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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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2
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Neale RE, Beedle V, Ebeling PR, Elliott T, Francis D, Girgis CM, Gordon L, Janda M, Jones G, Lucas RM, Mason RS, Monnington PK, Morahan J, Paxton G, Sinclair C, Shumack S, Smith J, Webb AR, Whiteman DC. Balancing the risks and benefits of sun exposure: A revised position statement for Australian adults. Aust N Z J Public Health 2024; 48:100117. [PMID: 38350754 DOI: 10.1016/j.anzjph.2023.100117] [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: 09/03/2023] [Revised: 11/11/2023] [Accepted: 11/21/2023] [Indexed: 02/15/2024] Open
Abstract
OBJECTIVE To describe the development of a new position statement regarding balancing the risks and benefits of sun exposure for Australian adults. METHODS We conducted a Sun Exposure Summit in March 2021, with presentations from invited experts and a workshop including representation from academic, clinical, policy, and patient stakeholder organisations. The group considered advice about balancing the risks and benefits of sun exposure for Australian adults and developed a revised consensus position statement. RESULTS The balance of risks and benefits of sun exposure is not the same for everybody. For people at very high risk of skin cancer, the risks of exposure likely outweigh the benefits; sun protection is essential. Conversely, people with deeply pigmented skin are at low risk of skin cancer but at high risk of vitamin D deficiency; routine sun protection is not recommended. For those at intermediate risk of skin cancer, sun protection remains a priority, but individuals may obtain sufficient sun exposure to maintain adequate vitamin D status. CONCLUSIONS The new position statement provides sun exposure advice that explicitly recognises the differing needs of Australia's diverse population. IMPLICATIONS FOR PUBLIC HEALTH Mass communication campaigns should retain the focus on skin cancer prevention. The new position statement will support the delivery of personalised advice.
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Affiliation(s)
- Rachel E Neale
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; University of Queensland, Brisbane, Australia.
| | | | - Peter R Ebeling
- Monash University, Melbourne, Australia; Healthy Bones Australia, Australia
| | - Thomas Elliott
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Christian M Girgis
- University of Sydney, Sydney, Australia; Australa and New Zealand Bone and Mineral Society, Australia
| | - Louisa Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; University of Queensland, Brisbane, Australia
| | | | - Graeme Jones
- Australa and New Zealand Bone and Mineral Society, Australia; University of Tasmania, Hobart, Australia
| | | | - Rebecca S Mason
- University of Sydney, Sydney, Australia; Healthy Bones Australia, Australia
| | | | | | | | | | | | - Jane Smith
- Royal Australian College of General Practitioners, Australia
| | - Ann R Webb
- University of Manchester, Manchester, United Kingdom
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; University of Queensland, Brisbane, Australia
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3
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Shi JJ, Mao CY, Guo YZ, Fan Y, Hao XY, Li SJ, Tian J, Hu ZW, Li MJ, Li JD, Ma DR, Guo MN, Zuo CY, Liang YY, Xu YM, Yang J, Shi CH. Joint analysis of proteome, transcriptome, and multi-trait analysis to identify novel Parkinson's disease risk genes. Aging (Albany NY) 2024; 16:1555-1580. [PMID: 38240717 PMCID: PMC10866412 DOI: 10.18632/aging.205444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
Genome-wide association studies (GWAS) have identified multiple risk variants for Parkinson's disease (PD). Nevertheless, how the risk variants confer the risk of PD remains largely unknown. We conducted a proteome-wide association study (PWAS) and summary-data-based mendelian randomization (SMR) analysis by integrating PD GWAS with proteome and protein quantitative trait loci (pQTL) data from human brain, plasma and CSF. We also performed a large transcriptome-wide association study (TWAS) and Fine-mapping of causal gene sets (FOCUS), leveraging joint-tissue imputation (JTI) prediction models of 22 tissues to identify and prioritize putatively causal genes. We further conducted PWAS, SMR, TWAS, and FOCUS using a multi-trait analysis of GWAS (MTAG) to identify additional PD risk genes to boost statistical power. In this large-scale study, we identified 16 genes whose genetically regulated protein abundance levels were associated with Parkinson's disease risk. We undertook a large-scale analysis of PD and correlated traits, through TWAS and FOCUS studies, and discovered 26 casual genes related to PD that had not been reported in previous TWAS. 5 genes (CD38, GPNMB, RAB29, TMEM175, TTC19) showed significant associations with PD at both the proteome-wide and transcriptome-wide levels. Our study provides new insights into the etiology and underlying genetic architecture of PD.
