1,130 differentially expressed transcripts to identify six differentially regulated transcriptional regulators, including Breast Cancer 1 (BRCA1) and the ETS-family transcription factor, ELK-1, which are predicted to regulate the majority of the other differentially expressed transcripts. BRCA1 is known for its role in cancers, but relatively little is known about its potential role in regulating neural progenitor cell fate. ELK-1 is a multifunctional transcription factor which regulates immediate early gene expression. We investigated the potential functions of BRCA1 and ELK-1 in activity-regulated neurogenesis in the tadpole visual system using in vivo time-lapse imaging to monitor the fate of GFP-expressing SOX2+ neural progenitor cells in the optic tectum. Our longitudinal in vivo imaging analysis showed that knockdown of either BRCA1 or ELK-1 altered the fates of neural progenitor cells and furthermore that the effects of visual experience on neurogenesis depend on BRCA1 and ELK-1 expression. These studies provide insight into the potential mechanisms by which neural activity affects neural progenitor cell fate.
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Affiliation(s)
- Lin-Chien Huang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Caroline R. McKeown
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Hai-Yan He
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Aaron C. Ta
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
| | - Hollis T. Cline
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA92037
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10
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Drake DM, Zhen D, Kerrebijn I, Or B, Gao S, Afsharian K, Tran J, Bhatia S, Cheng A, Wells PG. Breast cancer 1 (BRCA1) protection in altered gene expression and neurodevelopmental disorders due to physiological and ethanol-enhanced reactive oxygen species formation. Free Radic Biol Med 2023; 208:272-284. [PMID: 37541454 DOI: 10.1016/j.freeradbiomed.2023.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/08/2023] [Accepted: 08/02/2023] [Indexed: 08/06/2023]
Abstract
The breast cancer 1 (Brca1) susceptibility gene regulates the repair of reactive oxygen species (ROS)-mediated DNA damage, which is implicated in neurodevelopmental disorders. Alcohol (ethanol, EtOH) exposure during pregnancy causes fetal alcohol spectrum disorders (FASD), including abnormal brain function, associated with enhanced ROS-initiated DNA damage. Herein, oxidative DNA damage in fetal brains and neurodevelopmental disorders were enhanced in saline-exposed +/- vs. +/+ Brca1 littermates. A single EtOH exposure during gestation further enhanced oxidative DNA damage, altered the expression of developmental/DNA damage response genes in fetal brains, and resulted in neurodevelopmental disorders, all of which were BRCA1-dependent. Pretreatment with the ROS inhibitor phenylbutylnitrone (PBN) blocked DNA damage and some neurodevelopmental disorders in both saline- and EtOH-exposed progeny, corroborating a ROS-dependent mechanism. Fetal BRCA1 protects against altered gene expression and neurodevelopmental disorders caused by both physiological and EtOH-enhanced levels of ROS formation. BRCA1 deficiencies may enhance the risk for FASD.
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Affiliation(s)
- Danielle M Drake
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Danlin Zhen
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Isabel Kerrebijn
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Benjamin Or
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sophie Gao
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Kian Afsharian
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Jason Tran
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Shama Bhatia
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ashley Cheng
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Centre for Pharmaceutical Oncology, Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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11
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Ribeiro JH, Altinisik N, Rajan N, Verslegers M, Baatout S, Gopalakrishnan J, Quintens R. DNA damage and repair: underlying mechanisms leading to microcephaly. Front Cell Dev Biol 2023; 11:1268565. [PMID: 37881689 PMCID: PMC10597653 DOI: 10.3389/fcell.2023.1268565] [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: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
DNA-damaging agents and endogenous DNA damage constantly harm genome integrity. Under genotoxic stress conditions, the DNA damage response (DDR) machinery is crucial in repairing lesions and preventing mutations in the basic structure of the DNA. Different repair pathways are implicated in the resolution of such lesions. For instance, the non-homologous DNA end joining and homologous recombination pathways are central cellular mechanisms by which eukaryotic cells maintain genome integrity. However, defects in these pathways are often associated with neurological disorders, indicating the pivotal role of DDR in normal brain development. Moreover, the brain is the most sensitive organ affected by DNA-damaging agents compared to other tissues during the prenatal period. The accumulation of lesions is believed to induce cell death, reduce proliferation and premature differentiation of neural stem and progenitor cells, and reduce brain size (microcephaly). Microcephaly is mainly caused by genetic mutations, especially genes encoding proteins involved in centrosomes and DNA repair pathways. However, it can also be induced by exposure to ionizing radiation and intrauterine infections such as the Zika virus. This review explains mammalian cortical development and the major DNA repair pathways that may lead to microcephaly when impaired. Next, we discuss the mechanisms and possible exposures leading to DNA damage and p53 hyperactivation culminating in microcephaly.
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Affiliation(s)
- Jessica Honorato Ribeiro
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nazlican Altinisik
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Nicholas Rajan
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jay Gopalakrishnan
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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12
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Kou SH, Li J, Tam B, Lei H, Zhao B, Xiao F, Wang S. TP53 germline pathogenic variants in modern humans were likely originated during recent human history. NAR Cancer 2023; 5:zcad025. [PMID: 37304756 PMCID: PMC10251638 DOI: 10.1093/narcan/zcad025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
TP53 is crucial for maintaining genome stability and preventing oncogenesis. Germline pathogenic variation in TP53 damages its function, causing genome instability and increased cancer risk. Despite extensive study in TP53, the evolutionary origin of the human TP53 germline pathogenic variants remains largely unclear. In this study, we applied phylogenetic and archaeological approaches to identify the evolutionary origin of TP53 germline pathogenic variants in modern humans. In the phylogenic analysis, we searched 406 human TP53 germline pathogenic variants in 99 vertebrates distributed in eight clades of Primate, Euarchontoglires, Laurasiatheria, Afrotheria, Mammal, Aves, Sarcopterygii and Fish, but we observed no direct evidence for the cross-species conservation as the origin; in the archaeological analysis, we searched the variants in 5031 ancient human genomes dated between 45045 and 100 years before present, and identified 45 pathogenic variants in 62 ancient humans dated mostly within the last 8000 years; we also identified 6 pathogenic variants in 3 Neanderthals dated 44000 to 38515 years before present and 1 Denisovan dated 158 550 years before present. Our study reveals that TP53 germline pathogenic variants in modern humans were likely originated in recent human history and partially inherited from the extinct Neanderthals and Denisovans.
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Affiliation(s)
- Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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13
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Leung E, Taskina D, Schwab N, Hazrati LN. BRCA1 heterozygosity promotes DNA damage-induced senescence in a sex-specific manner following repeated mild traumatic brain injury. Front Neurosci 2023; 17:1225226. [PMID: 37638313 PMCID: PMC10450634 DOI: 10.3389/fnins.2023.1225226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Emerging evidence suggests cellular senescence, as a consequence of excess DNA damage and deficient repair, to be a driver of brain dysfunction following repeated mild traumatic brain injury (rmTBI). This study aimed to further investigate the role of deficient DNA repair, specifically BRCA1-related repair, on DNA damage-induced senescence. BRCA1, a repair protein involved in maintaining genomic integrity with multiple roles in the central nervous system, was previously reported to be significantly downregulated in post-mortem brains with a history of rmTBI. Here we examined the effects of impaired BRCA1-related repair on DNA damage-induced senescence and outcomes 1-week post-rmTBI using mice with a heterozygous knockout for BRCA1 in a sex-segregated manner. Altered BRCA1 repair with rmTBI resulted in altered anxiety-related behaviours in males and females using elevated zero maze and contextual fear conditioning. Evaluating molecular markers associated with DNA damage signalling and senescence-related pathways revealed sex-specific differences attributed to BRCA1, where females exhibited elevated DNA damage, impaired DNA damage signalling, and dampened senescence onset compared to males. Overall, the results from this study highlight sex-specific consequences of aberrant DNA repair on outcomes post-injury, and further support a need to develop sex-specific treatments following rmTBI.
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Affiliation(s)
- Emily Leung
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daria Taskina
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nicole Schwab
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lili-Naz Hazrati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
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14
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Chian JS, Li J, Wang SM. Evolutionary Origin of Human PALB2 Germline Pathogenic Variants. Int J Mol Sci 2023; 24:11343. [PMID: 37511102 PMCID: PMC10379391 DOI: 10.3390/ijms241411343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary origin of human PALB2 variants will promote a deeper understanding of the biological basis of PALB2 germline variation and its roles in human diseases. We tested the evolution origin for 1444 human PALB2 germline variants, including 484 pathogenic and 960 benign variants. We performed a phylogenic analysis by tracing the variants in 100 vertebrates. However, we found no evidence to show that cross-species conservation was the origin of PALB2 germline pathogenic variants, but it is indeed a rich source for PALB2 germline benign variants. We performed a paleoanthropological analysis by tracing the variants in over 5000 ancient humans. We identified 50 pathogenic in 71 ancient humans dated from 32,895 to 689 before the present, of which 90.1% were dated within the recent 10,000 years. PALB2 benign variants were also highly shared with ancient humans. Data from our study reveal that human PALB2 pathogenic variants mostly arose in recent human history.
