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Saad MN, Hamed M. Transcriptome-Wide Association Study Reveals New Molecular Interactions Associated with Melanoma Pathogenesis. Cancers (Basel) 2024; 16:2517. [PMID: 39061157 PMCID: PMC11274789 DOI: 10.3390/cancers16142517] [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: 05/23/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
A transcriptome-wide association study (TWAS) was conducted on genome-wide association study (GWAS) summary statistics of malignant melanoma of skin (UK Biobank dataset) and The Cancer Genome Atlas-Skin Cutaneous Melanoma (TCGA-SKCM) gene expression weights to identify melanoma susceptibility genes. The GWAS included 2465 cases and 449,799 controls, while the gene expression testing was conducted on 103 cases. Afterward, a gene enrichment analysis was applied to identify significant TWAS associations. The melanoma's gene-microRNA (miRNA) regulatory network was constructed from the TWAS genes and their corresponding miRNAs. At last, a disease enrichment analysis was conducted on the corresponding miRNAs. The TWAS detected 27 genes associated with melanoma with p-values less than 0.05 (the top three genes are LOC389458 (RBAK), C16orf73 (MEIOB), and EIF3CL). After the joint/conditional test, one gene (AMIGO1) was dropped, resulting in 26 significant genes. The Gene Ontology (GO) biological process associated the extended gene set (76 genes) with protein K11-linked ubiquitination and regulation of cell cycle phase transition. K11-linked ubiquitin chains regulate cell division. Interestingly, the extended gene set was related to different skin cancer subtypes. Moreover, the enriched pathways were nsp1 from SARS-CoV-2 that inhibit translation initiation in the host cell, cell cycle, translation factors, and DNA repair pathways full network. The gene-miRNA regulatory network identified 10 hotspot genes with the top three: TP53, BRCA1, and MDM2; and four hotspot miRNAs: mir-16, mir-15a, mir-125b, and mir-146a. Melanoma was among the top ten diseases associated with the corresponding (106) miRNAs. Our results shed light on melanoma pathogenesis and biologically significant molecular interactions.
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Affiliation(s)
- Mohamed N. Saad
- Biomedical Engineering Department, Faculty of Engineering, Minia University, Minia 61519, Egypt
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, 18057 Rostock, Germany;
| | - Mohamed Hamed
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, 18057 Rostock, Germany;
- Faculty of Media Engineering and Technology, German University in Cairo, Cairo 11835, Egypt
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2
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Zhang R, Lu Y, Bian Z, Zhou S, Xu L, Jiang F, Yuan S, Tan X, Chen X, Ding Y, Li X. Sleep, physical activity, and sedentary behaviors in relation to overall cancer and site-specific cancer risk: A prospective cohort study. iScience 2024; 27:109931. [PMID: 38974470 PMCID: PMC11225818 DOI: 10.1016/j.isci.2024.109931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 02/20/2024] [Accepted: 05/05/2024] [Indexed: 07/09/2024] Open
Abstract
Large prospective studies are required to better elucidate the associations of physical activity, sedentary behaviors (SBs), and sleep with overall cancer and site-specific cancer risk, accounting for the interactions with genetic predisposition. The study included 360,271 individuals in UK Biobank. After a median follow-up of 12.52 years, we found higher total physical activity (TPA) level and higher sleep scores were related to reduced risk of cancer while higher SB level showed a positive association with cancer. Compared with high TPA-healthy sleep group and low SB-healthy sleep group, low TPA-poor sleep group and high SB-poor sleep group had the highest risk for overall cancer, breast cancer, and lung cancer. Adherence to a more active exercise pattern was associated with a lower risk of cancer irrespective of genetic risk. Our study suggests that improving the quality of sleep and developing physical activity habits might yield benefits in mitigating the cancer risk.
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Affiliation(s)
- Rongqi Zhang
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Lu
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zilong Bian
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siyun Zhou
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liying Xu
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fangyuan Jiang
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shuai Yuan
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Xiao Tan
- Department of Big Data in Health Science, School of Public Health and Department of Psychiatry Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiangjun Chen
- Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, Hangzhou 310020, China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xue Li
- Department of Big Data in Health Science School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
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3
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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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4
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Pierce ES, Jindal C, Choi YM, Cassidy K, Efird JT. Pathogenic mechanisms and etiologic aspects of Mycobacterium avium subspecies paratuberculosis as an infectious cause of cutaneous melanoma. MEDCOMM - ONCOLOGY 2024; 3:e72. [PMID: 38831791 PMCID: PMC11145504 DOI: 10.1002/mog2.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Abstract
Infectious etiologies have previously been proposed as causes of both melanoma and non-melanoma skin cancer. This exploratory overview explains and presents the evidence for the hypothesis that a microorganism excreted in infected ruminant animal feces, Mycobacterium avium subspecies paratuberculosis (MAP), is the cause of some cases of cutaneous melanoma (CM). Occupational, residential, and recreational contact with MAP-contaminated feces, soil, sand, and natural bodies of water may confer a higher rate of CM. Included in our hypothesis are possible reasons for the differing rates and locations of CM in persons with white versus nonwhite skin, why CM develops underneath nails and in vulvar skin, why canine melanoma is an excellent model for human melanoma, and why the Bacille Calmette-Guérin (BCG) vaccine has demonstrated efficacy in the prevention and treatment of CM. The pathogenic mechanisms and etiologic aspects of MAP, as a transmittable agent underlying CM risk, are carefully deliberated in this paper. Imbalances in gut and skin bacteria, genetic risk factors, and vaccine prevention/therapy are also discussed, while acknowledging that the evidence for a causal association between MAP exposure and CM remains circumstantial.
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Affiliation(s)
- Ellen S. Pierce
- Independent Physician Researcher, Spokane Valley, Washington, USA
| | - Charulata Jindal
- School of Medicine and Public Health, University of Sydney, Sydney, New South Wales, Australia
| | - Yuk Ming Choi
- Provider Services, Signify Health, Dallas, Texas, USA
| | - Kaitlin Cassidy
- VA Boston Healthcare System, Cooperative Studies Program Coordinating Center, Boston, Massachusetts, USA
| | - Jimmy T. Efird
- VA Boston Healthcare System, Cooperative Studies Program Coordinating Center, Boston, Massachusetts, USA
- Department of Radiation Oncology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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5
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Fortes C, Mastroeni S, Levati L, Alotto M, Ricci F, D'Atri S. The potential impact of dietary choices on melanoma risk: an anti-inflammatory diet. GENES & NUTRITION 2024; 19:9. [PMID: 38783228 PMCID: PMC11119307 DOI: 10.1186/s12263-024-00745-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The role of inflammation in the aetiology of cancer is recognized. However, no study yet examined the association between an anti-inflammatory diet and cutaneous melanoma and explored whether it could be modified by genetic variations in cyclooxygenase-2 (COX-2), a key enzyme in inflammation. A case-control study was conducted in the IDI-IRCCS hospital in Rome, Italy with 273 cases of primary cutaneous melanoma and 269 controls frequency matched to cases. Information on socio-demographic and pigmentary characteristics, medical history, sun exposure and dietary habits were collected for all subjects. The - 765G > C polymorphism was identified in DNA extracted from blood samples. An anti-inflammatory diet score was created. Logistic regression models were fitted to obtain odds ratios (ORs) and 95% confidence intervals (CIs). A high anti-inflammatory diet score (≥ 8 anti-inflammatory dietary items) was associated with a decreased risk of cutaneous melanoma (OR: 0.29; 95%CI: 0.17-0.49, Ptrend < 0.0001) after adjusting for sex, age, education, number of common nevi, skin photo-type, solar lentigines and sunburns in childhood. COX-2 -765 G > C polymorphism was not an independent risk factor for cutaneous melanoma. Although interaction between - 765G > C genotypes and anti-inflammatory diet score was not statistically significant (p = 0.25), when stratified by -765 G > C genotypes the effect of the anti-inflammatory diet was slightly more pronounced for participants carrying - 765GG (OR: 0.17; 95%CI: 0.06-0.47, Ptrend < 0.001). Our study findings suggest that adherence to an anti-inflammatory diet is associated with a decreased risk of developing cutaneous melanoma. These results suggest the potential impact of dietary choices on melanoma risk.
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Affiliation(s)
- Cristina Fortes
- Epidemiology Unit, Istituto Dermopatico dell'Immacolata, IDI, Via dei Monti di Creta, 104, Roma, 00167, Italy.
| | - Simona Mastroeni
- National Centre for Disease Prevention and Health Promotion, Italian National Institute of Health (ISS), Rome, Italy
| | | | - Massimo Alotto
- Epidemiology Unit, Istituto Dermopatico dell'Immacolata, IDI, Via dei Monti di Creta, 104, Roma, 00167, Italy
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Xie Z, Zhang T, Kim S, Lu J, Zhang W, Lin CH, Wu MR, Davis A, Channa R, Giancardo L, Chen H, Wang S, Chen R, Zhi D. iGWAS: Image-based genome-wide association of self-supervised deep phenotyping of retina fundus images. PLoS Genet 2024; 20:e1011273. [PMID: 38728357 PMCID: PMC11111076 DOI: 10.1371/journal.pgen.1011273] [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: 12/08/2023] [Revised: 05/22/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
Existing imaging genetics studies have been mostly limited in scope by using imaging-derived phenotypes defined by human experts. Here, leveraging new breakthroughs in self-supervised deep representation learning, we propose a new approach, image-based genome-wide association study (iGWAS), for identifying genetic factors associated with phenotypes discovered from medical images using contrastive learning. Using retinal fundus photos, our model extracts a 128-dimensional vector representing features of the retina as phenotypes. After training the model on 40,000 images from the EyePACS dataset, we generated phenotypes from 130,329 images of 65,629 British White participants in the UK Biobank. We conducted GWAS on these phenotypes and identified 14 loci with genome-wide significance (p<5×10-8 and intersection of hits from left and right eyes). We also did GWAS on the retina color, the average color of the center region of the retinal fundus photos. The GWAS of retina colors identified 34 loci, 7 are overlapping with GWAS of raw image phenotype. Our results establish the feasibility of this new framework of genomic study based on self-supervised phenotyping of medical images.
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Affiliation(s)
- Ziqian Xie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Tao Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sangbae Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jiaxiong Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wanheng Zhang
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Cheng-Hui Lin
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Man-Ru Wu
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alexander Davis
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Roomasa Channa
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Luca Giancardo
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Han Chen
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Sui Wang
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Degui Zhi
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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7
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Chakraborty S, Guan Z, Kostrzewa CE, Shen R, Begg CB. Identifying somatic fingerprints of cancers defined by germline and environmental risk factors. Genet Epidemiol 2024. [PMID: 38686586 DOI: 10.1002/gepi.22565] [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: 07/27/2023] [Revised: 01/18/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Numerous studies over the past generation have identified germline variants that increase specific cancer risks. Simultaneously, a revolution in sequencing technology has permitted high-throughput annotations of somatic genomes characterizing individual tumors. However, examining the relationship between germline variants and somatic alteration patterns is hugely challenged by the large numbers of variants in a typical tumor, the rarity of most individual variants, and the heterogeneity of tumor somatic fingerprints. In this article, we propose statistical methodology that frames the investigation of germline-somatic relationships in an interpretable manner. The method uses meta-features embodying biological contexts of individual somatic alterations to implicitly group rare mutations. Our team has used this technique previously through a multilevel regression model to diagnose with high accuracy tumor site of origin. Herein, we further leverage topic models from computational linguistics to achieve interpretable lower-dimensional embeddings of the meta-features. We demonstrate how the method can identify distinctive somatic profiles linked to specific germline variants or environmental risk factors. We illustrate the method using The Cancer Genome Atlas whole-exome sequencing data to characterize somatic tumor fingerprints in breast cancer patients with germline BRCA1/2 mutations and in head and neck cancer patients exposed to human papillomavirus.