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Affiliation(s)
- Jing-Jing Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Cheng-Yuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Ya-Zhou Guo
- School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
| | - Yu Fan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Xiao-Yan Hao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Shuang-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jie Tian
- Zhengzhou Railway Vocational and Technical College, Zhengzhou 450000, Henan, China
| | - Zheng-Wei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Meng-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jia-Di Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Dong-Rui Ma
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Meng-Nan Guo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Chun-Yan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Yuan-Yuan Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
| | - Chang-He Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou 450000, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou 450000, Henan, China
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Mou SI, Sultana T, Chatterjee D, Faruk MO, Hosen MI. Comprehensive characterization of coding and non-coding single nucleotide polymorphisms of the Myoneurin (MYNN) gene using molecular dynamics simulation and docking approaches. PLoS One 2024; 19:e0296361. [PMID: 38165846 PMCID: PMC10760682 DOI: 10.1371/journal.pone.0296361] [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: 08/21/2023] [Accepted: 12/11/2023] [Indexed: 01/04/2024] Open
Abstract
Genome-wide association studies (GWAS) identified a coding single nucleotide polymorphism, MYNN rs10936599, at chromosome 3q. MYNN gene encodes myoneurin protein, which has been associated with several cancer pathogenesis and disease development processes. However, there needed to be a more detailed characterization of this polymorphism's (and other coding and non-coding polymorphisms) structural, functional, and molecular impact. The current study addressed this gap and analyzed different properties of rs10936599 and non-coding SNPs of MYNN via a thorough computational method. The variant, rs10936599, was predicted functionally deleterious by nine functionality prediction approaches, like SIFT, PolyPhen-2, and REVEL, etc. Following that, structural modifications were estimated through the HOPE server and Mutation3D. Moreover, the mutation was found in a conserved and active residue, according to ConSurf and CPORT. Further, the secondary structures were predicted, followed by tertiary structures, and there was a significant deviation between the native and variant models. Similarly, molecular simulation also showed considerable differences in the dynamic pattern of the wildtype and mutant structures. Molecular docking revealed that the variant binds with better docking scores with ligand NOTCH2. In addition to that, non-coding SNPs located at the MYNN locus were retrieved from the ENSEMBL database. These were found to disrupt the transcription factor binding regulatory regions; nonetheless, only two affect miRNA target sites. Again, eight non-coding variants were detected in the testes with normalized expression, whereas HaploReg v4.1 unveiled annotations for non-coding variants. In summary, in silico comprehensive characterization of coding and non-coding single nucleotide polymorphisms of MYNN gene will assist researchers to work on MYNN gene and establish their association with certain types of cancers.