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Affiliation(s)
- Jia Sheng Chian
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao
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15
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Qin Z, Li J, Tam B, Sinha S, Zhao B, Bhaskaran SP, Huang T, Wu X, Chian JS, Guo M, Kou SH, Lei H, Zhang L, Wang X, Lagniton PNP, Xiao F, Jiang X, Wang SM. Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population. Int J Cancer 2023; 152:1159-1173. [PMID: 36385461 PMCID: PMC10098510 DOI: 10.1002/ijc.34359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.
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Affiliation(s)
- Zixin Qin
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Shanmuga Priya Bhaskaran
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Teng Huang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaobing Wu
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jia Sheng Chian
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Maoni Guo
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Li Zhang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaoyu Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Philip Naderev P Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xinyang Jiang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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16
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Wang SM. A global perspective on the ethnic-specific BRCA variation and its implication in clinical application. JOURNAL OF THE NATIONAL CANCER CENTER 2023; 3:14-20. [PMID: 39036311 PMCID: PMC11256725 DOI: 10.1016/j.jncc.2022.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Pathogenic BRCA1 and BRCA2 (BRCA) variation is the genetic predisposition for high cancer risk affecting mostly breast and ovarian. BRCA variation information is widely used in clinical diagnosis, treatment, and prevention of BRCA-related cancer. The positive selection imposed on human BRCA leads to highly ethnic-specific BRCA variation to adapt different living environment on earth. Most of the human BRCA variants identified so far were from the European descendant populations and used as the standard reference for global human populations, whereas BRCA variation in other ethnic populations remains poorly characterized. This review addresses the origin of ethnic-specific BRCA variation, the importance of ethnic-specific BRCA variation in clinical application, the limitation of current BRCA variation data, and potential solutions to fill the gap.
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Affiliation(s)
- San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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17
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Bonfiglio F, Lasorsa VA, Cantalupo S, D'Alterio G, Aievola V, Boccia A, Ardito M, Furini S, Renieri A, Morini M, Stainczyk S, Westermann F, Paolella G, Eva A, Iolascon A, Capasso M. Inherited rare variants in homologous recombination and neurodevelopmental genes are associated with increased risk of neuroblastoma. EBioMedicine 2022; 87:104395. [PMID: 36493725 PMCID: PMC9732128 DOI: 10.1016/j.ebiom.2022.104395] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common solid extracranial paediatric tumour. Genome-wide association studies have driven the discovery of common risk variants, but no large study has investigated the contribution of rare variants to NB susceptibility. Here, we conducted a whole-exome sequencing (WES) of 664 NB cases and 822 controls and used independent validation datasets to identify genes with rare risk variants and involved pathways. METHODS WES was performed at 50× depth and variants were jointly called in cases and controls. We developed two models to identify mutations with high clinical impact (P/LP model) and to discover less penetrant risk mutations affecting non-canonical cancer pathways (RPV model). We performed a gene-level collapsing test using Firth's logistic regression in 242 selected cancer predisposition genes (CPGs) and a gene-sets burden analysis of biologically-informed pathways. FINDINGS Twelve percent of patients carried P/LP variants in CPGs and showed a significant enrichment (P = 2.3 × 10-4) compared to controls (6%). We identified P/LP variants in 45 CPGs enriched in homologous recombination (HR) pathway. The most P/LP enriched genes in NB were BRCA1, ALK and RAD51C. Additionally, we found higher RPV burden in gene-sets of neuron differentiation, neural tube development and synapse assembly, and in gene-sets associated with neurodevelopmental disorders (NDD). INTERPRETATION The high fraction of NB patients with P/LP variants indicates the need of genetic counselling. Furthermore, inherited rare variants predispose to NB development by affecting mechanisms related to HR and neurodevelopmental processes, and demonstrate that NDD genes are altered in NB at the germline level. FUNDING Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Lotta al Neuroblastoma, Associazione Oncologia Pediatrica e Neuroblastoma, Regione Campania, Associazione Giulio Adelfio onlus, and Italian Health Ministry.
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Affiliation(s)
- Ferdinando Bonfiglio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
| | - Vito Alessandro Lasorsa
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Sueva Cantalupo
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe D'Alterio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,European School of Medical Medicine, University of Milan, Milan, Italy
| | - Vincenzo Aievola
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Martina Ardito
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabine Stainczyk
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy,Corresponding author. Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Via Gaetano Salvatore 486, 80145 Napoli, Italy.
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18
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Ma C, Li C, Ma H, Yu D, Zhang Y, Zhang D, Su T, Wu J, Wang X, Zhang L, Chen CL, Zhang YE. Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum. Genome Biol 2022; 23:251. [PMID: 36474250 PMCID: PMC9724437 DOI: 10.1186/s13059-022-02821-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend to promote tumorigenesis, while the molecular atavism hypothesis predicts that PSGs involved in tumors may represent recently derived duplicates of unicellular genes. However, these predictions have not been tested. RESULTS By taking advantage of pan-cancer genomic data, we find the upregulation of PSGs across 13 cancer types, which is facilitated by copy-number gain and promoter hypomethylation. Meta-analyses indicate that upregulated PSGs (uPSGs) tend to promote tumorigenesis and to play cell cycle-related roles. The cell cycle-related uPSGs predominantly represent derived duplicates of unicellular genes. We prioritize 15 uPSGs and perform an in-depth analysis of one unicellular gene-derived duplicate involved in the cell cycle, DDX11. Genome-wide screening data and knockdown experiments demonstrate that DDX11 is broadly essential across cancer cell lines. Importantly, non-neutral amino acid substitution patterns and increased expression indicate that DDX11 has been under positive selection. Finally, we find that cell cycle-related uPSGs are also preferentially upregulated in the highly proliferative embryonic cerebrum. CONCLUSIONS Consistent with the predictions of the atavism and antagonistic pleiotropy hypotheses, primate-specific genes, especially those PSGs derived from cell cycle-related genes that emerged in unicellular ancestors, contribute to the early proliferation of the human cerebrum at the cost of hitchhiking by similarly highly proliferative cancer cells.
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Affiliation(s)
- Chenyu Ma
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Li
- School of Engineering Medicine, Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), and Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100191, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufei Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Dan Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianhan Su
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, 75005, Paris, France
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Chinese Institute for Brain Research, Beijing, 102206, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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19
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Shu S, Fu M, Chen X, Zhang N, Zhao R, Chang Y, Cui H, Liu Z, Wang X, Hua X, Li Y, Wang X, Wang X, Feng W, Song J. Cellular Landscapes of Nondiseased Human Cardiac Valves From End-Stage Heart Failure-Explanted Heart. Arterioscler Thromb Vasc Biol 2022; 42:1429-1446. [PMID: 36200446 DOI: 10.1161/atvbaha.122.318314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Exploring the mechanisms of valvular heart disease at the cellular level may be useful to identify new therapeutic targets; however, the comprehensive cellular landscape of nondiseased human cardiac valve leaflets remains unclear. METHODS The cellular landscapes of nondiseased human cardiac valve leaflets (5 aortic valves, 5 pulmonary valves, 5 tricuspid valves, and 3 mitral valves) from end-stage heart failure patients undergoing heart transplantation were explored using single-cell RNA sequencing. Bioinformatics was used to identify the cell types, describe the cell functions, and investigate cellular developmental trajectories and interactions. Differences among the 4 types of cardiac valves at the cellular level were summarized. Pathological staining was performed to validate the key findings of single-cell RNA sequencing. An integrative analysis of our single-cell data and published genome-wide association study-based and bulk RNA sequencing-based data provided insights into the cell-specific contributions to calcific aortic valve diseases. RESULTS Six cell types were identified among 128 412 cells from nondiseased human cardiac valve leaflets. Valvular interstitial cells were the largest population, followed by myeloid cells, lymphocytes, valvular endothelial cells, mast cells, and myofibroblasts. The 4 types of cardiac valve had distinct cellular compositions. The intercellular communication analysis revealed that valvular interstitial cells were at the center of the communication network. The integrative analysis of our single-cell RNA sequencing data revealed key cellular subpopulations involved in the pathogenesis of calcific aortic valve diseases. CONCLUSIONS The cellular landscape differed among the 4 types of nondiseased cardiac valve, which might explain their differences in susceptibility to pathological remodeling and valvular heart disease.
