1
|
Gerovska D, Fernández Moreno P, Zabala A, Araúzo-Bravo MJ. Cell-Free Genic Extrachromosomal Circular DNA Profiles of DNase Knockouts Associated with Systemic Lupus Erythematosus and Relation with Common Fragile Sites. Biomedicines 2023; 12:80. [PMID: 38255187 PMCID: PMC10813657 DOI: 10.3390/biomedicines12010080] [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: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Cell-free extrachromosomal circular DNA (cf-eccDNA) has been proposed as a promising early biomarker for disease diagnosis, progression and drug response. Its established biomarker features are changes in the number and length distribution of cf-eccDNA. Another novel promising biomarker is a set of eccDNA excised from a panel of genes specific to a condition compared to a control. Deficiencies in two endonucleases that specifically target DNA, Dnase1 and Dnase1l3, are associated with systemic lupus erythematosus (SLE). To study the genic eccDNA profiles in the case of their deficiencies, we mapped sequenced eccDNA data from plasma, liver and buffy coat from Dnase1 and Dnase1l3 knockouts (KOs), and wild type controls in mouse. Next, we performed an eccDNA differential analysis between KO and control groups using our DifCir algorithm. We found a specific genic cf-eccDNA fingerprint of the Dnase1l3 group compared to the wild type controls involving 131 genes; 26% of them were associated with human chromosomal fragile sites (CFSs) and with a statistically significant enrichment of CFS-associated genes. We found six genes in common with the genic cf-eccDNA profile of SLE patients with DNASE1L3 deficiency, namely Rorb, Mvb12b, Osbpl10, Fto, Tnik and Arhgap10; all of them were specific and present in all human plasma samples, and none of them were associated with CFSs. A not so distinctive genic cf-eccDNA difference involving only seven genes was observed in the case of the Dnase1 group compared to the wild type. In tissue-liver and buffy coat-we did not detect the same genic eccDNA difference observed in the plasma samples. These results point to a specific role of a set of genic eccDNA in plasma from DNase KOs, as well as a relation with CFS genes, confirming the promise of the genic cf-eccDNA in studying diseases and the need for further research on the relationship between eccDNA and CFSs.
Collapse
Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Patricia Fernández Moreno
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Aitor Zabala
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biogipuzkoa Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (P.F.M.); (A.Z.)
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
| |
Collapse
|
2
|
Hill HJ, Bonser D, Golic KG. Dicentric chromosome breakage in Drosophila melanogaster is influenced by pericentric heterochromatin and occurs in nonconserved hotspots. Genetics 2023; 224:iyad052. [PMID: 37010100 PMCID: PMC10213500 DOI: 10.1093/genetics/iyad052] [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: 10/18/2022] [Revised: 10/18/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Chromosome breakage plays an important role in the evolution of karyotypes and can produce deleterious effects within a single individual, such as aneuploidy or cancer. Forces that influence how and where chromosomes break are not fully understood. In humans, breakage tends to occur in conserved hotspots called common fragile sites (CFS), especially during replication stress. By following the fate of dicentric chromosomes in Drosophila melanogaster, we find that breakage under tension also tends to occur in specific hotspots. Our experimental approach was to induce sister chromatid exchange in a ring chromosome to generate a dicentric chromosome with a double chromatid bridge. In the following cell division, the dicentric bridges may break. We analyzed the breakage patterns of 3 different ring-X chromosomes. These chromosomes differ by the amount and quality of heterochromatin they carry as well as their genealogical history. For all 3 chromosomes, breakage occurs preferentially in several hotspots. Surprisingly, we found that the hotspot locations are not conserved between the 3 chromosomes: each displays a unique array of breakage hotspots. The lack of hotspot conservation, along with a lack of response to aphidicolin, suggests that these breakage sites are not entirely analogous to CFS and may reveal new mechanisms of chromosome fragility. Additionally, the frequency of dicentric breakage and the durability of each chromosome's spindle attachment vary significantly between the 3 chromosomes and are correlated with the origin of the centromere and the amount of pericentric heterochromatin. We suggest that different centromere strengths could account for this.
Collapse
Affiliation(s)
- Hunter J Hill
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Danielle Bonser
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
3
|
Li X, Shen X, Wang Z, Jiang H, Ma Z, Yu P, Yu Z, Qian X, Liu J. Gene expression profiling in nucleus pulposus of human ruptured lumbar disc herniation. Front Pharmacol 2022; 13:892594. [PMID: 36506585 PMCID: PMC9732013 DOI: 10.3389/fphar.2022.892594] [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: 05/10/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022] Open
Abstract
Purpose: To examine the differences in gene expression between ruptured and non-ruptured nucleus pulposus tissues of the intervertebral discs using gene chip technology. Methods: A total of 8 patients with nucleus pulposus from a lumbar disc herniation (LDH) undergoing discectomy in our hospital were selected, including 4 ruptured and 4 non-ruptured herniated nucleus pulposus cases. Total RNA was extracted from cells by using TRIzol reagent. Nucleus pulposus cDNA probes of the two groups were obtained by the single marker method and hybridized with a human gene expression profiling chip (Agilent). The fluorescence signal images were scanned by a laser, and the obtained genes were analyzed by bioinformatics. Results: There were 75 differentially expressed genes with more than 2-fold-changes, of which 56 were up-regulated and 19 were down-regulated. The differential expression of THSD7A, which was up-regulated 18 times, was the most significant, followed by CCL5, AQP3 and SDC4. Conclusion: THSD7A can be used as a characteristic differentially expressed gene in human ruptured nucleus pulposus. Moreover, CCL5, AQP3 and SDC4 may improve the chemotaxis of stem cell migration for self-healing of damaged disc tissue, increase water uptake by nucleus accumbens cells, and inhibit the inflammatory response, thus delaying the process of intervertebral disc degeneration.
