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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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2
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Holic L. Common skin cancers and their association with other non-cutaneous primary malignancies: a review of the literature. Med Oncol 2024; 41:157. [PMID: 38758457 DOI: 10.1007/s12032-024-02385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024]
Abstract
It has long been recognized that a history of skin cancer puts one at risk for additional primary skin cancers. However, more variable data exists for the risk of developing a non-cutaneous primary cancer following a diagnosis of skin cancer. The data are most variable for Basal Cell Carcinoma (BCC), the most common and least aggressive type of skin cancer. While early studies imply that BCC does not impart a larger risk of other primary non-cutaneous cancers, more recent studies with larger populations suggest otherwise. The cancers most significantly associated with BCC are lip, oropharyngeal, and salivary gland cancer. There is also burgeoning evidence to suggest a link between BCC and prostate, breast, and colorectal cancer, but more data are needed to draw a concrete conclusion. Squamous Cell Carcinoma (SCC), the second most common type of skin cancer, has a slightly more defined risk to other non-cutaneous primary malignancies. There is a notable link between SCC and non-Hodgkin's lymphoma (NHL), possibly due to immunosuppression. There is also an increased risk of other cancers derived from squamous epithelium following SCC, including oropharyngeal, lip, and salivary gland cancer. Some studies also suggest an increased risk of respiratory tract cancer following SCC, possibly due to shared risk factors. Melanoma, a more severe type of skin cancer, shows a well-defined risk of additional primary non-cutaneous malignancies. The most significant of these risks include NHL, thyroid cancer, prostate cancer, and breast cancer along with a host of other cancers. Each of these three main skin cancer types has a profile of genetic mutations that have also been linked to non-cutaneous malignancies. In this review, we discuss a selection of these genes to highlight the complex interplay between different tumorigenesis processes.
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Affiliation(s)
- Lindsay Holic
- Chicago Medical School at Rosalind Franklin University, North Chicago, IL, USA.
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3
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Woerner J, Sriram V, Nam Y, Verma A, Kim D. Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network. Bioinformatics 2024; 40:btae126. [PMID: 38527901 PMCID: PMC10963079 DOI: 10.1093/bioinformatics/btae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/17/2024] [Indexed: 03/27/2024] Open
Abstract
MOTIVATION Many diseases, particularly cardiometabolic disorders, exhibit complex multimorbidities with one another. An intuitive way to model the connections between phenotypes is with a disease-disease network (DDN), where nodes represent diseases and edges represent associations, such as shared single-nucleotide polymorphisms (SNPs), between pairs of diseases. To gain further genetic understanding of molecular contributors to disease associations, we propose a novel version of the shared-SNP DDN (ssDDN), denoted as ssDDN+, which includes connections between diseases derived from genetic correlations with intermediate endophenotypes. We hypothesize that a ssDDN+ can provide complementary information to the disease connections in a ssDDN, yielding insight into the role of clinical laboratory measurements in disease interactions. RESULTS Using PheWAS summary statistics from the UK Biobank, we constructed a ssDDN+ revealing hundreds of genetic correlations between diseases and quantitative traits. Our augmented network uncovers genetic associations across different disease categories, connects relevant cardiometabolic diseases, and highlights specific biomarkers that are associated with cross-phenotype associations. Out of the 31 clinical measurements under consideration, HDL-C connects the greatest number of diseases and is strongly associated with both type 2 diabetes and heart failure. Triglycerides, another blood lipid with known genetic causes in non-mendelian diseases, also adds a substantial number of edges to the ssDDN. This work demonstrates how association with clinical biomarkers can better explain the shared genetics between cardiometabolic disorders. Our study can facilitate future network-based investigations of cross-phenotype associations involving pleiotropy and genetic heterogeneity, potentially uncovering sources of missing heritability in multimorbidities. AVAILABILITY AND IMPLEMENTATION The generated ssDDN+ can be explored at https://hdpm.biomedinfolab.com/ddn/biomarkerDDN.
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Affiliation(s)
- Jakob Woerner
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Vivek Sriram
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Anurag Verma
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States
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Pellegrini C, Cardelli L, Ghiorzo P, Pastorino L, Potrony M, García-Casado Z, Elefanti L, Stefanaki I, Mastrangelo M, Necozione S, Aguilera P, Rodríguez-Hernández A, Di Nardo L, Rocco T, Del Regno L, Badenas C, Carrera C, Malvehy J, Requena C, Bañuls J, Stratigos AJ, Peris K, Menin C, Calista D, Nagore E, Puig S, Landi MT, Fargnoli MC. High- and intermediate-risk susceptibility variants in melanoma families from the Mediterranean area: A multicentre cohort from the MelaNostrum Consortium. J Eur Acad Dermatol Venereol 2023; 37:2498-2508. [PMID: 37611275 PMCID: PMC10842987 DOI: 10.1111/jdv.19461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Most of large epidemiological studies on melanoma susceptibility have been conducted on fair skinned individuals (US, Australia and Northern Europe), while Southern European populations, characterized by high UV exposure and dark-skinned individuals, are underrepresented. OBJECTIVES We report a comprehensive pooled analysis of established high- and intermediate-penetrance genetic variants and clinical characteristics of Mediterranean melanoma families from the MelaNostrum Consortium. METHODS Pooled epidemiological, clinical and genetic (CDKN2A, CDK4, ACD, BAP1, POT1, TERT, and TERF2IP and MC1R genes) retrospective data of melanoma families, collected within the MelaNostrum Consortium in Greece, Italy and Spain, were analysed. Univariate methods and multivariate logistic regression models were used to evaluate the association of variants with characteristics of families and of affected and unaffected family members. Subgroup analysis was performed for each country. RESULTS We included 839 families (1365 affected members and 2123 unaffected individuals). Pathogenic/likely pathogenic CDKN2A variants were identified in 13.8% of families. The strongest predictors of melanoma were ≥2 multiple primary melanoma cases (OR 8.1; 95% CI 3.3-19.7), >3 affected members (OR 2.6; 95% CI 1.3-5.2) and occurrence of pancreatic cancer (OR 4.8; 95% CI 2.4-9.4) in the family (AUC 0.76, 95% CI 0.71-0.82). We observed low frequency variants in POT1 (3.8%), TERF2IP (2.5%), ACD (0.8%) and BAP1 (0.3%). MC1R common variants (≥2 variants and ≥2 RHC variants) were associated with melanoma risk (OR 1.4; 95% CI 1.0-2.0 and OR 4.3; 95% CI 1.2-14.6, respectively). CONCLUSIONS Variants in known high-penetrance genes explain nearly 20% of melanoma familial aggregation in Mediterranean areas. CDKN2A melanoma predictors were identified with potential clinical relevance for cancer risk assessment.