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Affiliation(s)
- Songren Shu
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengxia Fu
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Chen
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruojin Zhao
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Chang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Cui
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zirui Liu
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohu Wang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiumeng Hua
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Li
- Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xianqiang Wang
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Feng
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease (S.S., M.F., X.C., N.Z., R.Z., Y.C., H.C., Z.L., Xiaohu Wang, X.H., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,The Cardiomyopathy Research Group (S.S., M.F., X.C., Y.C., H.C., Z.L., X.H., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Cardiovascular Surgery (Y.L., Xin Wang, Xianqiang Wang, W.F., J.S.), Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen' China (J.S.)
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20
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Zhuang J, Chen P, Wu Y, Luo Q, Wang Q, Chen S, Chen X, Jiang Z, Qiu J, Li Y, Yuan Z, Zhuang J. Brca1 Is Regulated by the Transcription Factor Gata3, and Its Silencing Promotes Neural Differentiation in Retinal Neurons. Int J Mol Sci 2022; 23:ijms232213860. [PMID: 36430332 PMCID: PMC9694312 DOI: 10.3390/ijms232213860] [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: 10/01/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Previous studies have indicated that Brca1 (Breast cancer suppressor gene 1) plays an important role in neural development and degenerative diseases. However, the bioactivity and regulatory mechanism of Brca1 expression in retinal neurocytes remain unclear. In the present study, our data indicated that Brca1 maintains the state of neuronal precursor cells. Brca1 silencing induces differentiation in 661W cells. Nestin, a marker of precursor cells, was significantly decreased in parallel with Brca1 silencing in 661W cells, whereas Map2 (Microtubule associated protein 2), a marker of differentiated neurons, was significantly increased. Neurite outgrowth was increased by ~4.0-fold in Brca1-silenced cells. Moreover, DNA affinity purification assays and ChIP assays demonstrated that Gata3 (GATA binding protein 3) regulates Brca1 transcription in 661W cells. Silencing or overexpressing Gata3 could significantly regulate the expression of Brca1 and affect its promoter inducibility. Furthermore, the expression of Gata3 generally occurred in parallel with that of Brca1 in developing mouse retinas. Both Gata3 and Brca1 are expressed in the neonatal mouse retina but are developmentally silenced with age. Exogenous Gata3 significantly inhibited neural activity by decreasing synaptophysin and neurite outgrowth. Thus, this study demonstrated that Brca1 is transcriptionally regulated by Gata3. Brca1/Gata3 silencing is involved in neuronal differentiation and maturation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhaohui Yuan
- Correspondence: (Z.Y.); (J.Z.); Tel.: +86-20-6667-8735 (J.Z.); Fax: +86-20-8733-3271 (J.Z.)
| | - Jing Zhuang
- Correspondence: (Z.Y.); (J.Z.); Tel.: +86-20-6667-8735 (J.Z.); Fax: +86-20-8733-3271 (J.Z.)
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21
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Qin Z, Huang T, Guo M, Wang SM. Distinct landscapes of deleterious variants in DNA damage repair system in ethnic human populations. Life Sci Alliance 2022; 5:5/9/e202101319. [PMID: 35595529 PMCID: PMC9122833 DOI: 10.26508/lsa.202101319] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/03/2022] Open
Abstract
Deleterious variants in the DNA damage repair system can cause genome instability and increase cancer risk. The highly ethnic-specific DDR deleterious variation from this study suggests its potential relationship with different disease susceptibility in ethnic human populations. Deleterious variants in DNA damage repair (DDR) system can cause genome instability and increase cancer risk. In this study, we analyzed the deleterious variants in DDR system in 16 ethnic human populations. From the genetic variants in 169 DDR genes involved in nine DDR pathways collected from 158,612 individuals of different ethnic background, we identified 1,781 deleterious variants in 81 DDR genes in eight DDR pathways (https://genemutation.fhs.um.edu.mo/dbddr-global/). Our analysis showed although the quantity of deleterious variants was loaded at a similar level, the landscape of the variants differed substantially among different populations that two-third of the variants were present in single ethnic populations, and the rest was mostly shared between the populations with closer geographic and genetic relationship. The highly ethnic-specific DDR deleterious variation suggests its potential relationship with different disease susceptibility in ethnic human populations.
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Affiliation(s)
- Zixin Qin
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
| | - Teng Huang
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
| | - Maoni Guo
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macau, China
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22
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Provasek VE, Mitra J, Malojirao VH, Hegde ML. DNA Double-Strand Breaks as Pathogenic Lesions in Neurological Disorders. Int J Mol Sci 2022; 23:ijms23094653. [PMID: 35563044 PMCID: PMC9099445 DOI: 10.3390/ijms23094653] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
The damage and repair of DNA is a continuous process required to maintain genomic integrity. DNA double-strand breaks (DSBs) are the most lethal type of DNA damage and require timely repair by dedicated machinery. DSB repair is uniquely important to nondividing, post-mitotic cells of the central nervous system (CNS). These long-lived cells must rely on the intact genome for a lifetime while maintaining high metabolic activity. When these mechanisms fail, the loss of certain neuronal populations upset delicate neural networks required for higher cognition and disrupt vital motor functions. Mammalian cells engage with several different strategies to recognize and repair chromosomal DSBs based on the cellular context and cell cycle phase, including homologous recombination (HR)/homology-directed repair (HDR), microhomology-mediated end-joining (MMEJ), and the classic non-homologous end-joining (NHEJ). In addition to these repair pathways, a growing body of evidence has emphasized the importance of DNA damage response (DDR) signaling, and the involvement of heterogeneous nuclear ribonucleoprotein (hnRNP) family proteins in the repair of neuronal DSBs, many of which are linked to age-associated neurological disorders. In this review, we describe contemporary research characterizing the mechanistic roles of these non-canonical proteins in neuronal DSB repair, as well as their contributions to the etiopathogenesis of selected common neurological diseases.
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Affiliation(s)
- Vincent E. Provasek
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
- College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Joy Mitra
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
- Correspondence: (J.M.); (M.L.H.)
| | - Vikas H. Malojirao
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
| | - Muralidhar L. Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (V.H.M.)
- College of Medicine, Texas A&M University, College Station, TX 77843, USA
- Department of Neurosciences, Weill Cornell Medical College, New York, NY 11021, USA
- Correspondence: (J.M.); (M.L.H.)
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23
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Li J, Zhao B, Huang T, Qin Z, Wang SM. Human BRCA pathogenic variants were originated during recent human history. Life Sci Alliance 2022; 5:5/5/e202101263. [PMID: 35165121 PMCID: PMC8860097 DOI: 10.26508/lsa.202101263] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/05/2023] Open
Abstract
BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.
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Affiliation(s)
- Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Bojin Zhao
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Teng Huang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Zixin Qin
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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24
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Ferdousi F, Furuya K, Sasaki K, Zheng YW, Oda T, Isoda H. DNA Microarray-Based Global Gene Expression Profiling in Human Amniotic Epithelial Cells Predicts the Potential of Microalgae-Derived Squalene for the Nervous System and Metabolic Health. Biomedicines 2021; 10:48. [PMID: 35052729 PMCID: PMC8772846 DOI: 10.3390/biomedicines10010048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 01/19/2023] Open
Abstract
In recent years, perinatal stem cells, such as human amniotic epithelial cells (hAECs), have attracted increasing interest as a novel tool of stem cell-based high-throughput drug screening. In the present study, we investigated the bioactivities of squalene (SQ) derived from ethanol extract (99.5%) of a microalgae Aurantiochytrium Sp. (EEA-SQ) in hAECs using whole-genome DNA microarray analysis. Tissue enrichment analysis showed that the brain was the most significantly enriched tissue by the differentially expressed genes (DEGs) between EEA-SQ-treated and control hAECs. Further gene set enrichment analysis and tissue-specific functional analysis revealed biological functions related to nervous system development, neurogenesis, and neurotransmitter modulation. Several adipose tissue-specific genes and functions were also enriched. Gene-disease association analysis showed nervous system-, metabolic-, and immune-related diseases were enriched. Altogether, our study suggests the potential health benefits of microalgae-derived SQ and we would further encourage investigation in EEA-SQ and its derivatives as potential therapeutics for nervous system- and metabolism-related diseases.
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Affiliation(s)
- Farhana Ferdousi
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba 305-8572, Japan; (F.F.); (K.S.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8575, Japan
- AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba 305-8572, Japan; (Y.-W.Z.); (T.O.)
| | - Kinji Furuya
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba 305-0005, Japan;
| | - Kazunori Sasaki
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba 305-8572, Japan; (F.F.); (K.S.)
- AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba 305-8572, Japan; (Y.-W.Z.); (T.O.)
| | - Yun-Wen Zheng
- AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba 305-8572, Japan; (Y.-W.Z.); (T.O.)
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba 305-0005, Japan;
| | - Tatsuya Oda
- AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba 305-8572, Japan; (Y.-W.Z.); (T.O.)