Collapse
Affiliation(s)
- Xiaochun Li
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Xueqiang Shen
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Zhiqiang Wang
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Hong Jiang
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Zhijia Ma
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Pengfei Yu
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Zhenhan Yu
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Xiang Qian
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Jintao Liu
- Suzhou Hospital of Traditional Chinese Medicine, Suzhou, China,Nanjing University of Traditional Chinese Medicine, Nanjing, China,*Correspondence: Jintao Liu,
| |
Collapse
|
4
|
Mirceta M, Shum N, Schmidt MHM, Pearson CE. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front Genet 2022; 13:985975. [PMID: 36468036 PMCID: PMC9714581 DOI: 10.3389/fgene.2022.985975] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/02/2022] [Indexed: 09/16/2023] Open
Abstract
Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.
Collapse
Affiliation(s)
- Mila Mirceta
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Shum
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Monika H. M. Schmidt
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
5
|
Balzano E, Di Tommaso E, Antoccia A, Pelliccia F, Giunta S. Characterization of Chromosomal Instability in Glioblastoma. Front Genet 2022; 12:810793. [PMID: 35154254 PMCID: PMC8831864 DOI: 10.3389/fgene.2021.810793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/23/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a malignant tumor of the central nervous system (CNS). The poor prognosis of GBM due to resistance to therapy has been associated with high chromosomal instability (CIN). Replication stress is a major cause of CIN that manifests as chromosome rearrangements, fragility, and breaks, including those cytologically expressed within specific chromosome regions named common fragile sites (CFSs). In this work, we characterized the expression of human CFSs in the glioblastoma U-251 MG cell line upon treatment with the inhibitor of DNA polymerase alpha aphidicolin (APH). We observed 52 gaps/breaks located within previously characterized CFSs. We found 17 to be CFSs in GBM cells upon treatment with APH, showing a frequency equal to at least 1% of the total gaps/breaks. We report that two CFSs localized to regions FRA2E (2p13/p12) and FRA2F (2q22) were only found in U-251 MG cells, but not lymphocytes or fibroblasts, after APH treatment. Notably, these glioblastoma-specific CFSs had a relatively high expression compared to the other CFSs with breakage frequency between ∼7 and 9%. Presence of long genes, incomplete replication, and delayed DNA synthesis during mitosis (MiDAS) after APH treatment suggest that an impaired replication process may contribute to this loci-specific fragility in U-251 MG cells. Altogether, our work offers a characterization of common fragile site expression in glioblastoma U-251 MG cells that may be further exploited for cytogenetic and clinical studies to advance our understanding of this incurable cancer.
Collapse
Affiliation(s)
- Elisa Balzano
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Elena Di Tommaso
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Antonio Antoccia
- Laboratory of Genetics and Cytogenetics, Dipartimento di Scienze, Università Degli Studi Roma Tre, Roma, Italy
| | - Franca Pelliccia
- Laboratory of Molecular Cytogenetics, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- *Correspondence: Franca Pelliccia, ; Simona Giunta,
| | - Simona Giunta
- Laboratory of Genome Evolution, Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
- *Correspondence: Franca Pelliccia, ; Simona Giunta,
| |
Collapse
|
6
|
Xia W, Gong D, Qin X, Cai Z. [MicroRNA-671-3p suppresses proliferation and invasion of breast cancer cells by targeting DEPTOR]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2020; 40:42-48. [PMID: 32376551 DOI: 10.12122/j.issn.1673-4254.2020.01.07] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To investigate the effects of miR-671-3p on the proliferation and invasion of breast cancer cells and explore the possible mechanism. METHODS We examined the expressions of miR-671-3p in human normal epithelial cells (MCF-10A) and breast cancer cell lines (MCF-7, MDA-MB-231, and SK-BR3) using RT-PCR. The effects of transfection with a miR-671-3p mimic or inhibitor on the proliferation, migration and invasion of MCF-7 cells were evaluated using CCK-8 assay and Transwell chamber assay. The target gene of miR-671-3p was predicated with Targetscan and validated by a dual luciferase reporter system and Western blotting. RESULTS The expression of miR-671-3p was significantly lower in breast cancer cells than in normal breast epithelial cells. Compared with negative control group, MCF-7 cells with miR-671-3p overexpression exhibited significantly reduced proliferation and invasion, whereas inhibition of miR-671-3p obviously promoted the cell proliferation and invasion. Luciferase reporter assay demonstrated that DEPTOR was the target gene of miR-671-3p, and miR-671-3p overexpression caused significant down-regulation of the protein expression of DEPTOR. CONCLUSIONS MiR-671-3p suppresses the proliferation and invasion of breast cancer cell line MCF-7 by directly targeting DEPTOR protein.