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Affiliation(s)
| | - Zoe Guan
- Mass General Research Institute, Boston, Massachusetts, USA
| | | | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Colin B Begg
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Primiero CA, Betz-Stablein B, Ascott N, D’Alessandro B, Gaborit S, Fricker P, Goldsteen A, González-Villà S, Lee K, Nazari S, Nguyen H, Ntouskos V, Pahde F, Pataki BE, Quintana J, Puig S, Rezze GG, Garcia R, Soyer HP, Malvehy J. A protocol for annotation of total body photography for machine learning to analyze skin phenotype and lesion classification. Front Med (Lausanne) 2024; 11:1380984. [PMID: 38654834 PMCID: PMC11035726 DOI: 10.3389/fmed.2024.1380984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Artificial Intelligence (AI) has proven effective in classifying skin cancers using dermoscopy images. In experimental settings, algorithms have outperformed expert dermatologists in classifying melanoma and keratinocyte cancers. However, clinical application is limited when algorithms are presented with 'untrained' or out-of-distribution lesion categories, often misclassifying benign lesions as malignant, or misclassifying malignant lesions as benign. Another limitation often raised is the lack of clinical context (e.g., medical history) used as input for the AI decision process. The increasing use of Total Body Photography (TBP) in clinical examinations presents new opportunities for AI to perform holistic analysis of the whole patient, rather than a single lesion. Currently there is a lack of existing literature or standards for image annotation of TBP, or on preserving patient privacy during the machine learning process. Methods This protocol describes the methods for the acquisition of patient data, including TBP, medical history, and genetic risk factors, to create a comprehensive dataset for machine learning. 500 patients of various risk profiles will be recruited from two clinical sites (Australia and Spain), to undergo temporal total body imaging, complete surveys on sun behaviors and medical history, and provide a DNA sample. This patient-level metadata is applied to image datasets using DICOM labels. Anonymization and masking methods are applied to preserve patient privacy. A two-step annotation process is followed to label skin images for lesion detection and classification using deep learning models. Skin phenotype characteristics are extracted from images, including innate and facultative skin color, nevi distribution, and UV damage. Several algorithms will be developed relating to skin lesion detection, segmentation and classification, 3D mapping, change detection, and risk profiling. Simultaneously, explainable AI (XAI) methods will be incorporated to foster clinician and patient trust. Additionally, a publicly released dataset of anonymized annotated TBP images will be released for an international challenge to advance the development of new algorithms using this type of data. Conclusion The anticipated results from this protocol are validated AI-based tools to provide holistic risk assessment for individual lesions, and risk stratification of patients to assist clinicians in monitoring for skin cancer.
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Affiliation(s)
- Clare A. Primiero
- Dermatology Department, Hospital Clinic and Fundació Clínic per la Recerca Biomèdica—IDIBAPS, Barcelona, Spain
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
| | - Brigid Betz-Stablein
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
| | | | | | | | - Paul Fricker
- Torus Actions & Belle.ai, Ramonville-Saint-Agne, France
| | | | | | - Katie Lee
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
| | - Sana Nazari
- Computer Vision and Robotics Group, University of Girona, Girona, Spain
| | - Hang Nguyen
- Torus Actions & Belle.ai, Ramonville-Saint-Agne, France
| | - Valsamis Ntouskos
- Remote Sensing Lab, National Technical University of Athens, Athens, Greece
| | | | - Balázs E. Pataki
- HUN-REN Institute for Computer Science and Control, Budapest, Hungary
| | | | - Susana Puig
- Dermatology Department, Hospital Clinic and Fundació Clínic per la Recerca Biomèdica—IDIBAPS, Barcelona, Spain
- Medicine Department, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Gisele G. Rezze
- Dermatology Department, Hospital Clinic and Fundació Clínic per la Recerca Biomèdica—IDIBAPS, Barcelona, Spain
| | - Rafael Garcia
- Computer Vision and Robotics Group, University of Girona, Girona, Spain
| | - H. Peter Soyer
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Josep Malvehy
- Dermatology Department, Hospital Clinic and Fundació Clínic per la Recerca Biomèdica—IDIBAPS, Barcelona, Spain
- Medicine Department, University of Barcelona, Barcelona, Spain
- CIBER de Enfermedades raras, Instituto de Salud Carlos III, Barcelona, Spain
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Keatley J, Law MH, Seviiri M, Olsen CM, Pandeya N, Ong JS, MacGregor S, Whiteman DC, Dusingize JC. Genetic predisposition to childhood obesity does not influence the risk of developing skin cancer in adulthood. Sci Rep 2024; 14:7854. [PMID: 38570581 PMCID: PMC10991302 DOI: 10.1038/s41598-024-58418-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/28/2024] [Indexed: 04/05/2024] Open
Abstract
The relationship between body mass index (BMI) and melanoma and other skin cancers remains unclear. The objective of this study was to employ the Mendelian randomization (MR) approach to evaluate the effects of genetically predicted childhood adiposity on the risk of developing skin cancer later in life. Two-sample MR analyses were conducted using summary data from genome-wide association study (GWAS) meta-analyses of childhood BMI, melanoma, cutaneous squamous cell carcinoma (cSCC), and basal cell carcinoma (BCC). We used the inverse-variance-weighted (IVW) methods to obtain a pooled estimate across all genetic variants for childhood BMI. We performed multiple sensitivity analyses to evaluate the potential influence of various assumptions on our findings. We found no evidence that genetically predicted childhood BMI was associated with risks of developing melanoma, cSCC, or BCC in adulthood (OR, 95% CI: melanoma: 1.02 (0.93-1.13), cSCC 0.94 (0.79-1.11), BCC 0.97 (0.84-1.12)). Our findings do not support the conclusions from observational studies that childhood BMI is associated with increased risks of melanoma, cSCC, or BCC in adulthood. Intervening on childhood adiposity will not reduce the risk of common skin cancers later in life.
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Affiliation(s)
- Jay Keatley
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Matthew H Law
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mathias Seviiri
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Catherine M Olsen
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nirmala Pandeya
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jue-Sheng Ong
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David C Whiteman
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jean Claude Dusingize
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
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10
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Ingold N, Seviiri M, Ong JS, Gordon S, Neale RE, Whiteman DC, Olsen CM, MacGregor S, Law MH. Genetic Analysis of Perceived Youthfulness Reveals Differences in How Men's and Women's Age Is Assessed. J Invest Dermatol 2024:S0022-202X(24)00180-5. [PMID: 38460809 DOI: 10.1016/j.jid.2024.02.019] [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: 06/07/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/11/2024]
Abstract
Skin aging is a natural process that occurs over time but can be accelerated by sun exposure. Measuring skin age in a large population can provide insight into the extent of skin damage from sun exposure and skin cancer risk. Understanding the genetics of skin aging, within and across sexes (males and females), could improve our understanding of the genetic drivers of both skin aging and skin cancer. We used UK Biobank data to examine the genetic overlap between perceived youthfulness and traits relevant to actinic photoaging. Our GWAS identified 22 genome-wide significant loci for women and 43 for men. The genetic correlation (rg) between perceived youthfulness in men and women was significantly less than unity (rg = 0.75, 95% confidence interval = 0.69-0.80), suggesting a gene-by-sex interaction. In women, perceived youthfulness was modestly correlated with keratinocyte cancer (rg = -0.19) and skin tanning (rg = 0.18). In men, perceived youthfulness was correlated with male-pattern baldness (rg = -0.23). This suggests that the genetic architecture of perceived youthfulness may differ between sexes, with genes influencing skin tanning and skin cancer susceptibility driving the difference in women, whereas genes influencing male-pattern baldness and other puberty-related traits drive the difference in men. We recommend that future genetic analysis of skin aging include a sex-stratified component.
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Affiliation(s)
- Nathan Ingold
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
| | - Mathias Seviiri
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jue-Sheng Ong
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Scott Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Rachel E Neale
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Herston, Australia
| | - David C Whiteman
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Public Health, University of Queensland, Herston, Australia
| | - Catherine M Olsen
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Faculty of Medicine, The University of Queensland, Herston, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia; Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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11
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Lee KJ, Soyer HP, Stark MS. The Skin Molecular Ecosystem Holds the Key to Nevogenesis and Melanomagenesis. J Invest Dermatol 2024; 144:456-465. [PMID: 37921715 DOI: 10.1016/j.jid.2023.09.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Early detection of melanoma is critical to good patient outcomes, but we still know little about the mechanisms of early melanoma development. Normal epidermis has many of the sequence variants and genetic architecture disruptions found in both benign nevi, melanomas, and other skin cancers, yet continues to behave more or less normally. One hypothesis is that many melanocytes in this context are "tumor competent" but are regulated by the microenvironment provided by the surrounding keratinocytes to inhibit progress to nevi or melanoma. There is evidence of accumulating disorder in several measures of the genomic and epigenomic landscape from normal skin through nevi to melanoma that may be key to promoting nevogenesis and melanomagenesis.
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Affiliation(s)
- Katie J Lee
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia.
| | - H Peter Soyer
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia; Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Mitchell S Stark
- Frazer Institute, the University of Queensland, Dermatology Research Centre, Queensland, Australia
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12
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Gibson TM, Karyadi DM, Hartley SW, Arnold MA, Berrington de Gonzalez A, Conces MR, Howell RM, Kapoor V, Leisenring WM, Neglia JP, Sampson JN, Turcotte LM, Chanock SJ, Armstrong GT, Morton LM. Polygenic risk scores, radiation treatment exposures and subsequent cancer risk in childhood cancer survivors. Nat Med 2024; 30:690-698. [PMID: 38454124 PMCID: PMC11029534 DOI: 10.1038/s41591-024-02837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/26/2024] [Indexed: 03/09/2024]
Abstract
Survivors of childhood cancer are at increased risk for subsequent cancers attributable to the late effects of radiotherapy and other treatment exposures; thus, further understanding of the impact of genetic predisposition on risk is needed. Combining genotype data for 11,220 5-year survivors from the Childhood Cancer Survivor Study and the St Jude Lifetime Cohort, we found that cancer-specific polygenic risk scores (PRSs) derived from general population, genome-wide association study, cancer loci identified survivors of European ancestry at increased risk of subsequent basal cell carcinoma (odds ratio per s.d. of the PRS: OR = 1.37, 95% confidence interval (CI) = 1.29-1.46), female breast cancer (OR = 1.42, 95% CI = 1.27-1.58), thyroid cancer (OR = 1.48, 95% CI = 1.31-1.67), squamous cell carcinoma (OR = 1.20, 95% CI = 1.00-1.44) and melanoma (OR = 1.60, 95% CI = 1.31-1.96); however, the association for colorectal cancer was not significant (OR = 1.19, 95% CI = 0.94-1.52). An investigation of joint associations between PRSs and radiotherapy found more than additive increased risks of basal cell carcinoma, and breast and thyroid cancers. For survivors with radiotherapy exposure, the cumulative incidence of subsequent cancer by age 50 years was increased for those with high versus low PRS. These findings suggest a degree of shared genetic etiology for these malignancy types in the general population and survivors, which remains evident in the context of strong radiotherapy-related risk.