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba 305-0005, Japan;
| | - Hiroko Isoda
- Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba 305-8572, Japan; (F.F.); (K.S.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8575, Japan
- AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), University of Tsukuba, Tsukuba 305-8572, Japan; (Y.-W.Z.); (T.O.)
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25
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Yoshida R. Hereditary breast and ovarian cancer (HBOC): review of its molecular characteristics, screening, treatment, and prognosis. Breast Cancer 2021; 28:1167-1180. [PMID: 32862296 PMCID: PMC8514387 DOI: 10.1007/s12282-020-01148-2] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022]
Abstract
Breast cancer is a common cancer affecting a large number of patients. Notably, 5-10% of all breast cancer patients are genetically predisposed to cancers. Although the most common breast cancer susceptibility genes are BRCA1 and BRCA2, which are also associated with the risk of developing ovarian and pancreatic cancer, advances in next-generation sequencing (NGS) analysis technology enabled the discovery of several non-BRCA genes responsible for breast and ovarian cancers. Studies on hereditary breast and ovarian cancer (HBOC) involve not only determining the predisposition to developing cancer, but also considering the current treatment for breast cancer, prevention of next cancer, risk diagnosis, and adoption of protective measures for relatives. We present a comprehensive review of HBOC, which will be a useful resource in the clinical setting. Many hereditary tumors, including HBOC, are syndromes characterized by the development of different types of cancer in succession. Taking advantage of knowing predisposition of susceptibility to cancer, it is important to continue and update cancer management protocols, which includes the adoption of preventive measures, countermeasures, and treatments, to accurately assess and prevent the impact of cancer on the quality of life of the next generation of patients.
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Affiliation(s)
- Reiko Yoshida
- Showa University Advanced Cancer Translational Research Institute, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan.
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26
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Akagawa R, Nabeshima YI, Kawauchi T. Alternative Functions of Cell Cycle-Related and DNA Repair Proteins in Post-mitotic Neurons. Front Cell Dev Biol 2021; 9:753175. [PMID: 34746147 PMCID: PMC8564117 DOI: 10.3389/fcell.2021.753175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Proper regulation of neuronal morphological changes is essential for neuronal migration, maturation, synapse formation, and high-order function. Many cytoplasmic proteins involved in the regulation of neuronal microtubules and the actin cytoskeleton have been identified. In addition, some nuclear proteins have alternative functions in neurons. While cell cycle-related proteins basically control the progression of the cell cycle in the nucleus, some of them have an extra-cell cycle-regulatory function (EXCERF), such as regulating cytoskeletal organization, after exit from the cell cycle. Our expression analyses showed that not only cell cycle regulators, including cyclin A1, cyclin D2, Cdk4/6, p21cip1, p27kip1, Ink4 family, and RAD21, but also DNA repair proteins, including BRCA2, p53, ATM, ATR, RAD17, MRE11, RAD9, and Hus1, were expressed after neurogenesis, suggesting that these proteins have alternative functions in post-mitotic neurons. In this perspective paper, we discuss the alternative functions of the nuclear proteins in neuronal development, focusing on possible cytoplasmic roles.
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Affiliation(s)
- Remi Akagawa
- Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe (FBRI), Kobe, Japan
| | - Yo-ichi Nabeshima
- Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe (FBRI), Kobe, Japan
| | - Takeshi Kawauchi
- Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe (FBRI), Kobe, Japan
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
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27
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Tarpey MD, Amorese AJ, LaFave ER, Minchew EC, Fisher-Wellman KH, McClung JM, Hvastkovs EG, Spangenburg EE. Skeletal Muscle Function Is Dependent Upon BRCA1 to Maintain Genomic Stability. Exerc Sport Sci Rev 2021; 49:267-273. [PMID: 34091499 PMCID: PMC8495729 DOI: 10.1249/jes.0000000000000265] [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: 11/21/2022]
Abstract
Breast Cancer gene 1 (BRCA1) is a large, multifunctional protein that regulates a variety of mechanisms in multiple different tissues. Our work established that Brca1 is expressed in skeletal muscle and localizes to the mitochondria and nucleus. Here, we propose BRCA1 expression is critical for the maintenance of force production and mitochondrial respiration in skeletal muscle.
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Affiliation(s)
- Michael D. Tarpey
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Adam J. Amorese
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Elizabeth R. LaFave
- East Carolina University, Department of Chemistry, 300 Science and Technology Bldg., Greenville, NC 27858
| | - Everett C. Minchew
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
| | - Kelsey H. Fisher-Wellman
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
| | - Joseph M. McClung
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
| | - Eli G. Hvastkovs
- East Carolina University, Department of Chemistry, 300 Science and Technology Bldg., Greenville, NC 27858
| | - Espen E. Spangenburg
- East Carolina University, Department of Physiology, Brody School of Medicine, Greenville, NC 27834
- East Carolina Diabetes and Obesity Institute, 115 Heart Dr, East Carolina University, Greenville NC, 27834
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28
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Drake DM, Wells PG. Novel mechanisms in alcohol neurodevelopmental disorders via BRCA1 depletion and BRCA1-dependent NADPH oxidase regulation. Redox Biol 2021; 48:102148. [PMID: 34736119 PMCID: PMC8577473 DOI: 10.1016/j.redox.2021.102148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/27/2022] Open
Abstract
The breast cancer 1 protein (BRCA1) facilitates DNA repair, preventing embryolethality and protecting the fetus from reactive oxygen species (ROS)-induced developmental disorders mediated by oxidatively damaged DNA. Alcohol (ethanol, EtOH) exposure during pregnancy causes fetal alcohol spectrum disorders (FASD), characterized by aberrant behaviour and enhanced ROS formation and proteasomal protein degradation. Herein, ROS-producing NADPH oxidase (NOX) activity was higher in Brca1 +/- vs. +/+ fetal and adult brains, and further enhanced by a single EtOH exposure. EtOH also enhanced catalase and proteasomal activities, while conversely reducing BRCA1 protein levels without affecting Brca1 gene expression. EtOH-initiated adaptive postnatal freezing behaviour was lost in Brca1 +/- progeny. Pretreatment with the free radical spin trap and ROS inhibitor phenylbutylnitrone blocked all EtOH effects, suggesting ROS-dependent mechanisms. This is the first in vivo evidence of NOX regulation by BRCA1, and of EtOH-induced, ROS-mediated depletion of BRCA1, revealing novel mechanisms of BRCA1 protection in FASD.
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Affiliation(s)
- Danielle M Drake
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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29
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Wang X, Wang SM. DNA damage repair system in C57BL/6 J mice is evolutionarily stable. BMC Genomics 2021; 22:669. [PMID: 34535077 PMCID: PMC8447752 DOI: 10.1186/s12864-021-07983-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022] Open
Abstract
Background DNA damage repair (DDR) system is vital in maintaining genome stability and survival. DDR consists of over 160 genes in 7 different pathways to repair specific type of DNA damage caused by external and internal damaging factors. The functional importance of DDR system implies that evolution could play important roles in maintaining its functional intactness to perform its function. Indeed, it has been observed that positive selection is present in BRCA1 and BRCA2 (BRCA), which are key genes in homologous recombination pathway of DDR system, in the humans and its close relatives of chimpanzee and bonobos. Efforts have been made to investigate whether the same selection could exist for BRCA in other mammals but found no evidence so far. However, as most of the studies in non-human mammals analyzed only a single or few individuals in the studied species, the observation may not reflect the true status in the given species. Furthermore, few studies have studied evolution selection in other DDR genes except BRCA. In current study, we used laboratory mouse C57BL/6 J as a model to address evolution selection on DDR genes in non-primate mammals by dynamically monitoring genetic variation across 30 generations in C57BL/6 J. Results Using exome sequencing, we collected coding sequences of 169 DDR genes from 44 C57BL/6 J individual genomes in 2018. We compared the coding sequences with the mouse reference genome sequences derived from 1998 C57BL/6 J DNA, and with the mouse Eve6B reference genome sequences derived from 2003 C57BL/6 J DNA, covering 30 generations of C57BL/6 J from 1998 to 2018. We didn’t identify meaningful coding variation in either Brca1 or Brca2, or in 167 other DDR genes across the 30 generations. In the meantime, we did identify 812 coding variants in 116 non-DNA damage repair genes during the same period, which served as a quality control to validate the reliability of our analytic pipeline and the negative results in DDR genes. Conclusions DDR genes in laboratory mouse strain C57BL/6 J were not under positive selection across its 30-generation period, highlighting the possibility that DDR system in rodents could be evolutionarily stable. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07983-7.
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Affiliation(s)
- Xiaoyu Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Taipa, Macau.
