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Monteil A, Guérineau NC, Gil-Nagel A, Parra-Diaz P, Lory P, Senatore A. New insights into the physiology and pathophysiology of the atypical sodium leak channel NALCN. Physiol Rev 2024; 104:399-472. [PMID: 37615954 DOI: 10.1152/physrev.00014.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Cell excitability and its modulation by hormones and neurotransmitters involve the concerted action of a large repertoire of membrane proteins, especially ion channels. Unique complements of coexpressed ion channels are exquisitely balanced against each other in different excitable cell types, establishing distinct electrical properties that are tailored for diverse physiological contributions, and dysfunction of any component may induce a disease state. A crucial parameter controlling cell excitability is the resting membrane potential (RMP) set by extra- and intracellular concentrations of ions, mainly Na+, K+, and Cl-, and their passive permeation across the cell membrane through leak ion channels. Indeed, dysregulation of RMP causes significant effects on cellular excitability. This review describes the molecular and physiological properties of the Na+ leak channel NALCN, which associates with its accessory subunits UNC-79, UNC-80, and NLF-1/FAM155 to conduct depolarizing background Na+ currents in various excitable cell types, especially neurons. Studies of animal models clearly demonstrate that NALCN contributes to fundamental physiological processes in the nervous system including the control of respiratory rhythm, circadian rhythm, sleep, and locomotor behavior. Furthermore, dysfunction of NALCN and its subunits is associated with severe pathological states in humans. The critical involvement of NALCN in physiology is now well established, but its study has been hampered by the lack of specific drugs that can block or agonize NALCN currents in vitro and in vivo. Molecular tools and animal models are now available to accelerate our understanding of how NALCN contributes to key physiological functions and the development of novel therapies for NALCN channelopathies.
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Affiliation(s)
- Arnaud Monteil
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
- Department of Physiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nathalie C Guérineau
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
| | - Antonio Gil-Nagel
- Department of Neurology, Epilepsy Program, Hospital Ruber Internacional, Madrid, Spain
| | - Paloma Parra-Diaz
- Department of Neurology, Epilepsy Program, Hospital Ruber Internacional, Madrid, Spain
| | - Philippe Lory
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
| | - Adriano Senatore
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-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: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
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Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
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Machine learning algorithm-generated and multi-center validated melanoma prognostic signature with inspiration for treatment management. Cancer Immunol Immunother 2023; 72:599-615. [PMID: 35998003 DOI: 10.1007/s00262-022-03279-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/12/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND Although immunotherapy and targeted treatments have dramatically improved the survival of melanoma patients, the intra- or intertumoral heterogeneity and drug resistance have hindered the further expansion of clinical benefits. METHODS The 96 combination frames constructed by ten machine learning algorithms identified a prognostic consensus signature based on 1002 melanoma samples from nine independent cohorts. Clinical features and 26 published signatures were employed to compare the predictive performance of our model. RESULTS A machine learning-based prognostic signature (MLPS) with the highest average C-index was developed via 96 algorithm combinations. The MLPS has a stable and excellent predictive performance for overall survival, superior to common clinical traits and 26 collected signatures. The low MLPS group with a better prognosis had significantly enriched immune-related pathways, tending to be an immune-hot phenotype and possessing potential immunotherapeutic responses to anti-PD-1, anti-CTLA-4, and MAGE-A3. On the contrary, the high MLPS group with more complex genomic alterations and poorer prognoses is more sensitive to the BRAF inhibitor dabrafenib, confirmed in patients with BRAF mutations. CONCLUSION MLPS could independently and stably predict the prognosis of melanoma, considered a promising biomarker to identify patients suitable for immunotherapy and those with BRAF mutations who would benefit from dabrafenib.
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Zhang Q, Zhao Y, Song Z, Zhang Q, Tian C, Li R, Zheng J, Yan L, Gu M, Jia X, Li M. Identification of THSD7B and PRMT9 mutations as risk factors for familial lung adenocarcinoma: A case report. Medicine (Baltimore) 2023; 102:e32872. [PMID: 36820582 PMCID: PMC9907970 DOI: 10.1097/md.0000000000032872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
RATIONALE Lung tumors arise from the unrestrained malignant growth of pulmonary epithelial cells. Lung cancer cases include both small and non-small cell lung cancers, with lung adenocarcinoma (LUAD) accounting for roughly half of all non-small cell lung cancer cases. Research focused on familial cancers suggests that approximately 8% of lung cancer cases are linked to genetic susceptibility or heritability. The precise genetic factors that underlie the onset of lung cancer, however, remain to be firmly established. PATIENT CONCERNS A 43-year-old presented with nodules in the lower left lung lobe. Following initial antibiotic treatment in a local hospital, these nodules remained present and the patient subsequently underwent the resection of the left lower lobe of the lung. The patient also had 4 family members with a history of LUAD. DIAGNOSIS Immunohistochemical staining results including cytokeratin 7 (+), TTF-1 (+), new aspartic proteinase A (+), CK5/6 (-), P63 (-), and Ki-67 (5%+) were consistent with a diagnosis of LUAD. INTERVENTION Whole exome sequencing analyses of 5 patients and 6 healthy family members were performed to explore potential mutations associated with familial LUAD. OUTCOMES Whole exome sequencing was conducted, confirming that the proband and their 4 other family members with LUAD harbored heterozygous THSD7B (c.A4000G:p.S1334G) mutations and homozygous PRMT9 (c.G40T:p.G14C) mutations, as further confirmed via Sanger sequencing. These mutations were predicted to be deleterious using the SIFT, PolyPhen2, and MutationTaster algorithms. Protein structure analyses indicated that the mutation of the serine at amino acid position 1334 in THSD7B to a glycine would reduce the minimum free energy from 8.08 kcal/mol to 68.57 kcal/mol. The identified mutation in the PRMT9 mutation was not present in the predicted protein structure. I-Mutant2.0 predictions indicated that both of these mutations (THSD7B:p.S1334G and PRMT9: p.G14C) were predicted to reduce protein stability. LESSONS Heterozygous THSD7B (c.A4000G:p.S1334G) and the homozygous PRMT9 (c.G40T:p.G14C) mutations were found to be linked to LUAD incidence in the analyzed family. Early analyses of these genetic loci and timely genetic counseling may provide benefits and aid in the early diagnosis of familial LUAD.
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Affiliation(s)
- Qianqian Zhang
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Yanwei Zhao
- Department of Radiotherapy, Liaocheng People’s Hospital, Liaocheng, China
| | - Zhaona Song
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Qiang Zhang
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Conghui Tian
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Rongrong Li
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Juan Zheng
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Lili Yan
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Mingliang Gu
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Xiaodong Jia
- Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, China
| | - Mingjun Li
- Department of Radiotherapy, Liaocheng People’s Hospital, Liaocheng, China
- * Correspondence: Mingjun Li, Department of Radiotherapy, Liaocheng People’s Hospital, 67 Dongchang West Road, Liaocheng, Shandong 252000, China (e-mail: )
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He J, Xu J, Chang Z, Yan J, Zhang L, Qin Y. NALCN is a potential biomarker and therapeutic target in human cancers. Front Genet 2023; 14:1164707. [PMID: 37152978 PMCID: PMC10154523 DOI: 10.3389/fgene.2023.1164707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Background: Sodium leak channel non-selective (NALCN), known as a voltage-independent Na+ channel, is increasingly considered to play vital roles in tumorigenesis and metastasis of human cancers. However, no comprehensive pan-cancer analysis of NALCN has been conducted. Our study aims to explore the potential diagnostic, prognostic and therapeutic value of NALCN in human cancers. Methods: Through comprehensive application of datasets from Human Protein Atlas (HPA), The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), Enhanced Version of Tumor Immune Estimation Resource (TIMER2.0), Tumor and Immune System Interaction Database (TISIDB), The University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cBioPortal, GeneMANIA and Search Tool for the Retrieval of Interaction Gene/Proteins (STRING) databases, we explored the potential roles of NALCN in different cancers. The differential expression, prognostic implications, pathological stages and grades, molecular and immune subtypes, diagnostic accuracy, tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR) genes, immune checkpoint genes, chemokine genes, major histocompatibility complex (MHC)-related genes, tumor-infiltrating immune cells (TIICs), promoter methylation, mutations, copy number alteration (CNA), and functional enrichment related to NALCN were analyzed. Results: Most cancers lowly expressed NALCN. Upregulated NALCN expression was associated with poor or better prognosis in different cancers. Moreover, NALCN was correlated with clinicopathological features in multiple cancers. NALCN showed high diagnostic accuracy in 5 caner types. NALCN is highly linked with immune-related biomarkers, immune-related genes and TIICs. Significant methylation changes and genetic alteration of NALCN can be observed in many cancers. Enrichment analysis showed that NALCN is closely related to multiple tumor-related signaling pathways. Conclusion: Our study revealed the vital involvement of NALCN in cancer. NALCN can be used as a prognostic biomarker for immune infiltration and clinical outcomes, and has potential diagnostic and therapeutic implications.
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Affiliation(s)
- Jian He
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Xu
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Zhiwei Chang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiaqin Yan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Limin Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanru Qin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Yanru Qin,
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Zholudeva AO, Lomakina ME, Orlova EA, Wang Y, Fokin AI, Polesskaya A, Gautreau AM, Alexandrova AY. The Role of the Adapter Protein Anks1a in the Regulation of Breast Cancer Cell Motility. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1651-1661. [PMID: 36717454 DOI: 10.1134/s0006297922120203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a critical step in tumor progression that leads to the acquisition by cancer cells the capacity for migration using the mesenchymal motility mode regulated by the Rac→WAVE→Arp2/3 signaling pathway. Earlier it was shown that proteins interacting with Rac can regulate mesenchymal migration and thus determine the metastatic potential of the cells. The search for new regulators of cell migration is an important theoretical and practical task. The adaptor protein Anks1a is one of the proteins interacting with Rac, whose expression is altered in many types of tumors. The aim of this study was to find whether Anks1a affects the migration of cancer cells and to identify the mechanism underlying this effect. It was suggested that Anks1a can influence cancer cell migration either as a Rac1 effector or by activating human epidermal growth factor receptor 2 (HER2) exchange. We investigated how upregulation and inhibition of Anks1a expression affected migration of breast cancer cells with different HER2 status. Anks1a was shown to interact with the activated form of Rac1. In the MDA-MB-231 cells (triple negative cancer), which lack HER2, Anks1a accumulated at the active cell edge, which is characterized by enrichment with active Rac1, whereas no such accumulation was observed in the HER2-overexpressing SK-BR-3 cells. Downregulation of the ANKS1a expression with esiRNA had almost no effect on the cancer cell motility, except a slight increase in the average migration rate of MDA-MB-231 cells. Among three cell lines tested, overexpression of Anks1a increased the migration rate of HER2-overexpressng SK-BR-3 cells only. We showed that Anks1a is an effector of activated Rac1, but its influence on the cell migration in this capacity was minimal, at least in the studied breast cancer cells. Anks1a affected the motility of breast cancer cells due to its involvement in the EGF receptor exchange.
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Affiliation(s)
- Anna O Zholudeva
- N. N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Maria E Lomakina
- N. N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.,CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Evgeniya A Orlova
- N. N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia
| | - Yanan Wang
- CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Artem I Fokin
- CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Anna Polesskaya
- CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Alexis M Gautreau
- CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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Minnai F, Noci S, Chierici M, Cotroneo CE, Bartolini B, Incarbone M, Tosi D, Mattioni G, Jurman G, Dragani TA, Colombo F. Genetic predisposition to lung adenocarcinoma outcome is a feature already present in patients' noninvolved lung tissue. Cancer Sci 2022; 114:281-294. [PMID: 36114746 PMCID: PMC9807507 DOI: 10.1111/cas.15591] [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: 04/14/2022] [Revised: 08/23/2022] [Accepted: 09/12/2022] [Indexed: 01/07/2023] Open
Abstract
Emerging evidence suggests that the prognosis of patients with lung adenocarcinoma can be determined from germline variants and transcript levels in nontumoral lung tissue. Gene expression data from noninvolved lung tissue of 483 lung adenocarcinoma patients were tested for correlation with overall survival using multivariable Cox proportional hazard and multivariate machine learning models. For genes whose transcript levels are associated with survival, we used genotype data from 414 patients to identify germline variants acting as cis-expression quantitative trait loci (eQTLs). Associations of eQTL variant genotypes with gene expression and survival were tested. Levels of four transcripts were inversely associated with survival by Cox analysis (CLCF1, hazard ratio [HR] = 1.53; CNTNAP1, HR = 2.17; DUSP14, HR = 1.78; and MT1F: HR = 1.40). Machine learning analysis identified a signature of transcripts associated with lung adenocarcinoma outcome that was largely overlapping with the transcripts identified by Cox analysis, including the three most significant genes (CLCF1, CNTNAP1, and DUSP14). Pathway analysis indicated that the signature is enriched for ECM components. We identified 32 cis-eQTLs for CNTNAP1, including 6 with an inverse correlation and 26 with a direct correlation between the number of minor alleles and transcript levels. Of these, all but one were prognostic: the six with an inverse correlation were associated with better prognosis (HR < 1) while the others were associated with worse prognosis. Our findings provide supportive evidence that genetic predisposition to lung adenocarcinoma outcome is a feature already present in patients' noninvolved lung tissue.