Collapse
Affiliation(s)
- Wei Xia
- Department of Cell biology, Southern Medical University, Guangzhou 510515, China.,Department of Clinical Laboratory, 74th Army Hospital of PLA, Guangzhou 510310, China
| | - Degui Gong
- Department of Clinical Laboratory, 74th Army Hospital of PLA, Guangzhou 510310, China
| | - Xiaoping Qin
- Department of Clinical Laboratory, 74th Army Hospital of PLA, Guangzhou 510310, China
| | - Zhuo Cai
- Department of Pharmacy, Air Force Hospital of Southern Theater Command of PLA, Guangzhou 510602, China
| |
Collapse
|
7
|
Panou V, Røe OD. Inherited Genetic Mutations and Polymorphisms in Malignant Mesothelioma: A Comprehensive Review. Int J Mol Sci 2020; 21:ijms21124327. [PMID: 32560575 PMCID: PMC7352726 DOI: 10.3390/ijms21124327] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Malignant mesothelioma (MM) is mainly caused by air-born asbestos but genetic susceptibility is also suspected to be a risk factor. Recent studies suggest an increasing number of candidate genes that may predispose to MM besides the well-characterized BRCA1-associated protein-1 gene. The aim of this review is to summarize the most important studies on germline mutations for MM. A total of 860 publications were retrieved from Scopus, PubMed and Web of Science, of which 81 met the inclusion criteria and were consider for this review. More than 50% of the genes that are reported to predispose to MM are involved in DNA repair mechanisms, and the majority of them have a role in the homologous recombination pathway. Genetic alterations in tumor suppressor genes involved in chromatin, transcription and hypoxia regulation have also been described. Furthermore, we identified several single nucleotide polymorphisms (SNPs) that may promote MM tumorigenesis as a result of an asbestos-gene interaction, including SNPs in DNA repair, carcinogen detoxification and other genes previously associated with other malignancies. The identification of inherited mutations for MM and an understanding of the underlying pathways may allow early detection and prevention of malignancies in high-risk individuals and pave the way for targeted therapies.
Collapse
Affiliation(s)
- Vasiliki Panou
- Department of Respiratory Medicine, Odense University Hospital, 5000 Odense, Denmark
- Department of Respiratory Medicine, Aalborg University Hospital, 9000 Aalborg, Denmark
- Clinical Institute, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Correspondence:
| | - Oluf Dimitri Røe
- Clinical Institute, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| |
Collapse
|
8
|
Impaired Replication Timing Promotes Tissue-Specific Expression of Common Fragile Sites. Genes (Basel) 2020; 11:genes11030326. [PMID: 32204553 PMCID: PMC7140878 DOI: 10.3390/genes11030326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022] Open
Abstract
Common fragile sites (CFSs) are particularly vulnerable regions of the genome that become visible as breaks, gaps, or constrictions on metaphase chromosomes when cells are under replicative stress. Impairment in DNA replication, late replication timing, enrichment of A/T nucleotides that tend to form secondary structures, the paucity of active or inducible replication origins, the generation of R-loops, and the collision between replication and transcription machineries on particularly long genes are some of the reported characteristics of CFSs that may contribute to their tissue-specific fragility. Here, we validated the induction of two CFSs previously found in the human fetal lung fibroblast line, Medical Research Council cell strain 5 (MRC-5), in another cell line derived from the same fetal tissue, Institute for Medical Research-90 cells (IMR-90). After induction of CFSs through aphidicolin, we confirmed the expression of the CFS 1p31.1 on chromosome 1 and CFS 3q13.3 on chromosome 3 in both fetal lines. Interestingly, these sites were found to not be fragile in lymphocytes, suggesting a role for epigenetic or transcriptional programs for this tissue specificity. Both these sites contained late-replicating genes NEGR1 (neuronal growth regulator 1) at 1p31.1 and LSAMP (limbic system-associated membrane protein) at 3q13.3, which are much longer, 0.880 and 1.4 Mb, respectively, than the average gene length. Given the established connection between long genes and CFS, we compiled information from the literature on all previously identified CFSs expressed in fibroblasts and lymphocytes in response to aphidicolin, including the size of the genes contained in each fragile region. Our comprehensive analysis confirmed that the genes found within CFSs are longer than the average human gene; interestingly, the two longest genes in the human genome are found within CFSs: Contactin Associated Protein 2 gene (CNTNAP2) in a lymphocytes’ CFS, and Duchenne muscular dystrophy gene (DMD) in a CFS expressed in both lymphocytes and fibroblasts. This indicates that the presence of very long genes is a unifying feature of all CFSs. We also obtained replication profiles of the 1p31.1 and 3q13.3 sites under both perturbed and unperturbed conditions using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence against bromodeoxyuridine (BrdU) on interphase nuclei. Our analysis of the replication dynamics of these CFSs showed that, compared to lymphocytes where these regions are non-fragile, fibroblasts display incomplete replication of the fragile alleles, even in the absence of exogenous replication stress. Our data point to the existence of intrinsic features, in addition to the presence of long genes, which affect DNA replication of the CFSs in fibroblasts, thus promoting chromosomal instability in a tissue-specific manner.
