1
|
Fröhlich A, Pfaff AL, Middlehurst B, Hughes LS, Bubb VJ, Quinn JP, Koks S. Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson's disease progression. Sci Rep 2024; 14:10932. [PMID: 38740892 DOI: 10.1038/s41598-024-61753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are transposable elements which represent a source of genetic variation. We previously demonstrated that the presence/absence of a human-specific SVA, termed SVA_67, correlated with the progression of Parkinson's disease (PD). In the present study, we demonstrate that SVA_67 acts as expression quantitative trait loci, thereby exhibiting a strong regulatory effect across the genome using whole genome and transcriptomic data from the Parkinson's progression markers initiative cohort. We further show that SVA_67 is polymorphic for its variable number tandem repeat domain which correlates with both regulatory properties in a luciferase reporter gene assay in vitro and differential expression of multiple genes in vivo. Additionally, this variation's utility as a biomarker is reflected in a correlation with a number of PD progression markers. These experiments highlight the plethora of transcriptomic and phenotypic changes associated with SVA_67 polymorphism which should be considered when investigating the missing heritability of neurodegenerative diseases.
Collapse
Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren S Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Hall A, Middlehurst B, Cadogan MAM, Reed X, Billingsley KJ, Bubb VJ, Quinn JP. A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models. Sci Rep 2024; 14:792. [PMID: 38191889 PMCID: PMC10774264 DOI: 10.1038/s41598-023-50307-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons represent mobile regulatory elements that have the potential to influence the surrounding genome when they insert into a locus. Evolutionarily recent mobilisation has resulted in loci in the human genome where a given retrotransposon might be observed to be present or absent, termed a retrotransposon insertion polymorphism (RIP). We previously observed that an SVA RIP ~ 2 kb upstream of LRIG2 on chromosome 1, the 'LRIG2 SVA', was associated with differences in local gene expression and methylation, and that the two were correlated. Here, we have used CRISPR-mediated deletion of the LRIG2 SVA in a cell line model to validate that presence of the retrotransposon is directly affecting local expression and provide evidence that is suggestive of a modest role for the SVA in modulating nearby methylation. Additionally, in leveraging an available Hi-C dataset we observed that the LRIG2 SVA was also involved in long-range chromatin interactions with a cluster of genes ~ 300 kb away, and that expression of these genes was to varying degrees associated with dosage of the SVA in both CRISPR cell line and population models. Altogether, these data support a regulatory role for SVAs in the modulation of gene expression, with the latter potentially involving chromatin looping, consistent with the model that RIPs may contribute to interpersonal differences in transcriptional networks.
Collapse
Affiliation(s)
- Ashley Hall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Max A M Cadogan
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Center for Alzheimer's and Related Dementias, National Institute on Aging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7BE, UK.
| |
Collapse
|
4
|
Fröhlich A, Hughes LS, Middlehurst B, Pfaff AL, Bubb VJ, Koks S, Quinn JP. CRISPR deletion of a SINE-VNTR- Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus. Front Neurol 2023; 14:1273036. [PMID: 37840928 PMCID: PMC10570551 DOI: 10.3389/fneur.2023.1273036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Background SINE-VNTR-Alu (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive elements exert regulatory functions. We have previously shown that the presence or absence of a specific SVA element, termed SVA_67, was associated with differential expression of several genes at the MAPT locus, a locus associated with Parkinson's Disease (PD) and frontotemporal dementia. However, we were not able to demonstrate that causation of differential gene expression was directed by the SVA due to lack of functional validation. Methods We performed CRISPR to delete SVA_67 in the HEK293 cell line. Quantification of target gene expression was performed using qPCR to assess the effects on expression in response to the deletion of SVA_67. Differences between CRISPR edit and control cell lines were analysed using two-tailed t-test with a minimum 95% confidence interval to determine statistical significance. Results In this study, we provide data highlighting the SVA-specific effect on differential gene expression. We demonstrate that the hemizygous deletion of the endogenous SVA_67 in CRISPR edited cell lines was associated with differential expression of several genes at the MAPT locus associated with neurodegenerative diseases including KANSL1, MAPT and LRRC37A. Discussion This data is consistent with our previous bioinformatic work of differential gene expression analysis using transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) cohort. As SVAs have regulatory influences on gene expression, and insertion polymorphisms contribute to interpersonal differences in expression patterns, these results highlight the potential contribution of these elements to complex diseases with potentially many genetic components, such as PD.
