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Johansson PA, Palmer JM, McGrath L, Warrier S, Hamilton HR, Beckman T, D'Mellow MG, Brooks KM, Glasson W, Hayward NK, Pritchard AL. Germline Variants in Patients Affected by Both Uveal and Cutaneous Melanoma. Pigment Cell Melanoma Res 2024. [PMID: 39315505 DOI: 10.1111/pcmr.13199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/25/2024]
Abstract
Uveal melanoma (UM) and nonacral cutaneous melanoma (CM) are distinct entities with varied genetic landscapes despite both arising from melanocytes. There are, however, similarities in that they most frequently affect people of European ancestry, and high penetrance germline variants in BAP1, POT1 and CDKN2A have been shown to predispose to both UM and CM. This study aims to further explore germline variants in patients affected by both UM and CM, shedding light on the underlying genetic mechanism causing these diseases. Using exome sequencing we analysed germline DNA samples from a cohort of 83 Australian patients diagnosed with both UM and CM. Eight (10%) patients were identified that carried pathogenic mutations in known melanoma predisposition genes POT1, MITF, OCA2, SLC45A2 and TYR. Three (4%) patients carried pathogenic variants in genes previously linked with other cancer syndromes (ATR, BRIP1 and MSH6) and another three cases carried monoallelic pathogenic variants in recessive cancer genes (xeroderma pigmentosum and Fanconi anaemia), indicating that reduced penetrance of phenotype in these individuals may contribute to the development of both UM and CM. These findings highlight the need for further studies characterising the role of these genes in melanoma susceptibility.
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Affiliation(s)
- Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- University of Queensland, Brisbane, Queensland, Australia
| | - Jane M Palmer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Lindsay McGrath
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - Sunil Warrier
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - Hayley R Hamilton
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Timothy Beckman
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - Matthew G D'Mellow
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kelly M Brooks
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- University of Queensland, Brisbane, Queensland, Australia
| | - William Glasson
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonia L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Genetics and Immunology, Division of Biomedical Science, University of the Highlands and Islands, Inverness, Scotland, UK
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2
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Ozturk A, Agbektas T, Huseynzada A, Guliyev R, Ganbarova R, Hasanova U, Tas A, Erkan S, Zontul C, Inandiklioglu N, Silig Y. In Silico and In Vitro Studies of Novel Azomethines on DNA Repair Genes in Gastric Cell Lines. Life (Basel) 2023; 13:1982. [PMID: 37895364 PMCID: PMC10607974 DOI: 10.3390/life13101982] [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: 09/04/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
We herein report the determination of the cytotoxic activity and expression profiles of some DNA repair genes of newly synthesized azomethines in the gastric cancer cell line (AGS). The studied novel compounds were synthesized by a condensation reaction and received compounds were characterized by 1H and 13C NMR spectroscopy methods. Furthermore, they were applied to the AGS cell line at eight different concentrations (0.1-50 µg/mL). Anticancer activities were determined using the MTT method. Expression levels of ATR, ERCC1, TOP2A, and ABCB1 genes were determined by the RT-PCR method. Biochemical parameters were also examined. The interaction of proteins with other proteins was investigated with the String v11 program. The IC50 values of compounds 1, 2, and 3 obtained after 72 h were 23.10, 8.93, and 1.58 µg/mL, respectively. The results demonstrate that the cytotoxic activity of compound 3 on AGS cancer cells is higher in comparison with other molecules. It was determined that the expression levels of ATR, TOP2A, and ABCB1 genes in compounds 1, 2, and 3 were decreased compared to the control group. In addition, it was determined that ERCC1 gene expression increased in compound 3, decreased in compound 2, and remained unchanged in compound 1 (p < 0.001). In AGS gastric cancer cells, a 64% decrease was detected for GST levels in compound 1, while a 38% decrease in GSH levels in compound 2. In addition, compounds 1-3 were examined at the molecular level with computational techniques and the docking studies revealed 4LN0 as a target protein.
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Affiliation(s)
- Alpaslan Ozturk
- Clinical Biochemistry, Etlik City Hospital, 06170 Ankara, Turkey
| | - Tugba Agbektas
- Department of Food Processing Technologies Services, Yıldızeli Vocational School, 58500 Sivas, Turkey;
| | - Alakbar Huseynzada
- Industrial Chemistry Research Laboratory, Baku State University, Z. Khalilov 33, Baku AZ1148, Azerbaijan; (A.H.); (R.G.); (R.G.); (U.H.)
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku AZ1010, Azerbaijan
- Department of Chemistry, Azerbaijan Engineers Union, Bashir Safaroglu 118, Baku AZ1022, Azerbaijan
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 33, Baku AZ1148, Azerbaijan
| | - Ruslan Guliyev
- Industrial Chemistry Research Laboratory, Baku State University, Z. Khalilov 33, Baku AZ1148, Azerbaijan; (A.H.); (R.G.); (R.G.); (U.H.)
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku AZ1010, Azerbaijan
| | - Rana Ganbarova
- Industrial Chemistry Research Laboratory, Baku State University, Z. Khalilov 33, Baku AZ1148, Azerbaijan; (A.H.); (R.G.); (R.G.); (U.H.)
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku AZ1010, Azerbaijan
| | - Ulviyya Hasanova
- Industrial Chemistry Research Laboratory, Baku State University, Z. Khalilov 33, Baku AZ1148, Azerbaijan; (A.H.); (R.G.); (R.G.); (U.H.)
- GPOGC SRI, Azerbaijan State Oil and Industry University, Baku AZ1010, Azerbaijan
- ICESCO Biomedical Materials Department, Baku State University, Z. Khalilov 33, Baku AZ1148, Azerbaijan
| | - Ayca Tas
- Department of Nutrition and Diet, Faculty of Health Sciences, Sivas Cumhuriyet University, 58140 Sivas, Turkey;
| | - Sultan Erkan
- Department of Chemistry, Faculty of Science, Sivas Cumhuriyet University, 58140 Sivas, Turkey;
| | - Cemile Zontul
- Department of Chemistry and Chemical Processing Technologies Services, Yıldızeli Vocational School, 58500 Sivas, Turkey;
| | - Nihal Inandiklioglu
- Department of Medical Biology, Faculty of Medicine, Yozgat Bozok University, 66100 Yozgat, Turkey;
| | - Yavuz Silig
- Department of Biochemistry, Faculty of Medicine, Sivas Cumhuriyet University, 58140 Sivas, Turkey;
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3
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Torres-Montaner A. Interactions between the DNA Damage Response and the Telomere Complex in Carcinogenesis: A Hypothesis. Curr Issues Mol Biol 2023; 45:7582-7616. [PMID: 37754262 PMCID: PMC10527771 DOI: 10.3390/cimb45090478] [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: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Contrary to what was once thought, direct cancer originating from normal stem cells seems to be extremely rare. This is consistent with a preneoplastic period of telomere length reduction/damage in committed cells that becomes stabilized in transformation. Multiple observations suggest that telomere damage is an obligatory step preceding its stabilization. During tissue turnover, the telomeres of cells undergoing differentiation can be damaged as a consequence of defective DNA repair caused by endogenous or exogenous agents. This may result in the emergence of new mechanism of telomere maintenance which is the final outcome of DNA damage and the initial signal that triggers malignant transformation. Instead, transformation of stem cells is directly induced by primary derangement of telomere maintenance mechanisms. The newly modified telomere complex may promote survival of cancer stem cells, independently of telomere maintenance. An inherent resistance of stem cells to transformation may be linked to specific, robust mechanisms that help maintain telomere integrity.
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Affiliation(s)
- Antonio Torres-Montaner
- Department of Pathology, Queen’s Hospital, Rom Valley Way, Romford, London RM7 OAG, UK;
- Departamento de Bioquímica y Biologia Molecular, Universidad de Cadiz, Puerto Real, 11510 Cadiz, Spain
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Bloch-Zupan A, Rey T, Jimenez-Armijo A, Kawczynski M, Kharouf N, Dure-Molla MDL, Noirrit E, Hernandez M, Joseph-Beaudin C, Lopez S, Tardieu C, Thivichon-Prince B, Dostalova T, Macek M, Alloussi ME, Qebibo L, Morkmued S, Pungchanchaikul P, Orellana BU, Manière MC, Gérard B, Bugueno IM, Laugel-Haushalter V. Amelogenesis imperfecta: Next-generation sequencing sheds light on Witkop's classification. Front Physiol 2023; 14:1130175. [PMID: 37228816 PMCID: PMC10205041 DOI: 10.3389/fphys.2023.1130175] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/06/2023] [Indexed: 05/27/2023] Open
Abstract
Amelogenesis imperfecta (AI) is a heterogeneous group of genetic rare diseases disrupting enamel development (Smith et al., Front Physiol, 2017a, 8, 333). The clinical enamel phenotypes can be described as hypoplastic, hypomineralized or hypomature and serve as a basis, together with the mode of inheritance, to Witkop's classification (Witkop, J Oral Pathol, 1988, 17, 547-553). AI can be described in isolation or associated with others symptoms in syndromes. Its occurrence was estimated to range from 1/700 to 1/14,000. More than 70 genes have currently been identified as causative. Objectives: We analyzed using next-generation sequencing (NGS) a heterogeneous cohort of AI patients in order to determine the molecular etiology of AI and to improve diagnosis and disease management. Methods: Individuals presenting with so called "isolated" or syndromic AI were enrolled and examined at the Reference Centre for Rare Oral and Dental Diseases (O-Rares) using D4/phenodent protocol (www.phenodent.org). Families gave written informed consents for both phenotyping and molecular analysis and diagnosis using a dedicated NGS panel named GenoDENT. This panel explores currently simultaneously 567 genes. The study is registered under NCT01746121 and NCT02397824 (https://clinicaltrials.gov/). Results: GenoDENT obtained a 60% diagnostic rate. We reported genetics results for 221 persons divided between 115 AI index cases and their 106 associated relatives from a total of 111 families. From this index cohort, 73% were diagnosed with non-syndromic amelogenesis imperfecta and 27% with syndromic amelogenesis imperfecta. Each individual was classified according to the AI phenotype. Type I hypoplastic AI represented 61 individuals (53%), Type II hypomature AI affected 31 individuals (27%), Type III hypomineralized AI was diagnosed in 18 individuals (16%) and Type IV hypoplastic-hypomature AI with taurodontism concerned 5 individuals (4%). We validated the genetic diagnosis, with class 4 (likely pathogenic) or class 5 (pathogenic) variants, for 81% of the cohort, and identified candidate variants (variant of uncertain significance or VUS) for 19% of index cases. Among the 151 sequenced variants, 47 are newly reported and classified as class 4 or 5. The most frequently discovered genotypes were associated with MMP20 and FAM83H for isolated AI. FAM20A and LTBP3 genes were the most frequent genes identified for syndromic AI. Patients negative to the panel were resolved with exome sequencing elucidating for example the gene involved ie ACP4 or digenic inheritance. Conclusion: NGS GenoDENT panel is a validated and cost-efficient technique offering new perspectives to understand underlying molecular mechanisms of AI. Discovering variants in genes involved in syndromic AI (CNNM4, WDR72, FAM20A … ) transformed patient overall care. Unravelling the genetic basis of AI sheds light on Witkop's AI classification.
