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Zhang W, Jiang Y, Ni Z, Zhou M, Liu L, Li X, Su S, Wang C. Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study. Animals (Basel) 2024; 14:1419. [PMID: 38791637 PMCID: PMC11117326 DOI: 10.3390/ani14101419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.
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Affiliation(s)
- Wei Zhang
- Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Yao Jiang
- National Animal Husbandry Service, Beijing 100125, China;
| | - Zelan Ni
- Anhui Provincial Livestock and Poultry Genetic Resources Conservation Center, Hefei 231283, China;
| | - Mei Zhou
- Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Linqing Liu
- Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Xiaoyu Li
- Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Shiguang Su
- Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Chonglong Wang
- Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
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Gasparini C, Iori S, Pietropoli E, Bonato M, Giantin M, Barbarossa A, Bardhi A, Pilastro A, Dacasto M, Pauletto M. Sub-acute exposure of male guppies (Poecilia reticulata) to environmentally relevant concentrations of PFOA and GenX induces significant changes in the testis transcriptome and reproductive traits. ENVIRONMENT INTERNATIONAL 2024; 187:108703. [PMID: 38705092 DOI: 10.1016/j.envint.2024.108703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
Poly- and perfluoroalkyl substances (PFAS) are frequently detected in the environment and are linked to adverse reproductive health outcomes in humans. Although legacy PFAS have been phased out due to their toxicity, alternative PFAS are increasingly used despite the fact that information on their toxic effects on reproductive traits is particularly scarce. Here, we exposed male guppies (Poecilia reticulata) for a short period (21 days) to an environmentally realistic concentration (1 ppb) of PFOA, a legacy PFAS, and its replacement compound, GenX, to assess their impact on reproductive traits and gene expression. Exposure to PFAS did not impair survival but instead caused sublethal effects. Overall, PFAS exposure caused changes in male sexual behaviour and had detrimental effects on sperm motility. Sublethal variations were also seen at the transcriptional level, with the modulation of genes involved in immune regulation, spermatogenesis, and oxidative stress. We also observed bioaccumulation of PFAS, which was higher for PFOA than for GenX. Our results offer a comprehensive comparison of these two PFAS and shed light on the toxicity of a newly emerging alternative to legacy PFAS. It is therefore evident that even at low concentrations and with short exposure, PFAS can have subtle yet significant effects on behaviour, fertility, and immunity. These findings underscore the potential ramifications of pollution under natural conditions and their impact on fish populations.
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Affiliation(s)
- C Gasparini
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy; National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - S Iori
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, I-35020 Agripolis Legnaro (Padova), Italy
| | - E Pietropoli
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, I-35020 Agripolis Legnaro (Padova), Italy
| | - M Bonato
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy
| | - M Giantin
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, I-35020 Agripolis Legnaro (Padova), Italy
| | - A Barbarossa
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, via Tolara di Sopra 50, I-40064 Ozzano dell'Emilia (Bologna), Italy; Health Sciences and Technologies-Interdepartmental Centre for Industrial Research (CIRI-SDV), Alma Mater Studiorum University of Bologna, I-40064 Ozzano dell'Emilia (Bologna), Italy
| | - A Bardhi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, via Tolara di Sopra 50, I-40064 Ozzano dell'Emilia (Bologna), Italy
| | - A Pilastro
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy; National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - M Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, I-35020 Agripolis Legnaro (Padova), Italy
| | - M Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università 16, I-35020 Agripolis Legnaro (Padova), Italy.
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Yang Z, Zhao A, Teng M, Li M, Wang H, Wang X, Liu Z, Zeng Q, Hu L, Hu J, Bao Z, Huang X. Signatures of selection in Mulinia lateralis underpinning its rapid adaptation to laboratory conditions. Evol Appl 2024; 17:e13657. [PMID: 38357357 PMCID: PMC10866071 DOI: 10.1111/eva.13657] [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: 08/05/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
The dwarf surf clam, Mulinia lateralis, is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five different generations were genotyped with 22,196 single nucleotide polymorphisms (SNPs) with the aim of uncovering the genetic basis of their adaptation to laboratory conditions. Results revealed that M. lateralis consistently maintained high genetic diversity across generations, characterized by high observed heterozygosity (H o: 0.2733-0.2934) and low levels of inbreeding (F is: -0.0244-0.0261). Population analysis indicated low levels of genetic differentiation among generations of M. lateralis during artificial breeding (F st <0.05). In total, 316 genomic regions exhibited divergent selection, with 168 regions under positive selection. Furthermore, 227 candidate genes were identified in the positive selection regions, which have functions including growth, stress resistance, and reproduction. Notably, certain selection signatures with significantly higher F st value were detected in genes associated with male reproduction, such as GAL3ST1, IFT88, and TSSK2, which were significantly upregulated during artificial breeding. This suggests a potential role of sperm-associated genes in the rapid evolutionary response of M. lateralis to selection in laboratory conditions. Overall, our findings highlight the phenotypic and genetic changes, as well as selection signatures, in M. lateralis during artificial breeding. This contributes to understanding their adaptation to laboratory conditions and underscores the potential for using this species to explore the adaptive evolution of bivalves.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Ang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Mingxuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Moli Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Xuefeng Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Zhi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding EngineeringSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
| | - Liping Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Yantai Marine Economic Research InstituteYantaiChina
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding EngineeringSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory of Tropical Marine Germplasm Resources and Breeding EngineeringSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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Pugacheva EM, Bhatt DN, Rivero-Hinojosa S, Tajmul M, Fedida L, Price E, Ji Y, Loukinov D, Strunnikov AV, Ren B, Lobanenkov VV. BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome Biol 2024; 25:40. [PMID: 38297316 PMCID: PMC10832218 DOI: 10.1186/s13059-024-03175-0] [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: 05/17/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mechanisms underpinning the activation of alternative promoters. RESULTS Here we describe how alternative cancer-testis-specific transcription is activated. We show that intergenic and intronic CTCF binding sites, which are transcriptionally inert in normal somatic cells, could be epigenetically reprogrammed into active de novo promoters in germ and cancer cells. BORIS/CTCFL, the testis-specific paralog of the ubiquitously expressed CTCF, triggers the epigenetic reprogramming of CTCF sites into units of active transcription. BORIS binding initiates the recruitment of the chromatin remodeling factor, SRCAP, followed by the replacement of H2A histone with H2A.Z, resulting in a more relaxed chromatin state in the nucleosomes flanking the CTCF binding sites. The relaxation of chromatin around CTCF binding sites facilitates the recruitment of multiple additional transcription factors, thereby activating transcription from a given binding site. We demonstrate that the epigenetically reprogrammed CTCF binding sites can drive the expression of cancer-testis genes, long noncoding RNAs, retro-pseudogenes, and dormant transposable elements. CONCLUSIONS Thus, BORIS functions as a transcription factor that epigenetically reprograms clustered CTCF binding sites into transcriptional start sites, promoting transcription from alternative promoters in both germ cells and cancer cells.
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Affiliation(s)
- Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Dharmendra Nath Bhatt
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Md Tajmul
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liron Fedida
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emma Price
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yon Ji
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, Center for Epigenomics, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, 92093-0653, USA
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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Akhtar MS, Akhter N, Talat A, Alharbi RA, Sindi AAA, Klufah F, Alyahyawi HE, Alruwetei A, Ahmad A, Zamzami MA, Deo S, Husain SA, Badi OA, Khan MJ. Association of mutation and expression of the brother of the regulator of imprinted sites (BORIS) gene with breast cancer progression. Oncotarget 2023; 14:528-541. [PMID: 37235839 DOI: 10.18632/oncotarget.28442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
INTRODUCTION The BORIS, 11 zinc-finger transcription factors, is a member of the cancer-testis antigen (CTA) family. It is mapped to chromosome number 20q13.2 and this region is genetically linked to the early onset of breast cancer. The current study analyzed the correlation between BORIS mutations and the expression of the protein in breast cancer cases. MATERIALS AND METHODS A population-based study including a total of 155 breast cancer tissue samples and an equal number of normal adjacent tissues from Indian female breast cancer patients was carried out. Mutations of the BORIS gene were detected by polymerase chain reaction-single standard confirmation polymorphisms (PCR-SSCP) and automated DNA sequencing and by immunohistochemistry for BORIS protein expression were performed. The observed findings were correlated with several clinicopathological parameters to find out the clinical relevance of associations. RESULTS Of all the cases 16.12% (25/155) showed mutations in the BORIS gene. The observed mutations present on codon 329 are missense, leading to Val> Ile (G>A) change on exon 5 of the BORIS gene. A significant association was observed between mutations of the BORIS gene and some clinicopathological features like nodal status (p = 0.013), estrogen receptor (ER) expression (p = 0.008), progesterone receptor (PR) expression (p = 0.039), clinical stage (p = 0.010) and menopausal status (p = 0.023). The protein expression analysis showed 20.64% (32/155) samples showing low or no expression (+), 34.19% (53/155) with moderate expression (++), and 45.17% (70/155) showing high expression (+++) of BORIS protein. A significant association was observed between the expression of BORIS protein and clinicopathological features like clinical stage (p = 0.013), nodal status (p = 0.049), ER expression (p = 0.039), and PR expression (p = 0.027). When mutation and protein expression were correlated in combination with clinicopathological parameters a significant association was observed in the category of high (+++) level of BORIS protein expression (p = 0.017). CONCLUSION The BORIS mutations and high protein expression occur frequently in carcinoma of the breast suggesting their association with the onset and progression of breast carcinoma. Further, the BORIS has the potential to be used as a biomarker.
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Affiliation(s)
- Mohammad Salman Akhtar
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naseem Akhter
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Arshi Talat
- Department of Orthodontics and Dentofacial Orthopedics, ITS Dental College, Hospital and Research Centre, Greater Noida, Delhi-NCR, India
| | - Raed A Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Faisal Klufah
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Hanan E Alyahyawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha, Saudi Arabia
| | - Abdulmohsen Alruwetei
- Department of Medical Laboratory, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Svs Deo
- Department of Surgical Oncology, BRA- IRCH, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Syed Akhtar Husain
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Osama A Badi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Torres-Flores U, Díaz-Espinosa F, López-Santaella T, Rebollar-Vega R, Vázquez-Jiménez A, Taylor IJ, Ortiz-Hernández R, Echeverría OM, Vázquez-Nin GH, Gutierrez-Ruiz MC, De la Rosa-Velázquez IA, Resendis-Antonio O, Hernández-Hernandez A. Spermiogenesis alterations in the absence of CTCF revealed by single cell RNA sequencing. Front Cell Dev Biol 2023; 11:1119514. [PMID: 37065848 PMCID: PMC10097911 DOI: 10.3389/fcell.2023.1119514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
CTCF is an architectonic protein that organizes the genome inside the nucleus in almost all eukaryotic cells. There is evidence that CTCF plays a critical role during spermatogenesis as its depletion produces abnormal sperm and infertility. However, defects produced by its depletion throughout spermatogenesis have not been fully characterized. In this work, we performed single cell RNA sequencing in spermatogenic cells with and without CTCF. We uncovered defects in transcriptional programs that explain the severity of the damage in the produced sperm. In the early stages of spermatogenesis, transcriptional alterations are mild. As germ cells go through the specialization stage or spermiogenesis, transcriptional profiles become more altered. We found morphology defects in spermatids that support the alterations in their transcriptional profiles. Altogether, our study sheds light on the contribution of CTCF to the phenotype of male gametes and provides a fundamental description of its role at different stages of spermiogenesis.