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Affiliation(s)
- Todd M Gibson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Danielle M Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen W Hartley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Arnold
- Department of Pathology, Children's Hospital of Colorado, University of Colorado, Denver, CO, USA
| | | | - Miriam R Conces
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Rebecca M Howell
- Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vidushi Kapoor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Joseph P Neglia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucie M Turcotte
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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13
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Lo Faro V, Bhattacharya A, Zhou W, Zhou D, Wang Y, Läll K, Kanai M, Lopera-Maya E, Straub P, Pawar P, Tao R, Zhong X, Namba S, Sanna S, Nolte IM, Okada Y, Ingold N, MacGregor S, Snieder H, Surakka I, Shortt J, Gignoux C, Rafaels N, Crooks K, Verma A, Verma SS, Guare L, Rader DJ, Willer C, Martin AR, Brantley MA, Gamazon ER, Jansonius NM, Joos K, Cox NJ, Hirbo J. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation. Cell Rep Med 2024; 5:101430. [PMID: 38382466 PMCID: PMC10897632 DOI: 10.1016/j.xcrm.2024.101430] [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: 01/05/2022] [Revised: 03/28/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Primary open-angle glaucoma (POAG), a leading cause of irreversible blindness globally, shows disparity in prevalence and manifestations across ancestries. We perform meta-analysis across 15 biobanks (of the Global Biobank Meta-analysis Initiative) (n = 1,487,441: cases = 26,848) and merge with previous multi-ancestry studies, with the combined dataset representing the largest and most diverse POAG study to date (n = 1,478,037: cases = 46,325) and identify 17 novel significant loci, 5 of which were ancestry specific. Gene-enrichment and transcriptome-wide association analyses implicate vascular and cancer genes, a fifth of which are primary ciliary related. We perform an extensive statistical analysis of SIX6 and CDKN2B-AS1 loci in human GTEx data and across large electronic health records showing interaction between SIX6 gene and causal variants in the chr9p21.3 locus, with expression effect on CDKN2A/B. Our results suggest that some POAG risk variants may be ancestry specific, sex specific, or both, and support the contribution of genes involved in programmed cell death in POAG pathogenesis.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Dan Zhou
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ying Wang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Esteban Lopera-Maya
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands
| | - Peter Straub
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Priyanka Pawar
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Serena Sanna
- University of Groningen, UMCG, Department of Genetics, Groningen, the Netherlands; Institute for Genetics and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka, Japan
| | - Nathan Ingold
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Queensland University of Technology, Brisbane, QLD, Australia; School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Queensland University of Technology, Brisbane, QLD, Australia
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ida Surakka
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Shortt
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Chris Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristy Crooks
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Anurag Verma
- Department of Medicine, Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | - Shefali S Verma
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Guare
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA; Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Medicine, Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA, USA; Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Cristen Willer
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milam A Brantley
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nomdo M Jansonius
- Department of Ophthalmology, Amsterdam University Medical Center (AMC), Amsterdam, the Netherlands
| | - Karen Joos
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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14
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Shao L, Zhao Y, Heinrich M, Prieto-Garcia JM, Manzoni C. Active natural compounds perturb the melanoma risk-gene network. G3 (BETHESDA, MD.) 2024; 14:jkad274. [PMID: 38035793 PMCID: PMC10849364 DOI: 10.1093/g3journal/jkad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Cutaneous melanoma is an aggressive type of skin cancer with a complex genetic landscape caused by the malignant transformation of melanocytes. This study aimed at providing an in silico network model based on the systematic profiling of the melanoma-associated genes considering germline mutations, somatic mutations, and genome-wide association study signals accounting for a total of 232 unique melanoma risk genes. A protein-protein interaction network was constructed using the melanoma risk genes as seeds and evaluated to describe the functional landscape in which the melanoma genes operate within the cellular milieu. Not only were the majority of the melanoma risk genes able to interact with each other at the protein level within the core of the network, but this showed significant enrichment for genes whose expression is altered in human melanoma specimens. Functional annotation showed the melanoma risk network to be significantly associated with processes related to DNA metabolism and telomeres, DNA damage and repair, cellular ageing, and response to radiation. We further explored whether the melanoma risk network could be used as an in silico tool to predict the efficacy of anti-melanoma phytochemicals, that are considered active molecules with potentially less systemic toxicity than classical cytotoxic drugs. A significant portion of the melanoma risk network showed differential expression when SK-MEL-28 human melanoma cells were exposed to the phytochemicals harmine and berberine chloride. This reinforced our hypothesis that the network modeling approach not only provides an alternative way to identify molecular pathways relevant to disease but it may also represent an alternative screening approach to prioritize potentially active compounds.
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Affiliation(s)
- Luying Shao
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX London, UK
| | - Yibo Zhao
- Department of Pharmacology, UCL School of Pharmacy, WC1N 1AX London, UK
| | - Michael Heinrich
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, WC1N 1AX London, UK
- Chinese Medicine Research Center, and Department of Pharmaceutical Sciences and Chinese Medicine Resources, College of Chinese Medicine, China Medical University, Taichung City 404333, Taiwan
| | - Jose M Prieto-Garcia
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Claudia Manzoni
- Department of Pharmacology, UCL School of Pharmacy, WC1N 1AX London, UK
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15
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Cornish N, Haycock P, Brenner H, Figueiredo JC, Galesloot TE, Grant RC, Johansson M, Mariosa D, McKay J, Pai R, Pellatt AJ, Samadder NJ, Shi J, Thibord F, Trégouët DA, Voegele C, Thirlwell C, Mumford A, Langdon R. Causal relationships between risk of venous thromboembolism and 18 cancers: a bidirectional Mendelian randomization analysis. Int J Epidemiol 2024; 53:dyad170. [PMID: 38124529 PMCID: PMC10859161 DOI: 10.1093/ije/dyad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND People with cancer experience high rates of venous thromboembolism (VTE). Risk of subsequent cancer is also increased in people experiencing their first VTE. The causal mechanisms underlying this association are not completely understood, and it is unknown whether VTE is itself a risk factor for cancer. METHODS We used data from large genome-wide association study meta-analyses to perform bidirectional Mendelian randomization analyses to estimate causal associations between genetic liability to VTE and risk of 18 different cancers. RESULTS We found no conclusive evidence that genetic liability to VTE was causally associated with an increased incidence of cancer, or vice versa. We observed an association between liability to VTE and pancreatic cancer risk [odds ratio for pancreatic cancer: 1.23 (95% confidence interval: 1.08-1.40) per log-odds increase in VTE risk, P = 0.002]. However, sensitivity analyses revealed this association was predominantly driven by a variant proxying non-O blood group, with inadequate evidence to suggest a causal relationship. CONCLUSIONS These findings do not support the hypothesis that genetic liability to VTE is a cause of cancer. Existing observational epidemiological associations between VTE and cancer are therefore more likely to be driven by pathophysiological changes which occur in the setting of active cancer and anti-cancer treatments. Further work is required to explore and synthesize evidence for these mechanisms.
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Affiliation(s)
- Naomi Cornish
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philip Haycock
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert C Grant
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Daniela Mariosa
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Andrew J Pellatt
- Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | | | - Catherine Voegele
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Chrissie Thirlwell
- University of Exeter Medical School, University of Exeter, Exeter, UK
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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16
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Primiero CA, Maas EJ, Wallingford CK, Soyer HP, McInerney-Leo AM. Genetic testing for familial melanoma. Ital J Dermatol Venerol 2024; 159:34-42. [PMID: 38287743 DOI: 10.23736/s2784-8671.23.07761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
While the average lifetime risk of melanoma worldwide is approximately 3%, those with inherited high-penetrance mutations face an increased lifetime risk of 52-84%. In countries of low melanoma incidence, such as in Southern Europe, familial melanoma genetic testing may be warranted when there are two first degree relatives with a melanoma diagnosis. Testing criteria for high incidence countries such as USA, or with very-high incidence, such as Australia and New Zealand, would require a threshold of 3 to 4 affected family members. A mutation in the most common gene associated with familial melanoma, CDKN2A, is identified in approximately 10-40% of those meeting testing criteria. However, the use of multi-gene panels covering additional less common risk genes can significantly increase the diagnostic yield. Currently, genetic testing for familial melanoma is typically conducted by qualified genetic counsellors, however with increasing demand on testing services and high incidence rate in certain countries, a mainstream model should be considered. With appropriate training, dermatologists are well placed to identify high risk individuals and offer melanoma genetic test in dermatology clinics. Genetic testing should be given in conjunction with pre- and post-test consultation. Informed patient consent should cover possible results, the limitations and implications of testing including inconclusive results, and potential for genetic discrimination. Previous studies reporting on participant outcomes of genetic testing for familial melanoma have found significant improvements in both sun protective behavior and screening frequency in mutation carriers.
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Affiliation(s)
- Clare A Primiero
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia
- Department of Dermatology, Hospital Clinic and Fundació Clínic per la Recerca Biomèdica - August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Ellie J Maas
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia
| | - Courtney K Wallingford
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia
| | - H Peter Soyer
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia -
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Australia
| | - Aideen M McInerney-Leo
- Frazer Institute, Dermatology Research Centre, The University of Queensland, Brisbane, Australia
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17
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Wang S, Chen J, Jin Z, Xing Y, Wang R. Natural hair color and skin cancers: A two-sample Mendelian randomization study. Gene 2024; 893:147940. [PMID: 37907182 DOI: 10.1016/j.gene.2023.147940] [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: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
Previous observational studies have indicated an association between hair color and the risk of melanoma and keratinocyte skin cancer (KSC); however, different hair colors show inconsistent effects on skin cancers. Here, we conducted a two-sample Mendelian randomization (MR) study to evaluate the causal relationship between natural hair color and skin cancers by using 211 single nucleotide polymorphisms as genetic instruments from a genome-wide meta-analysis of 360,270 individuals of European ancestry. Light hair colors (red, blonde, and light brown) were associated with high levels of cutaneous melanoma (CM) and KSC (CM-inverse variance weighted [IVW] odds ratio [OR]-red: 1.034, 95% confidence interval [CI]: 1.025-1.044, P < 0.001; OR-blonde: 1.008, 95% CI: 1.003-1.014, P = 0.003; OR-light brown: 1.006, 95% CI: 1.002-1.011, P = 0.009; KSC-IVW OR-red: 1.078, 95% CI: 1.053-1.103, P < 0.001; OR-blonde: 1.024, 95% CI: 1.009-1.040, P = 0.002; OR-light brown: 1.018, 95% CI: 1.004-1.033, P = 0.01). However, dark brown hair showed an inverse causal relationship with skin cancers (CM IVW OR: 0.987, 95% CI: 0.984-0.990, P < 0.001; KSC IVW OR: 0.979, 95% CI: 0.970-0.988, P < 0.001). Black hair was associated with a decreased risk of KSC (IVW OR: 0.954, 95% CI: 0.913-0.997, P = 0.036) but showed no causal relationship with CM. The present study provides strong MR evidence of a causal association between hair color and skin cancer. Secondary MR analyses enhances result robustness by replicating findings, exploring gender-specific effects, and providing a more comprehensive understanding of the complex relationship between hair color and skin cancers. More large-scale MR studies or randomized controlled trials are required to further investigate the mechanisms of the association between hair color and skin cancers.
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Affiliation(s)
- Shiting Wang
- Nanjing University of Chinese Medicine, Nanjing, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Jiaqi Chen
- Nanjing University of Chinese Medicine, Nanjing, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Zhichao Jin
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ying Xing
- Nanjing University of Chinese Medicine, Nanjing, China; Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ruiping Wang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
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18
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Atkinson C, McInerney-Leo AM, Proctor M, Lanagan C, Stevenson AJ, Dehkhoda F, Caole M, Maas E, Ainger S, Pritchard AL, Johansson PA, Leo P, Hayward NK, Sturm RA, Duncan EL, Gabrielli B. The ATM Ser49Cys Variant Effects ATM Function as a Regulator of Oncogene-Induced Senescence. Int J Mol Sci 2024; 25:1664. [PMID: 38338943 PMCID: PMC10855307 DOI: 10.3390/ijms25031664] [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: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
An apical component of the cell cycle checkpoint and DNA damage repair response is the ataxia-telangiectasia mutated (ATM) Ser/Thr protein kinase. A variant of ATM, Ser49Cys (rs1800054; minor allele frequency = 0.011), has been associated with an elevated risk of melanoma development; however, the functional consequence of this variant is not defined. ATM-dependent signalling in response to DNA damage has been assessed in a panel of patient-derived lymphoblastoid lines and primary human melanocytic cell strains heterozygous for the ATM Ser49Cys variant allele. The ATM Ser49Cys allele appears functional for acute p53-dependent signalling in response to DNA damage. Expression of the variant allele did reduce the efficacy of oncogene expression in inducing senescence. These findings demonstrate that the ATM 146C>G Ser49Cys allele has little discernible effect on the acute response to DNA damage but has reduced function observed in the chronic response to oncogene over-expression. Analysis of melanoma, naevus and skin colour genomics and GWAS analyses have demonstrated no association of this variant with any of these outcomes. The modest loss of function detected suggest that the variant may act as a modifier of other variants of ATM/p53-dependent signalling.