Collapse
Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Lauren S. Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
5
|
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.
Collapse
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
| | | |
Collapse
|
6
|
Loukinov D, Anderson AL, Mkrtichyan M, Ghochikyan A, Rivero-Hinojosa S, Tucker J, Lobanenkov V, Agadjanyan MG, Nelson EL. A Therapeutic Vaccine Targeting Rat BORIS (CTCFL) for the Treatment of Rat Breast Cancer Tumors. Int J Mol Sci 2023; 24:5976. [PMID: 36983050 PMCID: PMC10058450 DOI: 10.3390/ijms24065976] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer testis antigens are ideal for tumor immunotherapy due to their testis-restricted expression. We previously showed that an immunotherapeutic vaccine targeting the germ cell-specific transcription factor BORIS (CTCFL) was highly effective in treating aggressive breast cancer in the 4T1 mouse model. Here, we further tested the therapeutic efficacy of BORIS in a rat 13762 breast cancer model. We generated a recombinant VEE-VRP (Venezuelan Equine Encephalitis-derived replicon particle) vector-expressing modified rat BORIS lacking a DNA-binding domain (VRP-mBORIS). Rats were inoculated with the 13762 cells, immunized with VRP-mBORIS 48 h later, and then, subsequently, boosted at 10-day intervals. The Kaplan-Meier method was used for survival analysis. Cured rats were re-challenged with the same 13762 cells. We demonstrated that BORIS was expressed in a small population of the 13762 cells, called cancer stem cells. Treatment of rats with VRP-BORIS suppressed tumor growth leading to its complete disappearance in up to 50% of the rats and significantly improved their survival. This improvement was associated with the induction of BORIS-specific cellular immune responses measured by T-helper cell proliferation and INFγ secretion. The re-challenging of cured rats with the same 13762 cells indicated that the immune response prevented tumor growth. Thus, a therapeutic vaccine against rat BORIS showed high efficacy in treating the rat 13762 carcinoma. These data suggest that targeting BORIS can lead to the elimination of mammary tumors and cure animals even though BORIS expression is detected only in cancer stem cells.
Collapse
Affiliation(s)
- Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amanda Laust Anderson
- Center for Immunology, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA
| | | | | | | | - Jo Tucker
- Center for Immunology, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA
| | - Victor Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | | | - Edward L. Nelson
- Center for Immunology, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92868, USA
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Barnada SM, Isopi A, Tejada-Martinez D, Goubert C, Patoori S, Pagliaroli L, Tracewell M, Trizzino M. Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells. PLoS Genet 2022; 18:e1010225. [PMID: 35704668 PMCID: PMC9239442 DOI: 10.1371/journal.pgen.1010225] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/28/2022] [Accepted: 04/28/2022] [Indexed: 01/08/2023] Open
Abstract
Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that ~750 SVAs are co-opted as functional cis-regulatory elements in human induced pluripotent stem cells. These SVAs are significantly closer to genes and harbor more transcription factor binding sites than non-co-opted SVAs. We show that a long DNA motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs and that these two transcription factors bind consecutively on the TE sequence. We used CRISPRi to epigenetically repress active SVAs in stem cell-like NCCIT cells. Epigenetic perturbation of active SVAs strongly attenuated YY1/OCT4 binding and influenced neighboring gene expression. Ultimately, SVA repression resulted in ~3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA. In summary, we demonstrated that SVAs modulate human gene expression, and uncovered that location and sequence composition contribute to SVA domestication into gene regulatory networks. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated. Nearly half of the SVAs annotated in the human genome are exclusive to our species. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we filled this knowledge-gap by focusing on human induced pluripotent stem cells (iPSCs) and on a pluripotent-like cell line (NCCITs). Through the analysis of histone marks, gene expression profiles, and by means of genome editing (CRISPR-interference), we identified ~750 SVAs that work as enhancers and promoters in human pluripotent cells, and characterized a mechanism for SVA co-option involving the transcription factors OCT4 and YY1. With our CRISPR approach, we demonstrated that repressing the 750 active SVAs leads to alteration in the expression of ~3,000 genes.