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Affiliation(s)
- Francesca Minnai
- Institute for Biomedical TechnologiesNational Research CouncilSegrateItaly
| | - Sara Noci
- Department of ResearchFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Marco Chierici
- Data Science for Health Research UnitBruno Kessler FoundationTrentoItaly
| | | | - Barbara Bartolini
- Department of ResearchFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | | | - Davide Tosi
- Thoracic Surgery and Lung Transplantation UnitFondazione IRCCS Cà Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Giovanni Mattioni
- Thoracic Surgery and Lung Transplantation UnitFondazione IRCCS Cà Granda Ospedale Maggiore PoliclinicoMilanItaly
| | - Giuseppe Jurman
- Data Science for Health Research UnitBruno Kessler FoundationTrentoItaly
| | - Tommaso A. Dragani
- Department of ResearchFondazione IRCCS Istituto Nazionale dei TumoriMilanItaly
| | - Francesca Colombo
- Institute for Biomedical TechnologiesNational Research CouncilSegrateItaly
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Li Z, Wang D, Liao H, Zhang S, Guo W, Chen L, Lu L, Huang T, Cai YD. Exploring the Genomic Patterns in Human and Mouse Cerebellums Via Single-Cell Sequencing and Machine Learning Method. Front Genet 2022; 13:857851. [PMID: 35309141 PMCID: PMC8930846 DOI: 10.3389/fgene.2022.857851] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022] Open
Abstract
In mammals, the cerebellum plays an important role in movement control. Cellular research reveals that the cerebellum involves a variety of sub-cell types, including Golgi, granule, interneuron, and unipolar brush cells. The functional characteristics of cerebellar cells exhibit considerable differences among diverse mammalian species, reflecting a potential development and evolution of nervous system. In this study, we aimed to recognize the transcriptional differences between human and mouse cerebellum in four cerebellar sub-cell types by using single-cell sequencing data and machine learning methods. A total of 321,387 single-cell sequencing data were used. The 321,387 cells included 4 cell types, i.e., Golgi (5,048, 1.57%), granule (250,307, 77.88%), interneuron (60,526, 18.83%), and unipolar brush (5,506, 1.72%) cells. Our results showed that by using gene expression profiles as features, the optimal classification model could achieve very high even perfect performance for Golgi, granule, interneuron, and unipolar brush cells, respectively, suggesting a remarkable difference between the genomic profiles of human and mouse. Furthermore, a group of related genes and rules contributing to the classification was identified, which might provide helpful information for deepening the understanding of cerebellar cell heterogeneity and evolution.
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Affiliation(s)
- ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - HuiPing Liao
- Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - ShiQi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Lin Lu, ; Tao Huang, ; Yu-Dong Cai,
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Mousa M, Vurivi H, Kannout H, Uddin M, Alkaabi N, Mahboub B, Tay GK, Alsafar HS. Genome-wide association study of hospitalized COVID-19 patients in the United Arab Emirates. EBioMedicine 2021; 74:103695. [PMID: 34775353 PMCID: PMC8587122 DOI: 10.1016/j.ebiom.2021.103695] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The heterogeneity in symptomatology and phenotypic profile attributable to COVID-19 is widely unknown. The objective of this manuscript is to conduct a trans-ancestry genome wide association study (GWAS) meta-analysis of COVID-19 severity to improve the understanding of potentially causal targets for SARS-CoV-2. METHODS This cross-sectional study recruited 646 participants in the UAE that were divided into two phenotypic groups based on the severity of COVID-19 phenotypes, hospitalized (n=482) and non-hospitalized (n=164) participants. Hospitalized participants were COVID-19 patients that developed acute respiratory distress syndrome (ARDS), pneumonia or progression to respiratory failure that required supplemental oxygen therapy or mechanical ventilation support or had severe complications such as septic shock or multi-organ failure. We conducted a trans-ancestry meta-analysis GWAS of European (n=302), American (n=102), South Asian (n=99), and East Asian (n=107) ancestry populations. We also carried out comprehensive post-GWAS analysis, including enrichment of SNP associations in tissues and cell-types, expression quantitative trait loci and differential expression analysis. FINDINGS Eight genes demonstrated a strong association signal: VWA8 gene in locus 13p14·11 (SNP rs10507497; p=9·54 x10-7), PDE8B gene in locus 5q13·3 (SNP rs7715119; p=2·19 x10-6), CTSC gene in locus 11q14·2 (rs72953026; p=2·38 x10-6), THSD7B gene in locus 2q22·1 (rs7605851; p=3·07x10-6), STK39 gene in locus 2q24·3 (rs7595310; p=4·55 x10-6), FBXO34 gene in locus 14q22·3 (rs10140801; p=8·26 x10-6), RPL6P27 gene in locus 18p11·31 (rs11659676; p=8·88 x10-6), and METTL21C gene in locus 13q33·1 (rs599976; p=8·95 x10-6). The genes are expressed in the lung, associated to tumour progression, emphysema, airway obstruction, and surface tension within the lung, as well as an association to T-cell-mediated inflammation and the production of inflammatory cytokines. INTERPRETATION We have discovered eight highly plausible genetic association with hospitalized cases in COVID-19. Further studies must be conducted on worldwide population genetics to facilitate the development of population specific therapeutics to mitigate this worldwide challenge. FUNDING This review was commissioned as part of a project to study the host cell receptors of coronaviruses funded by Khalifa University's CPRA grant (Reference number 2020-004).
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Affiliation(s)
- Mira Mousa
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Hema Vurivi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Hussein Kannout
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Bassam Mahboub
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Guan K Tay
- Division of Psychiatry, Faculty of Health and Medical Sciences, the University of Western Australia, Crawley, Western Australia, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Habiba S Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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10
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Sun P, Lu Q, Li Z, Qin N, Jiang Y, Ma H, Jin G, Yu H, Dai J. Assessment of prognostic prediction models for gastric cancer using genomic and transcriptomic profiles. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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11
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Lee AJ, Jung I. Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. Genomics Inform 2021; 19:e3. [PMID: 33840167 PMCID: PMC8042303 DOI: 10.5808/gi.20073] [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: 12/03/2020] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer‒associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type‒specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer‒associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.
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Affiliation(s)
- Andrew J Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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12
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Brhane Y, Yang P, Christiani DC, Liu G, McLaughlin JR, Brennan P, Shete S, Field JK, Tardón A, Kohno T, Shiraishi K, Matsuo K, Bossé Y, Amos CI, Hung RJ. Genetic Determinants of Lung Cancer Prognosis in Never Smokers: A Pooled Analysis in the International Lung Cancer Consortium. Cancer Epidemiol Biomarkers Prev 2020; 29:1983-1992. [PMID: 32699080 PMCID: PMC7541720 DOI: 10.1158/1055-9965.epi-20-0248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/12/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer death worldwide, with 15% to 20% occurring in never smokers. To assess genetic determinants for prognosis among never smokers, we conducted a genome-wide investigation in the International Lung Cancer Consortium (ILCCO). METHODS Genomic and clinical data from 1,569 never-smoking patients with lung cancer of European ancestry from 10 ILCCO studies were included. HRs and 95% confidence intervals of overall survival were estimated. We assessed whether the associations were mediated through mRNA expression-based 1,553 normal lung tissues from the lung expression quantitative trait loci (eQTL) dataset and Genotype-Tissue Expression (GTEx). For cross-ethnicity generalization, we assessed the associations in a Japanese study (N = 887). RESULTS One locus at 13q22.2 was associated with lung adenocarcinoma survival at genome-wide level, with carriers of rs12875562-T allele exhibiting poor prognosis [HR = 1.71 (1.41-2.07), P = 3.60 × 10-8], and altered mRNA expression of LMO7DN in lung tissue (GTEx, P = 9.40 × 10-7; Lung eQTL dataset, P = 0.003). Furthermore, 2 of 11 independent loci that reached the suggestive significance level (P < 10-6) were significant eQTL affecting mRNA expression of nearby genes in lung tissues, including CAPZB at 1p36.13 and UBAC1 at 9q34.3. One locus encoding NWD2/KIAA1239 at 4p14 showed associations in both European [HR = 0.50 (0.38-0.66), P = 6.92 × 10-7] and Japanese populations [HR = 0.79 (0.67-0.94), P = 0.007]. CONCLUSIONS Based on the largest genomic investigation on the lung cancer prognosis of never smokers to date, we observed that lung cancer prognosis is affected by inherited genetic variants. IMPACT We identified one locus near LMO7DN at genome-wide level and several potential prognostic genes with cis-effect on mRNA expression. Further functional genomics work is required to understand their role in tumor progression.
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Affiliation(s)
- Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | | | | | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Canada
| | - John R McLaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Sanjay Shete
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Institute of Translational Medicine, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Adonina Tardón
- University of Oviedo, ISPA and CIBERESP, Faculty of Medicine, Campus del Cristo, Oviedo, Spain
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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13
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Jiang J, Ding Y, Wu M, Chen Y, Lyu X, Lu J, Wang H, Teng L. Integrated genomic analysis identifies a genetic mutation model predicting response to immune checkpoint inhibitors in melanoma. Cancer Med 2020; 9:8498-8518. [PMID: 32969604 PMCID: PMC7666739 DOI: 10.1002/cam4.3481] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/29/2020] [Accepted: 09/09/2020] [Indexed: 12/19/2022] Open
Abstract
Several biomarkers such as tumor mutation burden (TMB), neoantigen load (NAL), programmed cell‐death receptor 1 ligand (PD‐L1) expression, and lactate dehydrogenase (LDH) have been developed for predicting response to immune checkpoint inhibitors (ICIs) in melanoma. However, some limitations including the undefined cut‐off value, poor uniformity of test platform, and weak reliability of prediction have restricted the broad application in clinical practice. In order to identify a clinically actionable biomarker and explore an effective strategy for prediction, we developed a genetic mutation model named as immunotherapy score (ITS) for predicting response to ICIs therapy in melanoma, based on whole‐exome sequencing data from previous studies. We observed that patients with high ITS had better durable clinical benefit and survival outcomes than patients with low ITS in three independent cohorts, as well as in the meta‐cohort. Notably, the prediction capability of ITS was more robust than that of TMB. Remarkably, ITS was not only an independent predictor of ICIs therapy, but also combined with TMB or LDH to better predict response to ICIs than any single biomarker. Moreover, patients with high ITS harbored the immunotherapy‐sensitive characteristics including high TMB and NAL, ultraviolet light damage, impaired DNA damage repair pathway, arrested cell cycle signaling, and frequent mutations in NF1 and SERPINB3/4. Overall, these findings deserve prospective investigation in the future and may help guide clinical decisions on ICIs therapy for patients with melanoma.