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Affiliation(s)
- Caroline Atkinson
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Aideen M. McInerney-Leo
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Martina Proctor
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Catherine Lanagan
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | | | - Farhad Dehkhoda
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Mary Caole
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Ellie Maas
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Stephen Ainger
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Antonia L. Pritchard
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Peter A. Johansson
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Paul Leo
- Centre of Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Nicholas K. Hayward
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Richard A. Sturm
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 1UL, UK
| | - Brian Gabrielli
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
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Stark MS, Sturm RA, Pan Y, Smit DJ, Kommajosyula V, Lee KJ, Jagirdar K, McLean C, Duffy DL, Soyer HP, Mar VJ. Assessing the genetic risk of nodular melanoma using a candidate gene approach. Br J Dermatol 2024; 190:199-206. [PMID: 37766469 DOI: 10.1093/bjd/ljad365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Nodular melanoma (NM) is a challenge to diagnose early due to its rapid growth and more atypical clinical presentation, making it the largest contributor to melanoma mortality. OBJECTIVES Our study aim was to perform a rare-variant allele (RVA) analysis of whole-exome sequencing of patients with NM and non-NM (minor allele frequency ≤ 1% non-Finnish European) for a set of 500 candidate genes potentially implicated in melanoma. METHODS This study recruited 131 participants with NM and 194 with non-NM from South-east Queensland and patients with NM from Victoria to perform a comparative analysis of possible genetic differences or similarities between the two melanoma cohorts. RESULTS Phenotypic analysis revealed that a majority of patients diagnosed with NM were older males with a higher frequency of fair skin and red hair than is seen in the general population. The distribution of common melanoma polygenic risk scores was similar in patients with NM and non-NM, with over 28% in the highest quantile of scores. There was also a similar frequency of carriage of familial/high-penetrant melanoma gene and loss-of-function variants. We identified 39 genes by filtering 500 candidate genes based on the greatest frequency in NM compared with non-NM cases. The genes with RVAs of greatest frequency in NM included PTCH1, ARID2 and GHR. Rare variants in the SMO gene, which interacts with PTCH1 as ligand and receptor, were also identified, providing evidence that the Hedgehog pathway may contribute to NM risk. There was a cumulative effect in carrying multiple rare variants in the NM-associated genes. A 14.8-fold increased ratio for NM compared with non-NM was seen when two RVAs of the 39 genes were carried by a patient. CONCLUSIONS This study highlights the importance of considering frequency of RVA to identify those at risk of NM in addition to known high penetrance genes.
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Affiliation(s)
- Mitchell S Stark
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Richard A Sturm
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Yan Pan
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences
| | - Darren J Smit
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Varsha Kommajosyula
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Katie J Lee
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Kasturee Jagirdar
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Catriona McLean
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences
| | - David L Duffy
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - H Peter Soyer
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Victoria J Mar
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- School of Public Health and Preventive Medicine; Monash University, Melbourne, Vic, Australia
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20
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Dessinioti C, Stratigos AJ. Decoding the nodular melanoma subtype: what about genetics? Br J Dermatol 2024; 190:144-145. [PMID: 37976178 DOI: 10.1093/bjd/ljad445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/05/2023] [Accepted: 12/04/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Clio Dessinioti
- Skin Cancer and Melanoma Unit, 1st Department of Dermatology-Venereology, National and Kapodistrian University of Athens, Andreas Sygros Hospital, Athens , Greece
| | - Alexander J Stratigos
- Skin Cancer and Melanoma Unit, 1st Department of Dermatology-Venereology, National and Kapodistrian University of Athens, Andreas Sygros Hospital, Athens , Greece
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21
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Gholami M. Genetic variants and haplotype structures of miRNA host genes in cancer and obesity. J Biomol Struct Dyn 2024:1-7. [PMID: 38174558 DOI: 10.1080/07391102.2023.2300056] [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: 09/06/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
Cancer and obesity are two important public health problems. This study aimed to investigate the role of genetic variants and haplotypes of miRNA host genes in cancer and obesity. Data from the catalog of genome-wide association studies (GWAS) were used to find significant variants (index). Then, 1000-genome phase 3 data were used to find haplotypic variants (proxy) associated with these diseases. The candidate variants and haplotypes were identified from proxy and index variants. Finally, SNP function analysis was performed. All GWAS-significant cancer-associated miRNA host gene variants, including MIR4713HG, MIR663AHG, MIR99AHG and MIR4435-2HG, were also significantly associated with obesity. The rs703764 variant was common between cutaneous melanoma and obesity traits in the European population (P ≤ 5E-8). The rs2414098 variant was associated with endometrial cancer (P ≤ 5E-13), and the rs7173595 variant was associated with waist-hip ratio (P ≤ 5E-13) and new CGGCATCA haplotypic located at MIR4713HG was identified in the European population. In addition, the ATCTTGTT haplotype for rs17041868 in MIR4435-2HG was identified to be associated with obesity traits (waist-hip ratio and BMI) in the European population (P ≤ 5E-8). This study found that rs703764 is a common genetic marker between cancer and obesity. The CGGCATCA haplotype is common between endometrial cancer and waist-hip ratio. Also, ATCTTGTT haplotype is associated with obesity traits. These results indicate that the variants and haplotypes of miRNAs host genes play an important role between cancer and obesity in the European population. It is suggested to investigate the effect of these structures in other populations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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22
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Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, Dunham I, Stamatoyannopoulos J, Franceschini N, Machiela MJ, Berndt SI. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biol 2024; 25:3. [PMID: 38167104 PMCID: PMC10763681 DOI: 10.1186/s13059-023-03126-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The majority of disease-associated variants identified through genome-wide association studies are located outside of protein-coding regions. Prioritizing candidate regulatory variants and gene targets to identify potential biological mechanisms for further functional experiments can be challenging. To address this challenge, we developed FORGEdb ( https://forgedb.cancer.gov/ ; https://forge2.altiusinstitute.org/files/forgedb.html ; and https://doi.org/10.5281/zenodo.10067458 ), a standalone and web-based tool that integrates multiple datasets, delivering information on associated regulatory elements, transcription factor binding sites, and target genes for over 37 million variants. FORGEdb scores provide researchers with a quantitative assessment of the relative importance of each variant for targeted functional experiments.
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Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue 98121, Seattle, USA.
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue 98121, Seattle, USA
| | - María Gutierrez-Arcelus
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaozheng Yao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew Teschendorff
- CAS Key Lab of Computational Biology, Shanghai Institute for Biological Sciences, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Lendinez-Sanchez G, Diaz-Redondo T, Campos MI, Porta Pelayo J, Porta Pelayo JM, Muriel-López C. ATM Variant as a Cause of Hereditary Cutaneous Melanoma in a Spanish Family: Case Report. Case Rep Oncol 2024; 17:386-391. [PMID: 38415270 PMCID: PMC10898853 DOI: 10.1159/000536105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/30/2023] [Indexed: 02/29/2024] Open
Abstract
Introduction Ataxia-Telangiectasia Mutated (ATM) is a cancer predisposition gene; carriers of germline pathogenic variants have an increased risk of developing malignancies, including breast, prostate, pancreatic, and ovarian cancer. Most ATM variants are of uncertain significance. Findings from genome-wide association studies (GWAS) suggest that ATM may be a low-risk melanoma susceptibility locus. Case Report We report the case of a Hispanic family whose members who have presented cutaneous melanoma have been found to be carriers for the ATM pathogenic variant c.3747-1G>C (rs730881364), one of whom was diagnosed at 24 years old. Discussion We describe for the first time the possible clinical association between ATM (c.3747-1G>C) and familial melanoma. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site, assuming a variant that entails loss of functionality that is probably pathogenic and related to oncogenesis. However, we cannot exclude that cutaneous melanoma in both members and at an early age is the result of chance, environmental interaction, other uncontrolled external factors, or the interaction of other genetic alterations other than the ATM variant described in this study.
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Affiliation(s)
- Gonzalo Lendinez-Sanchez
- Department of Medical Oncology, Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Málaga, Spain
| | - Tamara Diaz-Redondo
- Department of Medical Oncology, Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Málaga, Spain
| | - Marcos Iglesias Campos
- Department of Medical Oncology, Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Málaga, Spain
| | | | | | - Carolina Muriel-López
- Department of Medical Oncology, Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Málaga, Spain
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24
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Liu M, Lan Y, Zhang H, Wu M, Zhang X, Leng L, Zheng H, Li J. Analysing the causal relationship between potentially protective and risk factors and cutaneous melanoma: A Mendelian randomization study. J Eur Acad Dermatol Venereol 2024; 38:102-111. [PMID: 37712456 DOI: 10.1111/jdv.19484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Previous observational studies reported altered melanoma risks in relation to many potential factors, such as coffee intake, smoking habits and photodamage-related conditions. Considering the susceptibility of epidemiological studies to residual confounders, there remains uncertainty about the actual causal roles of these reported factors in melanoma aetiology. OBJECTIVES This study aims to investigate the causal association between cutaneous melanoma (CM) and previously reported factors: coffee intake, alcohol consumption, lifetime smoking, socioeconomic status (SES), ease of skin tanning, childhood sunburn and facial ageing, providing insight into its underlying aetiology and preventative strategies. METHODS We utilized a two-sample MR analysis on data from the largest meta-analysis summary statistics of confirmed cutaneous melanoma including 30,134 patients. Genetic instrumental variables were constructed by identifying single nucleotide polymorphisms (SNPs) that associate with corresponding factors. Inverse variance weighted (IVW) was the primary MR method. For sensitivity and heterogeneity, MR Egger, weighted median, simple mode, weighted mode and MR Egger intercept tests were examined. RESULTS Cutaneous melanoma risks were found to be elevated in association with a predisposition towards ease of skin tanning (IVW: OR = 2.842, 95% CI 2.468-3.274, p < 0.001) and with childhood sunburn history (IVW: OR = 6.317, 95% CI 4.479-8.909, p < 0.001). Repeated MR after removing potential confounders and outliers demonstrated resolved horizontal pleiotropy and statistically significant results that closely mirrored the initial findings. Other potential factors, such as coffee intake, alcohol consumption, smoking and socioeconomic status (SES), indicated insignificant effects on melanoma risk in the analysis, and therefore, our Mendelian randomization study does not support their roles in modifying melanoma risks. CONCLUSIONS Our extensive MR analysis provides strong evidence of the causative role of ease of skin tanning and childhood sunburn history in elevating melanoma risk. Curtailing ultraviolet radiation (UVR) exposure may be the single best preventative strategy to reduce melanoma risk.
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Affiliation(s)
- Mingjuan Liu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- 4+4 M.D. Program, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yining Lan
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hanlin Zhang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mengyin Wu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyi Zhang
- Departments of Internal Medicine and Cellular & Molecular Physiology, Yale School of Medicine, Connecticut, New Haven, USA
| | - Ling Leng
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Heyi Zheng
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jun Li
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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25
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Dunlop KLA, Keogh LA, Smith AL, Aranda S, Aitken J, Watts CG, Smit AK, Janda M, Mann GJ, Cust AE, Rankin NM. Acceptability and appropriateness of a risk-tailored organised melanoma screening program: Qualitative interviews with key informants. PLoS One 2023; 18:e0287591. [PMID: 38091281 PMCID: PMC10718433 DOI: 10.1371/journal.pone.0287591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/08/2023] [Indexed: 12/18/2023] Open
Abstract
INTRODUCTION In Australia, opportunistic screening (occurring as skin checks) for the early detection of melanoma is common, and overdiagnosis is a recognised concern. Risk-tailored cancer screening is an approach to cancer control that aims to provide personalised screening tailored to individual risk. This study aimed to explore the views of key informants in Australia on the acceptability and appropriateness of risk-tailored organised screening for melanoma, and to identify barriers, facilitators and strategies to inform potential future implementation. Acceptability and appropriateness are crucial, as successful implementation will require a change of practice for clinicians and consumers. METHODS This was a qualitative study using semi-structured interviews. Key informants were purposively selected to ensure expertise in melanoma early detection and screening, prioritising senior or executive perspectives. Consumers were expert representatives. Data were analysed deductively using the Tailored Implementation for Chronic Diseases (TICD) checklist. RESULTS Thirty-six participants were interviewed (10 policy makers; 9 consumers; 10 health professionals; 7 researchers). Key informants perceived risk-tailored screening for melanoma to be acceptable and appropriate in principle. Barriers to implementation included lack of trial data, reluctance for low-risk groups to not screen, variable skill level in general practice, differing views on who to conduct screening tests, confusing public health messaging, and competing health costs. Key facilitators included the perceived opportunity to improve health equity and the potential cost-effectiveness of a risk-tailored screening approach. A range of implementation strategies were identified including strengthening the evidence for cost-effectiveness, engaging stakeholders, developing pathways for people at low risk, evaluating different risk assessment criteria and screening delivery models and targeted public messaging. CONCLUSION Key informants were supportive in principle of risk-tailored melanoma screening, highlighting important next steps. Considerations around risk assessment, policy and modelling the costs of current verses future approaches will help inform possible future implementation of risk-tailored population screening for melanoma.
