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Boccardi V, Cari L, Bastiani P, Scamosci M, Cecchetti R, Nocentini G, Mecocci P. Aberrant telomeric structures and serum markers of telomere dysfunction in healthy aging: a preliminary study. Biogerontology 2024:10.1007/s10522-024-10120-y. [PMID: 39001954 DOI: 10.1007/s10522-024-10120-y] [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: 01/21/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024]
Abstract
Telomeres undergo a progressive shortening process as individuals age, and it has been proposed that severely shortened and dysfunctional telomeres play a role in the aging process and the onset of age-related diseases in human beings. An emerging body of evidence indicates that the shortening of telomeres in cultured human cells is also influenced by other replication defects occurring within telomeric repeats. These abnormalities can be detected on metaphase chromosomes. Recent studies have also identified a set of serological markers for telomere dysfunction and DNA damage (elongation factor 1α [EF-1α], stathmin, and N-acetyl-glucosaminidase). With this study, the correlation between telomere abnormalities (by FISH) and these biomarkers as measured in blood serum (by ELISA) from a cohort of 22 healthy subjects at different ages (range 26-101 years) was analyzed. A strong positive correlation between aging and the presence of aberrant telomere structures, sister telomere loss (STL), and sister telomere chromatid fusions (STCF) was detected. When serum markers of telomere dysfunction were correlated with telomere abnormalities, we found that stathmin correlated with total aberrant telomeres structures (r = 0.431, p = 0.0453) and STCF (r = 0.533, p = 0.0107). These findings suggest that serum stathmin can be considered an easy-to-get marker of telomere dysfunction and may serve as valuable indicators of aging.
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Affiliation(s)
- Virginia Boccardi
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy.
- Department of Medicine and Surgery, Institute of Gerontology and Geriatrics, University of Perugia, Piazzale Gambuli 1, 06132, Perugia, Italy.
| | - Luigi Cari
- Department of Medicine and Surgery, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - Patrizia Bastiani
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Michela Scamosci
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Roberta Cecchetti
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
| | - Giuseppe Nocentini
- Department of Medicine and Surgery, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - Patrizia Mecocci
- Division of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Santa Maria Della Misericordia Hospital, Perugia, Italy
- Division of Clinical Geriatrics, NVS Department, Karolinska Institutet, Stockholm, Sweden
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2
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Krupina K, Goginashvili A, Cleveland DW. Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements. Nat Rev Genet 2024; 25:196-210. [PMID: 37938738 PMCID: PMC10922386 DOI: 10.1038/s41576-023-00663-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 11/09/2023]
Abstract
Complex chromosome rearrangements, known as chromoanagenesis, are widespread in cancer. Based on large-scale DNA sequencing of human tumours, the most frequent type of complex chromosome rearrangement is chromothripsis, a massive, localized and clustered rearrangement of one (or a few) chromosomes seemingly acquired in a single event. Chromothripsis can be initiated by mitotic errors that produce a micronucleus encapsulating a single chromosome or chromosomal fragment. Rupture of the unstable micronuclear envelope exposes its chromatin to cytosolic nucleases and induces chromothriptic shattering. Found in up to half of tumours included in pan-cancer genomic analyses, chromothriptic rearrangements can contribute to tumorigenesis through inactivation of tumour suppressor genes, activation of proto-oncogenes, or gene amplification through the production of self-propagating extrachromosomal circular DNAs encoding oncogenes or genes conferring anticancer drug resistance. Here, we discuss what has been learned about the mechanisms that enable these complex genomic rearrangements and their consequences in cancer.
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Affiliation(s)
- Ksenia Krupina
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Alexander Goginashvili
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
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3
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Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024; 262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [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: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. This gene shows not only loss-of-function mutations but also recurrent missense mutations with gain-of-function activity. We have studied the primary bone malignancy osteosarcoma, which harbours one of the most rearranged genomes of all cancers. This is odd since it primarily affects children and adolescents who have not lived the long life thought necessary to accumulate massive numbers of mutations. In osteosarcoma, TP53 is often disrupted by structural variants. Here, we show through combined whole-genome and transcriptome analyses of 148 osteosarcomas that TP53 structural variants commonly result in loss of coding parts of the gene while simultaneously preserving and relocating the promoter region. The transferred TP53 promoter region is fused to genes previously implicated in cancer development. Paradoxically, these erroneously upregulated genes are significantly associated with the TP53 signalling pathway itself. This suggests that while the classical tumour suppressor activities of TP53 are lost, certain parts of the TP53 signalling pathway that are necessary for cancer cell survival and proliferation are retained. In line with this, our data suggest that transposition of the TP53 promoter is an early event that allows for a new normal state of genome-wide rearrangements in osteosarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mahtab Bidgoli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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Borghini A, Ndreu R, Canale P, Campolo J, Marinaro I, Mercuri A, Turchi S, Andreassi MG. Telomere Length, Mitochondrial DNA, and Micronucleus Yield in Response to Oxidative Stress in Peripheral Blood Mononuclear Cells. Int J Mol Sci 2024; 25:1428. [PMID: 38338706 PMCID: PMC10855977 DOI: 10.3390/ijms25031428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Telomere shortening, chromosomal damage, and mitochondrial dysfunction are major initiators of cell aging and biomarkers of many diseases. However, the underlying correlations between nuclear and mitochondrial DNA alterations remain unclear. We investigated the relationship between telomere length (TL) and micronucleus (MN) and their association with mitochondrial DNA copy number (mtDNAcn) in peripheral blood mononuclear cells (PBMCs) in response to 100 μM and 200 μM of hydrogen peroxide (H2O2) at 44, 72, and 96 h. Significant TL shortening was observed after both doses of H2O2 and at all times (all p < 0.05). A concomitant increase in MN was found at 72 h (p < 0.01) and persisted at 96 h (p < 0.01). An increase in mtDNAcn (p = 0.04) at 200 µM of H2O2 was also found. In PBMCs treated with 200 µM H2O2, a significant inverse correlation was found between TL and MN (r = -0.76, p = 0.03), and mtDNA content was directly correlated with TL (r = 0.6, p = 0.04) and inversely related to MN (r = -0.78, p = 0.02). Telomere shortening is the main triggering mechanism of chromosomal damage in stimulated T lymphocytes under oxidative stress. The significant correlations between nuclear DNA damage and mtDNAcn support the notion of a telomere-mitochondria axis that might influence age-associated pathologies and be a target for the development of relevant anti-aging drugs.
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Affiliation(s)
- Andrea Borghini
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
| | - Rudina Ndreu
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
| | - Paola Canale
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
- Health Science Interdisciplinary Center, Sant’Anna School of Advanced Studies, 56124 Pisa, Italy
| | - Jonica Campolo
- CNR Institute of Clinical Physiology, ASST Grande Ospedale Metropolitano Niguarda, 20142 Milan, Italy;
| | - Irene Marinaro
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
| | - Antonella Mercuri
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
| | - Stefano Turchi
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
| | - Maria Grazia Andreassi
- CNR Institute of Clinical Physiology, 56124 Pisa, Italy; (R.N.); (P.C.); (I.M.); (A.M.); (S.T.); (M.G.A.)
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5
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Heng E, Thanedar S, Heng HH. The Importance of Monitoring Non-clonal Chromosome Aberrations (NCCAs) in Cancer Research. Methods Mol Biol 2024; 2825:79-111. [PMID: 38913304 DOI: 10.1007/978-1-0716-3946-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Cytogenetic analysis has traditionally focused on the clonal chromosome aberrations, or CCAs, and considered the large number of diverse non-clonal chromosome aberrations, or NCCAs, as insignificant noise. Our decade-long karyotype evolutionary studies have unexpectedly demonstrated otherwise. Not only the baseline of NCCAs is associated with fuzzy inheritance, but the frequencies of NCCAs can also be used to reliably measure genome or chromosome instability (CIN). According to the Genome Architecture Theory, CIN is the common driver of cancer evolution that can unify diverse molecular mechanisms, and genome chaos, including chromothripsis, chromoanagenesis, and polypoidal giant nuclear and micronuclear clusters, and various sizes of chromosome fragmentations, including extrachromosomal DNA, represent some extreme forms of NCCAs that play a key role in the macroevolutionary transition. In this chapter, the rationale, definition, brief history, and current status of NCCA research in cancer are discussed in the context of two-phased cancer evolution and karyotype-coded system information. Finally, after briefly describing various types of NCCAs, we call for more research on NCCAs in future cytogenetics.
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Affiliation(s)
- Eric Heng
- Stanford University, Stanford, CA, USA
| | - Sanjana Thanedar
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Henry H Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA.
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6
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Jiang H, Chan YW. Chromatin bridges: stochastic breakage or regulated resolution? Trends Genet 2024; 40:69-82. [PMID: 37891096 DOI: 10.1016/j.tig.2023.10.004] [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: 08/15/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
Genetic material is organized in the form of chromosomes, which need to be segregated accurately into two daughter cells in each cell cycle. However, chromosome fusion or the presence of unresolved interchromosomal linkages lead to the formation of chromatin bridges, which can induce DNA lesions and genome instability. Persistent chromatin bridges are trapped in the cleavage furrow and are broken at or after abscission, the final step of cytokinesis. In this review, we focus on recent progress in understanding the mechanism of bridge breakage and resolution. We discuss the molecular machinery and enzymes that have been implicated in the breakage and processing of bridge DNA. In addition, we outline both the immediate outcomes and genomic consequences induced by bridge breakage.
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Affiliation(s)
- Huadong Jiang
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Ying Wai Chan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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7
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Song C, Hu Z, Xu D, Bian H, Lv J, Zhu X, Zhang Q, Su L, Yin H, Lu T, Li Y. STING signaling in inflammaging: a new target against musculoskeletal diseases. Front Immunol 2023; 14:1227364. [PMID: 37492580 PMCID: PMC10363987 DOI: 10.3389/fimmu.2023.1227364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/20/2023] [Indexed: 07/27/2023] Open
Abstract
Stimulator of Interferon Gene (STING) is a critical signaling linker protein that plays a crucial role in the intrinsic immune response, particularly in the cytoplasmic DNA-mediated immune response in both pathogens and hosts. It is also involved in various signaling processes in vivo. The musculoskeletal system provides humans with morphology, support, stability, and movement. However, its aging can result in various diseases and negatively impact people's lives. While many studies have reported that cellular aging is a leading cause of musculoskeletal disorders, it also offers insight into potential treatments. Under pathological conditions, senescent osteoblasts, chondrocytes, myeloid cells, and muscle fibers exhibit persistent senescence-associated secretory phenotype (SASP), metabolic disturbances, and cell cycle arrest, which are closely linked to abnormal STING activation. The accumulation of cytoplasmic DNA due to chromatin escape from the nucleus following DNA damage or telomere shortening activates the cGAS-STING signaling pathway. Moreover, STING activation is also linked to mitochondrial dysfunction, epigenetic modifications, and impaired cytoplasmic DNA degradation. STING activation upregulates SASP and autophagy directly and indirectly promotes cell cycle arrest. Thus, STING may be involved in the onset and development of various age-related musculoskeletal disorders and represents a potential therapeutic target. In recent years, many STING modulators have been developed and used in the study of musculoskeletal disorders. Therefore, this paper summarizes the effects of STING signaling on the musculoskeletal system at the molecular level and current understanding of the mechanisms of endogenous active ligand production and accumulation. We also discuss the relationship between some age-related musculoskeletal disorders and STING, as well as the current status of STING modulator development.