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Affiliation(s)
- Junjie Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengjie Wu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiadong Lyu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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14
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Wang C, Yang D, Zhang X, Zhang X, Yang L, Wang P, Zhou W, Li H, Li Y, Nie H, Li Y. Association of PTEN Gene SNPs rs2299939 With PFS in Patients With Small Cell Lung Cancer Treated With Early Radiotherapy. Front Genet 2020; 11:298. [PMID: 32391045 PMCID: PMC7190978 DOI: 10.3389/fgene.2020.00298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
Lung cancer has higher morbidity and mortality than most cancers. It is common that there are some phenomenons of secondary drug resistance, radiotherapy resistance and poor prognosis during the treatment of small cell lung cancer (SCLC). Recent studies revealed that the single-nucleotide polymorphisms (SNPs) are associated with the curative effect among patients with the same pathological type and stage. Our study analyzed the start time of radiotherapy and the relationship between PTEN gene rs2299939 polymorphisms and survival time among 116 SCLC patients. The results showed that early radiotherapy significantly improved the time of survival in patients compared with late radiotherapy (P = 0.029). Simultaneously, the study found that patients with the rs2299939 AA genotype showed significant sensitivity to both early and late radiotherapy, but early radiotherapy is better. The median survival time of CC genotype patients was 12 months in the early radiotherapy group while it was 9 months in the late radiotherapy group, thus recommending early radiotherapy among these patients. In addition, it was found that rs2299939 could regulate the expression of related genes in peripheral blood and lung tissues by eQTL analysis. This study revealed that the early radiotherapy could prolong the PFS of SCLC and shall be performed in SCLC treatment.
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Affiliation(s)
- Chunbo Wang
- Department of Radiotherapy, The Third Affiliated Hospital of Harbin Medical University, Harbin, China.,School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Depeng Yang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiaoqing Zhang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Xiaohan Zhang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Lijun Yang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Pingping Wang
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenyang Zhou
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Huaxin Li
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Yiqun Li
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Huan Nie
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
| | - Yu Li
- School of Life Sciences and Technology, Harbin Institute of Technology, Harbin, China
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15
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Djamgoz MBA. Hyponatremia and Cancer Progression: Possible Association with Sodium-Transporting Proteins. Bioelectricity 2020; 2:14-20. [PMID: 34471833 DOI: 10.1089/bioe.2019.0035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hyponatremia, the phenomenon of serum sodium level falling below 135 mmol/L, is seen frequently in cancer patients and has been correlated with poor prognosis. Hyponatremia has classically been attributed to the "syndrome of inappropriate antidiuretic hormone secretion," leading to prolonged fluid retention. However, this is unlikely to be the only mechanism. In this study, we advance the hypothesis that upregulation of various sodium-transporting proteins during the cancer process makes a significant contribution to the pathophysiology of cancer-associated hyponatremia. Such sodium-transporting proteins include voltage-gated sodium channels, especially its hypoxia-promoted persistent current, epithelial sodium channels, and transient receptor potential channels. Thus, hyponatremia follows cancer, whereby drop in blood serum level occurs as a result of uptake of sodium from extracellular fluid by cancer cells. Indeed, the sodium content of cancer cells/tissues is higher than normal. In turn, the rise in the intracellular sodium concentration brings about a range of cellular effects, including extracellular acidification that promotes invasiveness and thus leads to poor prognosis. This perspective offers novel therapies for cancer and the associated hyponatremia.
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Affiliation(s)
- Mustafa B A Djamgoz
- Department of Life Sciences, Neuroscience Solutions to Cancer Research Group, Imperial College London, London, United Kingdom.,Biotechnology Research Centre, Cyprus International University, Lefkosa, North Cyprus
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16
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Ezzeldin N, El-Lebedy D, Mohammed A. Gene-environment and gene-gene interactions between CHRNA3 rs1051730, XRCC1 rs25487, and ERCC1 rs735482 variants highly elevate the risk of lung cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2019. [DOI: 10.1186/s43042-019-0034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Gene-gene and gene-environment interactions play an important role in cancer susceptibility. In this work, we studied the association of XRCC1 rs25487, ERCC1 rs735482, and CHRNA3 rs1051730 variants with lung cancer and assessed the modulatory effect of potential interaction between these variants on disease risk.
Results
In this study, 86 primary lung cancer patients and 64 control subjects were genotyped for CHRNA3 rs1051730, XRCC1 rs25487, and ERCC1 rs735482 by real-time PCR. The frequency of the three studied variants was higher among lung cancer patients than in control subjects, but with no statistical significance. ERCC1 rs735482 variant was associated with 6.9-fold increased risk to develop lung cancer among smokers (p = 0.03). Concomitant presence of CHRNA3 and ERCC1 wild alleles was associated with 2.7-fold elevated risk of lung cancer (p < 0.0001), while concomitant presence of CHRNA3 rs1051730 variant allele with ERCC1 wild allele was associated with 20-fold elevated risk (p < 0.000). Concomitant presence of both variants, ERCC1 rs735482 and CHRNA3 rs1051730, was associated with 9.9-fold elevated risk (p < 0.0001). Meanwhile, the concomitant presence of XRCC1 rs25487 with either ERCC1 rs735482 or CHRNA3 rs1051730 or both was not associated with increased risk of the disease.
Conclusion
Our results emphasize the role of gene-gene interaction in the pathogenesis of lung cancer. Large-scale further studies to clarify the underlying mechanisms are needed.
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Affiliation(s)
- Julia Kastner
- University of Maryland School of Medicine, Baltimore, MD
| | - Rydhwana Hossain
- University of Maryland School of Medicine, Cardiothoracic Imaging, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland Medical Center, Baltimore, MD
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18
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Hayashi M, Kawakubo H, Fukuda K, Mayanagi S, Nakamura R, Suda K, Hayashida T, Wada N, Kitagawa Y. THUMP domain containing 2 protein possibly induces resistance to cisplatin and 5-fluorouracil in in vitro human esophageal squamous cell carcinoma cells as revealed by transposon activation mutagenesis. J Gene Med 2019; 21:e3135. [PMID: 31656051 DOI: 10.1002/jgm.3135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/11/2019] [Accepted: 10/12/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Although chemotherapy is a core treatment for esophageal cancer, some patients develop drug resistance. Gene screening with transposons (i.e. mobile genetic elements) is a novel procedure for identifying chemotherapy-resistant genes. Transposon insertion can randomly affect nearby gene expression. By identifying the affected genes, candidate genes can be found. The present study aimed to identify cisplatin (CDDP)/5-fluorouracil (5-FU)-resistant genes in in vitro human esophageal squamous cell carcinoma with transposons. METHODS After establishing transposon-tagged cells, we obtained CDDP/5-FU-resistant colonies. A polymerase chain reaction and sequencing were used to identify the transposon inserted site and candidate CDDP/5-FU resistant genes. Focusing on one candidate gene, we confirmed CDDP/5-FU resistance by comparing the IC50 between drug-resistant and wild-type cells. Furthermore, we investigated gene expression by a real-time polymerase chain reaction. Finally, we mediated the candidate gene level with small interfering RNA to confirm the resistance. RESULTS Thirty-nine candidate genes for CDDP/5-FU resistance were identified. Nineteen were for CDDP resistance and 27 were for 5-FU resistance. Seven genes, THUMP domain-containing protein 2 (THUMPD2), nuclear factor interleukin-3-regulated protein (NFIL3), tyrosine-protein kinase transmembrane receptor 2 (ROR2), C-X-C chemokine receptor type 4 (CXCR4), thrombospondin type-1 domain-containing protein 2 (THSD7B) alpha-parvin (PARVA) and TEA domain transcription factor 1 (TEAD1), were detected as candidate genes in both colonies. Regarding THUMPD2, its expression was downregulated and knocking down THUMPD2 suggested drug resistance in both drugs. CONCLUSIONS Thirty-nine candidate genes were identified with transposons. The downregulation of THUMPD2 was suggested to play a role in multidrug resistance in in vitro esophageal squamous cell carcinoma.
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Affiliation(s)
- Masato Hayashi
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Hirofumi Kawakubo
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Kazumasa Fukuda
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Shuhei Mayanagi
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Rieko Nakamura
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Koichi Suda
- Department of Surgery, Fujita Health University Hospital, Toyoake, Aichi, Japan
| | - Testu Hayashida
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Norihito Wada
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University, School of Medicine, Tokyo, Japan
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Valdés MG, Galván-Femenía I, Ripoll VR, Duran X, Yokota J, Gavaldà R, Rafael-Palou X, de Cid R. Pipeline design to identify key features and classify the chemotherapy response on lung cancer patients using large-scale genetic data. BMC SYSTEMS BIOLOGY 2018; 12:97. [PMID: 30458782 PMCID: PMC6245589 DOI: 10.1186/s12918-018-0615-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND During the last decade, the interest to apply machine learning algorithms to genomic data has increased in many bioinformatics applications. Analyzing this type of data entails difficulties for managing high-dimensional data, class imbalance for knowledge extraction, identifying important features and classifying individuals. In this study, we propose a general framework to tackle these challenges with different machine learning algorithms and techniques. We apply the configuration of this framework on lung cancer patients, identifying genetic signatures for classifying response to drug treatment response. We intersect these relevant SNPs with the GWAS Catalog of the National Human Genome Research Institute and explore the Regulomedb, GTEx databases for functional analysis purposes. RESULTS The machine learning based solution proposed in this study is a scalable and flexible alternative to the classical uni-variate regression approach to analyze large-scale data. From 36 experiments executed using the machine learning framework design, we obtain good classification performance from the top 5 models with the highest cross-validation score and the smallest standard deviation. One thousand two hundred twenty four SNPs corresponding to the key features from the top 20 models (cross validation F1 mean >= 0.65) were compared with the GWAS Catalog finding no intersection with genome-wide significant reported hits. From these, new genetic signatures in MAE, CEP104, PRKCZ and ADRB2 show relevant biological regulatory functionality related to lung physiology. CONCLUSIONS We have defined a machine learning framework using data with an unbalanced large data-set of SNP-arrays and imputed genotyping data from a pharmacogenomics study in lung cancer patients subjected to first-line platinum-based treatment. This approach found genome signals with no genome-wide significance in the uni-variate regression approach (GWAS Catalog) that are valuable for classifying patients, only few of them with related biological function. The effect results of these variants can be explained by the recently proposed omnigenic model hypothesis, which states that complex traits can be influenced mostly by genes outside not only by the "core genes", mainly found by the genome-wide significant SNPs, but also by the rest of genes outside of the "core pathways" with apparent unrelated biological functionality.
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Affiliation(s)
- María Gabriela Valdés
- Eurecat. Technology Centre of Catalonia, Av. Diagonal 177, 9th floor, Barcelona, 08018 Spain
| | - Iván Galván-Femenía
- PMPPC-IGTP. Programa de Medicina Predictiva i Personalitzada del Càncer - Institut Germans Trias i Pujol (IGTP). Genomes for Life - GCAT lab Group, Badalona, Spain
| | - Vicent Ribas Ripoll
- Eurecat. Technology Centre of Catalonia, Av. Diagonal 177, 9th floor, Barcelona, 08018 Spain
| | - Xavier Duran
- PMPPC-IGTP. Programa de Medicina Predictiva i Personalitzada del Càncer - Institut Germans Trias i Pujol (IGTP). Genomes for Life - GCAT lab Group, Badalona, Spain
| | - Jun Yokota
- PMPPC-IGTP. Programa de Medicina Predictiva i Personalitzada del Càncer - Institut Germans Trias i Pujol (IGTP). CancerGenome Biology, Badalona, Spain
| | - Ricard Gavaldà
- Universitat Politècnica de Catalunya, Barcelona, Spain
- Barcelona Graduate School of Mathematics, BGSMath, Barcelona, Spain
| | - Xavier Rafael-Palou
- Eurecat. Technology Centre of Catalonia, Av. Diagonal 177, 9th floor, Barcelona, 08018 Spain
| | - Rafael de Cid
- PMPPC-IGTP. Programa de Medicina Predictiva i Personalitzada del Càncer - Institut Germans Trias i Pujol (IGTP). Genomes for Life - GCAT lab Group, Badalona, Spain
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20
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Prevarskaya N, Skryma R, Shuba Y. Ion Channels in Cancer: Are Cancer Hallmarks Oncochannelopathies? Physiol Rev 2018; 98:559-621. [PMID: 29412049 DOI: 10.1152/physrev.00044.2016] [Citation(s) in RCA: 272] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genomic instability is a primary cause and fundamental feature of human cancer. However, all cancer cell genotypes generally translate into several common pathophysiological features, often referred to as cancer hallmarks. Although nowadays the catalog of cancer hallmarks is quite broad, the most common and obvious of them are 1) uncontrolled proliferation, 2) resistance to programmed cell death (apoptosis), 3) tissue invasion and metastasis, and 4) sustained angiogenesis. Among the genes affected by cancer, those encoding ion channels are present. Membrane proteins responsible for signaling within cell and among cells, for coupling of extracellular events with intracellular responses, and for maintaining intracellular ionic homeostasis ion channels contribute to various extents to pathophysiological features of each cancer hallmark. Moreover, tight association of these hallmarks with ion channel dysfunction gives a good reason to classify them as special type of channelopathies, namely oncochannelopathies. Although the relation of cancer hallmarks to ion channel dysfunction differs from classical definition of channelopathies, as disease states causally linked with inherited mutations of ion channel genes that alter channel's biophysical properties, in a broader context of the disease state, to which pathogenesis ion channels essentially contribute, such classification seems absolutely appropriate. In this review the authors provide arguments to substantiate such point of view.