Collapse
Affiliation(s)
- Samantha M. Barnada
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Andrew Isopi
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Biochemistry and Molecular Pharmacology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Daniela Tejada-Martinez
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Clément Goubert
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Sruti Patoori
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Luca Pagliaroli
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Mason Tracewell
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Biochemistry and Molecular Pharmacology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region. Int J Mol Sci 2021; 22:ijms22041911. [PMID: 33671852 PMCID: PMC7917899 DOI: 10.3390/ijms22041911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are a subclass of transposable elements (TEs) that exist only in primate genomes. TE insertions can be co-opted as cis-regulatory elements (CREs); however, the regulatory potential of SVAs has predominantly been demonstrated using bioinformatic approaches and reporter gene assays. The objective of this study was to demonstrate SVA cis-regulatory activity by CRISPR (clustered regularly interspaced short palindromic repeats) deletion and subsequent measurement of direct effects on local gene expression. We identified a region on chromosome 17 that was enriched with human-specific SVAs. Comparative gene expression analysis at this region revealed co-expression of TRPV1 and TRPV3 in multiple human tissues, which was not observed in mouse, highlighting key regulatory differences between the two species. Furthermore, the intergenic region between TRPV1 and TRPV3 coding sequences contained a human specific SVA insertion located upstream of the TRPV3 promoter and downstream of the 3′ end of TRPV1, highlighting this SVA as a candidate to study its potential cis-regulatory activity on both genes. Firstly, we generated SVA reporter gene constructs and demonstrated their transcriptional regulatory activity in HEK293 cells. We then devised a dual-targeting CRISPR strategy to facilitate the deletion of this entire SVA sequence and generated edited HEK293 clonal cell lines containing homozygous and heterozygous SVA deletions. In edited homozygous ∆SVA clones, we observed a significant decrease in both TRPV1 and TRPV3 mRNA expression, compared to unedited HEK293. In addition, we also observed an increase in the variability of mRNA expression levels in heterozygous ∆SVA clones. Overall, in edited HEK293 with SVA deletions, we observed a disruption to the co-expression of TRPV1 and TRPV3. Here we provide an example of a human specific SVA with cis-regulatory activity in situ, supporting the role of SVA retrotransposons as contributors to species-specific gene expression.
Collapse
|
12
|
A SINE-VNTR- Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus. Int J Mol Sci 2020; 21:ijms21228486. [PMID: 33187279 PMCID: PMC7697779 DOI: 10.3390/ijms21228486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
The hominid SINE-VNTR-Alu (SVA) retrotransposons represent a repertoire of genomic variation which could have significant effects on genome function. A human-specific SVA in the promoter region of the gene leucine-rich repeats and immunoglobulin-like domains 2 (LRIG2), which we termed SVA_LRIG2, is a common retrotransposon insertion polymorphism (RIP), defined as an element which is polymorphic for its presence or absence in the genome. We hypothesised that this RIP might be associated with differential levels of expression of LRIG2. The RIP genotype of SVA_LRIG2 was determined in a subset of frontal cortex DNA samples from the North American Brain Expression Consortium (NABEC) cohort and was imputed for a larger set of that cohort. Utilising available frontal cortex total RNA-seq and CpG methylation data for this cohort, we observed that increased allele dosage of SVA_LRIG2 was non-significantly associated with a decrease in transcription from the region and significantly associated with increased methylation of the CpG probe nearest to SVA_LRIG2, i.e., SVA_LRIG2 is a significant methylation quantitative trait loci (mQTL) at the LRIG2 locus. These data are consistent with SVA_LRIG2 being a transcriptional regulator, which in part may involve epigenetic modulation.