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Affiliation(s)
- Chenyu Song
- Jiangsu CM Clinical Innovation Center of Degenerative Bone & Joint Disease, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Zhuoyi Hu
- Jiangsu CM Clinical Innovation Center of Degenerative Bone & Joint Disease, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Dingjun Xu
- Department of Orthopaedics, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Zhejiang, China
| | - Huihui Bian
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Juan Lv
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Xuanxuan Zhu
- Jiangsu CM Clinical Innovation Center of Degenerative Bone & Joint Disease, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Qiang Zhang
- Jiangsu CM Clinical Innovation Center of Degenerative Bone & Joint Disease, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Li Su
- Institute of Translational Medicine, Shanghai University, Shanghai, China
| | - Heng Yin
- Jiangsu CM Clinical Innovation Center of Degenerative Bone & Joint Disease, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Tong Lu
- Department of Critical Care Medicine, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, China
| | - Yinghua Li
- Institute of Translational Medicine, Shanghai University, Shanghai, China
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8
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Shih J, Sarmashghi S, Zhakula-Kostadinova N, Zhang S, Georgis Y, Hoyt SH, Cuoco MS, Gao GF, Spurr LF, Berger AC, Ha G, Rendo V, Shen H, Meyerson M, Cherniack AD, Taylor AM, Beroukhim R. Cancer aneuploidies are shaped primarily by effects on tumour fitness. Nature 2023; 619:793-800. [PMID: 37380777 PMCID: PMC10529820 DOI: 10.1038/s41586-023-06266-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Aneuploidies-whole-chromosome or whole-arm imbalances-are the most prevalent alteration in cancer genomes1,2. However, it is still debated whether their prevalence is due to selection or ease of generation as passenger events1,2. Here we developed a method, BISCUT, that identifies loci subject to fitness advantages or disadvantages by interrogating length distributions of telomere- or centromere-bounded copy-number events. These loci were significantly enriched for known cancer driver genes, including genes not detected through analysis of focal copy-number events, and were often lineage specific. BISCUT identified the helicase-encoding gene WRN as a haploinsufficient tumour-suppressor gene on chromosome 8p, which is supported by several lines of evidence. We also formally quantified the role of selection and mechanical biases in driving aneuploidy, finding that rates of arm-level copy-number alterations are most highly correlated with their effects on cellular fitness1,2. These results provide insight into the driving forces behind aneuploidy and its contribution to tumorigenesis.
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Affiliation(s)
- Juliann Shih
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Tufts University School of Medicine, Boston, MA, USA
- Department of Internal Medicine, Kirk Kerkorian School of Medicine at the University of Nevada, Las Vegas, NV, USA
| | - Shahab Sarmashghi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nadja Zhakula-Kostadinova
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shu Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yohanna Georgis
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephanie H Hoyt
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael S Cuoco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Galen F Gao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Liam F Spurr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ashton C Berger
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gavin Ha
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Veronica Rendo
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Matthew Meyerson
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrew D Cherniack
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison M Taylor
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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9
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Dhillon VS, Deo P, Fenech M. The Relationship between Telomere Length and Nucleoplasmic Bridges and Severity of Disease in Prostate Cancer Patients. Cancers (Basel) 2023; 15:3351. [PMID: 37444460 DOI: 10.3390/cancers15133351] [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: 05/16/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Telomeres are repetitive nucleotide (TTAGGG) sequences that stabilize the chromosome ends and play an important role in the prevention of cancer initiation and progression. Nucleoplasmic bridges (NPBs) are formed when chromatids remain joined together during mitotic anaphase either due to mis-repair of DNA breaks or due to chromatid end fusion as a result of telomere loss or telomere dysfunction. We tested the hypotheses that (i) telomere length (TL) is shorter in prostate cancer (PC) patients relative to healthy age-matched individuals, (ii) TL differs in different stages of PC and (iii) shorter TL is significantly correlated with NPBs formation in PC cases. TL was measured in whole blood by well-established quantitative PCR method and the frequency of NPBs was measured in lymphocytes using cytokinesis-block micronucleus cytome (CBMNcyt) assay. Our results indicate that TL is shorter and NPBs are increased in PC patients relative to age-matched healthy controls. Furthermore, TL was significantly shorter (p = 0.03) in patients with a Gleason score more than 7 and there was also a significant trend of decreasing TL across all three stages (p trend = 0.01; Gleason score <7, 7 and >7). Furthermore, TL was significantly inversely correlated with NPB frequency in PC patients (r = -0.316; p = 0.001) but not in controls (r = 0.163; p = 0.06) and their relationships became stronger with higher Gleason scores. More studies are required that can confirm our observations and explore mechanistic differences in the role of telomeres in NPB formation in PC cases relative to non-cancer cases.
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Affiliation(s)
- Varinderpal S Dhillon
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia
| | - Permal Deo
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia
| | - Michael Fenech
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia
- Genome Health Foundation, North Brighton 5048, Australia
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10
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Sanpedro-Luna JA, Jacinto-Vázquez JJ, Anastacio-Marcelino E, Posadas-Gutiérrez CM, Olmos-Pineda I, González-Bernal JA, Carcaño-Montiel M, Vega-Alvarado L, Vázquez-Cruz C, Sánchez-Alonso P. Telomerase RNA plays a major role in the completion of the life cycle in Ustilago maydis and shares conserved domains with other Ustilaginales. PLoS One 2023; 18:e0281251. [PMID: 36952474 PMCID: PMC10035886 DOI: 10.1371/journal.pone.0281251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/18/2023] [Indexed: 03/25/2023] Open
Abstract
The RNA subunit of telomerase is an essential component whose primary sequence and length are poorly conserved among eukaryotic organisms. The phytopathogen Ustilago maydis is a dimorphic fungus of the order Ustilaginales. We analyzed several species of Ustilaginales to computationally identify the TElomere RNA (TER) gene ter1. To confirm the identity of the TER gene, we disrupted the gene and characterized telomerase-negative mutants. Similar to catalytic TERT mutants, ter1Δ mutants exhibit phenotypes of growth delay, telomere shortening and low replicative potential. ter1-disrupted mutants were unable to infect maize seedlings in heterozygous crosses and showed defects such as cell cycle arrest and segregation failure. We concluded that ter1, which encodes the TER subunit of the telomerase of U. maydis, have similar and perhaps more extensive functions than trt1.
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Affiliation(s)
- Juan Antonio Sanpedro-Luna
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - José Juan Jacinto-Vázquez
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Estela Anastacio-Marcelino
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | | | - Iván Olmos-Pineda
- Facultad de Ciencias de la Computación, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Jesús Antonio González-Bernal
- Department of Computer Science and Engineering, The University of Texas Arlington, Arlington, Texas, United States of America
| | - Moisés Carcaño-Montiel
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México, México
| | - Candelario Vázquez-Cruz
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Patricia Sánchez-Alonso
- Instituto de Ciencias, Posgrado en Microbiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
- Instituto de Ciencias, Centro de Investigaciones Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, México
- * E-mail:
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11
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Prime SS, Cirillo N, Parkinson EK. Escape from Cellular Senescence Is Associated with Chromosomal Instability in Oral Pre-Malignancy. BIOLOGY 2023; 12:biology12010103. [PMID: 36671795 PMCID: PMC9855962 DOI: 10.3390/biology12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
An escape from cellular senescence through the development of unlimited growth potential is one of the hallmarks of cancer, which is thought to be an early event in carcinogenesis. In this review, we propose that the molecular effectors of senescence, particularly the inactivation of TP53 and CDKN2A, together with telomere attrition and telomerase activation, all lead to aneuploidy in the keratinocytes from oral potentially malignant disorders (OPMD). Premalignant keratinocytes, therefore, not only become immortal but also develop genotypic and phenotypic cellular diversity. As a result of these changes, certain clonal cell populations likely gain the capacity to invade the underlying connective tissue. We review the clinical implications of these changes and highlight a new PCR-based assay to identify aneuploid cell in fluids such as saliva, a technique that is extremely sensitive and could facilitate the regular monitoring of OPMD without the need for surgical biopsies and may avoid potential biopsy sampling errors. We also draw attention to recent studies designed to eliminate aneuploid tumour cell populations that, potentially, is a new therapeutic approach to prevent malignant transformations in OPMD.
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Affiliation(s)
- Stephen S. Prime
- Centre for Immunology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
- Correspondence: (S.S.P.); (E.K.P.)
| | - Nicola Cirillo
- Melbourne Dental School, University of Melbourne, 720 Swanson Street, Melbourne, VIC 3053, Australia
| | - E. Kenneth Parkinson
- Centre for Immunology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
- Correspondence: (S.S.P.); (E.K.P.)
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12
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Wilson C, Murnane JP. High-throughput screen to identify compounds that prevent or target telomere loss in human cancer cells. NAR Cancer 2022; 4:zcac029. [PMID: 36196242 PMCID: PMC9527662 DOI: 10.1093/narcan/zcac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/09/2022] [Accepted: 09/29/2022] [Indexed: 11/14/2022] Open
Abstract
Chromosome instability (CIN) is an early step in carcinogenesis that promotes tumor cell progression and resistance to therapy. Using plasmids integrated adjacent to telomeres, we have previously demonstrated that the sensitivity of subtelomeric regions to DNA double-strand breaks (DSBs) contributes to telomere loss and CIN in cancer. A high-throughput screen was created to identify compounds that affect telomere loss due to subtelomeric DSBs introduced by I-SceI endonuclease, as detected by cells expressing green fluorescent protein (GFP). A screen of a library of 1832 biologically-active compounds identified a variety of compounds that increase or decrease the number of GFP-positive cells following activation of I-SceI. A curated screen done in triplicate at various concentrations found that inhibition of classical nonhomologous end joining (C-NHEJ) increased DSB-induced telomere loss, demonstrating that C-NHEJ is functional in subtelomeric regions. Compounds that decreased DSB-induced telomere loss included inhibitors of mTOR, p38 and tankyrase, consistent with our earlier hypothesis that the sensitivity of subtelomeric regions to DSBs is a result of inappropriate resection during repair. Although this assay was also designed to identify compounds that selectively target cells experiencing telomere loss and/or chromosome instability, no compounds of this type were identified in the current screen.