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Affiliation(s)
- Ulises Torres-Flores
- Graduate Program in Experimental Biology, DCBS, Universidad Autónoma Metropolitana, Unidad Iztapalapa, México City, Mexico
- Biología de Células Individuales (BIOCELIN), Laboratorio de Investigación en Patología Experimental, Hospital Infantíl de México Federico Gómez, México City, Mexico
| | - Fernanda Díaz-Espinosa
- Biología de Células Individuales (BIOCELIN), Laboratorio de Investigación en Patología Experimental, Hospital Infantíl de México Federico Gómez, México City, Mexico
| | - Tayde López-Santaella
- Biología de Células Individuales (BIOCELIN), Laboratorio de Investigación en Patología Experimental, Hospital Infantíl de México Federico Gómez, México City, Mexico
| | - Rosa Rebollar-Vega
- Coordinación de la Investigación Científica-Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas yNutrición Salvador Zubirán, México City, Mexico
| | - Aarón Vázquez-Jiménez
- Coordinación de la Investigación Científica-Red de Apoyo a la Investigación-Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México City, Mexico
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Ian J. Taylor
- BD Life Sciences Informatics, Ashland, OR, United States
| | - Rosario Ortiz-Hernández
- Laboratorio de Microscopía Electrónica, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Olga M. Echeverría
- Laboratorio de Microscopía Electrónica, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gerardo H. Vázquez-Nin
- Laboratorio de Microscopía Electrónica, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María Concepción Gutierrez-Ruiz
- Laboratorio de Fisiología Celular y Medicina Traslacional, Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana-I, Mexico City, Mexico
| | - Inti Alberto De la Rosa-Velázquez
- Coordinación de la Investigación Científica-Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas yNutrición Salvador Zubirán, México City, Mexico
| | - Osbaldo Resendis-Antonio
- Coordinación de la Investigación Científica-Red de Apoyo a la Investigación-Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, México City, Mexico
- Human Systems Biology Laboratory, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
- *Correspondence: Osbaldo Resendis-Antonio, ; Abrahan Hernández-Hernandez,
| | - Abrahan Hernández-Hernandez
- Biología de Células Individuales (BIOCELIN), Laboratorio de Investigación en Patología Experimental, Hospital Infantíl de México Federico Gómez, México City, Mexico
- *Correspondence: Osbaldo Resendis-Antonio, ; Abrahan Hernández-Hernandez,
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Zhou S, Li L, Zhang M, Qin Y, Li B. The function of brother of the regulator of imprinted sites in cancer development. Cancer Gene Ther 2023; 30:236-244. [PMID: 36376421 DOI: 10.1038/s41417-022-00556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022]
Abstract
As Douglas Hanahan and Robert Weinberg compiled, there are nine hallmarks of cancer that are conducive to cancer cell development and survival. Previous studies showed that brother of the regulator of imprinted sites (BORIS) might promote cancer progression through these aspects. The competition between BORIS and CCCTC-binding factor (CTCF), which is crucial in the formation of chromatin loops, affects the normal function of CTCF and leads to neoplasia and deformity. In addition, BORIS belongs to the cancer-testis antigen families, which are potential targets in cancer diagnosis and treatment. Herein, we discuss the function and mechanisms of BORIS, especially in cancer development.
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Affiliation(s)
- Siqi Zhou
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China
| | - Lian Li
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China
| | - Ming Zhang
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China
| | - Yang Qin
- Department of Biochemistry and Molecular Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, No. 17, Section 3, South Renmin Road, Chengdu, 610041, Sichuan Province, China.
| | - Bo Li
- Department of Liver Surgery, West China Hospital, Sichuan University Medical School, 37 Guo Xue Road, Chengdu, 610041, Sichuan Province, China.
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8
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Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line. Proc Natl Acad Sci U S A 2022; 119:e2204071119. [PMID: 36179046 PMCID: PMC9549395 DOI: 10.1073/pnas.2204071119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This work originated from mining of cancer genome data and proceeded to analyze the effects of ectopic expression of meiotic cohesins in mitotic cells in culture. In the process, apart from conclusively answering the question on mechanisms for RAD21L toxicity and its underrepresentation in tumor transcriptomes, we found an association of meiotic cohesin binding with BORIS/CTCFL sites in the normal testis. We also elucidated the patterns and outcomes of meiotic cohesin binding to chromosomes in model cell lines. Furthermore, we uncovered that RAD21L-based meiotic cohesin possesses a self-contained chromosome restructuring activity able to trigger sustainable but imperfect mitotic arrest leading to chromosomal instability. The discovered epigenomic and genetic mechanisms can be relevant to chromosome instability in cancer. Many tumors express meiotic genes that could potentially drive somatic chromosome instability. While germline cohesin subunits SMC1B, STAG3, and REC8 are widely expressed in many cancers, messenger RNA and protein for RAD21L subunit are expressed at very low levels. To elucidate the potential of meiotic cohesins to contribute to genome instability, their expression was investigated in human cell lines, predominately in DLD-1. While the induction of the REC8 complex resulted in a mild mitotic phenotype, the expression of the RAD21L complex produced an arrested but viable cell pool, thus providing a source of DNA damage, mitotic chromosome missegregation, sporadic polyteny, and altered gene expression. We also found that genomic binding profiles of ectopically expressed meiotic cohesin complexes were reminiscent of their corresponding specific binding patterns in testis. Furthermore, meiotic cohesins were found to localize to the same sites as BORIS/CTCFL, rather than CTCF sites normally associated with the somatic cohesin complex. These findings highlight the existence of a germline epigenomic memory that is conserved in cells that normally do not express meiotic genes. Our results reveal a mechanism of action by unduly expressed meiotic cohesins that potentially links them to aneuploidy and chromosomal mutations in affected cells.
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Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. Genet Sel Evol 2022; 54:30. [PMID: 35484510 PMCID: PMC9052598 DOI: 10.1186/s12711-022-00718-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/05/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). RESULTS The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. CONCLUSIONS Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.
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10
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Berger T, Vanselow J, Conley A, Almand TJ, Nitta-Oda BS. Multifaceted epigenetic regulation of porcine testicular aromatase. Mol Cell Endocrinol 2022; 541:111526. [PMID: 34856344 DOI: 10.1016/j.mce.2021.111526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/27/2021] [Accepted: 11/28/2021] [Indexed: 11/20/2022]
Abstract
Testicular aromatase catalyzes the synthesis of estradiol, which contributes to regulation of porcine Sertoli cell proliferation and postpubertal maintenance of Sertoli cell numbers. Although aromatase enzymatic activity decreases with age and is persistently reprogrammed by prepubertal treatment with the aromatase inhibitor letrozole, the molecular bases for regulation have not been identified. DNA methylation was examined as a potential regulatory mechanism using DNA from Leydig cells isolated from 16-, 40-, and 68-week-old boars and from 68- week-old littermates treated with the aromatase inhibitor, letrozole. Methylation levels of individual CpG dinucleotides located in the distal untranslated exon 1 of the relevant aromatase encoding gene, CYP19A3, were quite high in Leydig cell DNA, and increased further with maturity of boar (P < 0.05), while aromatase activity and transcript abundance decreased more than two-fold. However, reduced aromatase activity following letrozole treatment was not accompanied by altered DNA methylation. Testicular expression of miR378 was altered by prepubertal treatment with letrozole. The data provide evidence for two different epigenetic mechanisms that regulate aromatase expression and enzymatic activity in the boar testis.
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Affiliation(s)
- Trish Berger
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA.
| | - Jens Vanselow
- Research Institute for Farm Animal Biology FBN, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
| | - Alan Conley
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Tana Jo Almand
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA.
| | - Barbara S Nitta-Oda
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA.