Collapse
|
9
|
Irony-Tur Sinai M, Kerem B. Genomic instability in fragile sites-still adding the pieces. Genes Chromosomes Cancer 2018; 58:295-304. [PMID: 30525255 DOI: 10.1002/gcc.22715] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/19/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic regions in normal chromosomes that exhibit genomic instability under DNA replication stress. As replication stress is an early feature of cancer development, CFSs are involved in the signature of genomic instability found in malignant tumors. The landscape of CFSs is tissue-specific and differs under different replication stress inducers. Nevertheless, the features underlying CFS sensitivity to replication stress are shared. Here, we review the events generating replication stress and discuss the unique characteristics of CFS regions and the cellular responses aimed to stabilizing these regions.
Collapse
Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, Israel
| |
Collapse
|
10
|
Abstract
Despite availability of sequence site-specific information resulting from years of sequencing and sequence feature curation, there have been few efforts to integrate and annotate this information. In this study, we update the number of human N-linked glycosylation sequons (NLGs), and we investigate cancer-relatedness of glycosylation-impacting somatic nonsynonymous single-nucleotide variation (nsSNV) by mapping human NLGs to cancer variation data and reporting the expected loss or gain of glycosylation sequon. We find 75.8% of all human proteins have at least one NLG for a total of 59,341 unique NLGs (includes predicted and experimentally validated). Only 27.4% of all NLGs are experimentally validated sites on 4,412 glycoproteins. With respect to cancer, 8,895 somatic-only nsSNVs abolish NLGs in 5,204 proteins and 12,939 somatic-only nsSNVs create NLGs in 7,356 proteins in cancer samples. nsSNVs causing loss of 24 NLGs on 23 glycoproteins and nsSNVs creating 41 NLGs on 40 glycoproteins are identified in three or more cancers. Of all identified cancer somatic variants causing potential loss or gain of glycosylation, only 36 have previously known disease associations. Although this work is computational, it builds on existing genomics and glycobiology research to promote identification and rank potential cancer nsSNV biomarkers for experimental validation.
Collapse
|
11
|
Brandariz L, Arriba M, García JL, Cano JM, Rueda D, Rubio E, Rodríguez Y, Pérez J, Vivas A, Sánchez C, Tapial S, Pena L, García-Arranz M, García-Olmo D, Urioste M, González-Sarmiento R, Perea J. Differential clinicopathological and molecular features within late-onset colorectal cancer according to tumor location. Oncotarget 2018; 9:15302-15311. [PMID: 29632645 PMCID: PMC5880605 DOI: 10.18632/oncotarget.24502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/10/2018] [Indexed: 12/12/2022] Open
Abstract
Background Since there is a predilection of some clinical and molecular features for a given tumor location, we assessed whether this can be confirmed in late-onset colorectal cancer (LOCRC). Results Right colon cancers showed features associated with sporadic Microsatellite Instability: predominance of female cases and BRAF mutations, and an important mucinous component. Left colon cancers developed a higher number of polyps and multiple primary CRCs, showed the strongest familial component, and had better prognosis. Rectal cancers showed a predominantly sporadic phenotype, with worse prognosis and a CpG Island Methylator Phenotype (CIMP)-High. No copy number alterations (CNAs) greater than or equal to 50% were observed in this LOCRC group, and the most recurrent alterations were losses at 5q13 and 14q11, and gains at 7q11, 7q21-q22, 19p13-p12, 19q13 and 20p11-q11. KRAS and PIK3CA were the only mutated genes showing differences according to the tumor location, mainly for right colon cancers. Materials and Methods We analyzed clinical and molecular characteristics of LOCRC at different tumor locations in order to determine if there are differential phenotypes related with the location in the colon. Conclusions Categorizing LOCRC according to tumor location appears to be an adequate first step to resolving the heterogeneity of this subset of CRC.