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Affiliation(s)
- Chris Wilson
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94143, USA
| | - John P Murnane
- To whom correspondence should be addressed. Tel: +1 415 680 4434;
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13
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Liddiard K, Aston-Evans AN, Cleal K, Hendrickson E, Baird D. POLQ suppresses genome instability and alterations in DNA repeat tract lengths. NAR Cancer 2022; 4:zcac020. [PMID: 35774233 PMCID: PMC9241439 DOI: 10.1093/narcan/zcac020] [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: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/10/2022] [Indexed: 11/26/2022] Open
Abstract
DNA polymerase theta (POLQ) is a principal component of the alternative non-homologous end-joining (ANHEJ) DNA repair pathway that ligates DNA double-strand breaks. Utilizing independent models of POLQ insufficiency during telomere-driven crisis, we found that POLQ - /- cells are resistant to crisis-induced growth deceleration despite sustaining inter-chromosomal telomere fusion frequencies equivalent to wild-type (WT) cells. We recorded longer telomeres in POLQ - / - than WT cells pre- and post-crisis, notwithstanding elevated total telomere erosion and fusion rates. POLQ - /- cells emerging from crisis exhibited reduced incidence of clonal gross chromosomal abnormalities in accordance with increased genetic heterogeneity. High-throughput sequencing of telomere fusion amplicons from POLQ-deficient cells revealed significantly raised frequencies of inter-chromosomal fusions with correspondingly depreciated intra-chromosomal recombinations. Long-range interactions culminating in telomere fusions with centromere alpha-satellite repeats, as well as expansions in HSAT2 and HSAT3 satellite and contractions in ribosomal DNA repeats, were detected in POLQ - / - cells. In conjunction with the expanded telomere lengths of POLQ - /- cells, these results indicate a hitherto unrealized capacity of POLQ for regulation of repeat arrays within the genome. Our findings uncover novel considerations for the efficacy of POLQ inhibitors in clinical cancer interventions, where potential genome destabilizing consequences could drive clonal evolution and resistant disease.
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Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Alys N Aston-Evans
- Dementia Research Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, UK
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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14
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A genetic programming-based approach for classifying pancreatic adenocarcinoma: the SICED experience. Soft comput 2022. [DOI: 10.1007/s00500-022-07383-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AbstractDuctal adenocarcinoma of the pancreas is a cancer with a high mortality rate. Among the main reasons for this baleful prognosis is that, in most patients, this neoplasm is diagnosed at a too advanced stage. Clinical oncology research is now particularly focused on decoding the cancer molecular onset by understanding the complex biological architecture of tumor cell proliferation. In this direction, machine learning has proved to be a valid solution in many sectors of the biomedical field, thanks to its ability to mine useful knowledge by biological and genetic data. Since the major risk factor is represented by genetic predisposition, the aim of this study is to find a mathematical model describing the complex relationship existing between genetic mutations of the involved genes and the onset of the disease. To this end, an approach based on evolutionary algorithms is proposed. In particular, genetic programming is used, which allows solving a symbolic regression problem through the use of genetic algorithms. The identification of these correlations is a typical objective of the diagnostic approach and is one of the most critical and complex activities in the presence of large amounts of data that are difficult to correlate through traditional statistical techniques. The mathematical model obtained highlights the importance of the complex relationship existing between the different gene’s mutations present in the tumor tissue of the group of patients considered.
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15
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Chromosomal Instability in Chronic Myeloid Leukemia: Mechanistic Insights and Effects. Cancers (Basel) 2022; 14:cancers14102533. [PMID: 35626137 PMCID: PMC9140097 DOI: 10.3390/cancers14102533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/15/2022] Open
Abstract
The most recent two decades have seen tremendous progress in the understanding and treatment of chronic myeloid leukemia, a disease defined by the characteristic Philadelphia chromosome and the ensuing BCR::ABL fusion protein. However, the biology of the disease extends beyond the Philadelphia chromosome into a nebulous arena of chromosomal and genetic instability, which makes it a genetically heterogeneous disease. The BCR::ABL oncoprotein creates a fertile backdrop for oxidative damage to the DNA, along with impairment of genetic surveillance and the favoring of imprecise error-prone DNA repair pathways. These factors lead to growing chromosomal instability, manifested as additional chromosomal abnormalities along with other genetic aberrations. This worsens with disease progression to accelerated and blast phase, and modulates responses to tyrosine kinase inhibitors. Treatment options that target the genetic aberrations that mitigate chromosome instability might be a potential area for research in patients with advanced phase CML.
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16
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Tools used to assay genomic instability in cancers and cancer meiomitosis. J Cell Commun Signal 2021; 16:159-177. [PMID: 34841477 DOI: 10.1007/s12079-021-00661-z] [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: 09/13/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022] Open
Abstract
Genomic instability is a defining characteristic of cancer and the analysis of DNA damage at the chromosome level is a crucial part of the study of carcinogenesis and genotoxicity. Chromosomal instability (CIN), the most common level of genomic instability in cancers, is defined as the rate of loss or gain of chromosomes through successive divisions. As such, DNA in cancer cells is highly unstable. However, the underlying mechanisms remain elusive. There is a debate as to whether instability succeeds transformation, or if it is a by-product of cancer, and therefore, studying potential molecular and cellular contributors of genomic instability is of high importance. Recent work has suggested an important role for ectopic expression of meiosis genes in driving genomic instability via a process called meiomitosis. Improving understanding of these mechanisms can contribute to the development of targeted therapies that exploit DNA damage and repair mechanisms. Here, we discuss a workflow of novel and established techniques used to assess chromosomal instability as well as the nature of genomic instability such as double strand breaks, micronuclei, and chromatin bridges. For each technique, we discuss their advantages and limitations in a lab setting. Lastly, we provide detailed protocols for the discussed techniques.
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17
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Wen J, Wang Y, Yuan M, Huang Z, Zou Q, Pu Y, Zhao B, Cai Z. Role of mismatch repair in aging. Int J Biol Sci 2021; 17:3923-3935. [PMID: 34671209 PMCID: PMC8495402 DOI: 10.7150/ijbs.64953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
A common feature of aging is the accumulation of genetic damage throughout life. DNA damage can lead to genomic instability. Many diseases associated with premature aging are a result of increased accumulation of DNA damage. In order to minimize these damages, organisms have evolved a complex network of DNA repair mechanisms, including mismatch repair (MMR). In this review, we detail the effects of MMR on genomic instability and its role in aging emphasizing on the association between MMR and the other hallmarks of aging, serving to drive or amplify these mechanisms. These hallmarks include telomere attrition, epigenetic alterations, mitochondrial dysfunction, altered nutrient sensing and cell senescence. The close relationship between MMR and these markers may provide prevention and treatment strategies, to reduce the incidence of age-related diseases and promote the healthy aging of human beings.
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Affiliation(s)
- Jie Wen
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China.,Department and Institute of Neurology, Guangdong Medical University, Guangdong, 524001, China.,Guangdong Key Laboratory of aging related cardio cerebral diseases, Guangdong, 524001, China
| | - Yangyang Wang
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Minghao Yuan
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Zhenting Huang
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Qian Zou
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Yinshuang Pu
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
| | - Bin Zhao
- Department and Institute of Neurology, Guangdong Medical University, Guangdong, 524001, China.,Guangdong Key Laboratory of aging related cardio cerebral diseases, Guangdong, 524001, China
| | - Zhiyou Cai
- Chongqing Key Laboratory of Neurodegenerative Diseases, Chongqing, 400013, China.,Department of Neurology, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, 400013, China
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18
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Jeon HJ, Oh JS. TRF1 Depletion Reveals Mutual Regulation Between Telomeres, Kinetochores, and Inner Centromeres in Mouse Oocytes. Front Cell Dev Biol 2021; 9:749116. [PMID: 34604243 PMCID: PMC8486315 DOI: 10.3389/fcell.2021.749116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022] Open
Abstract
In eukaryotic chromosomes, the centromere and telomere are two specialized structures that are essential for chromosome stability and segregation. Although centromeres and telomeres often are located in close proximity to form telocentric chromosomes in mice, it remained unclear whether these two structures influence each other. Here we show that TRF1 is required for inner centromere and kinetochore assembly in addition to its role in telomere protection in mouse oocytes. TRF1 depletion caused premature chromosome segregation by abrogating the spindle assembly checkpoint (SAC) and impairing kinetochore-microtubule (kMT) attachment, which increased the incidence of aneuploidy. Notably, TRF1 depletion disturbed the localization of Survivin and Ndc80/Hec1 at inner centromeres and kinetochores, respectively. Moreover, SMC3 and SMC4 levels significantly decreased after TRF1 depletion, suggesting that TRF1 is involved in chromosome cohesion and condensation. Importantly, inhibition of inner centromere or kinetochore function led to a significant decrease in TRF1 level and telomere shortening. Therefore, our results suggest that telomere integrity is required to preserve inner centromere and kinetochore architectures, and vice versa, suggesting mutual regulation between telomeres and centromeres.
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Affiliation(s)
- Hyuk-Joon Jeon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Jeong Su Oh
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
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19
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Kim E, Kim J, Kim C, Lee J. Long-read sequencing and de novo genome assemblies reveal complex chromosome end structures caused by telomere dysfunction at the single nucleotide level. Nucleic Acids Res 2021; 49:3338-3353. [PMID: 33693840 PMCID: PMC8034613 DOI: 10.1093/nar/gkab141] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/28/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Karyotype change and subsequent evolution is triggered by chromosome fusion and rearrangement events, which often occur when telomeres become dysfunctional. Telomeres protect linear chromosome ends from DNA damage responses (DDRs), and telomere dysfunction may result in genome instability. However, the complex chromosome end structures and the other possible consequences of telomere dysfunction have rarely been resolved at the nucleotide level due to the lack of the high-throughput methods needed to analyse these highly repetitive regions. Here we applied long-read sequencing technology to Caenorhabditis elegans survivor lines that emerged after telomere dysfunction. The survivors have preserved traces of DDRs in their genomes and our data revealed that variants generated by telomere dysfunction are accumulated along all chromosomes. The reconstruction of the chromosome end structures through de novo genome assemblies revealed diverse types of telomere damage processing at the nucleotide level. When telomeric repeats were totally eroded by telomere dysfunction, DDRs were mostly terminated by chromosome fusion events. We also partially reconstructed the most complex end structure and its DDR signatures, which would have been accumulated via multiple cell divisions. These finely resolved chromosome end structures suggest possible mechanisms regarding the repair processes after telomere dysfunction, providing insights into chromosome evolution in nature.