Collapse
|
13
|
Zhang Y, Song Y, Li C, Ren J, Fang M, Fang J, Wang X. Brother of regulator of imprinted sites inhibits cisplatin-induced DNA damage in non-small cell lung cancer. Oncol Lett 2020; 20:251. [PMID: 32994814 PMCID: PMC7509674 DOI: 10.3892/ol.2020.12114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 05/27/2020] [Indexed: 12/13/2022] Open
Abstract
Cisplatin (DDP) chemotherapy is the primary modality of treatment for non-small cell lung cancer (NSCLC). However, due to the occurrence of DDP resistance, only a limited number of patients benefit from this treatment regimen. Brother of Regulator of Imprinted Sites (BORIS) is expressed elevated in NSCLC. Whether BORIS is involved in the DDP resistance of NSCLC is currently undetermined. The association between BORIS expression and overall survival rate of 156 patients with NSCLC who received DDP chemotherapy was analyzed in the present study. In order to investigate the function of BORIS in DDP chemotherapy, BORIS was silenced or overexpressed in four NSCLC cell lines. The cell viabilities, apoptosis and DNA damage induced by DDP were evaluated in these cell lines. In addition, the regulations of DNA repair genes were assessed, including POLH, ERCC1, BRCA1, MSH6 and XPA. The present study demonstrated that high BORIS expression was associated with decreased overall survival rate in patients with NSCLC who received DDP chemotherapy. The patients who benefited and went into remission following DDP therapy expressed a relatively low level of BORIS, suggesting the potential function of BORIS in DDP resistance. Cell experiments revealed that NSCLC cells that had a higher proliferation rate and resisted DDP treatment expressed a relatively higher level of BORIS. Knockdown of BORIS in NSCLC cells induced DNA damage; inhibiting cell proliferation and sensitizing cells to DDP treatment. In contrast, BORIS overexpression suppressed DDP-induced DNA damage. Notably, the mismatch repair factor mutS homolog 6 (MSH6) was regulated by BORIS, indicating its association with BORIS-associated DDP resistance in NSCLC. The findings of the present study suggest that BORIS suppresses DNA damage and promotes the progression of NSCLC and DDP resistance. The present study indicates the potential application of BORIS in NSCLC therapy and prognosis.
Collapse
Affiliation(s)
- Yanmei Zhang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Yongfei Song
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Chao Li
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Juan Ren
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Mengdie Fang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| | - Jianfei Fang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China.,Department of Pathology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Xiaoju Wang
- Center for Molecular Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310012, P.R. China
| |
Collapse
|
14
|
Schmidt F, Kern F, Schulz MH. Integrative prediction of gene expression with chromatin accessibility and conformation data. Epigenetics Chromatin 2020; 13:4. [PMID: 32029002 PMCID: PMC7003490 DOI: 10.1186/s13072-020-0327-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Enhancers play a fundamental role in orchestrating cell state and development. Although several methods have been developed to identify enhancers, linking them to their target genes is still an open problem. Several theories have been proposed on the functional mechanisms of enhancers, which triggered the development of various methods to infer promoter-enhancer interactions (PEIs). The advancement of high-throughput techniques describing the three-dimensional organization of the chromatin, paved the way to pinpoint long-range PEIs. Here we investigated whether including PEIs in computational models for the prediction of gene expression improves performance and interpretability. RESULTS We have extended our [Formula: see text] framework to include DNA contacts deduced from chromatin conformation capture experiments and compared various methods to determine PEIs using predictive modelling of gene expression from chromatin accessibility data and predicted transcription factor (TF) motif data. We designed a novel machine learning approach that allows the prioritization of TFs binding to distal loop and promoter regions with respect to their importance for gene expression regulation. Our analysis revealed a set of core TFs that are part of enhancer-promoter loops involving YY1 in different cell lines. CONCLUSION We present a novel approach that can be used to prioritize TFs involved in distal and promoter-proximal regulatory events by integrating chromatin accessibility, conformation, and gene expression data. We show that the integration of chromatin conformation data can improve gene expression prediction and aids model interpretability.
Collapse
Affiliation(s)
- Florian Schmidt
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672 Singapore
| | - Fabian Kern
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Marcel H. Schulz
- High-throughput Genomics & Systems Biology, Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Computational Biology & Applied Algorithmics, Max-Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Institute of Cardiovascular Regeneration, Goethe-University, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner Site Rhein-Main, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| |
Collapse
|
15
|
Gianfrancesco O, Geary B, Savage AL, Billingsley KJ, Bubb VJ, Quinn JP. The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome. Int J Mol Sci 2019; 20:ijms20235977. [PMID: 31783611 PMCID: PMC6928650 DOI: 10.3390/ijms20235977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022] Open
Abstract
Retrotransposons can alter the regulation of genes both transcriptionally and post-transcriptionally, through mechanisms such as binding transcription factors and alternative splicing of transcripts. SINE-VNTR-Alu (SVA) retrotransposons are the most recently evolved class of retrotransposable elements, found solely in primates, including humans. SVAs are preferentially found at genic, high GC loci, and have been termed "mobile CpG islands". We hypothesise that the ability of SVAs to mobilise, and their non-random distribution across the genome, may result in differential regulation of certain pathways. We analysed SVA distribution patterns across the human reference genome and identified over-representation of SVAs at zinc finger gene clusters. Zinc finger proteins are able to bind to and repress SVA function through transcriptional and epigenetic mechanisms, and the interplay between SVAs and zinc fingers has been proposed as a major feature of genome evolution. We describe observations relating to the clustering patterns of both reference SVAs and polymorphic SVA insertions at zinc finger gene loci, suggesting that the evolution of this network may be ongoing in humans. Further, we propose a mechanism to direct future research and validation efforts, in which the interplay between zinc fingers and their epigenetic modulation of SVAs may regulate a network of zinc finger genes, with the potential for wider transcriptional consequences.