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Affiliation(s)
- Sadia Islam Mou
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tamanna Sultana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md. Omar Faruk
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
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Chen J, Epstein MP, Schildkraut JM, Kar SP. Mapping inherited genetic variation with opposite effects on autoimmune disease and cancer identifies candidate drug targets associated with the anti-tumor immune response. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.23.23300491. [PMID: 38234717 PMCID: PMC10793537 DOI: 10.1101/2023.12.23.23300491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Germline alleles near genes that encode certain immune checkpoints (CTLA4, CD200) are associated with autoimmune/autoinflammatory disease and cancer but in opposite directions. This motivates a systematic search for additional germline alleles which demonstrate this pattern with the aim of identifying potential cancer immunotherapeutic targets using human genetic evidence. Methods Pairwise fixed effect cross-disorder meta-analyses combining genome-wide association studies (GWAS) for breast, prostate, ovarian and endometrial cancers (240,540 cases/317,000 controls) and seven autoimmune/autoinflammatory diseases (112,631 cases/895,386 controls) coupled with in silico follow-up. To ensure detection of alleles with opposite effects on cancer and autoimmune/autoinflammatory disease, the signs on the beta coefficients in the autoimmune/autoinflammatory GWAS were reversed prior to meta-analyses. Results Meta-analyses followed by linkage disequilibrium clumping identified 312 unique, independent lead variants with Pmeta<5x10-8 associated with at least one of the cancer types at Pcancer<10-3 and one of the autoimmune/autoinflammatory diseases at Pauto<10-3. At each lead variant, the allele that conferred autoimmune/autoinflammatory disease risk was protective for cancer. Mapping each lead variant to its nearest gene as its putative functional target and focusing on genes with established immunological effects implicated 32 of the nearest genes. Tumor bulk RNA-Seq data highlighted that the tumor expression of 5/32 genes (IRF1, IKZF1, SPI1, SH2B3, LAT) were each strongly correlated (Spearman's ρ>0.5) with at least one intra-tumor T/myeloid cell infiltration marker (CD4, CD8A, CD11B, CD45) in every one of the cancer types. Tumor single-cell RNA-Seq data from all cancer types showed that the five genes were more likely to be expressed in intra-tumor immune versus malignant cells. The five lead SNPs corresponding to these genes were linked to them via expression quantitative trait locus mechanisms and at least one additional line of functional evidence. Proteins encoded by the genes were predicted to be druggable. Conclusion We provide population-scale germline genetic and functional genomic evidence to support further evaluation of the proteins encoded by IRF1, IKZF1, SPI1, SH2B3, and LAT as possible targets for cancer immunotherapy.
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Affiliation(s)
- Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Joellen M Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Siddhartha P Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Ovarian Cancer Programme, Cancer Research UK Cambridge Centre, Cambridge, UK
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6
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Brathovde M, Moger TA, Aalen OO, Grotmol T, Veierød MB, Valberg M. A lean additive frailty model: With an application to clustering of melanoma in Norwegian families. Stat Med 2023; 42:4207-4235. [PMID: 37527835 DOI: 10.1002/sim.9856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 06/25/2023] [Accepted: 07/09/2023] [Indexed: 08/03/2023]
Abstract
Additive frailty models are used to model correlated survival data. However, the complexity of the models increases with cluster size to the extent that practical usage becomes increasingly challenging. We present a modification of the additive genetic gamma frailty (AGGF) model, the lean AGGF (L-AGGF) model, which alleviates some of these challenges by using a leaner additive decomposition of the frailty. The performances of the models were compared and evaluated in a simulation study. The L-AGGF model was used to analyze population-wide data on clustering of melanoma in 2 391 125 two-generational Norwegian families, 1960-2015. Using this model, we could analyze the complete data set, while the original model limited the analysis to a restricted data set (with cluster sizes≤ 7 $$ \le 7 $$ ). We found a substantial clustering of melanoma in Norwegian families and large heterogeneity in melanoma risk across the population, where 52% of the frailty was attributed to the 10% of the population at highest unobserved risk. Due to the improved scalability, the L-AGGF model enables a wider range of analyses of population-wide data compared to the AGGF model. Moreover, the methods outlined here make it possible to perform these analyses in a computationally efficient manner.