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11
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Liang J, Liu X, Yang P, Yao Z, Qu K, Wang H, Zhang Z, Liang H, Cheng B, Li Z, Ru B, Zhang J, Qi Z, Wang E, Lei C, Chen H, Huang B, Huang Y. Copy number variation of GAL3ST1 gene is associated with growth traits of Chinese cattle. Anim Biotechnol 2022:1-7. [DOI: 10.1080/10495398.2021.1996385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Juntong Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, China
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhi Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Hongli Wang
- Jiaxian Animal Husbandry Bureau, Jiaxian, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | | | | | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou, China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Zengfang Qi
- Jiaxian Animal Husbandry Bureau, Jiaxian, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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12
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Ghieh F, Barbotin AL, Swierkowski-Blanchard N, Leroy C, Fortemps J, Gerault C, Hue C, Mambu Mambueni H, Jaillard S, Albert M, Bailly M, Izard V, Molina-Gomes D, Marcelli F, Prasivoravong J, Serazin V, Dieudonne MN, Delcroix M, Garchon HJ, Louboutin A, Mandon-Pepin B, Ferlicot S, Vialard F. OUP accepted manuscript. Hum Reprod 2022; 37:1334-1350. [PMID: 35413094 PMCID: PMC9156845 DOI: 10.1093/humrep/deac057] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- F Ghieh
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - A L Barbotin
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - N Swierkowski-Blanchard
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- Département de Gynécologie Obstétrique, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - C Leroy
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - J Fortemps
- Service d’Anatomie Pathologique, CHI de Poissy/Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - C Gerault
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - C Hue
- Department of Biotechnology and Health, UVSQ, Université Paris-Saclay, Inserm UMR 1173, Montigny-le-Bretonneux, France
| | - H Mambu Mambueni
- Department of Biotechnology and Health, UVSQ, Université Paris-Saclay, Inserm UMR 1173, Montigny-le-Bretonneux, France
| | - S Jaillard
- Service de Cytogénétique, CHU Rennes, Rennes, France
- INSERM, EHESP, IRSET—UMR_S 1085, Université Rennes 1, Rennes, France
| | - M Albert
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - M Bailly
- Département de Gynécologie Obstétrique, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - V Izard
- Service d’Urologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - D Molina-Gomes
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - F Marcelli
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - J Prasivoravong
- Institut de Biologie de la Reproduction-Spermiologie-CECOS, Hôpital Jeanne de Flandre, Centre Hospitalier et Universitaire, Lille, France
| | - V Serazin
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - M N Dieudonne
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - M Delcroix
- Département de Génétique, Laboratoire de Biologie Médicale, CHI de Poissy/Saint-Germain-en-Laye, Poissy, France
| | - H J Garchon
- Department of Biotechnology and Health, UVSQ, Université Paris-Saclay, Inserm UMR 1173, Montigny-le-Bretonneux, France
| | - A Louboutin
- Service d’Anatomie Pathologique, CHI de Poissy/Saint-Germain-en-Laye, Saint-Germain-en-Laye, France
| | - B Mandon-Pepin
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- École Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - S Ferlicot
- Service d’Anatomie Pathologique, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - F Vialard
- Correspondence address. Tel: +33-139-274-700; E-mail:
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13
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Rivero-Hinojosa S, Pugacheva EM, Kang S, Méndez-Catalá CF, Kovalchuk AL, Strunnikov AV, Loukinov D, Lee JT, Lobanenkov VV. The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis. Nat Commun 2021; 12:3846. [PMID: 34158481 PMCID: PMC8219828 DOI: 10.1038/s41467-021-24140-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/28/2021] [Indexed: 01/03/2023] Open
Abstract
CTCF is a key organizer of the 3D genome. Its specialized paralog, BORIS, heterodimerizes with CTCF but is expressed only in male germ cells and in cancer states. Unexpectedly, BORIS-null mice have only minimal germ cell defects. To understand the CTCF-BORIS relationship, mouse models with varied CTCF and BORIS levels were generated. Whereas Ctcf+/+Boris+/+, Ctcf+/-Boris+/+, and Ctcf+/+Boris-/- males are fertile, Ctcf+/-Boris-/- (Compound Mutant; CM) males are sterile. Testes with combined depletion of both CTCF and BORIS show reduced size, defective meiotic recombination, increased apoptosis, and malformed spermatozoa. Although CM germ cells exhibit only 25% of CTCF WT expression, chromatin binding of CTCF is preferentially lost from CTCF-BORIS heterodimeric sites. Furthermore, CM testes lose the expression of a large number of spermatogenesis genes and gain the expression of developmentally inappropriate genes that are "toxic" to fertility. Thus, a combined action of CTCF and BORIS is required to both repress pre-meiotic genes and activate post-meiotic genes for a complete spermatogenesis program.
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Affiliation(s)
- Samuel Rivero-Hinojosa
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, USA.
| | - Elena M Pugacheva
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Sungyun Kang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Claudia Fabiola Méndez-Catalá
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Genetics and Molecular Oncology, Building A4, Faculty of Higher Studies (FES) Iztacala, National Autonomous University of Mexico (UNAM), Tlalnepantla, State of Mexico, Mexico
| | - Alexander L Kovalchuk
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, Guangzhou, China
| | - Dmitri Loukinov
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Victor V Lobanenkov
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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14
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Sati L, Soygur B, Goksu E, Bassorgun CI, McGrath J. CTCFL expression is associated with cerebral vascular abnormalities. Tissue Cell 2021; 72:101528. [PMID: 33756271 DOI: 10.1016/j.tice.2021.101528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/06/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
CTCFL is expressed in testis, oocytes and embryonic stem cells, and is aberrantly expressed in malignant cells, and is classified as a cancer-testis gene. We have previously shown by using a tetracycline-inducible Ctcfl transgene that inappropriate expression of Ctcfl negatively impacts fetal development and causes early postnatal lethality in the mouse. The affected pups displayed severe vascular abnormalities and localized hemorrhages in the brain evocative of cerebral cavernous malformations (CCM) and arteriovenous malformations (AVM) in humans. Thus, we aim to analyze; a) the presence of CCM-related proteins CCM1/KRIT1, CCM2/malcavernin and CCM3/PDCD10 in Ctcfl transgenic animals and, b) whether there is CTCFL expression in human CCM and AVM tissues. Ctcfl transgenic animals exhibited increased CD31 expression in vascular areas of the dermis and periadnexal regions but no difference was observed for vWF and α-SMA expressions. CCM-related proteins CCM1/KRIT1, CCM2/malcavernin and CCM3/PDCD10 were aberrantly expressed in coronal sections of the head in transgenic animals. We also observed CTCFL expression in human CCMs and AVMs. The induced expression of CTCFL resulting in vascular brain malformations in mice combined with the presence of CTCFL in human vascular malformations provide new insights into the role of this gene in vascular development in humans.
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Affiliation(s)
- Leyla Sati
- Department of Histology and Embryology, Akdeniz University School of Medicine, Antalya, Turkey.
| | - Bikem Soygur
- Department of Histology and Embryology, Akdeniz University School of Medicine, Antalya, Turkey; Department of Obstetrics, Gynecology and Reproductive Sciences, Center for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Ethem Goksu
- Department of Neurosurgery, Akdeniz University School of Medicine, Antalya, Turkey
| | | | - James McGrath
- Departments of Genetics and Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
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15
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Ganteil A, Rodriguez-Ramilo ST, Ligonesche B, Larzul C. Characterization of Autozygosity in Pigs in Three-Way Crossbreeding. Front Genet 2021; 11:584556. [PMID: 33584790 PMCID: PMC7876413 DOI: 10.3389/fgene.2020.584556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Crossbreeding in livestock can be used to increase genetic diversity. The resulting increase in variability is related to the heterozygosity of the crossbred animal. The evolution of diversity during crossbreeding can be assessed using genomic data. The objective of this study was to describe patterns of runs of homozygosity (ROH) in animals resulting from three-way crossbreeding, from parental pure lines, and in their crossbred offspring. The crossbreeding scheme consisted of a first crossbreeding Pietrain boars and Large White sows, after which the offspring of the Pietrain × Large White were crossed with Duroc boars. The offspring of the second crossbreeding are called G0, the offspring of G0 boars and G0 sows are called G1. All the animals were genotyped using the Illumina SNP60 porcine chip. After filtering, analyses were performed with 2,336 animals and 48,579 autosomal single nucleotide polymorphism (SNP). The mean ROH-based inbreeding coefficients were shown to be 0.27 ± 0.05, 0.23 ± 0.04, and 0.26 ± 0.04 for Duroc, Large White, and Pietrain, respectively. ROH were detected in the Pietrain × Large White crossbred but the homozygous segments were fewer and smaller than in their parents. Similar results were obtained in the G0 crossbred. However, in the G1 crossbreds the number and the size of ROH were higher than in G0 parents. Similar ROH hotspots were detected on SSC1, SSC4, SSC7, SSC9, SSC13, SSC14, and SSC15 in both G0 and G1 animals. Long ROH (>16 Mb) were observed in G1 animals, suggesting regions with low recombination rates. The conservation of these homozygous segments in the three crossbred populations means that some haplotypes were shared between parental breeds. Gene annotation in ROH hotspots in G0 animals identified genes related to production traits including carcass composition and reproduction. These findings advance our understanding of how to manage genetic diversity in crossbred populations.
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Affiliation(s)
- Audrey Ganteil
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.,SAS NUCLEUS, Le Rheu, France
| | | | | | - Catherine Larzul
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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Aurrière J, Goudenège D, Baris OR, Boguenet M, May-Panloup P, Lenaers G, Khiati S. Cancer/Testis Antigens into mitochondria: a hub between spermatogenesis, tumorigenesis and mitochondrial physiology adaptation. Mitochondrion 2020; 56:73-81. [PMID: 33220498 DOI: 10.1016/j.mito.2020.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/18/2020] [Accepted: 11/02/2020] [Indexed: 01/05/2023]
Abstract
Cancer/Testis Antigens (CTAs) genes are expressed only during spermatogenesis and tumorigenesis. Both processes share common specific metabolic adaptation related to energy supply, with a glucose to lactate gradient, leading to changes in mitochondrial physiology paralleling CTAs expression. In this review, we address the role of CTAs in mitochondria (mitoCTAs), by reviewing all published data, and assessing the putative localization of CTAs by screening for the presence of a mitochondrial targeting sequence (MTS). We evidenced that among the 276 CTAs, five were already shown to interfere with mitochondrial activities and 67 display a potential MTS.
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Affiliation(s)
- Jade Aurrière
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - David Goudenège
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France; Departments of Biochemistry and Genetics, University Hospital Angers, Angers, France
| | - Olivier R Baris
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - Magalie Boguenet
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - Pascale May-Panloup
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France; Reproductive Biology Unit, Angers University Hospital, 49000 Angers, France
| | - Guy Lenaers
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France
| | - Salim Khiati
- MitoLab Team, Institut MitoVasc, CNRS UMR6015, INSERM U1083, Angers University, Angers, France.
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Early vertebrate origin of CTCFL, a CTCF paralog, revealed by proximity-guided shark genome scaffolding. Sci Rep 2020; 10:14629. [PMID: 32884037 PMCID: PMC7471279 DOI: 10.1038/s41598-020-71602-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022] Open
Abstract
The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in diverse animals. The gene encoding this protein has a paralog which was first identified to be expressed exclusively in the testis in mammals and designated as CTCFL (also called BORIS). CTCFL orthologs were reported only among amniotes, and thus CTCFL was once thought to have arisen in the amniote lineage. In this study, we identified elasmobranch CTCFL orthologs, and investigated its origin with the aid of a shark genome assembly improved by proximity-guided scaffolding. Our analysis employing evolutionary interpretation of syntenic gene location suggested an earlier timing of the gene duplication between CTCF and CTCFL than previously thought, that is, around the common ancestor of extant vertebrates. Also, our transcriptomic sequencing revealed a biased expression of the catshark CTCFL in the testis, suggesting the origin of the tissue-specific localization in mammals more than 400 million years ago. To understand the historical process of the functional consolidation of the long-standing chromatin regulator CTCF, its additional paralogs remaining in some of the descendant lineages for spatially restricted transcript distribution should be taken into consideration.
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18
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Torres-Flores U, Hernández-Hernández A. The Interplay Between Replacement and Retention of Histones in the Sperm Genome. Front Genet 2020; 11:780. [PMID: 32765595 PMCID: PMC7378789 DOI: 10.3389/fgene.2020.00780] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/30/2020] [Indexed: 12/21/2022] Open
Abstract
The genome of eukaryotes is highly organized within the cell nucleus, this organization per se elicits gene regulation and favors other mechanisms like cell memory throughout histones and their post-translational modifications. In highly specialized cells, like sperm, the genome is mostly organized by protamines, yet a significant portion of it remains organized by histones. This protamine-histone-DNA organization, known as sperm epigenome, is established during spermiogenesis. Specific histones and their post-translational modifications are retained at specific genomic sites and during embryo development these sites recapitulate their histone profile that harbored in the sperm nucleus. It is known that histones are the conduit of epigenetic memory from cell to cell, hence histones in the sperm epigenome may have a role in transmitting epigenetic memory from the sperm to the embryo. However, the exact function and mechanism of histone retention remains elusive. During spermatogenesis, most of the histones that organize the genome are replaced by protamines and their retention at specific regions may be deeply intertwined with the eviction and replacement mechanism. In this review we will cover some relevant aspects of histone replacement that in turn may help us to contextualize histone retention. In the end, we focus on the architectonical protein CTCF that is, so far, the only factor that has been directly linked to the histone retention process.