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Affiliation(s)
- Natalia Prevarskaya
- INSERM U-1003, Equipe Labellisée par la Ligue Nationale contre le Cancer et LABEX, Université Lille1 , Villeneuve d'Ascq , France ; Bogomoletz Institute of Physiology and International Center of Molecular Physiology, NASU, Kyiv-24, Ukraine
| | - Roman Skryma
- INSERM U-1003, Equipe Labellisée par la Ligue Nationale contre le Cancer et LABEX, Université Lille1 , Villeneuve d'Ascq , France ; Bogomoletz Institute of Physiology and International Center of Molecular Physiology, NASU, Kyiv-24, Ukraine
| | - Yaroslav Shuba
- INSERM U-1003, Equipe Labellisée par la Ligue Nationale contre le Cancer et LABEX, Université Lille1 , Villeneuve d'Ascq , France ; Bogomoletz Institute of Physiology and International Center of Molecular Physiology, NASU, Kyiv-24, Ukraine
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Hubert JN, Zerjal T, Hospital F. Cancer- and behavior-related genes are targeted by selection in the Tasmanian devil (Sarcophilus harrisii). PLoS One 2018; 13:e0201838. [PMID: 30102725 PMCID: PMC6089428 DOI: 10.1371/journal.pone.0201838] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/22/2018] [Indexed: 12/27/2022] Open
Abstract
Devil Facial Tumor Disease (DFTD) is an aggressive cancer notorious for its rare etiology and its impact on Tasmanian devil populations. Two regions underlying an evolutionary response to this cancer were recently identified using genomic time-series pre- and post-DTFD arrival. Here, we support that DFTD shaped the genome of the Tasmanian devil in an even more extensive way than previously reported. We detected 97 signatures of selection, including 148 protein coding genes having a human orthologue, linked to DFTD. Most candidate genes are associated with cancer progression, and an important subset of candidate genes has additional influence on social behavior. This confirms the influence of cancer on the ecology and evolution of the Tasmanian devil. Our work also demonstrates the possibility to detect highly polygenic footprints of short-term selection in very small populations.
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Affiliation(s)
- Jean-Noël Hubert
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | - Tatiana Zerjal
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Frédéric Hospital
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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22
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Kim JE, Choi J, Park J, Park C, Lee SM, Park SE, Song N, Chung S, Sung H, Han W, Lee JW, Park SK, Kim MK, Noh DY, Yoo KY, Kang D, Choi JY. Associations between genetic polymorphisms of membrane transporter genes and prognosis after chemotherapy: meta-analysis and finding from Seoul Breast Cancer Study (SEBCS). THE PHARMACOGENOMICS JOURNAL 2018; 18:633-645. [PMID: 29618765 DOI: 10.1038/s41397-018-0016-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/13/2017] [Accepted: 12/04/2017] [Indexed: 12/30/2022]
Abstract
Membrane transporters can be major determinants of the pharmacokinetic profiles of anticancer drugs. The associations between genetic variations of ATP-binding cassette (ABC) and solute carrier (SLC) genes and cancer survival were investigated through a meta-analysis and an association study in the Seoul Breast Cancer Study (SEBCS). Including the SEBCS, the meta-analysis was conducted among 38 studies of genetic variations of transporters on various cancer survivors. The population of SEBCS consisted of 1338 breast cancer patients who had been treated with adjuvant chemotherapy. A total of 7750 SNPs were selected from 453 ABC and/or SLC genes typed by an Affymetrix 6.0 chip. ABCB1 rs1045642 was associated with poor progression-free survival in a meta-analysis (HR = 1.33, 95% CI: 1.07-1.64). ABCB1, SLC8A1, and SLC12A8 were associated with breast cancer survival in SEBCS (Pgene < 0.05). ABCB1 rs1202172 was differentially associated with survival depending on the chemotherapy (Pinteraction = 0.035). Our finding provides suggestive associations of membrane transporters on cancer survival.
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Affiliation(s)
- Ji-Eun Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Jaesung Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - JooYong Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Chulbum Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Se Mi Lee
- College of Pharmacy Chonnam National University, Gwangju, Korea
| | - Seong Eun Park
- College of Pharmacy, Duksung Women's university, Seoul, Korea
| | - Nan Song
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Seokang Chung
- Division for New Health Technology Assessment, National Evidence-based Healthcare Collaborating Agency, Seoul, Korea
| | - Hyuna Sung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wonshik Han
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sue K Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Mi Kyung Kim
- Division of Cancer Epidemiology and Management, National Cancer Center, Goyang, Korea
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Keun-Young Yoo
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.,The Armed Forces Capital Hospital, Seongnam, Korea
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.,Institute of Environmental Medicine, Seoul National University Medical Research Center, Seoul, Korea
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea. .,Cancer Research Institute, Seoul National University, Seoul, Korea. .,Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea.
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23
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Bossé Y, Amos CI. A Decade of GWAS Results in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:363-379. [PMID: 28615365 PMCID: PMC6464125 DOI: 10.1158/1055-9965.epi-16-0794] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec, Canada.
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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24
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Galván-Femenía I, Guindo M, Duran X, Calabuig-Fariñas S, Mercader JM, Ramirez JL, Rosell R, Torrents D, Carreras A, Kohno T, Jantus-Lewintre E, Camps C, Perucho M, Sumoy L, Yokota J, de Cid R. Genomic profiling in advanced stage non-small-cell lung cancer patients with platinum-based chemotherapy identifies germline variants with prognostic value in SMYD2. Cancer Treat Res Commun 2018; 15:21-31. [PMID: 30207284 DOI: 10.1016/j.ctarc.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/26/2018] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE The aim of the study was to investigate the relationship between germline variations as a prognosis biomarker in patients with advanced Non-Small-Cell-Lung-Cancer (NSCLC) subjected to first-line platinum-based treatment. MATERIALS AND METHODS We carried out a two-stage genome-wide-association study in non-small-cell lung cancer patients with platinum-based chemotherapy in an exploratory sample of 181 NSCLC patients from Caucasian origin, followed by a validation on 356 NSCLC patients from the same ancestry (Valencia, Spain). RESULTS We identified germline variants in SMYD2 as a prognostic factor for survival in patients with advanced NSCLC receiving chemotherapy. SMYD2 alleles are associated to a decreased overall survival and with a reduced Time to Progression. In addition, enrichment pathway analysis identified 361 variants in 40 genes to be involved in poorer outcome in advanced-stage NSCLC patients. CONCLUSION Germline SMYD2 alleles are associated with bad clinical outcome of first-line platinum-based treatment in advanced NSCLC patients. This result supports the role of SMYD2 in the carcinogenic process, and might be used as prognostic signature directing patient stratification and the choice of therapy. MICROABSTRACT A two-Stage Genome wide association study in Caucasian population reveals germline genetic variation in SMYD2 associated to progression disease in first-line platinum-based treatment in advanced NSCLC patients. SMYD2 profiling might have prognostic / predictive value directing choice of therapy and enlighten current knowledge on pathways involved in human carcinogenesis as well in resistance to chemotherapy.
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Affiliation(s)
- Iván Galván-Femenía
- Genomes For life-GCAT Lab. Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Marta Guindo
- Barcelona Supercomputing Center (BSC-CNS), Joint BSC-CRG-IRB Research Program in Computational Biology, Carrer de Jordi Girona, 29-31, 08034 Barcelona, Spain.
| | - Xavier Duran
- Genomes For life-GCAT Lab. Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Sílvia Calabuig-Fariñas
- Department of Medical Oncology, Hospital General Universitario de Valencia, Avenida Tres Cruces, 2, 46014, València, Spain; Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Avda. Tres Cruces s/n 46014 València, Spain; Department of Pathology, Universitat de València, Av. de Blasco Ibáñez, 13, 46010 València, Spain.
| | - Josep Maria Mercader
- Barcelona Supercomputing Center (BSC-CNS), Joint BSC-CRG-IRB Research Program in Computational Biology, Carrer de Jordi Girona, 29-31, 08034 Barcelona, Spain.
| | - Jose Luis Ramirez
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Rafael Rosell
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - David Torrents
- Barcelona Supercomputing Center (BSC-CNS), Joint BSC-CRG-IRB Research Program in Computational Biology, Carrer de Jordi Girona, 29-31, 08034 Barcelona, Spain; ICREA, Catalan Institution for Research and Advanced Studies, Spain.
| | - Anna Carreras
- Genomes For life-GCAT Lab. Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Avda. Tres Cruces s/n 46014 València, Spain; Department of Pathology, Universitat de València, Av. de Blasco Ibáñez, 13, 46010 València, Spain; Molecular Oncology Laboratory, Fundación Hospital General Universitario de València, Avda. Tres Cruces s/n, 46014 València.
| | - Carlos Camps
- Department of Medical Oncology, Hospital General Universitario de Valencia, Avenida Tres Cruces, 2, 46014, València, Spain; Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, Avda. Tres Cruces s/n 46014 València, Spain; Department of Biotechnology, Universitat Politècnica de València, Camí de Vera, s/n, 46022 València, Spain; Department of Medicine, Universitat de València, Av. de Blasco Ibáñez, 13, 46010 València, Spain.
| | - Manuel Perucho
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Lauro Sumoy
- Genomics and Bioinformatics. Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Jun Yokota
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
| | - Rafael de Cid
- Genomes For life-GCAT Lab. Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Can Ruti Biomedical Campus, Crta de Can Ruti, Camí de les Escoles S/N, 08916 Badalona, Barcelona, Spain.
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25
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Shin KM, Hong MJ, Lee SY, Jin CC, Baek SA, Lee JH, Choi JE, Kang HG, Lee WK, Seok Y, Lee EB, Jeong JY, Yoo SS, Lee J, Cha SI, Kim CH, Kim YC, Oh IJ, Na KJ, Cho S, Jheon S, Park JY. Regulatory variants in cancer-related pathway genes predict survival of patients with surgically resected non-small cell lung cancer. Gene 2017; 646:56-63. [PMID: 29289609 DOI: 10.1016/j.gene.2017.12.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/20/2017] [Accepted: 12/27/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND We conducted this study to identify genetic variants in cancer-related pathway genes which can predict prognosis of NSCLC patients after surgery, using a comprehensive list of regulatory single nucleotide polymorphisms (SNPs) prioritized by RegulomeDB. METHOD A total of 509 potentially functional SNPs in cancer-related pathway genes selected from RegulomeDB were evaluated. These SNPs were analyzed in a discovery set (n=354), and a replication study was performed in an independent set (n=772). The association of the SNPs with overall survival (OS) and disease-free survival (DFS) were analyzed. RESULTS In the discovery set, 76 SNPs were significantly associated with OS or DFS. Among the 76 SNPs, the association was consistently observed for 5 SNPs (ERCC1 rs2298881C>A, BRCA2 rs3092989G>A, NELFE rs440454C>T, PPP2R4 rs2541164G>A, and LTBP4 rs3786527G>A) in the validation set. In combined analysis, ERCC1 rs2298881C>A, BRCA2 rs3092989, NELFE rs440454C>T, and PPP2R4 rs2541164G>A were significantly associated with OS and DFS (adjusted HR ·aHR· for OS=1.46, 0.62, 078, and 0.76, respectively; P=0.003, 0.002, 0.007, and 0.003 respectively; and aHR for DFS=1.27, 0.69, 0.86, and 0.82, respectively; P=0.02, 0.002, 0.03, and 0.008, respectively). The LTBP4 rs3786527G>A was significantly associated with better OS (aHR=0.75; P=0.003). CONCLUSION Our results suggest that five SNPs in the cancer-related pathway genes may be useful for the prediction of the prognosis in patients with surgically resected NSCLC.