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Affiliation(s)
- Mari Brathovde
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Tron A Moger
- Department of Health Management and Health Economics, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Odd O Aalen
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Marit B Veierød
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Morten Valberg
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
- Department of Community Medicine and Global Health, Institute of Health and Society, University of Oslo, Oslo, Norway
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Crescioli S, Correa I, Ng J, Willsmore ZN, Laddach R, Chenoweth A, Chauhan J, Di Meo A, Stewart A, Kalliolia E, Alberts E, Adams R, Harris RJ, Mele S, Pellizzari G, Black ABM, Bax HJ, Cheung A, Nakamura M, Hoffmann RM, Terranova-Barberio M, Ali N, Batruch I, Soosaipillai A, Prassas I, Ulndreaj A, Chatanaka MK, Nuamah R, Kannambath S, Dhami P, Geh JLC, MacKenzie Ross AD, Healy C, Grigoriadis A, Kipling D, Karagiannis P, Dunn-Walters DK, Diamandis EP, Tsoka S, Spicer J, Lacy KE, Fraternali F, Karagiannis SN. B cell profiles, antibody repertoire and reactivity reveal dysregulated responses with autoimmune features in melanoma. Nat Commun 2023; 14:3378. [PMID: 37291228 PMCID: PMC10249578 DOI: 10.1038/s41467-023-39042-y] [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: 06/01/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
B cells are known to contribute to the anti-tumor immune response, especially in immunogenic tumors such as melanoma, yet humoral immunity has not been characterized in these cancers to detail. Here we show comprehensive phenotyping in samples of circulating and tumor-resident B cells as well as serum antibodies in melanoma patients. Memory B cells are enriched in tumors compared to blood in paired samples and feature distinct antibody repertoires, linked to specific isotypes. Tumor-associated B cells undergo clonal expansion, class switch recombination, somatic hypermutation and receptor revision. Compared with blood, tumor-associated B cells produce antibodies with proportionally higher levels of unproductive sequences and distinct complementarity determining region 3 properties. The observed features are signs of affinity maturation and polyreactivity and suggest an active and aberrant autoimmune-like reaction in the tumor microenvironment. Consistent with this, tumor-derived antibodies are polyreactive and characterized by autoantigen recognition. Serum antibodies show reactivity to antigens attributed to autoimmune diseases and cancer, and their levels are higher in patients with active disease compared to post-resection state. Our findings thus reveal B cell lineage dysregulation with distinct antibody repertoire and specificity, alongside clonally-expanded tumor-infiltrating B cells with autoimmune-like features, shaping the humoral immune response in melanoma.
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Affiliation(s)
- Silvia Crescioli
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Isabel Correa
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Joseph Ng
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
- Research Department of Structural and Molecular Biology, University College London, London, UK
| | - Zena N Willsmore
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Roman Laddach
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, London, UK
| | - Alicia Chenoweth
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Jitesh Chauhan
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Alexander Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Eleni Kalliolia
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Elena Alberts
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Rebecca Adams
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Robert J Harris
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Silvia Mele
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Giulia Pellizzari
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Anna B M Black
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Heather J Bax
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Anthony Cheung
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Mano Nakamura
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Ricarda M Hoffmann
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Manuela Terranova-Barberio
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Niwa Ali
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Centre for Gene Therapy and Regenerative Medicine, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Antigona Ulndreaj
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miyo K Chatanaka
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rosamund Nuamah
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Shichina Kannambath
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Genomics Facility, Institute of Cancer Research, London, UK
| | - Pawan Dhami
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Jenny L C Geh
- St John's Institute of Dermatology, Guy's, King's, and St. Thomas' Hospitals NHS Foundation Trust, London, UK
- Department of Plastic Surgery at Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Ciaran Healy
- Department of Plastic Surgery at Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - David Kipling
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Panagiotis Karagiannis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, London, UK
| | - James Spicer
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Katie E Lacy
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
- Research Department of Structural and Molecular Biology, University College London, London, UK
| | - Sophia N Karagiannis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK.
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK.
