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Prashanth S, Radha Maniswami R, Rajajeyabalachandran G, Jegatheesan SK. SETDB1, an H3K9-specific methyltransferase: An attractive epigenetic target to combat cancer. Drug Discov Today 2024; 29:103982. [PMID: 38614159 DOI: 10.1016/j.drudis.2024.103982] [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: 10/12/2023] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) is an important epigenetic regulator catalyzing histone H3 lysine 9 (H3K9) methylation, specifically di-/tri-methylation. This regulation promotes gene silencing through heterochromatin formation. Aberrant SETDB1 expression, and its oncogenic role is evident in many cancers. Thus, SETDB1 is a valid target with novel therapeutic benefits. In this review, we explore the structural and biochemical features of SETDB1, its regulatory mechanisms, and its role in various cancers. We also discuss recent discoveries in small molecules targeting SETDB1 and provide suggestions for future research.
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Affiliation(s)
- Seema Prashanth
- Informatics, AI & ML, Jubilant Biosys Ltd., Bangalore, India
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2
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Herreros-Pomares A, Hervás D, Bagan-Debon L, Proaño A, Garcia D, Sandoval J, Bagan J. Oral cancers preceded by proliferative verrucous leukoplakia exhibit distinctive molecular features. Oral Dis 2024; 30:1072-1083. [PMID: 36892444 DOI: 10.1111/odi.14550] [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: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/10/2023]
Abstract
OBJECTIVE Proliferative verrucous leukoplakia (PVL) has high rates of malignant transformation into oral squamous cell carcinoma (OSCC), but the clinical and evolutionary pattern of OSCC from PVL (PVL-OSCC) is more favorable than that of OSCC not preceded by PVL (OSCC). Here, we aimed to explore the pathophysiologic differences between PVL-OSCC and OSCC through transcriptomic and DNA methylation analyses. MATERIALS AND METHODS In this case-control study, oral biopsies from 8 PVL-OSCC and 10 OSCC patients were obtained for global sequencing using RNAseq and a genome-wide DNA methylation analysis via the Infinium EPIC Platform (graphical abstract). RESULTS One hundred and thirty-three differentially expressed genes (DEGs) were detected, 94 of them upregulated in OSCC. Most of these genes were previously described in cancer and associated with prognosis. The integrative analysis revealed 26 DEGs, corresponding to 37 CpGs, whose promoters were regulated by DNA methylation. Twenty-nine of the CpGs were found as hypermethylated in PVL-OSCC. Only 5 of the genes that were aberrantly methylated and differentially expressed were upregulated in PVL-OSCC patients, whereas 21 were underexpressed. CONCLUSIONS PVL-OSCC patients presented lower expression of cancer-related genes. Hypermethylation of the promoter region of many genes was also noticed, indicating that DNA methylation could be a regulatory mechanism.
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Affiliation(s)
- Alejandro Herreros-Pomares
- Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain
| | - David Hervás
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Leticia Bagan-Debon
- Medicina Oral Unit, Stomatology Department, Valencia University, Valencia, Spain
| | - Alex Proaño
- Medicina Oral Unit, Stomatology Department, Valencia University, Valencia, Spain
| | - Diana Garcia
- Epigenomics Unit, Health Research Institute La Fe, Valencia, Spain
| | - Juan Sandoval
- Epigenomics Unit, Health Research Institute La Fe, Valencia, Spain
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Valencia, Spain
| | - Jose Bagan
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, Madrid, Spain
- Medicina Oral Unit, Stomatology Department, Valencia University, Valencia, Spain
- Department of Stomatology and Maxillofacial Surgery, Hospital General Universitario de Valencia, Valencia, Spain
- Precancer and oral cancer research group of Valencia University, Valencia, Spain
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3