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Affiliation(s)
- C Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - L Cardelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - P Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetica dei Tumori rari, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - L Pastorino
- IRCCS Ospedale Policlinico San Martino, Genetica dei Tumori rari, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - M Potrony
- Department of Biochemistry and Molecular Genetics, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Z García-Casado
- Laboratory of Molecular Biology, Instituto Valenciano de Oncología, València, Spain
| | - L Elefanti
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - I Stefanaki
- 1st Department of Dermatology-Venereology, Andreas Sygros Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - M Mastrangelo
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - S Necozione
- Epidemiology Unit, Department of Life, Health and Environmental Science, University of L'Aquila, L'Aquila, Italy
| | - P Aguilera
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | | | - L Di Nardo
- UOC Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - T Rocco
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Dermatology Unit, Ospedale San Salvatore, L'Aquila, Italy
| | - L Del Regno
- UOC Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - C Badenas
- Department of Biochemistry and Molecular Genetics, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - C Carrera
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - J Malvehy
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - C Requena
- Department of Dermatology, Instituto Valenciano de Oncología, València, Spain
| | - J Bañuls
- Department of Dermatology, Hospital General Universitario de Alicante, Alicante, Spain
| | - A J Stratigos
- 1st Department of Dermatology-Venereology, Andreas Sygros Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - K Peris
- UOC Dermatologia, Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
- Dermatologia, Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - C Menin
- Immunology and Diagnostic Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - D Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - E Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, València, Spain
| | - S Puig
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Biomedical Research Networking Center on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Department of Dermatology, Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - M T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - M C Fargnoli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
- Dermatology Unit, Ospedale San Salvatore, L'Aquila, Italy
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Woerner J, Sriram V, Nam Y, Verma A, Kim D. Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.11.23289852. [PMID: 37293013 PMCID: PMC10246076 DOI: 10.1101/2023.05.11.23289852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many diseases exhibit complex multimorbidities with one another. An intuitive way to model the connections between phenotypes is with a disease-disease network (DDN), where nodes represent diseases and edges represent associations, such as shared single-nucleotide polymorphisms (SNPs), between pairs of diseases. To gain further genetic understanding of molecular contributors to disease associations, we propose a novel version of the shared-SNP DDN (ssDDN), denoted as ssDDN+, which includes connections between diseases derived from genetic correlations with endophenotypes. We hypothesize that a ssDDN+ can provide complementary information to the disease connections in a ssDDN, yielding insight into the role of clinical laboratory measurements in disease interactions. Using PheWAS summary statistics from the UK Biobank, we constructed a ssDDN+ revealing hundreds of genetic correlations between disease phenotypes and quantitative traits. Our augmented network uncovers genetic associations across different disease categories, connects relevant cardiometabolic diseases, and highlights specific biomarkers that are associated with cross-phenotype associations. Out of the 31 clinical measurements under consideration, HDL-C connects the greatest number of diseases and is strongly associated with both type 2 diabetes and diabetic retinopathy. Triglycerides, another blood lipid with known genetics causes in non-mendelian diseases, also adds a substantial number of edges to the ssDDN. Our study can facilitate future network-based investigations of cross-phenotype associations involving pleiotropy and genetic heterogeneity, potentially uncovering sources of missing heritability in multimorbidities.
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Affiliation(s)
- Jakob Woerner
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Vivek Sriram
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Mensi C, Stella S, Dallari B, Rugarli S, Pesatori AC, Ceresoli GL, Consonni D. Second Primary Cancers in a Population-Based Mesothelioma Registry. Cancers (Basel) 2023; 15:cancers15061746. [PMID: 36980631 PMCID: PMC10046097 DOI: 10.3390/cancers15061746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Background: The presence of a second primary cancer (SPC) in patients with pleural mesothelioma (PM) may impact overall survival and suggest a common mechanism of carcinogenesis or an underlying germline genetic alteration. Methods: We evaluated the occurrence of SPCs within PM cases collected from 2000 to 2018 by the Lombardy Mesothelioma Registry and their prognostic implications. Kaplan–Meier analysis was performed to estimate median survival times, together with univariate and multivariate Cox regression models to estimate hazard ratios (HR) and 95% confidence intervals (CI) of death. Results: The median overall survival (OS) of the entire study population (N = 6646) was 10.9 months (95% CI: 10.4–11.2); patient age and histotype were the strongest prognostic factors. No substantial survival difference was observed by the presence of an SPC (10.5 months in 1000 patients with an SPC vs. 10.9 months in 5646 patients in the non-SPC group, HR 1.03, p = 0.40). Shorter OS in the SPC group was only observed in 150 patients with the non-epithelioid subtype (median OS of 5.4 vs. 7.1 months, HR 1.21, p = 0.03). Conclusions: The diagnosis of an SPC did not influence the outcome of PM patients in the overall study population but was associated with shorter OS in non-epithelioid cases. Further studies are needed to clarify the role of SPCs as markers of genetic susceptibility in mesothelioma.