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Affiliation(s)
- Eunkyeong Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Chuna Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon 34141, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea.,Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
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20
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Dewhurst SM, Yao X, Rosiene J, Tian H, Behr J, Bosco N, Takai KK, de Lange T, Imieliński M. Structural variant evolution after telomere crisis. Nat Commun 2021; 12:2093. [PMID: 33828097 PMCID: PMC8027843 DOI: 10.1038/s41467-021-21933-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/17/2021] [Indexed: 01/14/2023] Open
Abstract
Telomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of experimental telomere crisis identified in previous studies. We examine the spectrum of structural variants (SVs) instigated by natural telomere crisis. Eight spontaneous post-crisis clones did not show prominent patterns of BFB cycles or chromothripsis. Their crisis-induced genome rearrangements varied from infrequent simple SVs to more frequent and complex SVs. In contrast, BFB cycles and chromothripsis occurred in MRC5 fibroblast clones that escaped telomere crisis after CRISPR-controlled telomerase activation. This system revealed convergent evolutionary lineages altering one allele of chromosome 12p, where a short telomere likely predisposed to fusion. Remarkably, the 12p chromothripsis and BFB events were stabilized by independent fusions to chromosome 21. The data establish that telomere crisis can generate a wide spectrum of SVs implying that a lack of BFB patterns and chromothripsis in cancer genomes does not indicate absence of past telomere crisis.
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Affiliation(s)
- Sally M Dewhurst
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Xiaotong Yao
- Tri-Institutional Ph.D. Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Joel Rosiene
- Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Huasong Tian
- Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Julie Behr
- Tri-Institutional Ph.D. Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Nazario Bosco
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Kaori K Takai
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Titia de Lange
- Laboratory of Cell Biology and Genetics, Rockefeller University, New York, NY, USA.
| | - Marcin Imieliński
- Department of Pathology and Laboratory Medicine, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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21
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Jebaraj BMC, Stilgenbauer S. Telomere Dysfunction in Chronic Lymphocytic Leukemia. Front Oncol 2021; 10:612665. [PMID: 33520723 PMCID: PMC7844343 DOI: 10.3389/fonc.2020.612665] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Telomeres are nucleprotein structures that cap the chromosomal ends, conferring genomic stability. Alterations in telomere maintenance and function are associated with tumorigenesis. In chronic lymphocytic leukemia (CLL), telomere length is an independent prognostic factor and short telomeres are associated with adverse outcome. Though telomere length associations have been suggested to be only a passive reflection of the cell's replication history, here, based on published findings, we suggest a more dynamic role of telomere dysfunction in shaping the disease course. Different members of the shelterin complex, which form the telomere structure have deregulated expression and POT1 is recurrently mutated in about 3.5% of CLL. In addition, cases with short telomeres have higher telomerase (TERT) expression and activity. TERT activation and shelterin deregulation thus may be pivotal in maintaining the minimal telomere length necessary to sustain survival and proliferation of CLL cells. On the other hand, activation of DNA damage response and repair signaling at dysfunctional telomeres coupled with checkpoint deregulation, leads to terminal fusions and genomic complexity. In summary, multiple components of the telomere system are affected and they play an important role in CLL pathogenesis, progression, and clonal evolution. However, processes leading to shelterin deregulation as well as cell intrinsic and microenvironmental factors underlying TERT activation are poorly understood. The present review comprehensively summarizes the complex interplay of telomere dysfunction in CLL and underline the mechanisms that are yet to be deciphered.
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Affiliation(s)
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, University of Ulm, Ulm, Germany
- Klinik für Innere Medizin I, Universitätsklinikum des Saarlandes, Homburg, Germany
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22
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Shibayama Y, Takahashi K, Yamaguchi H, Yasuda J, Yamazaki D, Rahman A, Fujimori T, Fujisawa Y, Takai S, Furukawa T, Nakagawa T, Ohsaki H, Kobara H, Wong JH, Masaki T, Yuzawa Y, Kiyomoto H, Yachida S, Fujimoto A, Nishiyama A. Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H. Commun Biol 2020; 3:724. [PMID: 33247206 PMCID: PMC7695732 DOI: 10.1038/s42003-020-01434-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 10/23/2020] [Indexed: 12/13/2022] Open
Abstract
(Pro)renin receptor [(P)RR] has a role in various diseases, such as cardiovascular and renal disorders and cancer. Aberrant (P)RR expression is prevalent in pancreatic ductal adenocarcinoma (PDAC) which is the most common pancreatic cancer. Here we show whether aberrant expression of (P)RR directly leads to genomic instability in human pancreatic ductal epithelial (HPDE) cells. (P)RR-expressing HPDE cells show obvious cellular atypia. Whole genome sequencing reveals that aberrant (P)RR expression induces large numbers of point mutations and structural variations at the genome level. A (P)RR-expressing cell population exhibits tumour-forming ability, showing both atypical nuclei characterised by distinctive nuclear bodies and chromosomal abnormalities. (P)RR overexpression upregulates SWItch/Sucrose Non-Fermentable (SWI/SNF)-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 5 (SMARCA5) through a direct molecular interaction, which results in the failure of several genomic stability pathways. These data reveal that aberrant (P)RR expression contributes to the early carcinogenesis of PDAC. Yuki Shibayama et al. find that high expression of (pro)renin receptor [(P)RR] in human pancreatic ductal cells causes increased genomic instability, leading to the development of pancreatic ductal adenocarcinoma. They show that (P)RR exerts its carcinogenic effects through direct binding and activation of the chromatin regulator SMARCA5.
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Affiliation(s)
- Yuki Shibayama
- Department of Pharmacology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan
| | - Kazuo Takahashi
- Department of Nephrology, Fujita Health University School of Medicine, Aichi, 470-1192, Japan
| | - Hisateru Yamaguchi
- Division of Biomedical Polymer Science, Institute for Comprehensive Medical Science, Fujita Health University School of Medicine, Aichi, 470-1192, Japan.,Department of Medical Technology, School of Nursing and Medical Care, Yokkaichi Nursing and Medical Care University, Mie, 512-8045, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, 980-8573, Japan.,Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Miyagi, 981-1293, Japan
| | - Daisuke Yamazaki
- Department of Pharmacology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan
| | - Asadur Rahman
- Department of Pharmacology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan
| | - Takayuki Fujimori
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan.,Fujimori Clinic for Internal Medicine and Gastroenterology, Kagawa, 761-8075, Japan
| | - Yoshihide Fujisawa
- Health Science Research Center, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan
| | - Shinji Takai
- Department of Innovative Medicine, Graduate School of Medicine, Osaka Medical College, Osaka, 569-8686, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Miyagi, 980-8575, Japan
| | - Tsutomu Nakagawa
- Department of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Hiroyuki Ohsaki
- Department of Medical Biophysics, Kobe University Graduate School of Health Sciences, Hyogo, 654-0142, Japan
| | - Hideki Kobara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan
| | - Jing Hao Wong
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo, 113-0033, Japan
| | - Tsutomu Masaki
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan
| | - Yukio Yuzawa
- Department of Nephrology, Fujita Health University School of Medicine, Aichi, 470-1192, Japan
| | - Hideyasu Kiyomoto
- Community Medical Support, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, 980-8573, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Faculty of Medicine, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo, 113-0033, Japan.
| | - Akira Nishiyama
- Department of Pharmacology, Faculty of Medicine, Kagawa University, Kagawa, 761-0793, Japan.
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23
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Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci 2020; 21:ijms21218062. [PMID: 33137955 PMCID: PMC7662960 DOI: 10.3390/ijms21218062] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.
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24
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Esopi D, Graham MK, Brosnan-Cashman JA, Meyers J, Vaghasia A, Gupta A, Kumar B, Haffner MC, Heaphy CM, De Marzo AM, Meeker AK, Nelson WG, Wheelan SJ, Yegnasubramanian S. Pervasive promoter hypermethylation of silenced TERT alleles in human cancers. Cell Oncol (Dordr) 2020; 43:847-861. [PMID: 32468444 PMCID: PMC7581602 DOI: 10.1007/s13402-020-00531-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In cancers, maintenance of telomeres often occurs through activation of the catalytic subunit of telomerase, encoded by TERT. Yet, most cancers show only modest levels of TERT gene expression, even in the context of activating hotspot promoter mutations (C228T and C250T). The role of epigenetic mechanisms, including DNA methylation, in regulating TERT gene expression in cancer cells is as yet not fully understood. METHODS Here, we have carried out the most comprehensive characterization to date of TERT promoter methylation using ultra-deep bisulfite sequencing spanning the CpG island surrounding the core TERT promoter in 96 different human cell lines, including primary, immortalized and cancer cell types, as well as in control and reference samples. RESULTS In general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent C228T and C250T TERT promoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. However, at the allele-level, we generally found that hypermethylation of promoter sequences in cancer cells is associated with repressed expression, and the remaining unmethylated alleles marked with open chromatin are largely responsible for the observed TERT expression in cancer cells. CONCLUSIONS Our findings suggest that hypermethylation of the TERT promoter alleles signals transcriptional repression of those alleles, leading to attenuation of TERT activation in cancer cells. This type of fine tuning of TERT expression may account for the modest activation of TERT expression in most cancers.