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Affiliation(s)
- Ulises Torres-Flores
- Biología de Células Individuales (BIOCELIN), Laboratorio de Investigación en Patología Experimental, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Abrahan Hernández-Hernández
- Biología de Células Individuales (BIOCELIN), Laboratorio de Investigación en Patología Experimental, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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19
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Nishana M, Ha C, Rodriguez-Hernaez J, Ranjbaran A, Chio E, Nora EP, Badri SB, Kloetgen A, Bruneau BG, Tsirigos A, Skok JA. Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation. Genome Biol 2020; 21:108. [PMID: 32393311 PMCID: PMC7212617 DOI: 10.1186/s13059-020-02024-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ubiquitously expressed CTCF is involved in numerous cellular functions, such as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally only present in the testis. However, it is also aberrantly expressed in many cancers. While it is known that shared and unique zinc finger sequences in CTCF and CTCFL enable CTCFL to bind competitively to a subset of CTCF binding sites as well as its own unique locations, the impact of CTCFL on chromosome organization and gene expression has not been comprehensively analyzed in the context of CTCF function. Using an inducible complementation system, we analyze the impact of expressing CTCFL and CTCF-CTCFL chimeric proteins in the presence or absence of endogenous CTCF to clarify the relative and combined contribution of CTCF and CTCFL to chromosome organization and transcription. RESULTS We demonstrate that the N terminus of CTCF interacts with cohesin which explains the requirement for convergent CTCF binding sites in loop formation. By analyzing CTCF and CTCFL binding in tandem, we identify phenotypically distinct sites with respect to motifs, targeting to promoter/intronic intergenic regions and chromatin folding. Finally, we reveal that the N, C, and zinc finger terminal domains play unique roles in targeting each paralog to distinct binding sites to regulate transcription, chromatin looping, and insulation. CONCLUSION This study clarifies the unique and combined contribution of CTCF and CTCFL to chromosome organization and transcription, with direct implications for understanding how their co-expression deregulates transcription in cancer.
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Affiliation(s)
| | - Caryn Ha
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | | | - Ali Ranjbaran
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Erica Chio
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Elphege P Nora
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA
| | - Sana B Badri
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Andreas Kloetgen
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, 10016, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA.,Department of Pediatrics, University of California, San Francisco, CA, 94158, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA.,Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, 10016, USA
| | - Jane A Skok
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA. .,Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, 10016, USA.
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20
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Shi L, Wang L, Liu J, Deng T, Yan H, Zhang L, Liu X, Gao H, Hou X, Wang L, Zhao F. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population. J Anim Sci Biotechnol 2020; 11:46. [PMID: 32355558 PMCID: PMC7187514 DOI: 10.1186/s40104-020-00447-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/12/2020] [Indexed: 01/24/2023] Open
Abstract
Background Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and pedigree (FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. Results In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_total and FHOM, while the lowest was − 0.083 between FGRM and FPED. The correlations between FPED and FROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. Conclusion FROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
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Affiliation(s)
- Liangyu Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ligang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jiaxin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Tianyu Deng
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hua Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Longchao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xin Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hongmei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xinhua Hou
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lixian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (poultry) of Ministry of Agricuture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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21
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Debaugny RE, Skok JA. CTCF and CTCFL in cancer. Curr Opin Genet Dev 2020; 61:44-52. [PMID: 32334335 PMCID: PMC7893514 DOI: 10.1016/j.gde.2020.02.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/11/2020] [Accepted: 02/22/2020] [Indexed: 12/28/2022]
Abstract
CTCF plays a key role in organizing chromatin into TAD structures but it can also function as a transcription factor. CTCFL (CTCF-like), the paralog of CTCF, is normally transiently expressed in pre-meiotic male germ cells together with ubiquitously expressed CTCF. It plays a unique role in spermatogenesis by regulating expression of testis-specific genes. Genetic alterations in CTCF and its paralog CTCFL have both been found in numerous cancers, but it remains unknown to what extent CTCFL deregulates transcription on its own or by opposing CTCF. Here, we discuss some of the potential mechanisms by which these two proteins could alter gene regulation and contribute to oncogenic transcriptional programs.
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Affiliation(s)
- Roxanne E Debaugny
- Dept. of Pathology, New York University Langone Health, New York, NY 10016, USA
| | - Jane A Skok
- Dept. of Pathology, New York University Langone Health, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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22
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Large-scale chromatin organisation in interphase, mitosis and meiosis. Biochem J 2019; 476:2141-2156. [DOI: 10.1042/bcj20180512] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/17/2023]
Abstract
AbstractThe spatial configuration of chromatin is fundamental to ensure any given cell can fulfil its functional duties, from gene expression to specialised cellular division. Significant technological innovations have facilitated further insights into the structure, function and regulation of three-dimensional chromatin organisation. To date, the vast majority of investigations into chromatin organisation have been conducted in interphase and mitotic cells leaving meiotic chromatin relatively unexplored. In combination, cytological and genome-wide contact frequency analyses in mammalian germ cells have recently demonstrated that large-scale chromatin structures in meiotic prophase I are reminiscent of the sequential loop arrays found in mitotic cells, although interphase-like segmentation of transcriptionally active and inactive regions are also evident along the length of chromosomes. Here, we discuss the similarities and differences of such large-scale chromatin architecture, between interphase, mitotic and meiotic cells, as well as their functional relevance and the proposed modulatory mechanisms which underlie them.
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23
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Bergmaier P, Weth O, Dienstbach S, Boettger T, Galjart N, Mernberger M, Bartkuhn M, Renkawitz R. Choice of binding sites for CTCFL compared to CTCF is driven by chromatin and by sequence preference. Nucleic Acids Res 2019; 46:7097-7107. [PMID: 29860503 PMCID: PMC6101590 DOI: 10.1093/nar/gky483] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/23/2018] [Indexed: 01/22/2023] Open
Abstract
The two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types in addition to other cell types. Both factors share the highly conserved DNA binding domain and are bound to DNA sequences with an identical consensus. In contrast, both factors differ substantially in the number of bound sites in the genome. Here, we addressed the molecular features for this binding specificity. In contrast to CTCF we found CTCFL highly enriched at ‘open’ chromatin marked by H3K27 acetylation, H3K4 di- and trimethylation, H3K79 dimethylation and H3K9 acetylation plus the histone variant H2A.Z. CTCFL is enriched at transcriptional start sites and regions bound by transcription factors. Consequently, genes deregulated by CTCFL are highly cell specific. In addition to a chromatin-driven choice of binding sites, we determined nucleotide positions critical for DNA binding by CTCFL, but not by CTCF.
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Affiliation(s)
- Philipp Bergmaier
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Oliver Weth
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Sven Dienstbach
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Thomas Boettger
- Department Cardiac Development and Remodelling, Max-Planck-Institute, D61231 Bad Nauheim, Germany
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, 3000CA Rotterdam, The Netherlands
| | - Marco Mernberger
- Institute of Molecular Oncology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, 35392 Giessen, Germany
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24
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Hillman JC, Pugacheva EM, Barger CJ, Sribenja S, Rosario S, Albahrani M, Truskinovsky AM, Stablewski A, Liu S, Loukinov DI, Zentner GE, Lobanenkov VV, Karpf AR, Higgins MJ. BORIS Expression in Ovarian Cancer Precursor Cells Alters the CTCF Cistrome and Enhances Invasiveness through GALNT14. Mol Cancer Res 2019; 17:2051-2062. [PMID: 31292201 DOI: 10.1158/1541-7786.mcr-19-0310] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/07/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022]
Abstract
High-grade serous carcinoma (HGSC) is the most aggressive and predominant form of epithelial ovarian cancer and the leading cause of gynecologic cancer-related death. We have previously shown that CTCFL (also known as BORIS, Brother of the Regulator of Imprinted Sites) is expressed in most ovarian cancers, and is associated with global and promoter-specific DNA hypomethylation, advanced tumor stage, and poor prognosis. To explore its role in HGSC, we expressed BORIS in human fallopian tube secretory epithelial cells (FTSEC), the presumptive cells of origin for HGSC. BORIS-expressing cells exhibited increased motility and invasion, and BORIS expression was associated with alterations in several cancer-associated gene expression networks, including fatty acid metabolism, TNF signaling, cell migration, and ECM-receptor interactions. Importantly, GALNT14, a glycosyltransferase gene implicated in cancer cell migration and invasion, was highly induced by BORIS, and GALNT14 knockdown significantly abrogated BORIS-induced cell motility and invasion. In addition, in silico analyses provided evidence for BORIS and GALNT14 coexpression in several cancers. Finally, ChIP-seq demonstrated that expression of BORIS was associated with de novo and enhanced binding of CTCF at hundreds of loci, many of which correlated with activation of transcription at target genes, including GALNT14. Taken together, our data indicate that BORIS may promote cell motility and invasion in HGSC via upregulation of GALNT14, and suggests BORIS as a potential therapeutic target in this malignancy. IMPLICATIONS: These studies provide evidence that aberrant expression of BORIS may play a role in the progression to HGSC by enhancing the migratory and invasive properties of FTSEC.
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Affiliation(s)
- Joanna C Hillman
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Carter J Barger
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sirinapa Sribenja
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Spencer Rosario
- Department of Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Mustafa Albahrani
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Aimee Stablewski
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Dmitri I Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Gabriel E Zentner
- Department of Biology, Indiana University, Bloomington, Indiana.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
| | - Adam R Karpf
- Eppley Institute and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York.