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30
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Yang J, Qi L, Chiang HC, Yuan B, Li R, Hu Y. BRCA1 Antibodies Matter. Int J Biol Sci 2021; 17:3239-3254. [PMID: 34421362 PMCID: PMC8375228 DOI: 10.7150/ijbs.63115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/11/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer susceptibility gene 1 (BRCA1) encodes a tumor suppressor that is frequently mutated in familial breast and ovarian cancer patients. BRCA1 functions in multiple important cellular processes including DNA damage repair, cell cycle checkpoint activation, protein ubiquitination, chromatin remodeling, transcriptional regulation, as well as R-loop formation and apoptosis. A large number of BRCA1 antibodies have been generated and become commercially available over the past three decades, however, many commercial antibodies are poorly characterized and, when widely used, led to unreliable data. In search of reliable and specific BRCA1 antibodies (Abs), particularly antibodies recognizing mouse BRCA1, we performed a rigorous validation of a number of commercially available anti-BRCA1 antibodies, using proper controls in a panel of validation applications, including Western blot (WB), immunoprecipitation (IP), immunoprecipitation-mass spectrometry (IP-MS), chromatin immunoprecipitation (ChIP) and immunofluorescence (IF). Furthermore, we assessed the specificity of these antibodies to detect mouse BRCA1 protein through the use of testis tissue and mouse embryonic fibroblasts (MEFs) from Brca1+/+ and Brca1Δ11/Δ11 mice. We find that Ab1, D-9, 07-434 (for recognizing human BRCA1) and 287.17, 440621, BR-64 (for recognizing mouse BRCA1) are specific with high quality performance in the indicated assays. We share these results here with the goal of helping the community combat the common challenges associated with anti-BRCA1 antibody specificity and reproducibility and, hopefully, better understanding BRCA1 functions at cellular and tissue levels.
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Affiliation(s)
- Jing Yang
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Leilei Qi
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Huai-Chin Chiang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Bin Yuan
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Yanfen Hu
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
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31
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Leung E, Hazrati LN. Breast cancer type 1 and neurodegeneration: consequences of deficient DNA repair. Brain Commun 2021; 3:fcab117. [PMID: 34222870 PMCID: PMC8242133 DOI: 10.1093/braincomms/fcab117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
Numerous cellular processes, including toxic protein aggregation and oxidative stress, have been studied extensively as potential mechanisms underlying neurodegeneration. However, limited therapeutic efficacy targeting these processes has prompted other mechanisms to be explored. Previous research has emphasized a link between cellular senescence and neurodegeneration, where senescence induced by excess DNA damage and deficient DNA repair results in structural and functional changes that ultimately contribute to brain dysfunction and increased vulnerability for neurodegeneration. Specific DNA repair proteins, such as breast cancer type 1, have been associated with both stress-induced senescence and neurodegenerative diseases, however, specific mechanisms remain unclear. Therefore, this review explores DNA damage-induced senescence in the brain as a driver of neurodegeneration, with particular focus on breast cancer type 1, and its potential contribution to sex-specific differences associated with neurodegenerative disease.
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Affiliation(s)
- Emily Leung
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 Kings College Cir, Toronto, ON M5S 1A8, Canada
- The Hospital for Sick Children, 555 University Ave, Toronto, ON M5G 1X8, Canada
| | - Lili-Naz Hazrati
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 Kings College Cir, Toronto, ON M5S 1A8, Canada
- The Hospital for Sick Children, 555 University Ave, Toronto, ON M5G 1X8, Canada
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32
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Xu S, Wu X, Wang P, Cao SL, Peng B, Xu X. ASPM promotes homologous recombination-mediated DNA repair by safeguarding BRCA1 stability. iScience 2021; 24:102534. [PMID: 34142045 PMCID: PMC8184511 DOI: 10.1016/j.isci.2021.102534] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) is essential for ensuring genome stability. Abnormal spindle-like microcephaly-associated (ASPM) gene encodes a spindle protein that is commonly implicated in primary microcephaly. We found that ASPM is recruited to sites of DNA damage in a PARP2-dependent manner. ASPM interacts with BRCA1 and its E3 ligase HERC2, preventing HERC2 from accessing to BRCA1 and ensuring BRCA1 stability. Inhibition of ASPM expression promotes HERC2-mediated BRCA1 degradation, compromises HR repair efficiency and chromosome stability, and sensitizes cancer cells to ionizing radiation. Moreover, we observed a synergistic effect between ASPM and PARP inhibition in killing cancer cells. This research has uncovered a novel function for ASPM in facilitating HR-mediated repair of DSBs by ensuring BRCA1 stability. ASPM might constitute a promising target for synthetic lethality-based cancer therapy. ASPM is recruited to sites of DNA damage in a PARP2-dependent manner. ASPM promotes DSB-end resection to facilitate HR repair. ASPM prevents HERC2 from accessing to BRCA1 and ensuring BRCA1 stability. Inhibition of ASPM sensitizes cancer cells to ionizing radiation and PARP inhibitor.
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Affiliation(s)
- Shibin Xu
- College of Life Sciences, Capital Normal University, Beijing 100048, China.,Department of Chemistry, Capital Normal University, Beijing 100048, China.,Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xingxuan Wu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China.,Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Peipei Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China.,International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Sheng-Li Cao
- Department of Chemistry, Capital Normal University, Beijing 100048, China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China.,Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China.,International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China.,Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China.,International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
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33
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Mouse Models for Deciphering the Impact of Homologous Recombination on Tumorigenesis. Cancers (Basel) 2021; 13:cancers13092083. [PMID: 33923105 PMCID: PMC8123484 DOI: 10.3390/cancers13092083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) is a fundamental evolutionarily conserved process that plays prime role(s) in genome stability maintenance through DNA repair and through the protection and resumption of arrested replication forks. Many HR genes are deregulated in cancer cells. Notably, the breast cancer genes BRCA1 and BRCA2, two important HR players, are the most frequently mutated genes in familial breast and ovarian cancer. Transgenic mice constitute powerful tools to unravel the intricate mechanisms controlling tumorigenesis in vivo. However, the genes central to HR are essential in mammals, and their knockout leads to early embryonic lethality in mice. Elaborated strategies have been developed to overcome this difficulty, enabling one to analyze the consequences of HR disruption in vivo. In this review, we first briefly present the molecular mechanisms of HR in mammalian cells to introduce each factor in the HR process. Then, we present the different mouse models of HR invalidation and the consequences of HR inactivation on tumorigenesis. Finally, we discuss the use of mouse models for the development of targeted cancer therapies as well as perspectives on the future potential for understanding the mechanisms of HR inactivation-driven tumorigenesis in vivo.
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34
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Spatiotemporal 7q11.23 protein network analysis implicates the role of DNA repair pathway during human brain development. Sci Rep 2021; 11:8246. [PMID: 33859276 PMCID: PMC8050238 DOI: 10.1038/s41598-021-87632-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/25/2021] [Indexed: 01/10/2023] Open
Abstract
Recurrent deletions and duplications of chromosome 7q11.23 copy number variants (CNVs) are associated with several psychiatric disorders. Although phenotypic abnormalities have been observed in patients, causal genes responsible for CNV-associated diagnoses and traits are still poorly understood. Furthermore, the targeted human brain regions, developmental stages, protein networks, and signaling pathways, influenced by this CNV remain unclear. Previous works showed GTF2I involved in Williams-Beuren syndrome, but pathways affected by GTF2I are indistinct. We first constructed dynamic spatiotemporal networks of 7q11.23 genes by combining data from the brain developmental transcriptome with physical interactions of 7q11.23 proteins. Topological changes were observed in protein-protein interaction (PPI) networks throughout different stages of brain development. Early and late fetal periods of development in the cortex, striatum, hippocampus, and amygdale were observed as the vital periods and regions for 7q11.23 CNV proteins. CNV proteins and their partners are significantly enriched in DNA repair pathway. As a driver gene, GTF2I interacted with PRKDC and BRCA1 to involve in DNA repair pathway. The physical interaction between GTF2I with PRKDC was confirmed experimentally by the liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified that early and late fetal periods are crucial for 7q11.23 genes to affect brain development. Our results implicate that 7q11.23 CNV genes converge on the DNA repair pathway to contribute to the pathogenesis of psychiatric diseases.
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35
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Yamaguchi H, Kitami K, Wu X, He L, Wang J, Wang B, Komatsu Y. Alteration of DNA Damage Response Causes Cleft Palate. Front Physiol 2021; 12:649492. [PMID: 33854442 PMCID: PMC8039291 DOI: 10.3389/fphys.2021.649492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022] Open
Abstract
Cleft palate is one of the most common craniofacial birth defects, however, little is known about how changes in the DNA damage response (DDR) cause cleft palate. To determine the role of DDR during palatogenesis, the DDR process was altered using a pharmacological intervention approach. A compromised DDR caused by a poly (ADP-ribose) polymerase (PARP) enzyme inhibitor resulted in cleft palate in wild-type mouse embryos, with increased DNA damage and apoptosis. In addition, a mouse genetic approach was employed to disrupt breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2), known as key players in DDR. An ectomesenchymal-specific deletion of Brca1 or Brca2 resulted in cleft palate due to attenuation of cell survival. This was supported by the phenotypes of the ectomesenchymal-specific Brca1/Brca2 double-knockout mice. The cleft palate phenotype was rescued by superimposing p53 null alleles, demonstrating that the BRCA1/2-p53 DDR pathway is critical for palatogenesis. Our study highlights the importance of DDR in palatogenesis.