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Affiliation(s)
- Kyung Min Shin
- Department of Radiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Cheng Cheng Jin
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Sun Ah Baek
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won Kee Lee
- Biostatistics, Medical Research Collaboration Center in Kyungpook National University Hospital and Kyungpook National University School of Medicine, Daegu, Korea
| | - Yangki Seok
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea; Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eung Bae Lee
- Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea; Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Young Chul Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - In Jae Oh
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Kook Joo Na
- Department of Thoracic and Cardiovascular Surgery, Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Jae Yong Park
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Lung Cancer Center, Kyungpook National University Medical Center, Daegu, Republic of Korea; Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
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26
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Bulk E, Kramko N, Liashkovich I, Glaser F, Schillers H, Schnittler HJ, Oberleithner H, Schwab A. K Ca3.1 channel inhibition leads to an ICAM-1 dependent increase of cell-cell adhesion between A549 lung cancer and HMEC-1 endothelial cells. Oncotarget 2017; 8:112268-112282. [PMID: 29348824 PMCID: PMC5762509 DOI: 10.18632/oncotarget.22735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/14/2017] [Indexed: 12/14/2022] Open
Abstract
Early metastasis leads to poor prognosis of lung cancer patients, whose 5-year survival rate is only 15%. We could recently show that the Ca2+ sensitive K+ channel KCa3.1 promotes aggressive behavior of non-small cell lung cancer (NSCLC) cells and that it can serve as a prognostic marker in NSCLC. Since NSCLC patients die of metastases, we investigated whether KCa3.1 channels contribute to poor patient prognosis by regulating distinct steps of the metastatic cascade. We investigated the extravasation of NSCLC cells and focused on their adhesion to endothelial cells and on transendothelial migration. We quantified the adhesion forces between NSCLC cells and endothelial cells by applying single cell force spectroscopy, and we monitored transendothelial migration using live-cell imaging. Inhibition of KCa3.1 channels with senicapoc or KCa3.1 silencing increases the adhesion force of A549 lung cancer cells to human microvascular endothelial cells (HMEC-1). Western blotting, immunofluorescence staining and biotinylation assays indicate that the elevated adhesion force is due to increased expression of ICAM-1 in both cell lines when KCa3.1 channels are downregulated. Consistent with this interpretation, an anti-ICAM-1 blocking antibody abolishes the KCa3.1-dependent increase in adhesion. Senicapoc inhibits transendothelial migration of A549 cells by 50%. Selectively silencing KCa3.1 channels in either NSCLC or endothelial cells reveals that transendothelial migration depends predominantly on endothelial KCa3.1 channels. In conclusion, our findings disclose a novel function of KCa3.1 channels in cancer. KCa3.1 channels regulate ICAM-1 dependent cell-cell adhesion between endothelial and cancer cells that affects the transmigration step of the metastatic cascade.
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Affiliation(s)
- Etmar Bulk
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Nadzeya Kramko
- Institute of Anatomy and Vascular Biology, University of Muenster, Münster, Germany
| | - Ivan Liashkovich
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Felix Glaser
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Hermann Schillers
- Institute of Physiology II, University of Muenster, Münster, Germany
| | | | - Hans Oberleithner
- Institute of Physiology II, University of Muenster, Münster, Germany
| | - Albrecht Schwab
- Institute of Physiology II, University of Muenster, Münster, Germany
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27
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Jones CC, Bush WS, Crawford DC, Wenzlaff AS, Schwartz AG, Wiencke JK, Wrensch MR, Blot WJ, Chanock SJ, Grogan EL, Aldrich MC. Germline Genetic Variants and Lung Cancer Survival in African Americans. Cancer Epidemiol Biomarkers Prev 2017; 26:1288-1295. [PMID: 28619829 DOI: 10.1158/1055-9965.epi-16-0998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022] Open
Abstract
Background: African Americans have the highest lung cancer mortality in the United States. Genome-wide association studies (GWASs) of germline variants influencing lung cancer survival have not yet been conducted with African Americans. We examined five previously reported GWAS catalog variants and explored additional genome-wide associations among African American lung cancer cases.Methods: Incident non-small cell lung cancer cases (N = 286) in the Southern Community Cohort Study were genotyped on the Illumina HumanExome BeadChip. We used Cox proportional hazards models to estimate HRs and 95% confidence intervals (CIs) for overall mortality. Two independent African American studies (N = 316 and 298) were used for replication.Results: One previously reported variant, rs1878022 on 12q23.3, was significantly associated with mortality (HR = 0.70; 95% CI: 0.54-0.92). Replication findings were in the same direction, although attenuated (HR = 0.87 and 0.94). Meta-analysis had a HR of 0.83 (95% CI, 0.71-0.97). Analysis of common variants identified an association between chromosome 6q21.33 and mortality (HR = 0.46; 95% CI, 0.33-0.66).Conclusions: We identified an association between rs1878022 in CMKLR1 and lung cancer survival. However, our results in African Americans have a different direction of effect compared with a prior study in European Americans, suggesting a different genetic architecture or presence of gene-environment interactions. We also identified variants on chromosome 6 within the gene-rich HLA region, which has been previously implicated in lung cancer risk and survival.Impact: We found evidence that inherited genetic risk factors influence lung cancer survival in African Americans. Replication in additional populations is necessary to confirm potential genetic differences in lung cancer survival across populations. Cancer Epidemiol Biomarkers Prev; 26(8); 1288-95. ©2017 AACR.
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Affiliation(s)
- Carissa C Jones
- Department of Thoracic Surgery, Vanderbilt University Medical School, Nashville, Tennessee.,Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, Tennessee
| | - William S Bush
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dana C Crawford
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Angela S Wenzlaff
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - William J Blot
- Division of Epidemiology, Vanderbilt University Medical School, Nashville, Tennessee.,International Epidemiology Institute, Rockville, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical School, Nashville, Tennessee.,Tennessee Valley Health System Veterans Affairs, Nashville, Tennessee
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical School, Nashville, Tennessee. .,Vanderbilt Genetics Institute, Vanderbilt University Medical School, Nashville, Tennessee.,Division of Epidemiology, Vanderbilt University Medical School, Nashville, Tennessee
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28
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Molineros JE, Yang W, Zhou XJ, Sun C, Okada Y, Zhang H, Heng Chua K, Lau YL, Kochi Y, Suzuki A, Yamamoto K, Ma J, Bang SY, Lee HS, Kim K, Bae SC, Zhang H, Shen N, Looger LL, Nath SK. Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. Hum Mol Genet 2017; 26:1205-1216. [PMID: 28108556 DOI: 10.1093/hmg/ddx026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/13/2017] [Indexed: 01/13/2023] Open
Abstract
We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and to perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci. All five loci passed genome-wide significance: MYNN (rs10936599, Pmeta = 1.92 × 10-13, OR = 1.14), ATG16L2 (rs11235604, Pmeta = 8.87 × 10 -12, OR = 0.78), CCL22 (rs223881, Pmeta = 5.87 × 10-16, OR = 0.87), ANKS1A (rs2762340, Pmeta = 4.93 × 10-15, OR = 0.87) and RNASEH2C (rs1308020, Pmeta = 2.96 × 10-19, OR = 0.84) and co-located with annotated gene regulatory elements. The novel loci share genetic signatures with other reported SLE loci, including effects on gene expression, transcription factor binding, and epigenetic characteristics. Most (56%) of the correlated (r2 > 0.8) SNPs from the 82 SLE loci were implicated in differential expression (9.81 × 10-198 < P < 5 × 10-3) of cis-genes. Transcription factor binding sites for p53, MEF2A and E2F1 were significantly (P < 0.05) over-represented in SLE loci, consistent with apoptosis playing a critical role in SLE. Enrichment analysis revealed common pathways, gene ontology, protein domains, and cell type-specific expression. In summary, we provide evidence of five novel SLE susceptibility loci. Integrated bioinformatics using all 82 loci revealed that SLE susceptibility loci share many gene regulatory features, suggestive of conserved mechanisms of SLE etiopathogenesis.
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Affiliation(s)
- Julio E Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jianyang Ma
- Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Nan Shen
- Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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29
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Genetic susceptibility variants for lung cancer: replication study and assessment as expression quantitative trait loci. Sci Rep 2017; 7:42185. [PMID: 28181565 PMCID: PMC5299838 DOI: 10.1038/srep42185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival. Five of these SNPs acted as cis-eQTLs, being associated with the transcription of IREB2 (rs2568494, rs16969968, rs11634351, rs6495309), PSMA4 (rs6495309) and ERCC1 (rs735482), out of 10,821 genes analyzed in lung. For these three genes, we obtained experimental evidence of differential allelic expression in lung tissue, pointing to the existence of in-cis genomic variants that regulate their transcription. These results suggest that these SNPs exert their effects on cancer risk/outcome through the modulation of mRNA levels of their target genes.
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30
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Zhang Y, Wang DC, Shi L, Zhu B, Min Z, Jin J. Genome analyses identify the genetic modification of lung cancer subtypes. Semin Cancer Biol 2017; 42:20-30. [DOI: 10.1016/j.semcancer.2016.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/08/2016] [Indexed: 12/15/2022]
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31
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Lee H, Noh H, Mun J, Gu C, Sever S, Park S. Anks1a regulates COPII-mediated anterograde transport of receptor tyrosine kinases critical for tumorigenesis. Nat Commun 2016; 7:12799. [PMID: 27619642 PMCID: PMC5027278 DOI: 10.1038/ncomms12799] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/02/2016] [Indexed: 02/06/2023] Open
Abstract
ErbB2 signalling, which is amplified by EphA2 binding, is an important therapeutic target for breast cancer. Despite the importance of the EphA2/ErbB2 complex in promoting breast tumorigenesis, the mechanism by which these receptor tyrosine kinases (RTKs) are exported from the endoplasmic reticulum (ER) remains poorly understood. Here we report that the PTB adaptor Anks1a is specifically localized to the ER on its own serine phosphorylation. Once there, Anks1a acts as an important regulator of COPII-mediated EphA2 ER export. The Anks1a ankyrin repeat domain binds EphA2 and causes it to accumulate at sites of ER exit. Simultaneously, the Anks1a PTB domain binds Sec23. This induces internalization of EphA2 via COPII vesicles, while Anks1a remains behind on the ER membrane. EphA2 also binds ErbB2 in the ER and seems to load ErbB2 into growing COPII carriers. Together, our study reveals a novel mechanism that regulates the loading of RTKs into COPII vesicles. EphA2/ErbB2 complex is important in promoting breast cancer but the mechanism by which these receptor tyrosine kinases are exported from the endoplasmic reticulum is unknown. Here the authors show that Anks1a acts as a cargo adaptor in sorting EphA2 into COPII vesicles, thus modulating the surface level of EphA2.
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Affiliation(s)
- Haeryung Lee
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
| | - Hyuna Noh
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
| | - Jiyoung Mun
- Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam-Si, Gyeonggi-Do 13135, Korea
| | - Changkyu Gu
- Division of Nephrology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Sanja Sever
- Division of Nephrology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Soochul Park
- Department of Biological Science, Sookmyung Women's University, Chungpa-ro 47gil 100, Yongsan-gu, Seoul 140-742, Korea
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32
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Wang C, Nie H, Li Y, Liu G, Wang X, Xing S, Zhang L, Chen X, Chen Y, Li Y. The study of the relation of DNA repair pathway genes SNPs and the sensitivity to radiotherapy and chemotherapy of NSCLC. Sci Rep 2016; 6:26526. [PMID: 27246533 PMCID: PMC4887885 DOI: 10.1038/srep26526] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/04/2016] [Indexed: 12/18/2022] Open
Abstract
To analyze the relation between SNPs in DNA repair pathway-related genes and sensitivity of tumor radio-chemotherapy, 26 SNPs in 20 DNA repair genes were genotyped on 176 patients of NSCLC undertaking radio-chemotherapy treatment. In squamous cell carcinoma (SCC), as the rs2228000, rs2228001 (XPC), rs2273953 (TP73), rs2279744 (MDM2), rs2299939 (PTEN) and rs8178085, rs12334811 (DNA-PKcs) affected the sensitivity to chemotherapy, so did the rs8178085, rs12334811 to radiotherapy. Moreover rs344781, rs2273953 and rs12334811 were related with the survival time of SCC. In general, the “good” genotype GG (rs12334811) showed greater efficacy of radio-chemotherapy and MSF (24 months) on SCC. In adenocarcinoma, as the rs2699887 (PIK3), rs12334811 (DNA-PKcs) influenced the sensitivity to chemotherapy, so did the rs2299939, rs2735343 (PTEN) to radiotherapy. And rs402710, rs80270, rs2279744 and rs2909430 impacted the survival time of the adenocarcinoma patients. Both GG (rs2279744) and AG (rs2909430) showed a shorter survival time (MFS = 6). Additionally, some SNPs such as rs2228000, rs2228001 and rs344781 were found to regulate the expression of DNA repair pathway genes through eQTLs dataset analysis. These results indicate that SNPs in DNA repair pathway genes might regulate the expression and affect the DNA damage repair, and thereby impact the efficacy of radio-chemotherapy and the survival time of NSCLC.