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Affiliation(s)
- Kate L. A. Dunlop
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Louise A. Keogh
- Centre for Health Equity, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrea L. Smith
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia
| | - Sanchia Aranda
- School of Health Sciences, University of Melbourne, Melbourne, Australia
| | - Joanne Aitken
- Viertel Cancer Research Centre, Cancer Council Queensland, Brisbane, Queensland, Australia
| | - Caroline G. Watts
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia
- Surveillance, Evaluation & Research Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Amelia K. Smit
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Monika Janda
- Centre for Health Services Research, The University of Queensland, St Lucia, Queensland, Australia
| | - Graham J. Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales, Australia
| | - Anne E. Cust
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Nicole M. Rankin
- Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
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Lin S, Shen R, Huang J, Liu Y, Li H, Xu Q. Identification of genomic-wide genetic links between cutaneous melanoma and obesity-related physical traits via cFDR. Genes Genomics 2023; 45:1549-1562. [PMID: 37768517 DOI: 10.1007/s13258-023-01446-x] [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: 02/10/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Both epidemiological and clinical studies have suggested the comorbidity between cutaneous melanoma (CM) and obesity-related physical traits. However, it remains unclear about their shared genetic architecture. OBJECTIVE To determine the shared genetic architecture between CM and obesity-related physical traits through conditional false discovery rate (cFDR) analysis. METHOD Quantile-quantile plots were firstly built to assess the pleiotropic enrichment of shared single nucleotide polymorphisms between CM and each trait. Then, cFDR and conjunctional cFDR (ccFDR) were used to identify the shared risk loci between CM and each trait. Moreover, the functional evaluation of shared risk genes was carried out through analyses of expression quantitative trait loci (eQTL), Kyoto Encyclopedia of Genes and Genomes and gene ontology, respectively. Finally, single-cell sequence analysis was performed to locate the expression of eQTL-mapped genes in tissues. RESULTS Successive pleiotropic enrichment was found between CM and 5 obesity-related traits or height. 24 shared risk loci were identified between CM and 13 traits except appendicular lean mass using ccFDR analysis, with 17 novel and 4 validated loci. The functions of ccFDR-identified and eQTL-mapped genes were revealed to be mainly involved in cellular senescence, proliferation, meiotic nuclear division, cell cycle, and the metabolism of lipid, cholesterol and glucose. Single-cell sequence analysis showed that keratinocytes contribute to the occurrence and aggressiveness of CM through secreting paracrine cytokines. CONCLUSION Our findings demonstrate the significant genetic correlation between CM and obesity-related physical traits, which may provide a novel genetical basis for the pathogenesis and treatment of CM.
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Affiliation(s)
- Shen Lin
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Runnan Shen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jingqian Huang
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yanhan Liu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Hongpeng Li
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qingfang Xu
- Department of Dermato-Venereology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
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Liu M, Lan Y, Zhang H, Zhang X, Wu M, Yang L, Zhou J, Tong M, Leng L, Zheng H, Li J, Mi X. Telomere length is associated with increased risk of cutaneous melanoma: a Mendelian randomization study. Melanoma Res 2023; 33:475-481. [PMID: 37650705 DOI: 10.1097/cmr.0000000000000917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
RESULTS The MR analysis using two TL GWAS datasets revealed strong and consistent evidence that long TL is causally associated with an increased risk of CM. The analysis of the Codd et al. dataset found that long TL significantly predicted an elevated risk of CM (IVW OR = 2.411, 95% CI 2.092-2.780, P = 8.05E-34). Similarly, the analysis of the Li et al. dataset yielded consistent positive results across all MR methods, providing further robustness to the causal relationship (IVW OR = 2.324, 95% CI 1.516-3.565, P = 1.11E-04). The study provides evidence for a causal association between TL and CM susceptibility, indicating that longer TL increases the risk of developing CM and providing insight into the unique telomere biology in melanoma pathogenesis. Telomere maintenance pathways may be a potential target for preventing and treating CM.
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Affiliation(s)
- Mingjuan Liu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- 4 + 4 M.D. Program, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yining Lan
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Hanlin Zhang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Xinyi Zhang
- Departments of Internal Medicine
- Cellular & Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mengyin Wu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Leyan Yang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Jia Zhou
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Meiyi Tong
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Ling Leng
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Heyi Zheng
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Jun Li
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Xia Mi
- Department of Dermatology, Strategic Support Force Medical Center, Beijing, China
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Rashid S, Molotkov I, Klebanov N, Shaughnessy M, Daly MJ, Artomov M, Tsao H. Mendelian Randomization Analysis reveals Inverse Genetic Risks between Skin Cancers and Vitiligo. JID INNOVATIONS 2023; 3:100217. [PMID: 38034848 PMCID: PMC10685305 DOI: 10.1016/j.xjidi.2023.100217] [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: 04/19/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 12/02/2023] Open
Abstract
Several observational studies have demonstrated a consistent pattern of decreased melanoma risk among patients with vitiligo. More recently, this finding has been supported by a suggested genetic relationship between the two entities, with certain variants significantly associated with an increased risk of melanoma, basal cell carcinoma, and squamous cell carcinoma but a decreased risk of vitiligo. We compared 48 associated variants from a recently published GWAS and identified three variants-located in the TYR, MC1R-DEF8, and RALY-EIF2S2-ASIP-AHCY-ITCH loci- that correlated with an increased risk for melanoma, basal cell carcinoma, and squamous cell carcinoma and a decreased risk for vitiligo. We then used results of skin cancers and vitiligo GWAS to compare the shared genetic properties between these two traits through an unbiased Mendelian randomization analysis. Our results suggest that the inverse genetic relationship between common skin cancers and vitiligo is broader than previously reported owing to the influence of shared genome-wide significant associations.
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Affiliation(s)
- Sarem Rashid
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ivan Molotkov
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Nikolai Klebanov
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael Shaughnessy
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mark J. Daly
- Analytic & Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Mykyta Artomov
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Analytic & Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Hensin Tsao
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
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29
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Ingold N, Zhu G, Duffy DL, Mothershaw A, Martin NG, MacGregor S, Law MH. Counting nevi on the outer arm provides an accurate and feasible alternative to total body nevus count. J Eur Acad Dermatol Venereol 2023; 37:e1302-e1304. [PMID: 37328921 PMCID: PMC10615689 DOI: 10.1111/jdv.19279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023]
Affiliation(s)
- N Ingold
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - G Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - D L Duffy
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - A Mothershaw
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - N G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - S MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - M H Law
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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30
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Li J, Ji Y, Chen N, Dai L, Deng H. Colitis-associated carcinogenesis: crosstalk between tumors, immune cells and gut microbiota. Cell Biosci 2023; 13:194. [PMID: 37875976 PMCID: PMC10594787 DOI: 10.1186/s13578-023-01139-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. One of the main causes of colorectal cancer is inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD). Intestinal epithelial cells (IECs), intestinal mesenchymal cells (IMCs), immune cells, and gut microbiota construct the main body of the colon and maintain colon homeostasis. In the development of colitis and colitis-associated carcinogenesis, the damage, disorder or excessive recruitment of different cells such as IECs, IMCs, immune cells and intestinal microbiota play different roles during these processes. This review aims to discuss the various roles of different cells and the crosstalk of these cells in transforming intestinal inflammation to cancer, which provides new therapeutic methods for chemotherapy, targeted therapy, immunotherapy and microbial therapy.
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Affiliation(s)
- Junshu Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Yanhong Ji
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Na Chen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China
| | - Lei Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
| | - Hongxin Deng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Ke Yuan Road 4, No. 1 Gao Peng Street, Chengdu, 610041, China.
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31
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Jensen MR, Jelsig AM, Gerdes AM, Hölmich LR, Kainu KH, Lorentzen HF, Hansen MH, Bak M, Johansson PA, Hayward NK, Van Overeem Hansen T, Wadt KA. TINF2 is a major susceptibility gene in Danish patients with multiple primary melanoma. HGG ADVANCES 2023; 4:100225. [PMID: 37646013 PMCID: PMC10461021 DOI: 10.1016/j.xhgg.2023.100225] [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: 05/04/2023] [Accepted: 07/19/2023] [Indexed: 09/01/2023] Open
Abstract
TINF2 encodes the TINF2 protein, which is a subunit in the shelterin complex critical for telomere regulation. Three recent studies have associated six truncating germline variants in TINF2 that have previously been associated with a cancer predisposition syndrome (CPS) caused by elongation of the telomeres. This has added TINF2 to the long telomere syndrome genes, together with other telomere maintenance genes such as ACD, POT1, TERF2IP, and TERT. We report a clinical study of 102 Danish patients with multiple primary melanoma (MPM) in which a germline truncating variant in TINF2 (p.(Arg265Ter)) was identified in four unrelated participants. The telomere lengths of three variant carriers were >90% percentile. In a routine diagnostic setting, the variant was identified in two more families, including an additional MPM patient and monozygotic twins with thyroid cancer and other cancer types. A total of 10 individuals from six independent families were confirmed carriers, all with cancer history, predominantly melanoma. Our findings suggest a major role of TINF2 in Danish patients with MPM. In addition to melanoma, other cancers in the six families include thyroid, renal, breast, and sarcoma, supporting a CPS in which melanoma, thyroid cancer, and sarcoma predominate. Further studies are needed to establish the full spectrum of associated cancer types and characterize lifetime cancer risk in carriers.