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Affiliation(s)
- Agnes Bloch-Zupan
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Strasbourg, France
- Université de Strasbourg, Institut d’études avancées (USIAS), Strasbourg, France
- Hôpitaux Universitaires de Strasbourg (HUS), Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Centre de référence des maladies rares orales et dentaires, O-Rares, Filiére Santé Maladies rares TETE COU, European Reference Network ERN CRANIO, Strasbourg, France
- Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), IN-SERM U1258, CNRS- UMR7104, Illkirch, France
- Eastman Dental Institute, University College London, London, United Kingdom
| | - Tristan Rey
- Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), IN-SERM U1258, CNRS- UMR7104, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Laboratoires de diagnostic génétique, Institut de Génétique Médicale d’Alsace, Strasbourg, France
| | - Alexandra Jimenez-Armijo
- Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), IN-SERM U1258, CNRS- UMR7104, Illkirch, France
| | - Marzena Kawczynski
- Hôpitaux Universitaires de Strasbourg (HUS), Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Centre de référence des maladies rares orales et dentaires, O-Rares, Filiére Santé Maladies rares TETE COU, European Reference Network ERN CRANIO, Strasbourg, France
| | - Naji Kharouf
- Université de Strasbourg, Laboratoire de Biomatériaux et Bioingénierie, Inserm UMR_S 1121, Strasbourg, France
| | | | - Muriel de La Dure-Molla
- Rothschild Hospital, Public Assistance-Paris Hospitals (AP-HP), Reference Center for Rare Oral and Den-tal Diseases (O-Rares), Paris, France
| | - Emmanuelle Noirrit
- Centre Hospitalier Universitaire (CHU) Rangueil, Toulouse, Competence Center for Rare Oral and Den-tal Diseases, Toulouse, France
| | - Magali Hernandez
- Centre Hospitalier Régional Universitaire de Nancy, Université de Lorraine, Competence Center for Rare Oral and Dental Diseases, Nancy, France
| | - Clara Joseph-Beaudin
- Centre Hospitalier Universitaire de Nice, Competence Center for Rare Oral and Dental Diseases, Nice, France
| | - Serena Lopez
- Centre Hospitalier Universitaire de Nantes, Competence Center for Rare Oral and Dental Diseases, Nantes, France
| | - Corinne Tardieu
- APHM, Hôpitaux Universitaires de Marseille, Hôpital Timone, Competence Center for Rare Oral and Dental Diseases, Marseille, France
| | - Béatrice Thivichon-Prince
- Centre Hospitalier Universitaire de Lyon, Competence Center for Rare Oral and Dental Diseases, Lyon, France
| | | | - Tatjana Dostalova
- Department of Stomatology (TD) and Department of Biology and Medical Genetics (MM) Charles University 2nd Faculty of Medicine and Motol University Hospital, Prague, Czechia
| | - Milan Macek
- Department of Stomatology (TD) and Department of Biology and Medical Genetics (MM) Charles University 2nd Faculty of Medicine and Motol University Hospital, Prague, Czechia
| | | | - Mustapha El Alloussi
- Faculty of Dentistry, International University of Rabat, CReSS Centre de recherche en Sciences de la Santé, Rabat, Morocco
| | - Leila Qebibo
- Unité de génétique médicale et d’oncogénétique, CHU Hassan II, Fes, Morocco
| | | | | | - Blanca Urzúa Orellana
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Marie-Cécile Manière
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Strasbourg, France
- Hôpitaux Universitaires de Strasbourg (HUS), Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Centre de référence des maladies rares orales et dentaires, O-Rares, Filiére Santé Maladies rares TETE COU, European Reference Network ERN CRANIO, Strasbourg, France
| | - Bénédicte Gérard
- Hôpitaux Universitaires de Strasbourg, Laboratoires de diagnostic génétique, Institut de Génétique Médicale d’Alsace, Strasbourg, France
| | - Isaac Maximiliano Bugueno
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Strasbourg, France
- Hôpitaux Universitaires de Strasbourg (HUS), Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Centre de référence des maladies rares orales et dentaires, O-Rares, Filiére Santé Maladies rares TETE COU, European Reference Network ERN CRANIO, Strasbourg, France
- Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), IN-SERM U1258, CNRS- UMR7104, Illkirch, France
| | - Virginie Laugel-Haushalter
- Université de Strasbourg, Faculté de Chirurgie Dentaire, Strasbourg, France
- Université de Strasbourg, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), IN-SERM U1258, CNRS- UMR7104, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Laboratoires de diagnostic génétique, Institut de Génétique Médicale d’Alsace, Strasbourg, France
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Cybulski C, Zamani N, Kluźniak W, Milano L, Wokołorczyk D, Stempa K, Rudnicka H, Zhang S, Zadeh M, Huzarski T, Jakubowska A, Dębniak T, Lener M, Szwiec M, Domagała P, Samani AA, Narod S, Gronwald J, Masson JY, Lubiński J, Akbari MR. Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank. Am J Hum Genet 2023; 110:648-662. [PMID: 36977412 PMCID: PMC10119148 DOI: 10.1016/j.ajhg.2023.03.002] [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: 12/06/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023] Open
Abstract
Several breast cancer susceptibility genes have been discovered, but more are likely to exist. To identify additional breast cancer susceptibility genes, we used the founder population of Poland and performed whole-exome sequencing on 510 women with familial breast cancer and 308 control subjects. We identified a rare mutation in ATRIP (GenBank: NM_130384.3: c.1152_1155del [p.Gly385Ter]) in two women with breast cancer. At the validation phase, we found this variant in 42/16,085 unselected Polish breast cancer-affected individuals and in 11/9,285 control subjects (OR = 2.14, 95% CI = 1.13-4.28, p = 0.02). By analyzing the sequence data of the UK Biobank study participants (450,000 individuals), we identified ATRIP loss-of-function variants among 13/15,643 breast cancer-affected individuals versus 40/157,943 control subjects (OR = 3.28, 95% CI = 1.76-6.14, p < 0.001). Immunohistochemistry and functional studies showed the ATRIP c.1152_1155del variant allele is weakly expressed compared to the wild-type allele, and truncated ATRIP fails to perform its normal function to prevent replicative stress. We showed that tumors of women with breast cancer who have a germline ATRIP mutation have loss of heterozygosity at the site of ATRIP mutation and genomic homologous recombination deficiency. ATRIP is a critical partner of ATR that binds to RPA coating single-stranded DNA at sites of stalled DNA replication forks. Proper activation of ATR-ATRIP elicits a DNA damage checkpoint crucial in regulating cellular responses to DNA replication stress. Based on our observations, we conclude ATRIP is a breast cancer susceptibility gene candidate linking DNA replication stress to breast cancer.
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Affiliation(s)
- Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Neda Zamani
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Wojciech Kluźniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Larissa Milano
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Klaudia Stempa
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Helena Rudnicka
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Shiyu Zhang
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada
| | - Maryam Zadeh
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tomasz Huzarski
- Department of Clinical Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Tadeusz Dębniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marcin Lener
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Marek Szwiec
- Department of Surgery and Oncology, University of Zielona Góra, Zielona Góra, Poland
| | - Paweł Domagała
- Department of Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Amir Abbas Samani
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Humber River Hospital, University of Toronto, Toronto, ON, Canada
| | - Steven Narod
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Axis; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Jan Lubiński
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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6
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Chevarin M, Alcantara D, Albuisson J, Collonge-Rame MA, Populaire C, Selmani Z, Baurand A, Sawka C, Bertolone G, Callier P, Duffourd Y, Jonveaux P, Bignon YJ, Coupier I, Cornelis F, Cordier C, Mozelle-Nivoix M, Rivière JB, Kuentz P, Thauvin C, Boidot R, Ghiringhelli F, O'Driscoll M, Faivre L, Nambot S. The "extreme phenotype approach" applied to male breast cancer allows the identification of rare variants of ATR as potential breast cancer susceptibility alleles. Oncotarget 2023; 14:111-125. [PMID: 36749285 PMCID: PMC9904323 DOI: 10.18632/oncotarget.28358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
In oncogenetics, some patients could be considered as "extreme phenotypes", such as those with very early onset presentation or multiple primary malignancies, unusually high numbers of cancers of the same spectrum or rare cancer types in the same parental branch. For these cases, a genetic predisposition is very likely, but classical candidate gene panel analyses often and frustratingly remains negative. In the framework of the EX2TRICAN project, exploring unresolved extreme cancer phenotypes, we applied exome sequencing on rare familial cases with male breast cancer, identifying a novel pathogenic variant of ATR (p.Leu1808*). ATR has already been suspected as being a predisposing gene to breast cancer in women. We next identified 3 additional ATR variants in a cohort of both male and female with early onset and familial breast cancers (c.7762-2A>C; c.2078+1G>A; c.1A>G). Further molecular and cellular investigations showed impacts on transcripts for variants affecting splicing sites and reduction of ATR expression and phosphorylation of the ATR substrate CHEK1. This work further demonstrates the interest of an extended genetic analysis such as exome sequencing to identify very rare variants that can play a role in cancer predisposition in extreme phenotype cancer cases unexplained by classical cancer gene panels testing.