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25
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Loukinov D. Targeting CTCFL/BORIS for the immunotherapy of cancer. Cancer Immunol Immunother 2018; 67:1955-1965. [PMID: 30390146 PMCID: PMC11028242 DOI: 10.1007/s00262-018-2251-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 07/13/2018] [Indexed: 10/27/2022]
Abstract
Cancer vaccines have great potential in the fight against metastatic malignancies. Current anti-tumor immunotherapy is hindered by existing tolerance to tumor-associated antigens (TAA) and tumor escape using various mechanisms, highlighting the need for improved targets for immunotherapy. The cancer-testis antigen CTCFL/BORIS was discovered 16 years ago and possesses all features necessary for an ideal TAA. Recently CTCFL/BORIS has received additional attention as a target expressed in cancer stem cells (CSC). These cells drive tumor growth recurrence, metastasis, and treatment resistance. CTCFL/BORIS silencing leads to senescence and death of CSC. Therefore, an immunotherapeutic strategy that targets CTCFL/BORIS may lead to the selective destruction of CSC and potential eradication of metastatic disease. The high immunotherapeutic potential of CTCFL/BORIS antigen was shown in a stringent 4T1 mouse model of breast cancer. Using these highly metastatic, poorly immunogenic carcinoma cells inoculated into T-helper2 prone mice, we showed that DC fed with recombinant CTCFL/BORIS as an immunogen inhibited tumor growth and reduced the number of metastases in distant organs. About 20% of CTCFL/BORIS immunized animals were tumor free. 50% of animals remained metastasis free. Those having metastasis showed at least tenfold fewer metastases compared to controls. In a rat model of breast cancer, we showed that alphavirus-based CTCFL/BORIS immunotherapy was capable of cancer elimination as we were able to cure 50% of animals. Based on the above data, we believe that translation of CTCFL/BORIS-targeting immunotherapeutic strategies to the clinic will provide new avenues for improving survival of breast cancer patients with advanced metastatic disease.
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Affiliation(s)
- Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, NIAID/NIH, Twinbrook 1, Room 1329, 5640 Fishers Lane, Rockville, MD, 20852, USA.
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26
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Soltanian S, Dehghani H. BORIS: a key regulator of cancer stemness. Cancer Cell Int 2018; 18:154. [PMID: 30323717 PMCID: PMC6173857 DOI: 10.1186/s12935-018-0650-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
BORIS (CTCFL) is a DNA binding protein which is involved in tumorigenesis. Although, there are different opinions on the level of gene expression and function of BORIS in normal and cancer tissues, the results of many studies have classified BORIS as a protein belonging to cancer/testis (CT) genes, which are identified as a group of genes that are expressed normally in testis, and abnormally in various types of cancers. In testis, BORIS induces the expression of some male germ cell/testis specific genes, and plays crucial roles during spermatogenesis and production of sperm. In tumorigenesis, the role of BORIS in the expression induction of some CT genes and oncogenes, as well as increasing proliferation/viability of cancer cells has been demonstrated in many researches. In addition to cancer cells, some believe that BORIS is also expressed in normal conditions and plays a universal function in cell division and regulation of genes. The following is a comprehensive review on contradictory views on the expression pattern and biological function of BORIS in normal, as well as cancer cells/tissues, and presents some evidence that support the expression of BORIS in cancer stem cells (CSCs) and advanced stage/poorer differentiation grade of cancers. Boris is involved in the regulation of CSC cellular and molecular features such as self-renewal, chemo-resistance, tumorigenicity, sphere-forming ability, and migration capacity. Finally, the role of BORIS in regulating two important signaling pathways including Wnt/β-catenin and Notch in CSCs, and its ability in recruiting transcription factors or chromatin-remodeling proteins to induce tumorigenesis is discussed.
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Affiliation(s)
- Sara Soltanian
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hesam Dehghani
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, 91775-1793 Iran
- Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Stem Cells and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
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27
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Green CD, Ma Q, Manske GL, Shami AN, Zheng X, Marini S, Moritz L, Sultan C, Gurczynski SJ, Moore BB, Tallquist MD, Li JZ, Hammoud SS. A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. Dev Cell 2018; 46:651-667.e10. [PMID: 30146481 DOI: 10.1016/j.devcel.2018.07.025] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/03/2018] [Accepted: 07/30/2018] [Indexed: 02/07/2023]
Abstract
Spermatogenesis requires intricate interactions between the germline and somatic cells. Within a given cross section of a seminiferous tubule, multiple germ and somatic cell types co-occur. This cellular heterogeneity has made it difficult to profile distinct cell types at different stages of development. To address this challenge, we collected single-cell RNA sequencing data from ∼35,000 cells from the adult mouse testis and identified all known germ and somatic cells, as well as two unexpected somatic cell types. Our analysis revealed a continuous developmental trajectory of germ cells from spermatogonia to spermatids and identified candidate transcriptional regulators at several transition points during differentiation. Focused analyses delineated four subtypes of spermatogonia and nine subtypes of Sertoli cells; the latter linked to histologically defined developmental stages over the seminiferous epithelial cycle. Overall, this high-resolution cellular atlas represents a community resource and foundation of knowledge to study germ cell development and in vivo gametogenesis.
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Affiliation(s)
| | - Qianyi Ma
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel L Manske
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | | | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Simone Marini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lindsay Moritz
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Caleb Sultan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Bethany B Moore
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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28
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Jabbari K, Heger P, Sharma R, Wiehe T. The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis. Life (Basel) 2018; 8:life8010004. [PMID: 29385718 PMCID: PMC5871936 DOI: 10.3390/life8010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or “CTCF-like” (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach. We find that CTCF has 52 direct interaction partners while CTCFL only has 19. Almost all interactors already existed before the emergence of CTCF and CTCFL. The unique secondary loss of CTCF from several nematodes is paralleled by a loss of two of its interactors, the polycomb repressive complex subunit SuZ12 and the multifunctional transcription factor TYY1. In contrast to earlier studies reporting the absence of BORIS from birds, we present evidence for a multigene synteny block containing CTCFL that is conserved in mammals, reptiles, and several species of birds, indicating that not the entire lineage of birds experienced a loss of CTCFL. Within this synteny block, BORIS and its genomic neighbors seem to be partitioned into two nested chromatin loops. The high expression of SPO11, RAE1, RBM38, and PMEPA1 in male tissues suggests a possible link between CTCFL, meiotic recombination, and fertility-associated phenotypes. Using the 65,700 exomes and the 1000 genomes data, we observed a higher number of intergenic, non-synonymous, and loss-of-function mutations in CTCFL than in CTCF, suggesting a reduced strength of purifying selection, perhaps due to less functional constraint.
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Affiliation(s)
- Kamel Jabbari
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Peter Heger
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Ranu Sharma
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
| | - Thomas Wiehe
- Cologne Biocenter, Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Köln, Germany.
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29
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Zhao J, Wang Y, Liang Q, Xu Y, Sang J. MAGEA1 inhibits the expression of BORIS via increased promoter methylation. J Cell Sci 2018; 132:jcs.218628. [DOI: 10.1242/jcs.218628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/23/2018] [Indexed: 12/13/2022] Open
Abstract
Melanoma-associated antigen A1 (MAGEA1) and BORIS are members of the cancer testis antigens (CTA) family. Their functions and expression regulation mechanisms are not fully understood. In this study, we revealed new functions and regulatory mechanisms of MAGEA1 and BORIS in breast cancer cells, which were investigated in parental and genetically manipulated breast cancer cells via gene overexpression or siRNA interference-mediated down-regulation. We identified the interaction between MAGEA1 and CTCF, which was required for the binding of MAGEA1 to BORIS promoter and critical for the recruitment of DNMT3a. A protein complex containing MAGEA1, CTCF and DNMT3a will be formed before or after the conjunction with BORIS promoter. The binding of this complex to the BORIS promoter accounts for the hypermethylation and repression of BORIS expression, which results in cell death in the breast cancer cell lines tested. Multiple approaches are employed, including co-IP, GST-pull down, co-localization, cell death analyses using the Annexin V-FITC/PI double staining and caspase3 activation assays, ChIP and bisulfite sequencing PCR assays for methylation. These results have implications in the development of strategies in CTA-based immune therapeutics.
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Affiliation(s)
- Jizhong Zhao
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yueqing Wang
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qianjin Liang
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yan Xu
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, 1044 W. Walnut St. R4-W037, Indianapolis, IN 46202, USA
| | - Jianli Sang
- Key Laboratory of Cell Proliferation and Regulation, College of Life Sciences, Beijing Normal University, Beijing, China
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30
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Abstract
CCCTC-binding factor (CTCF) is a conserved, essential regulator of chromatin architecture containing a unique array of 11 zinc fingers (ZFs). Gene duplication and sequence divergence during early amniote evolution generated the CTCF paralog Brother Of the Regulator of Imprinted Sites (BORIS), which has a DNA binding specificity identical to that of CTCF but divergent N- and C-termini. While healthy somatic tissues express only CTCF, CTCF and BORIS are normally co-expressed in meiotic and post-meiotic germ cells, and aberrant activation of BORIS occurs in tumors and some cancer cell lines. This has led to a model in which CTCF and BORIS compete for binding to some but not all genomic target sites; however, regulation of CTCF and BORIS genomic co-occupancy is not well understood. We recently addressed this issue, finding evidence for two major classes of CTCF target sequences, some of which contain single CTCF target sites (1xCTSes) and others containing two adjacent CTCF motifs (2xCTSes). The functional and chromatin structural features of 2xCTSes are distinct from those of 1xCTS-containing regions bound by a CTCF monomer. We suggest that these previously overlooked classes of CTCF binding regions may have different roles in regulating diverse chromatin-based phenomena, and may impact our understanding of heritable epigenetic regulation in cancer cells and normal germ cells.
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Affiliation(s)
- Victor V Lobanenkov
- a Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health , 5601 Fishers Ln, Rockville , MD , USA
| | - Gabriel E Zentner
- b Department of Biology , Indiana University , 915 E 3rd St, Bloomington , IN 47405 , USA
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31
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Honke K. Biological functions of sulfoglycolipids and the EMARS method for identification of co-clustered molecules in the membrane microdomains. J Biochem 2017; 163:253-263. [DOI: 10.1093/jb/mvx078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/03/2017] [Indexed: 01/24/2023] Open
Affiliation(s)
- Koichi Honke
- Department of Biochemistry, Kochi University Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783–8505, Japan
- Center for Innovative and Translational Medicine, Kochi University Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783–8505, Japan
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32
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Teplyakov E, Wu Q, Liu J, Pugacheva EM, Loukinov D, Boukaba A, Lobanenkov V, Strunnikov A. The downregulation of putative anticancer target BORIS/CTCFL in an addicted myeloid cancer cell line modulates the expression of multiple protein coding and ncRNA genes. Oncotarget 2017; 8:73448-73468. [PMID: 29088719 PMCID: PMC5650274 DOI: 10.18632/oncotarget.20627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/23/2017] [Indexed: 12/27/2022] Open
Abstract
The BORIS/CTCFL gene, is a testis-specific CTCF paralog frequently erroneously activated in cancer, although its exact role in cancer remains unclear. BORIS is both a transcription factor and an architectural chromatin protein. BORIS' normal role is to establish a germline-like gene expression and remodel the epigenetic landscape in testis; it similarly remodels chromatin when activated in human cancer. Critically, at least one cancer cell line, K562, is dependent on BORIS for its self-renewal and survival. Here, we downregulate BORIS expression in the K562 cancer cell line to investigate downstream pathways regulated by BORIS. RNA-seq analyses of both mRNA and small ncRNAs, including miRNA and piRNA, in the knock-down cells revealed a set of differentially expressed genes and pathways, including both testis-specific and general proliferation factors, as well as proteins involved in transcription regulation and cell physiology. The differentially expressed genes included important transcriptional regulators such as SOX6 and LIN28A. Data indicate that both direct binding of BORIS to promoter regions and locus-control activity via long-distance chromatin domain regulation are involved. The sum of findings suggests that BORIS activation in leukemia does not just recapitulate the germline, but creates a unique regulatory network.