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Affiliation(s)
- Carolina Mensi
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Correspondence: ; Tel.: +39-02-55032595
| | - Simona Stella
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Barbara Dallari
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Sabrina Rugarli
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Angela Cecilia Pesatori
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Clinical and Community Science, Università degli Studi di Milano, 20122 Milan, Italy
| | | | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
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Schanknecht E, Bachari A, Nassar N, Piva T, Mantri N. Phytochemical Constituents and Derivatives of Cannabis sativa; Bridging the Gap in Melanoma Treatment. Int J Mol Sci 2023; 24:ijms24010859. [PMID: 36614303 PMCID: PMC9820847 DOI: 10.3390/ijms24010859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Melanoma is deadly, physically impairing, and has ongoing treatment deficiencies. Current treatment regimens include surgery, targeted kinase inhibitors, immunotherapy, and combined approaches. Each of these treatments face pitfalls, with diminutive five-year survival in patients with advanced metastatic invasion of lymph and secondary organ tissues. Polyphenolic compounds, including cannabinoids, terpenoids, and flavonoids; both natural and synthetic, have emerging evidence of nutraceutical, cosmetic and pharmacological potential, including specific anti-cancer, anti-inflammatory, and palliative utility. Cannabis sativa is a wellspring of medicinal compounds whose direct and adjunctive application may offer considerable relief for melanoma suffers worldwide. This review aims to address the diverse applications of C. sativa's biocompounds in the scope of melanoma and suggest it as a strong candidate for ongoing pharmacological evaluation.
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Affiliation(s)
- Ellen Schanknecht
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Ava Bachari
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia
| | - Nazim Nassar
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Terrence Piva
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Bundoora, VIC 3083, Australia
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- Correspondence:
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8
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Yu Y, Chang K, Chen JS, Bohlender RJ, Fowler J, Zhang D, Huang M, Chang P, Li Y, Wong J, Wang H, Gu J, Wu X, Schildkraut J, Cannon-Albright L, Ye Y, Zhao H, Hildebrandt MA, Permuth JB, Li D, Scheet P, Huff CD. A whole-exome case-control association study to characterize the contribution of rare coding variation to pancreatic cancer risk. HGG ADVANCES 2022; 3:100078. [PMID: 35047863 PMCID: PMC8756505 DOI: 10.1016/j.xhgg.2021.100078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/08/2021] [Indexed: 10/26/2022] Open
Abstract
Pancreatic cancer is a deadly disease that accounts for approximately 5% of cancer deaths worldwide, with a dismal 5-year survival rate of 10%. Known genetic risk factors explain only a modest proportion of the heritable risk of pancreatic cancer. We conducted a whole-exome case-control sequencing study in 1,591 pancreatic cancer cases and 2,134 cancer-free controls of European ancestry. In our gene-based analysis, ATM ranked first, with a genome-wide significant p value of 1 × 10-8. The odds ratio for protein-truncating variants in ATM was 24, which is substantially higher than prior estimates, although ours includes a broad 95% confidence interval (4.0-1000). SIK3 was the second highest ranking gene (p = 3.84 × 10-6, false discovery rate or FDR = 0.032). We observed nominally significant association signals in several genes of a priori interest, including BRCA2 (p = 4.3 × 10-4), STK11 (p = 0.003), PALB2 (p = 0.019), and TP53 (p = 0.037), and reported risk estimates for known pathogenic variants and variants of uncertain significance (VUS) in these genes. The rare variants in established susceptibility genes explain approximately 24% of log familial relative risk, which is comparable to the contribution from established common susceptibility variants (17%). In conclusion, this study provides new insights into the genetic susceptibility of pancreatic cancer, refining rare variant risk estimates in known pancreatic cancer susceptibility genes and identifying SIK3 as a novel candidate susceptibility gene. This study highlights the prominent importance of ATM truncating variants and the underappreciated role of VUS in pancreatic cancer etiology.
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Affiliation(s)
- Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle Chang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan J. Bohlender
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jerry Fowler
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Di Zhang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maosheng Huang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ping Chang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanan Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin Wong
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huamin Wang
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Center for Clinical Big Data and Analytics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, PR China
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lisa Cannon-Albright
- Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Yuanqing Ye
- Center for Clinical Big Data and Analytics, Bioinformatics and Big Data, The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, PR China
| | - Hua Zhao
- Department of Family Medicine and Population Health, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Jennifer B. Permuth
- Departments of Cancer Epidemiology and Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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9
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Huo J, Wang Y, Zhang Y, Wang W, Yang P, Zhao W, Zhang M, Cui L, Zhang D. The LncRNA MIR155HG is Upregulated by SP1 in Melanoma Cells and Drives Melanoma Progression via Modulating the MiR-485-3p/PSIP1 Axis. Anticancer Agents Med Chem 2022; 22:152-159. [PMID: 34225636 DOI: 10.2174/1871520621666210322092906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/03/2021] [Accepted: 01/18/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND MIR155HG is a long non-coding RNA (lncRNA) that has been shown to be dysregulated in a range of tumor types, but the functions of this lncRNA in melanoma remain to be explored. OBJECTIVES We explored the functions of lncRNA MIR155HG in melanoma progression. METHODS The expression of miR155HG was analyzed in clinical melanoma. Bioinformatics analysis was performed to assess the potential tumor-related functions of miR155HG. The interaction of miR155HG and SP1 and the inhibition of PSIP1 by miR-485-3p were analyzed by ChIP, luciferase reporter experiments, and the biological effects in melanoma were explored by colony formation assays, EdU cell proliferation assays, Transwell analysis, and intracranial melanoma mouse model. RESULTS Herein, we found that MIR155HG was markedly upregulated in melanoma cell lines and tissues. We further determined that the SP1 transcription factor was responsible for driving MIR155HG upregulation in melanoma. Elevated MIR155HG levels were linked to decreased overall survival (OS) in melanoma patients, and we further determined that MIR155HG expression was an independent predictor of melanoma patient prognosis. When MIR155HG was knocked down in melanoma cells, this impaired their proliferative, migratory, and invasive activity. By using predictive bioinformatics analyses, we identified miR-485-3p as a microRNA (miRNA) capable of binding to both MIR155HG and the 3' UTR of PSIP1. CONCLUSION Together, these results suggest that MIR155HG is capable of promoting melanoma cell proliferation via the miR-485-3p/PSIP1 axis. These novel findings provide new insights into the development of melanoma, potentially highlighting future avenues for therapeutic intervention.