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Affiliation(s)
- Martin Chevarin
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
| | - Diana Alcantara
- Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom
| | - Juliette Albuisson
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France
| | | | - Céline Populaire
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Zohair Selmani
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
| | - Amandine Baurand
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Sawka
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Geoffrey Bertolone
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Philippe Jonveaux
- Laboratoire de Génétique Médicale, INSERM U954, Hôpitaux de Brabois, Vandoeuvre les Nancy, France
| | - Yves-Jean Bignon
- Laboratoire d’Oncologie Moléculaire, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - François Cornelis
- Université Bordeaux, IMB, UMR 5251, Talence, France
- Service d’imagerie diagnostique et interventionnelle de l’adulte, Hôpital Pellegrin, CHU de Bordeaux, France
| | | | | | - Jean-Baptiste Rivière
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Paul Kuentz
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Christel Thauvin
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Romain Boidot
- Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France
| | - François Ghiringhelli
- Département d’oncologie médicale, INSERM LNC U1231, Centre Georges François Leclerc, Dijon, France
| | - Marc O'Driscoll
- Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom
| | - Laurence Faivre
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Sophie Nambot
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France
- Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
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7
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Drbohlavová T, Argalácsová S, Soukupová J, Vočka M. Germline Pathogenic Variants in Squamous Cell Carcinoma of the Head and Neck. Folia Biol (Praha) 2023; 69:107-115. [PMID: 38410968 DOI: 10.14712/fb2023069040107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) presents a significant global health problem with variable geographic distribution and risk factors, including tobacco and alcohol abuse, human papillomavirus infections, and genetic predisposition. While the majority of cases are sporadic, several well-defined hereditary syndromes have been associated with a higher risk of developing HNSCC including Li-Fraumeni syndrome, Fanconi anaemia, Bloom syndrome, familial atypical multiple mole melanoma, and dyskeratosis congenita. There is also evidence of familial clusters of HNSCC, suggesting a genetic component in the development of the disease. Germ-line genetic testing in HNSCC using next-generation sequencing has revealed a wide range of germline variants, some of which were not anticipated based on standard guidelines. These variants may influence treatment decisions and have the potential to be targeted with precision medicine in the future. Despite these advances, routine germline genetic testing for HNSCC is not currently recommended and remains reserved for HNSCC cases with early onset or strong family cancer history. However, the increasing availability of germline genetic testing warrants development of more comprehensive and standardized testing protocols. Germline genetic testing also has the potential to influence precision-guided treatment in HNSCC patients carrying germline pathogenic variants.
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Affiliation(s)
- Tereza Drbohlavová
- Institute of Radiation Oncology, First Faculty of Medicine, Charles University and Bulovka University Hospital, Prague, Czech Republic
| | - Soňa Argalácsová
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic.
| | - Jana Soukupová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
| | - Michal Vočka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Czech Republic
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8
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McCarthy-Leo C, Darwiche F, Tainsky MA. DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex. Cancers (Basel) 2022; 14:5278. [PMID: 36358700 PMCID: PMC9656488 DOI: 10.3390/cancers14215278] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 08/27/2023] Open
Abstract
Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Fatima Darwiche
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Michael A. Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Molecular Therapeutics Program, Karmanos Cancer Institute at Wayne State University School of Medicine, Detroit, MI 48201, USA
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9
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Pizzul P, Casari E, Gnugnoli M, Rinaldi C, Corallo F, Longhese MP. The DNA damage checkpoint: A tale from budding yeast. Front Genet 2022; 13:995163. [PMID: 36186482 PMCID: PMC9520983 DOI: 10.3389/fgene.2022.995163] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
Studies performed in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have led the way in defining the DNA damage checkpoint and in identifying most of the proteins involved in this regulatory network, which turned out to have structural and functional equivalents in humans. Subsequent experiments revealed that the checkpoint is an elaborate signal transduction pathway that has the ability to sense and signal the presence of damaged DNA and transduce this information to influence a multifaceted cellular response that is essential for cancer avoidance. This review focuses on the work that was done in Saccharomyces cerevisiae to articulate the checkpoint concept, to identify its players and the mechanisms of activation and deactivation.
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10
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Toss A, Quarello P, Mascarin M, Banna GL, Zecca M, Cinieri S, Peccatori FA, Ferrari A. Cancer Predisposition Genes in Adolescents and Young Adults (AYAs): a Review Paper from the Italian AYA Working Group. Curr Oncol Rep 2022; 24:843-860. [PMID: 35320498 PMCID: PMC9170630 DOI: 10.1007/s11912-022-01213-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW The present narrative systematic review summarizes current knowledge on germline gene mutations predisposing to solid tumors in adolescents and young adults (AYAs). RECENT FINDINGS AYAs with cancer represent a particular group of patients with specific challenging characteristics and yet unmet needs. A significant percentage of AYA patients carry pathogenic or likely pathogenic variants (PV/LPVs) in cancer predisposition genes. Nevertheless, knowledge on spectrum, frequency, and clinical implications of germline variants in AYAs with solid tumors is limited. The identification of PV/LPV in AYA is especially critical given the need for appropriate communicative strategies, risk of second primary cancers, need for personalized long-term surveillance, potential reproductive implications, and cascade testing of at-risk family members. Moreover, these gene alterations may potentially provide novel biomarkers and therapeutic targets that are lacking in AYA patients. Among young adults with early-onset phenotypes of malignancies typically presenting at later ages, the increased prevalence of germline PV/LPVs supports a role for genetic counseling and testing irrespective of tumor type.
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Affiliation(s)
- Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Quarello
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children's Hospital, Turin, Italy
- Department of Public Health and Paediatric Sciences, University of Torino, Turin, Italy
| | - Maurizio Mascarin
- AYA Oncology and Pediatric Radiotherapy Unit, Centro di Riferimento Oncologico IRCCS, Aviano, Italy
| | - Giuseppe Luigi Banna
- Candiolo Cancer Institute, FPO-IRCCS, SP142, km 3.95, 10060, Candiolo, Turin, Italy.
| | - Marco Zecca
- Department of Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Saverio Cinieri
- Medical Oncology Unit and Breast Unit Ospedale Perrino ASL, Brindisi, Italy
| | - Fedro Alessandro Peccatori
- Fertility and Procreation Unit, Gynecologic Oncology Program, European Institute of Oncology IRCCS, Milan, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
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11
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Ajaz S, Zaidi SEZ, Ali S, Siddiqa A, Memon MA. Germline Mutation Analysis in Sporadic Breast Cancer Cases With Clinical Correlations. Front Genet 2022; 13:820610. [PMID: 35356428 PMCID: PMC8959921 DOI: 10.3389/fgene.2022.820610] [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: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 11/15/2022] Open
Abstract
Demographics for breast cancers vary widely among nations. The frequency of germline mutations in breast cancers, which reflects the hereditary cases, has not been investigated adequately and accurately in highly-consanguineous Pakistani population. In the present discovery case series, germ-line mutations in twenty-seven breast cancer candidate genes were investigated in eighty-four sporadic breast cancer patients along with the clinical correlations. The germ-line variants were also assessed in two healthy gender-matched controls. The clinico-pathological features were evaluated by descriptive analysis and Pearson χ2 test (with significant p-value <0.05). The most frequent parameters associated with hereditary cancer cases are age and ethnicity. Therefore, the analyses were stratified on the basis of age (≤40 years vs. >40 years) and ethnicity. The breast cancer gene panel assay was carried out by BROCA, which is a genomic capture, massively parallel next generation sequencing assay on Illumina Hiseq2000 with 100bp read lengths. Copy number variations were determined by partially-mapped read algorithm. Once the mutation was identified, it was validated by Sanger sequencing. The ethnic analysis stratified on the basis of age showed that the frequency of breast cancer at young age (≤40 years) was higher in Sindhis (n = 12/19; 64%) in contrast to patients in other ethnic groups. Majority of the patients had stage III (38.1%), grade III (50%), tumor size 2–5 cm (54.8%), and invasive ductal carcinoma (81%). Overall, the analysis revealed germ-line mutations in 11.9% of the patients, which was not significantly associated with younger age or any particular ethnicity. The mutational spectrum was restricted to three genes: BRCA1, BRCA2, and TP53. The identified mutations consist of seven novel germ-line mutations, while three mutations have been reported previously. All the mutations are predicted to result in protein truncation. No mutations were identified in the remaining twenty-four candidate breast cancer genes. The present study provides the framework for the development of hereditary-based preventive and treatment strategies against breast cancers in Pakistani population.
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Affiliation(s)
- Sadia Ajaz
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
- *Correspondence: Sadia Ajaz, ,
| | - Sani-e-Zehra Zaidi
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Saleema Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Aisha Siddiqa
- Atomic Energy Medical Centre (AEMC), Jinnah Postgraduate Medical Centre (JPMC), Karachi, Pakistan
| | - Muhammad Ali Memon
- Atomic Energy Medical Centre (AEMC), Jinnah Postgraduate Medical Centre (JPMC), Karachi, Pakistan
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12
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Garcia FADO, de Andrade ES, de Campos Reis Galvão H, da Silva Sábato C, Campacci N, de Paula AE, Evangelista AF, Santana IVV, Melendez ME, Reis RM, Palmero EI. New insights on familial colorectal cancer type X syndrome. Sci Rep 2022; 12:2846. [PMID: 35181726 PMCID: PMC8857274 DOI: 10.1038/s41598-022-06782-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Familial colorectal cancer type X (FCCTX) is a heterogeneous colorectal cancer predisposition syndrome that, although displays a cancer pattern similar to Lynch syndrome, is mismatch repair proficient and does not exhibit microsatellite instability. Besides, its genetic etiology remains to be elucidated. In this study we performed germline exome sequencing of 39 cancer-affected patients from 34 families at risk for FCCTX. Variant classification followed the American College of Medical Genetics and Genomics (ACMG) guidelines. Pathogenic/likely pathogenic variants were identified in 17.65% of the families. Rare and potentially pathogenic alterations were identified in known hereditary cancer genes (CHEK2), in putative FCCTX candidate genes (OGG1 and FAN1) and in other cancer-related genes such as ATR, ASXL1, PARK2, SLX4 and TREX1. This study provides novel important clues that can contribute to the understanding of FCCTX genetic basis.