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Affiliation(s)
- Chunbo Wang
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China.,Department of Radiotherapy, Affiliated Tumour Hospital of Harbin Medical University
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Yiqun Li
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Guiyou Liu
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China.,Genome Analysis Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China
| | - Xu Wang
- Department of Radiotherapy, Beijing Miyun County Hospital
| | - Shijie Xing
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Liping Zhang
- Department of Radiotherapy, Affiliated Tumour Hospital of Harbin Medical University
| | - Xin Chen
- Department of Radiotherapy, Affiliated Tumour Hospital of Harbin Medical University
| | - Yue Chen
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Heilongjiang, China
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33
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Johnson N, De Ieso P, Migliorini G, Orr N, Broderick P, Catovsky D, Matakidou A, Eisen T, Goldsmith C, Dudbridge F, Peto J, dos-Santos-Silva I, Ashworth A, Ross G, Houlston RS, Fletcher O. Cytochrome P450 Allele CYP3A7*1C Associates with Adverse Outcomes in Chronic Lymphocytic Leukemia, Breast, and Lung Cancer. Cancer Res 2016; 76:1485-1493. [PMID: 26964624 PMCID: PMC4795533 DOI: 10.1158/0008-5472.can-15-1410] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CYP3A enzymes metabolize endogenous hormones and chemotherapeutic agents used to treat cancer, thereby potentially affecting drug effectiveness. Here, we refined the genetic basis underlying the functional effects of a CYP3A haplotype on urinary estrone glucuronide (E1G) levels and tested for an association between CYP3A genotype and outcome in patients with chronic lymphocytic leukemia (CLL), breast, or lung cancers. The most significantly associated SNP was rs45446698, an SNP that tags the CYP3A7*1C allele; this SNP was associated with a 54% decrease in urinary E1G levels. Genotyping this SNP in 1,008 breast cancer, 1,128 lung cancer, and 347 CLL patients, we found that rs45446698 was associated with breast cancer mortality (HR, 1.74; P = 0.03), all-cause mortality in lung cancer patients (HR, 1.43; P = 0.009), and CLL progression (HR, 1.62; P = 0.03). We also found borderline evidence of a statistical interaction between the CYP3A7*1C allele, treatment of patients with a cytotoxic agent that is a CYP3A substrate, and clinical outcome (Pinteraction = 0.06). The CYP3A7*1C allele, which results in adult expression of the fetal CYP3A7 gene, is likely to be the functional allele influencing levels of circulating endogenous sex hormones and outcome in these various malignancies. Further studies confirming these associations and determining the mechanism by which CYP3A7*1C influences outcome are required. One possibility is that standard chemotherapy regimens that include CYP3A substrates may not be optimal for the approximately 8% of cancer patients who are CYP3A7*1C carriers.
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Affiliation(s)
- Nichola Johnson
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK and Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | | | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Nick Orr
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK and Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Athena Matakidou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Timothy Eisen
- Department of Oncology, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
- Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Christy Goldsmith
- Imperial College, London, UK and The Harley Street Clinic, London, UK
| | - Frank Dudbridge
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Isabel dos-Santos-Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Alan Ashworth
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK and Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Gillian Ross
- The Royal Marsden NHS Foundation Trust, Fulham Road, London UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Olivia Fletcher
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK and Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
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Abstract
Adhesion G protein-coupled receptors (aGPCRs) have a long evolutionary history dating back to very basal unicellular eukaryotes. Almost every vertebrate is equipped with a set of different aGPCRs. Genomic sequence data of several hundred extinct and extant species allows for reconstruction of aGPCR phylogeny in vertebrates and non-vertebrates in general but also provides a detailed view into the recent evolutionary history of human aGPCRs. Mining these sequence sources with bioinformatic tools can unveil many facets of formerly unappreciated aGPCR functions. In this review, we extracted such information from the literature and open public sources and provide insights into the history of aGPCR in humans. This includes comprehensive analyses of signatures of selection, variability of human aGPCR genes, and quantitative traits at human aGPCR loci. As indicated by a large number of genome-wide genotype-phenotype association studies, variations in aGPCR contribute to specific human phenotypes. Our survey demonstrates that aGPCRs are significantly involved in adaptation processes, phenotype variations, and diseases in humans.
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Affiliation(s)
- Peter Kovacs
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, Medical Faculty, University of Leipzig, Liebigstr. 21, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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35
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Yang Y, Xu W, Liu D, Ding X, Su B, Sun Y, Gao W. PTEN polymorphisms contribute to clinical outcomes of advanced lung adenocarcinoma patients treated with platinum-based chemotherapy. Tumour Biol 2015; 37:7785-96. [PMID: 26695147 DOI: 10.1007/s13277-015-4651-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/14/2015] [Indexed: 12/22/2022] Open
Abstract
This study aimed to elucidate the impact of PTEN single nucleotide polymorphism (SNP) on clinical outcomes for advanced lung adenocarcinoma (LAC) patients treated with platinum-based chemotherapy. Three functional SNPs (rs11202607 G>A, rs701848 A>G, and rs11202592 G>C) of PTEN gene were genotyped by using DNA from blood samples of 618 advanced LAC patients, and their relationships with clinical outcomes were analyzed. The carriers of homozygous mutant of rs701848 and rs11202592 polymorphisms revealed significantly worse overall survival (OS) than those with heterozygote or wild-type homozygote (18.83 vs. 21.47 vs. 24.37 months, P = 0.034 and 13.40 vs. 19.03 vs. 21.90 months, P = 0.025, respectively). Subgroup analysis revealed that this association was particularly significant in tumor-lymph-node metastasis (TNM) stage III patients. The objective response rates (ORR) and disease control rates (DCR) of patients with genotype AA, AG, and GG in PTEN rs701848 polymorphism were statistically different (24.1 vs 16.6 vs 12.2 %, P = 0.017 and 82.7 vs 76.0 vs 70.2 %, P = 0.029, respectively). Haplotype analysis revealed a protective effect of the haplotype G-A-A (in the order of rs11202592, rs701848, and rs11202607) on chemotherapy efficacy and survival. Taken together, PTEN polymorphisms may contribute to survival and chemotherapy efficacy of advanced LAC patients treated with platinum-based agents.
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Affiliation(s)
- Yang Yang
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao-tong University, No. 241, Huaihaixi Road, Shanghai, 200030, China
| | - Wen Xu
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No. 507, Zhengmin Road, Shanghai, 200433, China
| | - Di Liu
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No. 507, Zhengmin Road, Shanghai, 200433, China
| | - Xi Ding
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No. 507, Zhengmin Road, Shanghai, 200433, China
| | - Bo Su
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, No. 507, Zhengmin Road, Shanghai, 200433, China
| | - Yifeng Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao-tong University, No. 241, Huaihaixi Road, Shanghai, 200030, China.
| | - Wen Gao
- Department of Thoracic Surgery, Shanghai Chest Hospital, School of Medicine, Shanghai Jiao-tong University, No. 241, Huaihaixi Road, Shanghai, 200030, China.
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36
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Burkhardt R, Kirsten H, Beutner F, Holdt LM, Gross A, Teren A, Tönjes A, Becker S, Krohn K, Kovacs P, Stumvoll M, Teupser D, Thiery J, Ceglarek U, Scholz M. Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood. PLoS Genet 2015; 11:e1005510. [PMID: 26401656 PMCID: PMC4581711 DOI: 10.1371/journal.pgen.1005510] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/17/2015] [Indexed: 01/23/2023] Open
Abstract
Profiling amino acids and acylcarnitines in whole blood spots is a powerful tool in the laboratory diagnosis of several inborn errors of metabolism. Emerging data suggests that altered blood levels of amino acids and acylcarnitines are also associated with common metabolic diseases in adults. Thus, the identification of common genetic determinants for blood metabolites might shed light on pathways contributing to human physiology and common diseases. We applied a targeted mass-spectrometry-based method to analyze whole blood concentrations of 96 amino acids, acylcarnitines and pathway associated metabolite ratios in a Central European cohort of 2,107 adults and performed genome-wide association (GWA) to identify genetic modifiers of metabolite concentrations. We discovered and replicated six novel loci associated with blood levels of total acylcarnitine, arginine (both on chromosome 6; rs12210538, rs17657775), propionylcarnitine (chromosome 10; rs12779637), 2-hydroxyisovalerylcarnitine (chromosome 21; rs1571700), stearoylcarnitine (chromosome 1; rs3811444), and aspartic acid traits (chromosome 8; rs750472). Based on an integrative analysis of expression quantitative trait loci in blood mononuclear cells and correlations between gene expressions and metabolite levels, we provide evidence for putative causative genes: SLC22A16 for total acylcarnitines, ARG1 for arginine, HLCS for 2-hydroxyisovalerylcarnitine, JAM3 for stearoylcarnitine via a trans-effect at chromosome 1, and PPP1R16A for aspartic acid traits. Further, we report replication and provide additional functional evidence for ten loci that have previously been published for metabolites measured in plasma, serum or urine. In conclusion, our integrative analysis of SNP, gene-expression and metabolite data points to novel genetic factors that may be involved in the regulation of human metabolism. At several loci, we provide evidence for metabolite regulation via gene-expression and observed overlaps with GWAS loci for common diseases. These results form a strong rationale for subsequent functional and disease-related studies.
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Affiliation(s)
- Ralph Burkhardt
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Holger Kirsten
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- Department for Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Frank Beutner
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Lesca M. Holdt
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Laboratory Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Arnd Gross
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Andrej Teren
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Heart Center Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Medical Department, Clinic for Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Susen Becker
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Knut Krohn
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Interdisciplinary Centre for Clinical Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig Germany
| | - Michael Stumvoll
- Medical Department, Clinic for Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
- Integrated Research and Treatment Center Adiposity Diseases, University of Leipzig, Leipzig Germany
| | - Daniel Teupser
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Laboratory Medicine, Ludwig-Maximilians University Munich, Munich, Germany
| | - Joachim Thiery
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Markus Scholz
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- * E-mail:
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37
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Wu C, Shi X, Cui Y, Ma S. A penalized robust semiparametric approach for gene-environment interactions. Stat Med 2015; 34:4016-30. [PMID: 26239060 DOI: 10.1002/sim.6609] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 06/28/2015] [Accepted: 07/06/2015] [Indexed: 11/09/2022]
Abstract
In genetic and genomic studies, gene-environment (G×E) interactions have important implications. Some of the existing G×E interaction methods are limited by analyzing a small number of G factors at a time, by assuming linear effects of E factors, by assuming no data contamination, and by adopting ineffective selection techniques. In this study, we propose a new approach for identifying important G×E interactions. It jointly models the effects of all E and G factors and their interactions. A partially linear varying coefficient model is adopted to accommodate possible nonlinear effects of E factors. A rank-based loss function is used to accommodate possible data contamination. Penalization, which has been extensively used with high-dimensional data, is adopted for selection. The proposed penalized estimation approach can automatically determine if a G factor has an interaction with an E factor, main effect but not interaction, or no effect at all. The proposed approach can be effectively realized using a coordinate descent algorithm. Simulation shows that it has satisfactory performance and outperforms several competing alternatives. The proposed approach is used to analyze a lung cancer study with gene expression measurements and clinical variables. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Cen Wu
- Department of Biostatistics, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, U.S.A.,Department of Statistics, Kansas State University, 1116 Mid-Campus Drive N., Manhattan, KS, 66506, U.S.A
| | - Xingjie Shi
- Department of Statistics, Nanjing University of Finance and Economics, Nanjing, China
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, 619 Red Cedar Rd, East Lansing, MI, 48824, U.S.A
| | - Shuangge Ma
- Department of Biostatistics, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06520, U.S.A.,VA Cooperative Studies Program Coordinating Center, West Haven, CT, 06516, U.S.A
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38
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Abstract
The severity of the toxic side effects of chemotherapy shows a great deal of interindividual variability, and much of this variation is likely genetically based. Simple DNA tests predictive of toxic side effects could revolutionize the way chemotherapy is carried out. Due to the challenges in identifying polymorphisms that affect toxicity in humans, we use Drosophila fecundity following oral exposure to carboplatin, gemcitabine and mitomycin C as a model system to identify naturally occurring DNA variants predictive of toxicity. We use the Drosophila Synthetic Population Resource (DSPR), a panel of recombinant inbred lines derived from a multiparent advanced intercross, to map quantitative trait loci affecting chemotoxicity. We identify two QTL each for carboplatin and gemcitabine toxicity and none for mitomycin. One QTL is associated with fly orthologs of a priori human carboplatin candidate genes ABCC2 and MSH2, and a second QTL is associated with fly orthologs of human gemcitabine candidate genes RRM2 and RRM2B. The third, a carboplatin QTL, is associated with a posteriori human orthologs from solute carrier family 7A, INPP4A&B, and NALCN. The fourth, a gemcitabine QTL that also affects methotrexate toxicity, is associated with human ortholog GPx4. Mapped QTL each explain a significant fraction of variation in toxicity, yet individual SNPs and transposable elements in the candidate gene regions fail to singly explain QTL peaks. Furthermore, estimates of founder haplotype effects are consistent with genes harboring several segregating functional alleles. We find little evidence for nonsynonymous SNPs explaining mapped QTL; thus it seems likely that standing variation in toxicity is due to regulatory alleles.