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Affiliation(s)
- Jia Huo
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Yuan Wang
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Yanfei Zhang
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Wei Wang
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Peiwen Yang
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Wenwei Zhao
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Miaomiao Zhang
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Lu Cui
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
| | - Dingwei Zhang
- Department of Dermatology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, China
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10
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Feng Q, Nickels E, Muskens IS, de Smith AJ, Gauderman WJ, Yee AC, Ricker C, Mack T, Leavitt AD, Godley LA, Wiemels JL. Increased burden of familial-associated early-onset cancer risk among minority Americans compared to non-Latino Whites. eLife 2021; 10:e64793. [PMID: 34155975 PMCID: PMC8219377 DOI: 10.7554/elife.64793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/04/2021] [Indexed: 01/11/2023] Open
Abstract
Background The role of race/ethnicity in genetic predisposition of early-onset cancers can be estimated by comparing family-based cancer concordance rates among ethnic groups. Methods We used linked California health registries to evaluate the relative cancer risks for first-degree relatives of patients diagnosed between ages 0 and 26, and the relative risks of developing distinct second primary malignancies (SPMs). From 1989 to 2015, we identified 29,631 cancer patients and 62,863 healthy family members. We calculated the standardized incident ratios (SIRs) of early-onset primary cancers diagnosed in proband siblings and mothers, as well as SPMs detected among early-onset patients. Analyses were stratified by self-identified race/ethnicity. Results Given probands with cancer, there were increased relative risks of any cancer for siblings and mothers (SIR = 3.32; 95% confidence interval [CI]: 2.85-3.85) and of SPMs (SIR = 7.27; 95% CI: 6.56-8.03). Given a proband with solid cancer, both Latinos (SIR = 4.98; 95% CI: 3.82-6.39) and non-Latino Blacks (SIR = 7.35; 95% CI: 3.36-13.95) exhibited significantly higher relative risk of any cancer in siblings and mothers when compared to non-Latino White subjects (SIR = 3.02; 95% CI: 2.12-4.16). For hematologic cancers, higher familial risk was evident for Asian/Pacific Islanders (SIR = 7.56; 95% CI: 3.26-14.90) compared to non-Latino whites (SIR = 2.69; 95% CI: 1.62-4.20). Conclusions The data support a need for increased attention to the genetics of early-onset cancer predisposition and environmental factors in race/ethnic minority families in the United States. Funding This work was supported by the V Foundation for funding this work (Grant FP067172).
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Affiliation(s)
- Qianxi Feng
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Eric Nickels
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
- Children's Hospital Los AngelesLos AngelesUnited States
| | - Ivo S Muskens
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Adam J de Smith
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - W James Gauderman
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Amy C Yee
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Charite Ricker
- Norris Comprehensive Cancer Center, USC Keck School of MedicineLos AngelesUnited States
| | - Thomas Mack
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
| | - Andrew D Leavitt
- Departments of Medicine and Laboratory Medicine, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy A Godley
- Departments of Medicine and Human Genetics, The University of ChicagoChicagoUnited States
| | - Joseph L Wiemels
- Department of Preventive Medicine, USC Keck School of MedicineLos AngelesUnited States
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11
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Abstract
Malignant melanoma is a neoplasm originating in the melanocytes in the skin. Although malignant melanoma is the third most common cutaneous cancer, it is recognized as the main cause of skin cancer-related mortality, and its incidence is rising. The natural history of malignant melanoma involves an inconsistent and insidious skin cancer with great metastatic potential. Increased ultra-violet (UV) skin exposure is undoubtedly the greatest risk factor for developing cutaneous melanoma; however, a plethora of risk factors are now recognized as causative. Moreover, modern oncology now considers melanoma proliferation a complex, multifactorial process with a combination of genetic, epigenetic, and environmental factors all known to be contributory to tumorgenesis. Herein, we wish to outline the epidemiological, molecular, and biological processes responsible for driving malignant melanoma proliferation.