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Affiliation(s)
- Evgeny Teplyakov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The University of the Chinese Academy of Sciences, Beijing, China
| | - Qiongfang Wu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - Jian Liu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Dmitry Loukinov
- NIH, NIAID, Laboratory of Immunogenetics, Rockville, MD, USA
| | - Abdelhalim Boukaba
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | | | - Alexander Strunnikov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China.,The University of the Chinese Academy of Sciences, Beijing, China
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33
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Ashapkin VV, Kutueva LI, Vanyushin BF. Aging as an Epigenetic Phenomenon. Curr Genomics 2017; 18:385-407. [PMID: 29081695 PMCID: PMC5635645 DOI: 10.2174/1389202918666170412112130] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/17/2016] [Accepted: 02/09/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging. Random errors in DNA methylation and other epigenetic marks during aging increase the transcriptional noise, and thus lead to enhanced phenotypic variation between cells of the same tissue. Such variation could cause progressive organ dysfunction observed in aged individuals. Multiple experimental data show that induction of NF-κB regulated gene sets occurs in various tissues of aged mammals. Upregulation of multiple miRNAs occurs at mid age leading to downregulation of enzymes and regulatory proteins involved in basic cellular functions, such as DNA repair, oxidative phosphorylation, intermediate metabolism, and others. CONCLUSION Strong evidence shows that all epigenetic systems contribute to the lifespan control in various organisms. Similar to other cell systems, epigenome is prone to gradual degradation due to the genome damage, stressful agents, and other aging factors. But unlike mutations and other kinds of the genome damage, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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34
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Giannoulatou E, Maher GJ, Ding Z, Gillis AJM, Dorssers LCJ, Hoischen A, Rajpert-De Meyts E, McVean G, Wilkie AOM, Looijenga LHJ, Goriely A. Whole-genome sequencing of spermatocytic tumors provides insights into the mutational processes operating in the male germline. PLoS One 2017; 12:e0178169. [PMID: 28542371 PMCID: PMC5439955 DOI: 10.1371/journal.pone.0178169] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/31/2022] Open
Abstract
Adult male germline stem cells (spermatogonia) proliferate by mitosis and, after puberty, generate spermatocytes that undertake meiosis to produce haploid spermatozoa. Germ cells are under evolutionary constraint to curtail mutations and maintain genome integrity. Despite constant turnover, spermatogonia very rarely form tumors, so-called spermatocytic tumors (SpT). In line with the previous identification of FGFR3 and HRAS selfish mutations in a subset of cases, candidate gene screening of 29 SpTs identified an oncogenic NRAS mutation in two cases. To gain insights in the etiology of SpT and into properties of the male germline, we performed whole-genome sequencing of five tumors (4/5 with matched normal tissue). The acquired single nucleotide variant load was extremely low (~0.2 per Mb), with an average of 6 (2-9) non-synonymous variants per tumor, none of which is likely to be oncogenic. The observed mutational signature of SpTs is strikingly similar to that of germline de novo mutations, mostly involving C>T transitions with a significant enrichment in the ACG trinucleotide context. The tumors exhibited extensive aneuploidy (50-99 autosomes/tumor) involving whole-chromosomes, with recurrent gains of chr9 and chr20 and loss of chr7, suggesting that aneuploidy itself represents the initiating oncogenic event. We propose that SpT etiology recapitulates the unique properties of male germ cells; because of evolutionary constraints to maintain low point mutation rate, rare tumorigenic driver events are caused by a combination of gene imbalance mediated via whole-chromosome aneuploidy. Finally, we propose a general framework of male germ cell tumor pathology that accounts for their mutational landscape, timing and cellular origin.
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Affiliation(s)
- Eleni Giannoulatou
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Geoffrey J. Maher
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Zhihao Ding
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ad J. M. Gillis
- Department of Pathology, Erasmus MC—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lambert C. J. Dorssers
- Department of Pathology, Erasmus MC—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ewa Rajpert-De Meyts
- Department of Growth & Reproduction, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | | | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Leendert H. J. Looijenga
- Department of Pathology, Erasmus MC—University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Anne Goriely
- Clinical Genetics Group, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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35
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Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells. Sci Rep 2017; 7:41279. [PMID: 28145452 PMCID: PMC5286509 DOI: 10.1038/srep41279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/19/2016] [Indexed: 12/14/2022] Open
Abstract
Despite sharing the same sequence specificity in vitro and in vivo, CCCTC-binding factor (CTCF) and its paralog brother of the regulator of imprinted sites (BORIS) are simultaneously expressed in germ cells. Recently, ChIP-seq analysis revealed two classes of CTCF/BORIS-bound regions: single CTCF target sites (1xCTSes) that are bound by CTCF alone (CTCF-only) or double CTCF target sites (2xCTSes) simultaneously bound by CTCF and BORIS (CTCF&BORIS) or BORIS alone (BORIS-only) in germ cells and in BORIS-positive somatic cancer cells. BORIS-bound regions (CTCF&BORIS and BORIS-only sites) are, on average, enriched for RNA polymerase II (RNAPII) binding and histone retention in mature spermatozoa relative to CTCF-only sites, but little else is known about them. We show that subsets of CTCF&BORIS and BORIS-only sites are occupied by several testis-specific transcriptional regulators (TSTRs) and associated with highly expressed germ cell-specific genes and histone retention in mature spermatozoa. We also demonstrate a physical interaction between BORIS and one of the analyzed TSTRs, TATA-binding protein (TBP)-associated factor 7-like (TAF7L). Our data suggest that CTCF and BORIS cooperate with additional TSTRs to regulate gene expression in developing male gametes and histone retention in mature spermatozoa, potentially priming certain regions of the genome for rapid activation following fertilization.
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36
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Pugacheva EM, Teplyakov E, Wu Q, Li J, Chen C, Meng C, Liu J, Robinson S, Loukinov D, Boukaba A, Hutchins AP, Lobanenkov V, Strunnikov A. The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. Epigenetics Chromatin 2016; 9:35. [PMID: 27588042 PMCID: PMC5007689 DOI: 10.1186/s13072-016-0084-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/18/2016] [Indexed: 12/20/2022] Open
Abstract
Background A common aberration in cancer is the activation of germline-specific proteins. The DNA-binding proteins among them could generate novel chromatin states, not found in normal cells. The germline-specific transcription factor BORIS/CTCFL, a paralog of chromatin architecture protein CTCF, is often erroneously activated in cancers and rewires the epigenome for the germline-like transcription program. Another common feature of malignancies is the changed expression and epigenetic states of genomic repeats, which could alter the transcription of neighboring genes and cause somatic mutations upon transposition. The role of BORIS in transposable elements and other repeats has never been assessed. Results The investigation of BORIS and CTCF binding to DNA repeats in the K562 cancer cells dependent on BORIS for self-renewal by ChIP-chip and ChIP-seq revealed three classes of occupancy by these proteins: elements cohabited by BORIS and CTCF, CTCF-only bound, or BORIS-only bound. The CTCF-only enrichment is characteristic for evolutionary old and inactive repeat classes, while BORIS and CTCF co-binding predominately occurs at uncharacterized tandem repeats. These repeats form staggered cluster binding sites, which are a prerequisite for CTCF and BORIS co-binding. At the same time, BORIS preferentially occupies a specific subset of the evolutionary young, transcribed, and mobile genomic repeat family, SVA. Unlike CTCF, BORIS prominently binds to the VNTR region of the SVA repeats in vivo. This suggests a role of BORIS in SVA expression regulation. RNA-seq analysis indicates that BORIS largely serves as a repressor of SVA expression, alongside DNA and histone methylation, with the exception of promoter capture by SVA. Conclusions Thus, BORIS directly binds to, and regulates SVA repeats, which are essentially movable CpG islands, via clusters of BORIS binding sites. This finding uncovers a new function of the global germline-specific transcriptional regulator BORIS in regulating and repressing the newest class of transposable elements that are actively transposed in human genome when activated. This function of BORIS in cancer cells is likely a reflection of its roles in the germline. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0084-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Evgeny Teplyakov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Qiongfang Wu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Jingjing Li
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Cheng Chen
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Chengcheng Meng
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Jian Liu
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Susan Robinson
- Laboratory of Immunogenetics, NIH, NIAID, Rockville, MD 20852 USA
| | - Dmitry Loukinov
- Laboratory of Immunogenetics, NIH, NIAID, Rockville, MD 20852 USA
| | - Abdelhalim Boukaba
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
| | - Andrew Paul Hutchins
- Department of Biology, Southern University of Science and Technology of China, Shenzhen, 518055 Guangdong China
| | | | - Alexander Strunnikov
- Molecular Epigenetics Laboratory, Guangzhou Institutes of Biomedicine and Health, Guangzhou, 510530 Guangdong China
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37
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Hernández-Hernández A, Lilienthal I, Fukuda N, Galjart N, Höög C. CTCF contributes in a critical way to spermatogenesis and male fertility. Sci Rep 2016; 6:28355. [PMID: 27345455 PMCID: PMC4921845 DOI: 10.1038/srep28355] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/01/2016] [Indexed: 11/21/2022] Open
Abstract
The CCCTC-binding factor (CTCF) is an architectural protein that governs chromatin organization and gene expression in somatic cells. Here, we show that CTCF regulates chromatin compaction necessary for packaging of the paternal genome into mature sperm. Inactivation of Ctcf in male germ cells in mice (Ctcf-cKO mice) resulted in impaired spermiogenesis and infertility. Residual spermatozoa in Ctcf-cKO mice displayed abnormal head morphology, aberrant chromatin compaction, impaired protamine 1 incorporation into chromatin and accelerated histone depletion. Thus, CTCF regulates chromatin organization during spermiogenesis, contributing to the functional organization of mature sperm.