Collapse
Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bethany Geary
- Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Abigail L. Savage
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Kimberley J. Billingsley
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GE, UK; (O.G.); (A.L.S.); (K.J.B.); (V.J.B.)
- Correspondence:
| |
Collapse
|
16
|
Patel D, Patel M, Datta S, Singh U. CGGBP1 regulates CTCF occupancy at repeats. Epigenetics Chromatin 2019; 12:57. [PMID: 31547883 PMCID: PMC6757366 DOI: 10.1186/s13072-019-0305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 12/27/2022] Open
Abstract
Background CGGBP1 is a repeat-binding protein with diverse functions in the regulation of gene expression, cytosine methylation, repeat silencing and genomic integrity. CGGBP1 has also been identified as a cooperator of histone-modifying enzymes and as a component of CTCF-containing complexes that regulate the enhancer–promoter looping. CGGBP1–CTCF cross talk in chromatin regulation has been hitherto unknown. Results Here, we report that the occupancy of CTCF at repeats depends on CGGBP1. Using ChIP-sequencing for CTCF, we describe its occupancy at repetitive DNA. Our results show that endogenous level of CGGBP1 ensures CTCF occupancy preferentially on repeats over canonical CTCF motifs. By combining CTCF ChIP-sequencing results with ChIP sequencing for three different kinds of histone modifications (H3K4me3, H3K9me3 and H3K27me3), we show that the CGGBP1-dependent repeat-rich CTCF-binding sites regulate histone marks in flanking regions. Conclusion CGGBP1 affects the pattern of CTCF occupancy. Our results posit CGGBP1 as a regulator of CTCF and its binding sites in interspersed repeats.
Collapse
Affiliation(s)
- Divyesh Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Manthan Patel
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Subhamoy Datta
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India
| | - Umashankar Singh
- HoMeCell Lab, Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, 382355, India.
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
Affiliation(s)
- Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, NIAID/NIH, Twinbrook 1, Room 1329, 5640 Fishers Lane, Rockville, MD, 20852, USA.
| |
Collapse
|
19
|
Mahmoud AM. Cancer testis antigens as immunogenic and oncogenic targets in breast cancer. Immunotherapy 2018; 10:769-778. [PMID: 29926750 PMCID: PMC6462849 DOI: 10.2217/imt-2017-0179] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/16/2018] [Indexed: 01/07/2023] Open
Abstract
Breast cancer cells frequently express tumor-associated antigens that can elicit immune responses to eradicate cancer. Cancer-testis antigens (CTAs) are a group of tumor-associated antigens that might serve as ideal targets for cancer immunotherapy because of their cancer-restricted expression and robust immunogenicity. Previous clinical studies reported that CTAs are associated with negative hormonal status, aggressive tumor behavior and poor survival. Furthermore, experimental studies have shown the ability of CTAs to induce both cellular and humoral immune responses. They also demonstrated the implication of CTAs in promoting cancer cell growth, inhibiting apoptosis and inducing cancer cell invasion and migration. In the current review, we attempt to address the immunogenic and oncogenic potential of CTAs and their current utilization in therapeutic interventions for breast cancer.
Collapse
Affiliation(s)
- Abeer M Mahmoud
- Department of Physical Therapy, College of Applied Health Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pathology, South Egypt Cancer Institute, Assiut University, Assiut 71111, Egypt
| |
Collapse
|
20
|
Cardelli M. The epigenetic alterations of endogenous retroelements in aging. Mech Ageing Dev 2018; 174:30-46. [PMID: 29458070 DOI: 10.1016/j.mad.2018.02.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 02/06/2023]
Abstract
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation. Indeed, most of the genomic CpG sites subjected to DNA methylation in the nuclear DNA are carried by these repetitive elements. As other parts of the genome, endogenous retroelements and other transposable elements are subjected to deep epigenetic alterations during aging, repeatedly observed in the context of organismal and cellular senescence, in human and other species. This review summarizes the current status of knowledge about the epigenetic alterations occurring in this large, non-genic portion of the genome in aging and age-related conditions, with a focus on the causes and the possible functional consequences of these alterations.