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Affiliation(s)
- Felipe Antonio de Oliveira Garcia
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | - Edilene Santos de Andrade
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | | | - Natália Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil. .,Department of Genetics, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
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13
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Targeting DNA Repair and Chromatin Crosstalk in Cancer Therapy. Cancers (Basel) 2021; 13:cancers13030381. [PMID: 33498525 PMCID: PMC7864178 DOI: 10.3390/cancers13030381] [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: 12/17/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Targeting aberrant DNA repair in cancers in addition to transcription and replication is an area of interest for cancer researchers. Inhibition of DNA repair selectively in cancer cells leads to cytotoxic or cytostatic effects and overcomes survival advantages imparted by chromosomal translocations or mutations. In this review, we highlight the relevance of DNA repair-linked events in developmental diseases and cancers and also discuss mechanisms to overcome these events that participate in different cellular processes. Abstract Aberrant DNA repair pathways that underlie developmental diseases and cancers are potential targets for therapeutic intervention. Targeting DNA repair signal effectors, modulators and checkpoint proteins, and utilizing the synthetic lethality phenomena has led to seminal discoveries. Efforts to efficiently translate the basic findings to the clinic are currently underway. Chromatin modulation is an integral part of DNA repair cascades and an emerging field of investigation. Here, we discuss some of the key advancements made in DNA repair-based therapeutics and what is known regarding crosstalk between chromatin and repair pathways during various cellular processes, with an emphasis on cancer.
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14
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Scott AJ, Tokaz MC, Jacobs MF, Chinnaiyan AM, Phillips TJ, Wilcox RA. Germline variants discovered in lymphoma patients undergoing tumor profiling: a case series. Fam Cancer 2021; 20:61-65. [PMID: 32504211 PMCID: PMC7719097 DOI: 10.1007/s10689-020-00192-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 11/29/2022]
Abstract
Clinical tumor sequencing protocols often depend on obtaining germline DNA from patients to aid in the identification of de novo variants in the tumor, and therefore come with the possibility for the incidental discovery of germline variants. Ninety-one adult patients with lymphoma were consented and enrolled in MIONCOSEQ, an IRB-approved tumor profiling protocol that utilizes an exome sequencing platform. Charts were retrospectively reviewed for germline variants from sequencing results, personal and/or family history of cancer and genetic counseling referral. After review of the 91 lymphoma cases, seven (8%) cases revealed germline variants. Only one of these, CHEK2 p.I157T, has been previously recovered as a germline variant in lymphoma. Two of the seven patients received genetic counseling, two died before genetic counseling could be arranged and three did not follow-up with a genetics provider. None of the patients had a personal or family history that would have otherwise suggested an indication for cancer genetics referral, especially notable as lymphoma is not traditionally associated with inherited cancer syndromes. Importantly, as only two of seven patients had appropriate genetic counseling for their variant, timely genetic counseling should be a critical part of all tumor profiling platforms that use non-tumor DNA.
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Affiliation(s)
- Anthony J Scott
- Division of Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA.
| | - Molly C Tokaz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michelle F Jacobs
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Tycel J Phillips
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ryan A Wilcox
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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15
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Lodovichi S, Cervelli T, Pellicioli A, Galli A. Inhibition of DNA Repair in Cancer Therapy: Toward a Multi-Target Approach. Int J Mol Sci 2020; 21:E6684. [PMID: 32932697 PMCID: PMC7554826 DOI: 10.3390/ijms21186684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Alterations in DNA repair pathways are one of the main drivers of cancer insurgence. Nevertheless, cancer cells are more susceptible to DNA damage than normal cells and they rely on specific functional repair pathways to survive. Thanks to advances in genome sequencing, we now have a better idea of which genes are mutated in specific cancers and this prompted the development of inhibitors targeting DNA repair players involved in pathways essential for cancer cells survival. Currently, the pivotal concept is that combining the inhibition of mechanisms on which cancer cells viability depends is the most promising way to treat tumorigenesis. Numerous inhibitors have been developed and for many of them, efficacy has been demonstrated either alone or in combination with chemo or radiotherapy. In this review, we will analyze the principal pathways involved in cell cycle checkpoint and DNA repair focusing on how their alterations could predispose to cancer, then we will explore the inhibitors developed or in development specifically targeting different proteins involved in each pathway, underscoring the rationale behind their usage and how their combination and/or exploitation as adjuvants to classic therapies could help in patients clinical outcome.
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Affiliation(s)
- Samuele Lodovichi
- Bioscience Department, University of Milan, Via Celoria 26, 20131 Milan, Italy;
| | - Tiziana Cervelli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy;
| | - Achille Pellicioli
- Bioscience Department, University of Milan, Via Celoria 26, 20131 Milan, Italy;
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy;
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16
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Wilhelm T, Said M, Naim V. DNA Replication Stress and Chromosomal Instability: Dangerous Liaisons. Genes (Basel) 2020; 11:E642. [PMID: 32532049 PMCID: PMC7348713 DOI: 10.3390/genes11060642] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosomal instability (CIN) is associated with many human diseases, including neurodevelopmental or neurodegenerative conditions, age-related disorders and cancer, and is a key driver for disease initiation and progression. A major source of structural chromosome instability (s-CIN) leading to structural chromosome aberrations is "replication stress", a condition in which stalled or slowly progressing replication forks interfere with timely and error-free completion of the S phase. On the other hand, mitotic errors that result in chromosome mis-segregation are the cause of numerical chromosome instability (n-CIN) and aneuploidy. In this review, we will discuss recent evidence showing that these two forms of chromosomal instability can be mechanistically interlinked. We first summarize how replication stress causes structural and numerical CIN, focusing on mechanisms such as mitotic rescue of replication stress (MRRS) and centriole disengagement, which prevent or contribute to specific types of structural chromosome aberrations and segregation errors. We describe the main outcomes of segregation errors and how micronucleation and aneuploidy can be the key stimuli promoting inflammation, senescence, or chromothripsis. At the end, we discuss how CIN can reduce cellular fitness and may behave as an anticancer barrier in noncancerous cells or precancerous lesions, whereas it fuels genomic instability in the context of cancer, and how our current knowledge may be exploited for developing cancer therapies.
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Affiliation(s)
- Therese Wilhelm
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris Saclay, Gustave Roussy, 94805 Villejuif, France; (T.W.); (M.S.)
- UMR144 Cell Biology and Cancer, Institut Curie, 75005 Paris, France
| | - Maha Said
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris Saclay, Gustave Roussy, 94805 Villejuif, France; (T.W.); (M.S.)
| | - Valeria Naim
- CNRS UMR9019 Genome Integrity and Cancers, Université Paris Saclay, Gustave Roussy, 94805 Villejuif, France; (T.W.); (M.S.)
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17
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Abstract
The hereditary nature of some forms of cancer was recognized long ago. Over time, recognition of associated findings led to the delineation of numerous hereditary cancer syndromes. Many of these syndromes also have cutaneous manifestations, the recognition of which can lead to their early identification. Recognition of these syndromes allows vigilant surveillance and preemptive treatment, which can dramatically impact the risks of morbidity and mortality for affected patients. The rise of rapid and accurate genetic testing now allows the early identification of asymptomatic at risk family members so that monitoring can be initiated as early as possible. The dermatologist plays a critical role in early identification of these syndromes and, in many cases, their treatment. This review summarizes many known hereditary cancer syndromes with cutaneous findings, their etiology, identification, evaluation, and management. Importantly, this is an ever evolving topic and new findings and syndromes will continue to be recognized. The dermatologist must be always alert to ensure they are detected.
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Affiliation(s)
- Ryan Ladd
- Department of Dermatology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Matthew Davis
- Department of Dermatology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Jonathan A Dyer
- Department of Dermatology, University of Missouri School of Medicine, Columbia, Missouri, USA.
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Shahamatdar S, He MX, Reyna MA, Gusev A, AlDubayan SH, Van Allen EM, Ramachandran S. Germline Features Associated with Immune Infiltration in Solid Tumors. Cell Rep 2020; 30:2900-2908.e4. [PMID: 32130895 PMCID: PMC7082123 DOI: 10.1016/j.celrep.2020.02.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 08/12/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
The immune composition of the tumor microenvironment influences response and resistance to immunotherapies. While numerous studies have identified somatic correlates of immune infiltration, germline features that associate with immune infiltrates in cancers remain incompletely characterized. We analyze seven million autosomal germline variants in the TCGA cohort and test for association with established immune-related phenotypes that describe the tumor immune microenvironment. We identify one SNP associated with the amount of infiltrating follicular helper T cells; 23 candidate genes, some of which are involved in cytokine-mediated signaling and others containing cancer-risk SNPs; and networks with genes that are part of the DNA repair and transcription elongation pathways. In addition, we find a positive association between polygenic risk for rheumatoid arthritis and amount of infiltrating CD8+ T cells. Overall, we identify multiple germline genetic features associated with tumor-immune phenotypes and develop a framework for probing inherited features that contribute to differences in immune infiltration.
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Affiliation(s)
- Sahar Shahamatdar
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Meng Xiao He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Boston, MA 02115, USA
| | - Matthew A Reyna
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322, USA; Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Saud H AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
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DNA damage response proteins and its role in tumor progression of uveal melanoma with patient outcome. Clin Transl Oncol 2020; 22:1472-1480. [PMID: 32124242 DOI: 10.1007/s12094-019-02281-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND The role of DNA damage response (DDR) proteins is poorly understood in uveal melanoma. ATR belongs to one of those proteins that induce DDR by arresting the cell cycle which leads to DNA repair. ATR is localized at position 23 on the same chromosome 3 where BAP1 is located at position 21.1 which is a known poor prognostic marker of UM. The aim of our study is to detect the expression of ATR at the protein and RNA levels and determine its prognostic significance. METHODS Expression of nuclear ATR was investigated on sixty-nine UM patients. Formalin-fixed paraffin-embedded choroidal melanoma samples were taken to evaluate the expression of ATR. Fifty samples were also validated by real-time PCR. Results of both protein and mRNA were then correlated with clinicopathological parameters. To determine the prognostic significance, Kaplan-Meier and multivariate analyses were performed. RESULTS Loss of ATR protein was seen in 72% cases which was statistically significant with epithelioid cell type (p = 0.005), tumor thickness (p = 0.016), mitotic figures (p = 0.001) and BAP1 loss (p < 0.001). At the transcriptional level loss of ATR was seen in 76% cases which were statistically significant with metastasis (p = 0.046), staging (0.044) and loss of BAP1 (p = 0.022). On multivariate analysis loss of ATR and tumor staging came out to be independent prognostic parameters. CONCLUSION Our data suggest that ATR might serve as a potential prognostic marker in UM patients and could serve as a potential therapeutic target.