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Affiliation(s)
- Hiroyuki Yamaguchi
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Kohei Kitami
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Xiao Wu
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Li He
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Jianbo Wang
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States
| | - Bin Wang
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Yoshihiro Komatsu
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX, United States.,Graduate Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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36
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Dumas G, Malesys S, Bourgeron T. Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition. Genome Res 2021; 31:484-496. [PMID: 33441416 PMCID: PMC7919455 DOI: 10.1101/gr.262113.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022]
Abstract
The human brain differs from that of other primates, but the genetic basis of these differences remains unclear. We investigated the evolutionary pressures acting on almost all human protein-coding genes (N = 11,667; 1:1 orthologs in primates) based on their divergence from those of early hominins, such as Neanderthals, and non-human primates. We confirm that genes encoding brain-related proteins are among the most strongly conserved protein-coding genes in the human genome. Combining our evolutionary pressure metrics for the protein-coding genome with recent data sets, we found that this conservation applied to genes functionally associated with the synapse and expressed in brain structures such as the prefrontal cortex and the cerebellum. Conversely, several genes presenting signatures commonly associated with positive selection appear as causing brain diseases or conditions, such as micro/macrocephaly, Joubert syndrome, dyslexia, and autism. Among those, a number of DNA damage response genes associated with microcephaly in humans such as BRCA1, NHEJ1, TOP3A, and RNF168 show strong signs of positive selection and might have played a role in human brain size expansion during primate evolution. We also showed that cerebellum granule neurons express a set of genes also presenting signatures of positive selection and that may have contributed to the emergence of fine motor skills and social cognition in humans. This resource is available online and can be used to estimate evolutionary constraints acting on a set of genes and to explore their relative contributions to human traits.
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Affiliation(s)
- Guillaume Dumas
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
- Department of Psychiatry, Université de Montreal, CHU Sainte-Justine Hospital, Montreal H3T 1C5, Quebec, Canada
| | - Simon Malesys
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris 75015, France
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37
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Interaction of maternal immune activation and genetic interneuronal inhibition. Brain Res 2021; 1759:147370. [PMID: 33600830 DOI: 10.1016/j.brainres.2021.147370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 11/24/2022]
Abstract
Genes and environment interact during intrauterine life, and potentially alter the developmental trajectory of the brain. This can result in life-long consequences on brain function. We have previously developed two transgenic mouse lines that suppress Gad1 expression in parvalbumin (PVALB) and neuropeptide Y (NPY) expressing interneuron populations using a bacterial artificial chromosome (BAC)-driven miRNA-based silencing technology. We were interested to assess if maternal immune activation (MIA), genetic interneuronal inhibition, and the combination of these two factors disrupt and result in long-term changes in neuroinflammatory gene expression, sterol biosynthesis, and acylcarnitine levels in the brain of maternally exposed offspring. Pregnant female WT mice were given a single intraperitoneal injection of saline or polyinosinic-polycytidilic acid [poly(I:C)] at E12.5. Brains of offspring were analyzed at postnatal day 90. We identified complex and persistent neuroinflammatory gene expression changes in the hippocampi of MIA-exposed offspring, as well in the hippocampi of Npy/Gad1 and Pvalb/Gad1 mice. In addition, both MIA and genetic inhibition altered the post-lanosterol sterol biosynthesis in the neocortex and disrupted the typical acylcarnitine profile. In conclusion, our findings suggest that both MIA and inhibition of interneuronal function have long-term consequences on critical homeostatic mechanisms of the brain, including immune function, sterol levels, and energy metabolism.
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38
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Chen Y, Sun J, Ju Z, Wang ZQ, Li T. Nbs1-mediated DNA damage repair pathway regulates haematopoietic stem cell development and embryonic haematopoiesis. Cell Prolif 2021; 54:e12972. [PMID: 33586242 PMCID: PMC7941224 DOI: 10.1111/cpr.12972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Objectives DNA damages pose threats to haematopoietic stem cells (HSC) maintenance and haematopoietic system homeostasis. Quiescent HSCs in adult mouse bone marrow are resistant to DNA damage, while human umbilical cord blood‐derived proliferative HSCs are prone to cell death upon ionizing radiation. Murine embryonic HSCs proliferate in foetal livers and divide symmetrically to generate HSC pool. How murine embryonic HSCs respond to DNA damages is not well‐defined. Materials and methods Mice models with DNA repair molecule Nbs1 or Nbs1/p53 specifically deleted in embryonic HSCs were generated. FACS analysis, in vitro and in vivo HSC differentiation assays, qPCR, immunofluorescence and Western blotting were used to delineate roles of Nbs1‐p53 signaling in HSCs and haematopoietic progenitors. Results Nbs1 deficiency results in persistent DNA breaks in embryonic HSCs, compromises embryonic HSC development and finally results in mouse perinatal lethality. The persistent DNA breaks in Nbs1 deficient embryonic HSCs render cell cycle arrest, while driving a higher rate of cell death in haematopoietic progenitors. Although Nbs1 deficiency promotes Atm‐Chk2‐p53 axis activation in HSCs and their progenies, ablation of p53 in Nbs1 deficient HSCs accelerates embryonic lethality. Conclusions Our study discloses that DNA double‐strand repair molecule Nbs1 is essential in embryonic HSC development and haematopoiesis. Persistent DNA damages result in distinct cell fate in HSCs and haematopoietic progenitors. Nbs1 null HSCs tend to be maintained through cell cycle arrest, while Nbs1 null haematopoietic progenitors commit cell death. The discrepancies are mediated possibly by different magnitude of p53 signaling.
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Affiliation(s)
- Yu Chen
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jie Sun
- Jiangsu Hansoh Pharmaceutical Group Co., Ltd., Lianyungang, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich-Schiller University of Jena, Jena, Germany
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.,NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
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39
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Yan Y, Yin Y, Feng X, Chen Y, Shi J, Weng H, Wang D. Homocysteine aggravates DNA damage by impairing the FA/Brca1 Pathway in NE4C murine neural stem cells. Int J Med Sci 2020; 17:2477-2486. [PMID: 33029090 PMCID: PMC7532487 DOI: 10.7150/ijms.49246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/24/2020] [Indexed: 11/05/2022] Open
Abstract
There is existing evidence that elevated homocysteine (Hcy) levels are risk factors for some neurodegenerative disorders. The pathogenesis of neurological diseases could be contributed to excessive cell dysfunction and death caused by defective DNA damage response (DDR) and accumulated DNA damage. Hcy is a neurotoxic amino acid and acts as a DNA damage inducer. However, it is not clear whether Hcy participates in the DDR. To investigate the effects of Hcy on DNA damage and the DDR, we employed mitomycin C (MMC) to cause DNA damage in NE4C murine neural stem cells (NSCs). Compared to treatment with MMC alone, we found that co-treatment with MMC and Hcy worsened DNA damage and increased death in NE4C cells. Intriguingly, in this DNA damage model mimicked by MMC, immunoblotting results showed that the monoubiquitination levels of Fanconi anemia complementation group I (Fanci) and Fanconi anemia complementation group D2 (Fancd2) were decreased to about 60.3% and 55.7% by supplementing cell culture medium with Hcy, indicating Hcy inactivates the function of Fanci and Fancd2 in DNA damage conditions. Given Breast Cancer 1 (BRCA1) is an important downstream of FANCD2, we next detected the interaction between Fancd2 and Brca1 in NE4C cells. Compared to treatment with MMC alone, the Fancd2-Brca1 interaction and the amount of Brca1 on chromatin were decreased when cells were co-exposed to MMC and Hcy, suggesting Hcy could impair the Fanconi anemia (FA)/Brca1 pathway. Taken together, our study demonstrates that Hcy may enhance cell death, which contributes to the accumulation of DNA damage and promotion of hypersensitivity to cytotoxicity by impairing the FA/Brca1 pathway in murine NSCs in the presence of DNA damage.