Collapse
Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, Italian National Research Center on Aging (INRCA), via Birarelli 8, 60121 Ancona, Italy.
| |
Collapse
|
21
|
CTCF driven TERRA transcription facilitates completion of telomere DNA replication. Nat Commun 2017; 8:2114. [PMID: 29235471 PMCID: PMC5727389 DOI: 10.1038/s41467-017-02212-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022] Open
Abstract
Telomere repeat DNA forms a nucleo-protein structure that can obstruct chromosomal DNA replication, especially under conditions of replication stress. Transcription of telomere repeats can initiate at subtelomeric CTCF-binding sites to generate telomere repeat-encoding RNA (TERRA), but the role of transcription, CTCF, and TERRA in telomere replication is not known. Here, we have used CRISPR/Cas9 gene editing to mutate CTCF-binding sites at the putative start site of TERRA transcripts for a class of subtelomeres. Under replication stress, telomeres lacking CTCF-driven TERRA exhibit sister-telomere loss and upon entry into mitosis, exhibit the formation of ultra-fine anaphase bridges and micronuclei. Importantly, these phenotypes could be rescued by the forced transcription of TERRA independent of CTCF binding. Our findings indicate that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription. Our findings also demonstrate that CTCF-driven TERRA transcription acts in cis to facilitate telomere repeat replication and chromosome stability. TERRA RNA is involved in maintaining stability during telomere repeat replication. Here the authors, by using CRISPR/Cas9, mutate CTCF-binding sites at start site of TERRA transcripts and find that subtelomeric CTCF facilitates telomeric DNA replication by promoting TERRA transcription.
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Anwar SL, Wulaningsih W, Lehmann U. Transposable Elements in Human Cancer: Causes and Consequences of Deregulation. Int J Mol Sci 2017; 18:E974. [PMID: 28471386 PMCID: PMC5454887 DOI: 10.3390/ijms18050974] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 01/04/2023] Open
Abstract
Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transposons, DNA transposons, and endogenous retroviruses that can invade the human genome with a substantial contribution in human evolution and genomic diversity. TEs are therefore firmly regulated from early embryonic development and during the entire course of human life by epigenetic mechanisms, in particular DNA methylation and histone modifications. The deregulation of TEs has been reported in some developmental diseases, as well as for different types of human cancers. To date, the role of TEs, the mechanisms underlying TE reactivation, and the interplay with DNA methylation in human cancers remain largely unexplained. We reviewed the loss of epigenetic regulation and subsequent genomic instability, chromosomal aberrations, transcriptional deregulation, oncogenic activation, and aberrations of non-coding RNAs as the potential mechanisms underlying TE deregulation in human cancers.
Collapse
Affiliation(s)
- Sumadi Lukman Anwar
- Division of Surgical Oncology, Department of Surgery Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover 30625, Germany.
- PILAR (Philippine and Indonesian Scholar) Research and Education, 20 Station Road, Cambridge CB1 2JD, UK.
| | - Wahyu Wulaningsih
- PILAR (Philippine and Indonesian Scholar) Research and Education, 20 Station Road, Cambridge CB1 2JD, UK.
- MRC (Medical Research Council) Unit for Lifelong Health and Ageing, University College London, London WC1B 5JU, UK.
- Division of Haematology/Oncology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.
| | - Ulrich Lehmann
- Institute of Pathology, Medizinische Hochschule Hannover, Hannover 30625, Germany.