Collapse
Affiliation(s)
- Lorena Brandariz
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - María Arriba
- Biochemistry Department, Gregorio Marañón University Hospital, Madrid, Spain
| | - Juan Luis García
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain
| | - Juana María Cano
- Oncology Department, Ciudad Real General Hospital, Ciudad Real, Spain
| | - Daniel Rueda
- Molecular Biology Laboratory, "12 de Octubre" Universitary Hospital, Madrid, Spain.,Digestive Cancer Research Group, "12 de Octubre" Research Institute, Madrid, Spain
| | - Eduardo Rubio
- Surgery Department, "12 de Octubre" Universitary Hospital, Madrid, Spain
| | - Yolanda Rodríguez
- Pathology Department, "12 de Octubre" Universitary Hospital, Madrid, Spain
| | - Jessica Pérez
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain
| | - Alfredo Vivas
- Surgery Department, "12 de Octubre" Universitary Hospital, Madrid, Spain
| | - Carmen Sánchez
- Surgery Department, "12 de Octubre" Universitary Hospital, Madrid, Spain
| | - Sandra Tapial
- Digestive Cancer Research Group, "12 de Octubre" Research Institute, Madrid, Spain
| | - Laura Pena
- Familial Cancer Clinical Unit, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Mariano García-Arranz
- Health Research Institute, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Damián García-Olmo
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Health Research Institute, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Centre (CNIO), Madrid, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, Madrid, Spain
| | - Rogelio González-Sarmiento
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain.,Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain
| | - José Perea
- Surgery Department, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Health Research Institute, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| |
Collapse
|
12
|
Expression, prognosis and functional role of Thsd7a in esophageal squamous cell carcinoma of Kazakh patients, Xinjiang. Oncotarget 2017; 8:60539-60557. [PMID: 28947992 PMCID: PMC5601160 DOI: 10.18632/oncotarget.16966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/01/2017] [Indexed: 12/12/2022] Open
Abstract
Thsd7a (Thrombospondin type 1 domain containing 7a) is a critical transmembrane protein. Studies have indicated that Thsd7a was associated with cytoskeletal organization, cell migration and filopodia formation. However, the involvement of Thsd7a remains elusive in human Esophageal Squamous Cell Carcinoma (ESCC). Consequently, immunohistochemistry and reverse transcription-polymerase chain reaction were utilized to study the correlation between the expression of Thsd7a and clinical-pathological characteristics. The influence of Thsd7a on apoptosis, cell proliferating activity, cell cycle, migratory and invasive capacity was determined in Eca 109 and EC 9706 cell lines in vitro. And the influence on proliferating activity was testified using naked mice model in vivo. In addition, the potential molecular mechanism was tested by microarray. It was discovered that there is a certain correlation between Thsd7a and the Kazakh ESCC. By knocking out Thsd7a, the invasion, migration and proliferation could be decreased. And it could also arrest the cell cycle at G1 phase and increase the apoptosis rate. It was further verified that Thsd7a had obvious effect on proliferation in naked mice with xenograft of Eca109 cells. Finally, it was uncovered by microarray analysis that a variety of tumor genes and pathways related to Thsd7a. Together, it was demonstrated that Thsd7a might have a certain degree of carcinogenesis in ESCC.
Collapse
|
13
|
Feng W, Chakraborty A. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:489-526. [PMID: 29357071 DOI: 10.1007/978-981-10-6955-0_21] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.
Collapse
Affiliation(s)
- Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| |
Collapse
|
14
|
Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells. Cell 2016; 164:644-55. [PMID: 26871630 DOI: 10.1016/j.cell.2015.12.039] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/23/2015] [Accepted: 12/21/2015] [Indexed: 12/25/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) by non-homologous end joining is critical for neural development, and brain cells frequently contain somatic genomic variations that might involve DSB intermediates. We now use an unbiased, high-throughput approach to identify genomic regions harboring recurrent DSBs in primary neural stem/progenitor cells (NSPCs). We identify 27 recurrent DSB clusters (RDCs), and remarkably, all occur within gene bodies. Most of these NSPC RDCs were detected only upon mild, aphidicolin-induced replication stress, providing a nucleotide-resolution view of replication-associated genomic fragile sites. The vast majority of RDCs occur in long, transcribed, and late-replicating genes. Moreover, almost 90% of identified RDC-containing genes are involved in synapse function and/or neural cell adhesion, with a substantial fraction also implicated in tumor suppression and/or mental disorders. Our characterization of NSPC RDCs reveals a basis of gene fragility and suggests potential impacts of DNA breaks on neurodevelopment and neural functions.
Collapse
|
15
|
PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1. Eur J Hum Genet 2016; 24:1598-1604. [PMID: 27329736 DOI: 10.1038/ejhg.2016.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/12/2016] [Accepted: 05/26/2016] [Indexed: 11/08/2022] Open
Abstract
Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5'-part from the 3'-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms.
Collapse
|
16
|
Lim HJ, Yang JL. Regulatory roles and therapeutic potential of microRNA in sarcoma. Crit Rev Oncol Hematol 2016; 97:118-30. [DOI: 10.1016/j.critrevonc.2015.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 07/15/2015] [Accepted: 08/04/2015] [Indexed: 02/01/2023] Open
|
17
|
Savelyeva L, Brueckner LM. Molecular characterization of common fragile sites as a strategy to discover cancer susceptibility genes. Cell Mol Life Sci 2014; 71:4561-75. [PMID: 25231336 PMCID: PMC11114050 DOI: 10.1007/s00018-014-1723-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 12/19/2022]
Abstract
The cytogenetic hypothesis that common fragile sites (cFSs) are hotspots of cancer breakpoints is increasingly supported by recent data from whole-genome profiles of different cancers. cFSs are components of the normal chromosome structure that are particularly prone to breakage under conditions of replication stress. In recent years, cFSs have become of increasing interest in cancer research, as they not only appear to be frequent targets of genomic alterations in progressive tumors, but also already in precancerous lesions. Despite growing evidence of their importance in disease development, most cFSs have not been investigated at the molecular level and most cFS genes have not been identified. In this review, we summarize the current data on molecularly characterized cFSs, their genetic and epigenetic characteristics, and put emphasis on less-studied cFS genes as potential contributors to cancer development.