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Wang L, Zhang Y, Li H, Peng J, Gao C, Yu Q, Gao P, Li L, Chen K, Ye F. Identification of an immune-related signature as a prognostic classifier for patients with early-stage head and neck squamous cell carcinoma. Transl Cancer Res 2024; 13:1367-1381. [PMID: 38617526 PMCID: PMC11009812 DOI: 10.21037/tcr-23-1791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is the most common type and accounts for 90% of all head and neck cancer cases. Despite advances in early diagnosis and treatment strategies-chemotherapy, surgical resection, and radiotherapy-5-year survival remains grim. For patients with early-stage HNSCC, accurately predicting clinical outcomes is challenging. Considering the pivotal role of the immune system in HNSCC, we developed a reliable immune-related gene signature (IRGS) and explored its predictive accuracy in patients with early-stage HNSCC. Methods We examined immune gene expression profiles and clinical information from 230 early-stage HNSCC specimens, including 100 cases from The Cancer Genome Atlas (TCGA), 49 cases from the Gene Expression Omnibus (GEO; GSE65858), and 81 cases from an independent clinical cohort. The prognostic signature was constructed using Kaplan-Meier analysis and the least absolute shrinkage and selection operator (LASSO) Cox algorithm. We also explored the IRGS-related biological pathways and immune landscape using bioinformatics analysis. Results A nine-immune-gene signature was generated to significantly stratify patients into high and low-risk groups. High risk patients exhibited shorter survival time [hazard ratio (HR) =13.795, 95% confidence interval (CI): 3.275-58.109, P<0.001]. The signature demonstrated robust prognostic ability in the training and validation sets and could independently predict overall survival (OS) and relapse-free survival (RFS). Subsequently, the receiver operating characteristic (ROC) curve and C-index confirmed the signature's predictive accuracy compared to clinical parameters. Additionally, cases classified as low risk showed more immune cell infiltration than high-risk cases. Conclusions Our novel IRGS is a reliable and robust classifier for accurate patient stratification and prognostic evaluation. Future studies will attempt to affirm the signature's clinical application to early-stage HNSCC.
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Affiliation(s)
- Le Wang
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yulin Zhang
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongmin Li
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jilin Peng
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Changhui Gao
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiuning Yu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Pei Gao
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Li
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kuisheng Chen
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Tumor Pathology, Zhengzhou, China
| | - Fanglei Ye
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Thean LF, Wong M, Lo M, Tan I, Wong E, Gao F, Tan E, Tang CL, Cheah PY. Functional annotation with expression validation identifies novel metastasis-relevant genes from post-GWAS risk loci in sporadic colorectal carcinomas. J Med Genet 2024; 61:276-283. [PMID: 37890997 DOI: 10.1136/jmg-2023-109517] [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: 07/17/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is the third highest incidence cancer and is the leading cause of cancer mortality worldwide. Metastasis to distal organ is the major cause of cancer mortality. However, the underlying genetic factors are unclear. This study aimed to identify metastasis-relevant genes and pathways for better management of metastasis-prone patients. METHODS A case-case genome-wide association study comprising 2677 sporadic Chinese CRC cases (1282 metastasis-positive vs 1395 metastasis-negative) was performed using the Human SNP6 microarray platform and analysed with the correlation/trend test based on the additive model. SNP variants with association testing -log10 p value ≥5 were imported into Functional Mapping and Annotation (FUMA) for functional annotation. RESULTS Glycolysis was uncovered as the top hallmark gene set. Transcripts from two of the five genes profiled, hematopoietic substrate 1 associated protein X 1 (HAX1) and hyaluronan-mediatedmotility receptor (HMMR), were significantly upregulated in the metastasis-positive tumours. In contrast to disease-risk variants, HAX1 appeared to act synergistically with HMMR in significantly impacting metastasis-free survival. Examining the subtype datasets with FUMA and Ingenuity Pathway Analysis (IPA) identified distinct pathways demonstrating sexual dimorphism in CRC metastasis. CONCLUSIONS Combining genome-wide association testing with in silico functional annotation and wet-bench validation identified metastasis-relevant genes that could serve as features to develop subtype-specific metastasis-risk signatures for tailored management of patients with stage I-III CRC.