| |
Collapse
|
25
|
Li Y, Li J, Wang Y, Zhang Y, Chu J, Sun C, Fu Z, Huang Y, Zhang H, Yuan H, Yin Y. Roles of cancer/testis antigens (CTAs) in breast cancer. Cancer Lett 2017; 399:64-73. [PMID: 28274891 DOI: 10.1016/j.canlet.2017.02.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 12/19/2022]
Abstract
Breast cancer is the most common cancer diagnosed and is the second leading cause of cancer death among women in the US. For breast cancer, early diagnosis and efficient therapy remains a significant clinical challenge. Therefore, it is necessary to identify novel tumor associated molecules to target for biomarker development and immunotherapy. In this regard, cancer testis antigens (CTAs) have emerged as a potential clinical biomarker targeting immunotherapy for various malignancies due to the nature of its characteristics. CTAs are a group of tumor associated antigens (TAAs) that display normal expression in immune-privileged organs, but display aberrant expression in several types of cancers, particularly in advanced cancers. Investigation of CTAs for the clinical management of breast malignancies indicates that these TAAs have potential roles as novel biomarkers, with increased specificity and sensitivity compared to those currently used in the clinic. Moreover, TAAs could be therapeutic targets for cancer immunotherapy. This review is an attempt to address the promising CTAs in breast cancer and their possible clinical implications as biomarkers and immunotherapeutic targets with particular focus on challenges and future interventions.
Collapse
Affiliation(s)
- Yongfei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Jun Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Yifan Wang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Yanhong Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Jiahui Chu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Chunxiao Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China; Nanjing Maternity and Child Health Medical Institute, Affiliated Obstetrics and Gynecology Hospital, Nanjing Medical University, Nanjing 210004, China
| | - Yi Huang
- Department of Pharmacology and Chemical Biology, Magee Women's Research Institute, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Hansheng Zhang
- School of Public Health, University of Maryland, College Park, MD 20742, USA
| | - Hongyan Yuan
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University. Nanjing 210004, China.
| |
Collapse
|
26
|
Zhang Y, Fang M, Song Y, Ren J, Fang J, Wang X. Brother of Regulator of Imprinted Sites (BORIS) suppresses apoptosis in colorectal cancer. Sci Rep 2017; 7:40786. [PMID: 28098226 PMCID: PMC5241680 DOI: 10.1038/srep40786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/09/2016] [Indexed: 11/09/2022] Open
Abstract
Identifying oncogenes that promote cancer cell proliferation or survival is critical for treatment of colorectal cancer. The Brother of Regulator of Imprinted Sites (BORIS) is frequently expressed in most types of cancer, but rarely in normal tissues. Aberrantly expressed BORIS relates to colorectal cancer, but its function in colorectal cancer cells remains unclear. In addition, previous studies indicated the significance of cytoplasm-localized BORIS in cancer cells. However, none of them investigated its function. Herein, we investigated the functions of BORIS in cancer cell proliferation and apoptosis and the role of cytoplasm-localized BORIS in colorectal cancer. BORIS expression correlated with colorectal cancer proliferation. BORIS overexpression promoted colorectal cancer cell growth, whereas BORIS knockdown suppressed cell proliferation. Sensitivity of colorectal cancer cells to 5-fluorouracil (5-FU) was inversely correlated with BORIS expression. These data suggest that BORIS functions as an oncogene in colorectal cancer. BORIS silencing induced reactive oxygen species (ROS) production and apoptosis, whereas BORIS supplementation inhibited apoptosis induced by BORIS short interfering RNA (siRNA), hydrogen peroxide (H2O2) or 5-FU. Introduction of BORIS-ZFdel showed that cytoplasmic localization of BORIS inhibited apoptosis but not ROS production. Our study highlights the anti-apoptotic function of BORIS in colorectal cancer.
Collapse
Affiliation(s)
- Yanmei Zhang
- Center for Molecular Medicine, Zhejiang Academy of Medical Science, Hangzhou, Zhejiang Province, 310012, P.R. China
| | - Mengdie Fang
- Center for Molecular Medicine, Zhejiang Academy of Medical Science, Hangzhou, Zhejiang Province, 310012, P.R. China
| | - Yongfei Song
- Center for Molecular Medicine, Zhejiang Academy of Medical Science, Hangzhou, Zhejiang Province, 310012, P.R. China
| | - Juan Ren
- Center for Molecular Medicine, Zhejiang Academy of Medical Science, Hangzhou, Zhejiang Province, 310012, P.R. China
| | - Jianfei Fang
- Center for Molecular Medicine, Zhejiang Academy of Medical Science, Hangzhou, Zhejiang Province, 310012, P.R. China
| | - Xiaoju Wang
- Center for Molecular Medicine, Zhejiang Academy of Medical Science, Hangzhou, Zhejiang Province, 310012, P.R. China
| |
Collapse
|