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Affiliation(s)
| | - Nicola Miller
- Surgery, National University of Ireland Galway, Galway, IRL
| | - Niall M McInerney
- Plastic, Aesthetic, and Reconstructive Surgery, Galway University Hospitals, Galway, IRL
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12
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Ulanja MB, Beutler BD, Antwi-Amoabeng D, Cohen PR, Moody AE, Rahman GA, Djankpa FT, Gullapalli N, Boampong-Konam K, Macaire JK, Bowman AT, Baral S, Bowles DW. Second primary malignancies in patients with melanoma in situ: Insights from the surveillance, epidemiology, and end results program. Cancer Epidemiol 2021; 72:101932. [PMID: 33773145 DOI: 10.1016/j.canep.2021.101932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/28/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Melanoma in situ (MIS) is among the most frequently diagnosed cancers in the United States. Emerging data suggest that MIS is associated with an increased risk of developing a second primary malignancy (SPM). OBJECTIVES To determine trends in MIS-associated SPMs and identify MIS-specific features that increase SPM risk. METHODS In this retrospective population-based study, we identified 90,075 patients who were diagnosed with MIS between 1973 and 2015 from the Surveillance, Epidemiology, and End Results database. The risk of developing an SPM among these individuals was compared to individuals without a diagnosis of MIS. The risk of developing an SPM among patients with a diagnosis of MIS was also increased over time. RESULTS Patients with a diagnosis of MIS had an increased relative risk (RR) of developing an SPM as compared to the general population with an identical age, sex, race, and follow-up period. The RR of a metachronous malignancy in MIS patients also increased over time, as follows: 1.16 (95 % CI: 1.07-1.26), 1.19 (95 % CI: 1.14-1.23), 1.30 (95 % CI: 1.27-1.33), and 1.52 (95 % CI: 1.49-1.56) in 1973-1982, 1983-1992, 1993-2002, and 2003-2015, respectively (P < 0.05). In addition, there was a direct correlation between the number of MIS lesions and SPM risk; ≥1, ≥2, and ≥3 tumors portended a 1.5-2, 2-3, and 4-5-fold increased risk of developing an SPM, respectively. CONCLUSIONS MIS is associated with an increased risk of developing an SPM and therefore individuals with a history of MIS may benefit from close medical surveillance.
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Affiliation(s)
- Mark B Ulanja
- University of Nevada, Reno School of Medicine, Department of Internal Medicine, Reno, NV, USA
| | - Bryce D Beutler
- University of Southern California, Keck School of Medicine, Department of Radiology, Los Angeles, CA, USA.
| | - Daniel Antwi-Amoabeng
- University of Nevada, Reno School of Medicine, Department of Internal Medicine, Reno, NV, USA
| | - Philip R Cohen
- Touro University California College of Osteopathic Medicine, Department of Dermatology, Vallejo, CA, USA; San Diego Family Dermatology, National City, CA, USA
| | - Alastair E Moody
- University of Utah School of Medicine, Department of Anesthesiology, Salt Lake City, UT, USA
| | - Ganiyu A Rahman
- Department of Surgery, University of Cape Coast, School of Medical Sciences, Cape Coast, Ghana
| | - Francis T Djankpa
- Department of Physiology, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Ghana
| | - Nageshwara Gullapalli
- University of Nevada, Reno School of Medicine, Department of Internal Medicine, Reno, NV, USA
| | | | - Jessica K Macaire
- Department of Surgery, University of Cape Coast, School of Medical Sciences, Cape Coast, Ghana
| | | | - Stefan Baral
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Daniel W Bowles
- University of Colorado School of Medicine, Department of Medical Oncology, Aurora, CO, USA; Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, USA
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13
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Yu H, Hemminki K. Genetic epidemiology of colorectal cancer and associated cancers. Mutagenesis 2021; 35:207-219. [PMID: 31424514 DOI: 10.1093/mutage/gez022] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
We review here data on familial risk in colorectal cancer (CRC) generated from the Swedish Family-Cancer Database, the largest resource of its kind in the world. Although the concordant familial risk for CRC (i.e. CRC risk in families of CRC patients) has been reasonably well established, the studies on discordant familial risks (i.e. CRC risk in families with any other cancers) are rare. Because different cancers could be caused by shared genetic susceptibility or shared environment, data of associations of discordant cancers may provide useful information for identifying common risk factors. In analyses between any of 33 discordant cancers relative risks (RRs) for discordant cancers were estimated in families with increasing numbers of probands with CRC; in the reverse analyses, RRs for CRC were estimated in families with increasing numbers of probands with discordant cancers. In separate analyses, hereditary non-polyposis colorectal cancer (HNPCC) families were excluded from the study, based on HNPCC related double primary cancers, to assess the residual familial RRs. We further reviewed familial risks of colon and rectal cancers separately in search for distinct discordant associations. The reviewed data suggested that colon cancer was associated with a higher familial risk for CRC compared to rectal cancer. The previous data had reported associations of CRC with melanoma, thyroid and eye cancers. Nervous system cancer was only associated with colon cancer, and lung cancer only associated with rectal cancer. The reviewed data on discordant association may provide guidance to gene identification and may help genetic counseling.
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Affiliation(s)
- Hongyao Yu
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany.,Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, Department of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
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14
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Informing patients about their mutation tests: CDKN2A c.256G>A in melanoma as an example. Hered Cancer Clin Pract 2020; 18:15. [PMID: 32760473 PMCID: PMC7393828 DOI: 10.1186/s13053-020-00146-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022] Open
Abstract
Background When germline mutations are suspected as causal in cancer, patient DNA may be sequenced to detect variants in relevant genes. If a particular mutation has not been reported in reliable family studies, genetic counselors are facing a dilemma of appropriately informing patients. Many sequencing facilities provide an interpretation of the findings based on the available sequence databases or on prediction tools that are curated from bioinformatics and mechanistic datasets. The counseling dilemma is exacerbated if the pedigree data are not informative but the in silico predictions suggest pathogenicity. Methods We present here a real world example of the c.256G > A CDKN2A variant, which was detected in one melanoma patient where two siblings were diagnosed with melanoma in situ. We investigated a detailed family history of the affected siblings in order to survey probability of the cancer risks within the context to this mutation. Results This c.256G > A CDKN2A variant was detected in one of the brothers and in the melanoma-free mother while the other brother in the family tested negative. The variant had been previously described in one patient from a melanoma family. In the family under investigation, the mother’s 16 first-and second-degree relatives had survived past the median onset age for melanoma and none presented melanoma. We tested the variant using multiple bioinformatic tools that all predicted deleteriousness of the variant. The genetic counseling report to the melanoma patient stated that the CDKN2A variant was ‘likely pathogenic’ and the disease was defined as ‘likely hereditary melanoma’. Conclusions The pedigree data showed at the most a low penetrance variant, which, if taken into consideration, might have altered the provided diagnosis. When dealing with ‘practically’ unknown variants the counselors would be advised to incorporate a detailed family history rather than basing predictions on functionality provided by sequencing facilities.