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Affiliation(s)
- Marlene Richter Jensen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne Marie Jelsig
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisbet Rosenkrantz Hölmich
- Department of Plastic and Reconstructive Surgery, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kati Hannele Kainu
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Dermatology and Allergology, Herlev and Gentofte Hospital, 2900 Gentofte, Denmark
| | | | | | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | | | | | - Thomas Van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin A.W. Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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32
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Kyrgiafini MA, Giannoulis T, Chatziparasidou A, Christoforidis N, Mamuris Z. Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility. Int J Mol Sci 2023; 24:15002. [PMID: 37834450 PMCID: PMC10573971 DOI: 10.3390/ijms241915002] [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: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Male infertility is a global health issue, affecting over 20 million men worldwide. Genetic factors are crucial in various male infertility forms, including teratozoospermia. Nonetheless, the genetic causes of male infertility remain largely unexplored. In this study, we employed whole-genome sequencing and RNA expression analysis to detect differentially expressed (DE) long-noncoding RNAs (lncRNAs) in teratozoospermia, along with mutations that are exclusive to teratozoospermic individuals within these DE lncRNAs regions. Bioinformatic tools were used to assess variants' impact on lncRNA structure, function, and lncRNA-miRNA interactions. Our analysis identified 1166 unique mutations in teratozoospermic men within DE lncRNAs, distinguishing them from normozoospermic men. Among these, 64 variants in 23 lncRNAs showed potential regulatory roles, 7 variants affected 4 lncRNA structures, while 37 variants in 17 lncRNAs caused miRNA target loss or gain. Pathway Enrichment and Gene Ontology analyses of the genes targeted by the affected miRNAs revealed dysregulated pathways in teratozoospermia and a link between male infertility and cancer. This study lists novel variants and lncRNAs associated for the first time with teratozoospermia. These findings pave the way for future studies aiming to enhance diagnosis and therapy in the field of male infertility.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Alexia Chatziparasidou
- Embryolab IVF Unit, St. 173-175 Ethnikis Antistaseos, Kalamaria, 55134 Thessaloniki, Greece
| | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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33
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Dusingize JC, Law MH, Seviiri M, Olsen CM, Pandeya N, Landi MT, Iles MM, Neale RE, Ong JS, MacGregor S, Whiteman DC. Genetic variants for smoking behaviour and risk of skin cancer. Sci Rep 2023; 13:16873. [PMID: 37803080 PMCID: PMC10558453 DOI: 10.1038/s41598-023-44144-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Observational studies have suggested that smoking may increase the risk of cutaneous squamous cell carcinoma (cSCC) while decreasing the risks of basal cell carcinoma (BCC), and melanoma. However, it remains possible that confounding by other factors may explain these associations. The aim of this investigation was to use Mendelian randomization (MR) to test whether smoking is associated with skin cancer, independently of other factors. Two-sample MR analyses were conducted to determine the causal effect of smoking measures on skin cancer risk using genome-wide association study (GWAS) summary statistics. We used the inverse-variance-weighted estimator to derive separate risk estimates across genetic instruments for all smoking measures. A genetic predisposition to smoking initiation was associated with lower risks of all skin cancer types, although none of the effect estimates reached statistical significance (OR 95% CI BCC 0.91, 0.82-1.01; cSCC 0.82, 0.66-1.01; melanoma 0.91, 0.82-1.01). Results for other measures were similar to smoking initiation with the exception of smoking intensity which was associated with a significantly reduced risk of melanoma (OR 0.67, 95% CI 0.51-0.89). Our findings support the findings of observational studies linking smoking to lower risks of melanoma and BCC. However, we found no evidence that smoking is associated with an elevated risk of cSCC; indeed, our results are most consistent with a decreased risk, similar to BCC and melanoma.
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Affiliation(s)
- Jean Claude Dusingize
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Matthew H Law
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Mathias Seviiri
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Catherine M Olsen
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Nirmala Pandeya
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Rachel E Neale
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jue-Sheng Ong
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stuart MacGregor
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David C Whiteman
- Departments of Population Health and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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34
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Ong JS, Seviiri M, Dusingize JC, Wu Y, Han X, Shi J, Olsen CM, Neale RE, Thompson JF, Saw RPM, Shannon KF, Mann GJ, Martin NG, Medland SE, Gordon SD, Scolyer RA, Long GV, Iles MM, Landi MT, Whiteman DC, MacGregor S, Law MH. Uncovering the complex relationship between balding, testosterone and skin cancers in men. Nat Commun 2023; 14:5962. [PMID: 37789011 PMCID: PMC10547720 DOI: 10.1038/s41467-023-41231-8] [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: 09/28/2022] [Accepted: 08/24/2023] [Indexed: 10/05/2023] Open
Abstract
Male-pattern baldness (MPB) is related to dysregulation of androgens such as testosterone. A previously observed relationship between MPB and skin cancer may be due to greater exposure to ultraviolet radiation or indicate a role for androgenic pathways in the pathogenesis of skin cancers. We dissected this relationship via Mendelian randomization (MR) analyses, using genetic data from recent male-only meta-analyses of cutaneous melanoma (12,232 cases; 20,566 controls) and keratinocyte cancers (KCs) (up to 17,512 cases; >100,000 controls), followed by stratified MR analysis by body-sites. We found strong associations between MPB and the risk of KC, but not with androgens, and multivariable models revealed that this relationship was heavily confounded by MPB single nucleotide polymorphisms involved in pigmentation pathways. Site-stratified MR analyses revealed strong associations between MPB with head and neck squamous cell carcinoma and melanoma, suggesting that sun exposure on the scalp, rather than androgens, is the main driver. Men with less hair covering likely explains, at least in part, the higher incidence of melanoma in men residing in countries with high ambient UV.
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Affiliation(s)
- Jue-Sheng Ong
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
| | - Mathias Seviiri
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Jean Claude Dusingize
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Yeda Wu
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Xikun Han
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Catherine M Olsen
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Nicholas G Martin
- Department of Mental Health & Neuroscience, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Sarah E Medland
- Department of Mental Health & Neuroscience, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Scott D Gordon
- Department of Mental Health & Neuroscience, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital & NSW Health Pathology, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Mark M Iles
- Leeds Institute of Medical Research & Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David C Whiteman
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Stuart MacGregor
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Matthew H Law
- Population Health Department, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia.
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35
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Yao Y, Pan L, Song W, Yuan Y, Yan S, Yu S, Chen S. Elsinochrome A induces cell apoptosis and autophagy in photodynamic therapy. J Cell Biochem 2023; 124:1346-1365. [PMID: 37555580 DOI: 10.1002/jcb.30451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/10/2023]
Abstract
Elsinochrome A (EA) is a perylene quinone natural photosensitizer, photosensitizer under light excitation generates reactive oxygen species (ROS) to induce apoptosis, so can be used for treating tumors, that is so-called photodynamic therapy (PDT). However, the molecular mechanism, especially related to apoptosis and autophagy, is still unclear. In this study, we aimed to explore the mechanism of EA-PDT-induced B16 cells apoptosis and autophagy. The action of EA-PDT on mitochondrial permeability transition pore (MPTP), mitochondrial membrane potential (MMP) and the mitochondrial function were researched by fluorescence technique and Extracellular Flux Analyzer. Illumina sequencing, tandem mass tags Quantitative Proteomics and Western Blot studied the mechanism at the gene and protein levels. The results indicated that EA-PDT had excellent phototoxicity in vitro. EA could bind to the mitochondria. EA-PDT for 5 min caused MPTP opening, MMP decreasing and abnormal mitochondrial function with a concentration-dependent characteristic. EA-PDT resulted in an increase intracellular ROS and the number of autophagosomes. Caspase2, caspase9 and tnf were upregulated, and bcl2, prkn, atg2, atg9 and atg10 were downregulated. Our results indicated that EA-PDT induced cell apoptosis and autophagy through the mediation of ROS/Atg/Parkin. This study can provide enlightenment for exploring potential targets of drug development for the PDT of melanoma.
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Affiliation(s)
- Yuanyuan Yao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lili Pan
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenlong Song
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yizhen Yuan
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuzhen Yan
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuqin Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuanglin Chen
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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36
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McGrath IM, Montgomery GW, Mortlock S. Genomic characterisation of the overlap of endometriosis with 76 comorbidities identifies pleiotropic and causal mechanisms underlying disease risk. Hum Genet 2023; 142:1345-1360. [PMID: 37410157 PMCID: PMC10449967 DOI: 10.1007/s00439-023-02582-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
Comorbid conditions can be driven by underlying pleiotropic and causal mechanisms that can provide insights into shared molecular and biological processes contributing to disease risk. Endometriosis is a chronic condition affecting one in nine women of reproductive age and poses many challenges including lengthy diagnostic delays and limited treatment efficacy owing to poor understanding of disease aetiology. To shed light on the underlying biological mechanisms and to identify potential risk factors, we examine the epidemiological and genomic relationship between endometriosis and its comorbidities. In the UK Biobank 292 ICD10 codes were epidemiologically correlated with endometriosis diagnosis, including gynaecological, immune, infection, pain, psychiatric, cancer, gastrointestinal, urinary, bone and cardiovascular traits. A subset of the identified comorbidities (n = 76) underwent follow-up genetic analysis. Whilst Mendelian randomisation suggested causality was not responsible for most comorbid relationships, 22 traits were genetically correlated with endometriosis, including pain, gynaecological and gastrointestinal traits, suggestive of a shared genetic background. Pleiotropic genetic variants and genes were identified using gene-based and colocalisation analysis. Shared genetic risk factors and potential target genes suggest a diverse collection of biological systems are involved in these comorbid relationships including coagulation factors, development of the female reproductive tract and cell proliferation. These findings highlight the diversity of traits with epidemiological and genomic overlap with endometriosis and implicate a key role for pleiotropy in the comorbid relationships.
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Affiliation(s)
- Isabelle M McGrath
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sally Mortlock
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Soo JK, Castle JT, Bennett DC. Preferential killing of melanoma cells by a p16-related peptide. Biol Open 2023; 12:bio059965. [PMID: 37522264 PMCID: PMC10445694 DOI: 10.1242/bio.059965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023] Open
Abstract
We report the identification of a synthetic, cell-penetrating peptide able to kill human melanoma cells efficiently and selectively, while being less toxic to normal human melanocytes and nontoxic to human fibroblasts. The peptide is based on the target-binding site of the melanoma suppressor and senescence effector p16 (also known as INK4A or CDKN2A), coupled to a cell-penetrating moiety. The killing is by apoptosis and appears to act by a route other than the canonical downstream target of p16 and CDK4, the retinoblastoma (RB) protein family, as it is also effective in HeLa cells and a melanocyte line expressing HPV E7 oncogenes, which both lack any active RB. There was varying toxicity to other types of cancer cell lines, such as glioblastoma. Melanoma cell killing by a p16-derived peptide was reported once before but only at a higher concentration, while selectivity and generality were not previously tested.
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Affiliation(s)
- Julia K. Soo
- Molecular & Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Joanna T. Castle
- Molecular & Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Dorothy C. Bennett
- Molecular & Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
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38
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Wong CK, Dite GS, Spaeth E, Murphy NM, Allman R. Melanoma risk prediction based on a polygenic risk score and clinical risk factors. Melanoma Res 2023; 33:293-299. [PMID: 37096571 PMCID: PMC10309112 DOI: 10.1097/cmr.0000000000000896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/30/2023] [Indexed: 04/26/2023]
Abstract
Melanoma is one of the most commonly diagnosed cancers in the Western world: third in Australia, fifth in the USA and sixth in the European Union. Predicting an individual's personal risk of developing melanoma may aid them in undertaking effective risk reduction measures. The objective of this study was to use the UK Biobank to predict the 10-year risk of melanoma using a newly developed polygenic risk score (PRS) and an existing clinical risk model. We developed the PRS using a matched case-control training dataset ( N = 16 434) in which age and sex were controlled by design. The combined risk score was developed using a cohort development dataset ( N = 54 799) and its performance was tested using a cohort testing dataset ( N = 54 798). Our PRS comprises 68 single-nucleotide polymorphisms and had an area under the receiver operating characteristic curve of 0.639 [95% confidence interval (CI) = 0.618-0.661]. In the cohort testing data, the hazard ratio per SD of the combined risk score was 1.332 (95% CI = 1.263-1.406). Harrell's C-index was 0.685 (95% CI = 0.654-0.715). Overall, the standardized incidence ratio was 1.193 (95% CI = 1.067-1.335). By combining a PRS and a clinical risk score, we have developed a risk prediction model that performs well in terms of discrimination and calibration. At an individual level, information on the 10-year risk of melanoma can motivate people to take risk-reduction action. At the population level, risk stratification can allow more effective population-level screening strategies to be implemented.