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8
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Neale RE, Lucas RM, Byrne SN, Hollestein L, Rhodes LE, Yazar S, Young AR, Berwick M, Ireland RA, Olsen CM. The effects of exposure to solar radiation on human health. Photochem Photobiol Sci 2023:10.1007/s43630-023-00375-8. [PMID: 36856971 PMCID: PMC9976694 DOI: 10.1007/s43630-023-00375-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 03/02/2023]
Abstract
This assessment by the Environmental Effects Assessment Panel (EEAP) of the Montreal Protocol under the United Nations Environment Programme (UNEP) evaluates the effects of ultraviolet (UV) radiation on human health within the context of the Montreal Protocol and its Amendments. We assess work published since our last comprehensive assessment in 2018. Over the last four years gains have been made in knowledge of the links between sun exposure and health outcomes, mechanisms, and estimates of disease burden, including economic impacts. Of particular note, there is new information about the way in which exposure to UV radiation modulates the immune system, causing both harms and benefits for health. The burden of skin cancer remains high, with many lives lost to melanoma and many more people treated for keratinocyte cancer, but it has been estimated that the Montreal Protocol will prevent 11 million cases of melanoma and 432 million cases of keratinocyte cancer that would otherwise have occurred in the United States in people born between 1890 and 2100. While the incidence of skin cancer continues to rise, rates have stabilised in younger populations in some countries. Mortality has also plateaued, partly due to the use of systemic therapies for advanced disease. However, these therapies are very expensive, contributing to the extremely high economic burden of skin cancer, and emphasising the importance and comparative cost-effectiveness of prevention. Photodermatoses, inflammatory skin conditions induced by exposure to UV radiation, can have a marked detrimental impact on the quality of life of sufferers. More information is emerging about their potential link with commonly used drugs, particularly anti-hypertensives. The eyes are also harmed by over-exposure to UV radiation. The incidence of cataract and pterygium is continuing to rise, and there is now evidence of a link between intraocular melanoma and sun exposure. It has been estimated that the Montreal Protocol will prevent 63 million cases of cataract that would otherwise have occurred in the United States in people born between 1890 and 2100. Despite the clearly established harms, exposure to UV radiation also has benefits for human health. While the best recognised benefit is production of vitamin D, beneficial effects mediated by factors other than vitamin D are emerging. For both sun exposure and vitamin D, there is increasingly convincing evidence of a positive role in diseases related to immune function, including both autoimmune diseases and infection. With its influence on the intensity of UV radiation and global warming, the Montreal Protocol has, and will have, both direct and indirect effects on human health, potentially changing the balance of the risks and benefits of spending time outdoors.
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Affiliation(s)
- R. E. Neale
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia ,School of Public Health, University of Queensland, Brisbane, QLD Australia
| | - R. M. Lucas
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, ACT Australia
| | - S. N. Byrne
- School of Medical Science, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia
| | - L. Hollestein
- Erasmus MC Cancer Institute, Rotterdam, The Netherlands ,Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - L. E. Rhodes
- Dermatology Research Centre, School of Biological Sciences, University of Manchester, Salford Royal Hospital, Northern Care Alliance NHS Trust, Manchester, UK
| | - S. Yazar
- Garvan Medical Research Institute, Sydney, NSW Australia
| | | | - M. Berwick
- University of New Mexico Comprehensive Cancer Center, Albuquerque, USA
| | - R. A. Ireland
- School of Medical Science, Faculty of Medicine and Health, University of Sydney, Sydney, NSW Australia
| | - C. M. Olsen
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia ,Frazer Institute, University of Queensland, Brisbane, QLD Australia
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9
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Uhl GR. Selecting the appropriate hurdles and endpoints for pentilludin, a novel antiaddiction pharmacotherapeutic targeting the receptor type protein tyrosine phosphatase D. Front Psychiatry 2023; 14:1031283. [PMID: 37139308 PMCID: PMC10149857 DOI: 10.3389/fpsyt.2023.1031283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/30/2023] [Indexed: 05/05/2023] Open
Abstract
Substance use disorders provide challenges for development of effective medications. Use of abused substances is likely initiated, sustained and "quit" by complex brain and pharmacological mechanisms that have both genetic and environmental determinants. Medical utilities of prescribed stimulants and opioids provide complex challenges for prevention: how can we minimize their contribution to substance use disorders while retaining medical benefits for pain, restless leg syndrome, attention deficit hyperactivity disorder, narcolepsy and other indications. Data required to support assessments of reduced abuse liability and resulting regulatory scheduling differs from information required to support licensing of novel prophylactic or therapeutic anti-addiction medications, adding further complexity and challenges. I describe some of these challenges in the context of our current efforts to develop pentilludin as a novel anti-addiction therapeutic for a target that is strongly supported by human and mouse genetic and pharmacologic studies, the receptor type protein tyrosine phosphatase D (PTPRD).