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15
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Pertesi M, Went M, Hansson M, Hemminki K, Houlston RS, Nilsson B. Genetic predisposition for multiple myeloma. Leukemia 2020; 34:697-708. [PMID: 31913320 DOI: 10.1038/s41375-019-0703-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/24/2019] [Indexed: 12/14/2022]
Abstract
Multiple myeloma (MM) is the second most common blood malignancy. Epidemiological family studies going back to the 1920s have provided evidence for familial aggregation, suggesting a subset of cases have an inherited genetic background. Recently, studies aimed at explaining this phenomenon have begun to provide direct evidence for genetic predisposition to MM. Genome-wide association studies have identified common risk alleles at 24 independent loci. Sequencing studies of familial cases and kindreds have begun to identify promising candidate genes where variants with strong effects on MM risk might reside. Finally, functional studies are starting to give insight into how identified risk alleles promote the development of MM. Here, we review recent findings in MM predisposition field, and highlight open questions and future directions.
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Affiliation(s)
- Maroulio Pertesi
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Kari Hemminki
- Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld, Heidelberg, Germany.,Faculty of Medicine and Biomedical Center, Charles University in Prague, 30605, Pilsen, Czech Republic
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden. .,Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.
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16
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Lakiotaki K, Georgakopoulos G, Castanas E, Røe OD, Borboudakis G, Tsamardinos I. A data driven approach reveals disease similarity on a molecular level. NPJ Syst Biol Appl 2019; 5:39. [PMID: 31666984 PMCID: PMC6814739 DOI: 10.1038/s41540-019-0117-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/26/2019] [Indexed: 02/06/2023] Open
Abstract
Could there be unexpected similarities between different studies, diseases, or treatments, on a molecular level due to common biological mechanisms involved? To answer this question, we develop a method for computing similarities between empirical, statistical distributions of high-dimensional, low-sample datasets, and apply it on hundreds of -omics studies. The similarities lead to dataset-to-dataset networks visualizing the landscape of a large portion of biological data. Potentially interesting similarities connecting studies of different diseases are assembled in a disease-to-disease network. Exploring it, we discover numerous non-trivial connections between Alzheimer's disease and schizophrenia, asthma and psoriasis, or liver cancer and obesity, to name a few. We then present a method that identifies the molecular quantities and pathways that contribute the most to the identified similarities and could point to novel drug targets or provide biological insights. The proposed method acts as a "statistical telescope" providing a global view of the constellation of biological data; readers can peek through it at: http://datascope.csd.uoc.gr:25000/.
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Affiliation(s)
| | | | - Elias Castanas
- Laboratory of Experimental Endocrinology, School of Medicine, University of Crete, Heraklion, Greece
| | - Oluf Dimitri Røe
- Norwegian University of Science and Technology, Department of Clinical Research and Molecular Medicine, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Cancer Clinic, Norway
- Clinical Cancer Research Center, Department of Clinical Medicine, Aalborg, Denmark
| | | | - Ioannis Tsamardinos
- Computer Science Department, University of Crete, Heraklion, Greece
- Gnosis Data Analysis PC, Heraklion Crete, Greece
- Institute of Computational and Applied Mathematics, Foundation for Research and Technology, Heraklion, Greece
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17
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Wei EX, Li X, Nan H. Having a first-degree relative with melanoma increases lifetime risk of melanoma, squamous cell carcinoma, and basal cell carcinoma. J Am Acad Dermatol 2019; 81:489-499. [DOI: 10.1016/j.jaad.2019.04.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/01/2019] [Accepted: 04/14/2019] [Indexed: 01/29/2023]
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18
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Middlebrooks CD, Stacey ML, Li Q, Snyder C, Shaw TG, Richardson-Nelson T, Rendell M, Ferguson C, Silberstein P, Casey MJ, Bailey-Wilson JE, Lynch HT. Analysis of the CDKN2A Gene in FAMMM Syndrome Families Reveals Early Age of Onset for Additional Syndromic Cancers. Cancer Res 2019; 79:2992-3000. [PMID: 30967399 DOI: 10.1158/0008-5472.can-18-1580] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/15/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022]
Abstract
Familial atypical multiple mole melanoma (FAMMM) syndrome is a hereditary cancer syndrome that results from mutations in several genes, including the CDKN2A gene. In addition to melanoma, certain other malignancies such as pancreatic cancer are known to occur more frequently in family members who carry the mutation. However, as these families have been followed over time, additional cancers have been observed in both carriers and noncarriers. We sought to determine whether these additional cancers occur at higher frequencies in carriers than noncarriers. We performed survival analyses using 10 FAMMM syndrome families (N = 1,085 individuals) as well as a mixed effects Cox regression, with age at last visit to the clinic or age at cancer diagnosis as our time variable. This analysis was done separately for the known FAMMM-related cancers and "other" cancer groups. The survival curves showed a significant age effect with carriers having a younger age at cancer onset than noncarriers for FAMMM-related cancers (as expected) as well as for newly associated cancers. The Cox regression reflected what was seen in the survival curves, with all models being highly significant (P = 7.15E-20 and P = 5.00E-13 for the FAMMM-related and other cancers, respectively). These analyses support the hypothesis that CDKN2A mutation carriers in FAMMM syndrome families have increased risk for early onset of several cancer types beyond the known cancers. Therefore, these individuals should be screened for additional cancers, and mutation screening should be extended to more than first-degree relatives of an index carrier patient. SIGNIFICANCE: This study shows that carriers of mutations in the CDKN2A gene in FAMMM syndrome are at increased risk for early onset of several cancer types beyond the known cancers.