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Affiliation(s)
- David Esopi
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Vertex Genetic Therapies, Watertown, MA USA
| | - Mindy Kim Graham
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jacqueline A. Brosnan-Cashman
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- American Association for Cancer Research, Publications Division, Boston, MA USA
| | - Jennifer Meyers
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Ajay Vaghasia
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Anuj Gupta
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | | | - Michael C. Haffner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Fred Hutchinson Cancer Research Center, Division of Human Biology, Seattle, Washington State USA
| | - Christopher M. Heaphy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Medicine, Boston University School of Medicine, Boston, MA USA
| | - Angelo M. De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alan K. Meeker
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - William G. Nelson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Sarah J. Wheelan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
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25
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Soman A, Liew CW, Teo HL, Berezhnoy NV, Olieric V, Korolev N, Rhodes D, Nordenskiöld L. The human telomeric nucleosome displays distinct structural and dynamic properties. Nucleic Acids Res 2020; 48:5383-5396. [PMID: 32374876 PMCID: PMC7261157 DOI: 10.1093/nar/gkaa289] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/01/2020] [Accepted: 05/05/2020] [Indexed: 12/21/2022] Open
Abstract
Telomeres protect the ends of our chromosomes and are key to maintaining genomic integrity during cell division and differentiation. However, our knowledge of telomeric chromatin and nucleosome structure at the molecular level is limited. Here, we aimed to define the structure, dynamics as well as properties in solution of the human telomeric nucleosome. We first determined the 2.2 Å crystal structure of a human telomeric nucleosome core particle (NCP) containing 145 bp DNA, which revealed the same helical path for the DNA as well as symmetric stretching in both halves of the NCP as that of the 145 bp ‘601’ NCP. In solution, the telomeric nucleosome exhibited a less stable and a markedly more dynamic structure compared to NCPs containing DNA positioning sequences. These observations provide molecular insights into how telomeric DNA forms nucleosomes and chromatin and advance our understanding of the unique biological role of telomeres.
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Affiliation(s)
- Aghil Soman
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Hsiang Ling Teo
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore.,Singapore Centre for Environmental Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Vincent Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Daniela Rhodes
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore.,School of Chemical and Biomolecular Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
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26
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Osako T, Lee H, Turashvili G, Chiu D, McKinney S, Joosten SEP, Wilkinson D, Nielsen TO, Zwart W, Emerman JT, Eaves CJ, Caldas C, Aparicio S. Age-correlated protein and transcript expression in breast cancer and normal breast tissues is dominated by host endocrine effects. ACTA ACUST UNITED AC 2020; 1:518-532. [DOI: 10.1038/s43018-020-0060-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 03/23/2020] [Indexed: 02/07/2023]
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27
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Micronucleus Assay: The State of Art, and Future Directions. Int J Mol Sci 2020; 21:ijms21041534. [PMID: 32102335 PMCID: PMC7073234 DOI: 10.3390/ijms21041534] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
During almost 40 years of use, the micronucleus assay (MN) has become one of the most popular methods to assess genotoxicity of different chemical and physical factors, including ionizing radiation-induced DNA damage. In this minireview, we focus on the position of MN among the other genotoxicity tests, its usefulness in different applications and visibility by international organizations, such as International Atomic Energy Agency, Organization for Economic Co-operation and Development and International Organization for Standardization. In addition, the mechanism of micronuclei formation is discussed. Finally, foreseen directions of the MN development are pointed, such as automation, buccal cells MN and chromothripsis phenomenon.
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28
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A Novel Tissue and Stem Cell Specific TERF1 Splice Variant Is Downregulated in Tumour Cells. Int J Mol Sci 2019; 21:ijms21010085. [PMID: 31877678 PMCID: PMC6981981 DOI: 10.3390/ijms21010085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 11/17/2022] Open
Abstract
In this study, we describe the identification of a novel splice variant of TERF1/PIN2, one of the main components of the telomeric shelterin complex. This new splice variant is identical to TERF1, apart from a 30 amino acid internal insertion near to the C-terminus of TERF1. Based on genome comparison analyses and RNA expression data, we show that this splice variant is conserved among hominidae but absent from all other species. RNA expression and histological analyses show specific expression in human spermatogonial and hematopoietic stem cells (HSCs), while all other analyzed tissues lack the expression of this TERF1-isoform, hence the name TERF1-tsi (TERF1-tissue-specific-isoform). In addition, we could not detect any expression in primary human cells and established cancer cell lines. Immunohistochemistry results involving two new rabbit polyclonal antibodies, generated against TERF1-tsi specific peptides, indicate nuclear localization of TERF1-tsi in a subset of spermatogonial stem cells. In line with this observation, immunofluorescence analyzes in various cell lines consistently revealed that ectopic TERF1-tsi localizes to the cell nucleus, mainly but not exclusively at telomeres. In a first attempt to evaluate the impact of TERF1-tsi in the testis, we have tested its expression in normal testis samples versus matched tumor samples from the same patients. Both RT-PCR and IHC show a specific downregulation of TERF1-tsi in tumor samples while the expression of TERF1 and PIN2 remains unchanged.
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29
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Chang AR, Ferrer CM, Mostoslavsky R. SIRT6, a Mammalian Deacylase with Multitasking Abilities. Physiol Rev 2019; 100:145-169. [PMID: 31437090 DOI: 10.1152/physrev.00030.2018] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian sirtuins have emerged in recent years as critical modulators of multiple biological processes, regulating cellular metabolism, DNA repair, gene expression, and mitochondrial biology. As such, they evolved to play key roles in organismal homeostasis, and defects in these proteins have been linked to a plethora of diseases, including cancer, neurodegeneration, and aging. In this review, we describe the multiple roles of SIRT6, a chromatin deacylase with unique and important functions in maintaining cellular homeostasis. We attempt to provide a framework for such different functions, for the ability of SIRT6 to interconnect chromatin dynamics with metabolism and DNA repair, and the open questions the field will face in the future, particularly in the context of putative therapeutic opportunities.
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Affiliation(s)
- Andrew R Chang
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts; and The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Christina M Ferrer
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts; and The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts; and The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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30
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Bach DH, Zhang W, Sood AK. Chromosomal Instability in Tumor Initiation and Development. Cancer Res 2019; 79:3995-4002. [PMID: 31350294 PMCID: PMC7694409 DOI: 10.1158/0008-5472.can-18-3235] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/26/2019] [Accepted: 05/09/2019] [Indexed: 12/15/2022]
Abstract
Chromosomal instability (CIN) is one of the major forms of genomic instability in various human cancers and is recognized as a common hallmark of tumorigenesis and heterogeneity. However, some malignant tumors show a paucity of chromosomal alterations, suggesting that tumor progression and evolution can occur in the absence of CIN. It is unclear whether CIN is stable between precursor lesions, primary tumor, and metastases or if it evolves during these steps. In this review, we describe the influence of CIN on the various steps in tumor initiation and development. Given the recognized significant effects of CIN in cancer, CIN-targeted therapeutics could have a major impact on improving clinical outcomes.
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Affiliation(s)
- Duc-Hiep Bach
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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31
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Tijhuis AE, Johnson SC, McClelland SE. The emerging links between chromosomal instability (CIN), metastasis, inflammation and tumour immunity. Mol Cytogenet 2019; 12:17. [PMID: 31114634 PMCID: PMC6518824 DOI: 10.1186/s13039-019-0429-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/15/2019] [Indexed: 02/06/2023] Open
Abstract
Many cancers possess an incorrect number of chromosomes, a state described as aneuploidy. Aneuploidy is often caused by Chromosomal Instability (CIN), a process of continuous chromosome mis-segregation. CIN is believed to endow tumours with enhanced evolutionary capabilities due to increased intratumour heterogeneity, and facilitating adaptive resistance to therapies. Recently, however, additional consequences and associations with CIN have been revealed, prompting the need to understand this universal hallmark of cancer in a multifaceted context. This review is focused on the investigation of possible links between CIN, metastasis and the host immune system in cancer development and treatment. We specifically focus on these links since most cancer deaths are due to the consequences of metastasis, and immunotherapy is a rapidly expanding novel avenue of cancer therapy.
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Affiliation(s)
- Andréa E. Tijhuis
- Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
| | - Sarah C. Johnson
- Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
| | - Sarah E. McClelland
- Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, London, UK
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32
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Robinson NJ, Taylor DJ, Schiemann WP. Stem cells, immortality, and the evolution of metastatic properties in breast cancer: telomere maintenance mechanisms and metastatic evolution. JOURNAL OF CANCER METASTASIS AND TREATMENT 2019; 5:39. [PMID: 31440584 PMCID: PMC6706062 DOI: 10.20517/2394-4722.2019.15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Breast cancer is the most significant cause of cancer-related death in women around the world. The vast majority of breast cancer-associated mortality stems from metastasis, which remains an incurable disease state. Metastasis results from evolution of clones that possess the insidious properties required for dissemination and colonization of distant organs. These clonal populations are descended from breast cancer stem cells (CSCs), which are also responsible for their prolonged maintenance and continued evolution. Telomeres impose a lifespan on cells that can be extended when they are actively elongated, as occurs in CSCs. Thus, changes in telomere structure serve to promote the survival of CSCs and subsequent metastatic evolution. The selection of telomere maintenance mechanism (TMM) has important consequences not only for CSC survival and evolution, but also for their coordination of various signaling pathways that choreograph the metastatic cascade. Targeting the telomere maintenance machinery may therefore provide a boon to the treatment of metastatic breast cancer. Here we review the two major TMMs and the roles they play in the development of stem and metastatic breast cancer cells. We also highlight current and future approaches to targeting these mechanisms in clinical settings to alleviate metastatic breast cancers.
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Affiliation(s)
- Nathaniel J. Robinson
- Department of Pathology, Case Western Reserve University
School of Medicine, Cleveland, OH 44106, USA
| | - Derek J. Taylor
- Department of Pharmacology, Case Western Reserve University
School of Medicine, Cleveland, OH 44106, USA
| | - William P. Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve
University, Cleveland, OH 44106 USA
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33
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Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
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Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
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34
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Alhamdow A, Lindh C, Hagberg J, Graff P, Westberg H, Krais AM, Albin M, Gustavsson P, Tinnerberg H, Broberg K. DNA methylation of the cancer-related genes F2RL3 and AHRR is associated with occupational exposure to polycyclic aromatic hydrocarbons. Carcinogenesis 2019; 39:869-878. [PMID: 29722794 PMCID: PMC6030939 DOI: 10.1093/carcin/bgy059] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/30/2018] [Indexed: 12/22/2022] Open
Abstract
Some polycyclic aromatic hydrocarbons (PAH) are known carcinogens and workplace PAH exposure may increase the risk of cancer. Monitoring early cancer-related changes can indicate whether the exposure is carcinogenic. Here, we enrolled 151 chimney sweeps, 152 controls and 19 creosote-exposed male workers from Sweden. We measured urinary PAH metabolites using LC/MS/MS, the cancer-related markers telomere length (TL) and mitochondrial DNA copy number (mtDNAcn) using qPCR, and DNA methylation of lung cancer-related genes F2RL3 and AHRR using pyrosequencing. The median 1-hydroxypyrene (PAH metabolite) concentrations were highest in creosote-exposed workers (8.0 μg/g creatinine) followed by chimney sweeps (0.34 μg/g creatinine) and controls (0.05 μg/g creatinine). TL and mtDNAcn did not differ between study groups. Chimney sweeps and creosote-exposed workers had significantly lower methylation of AHRR CpG site cg05575921 (88.1 and 84.9%, respectively) than controls (90%). Creosote-exposed workers (73.3%), but not chimney sweeps (76.6%) had lower methylation of F2RL3 cg03636183 than controls (76.7%). Linear regression analyses showed that chimney sweeps had lower AHRR cg05575921 methylation (B = -2.04; P < 0.057, adjusted for smoking and age) and lower average AHRR methylation (B = -2.05; P < 0.035), and non-smoking chimney sweeps had lower average F2RL3 methylation (B = -0.81; P < 0.042, adjusted for age) compared with controls. These cancer-related markers were not associated with urinary concentrations of PAH metabolites. In conclusion, although we found no associations with PAH metabolites in urine (short-term exposure), our results suggest dose-response relationship between PAH exposure and DNA hypomethylation of lung cancer-related loci. These findings indicate that further protective measures should be taken to reduce PAH exposure.