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20
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Precision medicine in Ewing sarcoma: a translational point of view. Clin Transl Oncol 2020; 22:1440-1454. [PMID: 32026343 DOI: 10.1007/s12094-020-02298-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022]
Abstract
Ewing sarcoma is a rare tumor that arises in bones of children and teenagers but, in 15% of the patients it is presented as a primary soft tissue tumor. Balanced reciprocal chimeric translocation t(11;22)(q24;q12), which encodes an oncogenic protein fusion (EWSR1/FLI1), is the most generalized and characteristic molecular event. Using conventional treatments, (chemotherapy, surgery and radiotherapy) long-term overall survival rate is 30% for patients with disseminated disease and 65-75% for patients with localized tumors. Urgent new effective drug development is a challenge. This review summarizes the preclinical and clinical investigational knowledge about prognostic and targetable biomarkers in Ewing sarcoma, finally suggesting a workflow for precision medicine committees.
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21
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Challenges in reporting pathogenic/potentially pathogenic variants in 94 cancer predisposing genes - in pediatric patients screened with NGS panels. Sci Rep 2020; 10:223. [PMID: 31937788 PMCID: PMC6959212 DOI: 10.1038/s41598-019-57080-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022] Open
Abstract
The benefit of reporting unsolicited findings in Next Generation Sequencing (NGS) related to cancer genes in children may have implications for family members, nevertheless, could also cause distress. We aimed to retrospectively investigate germline variants in 94 genes implicated in oncogenesis, in patients referred to NGS testing for various rare genetic diseases and reevaluate the utility of reporting different classes of pathogenicity. We used in silico prediction software to classify variants and conducted manual review to examine unsolicited findings frequencies in 145 children with rare diseases, that underwent sequencing - using a 4813 gene panel. The anonymized reanalysis revealed 18250 variants, of which 126 were considered after filtering. Six pathogenic variants (in BRCA1,BMPR1A,FANCA,FANCC,NBN genes) with cancer related phenotype and three unsolicited variants (in BRCA2,PALB2,RAD50 genes) were reported to patients. Additionally, three unsolicited variants in ATR, BLM (in two individuals), and FANCB genes presented potential cancer susceptibility, were not reported to patients. In retrospect, 4.8% (7/145) of individuals in our cohort had unsolicited NGS findings related to cancer. More efforts are needed to create an updatable consensus in reporting variants in cancer predisposing genes, especially for children. Consent process is crucial to inform of both value and risk of additional genetic information.
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Pilzecker B, Buoninfante OA, Jacobs H. DNA damage tolerance in stem cells, ageing, mutagenesis, disease and cancer therapy. Nucleic Acids Res 2019; 47:7163-7181. [PMID: 31251805 PMCID: PMC6698745 DOI: 10.1093/nar/gkz531] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA damage response network guards the stability of the genome from a plethora of exogenous and endogenous insults. An essential feature of the DNA damage response network is its capacity to tolerate DNA damage and structural impediments during DNA synthesis. This capacity, referred to as DNA damage tolerance (DDT), contributes to replication fork progression and stability in the presence of blocking structures or DNA lesions. Defective DDT can lead to a prolonged fork arrest and eventually cumulate in a fork collapse that involves the formation of DNA double strand breaks. Four principal modes of DDT have been distinguished: translesion synthesis, fork reversal, template switching and repriming. All DDT modes warrant continuation of replication through bypassing the fork stalling impediment or repriming downstream of the impediment in combination with filling of the single-stranded DNA gaps. In this way, DDT prevents secondary DNA damage and critically contributes to genome stability and cellular fitness. DDT plays a key role in mutagenesis, stem cell maintenance, ageing and the prevention of cancer. This review provides an overview of the role of DDT in these aspects.
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Affiliation(s)
- Bas Pilzecker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Olimpia Alessandra Buoninfante
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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23
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Cui Y, Dong H, Ma Y, Zhang D. Strategies for Applying Nonhomologous End Joining-Mediated Genome Editing in Prokaryotes. ACS Synth Biol 2019; 8:2194-2202. [PMID: 31525995 DOI: 10.1021/acssynbio.9b00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of genome editing technology based on the CRISPR/Cas system enabled revolutionary progress in genetic engineering. Double-strand breaks (DSBs), which can be induced by the CRISPR/Cas9 system, cause serious DNA damage that can be repaired by a homologous recombination (HR) system or the nonhomologous end joining (NHEJ) pathway. However, many bacterial species have a very weak HR system. Thus, the NHEJ pathway can be used in prokaryotes. Starting with a brief introduction of the mechanism of the NHEJ pathway, this review focuses on current research and details of applications of NHEJ in eukaryotes, which forms the theoretical basis for the application of the NHEJ system in prokaryotes.
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24
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Jacobs DI, Fukumura K, Bainbridge MN, Armstrong GN, Tsavachidis S, Gu X, Doddapaneni HV, Hu J, Jayaseelan JC, Muzny DM, Huse JT, Bondy ML. Elucidating the molecular pathogenesis of glioma: integrated germline and somatic profiling of a familial glioma case series. Neuro Oncol 2019; 20:1625-1633. [PMID: 30165405 DOI: 10.1093/neuonc/noy119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background The genomic characterization of sporadically arising gliomas has delineated molecularly and clinically distinct subclasses of disease. However, less is known about the molecular nature of gliomas that are familial in origin. We performed molecular subtyping of 163 tumor specimens from individuals with a family history of glioma and integrated germline and somatic genomic data to characterize the pathogenesis of 20 tumors in additional detail. Methods Immunohistochemical analyses were performed on formalin-fixed, paraffin-embedded tumor sections to determine molecular subtypes of glioma. For 20 cases, tumor DNA was exome sequenced on an Illumina HiSeq 2000 platform and copy number profiling was performed on the Illumina HumanOmniExpress BeadChip. Genotypes at glioma risk polymorphisms were determined from germline DNA profiled on the Illumina Infinium OncoArray and deleterious germline mutations were identified from germline sequencing data. Results All 3 molecular subtypes of sporadic glioma were represented in the overall case series, including molecular glioblastoma (n = 102), oligodendroglioma (n = 21), and astrocytoma (n = 20). Detailed profiling of 20 of these cases showed characteristic subtype-specific alterations at frequencies comparable to sporadic glioma cases. All 20 cases had alterations in genes regulating telomere length. Frequencies of common glioma risk alleles were similar to those among sporadic cases, and correlations between risk alleles and same-gene somatic mutations were not observed. Conclusions This study illustrates that the molecular characteristics of familial tumors profiled largely recapitulate what is known about sporadic glioma and that both germline and somatic molecular features target common core pathways involved in gliomagenesis. Key Points 1. Familial and sporadic gliomas display highly comparable molecular landscapes. 2. Germline and somatic molecular events target common core pathways involved in gliomagenesis. 3. Carriage of germline glioma risk variants is not associated with somatic events in the same gene.
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Affiliation(s)
- Daniel I Jacobs
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Kazutaka Fukumura
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Matthew N Bainbridge
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California
| | - Georgina N Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Spiridon Tsavachidis
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Gu
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Harsha V Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jianhong Hu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Joy C Jayaseelan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jason T Huse
- Departments of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
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25
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Abstract
The chemical treatment of cancer started with the realization that DNA damaging agents such as mustard gas present notable antitumoural properties. Consequently, early drug development focused on genotoxic chemicals, some of which are still widely used in the clinic. However, the efficacy of such therapies is often limited by the side effects of these drugs on healthy cells. A refinement to this approach is to use compounds that can exploit the presence of DNA damage in cancer cells. Given that replication stress (RS) is a major source of genomic instability in cancer, targeting the RS-response kinase ataxia telangiectasia and Rad3-related protein (ATR) has emerged as a promising alternative. With ATR inhibitors now entering clinical trials, we here revisit the biology behind this strategy and discuss potential biomarkers that could be used for a better selection of patients who respond to therapy.
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Affiliation(s)
- Emilio Lecona
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
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26
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Lang PY, Gershon TR. A New Way to Treat Brain Tumors: Targeting Proteins Coded by Microcephaly Genes?: Brain tumors and microcephaly arise from opposing derangements regulating progenitor growth. Drivers of microcephaly could be attractive brain tumor targets. Bioessays 2018; 40:e1700243. [PMID: 29577351 PMCID: PMC5910257 DOI: 10.1002/bies.201700243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/12/2018] [Indexed: 02/06/2023]
Abstract
New targets for brain tumor therapies may be identified by mutations that cause hereditary microcephaly. Brain growth depends on the repeated proliferation of stem and progenitor cells. Microcephaly syndromes result from mutations that specifically impair the ability of brain progenitor or stem cells to proliferate, by inducing either premature differentiation or apoptosis. Brain tumors that derive from brain progenitor or stem cells may share many of the specific requirements of their cells of origin. These tumors may therefore be susceptible to disruptions of the protein products of genes that are mutated in microcephaly. The potential for the products of microcephaly genes to be therapeutic targets in brain tumors are highlighted hereby reviewing research on EG5, KIF14, ASPM, CDK6, and ATR. Treatments that disrupt these proteins may open new avenues for brain tumor therapy that have increased efficacy and decreased toxicity.
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Affiliation(s)
- Patrick Y. Lang
- Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Neurology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Timothy R. Gershon
- Department of Neurology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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27
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Polverini PJ, D'Silva NJ, Lei YL. Precision Therapy of Head and Neck Squamous Cell Carcinoma. J Dent Res 2018; 97:614-621. [PMID: 29649374 DOI: 10.1177/0022034518769645] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Precision medicine is an approach to disease prevention and treatment that takes into account genetic variability and environmental and lifestyle influences that are unique to each patient. It facilitates stratification of patient populations that vary in their susceptibility to disease and response to therapy. Shared databases and the implementation of new technology systems designed to advance the integration of this information will enable health care providers to more accurately predict and customize prevention and treatment strategies for patients. Although precision medicine has had a limited impact in most areas of medicine, it has been shown to be an increasingly successful approach to cancer therapy. Despite early promising results targeting aberrant signaling pathways or inhibitors designed to block tumor-driven processes such as angiogenesis, limited success emphasizes the need to discover new biomarkers and treatment targets that are more reliable in predicting response to therapy and result in better health outcomes. Recent successes in the use of immunity-inducing antibodies have stimulated increased interest in the use of precision immunotherapy of head and neck squamous cell carcinoma. Using next-generation sequencing, the precise profiling of tumor-infiltrating lymphocytes has great promise to identify hypoimmunogenic cancer that would benefit from a rationally designed combinatorial approach. Continued interrogation of tumors will reveal new actionable targets with increasing therapeutic efficacy and fulfill the promise of precision therapy of head and neck cancer.