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Affiliation(s)
- Lai Fun Thean
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Michelle Wong
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Michelle Lo
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Iain Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Evelyn Wong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Fei Gao
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Emile Tan
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Choong Leong Tang
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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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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Klengel T, Dan S, Hall J, Holsen L. Divergent transcriptomic profiles in depressed individuals with hyper- and hypophagia implicating inflammatory status. RESEARCH SQUARE 2023:rs.3.rs-3385061. [PMID: 38014188 PMCID: PMC10680913 DOI: 10.21203/rs.3.rs-3385061/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Major Depressive Disorder (MDD) is a heterogenous and etiologically complex disease encompassing a broad spectrum of psychopathology, presumably arising from distinct pathophysiological mechanisms. Divergent appetitive phenotypes including Hyperphagic MDD (characterized by an increased appetite) and Hypophagic MDD (characterized by a decrease in appetite) are important clinical characteristics that are closely related to comorbidities, including cardiometabolic disorders. Prior evidence supports the notion that hyperphagia is associated with atypical depression, decreased stress-hormone signaling, a pro-inflammatory status, hypersomnia, and poorer clinical outcomes. Yet, our understanding of the underlying mechanisms of Hyperphagic and Hypophagic MDD is limited, and knowledge of associated biological correlates of these endophenotypes remain fragmented. We performed an exploratory study on peripheral blood RNA profiling using bulk RNAseq in unmedicated individuals with Hyperphagic and Hypophagic MDD (n=8 and n=13, respectively) and discovered individual genes and gene pathways associated with appetitive phenotypes. In addition, we used the Maastricht Acute Stress Task to uncover stress-related transcriptomic profiles in Hyper- and Hypophagic MDD.
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Affiliation(s)
| | - Shu Dan
- Brigham and Women's Hospital/Harvard Medical School
| | - Julia Hall
- Brigham and Women's Hospital/Harvard Medical School
| | - Laura Holsen
- Brigham and Women's Hospital/Harvard Medical School
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Dan S, Hall J, Holsen LM, Klengel T. Divergent transcriptomic profiles in depressed individuals with hyper- and hypophagia implicating inflammatory status. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.25.23296077. [PMID: 37808707 PMCID: PMC10557809 DOI: 10.1101/2023.09.25.23296077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Major Depressive Disorder (MDD) is a heterogenous and etiologically complex disease encompassing a broad spectrum of psychopathology, presumably arising from distinct pathophysiological mechanisms. Divergent appetitive phenotypes including Hyperphagic MDD (characterized by an increased appetite) and Hypophagic MDD (characterized by a decrease in appetite) are important clinical characteristics that are closely related to comorbidities, including cardiometabolic disorders. Prior evidence supports the notion that hyperphagia is associated with atypical depression, decreased stress-hormone signaling, a pro-inflammatory status, hypersomnia, and poorer clinical outcomes. Yet, our understanding of the underlying mechanisms of Hyperphagic and Hypophagic MDD is limited, and knowledge of associated biological correlates of these endophenotypes remain fragmented. We performed an exploratory study on peripheral blood RNA profiling using bulk RNAseq in unmedicated individuals with Hyperphagic and Hypophagic MDD (n=8 and n=13, respectively) and discovered individual genes and gene pathways associated with appetitive phenotypes. In addition, we used the Maastricht Acute Stress Task to uncover stress-related transcriptomic profiles in Hyper- and Hypophagic MDD.
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Zhu L, Tu D, Li R, Li L, Zhang W, Jin W, Li T, Zhu H. The diagnostic significance of the ZNF gene family in pancreatic cancer: a bioinformatics and experimental study. Front Genet 2023; 14:1089023. [PMID: 37396042 PMCID: PMC10311482 DOI: 10.3389/fgene.2023.1089023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 06/06/2023] [Indexed: 07/04/2023] Open
Abstract
Background: Pancreatic adenocarcinoma (PAAD) is among the most devastating of all cancers with a poor survival rate. Therefore, we established a zinc finger (ZNF) protein-based prognostic prediction model for PAAD patients. Methods: The RNA-seq data for PAAD were downloaded from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Differentially expressed ZNF protein genes (DE-ZNFs) in PAAD and normal control tissues were screened using the "lemma" package in R. An optimal risk model and an independent prognostic value were established by univariate and multivariate Cox regression analyses. Survival analyses were performed to assess the prognostic ability of the model. Results: We constructed a ZNF family genes-related risk score model that is based on the 10 DE-ZNFs (ZNF185, PRKCI, RTP4, SERTAD2, DEF8, ZMAT1, SP110, U2AF1L4, CXXC1, and RMND5B). The risk score was found to be a significant independent prognostic factor for PAAD patients. Seven significantly differentially expressed immune cells were identified between the high- and low-risk patients. Then, based on the prognostic genes, we constructed a ceRNA regulatory network that includes 5 prognostic genes, 7 miRNAs and 35 lncRNAs. Expression analysis showed ZNF185, PRKCI and RTP4 were significantly upregulated, while ZMAT1 and CXXC1 were significantly downregulated in the PAAD samples in all TCGA - PAAD, GSE28735 and GSE15471 datasets. Moreover, the upregulation of RTP4, SERTAD2, and SP110 were verified by the cell experiments. Conclusion: We established and validated a novel, Zinc finger protein family - related prognostic risk model for patients with PAAD, that has the potential to inform patient management.