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Affiliation(s)
| | | | - Erika Spaeth
- Phenogen Sciences Inc., Charlotte, North Carolina, USA
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Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet 2023; 110:1138-1161. [PMID: 37339630 PMCID: PMC10357503 DOI: 10.1016/j.ajhg.2023.05.013] [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: 07/13/2022] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
Autoimmunity and cancer represent two different aspects of immune dysfunction. Autoimmunity is characterized by breakdowns in immune self-tolerance, while impaired immune surveillance can allow for tumorigenesis. The class I major histocompatibility complex (MHC-I), which displays derivatives of the cellular peptidome for immune surveillance by CD8+ T cells, serves as a common genetic link between these conditions. As melanoma-specific CD8+ T cells have been shown to target melanocyte-specific peptide antigens more often than melanoma-specific antigens, we investigated whether vitiligo- and psoriasis-predisposing MHC-I alleles conferred a melanoma-protective effect. In individuals with cutaneous melanoma from both The Cancer Genome Atlas (n = 451) and an independent validation set (n = 586), MHC-I autoimmune-allele carrier status was significantly associated with a later age of melanoma diagnosis. Furthermore, MHC-I autoimmune-allele carriers were significantly associated with decreased risk of developing melanoma in the Million Veteran Program (OR = 0.962, p = 0.024). Existing melanoma polygenic risk scores (PRSs) did not predict autoimmune-allele carrier status, suggesting these alleles provide orthogonal risk-relevant information. Mechanisms of autoimmune protection were neither associated with improved melanoma-driver mutation association nor improved gene-level conserved antigen presentation relative to common alleles. However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte-conserved antigens and loss of heterozygosity of autoimmune alleles caused the greatest reduction in presentation for several conserved antigens across individuals with loss of HLA alleles. Overall, this study presents evidence that MHC-I autoimmune-risk alleles modulate melanoma risk unaccounted for by current PRSs.
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Affiliation(s)
- James V Talwar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - David Laub
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Meghana S Pagadala
- Biomedical Science Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - McKenna Lewis
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Georg E Luebeck
- Public Health Sciences Division, Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Cuiping Pan
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA
| | - Frederick N Dong
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Kyriacos Markianos
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02115, USA
| | - Craig C Teerlink
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Julie Lynch
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard Hauger
- VA San Diego Healthcare System, La Jolla, CA, USA; Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA; Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Wesley K Thompson
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK 74136, USA
| | - Kit Curtius
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Laboratory of Immunology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Division of Hematology and Oncology, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
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Simonin-Wilmer I, Ossio R, Leddin EM, Harland M, Pooley KA, Martil de la Garza MG, Obolenski S, Hewinson J, Wong CC, Iyer V, Taylor JC, Newton-Bishop JA, Bishop DT, Cisneros GA, Iles MM, Adams DJ, Robles-Espinoza CD. Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort. J Med Genet 2023; 60:692-696. [PMID: 36539277 PMCID: PMC10279804 DOI: 10.1136/jmg-2022-108776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022]
Abstract
Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumour types, including melanoma, glioma, leukaemia and cardiac angiosarcoma. We sequenced all coding exons of the POT1 gene in 2928 European-descent melanoma cases and 3298 controls, identifying 43 protein-changing genetic variants. We performed POT1-telomere binding assays for all missense and stop-gained variants, finding nine variants that impair or disrupt protein-telomere complex formation, and we further define the role of variants in the regulation of telomere length and complex formation through molecular dynamics simulations. We determine that POT1 coding variants are a minor contributor to melanoma burden in the general population, with only about 0.5% of melanoma cases carrying germline pathogenic variants in this gene, but should be screened in individuals with a strong family history of melanoma and/or multiple malignancies.
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Affiliation(s)
- Irving Simonin-Wilmer
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Qro, Mexico
| | - Raul Ossio
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Qro, Mexico
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas, USA
| | - Mark Harland
- Section of Epidemiolgy and Biostatistics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
| | - Karen A Pooley
- Centre for Cancer Genetic Epidemiology, Cambridge University, Cambridge, UK
| | | | | | - James Hewinson
- CASM, Wellcome Sanger Institute, Hinxton, UK
- CeGaT GmbH, Tübingen, Germany
| | - Chi C Wong
- CASM, Wellcome Sanger Institute, Hinxton, UK
| | - Vivek Iyer
- CASM, Wellcome Sanger Institute, Hinxton, UK
| | - John C Taylor
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Julia A Newton-Bishop
- Section of Epidemiolgy and Biostatistics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, UK
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, University of Leeds, Leeds, UK
| | - Gerardo Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas, USA
- Department of Physics, The University of Texas at Dallas, Richardson, Texas, USA
| | - Mark M Iles
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | | | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Qro, Mexico
- CASM, Wellcome Sanger Institute, Hinxton, UK
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41
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Badré A, Pan C. Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis. PLoS Comput Biol 2023; 19:e1011211. [PMID: 37418352 DOI: 10.1371/journal.pcbi.1011211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/23/2023] [Indexed: 07/09/2023] Open
Abstract
Many complex diseases share common genetic determinants and are comorbid in a population. We hypothesized that the co-occurrences of diseases and their overlapping genetic etiology can be exploited to simultaneously improve multiple diseases' polygenic risk scores (PRS). This hypothesis was tested using a multi-task learning (MTL) approach based on an explainable neural network architecture. We found that parallel estimations of the PRS for 17 prevalent cancers in a pan-cancer MTL model were generally more accurate than independent estimations for individual cancers in comparable single-task learning (STL) models. Such performance improvement conferred by positive transfer learning was also observed consistently for 60 prevalent non-cancer diseases in a pan-disease MTL model. Interpretation of the MTL models revealed significant genetic correlations between the important sets of single nucleotide polymorphisms used by the neural network for PRS estimation. This suggested a well-connected network of diseases with shared genetic basis.
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Affiliation(s)
- Adrien Badré
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Chongle Pan
- School of Computer Science, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
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42
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Katki HA, Berndt SI, Machiela MJ, Stewart DR, Garcia-Closas M, Kim J, Shi J, Yu K, Rothman N. Increase in power by obtaining 10 or more controls per case when type-1 error is small in large-scale association studies. BMC Med Res Methodol 2023; 23:153. [PMID: 37386403 PMCID: PMC10308790 DOI: 10.1186/s12874-023-01973-x] [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: 02/06/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The rule of thumb that there is little gain in statistical power by obtaining more than 4 controls per case, is based on type-1 error α = 0.05. However, association studies that evaluate thousands or millions of associations use smaller α and may have access to plentiful controls. We investigate power gains, and reductions in p-values, when increasing well beyond 4 controls per case, for small α. METHODS We calculate the power, the median expected p-value, and the minimum detectable odds-ratio (OR), as a function of the number of controls/case, as α decreases. RESULTS As α decreases, at each ratio of controls per case, the increase in power is larger than for α = 0.05. For α between 10-6 and 10-9 (typical for thousands or millions of associations), increasing from 4 controls per case to 10-50 controls per case increases power. For example, a study with power = 0.2 (α = 5 × 10-8) with 1 control/case has power = 0.65 with 4 controls/case, but with 10 controls/case has power = 0.78, and with 50 controls/case has power = 0.84. For situations where obtaining more than 4 controls per case provides small increases in power beyond 0.9 (at small α), the expected p-value can decrease by orders-of-magnitude below α. Increasing from 1 to 4 controls/case reduces the minimum detectable OR toward the null by 20.9%, and from 4 to 50 controls/case reduces by an additional 9.7%, a result which applies regardless of α and hence also applies to "regular" α = 0.05 epidemiology. CONCLUSIONS At small α, versus 4 controls/case, recruiting 10 or more controls/cases can increase power, reduce the expected p-value by 1-2 orders of magnitude, and meaningfully reduce the minimum detectable OR. These benefits of increasing the controls/case ratio increase as the number of cases increases, although the amount of benefit depends on exposure frequencies and true OR. Provided that controls are comparable to cases, our findings suggest greater sharing of comparable controls in large-scale association studies.
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Affiliation(s)
- Hormuzd A Katki
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Sun J, Wang L, Zhou X, Hu L, Yuan S, Bian Z, Chen J, Zhu Y, Farrington SM, Campbell H, Ding K, Zhang D, Dunlop MG, Theodoratou E, Li X. Cross-cancer pleiotropic analysis identifies three novel genetic risk loci for colorectal cancer. Hum Mol Genet 2023; 32:2093-2102. [PMID: 36928917 PMCID: PMC10244225 DOI: 10.1093/hmg/ddad044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND To understand the shared genetic basis between colorectal cancer (CRC) and other cancers and identify potential pleiotropic loci for compensating the missing genetic heritability of CRC. METHODS We conducted a systematic genome-wide pleiotropy scan to appraise associations between cancer-related genetic variants and CRC risk among European populations. Single nucleotide polymorphism (SNP)-set analysis was performed using data from the UK Biobank and the Study of Colorectal Cancer in Scotland (10 039 CRC cases and 30 277 controls) to evaluate the overlapped genetic regions for susceptibility of CRC and other cancers. The variant-level pleiotropic associations between CRC and other cancers were examined by CRC genome-wide association study meta-analysis and the pleiotropic analysis under composite null hypothesis (PLACO) pleiotropy test. Gene-based, co-expression and pathway enrichment analyses were performed to explore potential shared biological pathways. The interaction between novel genetic variants and common environmental factors was further examined for their effects on CRC. RESULTS Genome-wide pleiotropic analysis identified three novel SNPs (rs2230469, rs9277378 and rs143190905) and three mapped genes (PIP4K2A, HLA-DPB1 and RTEL1) to be associated with CRC. These genetic variants were significant expressions quantitative trait loci in colon tissue, influencing the expression of their mapped genes. Significant interactions of PIP4K2A and HLA-DPB1 with environmental factors, including smoking and alcohol drinking, were observed. All mapped genes and their co-expressed genes were significantly enriched in pathways involved in carcinogenesis. CONCLUSION Our findings provide an important insight into the shared genetic basis between CRC and other cancers. We revealed several novel CRC susceptibility loci to help understand the genetic architecture of CRC.
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Affiliation(s)
- Jing Sun
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lijuan Wang
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Xuan Zhou
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lidan Hu
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310005, China
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Zilong Bian
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Chen
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yingshuang Zhu
- Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Kefeng Ding
- Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, The School of Public Health of Qingdao University, Qingdao 266071, China
| | - Malcolm G Dunlop
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China
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44
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Wallingford CK, Demeshko A, Krishnakripa AK, Smit D, Duffy DL, Betz-Stablein B, Pflugfelder A, Jagirdar K, Holland E, Mann GJ, Primiero CA, Yanes T, Malvehy J, Badenas C, Carrera C, Aguilera P, Olsen C, Ward SV, Haass NK, Sturm RA, Puig S, Whiteman D, Law MH, Cust AE, Potrony M, Soyer H P, McInerney-Leo AM. The MC1R r allele does not increase melanoma risk in MITF E318K carriers. Br J Dermatol 2023; 188:770-776. [PMID: 36879448 PMCID: PMC10230961 DOI: 10.1093/bjd/ljad041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/18/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Population-wide screening for melanoma is not cost-effective, but genetic characterization could facilitate risk stratification and targeted screening. Common Melanocortin-1 receptor (MC1R) red hair colour (RHC) variants and Microphthalmia-associated transcription factor (MITF) E318K separately confer moderate melanoma susceptibility, but their interactive effects are relatively unexplored. OBJECTIVES To evaluate whether MC1R genotypes differentially affect melanoma risk in MITF E318K+ vs. E318K- individuals. MATERIALS AND METHODS Melanoma status (affected or unaffected) and genotype data (MC1R and MITF E318K) were collated from research cohorts (five Australian and two European). In addition, RHC genotypes from E318K+ individuals with and without melanoma were extracted from databases (The Cancer Genome Atlas and Medical Genome Research Bank, respectively). χ2 and logistic regression were used to evaluate RHC allele and genotype frequencies within E318K+/- cohorts depending on melanoma status. Replication analysis was conducted on 200 000 general-population exomes (UK Biobank). RESULTS The cohort comprised 1165 MITF E318K- and 322 E318K+ individuals. In E318K- cases MC1R R and r alleles increased melanoma risk relative to wild type (wt), P < 0.001 for both. Similarly, each MC1R RHC genotype (R/R, R/r, R/wt, r/r and r/wt) increased melanoma risk relative to wt/wt (P < 0.001 for all). In E318K+ cases, R alleles increased melanoma risk relative to the wt allele [odds ratio (OR) 2.04 (95% confidence interval 1.67-2.49); P = 0.01], while the r allele risk was comparable with the wt allele [OR 0.78 (0.54-1.14) vs. 1.00, respectively]. E318K+ cases with the r/r genotype had a lower but not significant melanoma risk relative to wt/wt [OR 0.52 (0.20-1.38)]. Within the E318K+ cohort, R genotypes (R/R, R/r and R/wt) conferred a significantly higher risk compared with non-R genotypes (r/r, r/wt and wt/wt) (P < 0.001). UK Biobank data supported our findings that r did not increase melanoma risk in E318K+ individuals. CONCLUSIONS RHC alleles/genotypes modify melanoma risk differently in MITF E318K- and E318K+ individuals. Specifically, although all RHC alleles increase risk relative to wt in E318K- individuals, only MC1R R increases melanoma risk in E318K+ individuals. Importantly, in the E318K+ cohort the MC1R r allele risk is comparable with wt. These findings could inform counselling and management for MITF E318K+ individuals.