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Affiliation(s)
- Ayman Alhamdow
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christian Lindh
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jessika Hagberg
- MTM Research Centre, School of Science and Technology, Örebro University, Örebro, Sweden.,Department of Occupational and Environmental Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Pål Graff
- Department of Occupational and Environmental Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,National Institute of Occupational Health, Oslo, Norway
| | - Håkan Westberg
- MTM Research Centre, School of Science and Technology, Örebro University, Örebro, Sweden.,Department of Occupational and Environmental Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Annette M Krais
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Maria Albin
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Centre for Occupational and Environmental Medicine (CAMM), Stockholm County Council, Stockholm, Sweden
| | - Per Gustavsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine (CAMM), Stockholm County Council, Stockholm, Sweden
| | - Håkan Tinnerberg
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Karin Broberg
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
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35
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Henry MP, Hawkins JR, Boyle J, Bridger JM. The Genomic Health of Human Pluripotent Stem Cells: Genomic Instability and the Consequences on Nuclear Organization. Front Genet 2019; 9:623. [PMID: 30719030 PMCID: PMC6348275 DOI: 10.3389/fgene.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are increasingly used for cell-based regenerative therapies worldwide, with embryonic and induced pluripotent stem cells as potential treatments for debilitating and chronic conditions, such as age-related macular degeneration, Parkinson's disease, spinal cord injuries, and type 1 diabetes. However, with the level of genomic anomalies stem cells generate in culture, their safety may be in question. Specifically, hPSCs frequently acquire chromosomal abnormalities, often with gains or losses of whole chromosomes. This review discusses how important it is to efficiently and sensitively detect hPSC aneuploidies, to understand how these aneuploidies arise, consider the consequences for the cell, and indeed the individual to whom aneuploid cells may be administered.
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Affiliation(s)
- Marianne P Henry
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom.,Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
| | - J Ross Hawkins
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Jennifer Boyle
- Advanced Therapies Division, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Joanna M Bridger
- Laboratory of Nuclear and Genomic Health, Division of Biosciences, Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, United Kingdom
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36
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Nassour J, Radford R, Correia A, Fusté JM, Schoell B, Jauch A, Shaw RJ, Karlseder J. Autophagic cell death restricts chromosomal instability during replicative crisis. Nature 2019; 565:659-663. [PMID: 30675059 PMCID: PMC6557118 DOI: 10.1038/s41586-019-0885-0] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022]
Abstract
Replicative crisis is a senescence-independent process that acts as a final barrier against oncogenic transformation by eliminating pre-cancerous cells with disrupted cell cycle checkpoints1. It functions as a potent tumour suppressor and culminates in extensive cell death. Cells rarely evade elimination and evolve towards malignancy, but the mechanisms that underlie cell death in crisis are not well understood. Here we show that macroautophagy has a dominant role in the death of fibroblasts and epithelial cells during crisis. Activation of autophagy is critical for cell death, as its suppression promoted bypass of crisis, continued proliferation and accumulation of genome instability. Telomere dysfunction specifically triggers autophagy, implicating a telomere-driven autophagy pathway that is not induced by intrachromosomal breaks. Telomeric DNA damage generates cytosolic DNA species with fragile nuclear envelopes that undergo spontaneous disruption. The cytosolic chromatin fragments activate the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) pathway and engage the autophagy machinery. Our data suggest that autophagy is an integral component of the tumour suppressive crisis mechanism and that loss of autophagy function is required for the initiation of cancer.
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Affiliation(s)
- Joe Nassour
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Robert Radford
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Adriana Correia
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Brigitte Schoell
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Reuben J Shaw
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, La Jolla, CA, USA.
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37
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Gisselsson D, Lichtenzstejn D, Kachko P, Karlsson J, Manor E, Mai S. Clonal evolution through genetic bottlenecks and telomere attrition: Potential threats to in vitro data reproducibility. Genes Chromosomes Cancer 2018; 58:452-461. [PMID: 30255964 DOI: 10.1002/gcc.22685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Tissue cultures of immortalized human cells, also known as established cell lines, are broadly accessible and cost-efficient tools for biomedical research. We here review potential genetic sources of systematic error in cell line experiments due to clonal evolution in vitro. In particular, the authors highlight alterations in telomere function over prolonged culture and population bottlenecks, respectively, as two commonly overlooked phenomena that can result in significant alterations in cell line genotypes over just one or a few passages in vitro. These alterations may include changes in mutation status of oncogenes and large scale chromosomal imbalances. We introduce a simple list of factors to be avoided in order to reduce the risk of data misinterpretation due to clonal evolution, including unacknowledged in vitro selection pressures, prolonged culture per se, harsh population size reductions, experiments at early phases after establishment, and the employment of cell lines not sufficiently analyzed by high resolution genetic techniques.
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Affiliation(s)
- David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Division of Oncology-Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Daniel Lichtenzstejn
- Cell Biology, Research Institute of Oncology and Hematology, The Genomic Centre for Cancer Research and Diagnosis, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
| | - Polina Kachko
- Shraga Segal Department of Microbiology, Immunology and Genetics, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Esther Manor
- Shraga Segal Department of Microbiology, Immunology and Genetics, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Sabine Mai
- Cell Biology, Research Institute of Oncology and Hematology, The Genomic Centre for Cancer Research and Diagnosis, CancerCare Manitoba, University of Manitoba, Winnipeg, Canada
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38
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Influence of aging in the modulation of epigenetic biomarkers of carcinogenesis after exposure to air pollution. Exp Gerontol 2018; 110:125-132. [DOI: 10.1016/j.exger.2018.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/11/2018] [Accepted: 05/25/2018] [Indexed: 11/19/2022]
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39
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Sikdar N, Saha G, Dutta A, Ghosh S, Shrikhande SV, Banerjee S. Genetic Alterations of Periampullary and Pancreatic Ductal Adenocarcinoma: An Overview. Curr Genomics 2018; 19:444-463. [PMID: 30258276 PMCID: PMC6128383 DOI: 10.2174/1389202919666180221160753] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 02/06/2023] Open
Abstract
Pancreatic Ductal AdenoCarcinoma (PDAC) is one of the most lethal malignancies of all solid cancers. Precancerous lesions for PDAC include PanIN, IPMNs and MCNs. PDAC has a poor prognosis with a 5-year survival of approximately 6%. Whereas Periampulary AdenoCarcinoma (PAC) having four anatomic subtypes, pancreatic, Common Bile Duct (CBD), ampullary and duodenum shows relative better prognosis. The highest incidence of PDAC has been reported with black with respect to white population. Similarly, incidence rate of PAC also differs with different ethnic populations. Several lifestyle, environmental and occupational exposures including long-term diabetes, obesity, and smoking, have been linked to PDAC, however, for PAC the causal risk factors were poorly described. It is now clear that PDAC and PAC are a multi-stage process resulting from the accumulation of genomic alterations in the somatic DNA of normal cells as well as inherited mutations. Approximately 10% of PDAC have a familial inheritance. Germline mutations in CDKN2A, BRCA2, STK11, PALB2, PRSS1, etc., as well as certain syndromes have been well associated with predisposition to PDAC. KRAS, CDKN2A, TP53 and SMAD4 are the 4 "mountains" (high-frequency driver genes) which have been known to earliest somatic alterations for PDAC while relatively less frequent in PAC. Our understanding of the molecular carcinogenesis has improved in the last few years due to extensive research on PDAC which was not well explored in case of PAC. The genetic alterations that have been identified in PDAC and different subgroups of PAC are important implications for the development of genetic screening test, early diagnosis, and prognostic genetic markers. The present review will provide a brief overview of the incidence and prevalence of PDAC and PAC, mainly, increased risk in India, the several kinds of risk factors associated with the diseases as well as required genetic alterations for disease initiation and progression.
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Affiliation(s)
- Nilabja Sikdar
- Address correspondence to this author at the Human Genetics Unit, Indian Statistical Institute, 203, B.T. Road Kolkata 700108, India; Tel (1): +91-33
-25773240 (L); (2): +91-9830780397 (M); Fax: +91 33 35773049;, E-mail:
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40
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Svahn F, Paulsson JO, Stenman A, Fotouhi O, Mu N, Murtha TD, Korah R, Carling T, Bäckdahl M, Wang N, Juhlin CC, Larsson C. TERT promoter hypermethylation is associated with poor prognosis in adrenocortical carcinoma. Int J Mol Med 2018; 42:1675-1683. [PMID: 29956721 DOI: 10.3892/ijmm.2018.3735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/11/2018] [Indexed: 11/05/2022] Open
Abstract
Telomere maintenance, most commonly achieved by telomerase activation through induction of the telomerase reverse transcriptase (TERT) gene, is required for cell immortalization, a hallmark of cancer. Adrenocortical carcinoma (ACC) is an endocrine tumor for which TERT promoter mutations and telomerase activation have been reported. The present study assessed alterations of the TERT gene locus and telomere length in relation to clinical characteristics in ACC. In total, 38 cases of ACC with known TERT promoter mutational status were included. TERT promoter methylation densities were assessed by pyrosequencing, and TERT copy numbers and telomere length were determined by quantitative polymerase chain reaction analysis, followed by comparison of the mRNA expression of TERT and clinical parameters. The ACC tissue samples showed increased TERT copy numbers, compared with normal adrenal tissue (NAT) samples (P=0.001). Mutually exclusive TERT copy number gains or promoter mutation were present in 70% of the ACC samples. The ACC tissues exhibited higher levels of CpG promoter methylation of all eight CpG sites investigated within the ‑578 to ‑541 bp (Region A), compared with the NATs (P=0.001). High methylation density at this region was associated with metastatic disease and/or relapse, poor survival rates and higher European Network for the Study of Adrenal Tumor stage (P<0.05). The mRNA expression of TERT was inversely correlated with methylation density at ‑162 to ‑100 bp (Region B). Correlation was observed between relative telomere length and the gene expression of TERT. It was concluded that epigenetic alterations of the TERT promoter are frequent and associated with advanced disease and poorer clinical outcome in ACC.