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Affiliation(s)
- Lei Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Dong Tu
- Department of Cardiothoracic Surgery, No. 920 Hospital of the PLA Joint Logistics Support Force, Kunming, China
| | - Ruixue Li
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lin Li
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wenjie Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Wenxiang Jin
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Tiehan Li
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Hong Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
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Calbet‐Llopart N, Combalia M, Kiroglu A, Potrony M, Tell‐Martí G, Combalia A, Brugues A, Podlipnik S, Carrera C, Puig S, Malvehy J, Puig‐Butillé JA. Common genetic variants associated with melanoma risk or naevus count in patients with wildtype MC1R melanoma. Br J Dermatol 2022; 187:753-764. [PMID: 35701387 PMCID: PMC9804579 DOI: 10.1111/bjd.21707] [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: 03/07/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Hypomorphic MC1R variants are the most prevalent genetic determinants of melanoma risk in the white population. However, the genetic background of patients with wildtype (WT) MC1R melanoma is poorly studied. OBJECTIVES To analyse the role of candidate common genetic variants on the melanoma risk and naevus count in Spanish patients with WT MC1R melanoma. METHODS We examined 753 individuals with WT MC1R from Spain (497 patients and 256 controls). We used OpenArray reverse-transcriptase polymerase chain reaction to genotype a panel of 221 common genetic variants involved in melanoma, naevogenesis, hormonal pathways and proinflammatory pathways. Genetic models were tested using multivariate logistic regression models. Nonparametric multifactor dimensionality reduction (MDR) was used to detect gene-gene interactions within each biological subgroup of variants. RESULTS We found that variant rs12913832 in the HERC2 gene, which is associated with blue eye colour, increased melanoma risk in individuals with WT MC1R [odds ratio (OR) 1·97, 95% confidence interval (CI) 1·48-2·63; adjusted P < 0·001; corrected P < 0·001]. We also observed a trend between the rs3798577 variant in the oestrogen receptor alpha gene (ESR1) and a lower naevus count, which was restricted to female patients with WT MC1R (OR 0·51, 95% CI 0·33-0·79; adjusted P = 0·002; corrected P = 0·11). This sex-dependent association was statistically significant in a larger cohort of patients with melanoma regardless of their MC1R status (n = 1497; OR 0·71, 95% CI 0·57-0·88; adjusted P = 0·002), reinforcing the hypothesis of an association between hormonal pathways and susceptibility to melanocytic proliferation. Last, the MDR analysis revealed four genetic combinations associated with melanoma risk or naevus count in patients with WT MC1R. CONCLUSIONS Our data suggest that epistatic interaction among common variants related to melanocyte biology or proinflammatory pathways might influence melanocytic proliferation in individuals with WT MC1R. What is already known about this topic? Genetic variants in the MC1R gene are the most prevalent melanoma genetic risk factor in the white population. Still, 20-40% of cases of melanoma occur in individuals with wildtype MC1R. Multiple genetic variants have a pleiotropic effect in melanoma and naevogenesis. Additional variants in unexplored pathways might also have a role in melanocytic proliferation in these patients. Epidemiological evidence suggests an association of melanocytic proliferation with hormonal pathways and proinflammatory pathways. What does this study add? Variant rs12913832 in the HERC2 gene, which is associated with blue eye colour, increases the melanoma risk in individuals with wildtype MC1R. Variant rs3798577 in the oestrogen receptor gene is associated with naevus count regardless of the MC1R status in female patients with melanoma. We report epistatic interactions among common genetic variants with a role in modulating the risk of melanoma or the number of naevi in individuals with wildtype MC1R. What is the translational message? We report a potential role of hormonal signalling pathways in melanocytic proliferation, providing a basis for better understanding of sex-based differences observed at the epidemiological level. We show that gene-gene interactions among common genetic variants might be responsible for an increased risk for melanoma development in individuals with a low-risk phenotype, such as darkly pigmented hair and skin.