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Affiliation(s)
- Yana Yan
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, P. R. China
| | - Yandan Yin
- Department of Pediatrics, Taizhou Women and Children's Hospital of Wenzhou Medical University, Taizhou 318000, Zhejiang, P. R. China
| | - Xiaofang Feng
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, P. R. China
| | - Yuan Chen
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, P. R. China
| | - Jiamin Shi
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, P. R. China
| | - Huachun Weng
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, P. R. China
| | - Dan Wang
- Department of Pediatrics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, P. R. China
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40
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Cell polarity and oncogenesis: common mutations contribute to altered cellular polarity and promote malignancy. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00313-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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41
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Bhatia S, Wells PG. Quantifying Activity for Repair of the DNA Lesion 8-Oxoguanine by Oxoguanine Glycosylase 1 (OGG1) in Mouse Adult and Fetal Brain Nuclear Extracts Using Biotin-Labeled DNA. Methods Mol Biol 2019; 1965:329-349. [PMID: 31069685 DOI: 10.1007/978-1-4939-9182-2_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reactive oxygen species (ROS)-initiated DNA lesion 8-oxoguanine (8-oxoG) is commonly used as a biomarker to measure oxidative stress levels in tissue samples from animals and humans. This lesion also can play a pathogenic role in cancer, birth defects, and neurodegeneration, among other disorders. The level of 8-oxoG may be enhanced due to ROS-initiating environmental factors (e.g., drugs, gamma radiation, microbial infection) or due to a decrease in the activity of oxoguanine glycosylase 1 (OGG1), an enzyme that repairs this lesion. Measurement of the activity of OGG1 can be useful in elucidating mechanisms and complements measurements of 8-oxoG levels in tissues of interest. This protocol describes an assay for measuring the activity of 8-oxoG in mouse adult and fetal brain tissues. Briefly, a synthetic duplex containing the 8-oxoG residue in one of the nucleotides (49-mer), labeled with biotin at the 3'-end, is incubated with protein extract from the tissue of interest containing OGG1, which cleaves the 8-oxoG residue producing a cleavage product of ~27-mer. The percent cleavage quantifies the activity of OGG1 in that tissue. The biotin tag allows rapid and sensitive detection of the cleavage product via chemiluminescence, avoiding the problems of safety and short half-lives of radionuclides encountered in assays employing a radioactively-labeled substrate.
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Affiliation(s)
- Shama Bhatia
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, University of Toronto, Toronto, ON, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, University of Toronto, Toronto, ON, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
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42
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Artificial Intelligence and the detection of pediatric concussion using epigenomic analysis. Brain Res 2019; 1726:146510. [PMID: 31628932 DOI: 10.1016/j.brainres.2019.146510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022]
Abstract
Concussion, also referred to as mild traumatic brain injury (mTBI) is the most common type of traumatic brain injury. Currently concussion is an area ofintensescientific interest to better understand the biological mechanisms and for biomarker development. We evaluated whole genome-wide blood DNA cytosine ('CpG') methylation in 17 pediatric concussion isolated cases and 18 unaffected controls using Illumina Infinium MethylationEPIC assay. Pathway analysis was performed using Ingenuity Pathway Analysis to help elucidate the epigenetic and molecular mechanisms of the disorder. Area under the receiver operating characteristics (AUC) curves and FDR p-values were calculated for mTBI detection based on CpG methylation levels. Multiple Artificial Intelligence (AI) platforms including Deep Learning (DL), the newest form of AI, were used to predict concussion based on i) CpG methylation markers alone, and ii) combined epigenetic, clinical and demographic predictors. We found 449 CpG sites (473 genes), those were statistically significantly methylated in mTBI compared to controls. There were four CpGs with excellent individual accuracy (AUC ≥ 0.90-1.00) while 119 displayed good accuracy (AUC ≥ 0.80-0.89) for the prediction of mTBI. The CpG methylation changes ≥10% were observed in many CpG loci after concussion suggesting biological significance. Pathway analysis identified several biologically important neurological pathways that were perturbed including those associated with: impaired brain function, cognition, memory, neurotransmission, intellectual disability and behavioral change and associated disorders. The combination of epigenomic and clinical predictors were highly accurate for the detection of concusion using AI techniques. Using DL/AI, a combination of epigenomic and clinical markers had sensitivity and specificity ≧95% for prediction of mTBI. In this novel study, we identified significant methylation changes in multiple genes in response to mTBI. Gene pathways that were epigenetically dysregulated included several known to be involved in neurological function, thus giving biological plausibility to our findings.
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43
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Bhatia S, Drake DM, Miller L, Wells PG. Oxidative stress and DNA damage in the mechanism of fetal alcohol spectrum disorders. Birth Defects Res 2019; 111:714-748. [PMID: 31033255 DOI: 10.1002/bdr2.1509] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 12/18/2022]
Abstract
This review covers molecular mechanisms involving oxidative stress and DNA damage that may contribute to morphological and functional developmental disorders in animal models resulting from exposure to alcohol (ethanol, EtOH) in utero or in embryo culture. Components covered include: (a) a brief overview of EtOH metabolism and embryopathic mechanisms other than oxidative stress; (b) mechanisms within the embryo and fetal brain by which EtOH increases the formation of reactive oxygen species (ROS); (c) critical embryonic/fetal antioxidative enzymes and substrates that detoxify ROS; (d) mechanisms by which ROS can alter development, including ROS-mediated signal transduction and oxidative DNA damage, the latter of which leads to pathogenic genetic (mutations) and epigenetic changes; (e) pathways of DNA repair that mitigate the pathogenic effects of DNA damage; (f) related indirect mechanisms by which EtOH enhances risk, for example by enhancing the degradation of some DNA repair proteins; and, (g) embryonic/fetal pathways like NRF2 that regulate the levels of many of the above components. Particular attention is paid to studies in which chemical and/or genetic manipulation of the above mechanisms has been shown to alter the ability of EtOH to adversely affect development. Alterations in the above components are also discussed in terms of: (a) individual embryonic and fetal determinants of risk and (b) potential risk biomarkers and mitigating strategies. FASD risk is likely increased in progeny which/who are biochemically predisposed via genetic and/or environmental mechanisms, including enhanced pathways for ROS formation and/or deficient pathways for ROS detoxification or DNA repair.
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Affiliation(s)
- Shama Bhatia
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Centre for Pharmaceutical Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Danielle M Drake
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Centre for Pharmaceutical Oncology, University of Toronto, Toronto, Ontario, Canada
| | | | - Peter G Wells
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada.,Centre for Pharmaceutical Oncology, University of Toronto, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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44
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Duraikannu A, Krishnan A, Chandrasekhar A, Zochodne DW. Beyond Trophic Factors: Exploiting the Intrinsic Regenerative Properties of Adult Neurons. Front Cell Neurosci 2019; 13:128. [PMID: 31024258 PMCID: PMC6460947 DOI: 10.3389/fncel.2019.00128] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/14/2019] [Indexed: 01/19/2023] Open
Abstract
Injuries and diseases of the peripheral nervous system (PNS) are common but frequently irreversible. It is often but mistakenly assumed that peripheral neuron regeneration is robust without a need to be improved or supported. However, axonal lesions, especially those involving proximal nerves rarely recover fully and injuries generally are complicated by slow and incomplete regeneration. Strategies to enhance the intrinsic growth properties of reluctant adult neurons offer an alternative approach to consider during regeneration. Since axons rarely regrow without an intimately partnered Schwann cell (SC), approaches to enhance SC plasticity carry along benefits to their axon partners. Direct targeting of molecules that inhibit growth cone plasticity can inform important regenerative strategies. A newer approach, a focus of our laboratory, exploits tumor suppressor molecules that normally dampen unconstrained growth. However several are also prominently expressed in stable adult neurons. During regeneration their ongoing expression “brakes” growth, whereas their inhibition and knockdown may enhance regrowth. Examples have included phosphatase and tensin homolog deleted on chromosome ten (PTEN), a tumor suppressor that inhibits PI3K/pAkt signaling, Rb1, the protein involved in retinoblastoma development, and adenomatous polyposis coli (APC), a tumor suppressor that inhibits β-Catenin transcriptional signaling and its translocation to the nucleus. The identification of several new targets to manipulate the plasticity of regenerating adult peripheral neurons is exciting. How they fit with canonical regeneration strategies and their feasibility require additional work. Newer forms of nonviral siRNA delivery may be approaches for molecular manipulation to improve regeneration.
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Affiliation(s)
- Arul Duraikannu
- Division of Neurology, Department of Medicine, and Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Anand Krishnan
- Division of Neurology, Department of Medicine, and Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Ambika Chandrasekhar
- Division of Neurology, Department of Medicine, and Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Douglas W Zochodne
- Division of Neurology, Department of Medicine, and Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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45
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Overexpression of BRCA1 in Neural Stem Cells Enhances Cell Survival and Functional Recovery after Transplantation into Experimental Ischemic Stroke. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:8739730. [PMID: 31073355 PMCID: PMC6470423 DOI: 10.1155/2019/8739730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/16/2018] [Indexed: 01/09/2023]
Abstract
Transplantation of neural stem cells (NSCs) is a promising therapy for ischemic stroke. However, the effectiveness of this approach is limited by grafted cell death. Breast cancer susceptibility protein 1 (BRCA1) could suppress apoptosis in neural progenitors and modulate oxidative stress in neurons. In this study, we found that BRCA1 was upregulated by oxygen-glucose deprivation/reoxygenation (OGD/R). Overexpression of BRCA1 in NSCs reduced cell apoptosis and oxidative stress after OGD/R insult. The molecule overexpression also stimulated cellular proliferation in OGD/R NSCs and increased the survival rate of grafted cells. Further, the transplantation of BRCA1-transfected NSCs into mice with ischemic stroke increased brain-derived neurotropic factor and nerve growth factor expression in the brain and elicited neurological function improvement. In addition, we found that RING finger domain and BRCT domain of BRCA1 could physically interact with p53 in NSCs. The cross talk between BRCA1 RING finger domain and p53 was responsible for p53 ubiquitination and degradation. Our findings indicate that modification with BRCA1 could enhance the efficacy of NSCs transplantation in ischemic stroke.