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Affiliation(s)
- P J Polverini
- 1 Department of Periodontics and Oral Medicine, Division of Oral Medicine, Pathology, and Radiology, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,2 Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.,3 Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - N J D'Silva
- 1 Department of Periodontics and Oral Medicine, Division of Oral Medicine, Pathology, and Radiology, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,2 Department of Pathology, University of Michigan Health System, Ann Arbor, MI, USA.,3 Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Y L Lei
- 1 Department of Periodontics and Oral Medicine, Division of Oral Medicine, Pathology, and Radiology, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,3 Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,4 Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA
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28
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ATM and ATR play complementary roles in the behavior of excitatory and inhibitory vesicle populations. Proc Natl Acad Sci U S A 2017; 115:E292-E301. [PMID: 29279380 DOI: 10.1073/pnas.1716892115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ATM (ataxia-telangiectasia mutated) and ATR (ATM and Rad3-related) are large PI3 kinases whose human mutations result in complex syndromes that include a compromised DNA damage response (DDR) and prominent nervous system phenotypes. Both proteins are nuclear-localized in keeping with their DDR functions, yet both are also found in cytoplasm, including on neuronal synaptic vesicles. In ATM- or ATR-deficient neurons, spontaneous vesicle release is reduced, but a drop in ATM or ATR level also slows FM4-64 dye uptake. In keeping with this, both proteins bind to AP-2 complex components as well as to clathrin, suggesting roles in endocytosis and vesicle recycling. The two proteins play complementary roles in the DDR; ATM is engaged in the repair of double-strand breaks, while ATR deals mainly with single-strand damage. Unexpectedly, this complementarity extends to these proteins' synaptic function as well. Superresolution microscopy and coimmunoprecipitation reveal that ATM associates exclusively with excitatory (VGLUT1+) vesicles, while ATR associates only with inhibitory (VGAT+) vesicles. The levels of ATM and ATR respond to each other; when ATM is deficient, ATR levels rise, and vice versa. Finally, blocking NMDA, but not GABA, receptors causes ATM levels to rise while ATR levels respond to GABA, but not NMDA, receptor blockade. Taken together, our data suggest that ATM and ATR are part of the cellular "infrastructure" that maintains the excitatory/inhibitory balance of the nervous system. This idea has important implications for the human diseases resulting from their genetic deficiency.
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29
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ATR Mutations Promote the Growth of Melanoma Tumors by Modulating the Immune Microenvironment. Cell Rep 2017; 18:2331-2342. [PMID: 28273450 DOI: 10.1016/j.celrep.2017.02.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/22/2016] [Accepted: 02/13/2017] [Indexed: 12/26/2022] Open
Abstract
Melanomas accumulate a high burden of mutations that could potentially generate neoantigens, yet somehow suppress the immune response to facilitate continued growth. In this study, we identify a subset of human melanomas that have loss-of-function mutations in ATR, a kinase that recognizes and repairs UV-induced DNA damage and is required for cellular proliferation. ATR mutant tumors exhibit both the accumulation of multiple mutations and the altered expression of inflammatory genes, resulting in decreased T cell recruitment and increased recruitment of macrophages known to spur tumor invasion. Taken together, these studies identify a mechanism by which melanoma cells modulate the immune microenvironment to promote continued growth.
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Jeannon JP, Tanaka A, Thavaraj S, Guerrero-Urbano T, McGrath JA, Tavassoli M. ATR gene mutations in HPV negative oropharyngeal cancer. Oral Oncol 2017; 65:121-123. [PMID: 28017652 DOI: 10.1016/j.oraloncology.2016.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Jean-Pierre Jeannon
- Department of Head & Neck Oncology, Guy's & ST Thomas' NHS Foundation Trust, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Akio Tanaka
- Department of Dermatology, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Selvam Thavaraj
- Department of Head & Neck Pathology, Mucosal and Salivary Biology King's College London, SE1 9RT, United Kingdom
| | - Teresa Guerrero-Urbano
- Department of Head & Neck Oncology,Guy's & ST Thomas' NHS Foundation Trust, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London, Guy's Campus, London SE1 9RT, United Kingdom
| | - Mahvash Tavassoli
- Department of Molecular Oncology, King's College London, Guy's Campus, SE1 9RT, United Kingdom.
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31
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Patil V, Pal J, Somasundaram K. Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing. Oncotarget 2016; 6:43452-71. [PMID: 26496030 PMCID: PMC4791243 DOI: 10.18632/oncotarget.6171] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/05/2015] [Indexed: 01/22/2023] Open
Abstract
Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM- EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes- ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.
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Affiliation(s)
- Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Jagriti Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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32
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Johnson CA, Collis SJ. Ciliogenesis and the DNA damage response: a stressful relationship. Cilia 2016; 5:19. [PMID: 27335639 PMCID: PMC4916530 DOI: 10.1186/s13630-016-0040-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/22/2016] [Indexed: 01/27/2023] Open
Abstract
Both inherited and sporadic mutations can give rise to a plethora of human diseases. Through myriad diverse cellular processes, sporadic mutations can arise through a failure to accurately replicate the genetic code or by inaccurate separation of duplicated chromosomes into daughter cells. The human genome has therefore evolved to encode a large number of proteins that work together with regulators of the cell cycle to ensure that it remains error-free. This is collectively known as the DNA damage response (DDR), and genome stability mechanisms involve a complex network of signalling and processing factors that ensure redundancy and adaptability of these systems. The importance of genome stability mechanisms is best illustrated by the dramatic increased risk of cancer in individuals with underlying disruption to genome maintenance mechanisms. Cilia are microtubule-based sensory organelles present on most vertebrate cells, where they facilitate transduction of external signals into the cell. When not embedded within the specialised ciliary membrane, components of the primary cilium's basal body help form the microtubule organising centre that controls cellular trafficking and the mitotic segregation of chromosomes. Ciliopathies are a collection of diseases associated with functional disruption to cilia function through a variety of different mechanisms. Ciliopathy phenotypes can vary widely, and although some cellular overgrowth phenotypes are prevalent in a subset of ciliopathies, an increased risk of cancer is not noted as a clinical feature. However, recent studies have identified surprising genetic and functional links between cilia-associated proteins and genome maintenance factors. The purpose of this mini-review is to therefore highlight some of these discoveries and discuss their implications with regards to functional crosstalk between the DDR and ciliogenesis pathways, and how this may impact on the development of human disease.
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Affiliation(s)
- Colin A. Johnson
- />Section of Ophthalmology and Neurosciences, Wellcome Trust Brenner Building, Leeds Institute of Molecular Medicine, St. James’s University Hospital, Leeds, LS9 7TF UK
| | - Spencer J. Collis
- />Genome Stability Group, Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, Medical School, University of Sheffield, Beech Hill Road, Sheffield, S10 2RX UK
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Abstract
ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely.
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Affiliation(s)
- Gururaj Rao Kidiyoor
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Marco Foiani
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy.
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Ge R, Zhou M, Luo Y, Meng Q, Mai G, Ma D, Wang G, Zhou F. McTwo: a two-step feature selection algorithm based on maximal information coefficient. BMC Bioinformatics 2016; 17:142. [PMID: 27006077 PMCID: PMC4804474 DOI: 10.1186/s12859-016-0990-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/14/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND High-throughput bio-OMIC technologies are producing high-dimension data from bio-samples at an ever increasing rate, whereas the training sample number in a traditional experiment remains small due to various difficulties. This "large p, small n" paradigm in the area of biomedical "big data" may be at least partly solved by feature selection algorithms, which select only features significantly associated with phenotypes. Feature selection is an NP-hard problem. Due to the exponentially increased time requirement for finding the globally optimal solution, all the existing feature selection algorithms employ heuristic rules to find locally optimal solutions, and their solutions achieve different performances on different datasets. RESULTS This work describes a feature selection algorithm based on a recently published correlation measurement, Maximal Information Coefficient (MIC). The proposed algorithm, McTwo, aims to select features associated with phenotypes, independently of each other, and achieving high classification performance of the nearest neighbor algorithm. Based on the comparative study of 17 datasets, McTwo performs about as well as or better than existing algorithms, with significantly reduced numbers of selected features. The features selected by McTwo also appear to have particular biomedical relevance to the phenotypes from the literature. CONCLUSION McTwo selects a feature subset with very good classification performance, as well as a small feature number. So McTwo may represent a complementary feature selection algorithm for the high-dimensional biomedical datasets.
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Affiliation(s)
- Ruiquan Ge
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P.R. China
| | - Manli Zhou
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P.R. China
| | - Youxi Luo
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China
- School of Science, Hubei University of Technology, Wuhan, Hubei, 430068, P.R. China
| | - Qinghan Meng
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, P.R. China
| | - Guoqin Mai
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China
| | - Dongli Ma
- Shenzhen Children's Hospital, Shenzhen, Guangdong, 518026, P.R. China.
| | - Guoqing Wang
- Department of Pathogenobiology, Basic Medical College of Jilin University, Changchun, Jilin, China.
| | - Fengfeng Zhou
- Shenzhen Institutes of Advanced Technology, and Key Lab for Health Informatics, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, Guangdong, 518055, P.R. China.