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Affiliation(s)
- Neus Calbet‐Llopart
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain
| | - Marc Combalia
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Anil Kiroglu
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Miriam Potrony
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain,Biochemistry and Molecular Genetics DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Gemma Tell‐Martí
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain
| | - Andrea Combalia
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Albert Brugues
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Sebastian Podlipnik
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
| | - Cristina Carrera
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain
| | - Susana Puig
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain
| | - Josep Malvehy
- Dermatology DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain
| | - Joan Anton Puig‐Butillé
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)Instituto de Salud Carlos IIIBarcelonaSpain,Molecular Biology CORE, Biochemistry and Molecular Genetics DepartmentMelanoma Group, Hospital Clínic de Barcelona, IDIBAPS, University of BarcelonaBarcelonaSpain
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10
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Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschläger O, Bordusa F. Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:237-246. [PMID: 35474152 PMCID: PMC9510119 DOI: 10.1007/s12104-022-10086-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The dysbindin domain-containing protein 1 (DBNDD1) is a conserved protein among higher eukaryotes whose structure and function are poorly investigated so far. Here, we present the backbone and side chain nuclear magnetic resonance assignments for the human DBNDD1 protein. Our chemical-shift based secondary structure analysis reveals the human DBNDD1 as an intrinsically disordered protein.
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Affiliation(s)
- Christoph Wiedemann
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany.
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Biostructural Interactions, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
| | - Kingsley Benjamin Obika
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Sandra Liebscher
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Jan Jirschitzka
- Department of Chemistry, Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany
| | - Oliver Ohlenschläger
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Frank Bordusa
- Charles Tanford Protein Centre, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
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Wang P, Sun X, Miao Q, Mi H, Cao M, Zhao S, Wang Y, Shu Y, Li W, Xu H, Bai D, Zhang Y. Novel genetic associations with five aesthetic facial traits: A genome-wide association study in the Chinese population. Front Genet 2022; 13:967684. [PMID: 36035146 PMCID: PMC9411802 DOI: 10.3389/fgene.2022.967684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The aesthetic facial traits are closely related to life quality and strongly influenced by genetic factors, but the genetic predispositions in the Chinese population remain poorly understood. Methods: A genome-wide association studies (GWAS) and subsequent validations were performed in 26,806 Chinese on five facial traits: widow’s peak, unibrow, double eyelid, earlobe attachment, and freckles. Functional annotation was performed based on the expression quantitative trait loci (eQTL) variants, genome-wide polygenic scores (GPSs) were developed to represent the combined polygenic effects, and single nucleotide polymorphism (SNP) heritability was presented to evaluate the contributions of the variants. Results: In total, 21 genetic associations were identified, of which ten were novel: GMDS-AS1 (rs4959669, p = 1.29 × 10−49) and SPRED2 (rs13423753, p = 2.99 × 10−14) for widow’s peak, a previously unreported trait; FARSB (rs36015125, p = 1.96 × 10−21) for unibrow; KIF26B (rs7549180, p = 2.41 × 10−15), CASC2 (rs79852633, p = 4.78 × 10−11), RPGRIP1L (rs6499632, p = 9.15 × 10−11), and PAX1 (rs147581439, p = 3.07 × 10−8) for double eyelid; ZFHX3 (rs74030209, p = 9.77 × 10−14) and LINC01107 (rs10211400, p = 6.25 × 10−10) for earlobe attachment; and SPATA33 (rs35415928, p = 1.08 × 10−8) for freckles. Functionally, seven identified SNPs tag the missense variants and six may function as eQTLs. The combined polygenic effect of the associations was represented by GPSs and contributions of the variants were evaluated using SNP heritability. Conclusion: These identifications may facilitate a better understanding of the genetic basis of features in the Chinese population and hopefully inspire further genetic research on facial development.