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Affiliation(s)
- Fredrika Svahn
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Johan O Paulsson
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Adam Stenman
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Omid Fotouhi
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Ninni Mu
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Timothy D Murtha
- Department of Surgery, Yale School of Medicine, Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT 06520, USA
| | - Reju Korah
- Department of Surgery, Yale School of Medicine, Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT 06520, USA
| | - Tobias Carling
- Department of Surgery, Yale School of Medicine, Yale Endocrine Neoplasia Laboratory, Yale School of Medicine, New Haven, CT 06520, USA
| | - Martin Bäckdahl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, SE‑17176 Stockholm, Sweden
| | - Na Wang
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - C Christofer Juhlin
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology‑Pathology, Karolinska Institutet, Karolinska University Hospital, Cancer Center Karolinska, SE‑17176 Stockholm, Sweden
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41
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Cleal K, Norris K, Baird D. Telomere Length Dynamics and the Evolution of Cancer Genome Architecture. Int J Mol Sci 2018; 19:E482. [PMID: 29415479 PMCID: PMC5855704 DOI: 10.3390/ijms19020482] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 02/06/2023] Open
Abstract
Telomeres are progressively eroded during repeated rounds of cell division due to the end replication problem but also undergo additional more substantial stochastic shortening events. In most cases, shortened telomeres induce a cell-cycle arrest or trigger apoptosis, although for those cells that bypass such signals during tumour progression, a critical length threshold is reached at which telomere dysfunction may ensue. Dysfunction of the telomere nucleoprotein complex can expose free chromosome ends to the DNA double-strand break (DSB) repair machinery, leading to telomere fusion with both telomeric and non-telomeric loci. The consequences of telomere fusions in promoting genome instability have long been appreciated through the breakage-fusion-bridge (BFB) cycle mechanism, although recent studies using high-throughput sequencing technologies have uncovered evidence of involvement in a wider spectrum of genomic rearrangements including chromothripsis. A critical step in cancer progression is the transition of a clone to immortality, through the stabilisation of the telomere repeat array. This can be achieved via the reactivation of telomerase, or the induction of the alternative lengthening of telomeres (ALT) pathway. Whilst telomere dysfunction may promote genome instability and tumour progression, by limiting the replicative potential of a cell and enforcing senescence, telomere shortening can act as a tumour suppressor mechanism. However, the burden of senescent cells has also been implicated as a driver of ageing and age-related pathology, and in the promotion of cancer through inflammatory signalling. Considering the critical role of telomere length in governing cancer biology, we review questions related to the prognostic value of studying the dynamics of telomere shortening and fusion, and discuss mechanisms and consequences of telomere-induced genome rearrangements.
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Affiliation(s)
- Kez Cleal
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
| | - Kevin Norris
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
| | - Duncan Baird
- Division of Cancer and Genetics, School of Medicine, UHW Main Building, Cardiff CF14 4XN, UK.
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42
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Baudoin NC, Cimini D. A guide to classifying mitotic stages and mitotic defects in fixed cells. Chromosoma 2018; 127:215-227. [PMID: 29411093 DOI: 10.1007/s00412-018-0660-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 12/12/2022]
Abstract
Cell division is fundamental to life and its perturbation can disrupt organismal development, alter tissue homeostasis, and cause disease. Analysis of mitotic abnormalities provides insight into how certain perturbations affect the fidelity of cell division and how specific cellular structures, molecules, and enzymatic activities contribute to the accuracy of this process. However, accurate classification of mitotic defects is instrumental for correct interpretation of data and formulation of new hypotheses. In this article, we provide guidelines for identifying specific mitotic stages and for classifying normal and deviant mitotic phenotypes. We hope this will clarify confusion about how certain defects are classified and help investigators avoid misnomers, misclassification, and/or misinterpretation, thus leading to a unified and standardized system to classify mitotic defects.
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Affiliation(s)
- Nicolaas C Baudoin
- Department of Biological Sciences and Biocomplexity Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA
| | - Daniela Cimini
- Department of Biological Sciences and Biocomplexity Institute, Virginia Tech, 1015 Life Science Circle, Blacksburg, VA, 24061, USA.
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43
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Feiler MO, Patel D, Li H, Meacham PJ, Watson GE, Shamlaye C, Yeates A, Broberg K, van Wijngaarden E. The association between early-life relative telomere length and childhood neurodevelopment. Neurotoxicology 2018; 65:22-27. [PMID: 29360532 DOI: 10.1016/j.neuro.2018.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/17/2018] [Accepted: 01/19/2018] [Indexed: 12/11/2022]
Abstract
PURPOSE To examine the association between telomere length and neurodevelopment in children. METHODS We examined the relationship between relative telomere length (rTL) and neurodevelopmental outcomes at 9 and 30 months, and 5 years of age in children enrolled in the Seychelles Child Development Study Nutrition Cohort 1 (NC1). Relative telomere length was measured in cord blood and in child blood at age five. Multivariable linear regression examined associations between neurodevelopmental outcomes and rTL adjusting for relevant covariates. RESULTS Mean rTL was 1.18 at birth and 0.71 at age five. Increased cord blood rTL was associated with better scores on two neurodevelopmental tests, the psychomotor developmental index (β = 4.01; 95% confidence interval (CI) = 0.17, 7.85) at age 30 months, and the Woodcock Johnson test of achievement letter-word score (β = 2.88; CI = 1.21-4.56) at age five. The Woodcock Johnson test of achievement letter-word score remained statistically significant after two outliers were excluded (β = 2.83; CI = 0.69, 4.97); the psychomotor developmental index did not (β = 3.62; CI = -1.28, 8.52). None of the neurodevelopmental outcomes at age five were associated with five-year rTL. CONCLUSION Although increased cord blood rTL was associated with better test scores for a few neurodevelopmental outcomes, this study found little consistent evidence of an association between rTL and neurodevelopment. Future studies with a larger sample size, longer follow-up, and other relevant biological markers (e.g. oxidative stress) are needed to clarify the role of rTL in neurodevelopment and its relevance as a potential surrogate measure for oxidative stress in the field of developmental neurotoxicity.
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Affiliation(s)
| | - Deven Patel
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Huiqi Li
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Philip J Meacham
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Gene E Watson
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | | | | | - Karin Broberg
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Edwin van Wijngaarden
- University of Rochester School of Medicine and Dentistry, Rochester, NY, United States.
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44
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Habib AGK, Sugiura K, Ueno M. Chromosome passenger complex is required for the survival of cells with ring chromosomes in fission yeast. PLoS One 2018; 13:e0190523. [PMID: 29298360 PMCID: PMC5752009 DOI: 10.1371/journal.pone.0190523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/15/2017] [Indexed: 11/25/2022] Open
Abstract
Ring chromosomes are circular chromosomal abnormalities that have been reported in association with some genetic disorders and cancers. In Schizosaccharomyces pombe, lack of function of protection of telomere 1 (Pot1) or telomerase catalytic subunit (Trt1) results in survivors with circular chromosomes. Hitherto, it is poorly understood how cells with circular chromosomes survive and how circular chromosomes are maintained. Fission yeast Cut17/Bir1, Ark1, Pic1, and Nbl1 is a conserved chromosome passenger complex (CPC) functioning mainly throughout mitosis. Here, using a temperature-sensitive mutant of CPC subunits, we determined that CPC is synthetically lethal in combination with either Pot1 or Trt1. The pot1Δ pic1-T269 double mutant, which has circular chromosomes, showed a high percentage of chromosome mis-segregation and DNA damage foci at 33°C. We furthermore found that neither Shugoshin Sgo2 nor heterochromatin protein Swi6, which contribute to the centromeric localization of CPC, were required for the survival in the absence of Pot1. Both the pot1Δ sgo2Δ and pot1Δ swi6Δ double mutants displayed a high percentage of DNA damage foci, but a low percentage of chromosome mis-segregation, suggesting the link between the high percentage of chromosome mis-segregation and the lethality of the CPC pot1Δ double mutant. Our results suggest that CPC is required for the survival of cells with circular chromosomes and sheds light on the possible roles of CPC in the maintenance of circular chromosomes.
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Affiliation(s)
- Ahmed G. K. Habib
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, Beni-Suef, Egypt
| | - Kanako Sugiura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Masaru Ueno
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
- * E-mail:
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45
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Suraweera N, Mouradov D, Li S, Jorissen RN, Hampson D, Ghosh A, Sengupta N, Thaha M, Ahmed S, Kirwan M, Aleva F, Propper D, Feakins RM, Vulliamy T, Elwood NJ, Tian P, Ward RL, Hawkins NJ, Xu ZZ, Molloy PL, Jones IT, Croxford M, Gibbs P, Silver A, Sieber OM. Relative telomere lengths in tumor and normal mucosa are related to disease progression and chromosome instability profiles in colorectal cancer. Oncotarget 2017; 7:36474-36488. [PMID: 27167335 PMCID: PMC5095014 DOI: 10.18632/oncotarget.9015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/10/2016] [Indexed: 01/02/2023] Open
Abstract
Telomeric dysfunction is linked to colorectal cancer (CRC) initiation. However, the relationship of normal tissue and tumor telomere lengths with CRC progression, molecular features and prognosis is unclear. Here, we measured relative telomere length (RTL) by real-time quantitative PCR in 90 adenomas (aRTL), 419 stage I-IV CRCs (cRTL) and adjacent normal mucosa (nRTL). Age-adjusted RTL was analyzed against germline variants in telomere biology genes, chromosome instability (CIN), microsatellite instability (MSI), CpG island methylator phenotype (CIMP), TP53, KRAS, BRAF mutations and clinical outcomes. In 509 adenoma or CRC patients, nRTL decreased with advancing age. Female gender, proximal location and the TERT rs2736100 G allele were independently associated with longer age-adjusted nRTL. Adenomas and carcinomas exhibited telomere shortening in 79% and 67% and lengthening in 7% and 15% of cases. Age-adjusted nRTL and cRTL were independently associated with tumor stage, decreasing from adenoma to stage III and leveling out or increasing from stage III to IV, respectively. Cancer MSI, CIMP, TP53, KRAS and BRAF status were not related to nRTL or cRTL. Near-tetraploid CRCs exhibited significantly longer cRTLs than CIN- and aneuploidy CRCs, while cRTL was significantly shorter in CRCs with larger numbers of chromosome breaks. Age-adjusted nRTL, cRTL or cRTL:nRTL ratios were not associated with disease-free or overall survival in stage II/III CRC. Taken together, our data show that both normal mucosa and tumor RTL are independently associated with CRC progression, and highlight divergent associations of CRC telomere length with tumor CIN profiles.