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Marouf C, Göhler S, Filho MIDS, Hajji O, Hemminki K, Nadifi S, Försti A. Analysis of functional germline variants in APOBEC3 and driver genes on breast cancer risk in Moroccan study population. BMC Cancer 2016; 16:165. [PMID: 26920143 PMCID: PMC4768349 DOI: 10.1186/s12885-016-2210-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/21/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most prevalent cancer in women and a major public health problem in Morocco. Several Moroccan studies have focused on studying this disease, but more are needed, especially at the genetic and molecular levels. Therefore, we investigated the potential association of several functional germline variants in the genes commonly mutated in sporadic breast cancer. METHODS In this case-control study, we examined 36 single nucleotide polymorphisms (SNPs) in 13 genes (APOBEC3A, APOBEC3B, ARID1B, ATR, MAP3K1, MLL2, MLL3, NCOR1, RUNX1, SF3B1, SMAD4, TBX3, TTN), which were located in the core promoter, 5'-and 3'UTR or which were nonsynonymous SNPs to assess their potential association with inherited predisposition to breast cancer development. Additionally, we identified a ~29.5-kb deletion polymorphism between APOBEC3A and APOBEC3B and explored possible associations with BC. A total of 226 Moroccan breast cancer cases and 200 matched healthy controls were included in this study. RESULTS The analysis showed that12 SNPs in 8 driver genes, 4 SNPs in APOBEC3B gene and 1 SNP in APOBEC3A gene were associated with BC risk and/or clinical outcome at P ≤ 0.05 level. RUNX1_rs8130963 (odds ratio (OR) = 2.25; 95 % CI 1.42-3.56; P = 0.0005; dominant model), TBX3_rs8853 (OR = 2.04; 95 % CI 1.38-3.01; P = 0.0003; dominant model), TBX3_rs1061651 (OR= 2.14; 95 % CI1.43-3.18; P = 0.0002; dominant model), TTN_rs12465459 (OR = 2.02; 95 % confidence interval 1.33-3.07; P = 0.0009; dominant model), were the most significantly associated SNPs with BC risk. A strong association with clinical outcome were detected for the genes SMAD4 _rs3819122 with tumor size (OR = 0.45; 95 % CI 0.25-0.82; P = 0.009) and TTN_rs2244492 with estrogen receptor (OR = 0.45; 95 % CI 0.25-0.82; P = 0.009). CONCLUSION Our results suggest that genetic variations in driver and APOBEC3 genes were associated with the risk of BC and may have impact on clinical outcome. However, the reported association between the deletion polymorphism and BC risk was not confirmed in the Moroccan population. These preliminary findings require replication in larger studies.
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Affiliation(s)
- Chaymaa Marouf
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Laboratory of Genetics and Molecular Pathology-Medical School of Casablanca, Casablanca, Morocco. .,University Hassan II Ain Chock, Center Of Doctoral Sciences "In Health Sciences", Casablanca, Morocco.
| | - Stella Göhler
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | | | - Omar Hajji
- Department of Oncology, Littoral Clinic, Casablanca, Morocco.
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
| | - Sellama Nadifi
- Laboratory of Genetics and Molecular Pathology-Medical School of Casablanca, Casablanca, Morocco. .,University Hassan II Ain Chock, Center Of Doctoral Sciences "In Health Sciences", Casablanca, Morocco.
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden.
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Mes SW, Leemans CR, Brakenhoff RH. Applications of molecular diagnostics for personalized treatment of head and neck cancer: state of the art. Expert Rev Mol Diagn 2016; 16:205-21. [PMID: 26620464 DOI: 10.1586/14737159.2016.1126512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Squamous cell carcinomas of the head and neck are the sixth most frequent tumors worldwide. Risk factors are carcinogenic exposure, infection with the human papillomavirus (HPV) and genetic predisposition. Lymph node metastasis in the neck and HPV status are major prognostic factors. There are several important clinical challenges that determine the research agenda in head and neck cancer. The first is more accurate staging, particularly of occult metastatic lymph nodes in the neck. A second challenge is the lack of biomarkers for personalized therapy. There are a number of treatment modalities that can be employed both single and in combination, but at present only site and stage of the tumor are used for treatment planning. Provided here is an overview of the successes and failures of molecular diagnostic approaches that have been and are being evaluated to address these clinical challenges.
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Affiliation(s)
- Steven W Mes
- a Department of Otolaryngology-Head and Neck Surgery , VU University Medical Center , Amsterdam , The Netherlands
| | - C René Leemans
- a Department of Otolaryngology-Head and Neck Surgery , VU University Medical Center , Amsterdam , The Netherlands
| | - Ruud H Brakenhoff
- a Department of Otolaryngology-Head and Neck Surgery , VU University Medical Center , Amsterdam , The Netherlands
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37
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Abstract
DNA is vulnerable to damage resulting from endogenous metabolites, environmental and dietary carcinogens, some anti-inflammatory drugs, and genotoxic cancer therapeutics. Cells respond to DNA damage by activating complex signalling networks that decide cell fate, promoting not only DNA repair and survival but also cell death. The decision between cell survival and death following DNA damage rests on factors that are involved in DNA damage recognition, and DNA repair and damage tolerance, as well as on factors involved in the activation of apoptosis, necrosis, autophagy and senescence. The pathways that dictate cell fate are entwined and have key roles in cancer initiation and progression. Furthermore, they determine the outcome of cancer therapy with genotoxic drugs. Understanding the molecular basis of these pathways is important not only for gaining insight into carcinogenesis, but also in promoting successful cancer therapy. In this Review, we describe key decision-making nodes in the complex interplay between cell survival and death following DNA damage.
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Affiliation(s)
- Wynand P Roos
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
| | - Adam D Thomas
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
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38
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Abstract
ATM and ATR signaling pathways are well conserved throughout evolution and are central to the maintenance of genome integrity. Although the role of both ATM and ATR in DNA repair, cell cycle regulation and apoptosis have been well studied, both still remain in the focus of current research activities owing to their role in cancer. Recent advances in the field suggest that these proteins have an additional function in maintaining cellular homeostasis under both stressed and non-stressed conditions. In this Cell Science at a Glance article and the accompanying poster, we present an overview of recent advances in ATR and ATM research with emphasis on that into the modes of ATM and ATR activation, the different signaling pathways they participate in - including those that do not involve DNA damage - and highlight their relevance in cancer.
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Affiliation(s)
- Poorwa Awasthi
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg 80, Lucknow 226001, India Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR campus, Lucknow 226001, India
| | - Marco Foiani
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus Via Adamello 16, Milan 20139, Italy DSBB-Università degli Studi di Milano, Milan 20133, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg 80, Lucknow 226001, India Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR campus, Lucknow 226001, India
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Rawal RM, Joshi MN, Bhargava P, Shaikh I, Pandit AS, Patel RP, Patel S, Kothari K, Shah M, Saxena A, Bagatharia SB. Tobacco habituated and non-habituated subjects exhibit different mutational spectrums in head and neck squamous cell carcinoma. 3 Biotech 2015; 5:685-696. [PMID: 28324520 PMCID: PMC4569615 DOI: 10.1007/s13205-014-0267-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/15/2014] [Indexed: 12/28/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common non-skin cancer in the world. Tobacco chewing is implicated with most of the cases of HNSCC but this type of cancer is increasing in non-tobacco chewers as well. This study was instigated to provide comprehensive variant and gene-level data in HNSCC subjects of the Indian population and fill the gap in the literature on comparative assessment of gene mutations in cancer subjects with a habit of tobacco and those without any habit using targeted amplicon sequencing. We performed targeted Amplicon sequencing of 409 tumor suppressor genes and oncogenes, frequently mutated across many cancer types, including head and neck. DNA from primary tumor tissues and matched blood was analyzed for HNSCC patients with a habit of tobacco and those without any habit. PDE4DIP, SYNE1, and NOTCH1 emerged as the highly mutated genes in HNSCC. A total of 39 candidate causal variants in 22 unique cancer driver genes were identified in non-habitual (WoH) and habitual (WH) subjects. Comparison of genes from both the subjects, showed seven unique cancer driver genes (KIT, ATM, RNF213, GATA2, DST, RET, CYP2C19) in WoH, while WH showed five (IL7R, PKHD1, MLL3, PTPRD, MAPK8) and 10 genes (SETD2, ATR, CDKN2A, NCOA4, TP53, SYNE1, KAT6B, THBS1, PTPRT, and FGFR3) were common to both subjects. In addition to this NOTCH1, NOTCH2, and NOTCH4 gene were found to be mutated only in habitual subjects. These findings strongly support a causal role for tobacco, acting via PI3K and MAPK pathway inhibition and stimulation of various genes leading to oncogenic transformations in case of tobacco chewers. In case of non-tobacco chewers it appears that mutations in the pathway affecting the squamous epithelial lineage and DNA repair genes lead to HNSCC. Somatic mutation in CYP2C19 gene in the non-habitual subjects suggests that this gene may have a tobacco independent role in development and progression of HNSCC. In addition to sharing high mutation rate, NOTCH gene family was found to be mutated only in habitual sample. Further, presence of mutated genes not earlier reported to be involved in HNSCC, suggest that the Indian sub-continent may have different sets of genes, as compared to other parts of the world, involved in the development and progression of HNSCC.
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Affiliation(s)
- Rakesh M Rawal
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Madhvi N Joshi
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Poonam Bhargava
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Inayat Shaikh
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Aanal S Pandit
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Riddhi P Patel
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Shanaya Patel
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Kiran Kothari
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Manoj Shah
- Gujarat Cancer and Research Institute, Gujarat Cancer Society, Civil Hospital Campus, Asarwa, Ahmedabad, 380 016, Gujarat, India
| | - Akshay Saxena
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India
| | - Snehal B Bagatharia
- Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat, 11th Block, 9th Floor, Udyog Bhavan, Gandhinagar, 382 011, Gujarat, India.
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Bertelsen B, Nazaryan-Petersen L, Sun W, Mehrjouy MM, Xie G, Chen W, Hjermind LE, Taschner PEM, Tümer Z. A germline chromothripsis event stably segregating in 11 individuals through three generations. Genet Med 2015; 18:494-500. [PMID: 26312826 DOI: 10.1038/gim.2015.112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/01/2015] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Parentally transmitted germ-line chromothripsis (G-CTH) has been identified in only a few cases. Most of these rearrangements were stably transmitted, in an unbalanced form, from a healthy mother to her child with congenital abnormalities probably caused by de novo copy-number changes of dosage sensitive genes. We describe a G-CTH transmitted through three generations in 11 healthy carriers. METHODS Conventional cytogenetic analysis, mate-pair sequencing, and polymerase chain reaction (PCR) were used to identify the chromosome rearrangement and characterize the breakpoints in all three generations. RESULTS We identified an apparently balanced translocation t(3;5), later shown to be a G-CTH, in all individuals of a three-generation family. The G-CTH stably segregated without occurrence of additional rearrangements; however, several spontaneous abortions were reported, possibly due to unbalanced transmission. Although seven protein-coding genes are interrupted, no clinical features can be definitively attributed to the affected genes. However, it can be speculated that truncation of one of these genes, encoding ataxia-telangiectasia and Rad3-related protein kinase (ATR), a key component of the DNA damage response, may be related to G-CTH formation. CONCLUSION G-CTH rearrangements are not always associated with abnormal phenotypes and may be misinterpreted as balanced two-way translocations, suggesting that G-CTH is an underdiagnosed phenomenon.Genet Med 18 5, 494-500.