Collapse
Affiliation(s)
- Larissa Savelyeva
- Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany,
| | | |
Collapse
|
18
|
Georgakilas AG, Tsantoulis P, Kotsinas A, Michalopoulos I, Townsend P, Gorgoulis VG. Are common fragile sites merely structural domains or highly organized "functional" units susceptible to oncogenic stress? Cell Mol Life Sci 2014; 71:4519-44. [PMID: 25238782 PMCID: PMC4232749 DOI: 10.1007/s00018-014-1717-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 08/28/2014] [Indexed: 01/07/2023]
Abstract
Common fragile sites (CFSs) are regions of the genome with a predisposition to DNA double-strand breaks in response to intrinsic (oncogenic) or extrinsic replication stress. CFS breakage is a common feature in carcinogenesis from its earliest stages. Given that a number of oncogenes and tumor suppressors are located within CFSs, a question that emerges is whether fragility in these regions is only a structural “passive” incident or an event with a profound biological effect. Furthermore, there is sparse evidence that other elements, like non-coding RNAs, are positioned with them. By analyzing data from various libraries, like miRbase and ENCODE, we show a prevalence of various cancer-related genes, miRNAs, and regulatory binding sites, such as CTCF within CFSs. We propose that CFSs are not only susceptible structural domains, but highly organized “functional” entities that when targeted, severe repercussion for cell homeostasis occurs.
Collapse
Affiliation(s)
- Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece
| | | | | | | | | | | |
Collapse
|
19
|
Gao G, Kasperbauer JL, Tombers NM, Wang V, Mayer K, Smith DI. A selected group of large common fragile site genes have decreased expression in oropharyngeal squamous cell carcinomas. Genes Chromosomes Cancer 2014; 53:392-401. [DOI: 10.1002/gcc.22150] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 01/11/2023] Open
Affiliation(s)
- Ge Gao
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN
| | | | | | - Vivian Wang
- Mayo Medical Genome Facilities; Mayo Clinic; Rochester MN
| | - Kevin Mayer
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN
| | - David I. Smith
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; Mayo Clinic; Rochester MN
| |
Collapse
|
20
|
White NM, Feng FY, Maher CA. Recurrent rearrangements in prostate cancer: causes and therapeutic potential. Curr Drug Targets 2014; 14:450-9. [PMID: 23410129 DOI: 10.2174/1389450111314040006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/13/2012] [Accepted: 02/06/2013] [Indexed: 11/22/2022]
Abstract
DNA damage and genetic rearrangements are hallmarks of cancer. However, gene fusions as driver mutations in cancer have classically been a distinction in leukemia and other rare instances until recently with the discovery of gene fusion events occurring in 50 to 75% of prostate cancer patients. The discovery of the TMPRSS2-ERG fusion sparked an onslaught of discovery and innovation resulting in a delineation of prostate cancer via a molecular signature of gene fusion events. The increased commonality of high-throughput sequencing data coupled with improved bioinformatics approaches not only elucidated the molecular underpinnings of prostate cancer progression, but the mechanisms of gene fusion biogenesis. Interestingly, the androgen receptor (AR), already known to play a significant role in prostate cancer tumorigenesis, has recently been implicated in the processes resulting in gene fusions by inducing the spatial proximity of genes involved in rearrangements, promoting the formation of double-strand DNA breaks (DSB), and facilitating the recruitment of proteins for non-homologous end-joining (NHEJ). Our increased understanding of the mechanisms inducing genomic instability may lead to improved diagnostic and therapeutic strategies. To date, the majority of prostate cancer patients can be molecularly stratified based on their gene fusion status thereby increasing the potential for tailoring more specific and effective therapies.