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39
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Galvan A, Colombo F, Frullanti E, Dassano A, Noci S, Wang Y, Eisen T, Matakidou A, Tomasello L, Vezzalini M, Sorio C, Dugo M, Ambrogi F, Iacobucci I, Martinelli G, Incarbone M, Alloisio M, Nosotti M, Tosi D, Santambrogio L, Pelosi G, Pastorino U, Houlston RS, Dragani TA. Germline polymorphisms and survival of lung adenocarcinoma patients: a genome-wide study in two European patient series. Int J Cancer 2015; 136:E262-71. [PMID: 25196286 DOI: 10.1002/ijc.29195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 11/09/2022]
Abstract
In lung cancer, the survival of patients with the same clinical stage varies widely for unknown reasons. In this two-phase study, we examined the hypothesis that germline variations influence the survival of patients with lung adenocarcinoma. First, we analyzed existing genotype and clinical data from 289 UK-resident patients with lung adenocarcinoma, identifying 86 single nucleotide polymorphisms (SNPs) that associated with survival (p < 0.01). We then genotyped these candidate SNPs in a validation series of 748 patients from Italy that resulted genetically compatible with the UK series based on principal component analysis. In a Cox proportional hazard model adjusted for age, sex and clinical stage, four SNPs were confirmed on the basis of their having a hazard ratio (HR) indicating the same direction of effect in the two series and p < 0.05. The strongest association was provided by rs2107561, an intronic SNP of PTPRG, protein tyrosine phosphatase, receptor type, G; the C allele was associated with poorer survival in both patient series (pooled analysis loge HR = 0.31; 95% CI: 0.15-0.46, p = 8.5 × 10(-5) ). PTPRG mRNA levels in 43 samples of lung adenocarcinoma were 40% of those observed in noninvolved lung tissue from the same patients. PTPRG overexpression significantly inhibited the clonogenicity of A549 lung carcinoma cells and the anchorage-independent growth of the NCI-H460 large cell lung cancer line. These four germline variants represent promising candidates that, with further study, may help predict clinical outcome. In addition, the PTPRG locus may have a role in tumor progression.
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Demirkan A, Henneman P, Verhoeven A, Dharuri H, Amin N, van Klinken JB, Karssen LC, de Vries B, Meissner A, Göraler S, van den Maagdenberg AMJM, Deelder AM, C ’t Hoen PA, van Duijn CM, van Dijk KW. Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. PLoS Genet 2015; 11:e1004835. [PMID: 25569235 PMCID: PMC4287344 DOI: 10.1371/journal.pgen.1004835] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 10/16/2014] [Indexed: 12/20/2022] Open
Abstract
Metabolite quantitative traits carry great promise for epidemiological studies, and their genetic background has been addressed using Genome-Wide Association Studies (GWAS). Thus far, the role of less common variants has not been exhaustively studied. Here, we set out a GWAS for metabolite quantitative traits in serum, followed by exome sequence analysis to zoom in on putative causal variants in the associated genes. 1H Nuclear Magnetic Resonance (1H-NMR) spectroscopy experiments yielded successful quantification of 42 unique metabolites in 2,482 individuals from The Erasmus Rucphen Family (ERF) study. Heritability of metabolites were estimated by SOLAR. GWAS was performed by linear mixed models, using HapMap imputations. Based on physical vicinity and pathway analyses, candidate genes were screened for coding region variation using exome sequence data. Heritability estimates for metabolites ranged between 10% and 52%. GWAS replicated three known loci in the metabolome wide significance: CPS1 with glycine (P-value = 1.27×10−32), PRODH with proline (P-value = 1.11×10−19), SLC16A9 with carnitine level (P-value = 4.81×10−14) and uncovered a novel association between DMGDH and dimethyl-glycine (P-value = 1.65×10−19) level. In addition, we found three novel, suggestively significant loci: TNP1 with pyruvate (P-value = 1.26×10−8), KCNJ16 with 3-hydroxybutyrate (P-value = 1.65×10−8) and 2p12 locus with valine (P-value = 3.49×10−8). Exome sequence analysis identified potentially causal coding and regulatory variants located in the genes CPS1, KCNJ2 and PRODH, and revealed allelic heterogeneity for CPS1 and PRODH. Combined GWAS and exome analyses of metabolites detected by high-resolution 1H-NMR is a robust approach to uncover metabolite quantitative trait loci (mQTL), and the likely causative variants in these loci. It is anticipated that insight in the genetics of intermediate phenotypes will provide additional insight into the genetics of complex traits. Human metabolic individuality is under strict control of genetic and environmental factors. In our study, we aimed to find the genetic determinants of circulating molecules in sera of large set of individuals representing the general population. First, we performed a hypothesis-free genome wide screen in this population to identify genetic regions of interest. Our study confirmed four known gene metabolite connections, but also pointed to four novel ones. Genome-wide screens enriched for common intergenic variants may miss causal genetic variations directly changing the protein sequence. To investigate this further, we zoomed into regions of interest and tested whether the association signals obtained in the first stage were direct, or whether they represent causal variations, which were not captured in the initial panel. These subsequent tests showed that protein coding and regulatory variations are involved in metabolite levels. For two genomic regions we also found that genes harbour more than one causal variant influencing metabolite levels independent of each other. We also observed strong connection between markers of cardio-metabolic health and metabolites. Taken together, our novel loci are of interest for further research to investigate the causal relation to for instance type 2 diabetes and cardiovascular disease.
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Affiliation(s)
- Ayşe Demirkan
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter Henneman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Harish Dharuri
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jan Bert van Klinken
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lennart C. Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Boukje de Vries
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Axel Meissner
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sibel Göraler
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Arn M. J. M. van den Maagdenberg
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - André M. Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A. C ’t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands
- * E-mail:
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Niu XM, Lu S. Acetylcholine receptor pathway in lung cancer: New twists to an old story. World J Clin Oncol 2014; 5:667-676. [PMID: 25302169 PMCID: PMC4129531 DOI: 10.5306/wjco.v5.i4.667] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/17/2014] [Accepted: 06/11/2014] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies revealed that allelic variation in the α5-α3-β4 nicotine acetylcholine receptor (nAChR) cluster on chromosome 15q24-15q25.1 was associated with lung cancer risk. nAChRs are membrane ligand-gated cation channels whose activation is triggered by the binding of the endogenous neurotransmitter acetylcholine (ACh) or other biologic compounds including nicotine. nAChRs have been found on lung cancer cells, underscoring the idea that the non-neuronal nAChR pathway has important implications for lung cancer. Several studies focusing on the treatment with nAChR antagonists with improved selectivity might trigger novel strategies for the intervention and prevention of lung cancer. Here we review the genetic risk factors for lung cancer in the nAChR gene cluster, the roles of nicotine receptors, and the molecular mechanisms of acetylcholine receptor pathways to lead to more opportunities for intervention and prevention of lung cancer.
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Murphy SJ, Wigle DA, Lima JF, Harris FR, Johnson SH, Halling G, Asiedu MK, Seto CT, Terra S, Kosari F, Peikert T, Yang P, Aubry MC, Vasmatzis G. Genomic rearrangements define lineage relationships between adjacent lepidic and invasive components in lung adenocarcinoma. Cancer Res 2014; 74:3157-67. [PMID: 24879567 DOI: 10.1158/0008-5472.can-13-1727] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The development of adenocarcinoma of the lung is believed to proceed from in situ disease (adenocarcinoma in situ, AIS) to minimally invasive disease with prominent lepidic growth (minimally invasive adenocarcinoma, MIA), then to fully invasive adenocarcinoma (AD), but direct evidence for this model has been lacking. Because some lung adenocarcinomas show prominent lepidic growth (AD-L), we designed a study to address the lineage relationship between the lepidic (noninvasive) component (L) and the adjacent nonlepidic growth component representing invasive disease within individual tumors. Lineage relationships were evaluated by next-generation DNA sequencing to define large genomic rearrangements in microdissected tissue specimens collected by laser capture. We found a strong lineage relationship between the majority of adjacent lepidic and invasive components, supporting a putative AIS-AD transition. Notably, many rearrangements were detected in the less aggressive lepidic component, although the invasive component exhibited an overall higher rate of genomic rearrangement. Furthermore, a significant number of genomic rearrangements were present in histologically normal lung adjacent to tumor, but not in host germline DNA, suggesting field defects restricted to zonal regions near a tumor. Our results offer a perspective on the genetic pathogenesis underlying adenocarcinoma development and its clinical management.
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Affiliation(s)
- Stephen J Murphy
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Dennis A Wigle
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Joema Felipe Lima
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Faye R Harris
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Sarah H Johnson
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Geoffrey Halling
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Michael K Asiedu
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Charlie T Seto
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Simone Terra
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Farhad Kosari
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Tobias Peikert
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ping Yang
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MinnesotaAuthors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Marie-Christine Aubry
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Authors' Affiliations: Departments of Molecular Medicine, General Thoracic Surgery, Pulmonary and Critical Care Medicine, Health Sciences Research, and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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Tang S, Pan Y, Wang Y, Hu L, Cao S, Chu M, Dai J, Shu Y, Xu L, Chen J, Jin G, Hu Z, Ma H, Shen H. Genome-wide association study of survival in early-stage non-small cell lung cancer. Ann Surg Oncol 2014; 22:630-5. [PMID: 25145502 DOI: 10.1245/s10434-014-3983-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Lung cancer, especially non-small cell lung cancer (NSCLC), is the leading cause of cancer-related deaths all over the world. Studies have indicated that molecular biomarkers, including genetic variants, may provide additional values for the targeted treatments and clinical outcomes of NSCLC patients. To better understand the effects of molecular biomarkers on the treatment of NSCLC, we conducted a genome-wide analysis to investigate the prognostic implications of genetic variants in early-stage NSCLC patients with surgery. METHODS A genome wide scan of 906,703 single-nucleotide polymorphisms (SNPs) was conducted in a cohort with 365 early-stage NSCLC patients with surgery, followed by a fast-track replication in another independent cohort of 327 NSCLC patients from Nanjing, China. Cox models were used to screen and validate significant SNPs associated with the overall survival of early-stage NSCLC patients. RESULTS We found that rs10023113 in calcium/calmodulin-dependent protein kinase II delta (CAMK2D) was consistently associated with survival of early-stage NSCLC in the GWAS scan and the replication cohort [GWAS scan: hazard ratio (HR) 2.84; 95 % confidence interval (CI) 1.90-4.23, P = 1.29 × 10(-6); replication cohort: HR 2.19, 95 % CI 1.15-4.21, P = 1.80 × 10(-2)]. When combining all the patients, the results showed that the variant allele of rs10023113 was significantly associated with poor prognosis of early-stage NSCLC with P value of 3.40 × 10(-7) (HR 2.30, 95 % CI 1.67-3.17). CONCLUSIONS These findings suggest that CAMK2D rs10023113 may be a potentially prognostic marker for overall survival of early-stage NSCLC patients in Chinese population.