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Affiliation(s)
| | - Ingrid Lilienthal
- Karolinska Institutet, Department of Cell and Molecular Biology, Berzelius väg 35, 171 77 Stockholm, Sweden
| | - Nanaho Fukuda
- Karolinska Institutet, Department of Cell and Molecular Biology, Berzelius väg 35, 171 77 Stockholm, Sweden
| | - Niels Galjart
- Department of Cell Biology and Genetics, Erasmus MC, 2040 CA Rotterdam, The Netherlands
| | - Christer Höög
- Karolinska Institutet, Department of Cell and Molecular Biology, Berzelius väg 35, 171 77 Stockholm, Sweden
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38
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Pugacheva EM, Rivero-Hinojosa S, Espinoza CA, Méndez-Catalá CF, Kang S, Suzuki T, Kosaka-Suzuki N, Robinson S, Nagarajan V, Ye Z, Boukaba A, Rasko JEJ, Strunnikov AV, Loukinov D, Ren B, Lobanenkov VV. Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions. Genome Biol 2015; 16:161. [PMID: 26268681 PMCID: PMC4562119 DOI: 10.1186/s13059-015-0736-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 12/22/2022] Open
Abstract
Background CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation. Results Here we show that these two proteins co-occupy a specific subset of regulatory elements consisting of clustered CTCF binding motifs (termed 2xCTSes). BORIS occupancy at 2xCTSes is largely invariant in BORIS-positive cancer cells, with the genomic pattern recapitulating the germline-specific BORIS binding to chromatin. In contrast to the single-motif CTCF target sites (1xCTSes), the 2xCTS elements are preferentially found at active promoters and enhancers, both in cancer and germ cells. 2xCTSes are also enriched in genomic regions that escape histone to protamine replacement in human and mouse sperm. Depletion of the BORIS gene leads to altered transcription of a large number of genes and the differentiation of K562 cells, while the ectopic expression of this CTCF paralog leads to specific changes in transcription in MCF7 cells. Conclusions We discover two functionally and structurally different classes of CTCF binding regions, 2xCTSes and 1xCTSes, revealed by their predisposition to bind BORIS. We propose that 2xCTSes play key roles in the transcriptional program of cancer and germ cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0736-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Samuel Rivero-Hinojosa
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Celso A Espinoza
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, San Diego School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Claudia Fabiola Méndez-Catalá
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Sungyun Kang
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Teruhiko Suzuki
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.,Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Natsuki Kosaka-Suzuki
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Susan Robinson
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Abdelhalim Boukaba
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA. .,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, Moores Cancer Center, San Diego School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
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39
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Expression of the CTCFL Gene during Mouse Embryogenesis Causes Growth Retardation, Postnatal Lethality, and Dysregulation of the Transforming Growth Factor β Pathway. Mol Cell Biol 2015; 35:3436-45. [PMID: 26169830 DOI: 10.1128/mcb.00381-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 07/06/2015] [Indexed: 12/12/2022] Open
Abstract
CTCFL, a paralog of CTCF, also known as BORIS (brother of regulator of imprinted sites), is a testis-expressed gene whose function is largely unknown. Its product is a cancer testis antigen (CTA), and it is often expressed in tumor cells and also seen in two benign human vascular malformations, juvenile angiofibromas and infantile hemangiomas. To understand the function of Ctcfl, we created tetracycline-inducible Ctcfl transgenic mice. We show that Ctcfl expression during embryogenesis results in growth retardation, eye malformations, multiorgan pathologies, vascular defects, and neonatal death. This phenotype resembles prior mouse models that perturb the transforming growth factor β (TGFB) pathway. Embryonic stem (ES) cells with the Ctcfl transgene reproduce the phenotype in ES cell-tetraploid chimeras. Transcriptome sequencing of the Ctcfl ES cells revealed 14 genes deregulated by Ctcfl expression. Bioinformatic analysis revealed the TGFB pathway as most affected by embryonic Ctcfl expression. Understanding the consequence of Ctcfl expression in nontesticular cells and elucidating downstream targets of Ctcfl could explain the role of its product as a CTA and its involvement in two, if not more, human vascular malformations.
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40
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Franco MM, Prickett AR, Oakey RJ. The role of CCCTC-binding factor (CTCF) in genomic imprinting, development, and reproduction. Biol Reprod 2014; 91:125. [PMID: 25297545 DOI: 10.1095/biolreprod.114.122945] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CCCTC-binding factor (CTCF) is the major protein involved in insulator activity in vertebrates, with widespread DNA binding sites in the genome. CTCF participates in many processes related to global chromatin organization and remodeling, contributing to the repression or activation of gene transcription. It is also involved in epigenetic reprogramming and is essential during gametogenesis and embryo development. Abnormal DNA methylation patterns at CTCF motifs may impair CTCF binding to DNA, and are related to fertility disorders in mammals. Therefore, CTCF and its binding sites are important candidate regions to be investigated as molecular markers for gamete and embryo quality. This article reviews the role of CTCF in genomic imprinting, gametogenesis, and early embryo development and, moreover, highlights potential opportunities for environmental influences associated with assisted reproductive techniques (ARTs) to affect CTCF-mediated processes. We discuss the potential use of CTCF as a molecular marker for assessing gamete and embryo quality in the context of improving the efficiency and safety of ARTs.
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Affiliation(s)
- Maurício M Franco
- Embrapa Genetic Resources & Biotechnology, Laboratory of Animal Reproduction, Parque Estação Biológica, Brasília, Brazil
| | - Adam R Prickett
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Rebecca J Oakey
- Department of Medical & Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
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Shin HS, Seo JH, Jeong SH, Park SW, Park Y, Son SW, Kim JS, Kang HG. Exposure of pregnant mice to chlorpyrifos-methyl alters embryonic H19 gene methylation patterns. ENVIRONMENTAL TOXICOLOGY 2014; 29:926-935. [PMID: 23125134 DOI: 10.1002/tox.21820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/11/2012] [Accepted: 09/23/2012] [Indexed: 06/01/2023]
Abstract
The aim of this study was to identify whether chlorpyrifos methyl (CPM) exposure during pregnancy leads to changes in the methylation patterns of H19 gene. CPM 4, 20, 100 mg/kg bw/day was administered to 4 pregnant mice per group between 7 and 12 days post coitum (d.p.c.). Pregnant mice were killed at 13 d.p.c. The genomic methylation in primordial germ cells (PGCs) and fetal organs (the liver, intestine, and placenta) was examined. Four polymorphism sites in the H19 alleles of maternal (C57BL/6J) and paternal (CAST/Ei) alleles were identified at nucleotide position 1407, 1485, 1566, and 1654. The methylation patterns of 17 CpG sites were analyzed. The methylation level in male and female PGCs was not altered by CPM treatment in the maternal allele H19. The methylation level of the paternal H19 allele was altered in only male PGCs in response to the CPM treatment. The methylation level at a binding site for the transcriptional regulator CTCF2 was higher than that at the CTCF1 binding site in all CPM-treated groups. In the placenta, the aggregate methylation level of H19 was 56.89%in control group. But, those levels were ranged from 47.7% to 49.89% after treatment with increasing doses of CPM. H19 gene from the liver and intestine of 13 d.p.c. fetuses treated with CPM was hypomethylated as compared with controls, although H19 mRNA expression was unaltered. In the placenta, H19 expression was slightly increased in the CPM-treated group, although not significantly. IGF2 expression levels were not significantly changed in the placenta. In conclusion, CPM exposure during pregnancy alters the methylation status of the H19 gene in PGCs and embryonic tissues. We infer that these alterations are likely related to changes in DNA demethylase activity.
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Affiliation(s)
- Hyo-Sook Shin
- Toxicology & Residue Chemistry Division, Animal, Plant and Fisheries Quarantine and Inspection Agency, 175 Anyangro, Anyang-si, Gyeonggi-do 430-757, Republic of Korea
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Zampieri M, Ciccarone F, Palermo R, Cialfi S, Passananti C, Chiaretti S, Nocchia D, Talora C, Screpanti I, Caiafa P. The epigenetic factor BORIS/CTCFL regulates the NOTCH3 gene expression in cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:813-25. [PMID: 24984200 DOI: 10.1016/j.bbagrm.2014.06.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 11/29/2022]
Abstract
Aberrant upregulation of NOTCH3 gene plays a critical role in cancer pathogenesis. However, the underlying mechanisms are still unknown. We tested here the hypothesis that aberrant epigenetic modifications in the NOTCH3 promoter region might account for its upregulation in cancer cells. We compared DNA and histone methylation status of NOTCH3 promoter region in human normal blood cells and T cell acute lymphoblastic leukemia (T-ALL) cell lines, differentially expressing NOTCH3. We found that histone methylation, rather than DNA hypomethylation, contributes towards establishing an active chromatin status of NOTCH3 promoter in NOTCH3 overexpressing cancer cells. We discovered that the chromatin regulator protein BORIS/CTCFL plays an important role in regulating NOTCH3 gene expression. We observed that BORIS is present in T-ALL cell lines as well as in cell lines derived from several solid tumors overexpressing NOTCH3. Moreover, BORIS targets NOTCH3 promoter in cancer cells and it is able to induce and to maintain a permissive/active chromatin conformation. Importantly, the association between NOTCH3 overexpression and BORIS presence was confirmed in primary T-ALL samples from patients at the onset of the disease. Overall, our results provide novel insights into the determinants of NOTCH3 overexpression in cancer cells, by revealing a key role for BORIS as the main mediator of transcriptional deregulation of NOTCH3.
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Affiliation(s)
- Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Rocco Palermo
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Samantha Cialfi
- Department of Molecular Medicine, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy
| | - Claudio Passananti
- Institute of Molecular Biology & Pathology CNR, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Sabina Chiaretti
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Nocchia
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy
| | - Claudio Talora
- Department of Molecular Medicine, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy
| | - Isabella Screpanti
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy; Department of Molecular Medicine, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy.
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy & Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy.