Collapse
Affiliation(s)
- Nicole M White
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | | | | |
Collapse
|
21
|
Cadby G, Mukherjee S, Musk A(B, Reid A, Garlepp M, Dick I, Robinson C, Hui J, Fiorito G, Guarrera S, Beilby J, Melton PE, Moses EK, Ugolini D, Mirabelli D, Bonassi S, Magnani C, Dianzani I, Matullo G, Robinson B, Creaney J, Palmer LJ. A genome-wide association study for malignant mesothelioma risk. Lung Cancer 2013; 82:1-8. [DOI: 10.1016/j.lungcan.2013.04.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/30/2013] [Accepted: 04/21/2013] [Indexed: 10/26/2022]
|
22
|
Common Fragile Site Profiling in Epithelial and Erythroid Cells Reveals that Most Recurrent Cancer Deletions Lie in Fragile Sites Hosting Large Genes. Cell Rep 2013; 4:420-8. [DOI: 10.1016/j.celrep.2013.07.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/05/2013] [Accepted: 07/02/2013] [Indexed: 01/22/2023] Open
|
23
|
Matullo G, Guarrera S, Betti M, Fiorito G, Ferrante D, Voglino F, Cadby G, Di Gaetano C, Rosa F, Russo A, Hirvonen A, Casalone E, Tunesi S, Padoan M, Giordano M, Aspesi A, Casadio C, Ardissone F, Ruffini E, Betta PG, Libener R, Guaschino R, Piccolini E, Neri M, Musk AWB, de Klerk NH, Hui J, Beilby J, James AL, Creaney J, Robinson BW, Mukherjee S, Palmer LJ, Mirabelli D, Ugolini D, Bonassi S, Magnani C, Dianzani I. Genetic variants associated with increased risk of malignant pleural mesothelioma: a genome-wide association study. PLoS One 2013; 8:e61253. [PMID: 23626673 PMCID: PMC3634031 DOI: 10.1371/journal.pone.0061253] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/06/2013] [Indexed: 12/19/2022] Open
Abstract
Asbestos exposure is the main risk factor for malignant pleural mesothelioma (MPM), a rare aggressive tumor. Nevertheless, only 5-17% of those exposed to asbestos develop MPM, suggesting the involvement of other environmental and genetic risk factors. To identify the genetic risk factors that may contribute to the development of MPM, we conducted a genome-wide association study (GWAS; 370,000 genotyped SNPs, 5 million imputed SNPs) in Italy, among 407 MPM cases and 389 controls with a complete history of asbestos exposure. A replication study was also undertaken and included 428 MPM cases and 1269 controls from Australia. Although no single marker reached the genome-wide significance threshold, several associations were supported by haplotype-, chromosomal region-, gene- and gene-ontology process-based analyses. Most of these SNPs were located in regions reported to harbor aberrant alterations in mesothelioma (SLC7A14, THRB, CEBP350, ADAMTS2, ETV1, PVT1 and MMP14 genes), causing at most a 2-3-fold increase in MPM risk. The Australian replication study showed significant associations in five of these chromosomal regions (3q26.2, 4q32.1, 7p22.2, 14q11.2, 15q14). Multivariate analysis suggested an independent contribution of 10 genetic variants, with an Area Under the ROC Curve (AUC) of 0.76 when only exposure and covariates were included in the model, and of 0.86 when the genetic component was also included, with a substantial increase of asbestos exposure risk estimation (odds ratio, OR: 45.28, 95% confidence interval, CI: 21.52-95.28). These results showed that genetic risk factors may play an additional role in the development of MPM, and that these should be taken into account to better estimate individual MPM risk in individuals who have been exposed to asbestos.
Collapse
Affiliation(s)
- Giuseppe Matullo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Marta Betti
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Daniela Ferrante
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | | | - Gemma Cadby
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Nedlands, Western Australia, Australia
| | - Cornelia Di Gaetano
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Fabio Rosa
- Human Genetics Foundation, HuGeF, Turin, Italy
| | - Alessia Russo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Ari Hirvonen
- Centre of Expertise for Health and Work Ability, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Elisabetta Casalone
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Sara Tunesi
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marina Padoan
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Mara Giordano
- Laboratory of Genetics, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Anna Aspesi
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Caterina Casadio
- Thoracic Surgery Unit, University of Piemonte Orientale, Novara, Italy
| | - Francesco Ardissone
- Chest Surgery, Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Enrico Ruffini
- Thoracic Surgery Unit, University of Turin, Turin, Italy
| | - Pier Giacomo Betta
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberta Libener
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberto Guaschino
- Transfusion Centre, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Ezio Piccolini
- Pneumology Unit, Santo Spirito Hospital, Casale Monferrato, Italy
| | - Monica Neri
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Arthur W. B. Musk
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Nicholas H. de Klerk
- Centre for Child Health Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Jennie Hui
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - John Beilby
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Alan L. James
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Jenette Creaney
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Bruce W. Robinson
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sutapa Mukherjee
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Women's College Research Institute and Women's College Hospital, Toronto, Ontario, Canada
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Dario Mirabelli
- Unit of Cancer Epidemiology, CPO-Piemonte and University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Donatella Ugolini
- Department of Internal Medicine, University of Genoa and IRCSS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Irma Dianzani
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| |
Collapse
|
24
|
Common fragile sites: genomic hotspots of DNA damage and carcinogenesis. Int J Mol Sci 2012; 13:11974-11999. [PMID: 23109895 PMCID: PMC3472787 DOI: 10.3390/ijms130911974] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/09/2012] [Accepted: 09/05/2012] [Indexed: 01/08/2023] Open
Abstract
Genomic instability, a hallmark of cancer, occurs preferentially at specific genomic regions known as common fragile sites (CFSs). CFSs are evolutionarily conserved and late replicating regions with AT-rich sequences, and CFS instability is correlated with cancer. In the last decade, much progress has been made toward understanding the mechanisms of chromosomal instability at CFSs. However, despite tremendous efforts, identifying a cancer-associated CFS gene (CACG) remains a challenge and little is known about the function of CACGs at most CFS loci. Recent studies of FATS (for Fragile-site Associated Tumor Suppressor), a new CACG at FRA10F, reveal an active role of this CACG in regulating DNA damage checkpoints and suppressing tumorigenesis. The identification of FATS may inspire more discoveries of other uncharacterized CACGs. Further elucidation of the biological functions and clinical significance of CACGs may be exploited for cancer biomarkers and therapeutic benefits.