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46
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Wezyk M, Szybinska A, Wojsiat J, Szczerba M, Day K, Ronnholm H, Kele M, Berdynski M, Peplonska B, Fichna JP, Ilkowski J, Styczynska M, Barczak A, Zboch M, Filipek-Gliszczynska A, Bojakowski K, Skrzypczak M, Ginalski K, Kabza M, Makalowska I, Barcikowska-Kotowicz M, Wojda U, Falk A, Zekanowski C. Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease. J Alzheimers Dis 2019; 62:175-202. [PMID: 29439343 DOI: 10.3233/jad-170830] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The BRCA1 protein, one of the major players responsible for DNA damage response has recently been linked to Alzheimer's disease (AD). Using primary fibroblasts and neurons reprogrammed from induced pluripotent stem cells (iPSC) derived from familial AD (FAD) patients, we studied the role of the BRCA1 protein underlying molecular neurodegeneration. By whole-transcriptome approach, we have found wide range of disturbances in cell cycle and DNA damage response in FAD fibroblasts. This was manifested by significantly increased content of BRCA1 phosphorylated on Ser1524 and abnormal ubiquitination and subcellular distribution of presenilin 1 (PS1). Accordingly, the iPSC-derived FAD neurons showed increased content of BRCA1(Ser1524) colocalized with degraded PS1, accompanied by an enhanced immunostaining pattern of amyloid-β. Finally, overactivation of BRCA1 was followed by an increased content of Cdc25C phosphorylated on Ser216, likely triggering cell cycle re-entry in FAD neurons. This study suggests that overactivated BRCA1 could both influence PS1 turnover leading to amyloid-β pathology and promote cell cycle re-entry-driven cell death of postmitotic neurons in AD.
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Affiliation(s)
- Michalina Wezyk
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Szybinska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Wojsiat
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcelina Szczerba
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Kelly Day
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Harriet Ronnholm
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mariusz Berdynski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland.,Department of Pharmacology and Clinical Neuroscience, Umea Universitet, Umea, Sweden
| | - Beata Peplonska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Piotr Fichna
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jan Ilkowski
- Department of Emergency Medicine, Faculty of Health Sciences, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Styczynska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Marzena Zboch
- Center of Alzheimer's Disease of Wroclaw Medical University, Scinawa, Poland
| | - Anna Filipek-Gliszczynska
- Clinical Department of Neurology, Extrapyramidal Disorders and Alzheimer's Outpatient Clinic, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Krzysztof Bojakowski
- Clinical Department of General and Vascular Surgery, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michal Kabza
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Maria Barcikowska-Kotowicz
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cezary Zekanowski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
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47
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Herold S, Kalb J, Büchel G, Ade CP, Baluapuri A, Xu J, Koster J, Solvie D, Carstensen A, Klotz C, Rodewald S, Schülein-Völk C, Dobbelstein M, Wolf E, Molenaar J, Versteeg R, Walz S, Eilers M. Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase. Nature 2019; 567:545-549. [PMID: 30894746 DOI: 10.1038/s41586-019-1030-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 02/18/2019] [Indexed: 01/17/2023]
Abstract
MYC is an oncogenic transcription factor that binds globally to active promoters and promotes transcriptional elongation by RNA polymerase II (RNAPII)1,2. Deregulated expression of the paralogous protein MYCN drives the development of neuronal and neuroendocrine tumours and is often associated with a particularly poor prognosis3. Here we show that, similar to MYC, activation of MYCN in human neuroblastoma cells induces escape of RNAPII from promoters. If the release of RNAPII from transcriptional pause sites (pause release) fails, MYCN recruits BRCA1 to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. Mechanistically, BRCA1 stabilizes mRNA decapping complexes and enables MYCN to suppress R-loop formation in promoter-proximal regions. Recruitment of BRCA1 requires the ubiquitin-specific protease USP11, which binds specifically to MYCN when MYCN is dephosphorylated at Thr58. USP11, BRCA1 and MYCN stabilize each other on chromatin, preventing proteasomal turnover of MYCN. Because BRCA1 is highly expressed in neuronal progenitor cells during early development4 and MYC is less efficient than MYCN in recruiting BRCA1, our findings indicate that a cell-lineage-specific stress response enables MYCN-driven tumours to cope with deregulated RNAPII function.
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Affiliation(s)
- Steffi Herold
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Jacqueline Kalb
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Gabriele Büchel
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Carsten P Ade
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jiajia Xu
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Daniel Solvie
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Anne Carstensen
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christina Klotz
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sabrina Rodewald
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Christina Schülein-Völk
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jan Molenaar
- Department of Translational Research, Prinses Máxima Centrum voor Kinderoncologie, Utrecht, The Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.
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48
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Abstract
MYC is an oncogenic transcription factor that binds globally to active promoters and promotes transcriptional elongation by RNA polymerase II (RNAPII)1,2. Deregulated expression of the paralogous protein MYCN drives the development of neuronal and neuroendocrine tumours and is often associated with a particularly poor prognosis3. Here we show that, similar to MYC, activation of MYCN in human neuroblastoma cells induces escape of RNAPII from promoters. If the release of RNAPII from transcriptional pause sites (pause release) fails, MYCN recruits BRCA1 to promoter-proximal regions. Recruitment of BRCA1 prevents MYCN-dependent accumulation of stalled RNAPII and enhances transcriptional activation by MYCN. Mechanistically, BRCA1 stabilizes mRNA decapping complexes and enables MYCN to suppress R-loop formation in promoter-proximal regions. Recruitment of BRCA1 requires the ubiquitin-specific protease USP11, which binds specifically to MYCN when MYCN is dephosphorylated at Thr58. USP11, BRCA1 and MYCN stabilize each other on chromatin, preventing proteasomal turnover of MYCN. Because BRCA1 is highly expressed in neuronal progenitor cells during early development4 and MYC is less efficient than MYCN in recruiting BRCA1, our findings indicate that a cell-lineage-specific stress response enables MYCN-driven tumours to cope with deregulated RNAPII function.
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49
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Niego A, Benítez-Burraco A. Williams Syndrome, Human Self-Domestication, and Language Evolution. Front Psychol 2019; 10:521. [PMID: 30936846 PMCID: PMC6431629 DOI: 10.3389/fpsyg.2019.00521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/22/2019] [Indexed: 01/06/2023] Open
Abstract
Language evolution resulted from changes in our biology, behavior, and culture. One source of these changes might be human self-domestication. Williams syndrome (WS) is a clinical condition with a clearly defined genetic basis which results in a distinctive behavioral and cognitive profile, including enhanced sociability. In this paper we show evidence that the WS phenotype can be satisfactorily construed as a hyper-domesticated human phenotype, plausibly resulting from the effect of the WS hemideletion on selected candidates for domestication and neural crest (NC) function. Specifically, we show that genes involved in animal domestication and NC development and function are significantly dysregulated in the blood of subjects with WS. We also discuss the consequences of this link between domestication and WS for our current understanding of language evolution.
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Affiliation(s)
- Amy Niego
- Ph.D. Program, Faculty of Humanities, University of Huelva, Huelva, Spain
| | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
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50
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Abstract
Known for its tumor suppressor activity in breast and ovarian cancers, the breast cancer 1 susceptibility gene (Brca1) is involved in a variety of cellular pathways including DNA repair, antioxidant signaling, apoptosis, and cell cycle regulation. BRCA1 can translocate between the cytoplasm and nucleus to perform its various roles. Herein is a procedure for measuring BRCA1 protein levels in the whole cell lysate (WCL), as well as in the nuclear (N) and cytoplasmic (C) fractions of mouse tissues at different gestational ages. The method employs multiple loading controls to ensure proper separation of fractions and a total protein stain for more consistent comparisons of dissimilar samples. This method is useful for identifying BRCA1 deficiencies and localization in a variety of research fields, including development, neurodegeneration, and cancer.
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Affiliation(s)
- Danielle M Drake
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, University of Toronto, Toronto, ON, Canada
| | - Peter G Wells
- Department of Pharmaceutical Sciences and Centre for Pharmaceutical Oncology, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
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