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Okahara K, Kizuka Y, Kitazume S, Ota F, Nakajima K, Hirabayashi Y, Maekawa M, Yoshikawa T, Taniguchi N. Ceramide galactosyltransferase expression is regulated positively by Nkx2.2 and negatively by OLIG2. Glycobiology 2014; 24:926-34. [DOI: 10.1093/glycob/cwu042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Cheema Z, Hari-Gupta Y, Kita GX, Farrar D, Seddon I, Corr J, Klenova E. Expression of the cancer-testis antigen BORIS correlates with prostate cancer. Prostate 2014; 74:164-76. [PMID: 24123052 DOI: 10.1002/pros.22738] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 09/11/2013] [Indexed: 11/09/2022]
Abstract
BACKGROUND BORIS, a paralogue of the transcription factor CTCF, is a member of the cancer-testis antigen (CT) family. BORIS is normally present at high levels in the testis; however it is aberrantly expressed in various tumors and cancer cell lines. The main objectives of this study were to investigate BORIS expression together with sub-cellular localization in both prostate cell lines and tumor tissues, and assess correlations between BORIS and clinical/pathological characteristics. METHODS We examined BORIS mRNA expression, protein levels and cellular localization in a panel of human prostate tissues, cancer and benign, together with a panel prostate cell lines. We also compared BORIS levels and localization with clinical/pathological characteristics in prostate tumors. RESULTS BORIS was detected in all inspected prostate cancer cell lines and tumors, but was absent in benign prostatic hyperplasia. Increased levels of BORIS protein positively correlated with Gleason score, T-stage and androgen receptor (AR) protein levels in prostate tumors. The relationship between BORIS and AR was further highlighted in prostate cell lines by the ability of ectopically expressed BORIS to activate the endogenous AR mRNA and protein. BORIS localization in the nucleus plus cytoplasm was also associated with higher BORIS levels and Gleason score. CONCLUSIONS Detection of BORIS in prostate tumors suggests potential applications of BORIS as a biomarker for prostate cancer diagnosis, as an immunotherapy target and, potentially, a prognostic marker of more aggressive prostate cancer. The ability of BORIS to activate the AR gene indicates BORIS involvement in the growth and development of prostate tumors.
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Affiliation(s)
- Zubair Cheema
- School of Biological Sciences, University of Essex, Colchester, UK; Department of Urology, Colchester Hospital University NHS Foundation Trust, Colchester, UK
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Marshall AD, Bailey CG, Rasko JEJ. CTCF and BORIS in genome regulation and cancer. Curr Opin Genet Dev 2013; 24:8-15. [PMID: 24657531 DOI: 10.1016/j.gde.2013.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 10/25/2022]
Abstract
CTCF plays a vital role in chromatin structure and function. CTCF is ubiquitously expressed and plays diverse roles in gene regulation, imprinting, insulation, intra/interchromosomal interactions, nuclear compartmentalisation, and alternative splicing. CTCF has a single paralogue, the testes-specific CTCF-like gene (CTCFL)/BORIS. CTCF and BORIS can be deregulated in cancer. The tumour suppressor gene CTCF can be mutated or deleted in cancer, or CTCF DNA binding can be altered by epigenetic changes. BORIS is aberrantly expressed frequently in cancer, leading some to propose a pro-tumourigenic role for BORIS. However, BORIS can inhibit cell proliferation, and is mutated in cancer similarly to CTCF suggesting BORIS activation in cancer may be due to global genetic or epigenetic changes typical of malignant transformation.
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Affiliation(s)
- Amy D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Missenden Road, Camperdown 2050, NSW, Australia; Sydney Medical School, University of Sydney, Sydney 2006, NSW, Australia; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown 2050, NSW, Australia.
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Kong A, Thorleifsson G, Frigge ML, Masson G, Gudbjartsson DF, Villemoes R, Magnusdottir E, Olafsdottir SB, Thorsteinsdottir U, Stefansson K. Common and low-frequency variants associated with genome-wide recombination rate. Nat Genet 2013; 46:11-6. [PMID: 24270358 DOI: 10.1038/ng.2833] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 10/31/2013] [Indexed: 12/14/2022]
Abstract
Meiotic recombination contributes to genetic diversity by yielding new combinations of alleles. Individuals vary with respect to the genome-wide recombination counts in their gametes. Exploiting data resources in Iceland, we compiled a data set consisting of 35,927 distinct parents and 71,929 parent-offspring pairs. Within this data set, we called over 2.2 million recombination events and imputed variants with sequence-level resolution from 2,261 whole genome-sequenced individuals into the parents to search for variants influencing recombination rate. We identified 13 variants in 8 regions that are associated with genome-wide recombination rate, 8 of which were previously unknown. Three of these variants associate with male recombination rate only, seven variants associate with female recombination rate only and three variants affect both. Two are low-frequency variants with large effects, one of which is estimated to increase the male and female genetic maps by 111 and 416 cM, respectively. This variant, located in an intron, would not be found by exome sequencing.
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Affiliation(s)
- Augustine Kong
- 1] deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. [2] Faculty of Physical Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Daniel F Gudbjartsson
- 1] deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. [2] Faculty of Physical Sciences, School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Unnur Thorsteinsdottir
- 1] deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. [2] Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- 1] deCODE Genetics/Amgen, Inc., Reykjavik, Iceland. [2] Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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Abstract
Tumor cells frequently exhibit widespread epigenetic aberrations that significantly alter the repertoire of expressed proteins. In particular, it has been known for nearly 25 years that tumors frequently reactivate genes whose expression is typically restricted to germ cells. These gene products are classified as cancer/testis antigens (CTAs) owing to their biased expression pattern and their immunogenicity in cancer patients. While these genes have been pursued as targets for anticancer vaccines, whether these reactivated testis proteins have roles in supporting tumorigenic features is less studied. Recent evidence now indicates that these proteins can be directly employed by the tumor cell regulatory environment to support cell-autonomous behaviors. Here, we review the history of the CTA field and present recent findings indicating that CTAs can play functional roles in supporting tumorigenesis.
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Tiffen JC, Bailey CG, Marshall AD, Metierre C, Feng Y, Wang Q, Watson SL, Holst J, Rasko JEJ. The cancer-testis antigen BORIS phenocopies the tumor suppressor CTCF in normal and neoplastic cells. Int J Cancer 2013; 133:1603-13. [PMID: 23553099 DOI: 10.1002/ijc.28184] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/15/2013] [Indexed: 11/10/2022]
Abstract
BORIS and CTCF are paralogous, multivalent 11-zinc finger transcription factors that play important roles in organizing higher-order chromatin architecture. BORIS is a cancer-testis antigen with a poorly defined function in cancer, although it has been hypothesized to exhibit oncogenic properties. CTCF, however, has been postulated as a candidate tumor suppressor. We collated the genetic lesions in BORIS and CTCF from multiple cancers identified using high-throughput genomics. In BORIS, nonsense and missense mutations are evenly distributed. In CTCF, recurrent mutations are mostly clustered in the conserved zinc finger domain and at residues critical for contacting DNA and zinc ion co-ordination. Three missense mutations are common to both proteins. We used an inducible lentivector to express wildtype BORIS or CTCF in primary cells and cancer cell lines in order to define their functional differences. Both BORIS and CTCF caused a significant decrease in cell proliferation and clonogenic capacity, without alteration of specific cell cycle phases. Both BORIS and CTCF conferred protective effects in primary cells and some cancer cells during UV damage-induced apoptosis. Using a bioluminescent MCF-7 orthotopic breast cancer model in vivo, we demonstrated that CTCF and BORIS suppressed breast cancer growth. These findings provide further evidence that CTCF behaves as a tumor suppressor, and show BORIS has a similar growth inhibitory effect in vitro and in vivo. Hence, acquired zinc finger mutations may disrupt these functions, thereby contributing to tumor growth and development.
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Affiliation(s)
- Jessamy C Tiffen
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW 2050, Australia
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Honke K. Biosynthesis and biological function of sulfoglycolipids. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2013; 89:129-138. [PMID: 23574804 PMCID: PMC3669731 DOI: 10.2183/pjab.89.129] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 02/19/2013] [Indexed: 06/02/2023]
Abstract
Sulfation confers negative charge on glycolipids and the attached sulfate group presents a part of determinants for the molecular interactions. Mammalian sulfoglycolipids are comprised of two major members, sulfatide (SO3-3Gal-ceramide) and seminolipid (SO3-3Gal-alkylacylglycerol). Sulfatide is abundant in the myelin sheath and seminolipid is unique to the spermatogenic cells. The carbohydrate moiety of sulfatide and seminolipid is biosynthesized via sequential reactions catalyzed by common enzymes: ceramide galactosyltransferase (CGT) and cerebroside sulfotransferase (CST). To elucidate the biological function of sulfoglycolipids, we have purified CST, cloned the CST gene, and generated CST-knockout mice. CST-null mice completely lack sulfoglycolipids all over the body. CST-null mice manifest some neurological disorders due to myelin dysfunction, an aberrant enhancement of oligodendrocyte terminal differentiation, and an arrest of spermatogenesis. CST-deficiency ameliorates L-selectin-dependent monocyte infiltration in the renal interstitial inflammation, indicating that sulfatide is an endogenous ligand of L-selectin. Studies on the molecular mechanisms underlying the biological events for which sulfoglycolipids are essential are ongoing
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Affiliation(s)
- Koichi Honke
- Department of Biochemistry and Kochi System Glycobiology Center, Kochi University Medical School, Kochi, Japan.
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Sheng X, Nakajima T, Wang L, Zhang X, Kamijo Y, Takahashi K, Tanaka N, Sugiyama E, Kyogashima M, Aoyama T, Hara A. Attenuation of kidney injuries maintains serum sulfatide levels dependent on hepatic synthetic ability: a possible involvement of oxidative stress. TOHOKU J EXP MED 2012; 227:1-12. [PMID: 22499158 DOI: 10.1620/tjem.227.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Serum sulfatides are the major glycosphingolipids in lipoproteins. Although serum sulfatides are mainly synthesized and secreted by the liver, they are significantly decreased when the kidneys are impaired. Our recent experimental study using a murine protein-overload nephropathy model suggested a hypothetical mechanism whereby serum sulfatides were reduced due to kidney dysfunction. This was the result of decreased hepatic expression of a sulfatide synthetic enzyme, cerebroside sulfotransferase (CST), which is associated with systemic enhancement of oxidative stress. However, there is a possibility that the experimental process, protein-overload itself, directly affected the sulfatide metabolism and oxidative stress in the liver. To determine whether kidney dysfunction actually reduces the hepatic synthesis of sulfatides via oxidative stress, we examined sulfatide levels, the hepatic content of metabolic sulfatide enzymes, and the degree of oxidative stress in protein-overload mice subjected to renoprotective therapy using clofibrate, a representative hypolipidemic medicine. Protein-overload mice exhibited marked kidney injuries, enhancement of hepatic oxidative stress, decreased levels of serum and hepatic sulfatides, and decreased expression of hepatic CST. The clofibrate treatment attenuated kidney damage and hepatic oxidative stress while maintaining serum/hepatic sulfatide levels and hepatic CST content in the mice. Because clofibrate monotherapy without protein-overload treatment only minimally affected these hepatic parameters, the hepatic synthesis of sulfatides appeared to be strongly influenced by kidney dysfunction and subsequent oxidative stress. This study suggests that the crosstalk between kidney dysfunction and hepatic sulfatide metabolism is mediated by oxidative stress. These results should help to understand the phenomenon in patients with end-stage kidney disease.
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Affiliation(s)
- Xiaona Sheng
- Department of Metabolic Regulation, Institute on Aging and Adaptation, Shinshu University Graduate School of Medicine, Matsumoto, Japan
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