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Affiliation(s)
- Peiqi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xinghan Sun
- Genomic & Phenomic Data Center, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Qiang Miao
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Mi
- Department of Biobank, Chengdu 23Mofang Biotechnology Co., Ltd, Chengdu, China
| | - Minyuan Cao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shan Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yiyi Wang
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Department of Dermatology, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- Department of Laboratory Medicine/Research Center of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
| | - Yan Zhang
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy, Department of Thoracic Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ding Bai, ; Yan Zhang,
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12
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Zhang Y. SPATA33 affects the formation of cell adhesion complex by interacting with CTNNA3 in TM4 cells. Cell Tissue Res 2022; 389:145-157. [PMID: 35536443 DOI: 10.1007/s00441-022-03631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
Communication between Sertoli cell is essential during spermatogenesis and testicular development in mice, and the dynamic balance of this communication is regulated by some adhesion proteins. In this study, we found that SPATA33 and CTNNA3 were involved in this process. Quantitative real-time PCR and western blotting showed similar trend of expression of two proteins in the testis of mice of different ages. Subsequently, CRISPR-Cas9 technique was used to prepare Spata33 knockout cell lines with TM4 cells, cell wound scratch assay showed that Spata33 gene knockout affected cell migration, and flow cytometry assay showed that Spata33 knockout resulted in a decreased percentage of G1 phase cells in TM4 cell line. In addition, phalloidin staining assay showed that Spata33 gene knockout disrupted the formation of F-actin. Moreover, the protein immunoprecipitation experiment showed the interaction between SPATA33 and CTNNA3, which affected the interaction between CTNNA3 and CTNNB1. SPATA33 inhibits the formation of CDH1-CTNNB1-CTNNA3 complex through its interaction with CTNNA3, thus weakening adhesion between Sertoli cell and promoting cell migration.
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Affiliation(s)
- Ying Zhang
- Luoyang Normal University, Luoyang, 471934, Henan, China.
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13
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Marley AR, Li M, Champion VL, Song Y, Han J, Li X. Citrus-Gene interaction and melanoma risk in the UK Biobank. Int J Cancer 2022; 150:976-983. [PMID: 34724200 PMCID: PMC10015424 DOI: 10.1002/ijc.33862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 09/29/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022]
Abstract
High citrus consumption may increase melanoma risk; however, little is known about the biological mechanisms of this association, or whether it is modified by genetic variants. We conducted a genome-wide analysis of gene-citrus consumption interactions on melanoma risk among 1563 melanoma cases and 193 296 controls from the UK Biobank. Both the 2-degrees-of-freedom (df) joint test of genetic main effect and gene-environment (G-E) interaction and the standard 1-df G-E interaction test were performed. Three index SNPs (lowest P-value SNP among highly correlated variants [r2 > .6]) were identified from among the 365 genome-wide significant 2-df test results (rs183783391 on chromosome 3 [MITF], rs869329 on chromosome 9 [MTAP] and rs11446223 on chromosome 16 [DEF8]). Although all three were statistically significant for the 2-df test (4.25e-08, 1.98e-10 and 4.93e-13, respectively), none showed evidence of interaction according to the 1-df test (P = .73, .24 and .12, respectively). Eight nonindex, 2-df test significant SNPs on chromosome 16 were significant (P < .05) according to the 1-df test, providing evidence of citrus-gene interaction. Seven of these SNPs were mapped to AFG3L1P (rs199600347, rs111822773, rs113178244, rs3803683, rs73283867, rs78800020, rs73283871), and one SNP was mapped to GAS8 (rs74583214). We identified several genetic loci that may elucidate the association between citrus consumption and melanoma risk. Further studies are needed to confirm these findings.