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Affiliation(s)
- Nirosha Suraweera
- Centre for Digestive Diseases, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Shan Li
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia
| | - Robert N Jorissen
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Debbie Hampson
- Centre for Digestive Diseases, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Anil Ghosh
- Centre for Digestive Diseases, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Neel Sengupta
- Centre for Digestive Diseases, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Mohamed Thaha
- Centre for Digestive Diseases, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK.,Academic Surgical Unit, The Royal London Hospital, Whitechapel, London, UK
| | - Shafi Ahmed
- Academic Surgical Unit, The Royal London Hospital, Whitechapel, London, UK
| | - Michael Kirwan
- Centre for Paediatrics, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Floor Aleva
- Department of Medical Oncology, St Bartholomew's Hospital, Little Britain, London, UK
| | - David Propper
- Department of Medical Oncology, St Bartholomew's Hospital, Little Britain, London, UK
| | - Roger M Feakins
- Department of Pathology, The Royal London Hospital, Whitechapel, London, UK
| | - Tom Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Ngaire J Elwood
- Cord Blood Research, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Pei Tian
- Cord Blood Research, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Robyn L Ward
- The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas J Hawkins
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Zheng-Zhou Xu
- CSIRO Preventative Health Flagship, North Ryde, NSW, Australia
| | - Peter L Molloy
- CSIRO Preventative Health Flagship, North Ryde, NSW, Australia
| | - Ian T Jones
- Department of Colorectal Surgery, Royal Melbourne Hospital, Parkville, Victoria, Australia.,Department of Surgery, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew Croxford
- Department of Colorectal Surgery, Western Hospital, Footscray, Victoria, Australia
| | - Peter Gibbs
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Andrew Silver
- Centre for Digestive Diseases, Blizard Institute, Barts and The London School of Medicine and Dentistry, Whitechapel, London, UK
| | - Oliver M Sieber
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medial Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.,Department of Surgery, The University of Melbourne, Parkville, Victoria, Australia.,School of Biomedical Sciences, Monash University, Victoria, Australia
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46
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Hata T, Dal Molin M, McGregor-Das A, Song TJ, Wolfgang C, Eshleman JR, Hruban RH, Goggins M. Simple Detection of Telomere Fusions in Pancreatic Cancer, Intraductal Papillary Mucinous Neoplasm, and Pancreatic Cyst Fluid. J Mol Diagn 2017; 20:46-55. [PMID: 29229290 DOI: 10.1016/j.jmoldx.2017.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/06/2017] [Accepted: 09/14/2017] [Indexed: 02/06/2023] Open
Abstract
Telomere end-to-end fusions are an important source of chromosomal instability that arise in cells with critically shortened telomeres. We developed a nested real-time quantitative PCR method for telomere fusion detection in pancreatic ductal adenocarcinomas, intraductal papillary mucinous neoplasms (IPMNs), and IPMN cyst fluids. Ninety-one pancreatic cancer cell lines and xenograft samples, 93 IPMNs, and 93 surgically aspirated IPMN cyst fluid samples were analyzed. The association between telomere shortening, telomerase activity, and telomere fusion detection was evaluated. Telomere fusions were detected in 56 of 91 pancreatic cancers (61.5%). Telomere fusion-positive cell lines had significantly shorter telomere lengths than fusion-negative lines (P = 0.003). Telomere fusions were undetectable in normal pancreas or IPMNs with low-grade dysplasia (0.0%) and were detected in IPMN with high-grade dysplasia (HGD; 48.0%) (P < 0.001). In IPMN cyst fluids, telomere fusions were more frequent in IPMNs with HGD (26.9%) or associated invasive cancer (42.9%) than IPMN with intermediate-grade dysplasia (15.4%) or low-grade dysplasia (0%) (P = 0.025). Telomerase activity levels were higher in cyst fluids with fusions than in those without (P = 0.0414). Cyst fluid telomere fusion status was an independent predictor of HGD/invasive cancer by multivariate analysis (odds ratio, 6.23; 95% CI, 1.61-28.0). Telomere fusions are detected in later stages of IPMN progression and can serve as a marker for predicting the presence of HGD and/or invasive cancer.
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Affiliation(s)
- Tatsuo Hata
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marco Dal Molin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anne McGregor-Das
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tae Jun Song
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher Wolfgang
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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47
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Muraki K, Murnane JP. The DNA damage response at dysfunctional telomeres, and at interstitial and subtelomeric DNA double-strand breaks. Genes Genet Syst 2017; 92:135-152. [PMID: 29162774 DOI: 10.1266/ggs.17-00014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In mammals, DNA double-strand breaks (DSBs) are primarily repaired by classical non-homologous end joining (C-NHEJ), although homologous recombination repair and alternative NHEJ (A-NHEJ), which involve DSB processing, can also occur. These pathways are tightly regulated to maintain chromosome integrity. The ends of chromosomes, called telomeres, contain telomeric DNA that forms a cap structure in cooperation with telomeric proteins to prevent the activation of the DNA damage response and chromosome fusion at chromosome termini. Telomeres and subtelomeric regions are poor substrates for DNA replication; therefore, regions near telomeres are prone to replication fork stalling and chromosome breakage. Moreover, DSBs near telomeres are poorly repaired. As a result, when DSBs occur near telomeres in normal cells, the cells stop proliferating, while in cancer cells, subtelomeric DSBs induce rearrangements due to the absence of cell cycle checkpoints. The sensitivity of subtelomeric regions to DSBs is due to the improper regulation of processing, because although C-NHEJ is functional at subtelomeric DSBs, excessive processing results in an increased frequency of large deletions and chromosome rearrangements involving A-NHEJ.
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Affiliation(s)
- Keiko Muraki
- Institute for Protein Research, Osaka University.,Department of Radiation Oncology, University of California, San Francisco
| | - John P Murnane
- Department of Radiation Oncology, University of California, San Francisco
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48
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Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun 2017; 8:1221. [PMID: 29089486 PMCID: PMC5663922 DOI: 10.1038/s41467-017-01355-0] [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: 12/07/2013] [Accepted: 09/12/2017] [Indexed: 11/23/2022] Open
Abstract
Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, we build a compendium of 2218 primary tumours across 12 human cancer types and systematically screen for homozygous deletions, aiming to identify rare tumour suppressors. Our analysis defines 96 genomic regions recurrently targeted by homozygous deletions. These recurrent homozygous deletions occur either over tumour suppressors or over fragile sites, regions of increased genomic instability. We construct a statistical model that separates fragile sites from regions showing signatures of positive selection for homozygous deletions and identify candidate tumour suppressors within those regions. We find 16 established tumour suppressors and propose 27 candidate tumour suppressors. Several of these genes (including MGMT, RAD17, and USP44) show prior evidence of a tumour suppressive function. Other candidate tumour suppressors, such as MAFTRR, KIAA1551, and IGF2BP2, are novel. Our study demonstrates how rare tumour suppressors can be identified through copy number meta-analysis. Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, the authors conduct pan-cancer analyses and apply statistical modelling to identify 27 candidate tumour suppressors, including MAFTRR, KIAA1551, and IGF2BP2.
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49
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de Sá Junior PL, Câmara DAD, Porcacchia AS, Fonseca PMM, Jorge SD, Araldi RP, Ferreira AK. The Roles of ROS in Cancer Heterogeneity and Therapy. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2467940. [PMID: 29123614 PMCID: PMC5662836 DOI: 10.1155/2017/2467940] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/03/2017] [Accepted: 08/27/2017] [Indexed: 12/23/2022]
Abstract
Cancer comprises a group of heterogeneous diseases encompassing high rates of morbidity and mortality. Heterogeneity, which is a hallmark of cancer, is one of the main factors related to resistance to chemotherapeutic agents leading to poor prognosis. Heterogeneity is profoundly affected by increasing levels of ROS. Under low concentrations, ROS may function as signaling molecules favoring tumorigenesis and heterogeneity, while under high ROS concentrations, these species may work as cancer modulators due to their deleterious, genotoxic or even proapoptotic effect on cancer cells. This double-edged sword effect represented by ROS relies on their ability to cause genetic and epigenetic modifications in DNA structure. Antitumor therapeutic approaches may use molecules that prevent the ROS formation precluding carcinogenesis or use chemical agents that promote a sudden increase of ROS causing considerable oxidative stress inside tumor mass. Therefore, herein, we review what ROS are and how they are produced in normal and in cancer cells while providing an argumentative discussion about their role in cancer pathophysiology. We also describe the various sources of ROS in cancer and their role in tumor heterogeneity. Further, we also discuss some therapeutic strategies from the current landscape of cancer heterogeneity, ROS modulation, or ROS production.
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Affiliation(s)
| | - Diana Aparecida Dias Câmara
- Laboratory of Genetics, Butantan Institute, Sao Paulo, SP, Brazil
- Morphology and Genetic Department, University Federal of Sao Paulo, Sao Paulo, SP, Brazil
| | | | | | - Salomão Doria Jorge
- Department of Immunology, Laboratory of Tumor Immunology, Institute of Biomedical Science, University of Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Adilson Kleber Ferreira
- Department of Immunology, Laboratory of Tumor Immunology, Institute of Biomedical Science, University of Sao Paulo, Sao Paulo, SP, Brazil
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50
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Olsson M, Wapstra E, Friesen CR. Evolutionary ecology of telomeres: a review. Ann N Y Acad Sci 2017; 1422:5-28. [DOI: 10.1111/nyas.13443] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Mats Olsson
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
- School of Biological Sciences The University of Wollongong Wollongong New South Wales Australia
| | - Erik Wapstra
- School of Biological Sciences University of Tasmania Hobart Tasmania Australia
| | - Christopher R. Friesen
- School of Life and Environmental Sciences University of Sydney Sydney New South Wales Australia
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