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Affiliation(s)
- Birgitte Bertelsen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Lusine Nazaryan-Petersen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Wei Sun
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Mana M Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Gangcai Xie
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lena E Hjermind
- Neurogenetics Clinic, Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, and Department of Cellular and Molecular Medicine, Section of Neurogenetics, University of Copenhagen, Copenhagen, Denmark
| | - Peter E M Taschner
- Generade Center of Expertise Genomics; University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Zeynep Tümer
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
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Torgovnick A, Schumacher B. DNA repair mechanisms in cancer development and therapy. Front Genet 2015; 6:157. [PMID: 25954303 PMCID: PMC4407582 DOI: 10.3389/fgene.2015.00157] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/07/2015] [Indexed: 01/18/2023] Open
Abstract
DNA damage has been long recognized as causal factor for cancer development. When erroneous DNA repair leads to mutations or chromosomal aberrations affecting oncogenes and tumor suppressor genes, cells undergo malignant transformation resulting in cancerous growth. Genetic defects can predispose to cancer: mutations in distinct DNA repair systems elevate the susceptibility to various cancer types. However, DNA damage not only comprises a root cause for cancer development but also continues to provide an important avenue for chemo- and radiotherapy. Since the beginning of cancer therapy, genotoxic agents that trigger DNA damage checkpoints have been applied to halt the growth and trigger the apoptotic demise of cancer cells. We provide an overview about the involvement of DNA repair systems in cancer prevention and the classes of genotoxins that are commonly used for the treatment of cancer. A better understanding of the roles and interactions of the highly complex DNA repair machineries will lead to important improvements in cancer therapy.
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Affiliation(s)
- Alessandro Torgovnick
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases Research Center, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases Research Center, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
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Abstract
With improved genetic testing and genomic sequencing, abnormalities are increasingly being identified in affected or germline tissues in DNA of patients with vascular tumors, vascular malformations, and lymphedema. Recognition of the genetics of vascular anomalies should help clinicians make more specific diagnoses, anticipate diagnosis-specific morbidities, provide better genetic counseling, and have a better understanding of the pathogenesis of these anomalies. Growing pharmacologic options, including therapies targeted to specific mutations, with obvious parallels to cancer treatment now allow the pediatric hematologist-oncologist to assume a more prominent role in clinical care and research for patients with these diagnoses. We summarize genes and genetic loci that have been associated with vascular anomalies and offer guidelines for patient evaluations.
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Razzouk S. Translational genomics and head and neck cancer: toward precision medicine. Clin Genet 2014; 86:412-21. [PMID: 25143247 DOI: 10.1111/cge.12487] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/12/2014] [Accepted: 08/18/2014] [Indexed: 12/19/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) comprise a wide spectrum of neoplasms with different tumor biologies, prognosis and response to therapies. Current tumor classification and traditional diagnostic methods (e.g. clinical assessment, histopathology) are limited in their capacity to determine prognosis and clinical decision-making. Despite recent improvements in treatment, the outcome for patients with HNSCC remains poor. Similar to most tumors, several patient-related factors, (e.g. genetics and environment) and disease-related factors (e.g. tumor location, TMN staging) play a significant role on survival. Thus, the problem in defining the prognosis is that the clinical course and response to treatment differ considerably among patients. Such interindividual variability is related to the heterogeneity of the tumor, genetic and epigenetic variations, thus reflecting the interaction of multiple biological components that result in a unique phenotype. Integrative genomics are developed to identify the molecular pathways leading to cancer at the individual level and find novel prognostic markers for HNSCC, hence tailoring a treatment accordingly. Such genetic-based personalized diagnosis allows tumor stratification and implementation of targeted therapy. Modern medicine includes new drugs that disrupt the implicated molecules and their signaling pathways. Here, we summarize the current state of knowledge that elucidates the translation of genetic data into clinical benefit.
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Affiliation(s)
- S Razzouk
- Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York City, NY; Private practice, Beirut, Lebanon
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Riaz N, Morris LG, Lee W, Chan TA. Unraveling the molecular genetics of head and neck cancer through genome-wide approaches. Genes Dis 2014; 1:75-86. [PMID: 25642447 PMCID: PMC4310010 DOI: 10.1016/j.gendis.2014.07.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/15/2022] Open
Abstract
The past decade has seen an unprecedented increase in our understanding of the biology and etiology of head and neck squamous cell carcinomas (HNSCC). Genome-wide sequencing projects have identified a number of recurrently mutated genes, including unexpected alterations in the NOTCH pathway and chromatin related genes. Gene-expression profiling has identified 4 distinct genetic subtypes which show some parallels to lung squamous cell carcinoma biology. The identification of the human papilloma virus as one causative agent in a subset of oropharyngeal cancers and their association with a favorable prognosis has opened up avenues for new therapeutic strategies. The expanding knowledge of the underlying molecular abnormalities in this once very poorly understood cancer should allow for increasingly rational clinical trial design and improved patient outcomes.
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Affiliation(s)
- Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Luc G. Morris
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - William Lee
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Timothy A. Chan
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Human Oncology and Pathogenesis, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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46
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Genetic Susceptibility to Head and Neck Squamous Cell Carcinoma. Int J Radiat Oncol Biol Phys 2014; 89:38-48. [DOI: 10.1016/j.ijrobp.2013.09.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/16/2013] [Accepted: 09/17/2013] [Indexed: 01/28/2023]
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47
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Genetic screens in mice for genome integrity maintenance and cancer predisposition. Curr Opin Genet Dev 2013; 24:1-7. [PMID: 24657530 DOI: 10.1016/j.gde.2013.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/16/2013] [Accepted: 10/19/2013] [Indexed: 12/26/2022]
Abstract
Genome instability is a feature of nearly all cancers and can be exploited for therapy. In addition, a growing number of genome maintenance genes have been associated with developmental disorders. Efforts to understand the role of genome instability in these processes will be greatly facilitated by a more comprehensive understanding of their genetic network. We highlight recent genetic screens in model organisms that have assisted in the discovery of novel regulators of genome stability and focus on the contribution of mice as a model organism to understanding the role of genome instability during embryonic development, tumour formation and cancer therapy.
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Sproul CD, Rao S, Ibrahim JG, Kaufmann WK, Cordeiro-Stone M. Is activation of the intra-S checkpoint in human fibroblasts an important factor in protection against UV-induced mutagenesis? Cell Cycle 2013; 12:3555-63. [PMID: 24091629 DOI: 10.4161/cc.26590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The ATR/CHK1-dependent intra-S checkpoint inhibits replicon initiation and replication fork progression in response to DNA damage caused by UV (UV) radiation. It has been proposed that this signaling cascade protects against UV-induced mutations by reducing the probability that damaged DNA will be replicated before it can be repaired. Normal human fibroblasts (NHF) were depleted of ATR or CHK1, or treated with the CHK1 kinase inhibitor TCS2312, and the UV-induced mutation frequency at the HPRT locus was measured. Despite clear evidence of S-phase checkpoint abrogation, neither ATR/CHK1 depletion nor CHK1 inhibition caused an increase in the UV-induced HPRT mutation frequency. These results question the premise that the UV-induced intra-S checkpoint plays a prominent role in protecting against UV-induced mutagenesis.
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Affiliation(s)
- Christopher D Sproul
- Curriculum in Toxicology; University of North Carolina-Chapel Hill; Chapel Hill, NC USA
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New findings in genodermatoses. Dermatol Clin 2013; 31:303-15. [PMID: 23557657 DOI: 10.1016/j.det.2012.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New technologies are accelerating the pace at which genetic defects leading to inherited skin disease are elucidated. Translation of these genetic discoveries into new therapies for patients with inherited skin diseases has not been as rapid but the pace is now accelerating. This article summarizes recent findings in genetic skin diseases, the scope of advances being made, the role of new DNA analysis technologies in these discoveries, as well as highlighting some examples of how an understanding of the genetic cause of inherited skin diseases can lead to therapeutic interventions for patients.
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Mokrani-Benhelli H, Gaillard L, Biasutto P, Le Guen T, Touzot F, Vasquez N, Komatsu J, Conseiller E, Pïcard C, Gluckman E, Francannet C, Fischer A, Durandy A, Soulier J, de Villartay JP, Cavazzana-Calvo M, Revy P. Primary microcephaly, impaired DNA replication, and genomic instability caused by compound heterozygous ATR mutations. Hum Mutat 2012; 34:374-84. [PMID: 23111928 DOI: 10.1002/humu.22245] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 10/22/2012] [Indexed: 11/10/2022]
Abstract
Ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) kinases are two key regulators of DNA-damage responses (DDR) that are mainly activated in response to DNA double-strand breaks and single-stranded DNA damages, respectively. Seckel syndrome, a rare genetic disorder characterized by a microcephaly and a markedly reduced body size, has been associated with defective ATR-dependent DNA damage signaling. However, the only human genetic ATR defect reported so far is a hypomorphic splicing mutation identified in five related individuals with Seckel syndrome. Here, we report the first case of primary microcephaly with compound heterozygous mutations in ATR: a 540 kb genomic deletion on one allele and a missense mutation leading to splice dysregulation on the other, which ultimately lead to a sharp decrease in ATR expression. DNA combing technology revealed a profound spontaneous alteration of several DNA replication parameters in patient's cells and FISH analyses highlighted the genomic instability caused by ATR deficiency. Collectively, our results emphasize the crucial role for ATR in the control of DNA replication, and reinforce the complementary and nonredundant contributions of ATM and ATR in human cells to face DNA damages and warrant genome integrity.
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