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Affiliation(s)
- Andrew R Marley
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, Indiana, USA
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University School of Public health, Bloomington, Indiana, USA
| | - Victoria L Champion
- Department of Community Health Systems, Indiana University School of Nursing, Indianapolis, Indiana, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
| | - Yiqing Song
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, Indiana, USA
| | - Jiali Han
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, Indiana, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
| | - Xin Li
- Department of Epidemiology, Indiana University Richard M. Fairbanks School of Public Health, Indianapolis, Indiana, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana, USA
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14
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Leyton E, Matus D, Espinoza S, Benitez JM, Cortés BI, Gomez W, Arévalo NB, Murgas P, Manque P, Woehlbier U, Duran-Aniotz C, Hetz C, Behrens MI, SanMartín CD, Nassif M. DEF8 and Autophagy-Associated Genes Are Altered in Mild Cognitive Impairment, Probable Alzheimer’s Disease Patients, and a Transgenic Model of the Disease. J Alzheimers Dis 2021; 82:S163-S178. [DOI: 10.3233/jad-201264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background: Disturbances in the autophagy/endolysosomal systems are proposed as early signatures of Alzheimer’s disease (AD). However, few studies are available concerning autophagy gene expression in AD patients. Objective: To explore the differential expression of classical genes involved in the autophagy pathway, among them a less characterized one, DEF8 (Differentially expressed in FDCP 8), initially considered a Rubicon family member, in peripheral blood mononuclear cells (PBMCs) from individuals with mild cognitive impairment (MCI) and probable AD (pAD) and correlate the results with the expression of DEF8 in the brain of 5xFAD mice. Method: By real-time PCR and flow cytometry, we evaluated autophagy genes levels in PBMCs from MCI and pAD patients. We evaluated DEF8 levels and its localization in brain samples of the 5xFAD mice by real-time PCR, western blot, and immunofluorescence. Results: Transcriptional levels of DEF8 were significantly reduced in PBMCs of MCI and pAD patients compared with healthy donors, correlating with the MoCA and MoCA-MIS cognitive tests scores. DEF8 protein levels were increased in lymphocytes from MCI but not pAD, compared to controls. In the case of brain samples from 5xFAD mice, we observed a reduced mRNA expression and augmented protein levels in 5xFAD compared to age-matched wild-type mice. DEF8 presented a neuronal localization. Conclusion: DEF8, a protein proposed to act at the final step of the autophagy/endolysosomal pathway, is differentially expressed in PBMCs of MCI and pAD and neurons of 5xFAD mice. These results suggest a potential role for DEF8 in the pathophysiology of AD.
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Affiliation(s)
- Esteban Leyton
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Escuela de Tecnología Médica, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Diego Matus
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Escuela de Tecnología Médica, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Sandra Espinoza
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - José Matías Benitez
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Bastián I. Cortés
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Wileidy Gomez
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Nohela B. Arévalo
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Paola Murgas
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Immunology Laboratory, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Patricio Manque
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - Ute Woehlbier
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Claudia Duran-Aniotz
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibañez, Santiago, Chile
| | - Claudio Hetz
- Biomedical Neuroscience Institute, Faculty of Medicine, University of Chile, Santiago, Chile
- Center for Geroscience, Brain Health, and Metabolism (GERO), Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, University of Chile, Santiago, Chile
- Buck Institute for Research on Aging, Novato, CA, USA
| | - María Isabel Behrens
- Departamento de Neurociencia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Neurología y Neurocirugía, Hospital Clínico Universidad de Chile, Santiago, Chile
- Centro de Investigación Clínica Avanzada (CICA), Hospital Clínico Universidad de Chile, Santiago, Chile
- Departamento de Neurología y Psiquiatría, Clínica Alemana de Santiago
| | - Carol D. SanMartín
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Escuela de Tecnología Médica, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Departamento de Neurociencia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Melissa Nassif
- Laboratory of Neuroprotection and Autophagy, Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Center for Integrative Biology, Faculty of Science, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Insights into Genetic Susceptibility to Melanoma by Gene Panel Testing: Potential Pathogenic Variants in ACD, ATM, BAP1, and POT1. Cancers (Basel) 2020; 12:cancers12041007. [PMID: 32325837 PMCID: PMC7226507 DOI: 10.3390/cancers12041007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
The contribution of recently established or candidate susceptibility genes to melanoma missing heritability has yet to be determined. Multigene panel testing could increase diagnostic yield and better define the role of candidate genes. We characterized 273 CDKN2A/ARF and CDK4-negative probands through a custom-designed targeted gene panel that included CDKN2A/ARF, CDK4, ACD, BAP1, MITF, POT1, TERF2IP, ATM, and PALB2. Co-segregation, loss of heterozygosity (LOH)/protein expression analysis, and splicing characterization were performed to improve variant classification. We identified 16 (5.9%) pathogenic and likely pathogenic variants in established high/medium penetrance cutaneous melanoma susceptibility genes (BAP1, POT1, ACD, MITF, and TERF2IP), including two novel variants in BAP1 and 4 in POT1. We also found four deleterious and five likely deleterious variants in ATM (3.3%). Thus, including potentially deleterious variants in ATM increased the diagnostic yield to about 9%. Inclusion of rare variants of uncertain significance would increase the overall detection yield to 14%. At least 10% of melanoma missing heritability may be explained through panel testing in our population. To our knowledge, this is the highest frequency of putative ATM deleterious variants reported in melanoma families, suggesting a possible role in melanoma susceptibility, which needs further investigation.
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