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Affiliation(s)
- Candace D Middlebrooks
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Mark L Stacey
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska
| | - Qing Li
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Carrie Snyder
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska
| | - Trudy G Shaw
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska
| | | | - Marc Rendell
- The Rose Salter Medical Research Foundation, Newport Coast, California
| | - Claire Ferguson
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska
| | - Peter Silberstein
- Department of Hematology/Oncology, Creighton University, Omaha, Omaha, Nebraska
| | - Murray J Casey
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska.,Department of Obstetrics and Gynecology, Creighton University, Omaha, Omaha, Nebraska
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland.
| | - Henry T Lynch
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska
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19
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Rauca VF, Vlase L, Casian T, Sesarman A, Gheldiu AM, Mocan A, Banciu M, Toiu A. Biologically Active Ajuga Species Extracts Modulate Supportive Processes for Cancer Cell Development. Front Pharmacol 2019; 10:334. [PMID: 31024305 PMCID: PMC6460044 DOI: 10.3389/fphar.2019.00334] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
Backround:Ajuga species have been used in traditional medicine for their diuretic, anti-inflammatory, wound-healing, and hepatoprotective properties. Purpose: The phytochemical profile and anticancer potential of three Ajuga sp. (A. genevensis, A. chamaepitys, and A. laxmannii) from Romania was investigated. Materials and Methods: The phytochemicals were extracted from the aerial parts of Ajuga sp. by using different solvents and methods. The hydroalcoholic extracts were examined for total phenolic, flavonoid and iridoid contents, and HPLC/MS was used to analyze the polyphenolic compounds and iridoids. The phytochemical profile was also evaluated by principal component analysis in connection with antitumor efficacy of extracts. The antiproliferative potential was evaluated using the ELISA BrdU-colorimetric immunoassay. Western Blot with regard to inflammatory protein NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) p65 subunit expression in cell lysates was performed. Quantification of oxidative stress marker malondialdehyde (MDA) was determined by high-performance liquid chromatography (HPLC). Enzymatic and non-enzymatic antioxidant capability was assessed by measuring catalase activity and by evaluating the total antioxidant capacity (TAC) of treated cells. Results:Ajuga laxmannii ethanol extract showed the highest total phenolic and flavonoid content, while A. genevensis ethanol extract was more abundant in iridoids. The overall cytostatic effect of the investigated plant extracts was exerted through strong inhibitory actions on NF-κB, the key molecule involved in the inflammatory response and via oxidative stress modulatory effects in both murine colon carcinoma and melanoma cell lines. Conclusion:Ajuga laxmannii showed the most significant antitumor activity and represents an important source of bioactive compounds, possibly an additional form of treatment alongside conventional anticancer drugs.
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Affiliation(s)
- Valentin-Florian Rauca
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Romania.,Molecular Biology Centre, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Tibor Casian
- Department of Pharmaceutical Technology and Biopharmacy, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Sesarman
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Romania.,Molecular Biology Centre, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Ana-Maria Gheldiu
- Department of Pharmaceutical Botany, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andrei Mocan
- Department of Pharmaceutical Botany, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Manuela Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Romania.,Molecular Biology Centre, Institute for Interdisciplinary Research in Bio-Nano-Sciences, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Anca Toiu
- Department of Pharmacognosy, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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20
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Chattopadhyay S, Hemminki A, Försti A, Sundquist K, Sundquist J, Hemminki K. Familial Risks and Mortality in Second Primary Cancers in Melanoma. JNCI Cancer Spectr 2019; 2:pky068. [PMID: 31360883 PMCID: PMC6649697 DOI: 10.1093/jncics/pky068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/09/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022] Open
Abstract
Background Malignant melanoma (MM) patients are at increasing risk of developing second primary cancers (SPCs). We assessed mortality and risk of SPCs in MM patients with siblings or parents affected with same cancer compared with that of the general population. Methods We used the Swedish Family-Cancer Database to assess relative risks (RRs) and causes of death in SPCs until 2015 in patients with a MM diagnosis between 1958 and 2015. We identified 35 451patients with MM among whom 3212 received a subsequent diagnosis of SPC. RRs of SPCs after MM diagnosis were calculated stratifying over concordant family history of cancer in first-degree relatives. Results Familial RRs were increased for second melanoma (RR = 19.28, 95% CI = 16.71 to 22.25), squamous cell skin cancer (RR = 7.58, 95% CI = 5.57 to 10.29), leukemia (RR = 5.69, 95% CI = 2.96 to 10.94), bladder (RR = 4.15, 95% CI = 2.50 to 6.89), ovarian (RR = 3.89, 95% CI = 1.46 to 10.37), kidney cancer (RR = 3.77, 95% CI = 1.57 to 9.06), cancer of unknown primary (RR = 3.67, 95% CI = 1.65 to 8.16), nervous system (RR = 2.88, 95% CI = 1.20 to 6.93), breast (RR = 2.34, 95% CI = 1.92 to 2.84), lung (RR = 2.24, 95% CI = 1.50 to 3.35), and prostate cancer (RR = 2.22, 95% CI = 1.89 to 2.61) with statistical significance. For all cancers, familial RR was in excess (2.09, 95% CI = 2.02 to 2.16 vs 1.78, 95% CI = 1.69 to 1.87; Ptrend < .0001). Cause of death in MM patients with SPC is shown to be dependent on the cancer site though SPCs contributed to majority of deaths. Conclusions SPCs appear higher with prior family history of cancer and contribute to mortality. SPC was the most common cause of death in patients with SPC and is almost uniformly the major contributing cause of death for all cancer sites. For improved survival in MM patients, prevention and early detection of SPCs would be important.