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Affiliation(s)
- George R. Uhl
- Departments of Neurology and Pharmacology, University of Maryland School of Medicine, Neurology Service, VA Maryland Healthcare System, Baltimore, MD, United States
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- *Correspondence: George R. Uhl
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10
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Seviiri M, Scolyer RA, Bishop DT, Newton-Bishop JA, Iles MM, Lo SN, Stretch JR, Saw RPM, Nieweg OE, Shannon KF, Spillane AJ, Gordon SD, Olsen CM, Whiteman DC, Landi MT, Thompson JF, Long GV, MacGregor S, Law MH. Higher polygenic risk for melanoma is associated with improved survival in a high ultraviolet radiation setting. J Transl Med 2022; 20:403. [PMID: 36064556 PMCID: PMC9446843 DOI: 10.1186/s12967-022-03613-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/24/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The role of germline genetic factors in determining survival from cutaneous melanoma (CM) is not well understood. OBJECTIVE To perform a genome-wide association study (GWAS) meta-analysis of melanoma-specific survival (MSS), and test whether a CM-susceptibility polygenic risk score (PRS) is associated with MSS. METHODS We conducted two Cox proportional-hazard GWAS of MSS using data from the Melanoma Institute Australia, a high ultraviolet (UV) radiation setting (MIA; 5,762 patients with melanoma; 800 melanoma deaths) and UK Biobank (UKB: 5,220 patients with melanoma; 241 melanoma deaths), and combined them in a fixed-effects meta-analysis. Significant (P < 5 × 10-8) results were investigated in the Leeds Melanoma Cohort (LMC; 1,947 patients with melanoma; 370 melanoma deaths). We also developed a CM-susceptibility PRS using a large independent GWAS meta-analysis (23,913 cases, 342,870 controls). The PRS was tested for an association with MSS in the MIA and UKB cohorts. RESULTS Two loci were significantly associated with MSS in the meta-analysis of MIA and UKB with lead SNPs rs41309643 (G allele frequency 1.6%, HR = 2.09, 95%CI = 1.61-2.71, P = 2.08 × 10-8) on chromosome 1, and rs75682113 (C allele frequency 1.8%, HR = 2.38, 95%CI = 1.77-3.21, P = 1.07 × 10-8) on chromosome 7. While neither SNP replicated in the LMC, rs75682113 was significantly associated in the combined discovery and replication sets. After adjusting for age at diagnosis, sex and the first ten principal components, a one standard deviation increase in the CM-susceptibility PRS was associated with improved MSS in the discovery meta-analysis (HR = 0.88, 95% CI = 0.83-0.94, P = 6.93 × 10-5; I2 = 88%). However, this was only driven by the high UV setting cohort (MIA HR = 0.84, 95% CI = 0.78-0.90). CONCLUSION We found two loci potentially associated with MSS. Increased genetic susceptibility to develop CM is associated with improved MSS in a high UV setting.
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Affiliation(s)
- Mathias Seviiri
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006 Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD Australia
- Center for Genomics and Personalised Health, Queensland University of Technology, Brisbane, 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
- Department of Tissue Oncology and Diagnostic Pathology, Royal Prince Alfred Hospital, Sydney, NSW Australia
- NSW Health Pathology, Sydney, NSW Australia
| | - D. Timothy Bishop
- Division of Haematology and Immunology, Leeds Institute of Medical Research at St James’, University of Leeds, Leeds, UK
| | - Julia A. Newton-Bishop
- Division of Haematology and Immunology, Leeds Institute of Medical Research at St James’, University of Leeds, Leeds, UK
| | - Mark M. Iles
- St James’s Institute of Medical Research, University of Leeds, Leeds, UK
- Leeds Institute of Data Analytics, University of Leeds, Leeds, UK
| | - Serigne N. Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW Australia
| | - Johnathan R. Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW Australia
| | - Robyn P. M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, NSW Australia
| | - Omgo E. Nieweg
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, 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, Camperdown, NSW Australia
- Sydney Head & Neck Cancer Institute, Chris O’Brien Lifehouse Cancer Center, Sydney, NSW Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW Australia
- Department of Breast and Melanoma Surgery, Royal North Shore Hospital, Sydney, NSW Australia
| | - Scott D. Gordon
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Catherine M. Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD Australia
| | - David C. Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - John F. Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, 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, Mater Hospital, North Sydney, NSW Australia
- Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW Australia
| | - Stuart MacGregor
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006 Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD Australia
| | - Matthew H. Law
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006 Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD Australia
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