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Affiliation(s)
- Courtney K Wallingford
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Anastassia Demeshko
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | | | - Darren J Smit
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - David L Duffy
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Brigid Betz-Stablein
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Annette Pflugfelder
- Center of Dermato-Oncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Kasturee Jagirdar
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- Biochemistry and Molecular Biology Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elizabeth Holland
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, Australia
| | - Graham J Mann
- The Melanoma Institute Australia, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Clare A Primiero
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Tatiane Yanes
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Josep Malvehy
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cèlia Badenas
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain
| | - Cristina Carrera
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Paula Aguilera
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Catherine M Olsen
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Sarah V Ward
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
| | - Nikolas K Haass
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Richard A Sturm
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Susana Puig
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD, 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, Australia
| | - Anne E Cust
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, Australia
- The Melanoma Institute Australia, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Miriam Potrony
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain
| | - H Peter Soyer
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Australia
| | - Aideen M McInerney-Leo
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
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45
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Cornish N, Haycock P, Brenner H, Figueiredo JC, Galesloot T, Grant RC, Johansson M, Mariosa D, McKay J, Pai R, Pellatt AJ, Samadder NJ, Shi J, Thibord F, Trégouët DA, Voegele C, Thirlwell C, Mumford A, Langdon R. Causal relationships between risk of venous thromboembolism and 18 cancers: a bidirectional Mendelian randomisation analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23289792. [PMID: 37292802 PMCID: PMC10246038 DOI: 10.1101/2023.05.16.23289792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background People with cancer experience high rates of venous thromboembolism (VTE). Additionally, risk of subsequent cancer is increased in people experiencing their first VTE. The causal mechanisms underlying this association are not completely understood, and it is unknown whether VTE is itself a risk factor for cancer. Methods We used data from large genome-wide association study meta-analyses to perform bi-directional Mendelian randomisation analyses to estimate causal associations between genetically-proxied lifetime risk of VTE and risk of 18 different cancers. Results We found no conclusive evidence that genetically-proxied lifetime risk of VTE was causally associated with an increased incidence of cancer, or vice-versa. We observed an association between VTE and pancreatic cancer risk (odds ratio for pancreatic cancer 1.23 (95% confidence interval 1.08 - 1.40) per log-odds increase in risk of VTE, P = 0.002). However, sensitivity analyses revealed this association was predominantly driven by a variant proxying non-O blood group, with inadequate evidence from Mendelian randomisation to suggest a causal relationship. Conclusions These findings do not support the hypothesis that genetically-proxied lifetime risk of VTE is a cause of cancer. Existing observational epidemiological associations between VTE and cancer are therefore more likely to be driven by pathophysiological changes which occur in the setting of active cancer and anti-cancer treatments. Further work is required to explore and synthesise evidence for these mechanisms.
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Affiliation(s)
- Naomi Cornish
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philip Haycock
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jane C. Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles CA
| | - Tessel Galesloot
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert C Grant
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Daniela Mariosa
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rish Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Arizona, Scottsdale, USA
| | - Andrew J Pellatt
- Division of Cancer Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA
| | | | - Catherine Voegele
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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46
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Bhave P, Wong J, McInerney-Leo A, Cust AE, Lawn C, Janda M, Mar VJ. Management of cutaneous melanoma in Australia: a narrative review. Med J Aust 2023; 218:426-431. [PMID: 37120760 DOI: 10.5694/mja2.51910] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/05/2023] [Accepted: 02/28/2023] [Indexed: 05/01/2023]
Affiliation(s)
- Prachi Bhave
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, VIC
- Alfred Hospital, Melbourne, VIC
| | | | - Aideen McInerney-Leo
- Dermatology Research Centre, University of Queensland Diamantina Institute for Cancer Immunology and Metabolic Medicine, Brisbane, QLD
- Australian Centre of Excellence in Melanoma Imaging, Brisbane, QLD
| | - Anne E Cust
- Australian Centre of Excellence in Melanoma Imaging, Brisbane, QLD
- Melanoma Institute Australia, Sydney, NSW
| | - Craig Lawn
- Melanoma Institute Australia, Sydney, NSW
- Centre of Excellence in Melanoma Imaging, Brisbane, QLD
| | - Monika Janda
- Centre for Health Services Research, University of Queensland, Brisbane, QLD
| | - Victoria J Mar
- Alfred Hospital, Melbourne, VIC
- Monash University, Melbourne, VIC
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Abstract
Over the past decade, melanoma has led the field in new cancer treatments, with impressive gains in on-treatment survival but more modest improvements in overall survival. Melanoma presents heterogeneity and transcriptional plasticity that recapitulates distinct melanocyte developmental states and phenotypes, allowing it to adapt to and eventually escape even the most advanced treatments. Despite remarkable advances in our understanding of melanoma biology and genetics, the melanoma cell of origin is still fiercely debated because both melanocyte stem cells and mature melanocytes can be transformed. Animal models and high-throughput single-cell sequencing approaches have opened new opportunities to address this question. Here, we discuss the melanocytic journey from the neural crest, where they emerge as melanoblasts, to the fully mature pigmented melanocytes resident in several tissues. We describe a new understanding of melanocyte biology and the different melanocyte subpopulations and microenvironments they inhabit, and how this provides unique insights into melanoma initiation and progression. We highlight recent findings on melanoma heterogeneity and transcriptional plasticity and their implications for exciting new research areas and treatment opportunities. The lessons from melanocyte biology reveal how cells that are present to protect us from the damaging effects of ultraviolet radiation reach back to their origins to become a potentially deadly cancer.
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Affiliation(s)
- Patricia P Centeno
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Valeria Pavet
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK
| | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK.
- Oncodrug Ltd, Alderly Park, Macclesfield, UK.
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48
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Lee OW, Rodrigues C, Lin SH, Luo W, Jones K, Brown DW, Zhou W, Karlins E, Khan SM, Baulande S, Raynal V, Surdez D, Reynaud S, Rubio RA, Zaidi S, Grossetête S, Ballet S, Lapouble E, Laurence V, Pierron G, Gaspar N, Corradini N, Marec-Bérard P, Rothman N, Dagnall CL, Burdett L, Manning M, Wyatt K, Yeager M, Chari R, Leisenring WM, Kulozik AE, Kriebel J, Meitinger T, Strauch K, Kirchner T, Dirksen U, Mirabello L, Tucker MA, Tirode F, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Romero-Pérez L, Hartmann W, Metzler M, Diver WR, Lori A, Freedman ND, Hoover RN, Morton LM, Chanock SJ, Grünewald TGP, Delattre O, Machiela MJ. Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding. Am J Hum Genet 2023; 110:427-441. [PMID: 36787739 PMCID: PMC10027473 DOI: 10.1016/j.ajhg.2023.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Ewing sarcoma (EwS) is a rare bone and soft tissue malignancy driven by chromosomal translocations encoding chimeric transcription factors, such as EWSR1-FLI1, that bind GGAA motifs forming novel enhancers that alter nearby expression. We propose that germline microsatellite variation at the 6p25.1 EwS susceptibility locus could impact downstream gene expression and EwS biology. We performed targeted long-read sequencing of EwS blood DNA to characterize variation and genomic features important for EWSR1-FLI1 binding. We identified 50 microsatellite alleles at 6p25.1 and observed that EwS-affected individuals had longer alleles (>135 bp) with more GGAA repeats. The 6p25.1 GGAA microsatellite showed chromatin features of an EWSR1-FLI1 enhancer and regulated expression of RREB1, a transcription factor associated with RAS/MAPK signaling. RREB1 knockdown reduced proliferation and clonogenic potential and reduced expression of cell cycle and DNA replication genes. Our integrative analysis at 6p25.1 details increased binding of longer GGAA microsatellite alleles with acquired EWSR-FLI1 to promote Ewing sarcomagenesis by RREB1-mediated proliferation.
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Affiliation(s)
- Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Calvin Rodrigues
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wen Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Virginie Raynal
- ICGex Next-Generation Sequencing Platform, PSL Université, Research Center, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Stephanie Reynaud
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Rebeca Alba Rubio
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Sakina Zaidi
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Stelly Ballet
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Eve Lapouble
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | | | - Gaelle Pierron
- SIREDO Oncology Centre, Institut Curie, 75005 Paris, France; Unité de Génétique Somatique, Department of Genetics, Institut Curie Hospital, 75005 Paris, France
| | - Nathalie Gaspar
- Department of Oncology for Child and Adolescent, Institut Gustave Roussy, 94800 Villejuif, France
| | - Nadège Corradini
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Perrine Marec-Bérard
- Institute for Paediatric Haematology and Oncology, Leon Bérard Cancer Centre, University of Lyon, 69008 Lyon, France
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Michelle Manning
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Kathleen Wyatt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Raj Chari
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; Genome Modification Core Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andreas E Kulozik
- University Children's Hospital of Heidelberg, 69120 Heidelberg, Germany
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 München-Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, 80539 Munich, Germany
| | - Thomas Kirchner
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany
| | - Uta Dirksen
- University Children's Hospital of Essen, 45147 Essen, Germany
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Franck Tirode
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama, Birmingham, AL 35294, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard- Domagk Institute of Pathology, University Hospital of Münster, 48149 Münster, Germany
| | - Markus Metzler
- University Children's Hospital of Erlangen, 91054 Erlangen, Germany
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Adriana Lori
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, 80337 Munich, Germany; Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Olivier Delattre
- Inserm U830, PSL Université, Research Center, Institut Curie, 75005 Paris, France; SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
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49
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Xie H, Cao X, Zhang S, Sha Q. Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies. Genet Epidemiol 2023; 47:185-197. [PMID: 36691904 DOI: 10.1002/gepi.22513] [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: 06/14/2022] [Revised: 11/16/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023]
Abstract
In genome-wide association studies (GWAS) for thousands of phenotypes in biobanks, most binary phenotypes have substantially fewer cases than controls. Many widely used approaches for joint analysis of multiple phenotypes produce inflated type I error rates for such extremely unbalanced case-control phenotypes. In this research, we develop a method to jointly analyze multiple unbalanced case-control phenotypes to circumvent this issue. We first group multiple phenotypes into different clusters based on a hierarchical clustering method, then we merge phenotypes in each cluster into a single phenotype. In each cluster, we use the saddlepoint approximation to estimate the p value of an association test between the merged phenotype and a single nucleotide polymorphism (SNP) which eliminates the issue of inflated type I error rate of the test for extremely unbalanced case-control phenotypes. Finally, we use the Cauchy combination method to obtain an integrated p value for all clusters to test the association between multiple phenotypes and a SNP. We use extensive simulation studies to evaluate the performance of the proposed approach. The results show that the proposed approach can control type I error rate very well and is more powerful than other available methods. We also apply the proposed approach to phenotypes in category IX (diseases of the circulatory system) in the UK Biobank. We find that the proposed approach can identify more significant SNPs than the other viable methods we compared with.
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Affiliation(s)
- Hongjing Xie
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, USA
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50
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Johansson PA, Palmer JM, Hamilton HR, Whiteman DC, Pritchard AL, Hayward NK. Germline Variants in Childhood Cutaneous Melanoma. J Invest Dermatol 2023:S0022-202X(23)00155-0. [PMID: 36863448 DOI: 10.1016/j.jid.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Affiliation(s)
- Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jane M Palmer
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hayley R Hamilton
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonia L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Genetics and Immunology Group, University of the Highlands and Islands, Inverness, United Kingdom
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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