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Affiliation(s)
- Subhayan Chattopadhyay
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Germany
| | - Akseli Hemminki
- Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Cancer Gene Therapy Group, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ) Heidelberg, Germany.,Cancer Gene Therapy Group, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kristina Sundquist
- Cancer Gene Therapy Group, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.,Center for Community-based Healthcare Research and Education (CoHRE) Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden.,Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY.,Center for Community-based Healthcare Research and Education (CoHRE) Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Kari Hemminki
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
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Impact of family history of cancer on risk and mortality of second cancers in patients with prostate cancer. Prostate Cancer Prostatic Dis 2018; 22:143-149. [PMID: 30185889 DOI: 10.1038/s41391-018-0089-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Survival rates are increasing in patients with prostate cancer, and second primary cancers (SPCs) are becoming more common in these patients. However, the etiology and clinical consequences of SPCs are not well-known. We define the impact of family history on SPC and causes of mortality in these patients. PATIENTS AND METHODS A nation-wide cohort study based on the Swedish Family-Cancer Database covering 4.4 million men and 80,449 prostate cancers diagnosed between 1990 and 2015. Relative risks (RRs) and cumulative incidence for SPCs and for familial SPC were calculated for prostate cancer patients. RESULTS SPC was diagnosed in 6,396 men and more than a third of these patients had a first-degree family history of any cancer; the familial risk was 1.37 (95% CI: 1.27-1.40), compared to 1.10 (1.08-1.16), without a family history. Cumulative incidence by the age of 83 years reached 21% for prostate cancer alone, 28% in those with SPC, and 35% in patients with SPC and family history. Family history was associated with the risk of seven specific SPCs, including colorectal, lung, kidney, bladder and skin (both melanoma and squamous cell) cancers, and leukemia. Colorectal and lung cancers were common SPCs, and family history doubled the risk of these SPCs. In patients with SPC, half of all causes of death were due to SPC and only 12.77% were due to prostate cancer. Most deaths in SPC were caused by lung and colorectal cancers. CONCLUSIONS SPCs were an important cause of death in patients with prostate cancer and family history was an important risk factor for SPCs. Prevention of SPC should be essential when prostate cancer survival rates are being improved and this could start by conducting a thorough assessment of family history at the time of prostate cancer diagnosis.
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Familial associations of male breast cancer with other cancers. Breast Cancer Res Treat 2017; 166:897-902. [PMID: 28836035 DOI: 10.1007/s10549-017-4468-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/16/2017] [Indexed: 10/19/2022]
Abstract
PURPOSE Male breast cancer is associated with female breast cancer in families but whether male breast cancer clusters with other discordant cancers has not been studied. As concordant male breast cancers are utterly rare, discordant associations of male breast cancer with other cancers may reveal genetic and possible environmental risk factors contributing to male breast cancer susceptibility. METHODS We calculated relative risks (RRs) for male breast cancer in families with discordant cancers, and conversely, for discordant cancers in families of male breast cancer patients, based on 15.7 million individuals in the Swedish Family-Cancer Database. RESULTS Among 1428 male breast cancer patients, 16.2% had a female relative diagnosed with breast cancer. Ovarian and female anal cancers showed the strongest associations with male breast cancer (p value < 0.0005). The other significant associations included colorectal, small intestinal, and thyroid cancers, cancer of unknown primary and non-Hodgkin lymphoma but these were each based on a single positive association with male breast cancer. The RRs for male breast cancer were increased in families in which multiple patients were diagnosed with diverse cancers, reaching an RR of 2.58 when three or more family members were affected. CONCLUSIONS The results suggest that male breast cancer shares susceptibility with a number of other cancers but confirmation is needed in other datasets.
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Yu H, Hemminki A, Sundquist K, Hemminki K. Familial Associations of Colorectal Cancer with Other Cancers. Sci Rep 2017; 7:5243. [PMID: 28701784 PMCID: PMC5507930 DOI: 10.1038/s41598-017-05732-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/02/2017] [Indexed: 11/26/2022] Open
Abstract
Colorectal cancer (CRC) has a strong familial component which extends to discordant cancers (ie non-CRC tumors). This is best seen in cancer syndromes such as hereditary non-polyposis colorectal cancer (HNPCC) which predisposes to several tumor types. Population-based family studies have also found discordant associations for CRC but they have included cancers which manifest in HNPCC, and there is no convincing evidence of discordant associations beyond the known syndromes. We address familial associations of non-CRC tumors with CRC using the resources of the Swedish Family-Cancer Database and applying a powerful approach of assessing familial relative risks in families of increasing numbers of patients with discordant cancers. Among 1.8 million cancer patients and over 200,000 CRC cases consistent familial associations of CRC was observed for several HNPCC related cancers. However, for small intestinal, pancreatic and nervous system cancers RRs remained essentially unchanged when potential HNPCC families were excluded, suggesting involvement of genes not related to HNPCC. Two independent associations of CRC were found for melanoma, thyroid and eye cancers and these appeared not to be related to known syndromes. A number of other cancers associated with CRC in single analyses and independent studies are required to assess the relevance of such findings.
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Affiliation(s)
- Hongyao Yu
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.
| | - Akseli Hemminki
- Cancer Gene Therapy Group, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, 205 02, Malmö, Sweden
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, 205 02, Malmö, Sweden
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