Collapse
|
25
|
Fungtammasan A, Walsh E, Chiaromonte F, Eckert KA, Makova KD. A genome-wide analysis of common fragile sites: what features determine chromosomal instability in the human genome? Genome Res 2012; 22:993-1005. [PMID: 22456607 PMCID: PMC3371707 DOI: 10.1101/gr.134395.111] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Chromosomal common fragile sites (CFSs) are unstable genomic regions that break under replication stress and are involved in structural variation. They frequently are sites of chromosomal rearrangements in cancer and of viral integration. However, CFSs are undercharacterized at the molecular level and thus difficult to predict computationally. Newly available genome-wide profiling studies provide us with an unprecedented opportunity to associate CFSs with features of their local genomic contexts. Here, we contrasted the genomic landscape of cytogenetically defined aphidicolin-induced CFSs (aCFSs) to that of nonfragile sites, using multiple logistic regression. We also analyzed aCFS breakage frequencies as a function of their genomic landscape, using standard multiple regression. We show that local genomic features are effective predictors both of regions harboring aCFSs (explaining ∼77% of the deviance in logistic regression models) and of aCFS breakage frequencies (explaining ∼45% of the variance in standard regression models). In our optimal models (having highest explanatory power), aCFSs are predominantly located in G-negative chromosomal bands and away from centromeres, are enriched in Alu repeats, and have high DNA flexibility. In alternative models, CpG island density, transcription start site density, H3K4me1 coverage, and mononucleotide microsatellite coverage are significant predictors. Also, aCFSs have high fragility when colocated with evolutionarily conserved chromosomal breakpoints. Our models are predictive of the fragility of aCFSs mapped at a higher resolution. Importantly, the genomic features we identified here as significant predictors of fragility allow us to draw valuable inferences on the molecular mechanisms underlying aCFSs.
Collapse
Affiliation(s)
- Arkarachai Fungtammasan
- The Integrative Biosciences Graduate Program, Bioinformatics and Genomics Option, Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | |
Collapse
|
26
|
Abstract
A number of genes involved in tumorigenesis have been known to be controlled by signal transducer and activator of transcription 3 (STAT3) and NF-κB, either synergistically or individually. In starved cancer cells, we found that NF-κB was activated through endoplasmic reticulum stress signals, which depend on reactive oxygen species, cytosolic calcium and preserved translation of NF-κB p65 subunit, but independent of IκBα serine phosphorylation, thereby resulting in IL6 induction. STAT3 was required for proper induction of IL6 by NF-κB. They existed as identical nuclear complexes in proximal IL6 promoters, and STAT3 had critical roles in binding to IL6 promoters as well as nuclear retention of NF-κB. The conditioned media from starved cancer cells contained various secretory factors, such as IL6, IL9, VWF (von Willebrand factor), FREM1 (FRAS1 related extracellular matrix 1), SAA1 (serum amyloid A1), SDK1 (sidekick homolog 1) and ADAM12 (ADAM metallopeptidase domain 12), induced by NF-κB and STAT3 and promoted clonogenic capacities of cancer cells, and proliferation and migration of human umbilical vein endothelial cells. These results suggest novel survival strategies of cancer cells by which two oncogenic transcriptional factors, NF-κB and STAT3, are activated simultaneously by an intrinsic mechanism during stressful conditions of cancer cells, and they cooperatively induce various survival factors.
Collapse
|
27
|
Common fragile sites: mechanisms of instability revisited. Trends Genet 2011; 28:22-32. [PMID: 22094264 DOI: 10.1016/j.tig.2011.10.003] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/05/2011] [Accepted: 10/05/2011] [Indexed: 12/22/2022]
Abstract
Common fragile sites (CFSs) are large chromosomal regions prone to breakage upon replication stress that are considered a driving force of oncogenesis. CFSs were long believed to contain sequences blocking fork progression, thus impeding replication completion and leading to DNA breaks upon chromosome condensation. However, recent studies show that delayed completion of DNA replication instead depends on a regional paucity in initiation events. Because the distribution and the timing of these events are cell type dependent, different chromosomal regions can be committed to fragility in different cell types. These new data reveal the epigenetic nature of CFSs and open the way to a reevaluation of the role played by these sites in the formation of chromosome rearrangements found in tumors from different tissues.
Collapse
|