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Affiliation(s)
- Shaowen Tang
- Department of Epidemiology and Biostatistics and Ministry of Education Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
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Yang IA, Holloway JW, Fong KM. Genetic susceptibility to lung cancer and co-morbidities. J Thorac Dis 2014; 5 Suppl 5:S454-62. [PMID: 24163739 DOI: 10.3978/j.issn.2072-1439.2013.08.06] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 12/18/2022]
Abstract
Lung cancer is a leading cause of cancer death and disease burden in many countries. Understanding of the biological pathways involved in lung cancer aetiology is required to identify key biomolecules that could be of significant clinical value, either as predictive, prognostic or diagnostic markers, or as targets for the development of novel therapies to treat this disease, in addition to smoking avoidance strategies. Genome-wide association studies (GWAS) have enabled significant progress in the past 5 years in investigating genetic susceptibility to lung cancer. Large scale, multi-cohort GWAS of mainly Caucasian, smoking, populations have identified strong associations for lung cancer mapped to chromosomal regions 15q [nicotinic acetylcholine receptor (nAChR) subunits: CHRNA3, CHRNA5], 5p (TERT-CLPTM1L locus) and 6p (BAT3-MSH5). Some studies in Asian populations of smokers have found similar risk loci, whereas GWAS in never smoking Asian females have identified associations in other chromosomal regions, e.g., 3q (TP63), that are distinct from smoking-related lung cancer risk loci. GWAS of smoking behaviour have identified risk loci for smoking quantity at 15q (similar genes to lung cancer susceptibility: CHRNA3, CHRNA5) and 19q (CYP2A6). Other genes have been mapped for smoking initiation and smoking cessation. In chronic obstructive pulmonary disease (COPD), which is a known risk factor for lung cancer, GWAS in large cohorts have also found CHRNA3 and CHRNA5 single nucleotide polymorphisms (SNPs) mapping at 15q as risk loci, as well as other regions at 4q31 (HHIP), 4q24 (FAM13A) and 5q (HTR4). The overlap in risk loci between lung cancer, smoking behaviour and COPD may be due to the effects of nicotine addiction; however, more work needs to be undertaken to explore the potential direct effects of nicotine and its metabolites in gene-environment interaction in these phenotypes. Goals of future genetic susceptibility studies of lung cancer should focus on refining the strongest risk loci in a wide range of populations with lung cancer, and integrating other clinical and biomarker information, in order to achieve the aim of personalised therapy for lung cancer.
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Affiliation(s)
- Ian A Yang
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia; ; UQ Thoracic Research Centre, The University of Queensland, Brisbane, Australia
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Cochet-Bissuel M, Lory P, Monteil A. The sodium leak channel, NALCN, in health and disease. Front Cell Neurosci 2014; 8:132. [PMID: 24904279 PMCID: PMC4033012 DOI: 10.3389/fncel.2014.00132] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/28/2014] [Indexed: 12/12/2022] Open
Abstract
Ion channels are crucial components of cellular excitability and are involved in many neurological diseases. This review focuses on the sodium leak, G protein-coupled receptors (GPCRs)-activated NALCN channel that is predominantly expressed in neurons where it regulates the resting membrane potential and neuronal excitability. NALCN is part of a complex that includes not only GPCRs, but also UNC-79, UNC-80, NLF-1 and src family of Tyrosine kinases (SFKs). There is growing evidence that the NALCN channelosome critically regulates its ion conduction. Both in mammals and invertebrates, animal models revealed an involvement in many processes such as locomotor behaviors, sensitivity to volatile anesthetics, and respiratory rhythms. There is also evidence that alteration in this NALCN channelosome can cause a wide variety of diseases. Indeed, mutations in the NALCN gene were identified in Infantile Neuroaxonal Dystrophy (INAD) patients, as well as in patients with an Autosomal Recessive Syndrome with severe hypotonia, speech impairment, and cognitive delay. Deletions in NALCN gene were also reported in diseases such as 13q syndrome. In addition, genes encoding NALCN, NLF- 1, UNC-79, and UNC-80 proteins may be susceptibility loci for several diseases including bipolar disorder, schizophrenia, Alzheimer's disease, autism, epilepsy, alcoholism, cardiac diseases and cancer. Although the physiological role of the NALCN channelosome is poorly understood, its involvement in human diseases should foster interest for drug development in the near future. Toward this goal, we review here the current knowledge on the NALCN channelosome in physiology and diseases.
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Affiliation(s)
- Maud Cochet-Bissuel
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Universités Montpellier 1&2 Montpellier, France ; INSERM, U 661 Montpellier, France ; LabEx 'Ion Channel Science and Therapeutics' Montpellier, France
| | - Philippe Lory
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Universités Montpellier 1&2 Montpellier, France ; INSERM, U 661 Montpellier, France ; LabEx 'Ion Channel Science and Therapeutics' Montpellier, France
| | - Arnaud Monteil
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Universités Montpellier 1&2 Montpellier, France ; INSERM, U 661 Montpellier, France ; LabEx 'Ion Channel Science and Therapeutics' Montpellier, France
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Yoo SS, Hong MJ, Jeon HS, Lee WK, Lee SY, Lee J, Cha SI, Kim CH, Lee E, Park JY. Replication of results of a genome-wide association study on lung cancer survival in a Korean population. Cancer Genet 2014; 207:35-9.e1-2. [PMID: 24525039 DOI: 10.1016/j.cancergen.2013.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/09/2013] [Accepted: 12/30/2013] [Indexed: 11/26/2022]
Abstract
Recently, a genome-wide association study (GWAS) identified single nucleotide polymorphisms (SNPs) that may influence the prognosis of early-stage non-small cell lung cancer (NSCLC) in Caucasians. We attempted to replicate the impact of genetic variants identified in the GWAS on lung cancer survival in a Korean population. A total of 363 patients with surgically resected NSCLCs were enrolled, and 12 SNPs were genotyped using the SEQUENOM MassARRAY iPLEX assay, TaqMan assay, or a polymerase chain reaction-restriction fragment length polymorphism analysis. The association between genotypes and overall survival (OS) was analyzed. Among the 12 SNPs, the rs6034368T>C was associated with OS. Patients with the rs6034368C allele showed a better OS than the patients with the rs6034368T allele (adjusted hazard ratio = 0.72, confidence interval = 0.56-0.93, P = 0.01). The rs12446308A>G had an effect on OS, but it was marginally significant (under a codominant model, adjusted hazard ratio = 1.85, confidence interval = 0.98-3.47, P = 0.06). We identified that the rs6034368T>C was associated with survival in early-stage NSCLC in a Korean population.
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Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea; Lung Cancer Center, Kyungpoook National University Medical Center, Daegu, Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Hyo-Sung Jeon
- Lung Cancer Center, Kyungpoook National University Medical Center, Daegu, Korea; Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea
| | - Won Kee Lee
- Department of Preventive Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Shin Yup Lee
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea; Lung Cancer Center, Kyungpoook National University Medical Center, Daegu, Korea
| | - Jaehee Lee
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Seung Ick Cha
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Chang Ho Kim
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea
| | - Eungbae Lee
- Lung Cancer Center, Kyungpoook National University Medical Center, Daegu, Korea; Department of Thoracic Surgery, Kyungpook National University School of Medicine, Daegu, Korea
| | - Jae Yong Park
- Department of Internal Medicine, Kyungpook National University School of Medicine, Daegu, Korea; Lung Cancer Center, Kyungpoook National University Medical Center, Daegu, Korea; Department of Biochemistry and Cell Biology, Kyungpook National University School of Medicine, Daegu, Korea.
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Abstract
miR-17∼92 is a polycistronic microRNA (miR) cluster (consisting of miR-17, miR-18a, miR-19a, miR-19b, miR-20a, and miR-92a) which frequently is overexpressed in several solid and lymphoid malignancies. Loss- and gain-of-function studies have revealed the role of miR-17∼92 in heart, lung, and B-cell development and in Myc-induced B-cell lymphomas, respectively. Recent studies indicate that overexpression of this locus leads to lymphoproliferation, but no experimental proof that dysregulation of this cluster causes B-cell lymphomas or leukemias is available. To determine whether miR-17∼92- overexpression induces lymphomagenesis/leukemogenesis, we generated a B-cell-specific transgenic mouse model with targeted overexpression of this cluster in B cells. The miR-17∼92 overexpression was driven by the Eµ-enhancer and Ig heavy-chain promoter, and a 3' GFP tag was added to the transgene to track the miR expression. Expression analysis using Northern Blot and quantitative RT-PCR confirmed 2.5- to 25-fold overexpression of all six miRs in the transgenic mice spleens as compared with spleens from wild-type mice. Eµ-miR-17∼92 mice developed B-cell malignancy by the age of 12-18 mo with a penetrance of ∼80% (49% splenic B-cell lymphoproliferative disease, 28% lymphoma). At this stage mice exhibited severe splenomegaly with abnormal B-cell-derived white pulp expansion and enlarged lymph nodes. Interestingly, we found three classes of B-cell lymphomas/leukemias at varying grades of differentiation. These included expansion of CD19(+) and CD5(+) double-positive B cells similar to the aggressive form of human B-cell chronic lymphocytic leukemia, B220(+) CD43(+) B1-cell proliferation, and a CD19(+) aggressive diffuse large B-cell lymphoma-like disease, as assessed by flow cytometry and histopathological analysis.
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Galvan A, Frullanti E, Anderlini M, Manenti G, Noci S, Dugo M, Ambrogi F, De Cecco L, Spinelli R, Piazza R, Pirola A, Gambacorti-Passerini C, Incarbone M, Alloisio M, Tosi D, Nosotti M, Santambrogio L, Pastorino U, Dragani TA. Gene expression signature of non-involved lung tissue associated with survival in lung adenocarcinoma patients. Carcinogenesis 2013; 34:2767-73. [PMID: 23978379 DOI: 10.1093/carcin/bgt294] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Lung adenocarcinoma patients of similar clinical stage and undergoing the same treatments often have marked interindividual variations in prognosis. These clinical discrepancies may be due to the genetic background modulating an individual's predisposition to fighting cancer. Herein, we hypothesized that the lung microenvironment, as reflected by its expression profile, may affect lung adenocarcinoma patients' survival. The transcriptome of non-involved lung tissue, excised from a discovery series of 204 lung adenocarcinoma patients, was evaluated using whole-genome expression microarrays (with probes corresponding to 28 688 well-annotated coding sequences). Genes associated with survival status at 60 months were identified by Cox regression analysis (adjusted for gender, age and clinical stage) and retested in a validation series of 78 additional cases. RNA-Seq analysis from non-involved lung tissue of 12 patients was performed to characterize the different isoforms of candidate genes. Ten genes for which the loge-transformed hazard ratios expressed the same direction of effect in the discovery (P < 1.0 × 10(-3)) and validation series comprised the gene expression signature associated with survival: CNTNAP1, PKNOX1, FAM156A, FRMD8, GALNTL1, TXNDC12, SNTB1, PPP3R1, SNX10 and SERPINH1. RNA sequencing highlighted the complex expression pattern of these genes in non-involved lung tissue from different patients and permitted the detection of a read-through gene fusion between PPP3R1 and the flanking gene (CNRIP1) as well as a novel isoform of CNTNAP1. Our findings support the hypothesis that individual genetic characteristics, evidenced by the expression pattern of non-involved tissue, influence the outcome of lung adenocarcinoma patients.
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Powell CA, Halmos B, Nana-Sinkam SP. Update in lung cancer and mesothelioma 2012. Am J Respir Crit Care Med 2013; 188:157-66. [PMID: 23855692 PMCID: PMC3778761 DOI: 10.1164/rccm.201304-0716up] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Charles A Powell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Köroğlu Ç, Seven M, Tolun A. Recessive truncating NALCN mutation in infantile neuroaxonal dystrophy with facial dysmorphism. J Med Genet 2013; 50:515-20. [PMID: 23749988 DOI: 10.1136/jmedgenet-2013-101634] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Infantile neuroaxonal dystrophy (INAD) is a recessive disease that results in total neurological degeneration and death in childhood. PLA2G6 mutation is the underlying genetic defect, but rare genetic heterogeneity has been demonstrated. One of the five families we studied did not link to PLA2G6 locus, and in the family one of the two affected siblings additionally had atypical features including facial dysmorphism, pectus carinatum, scoliosis, pes varus, zygodactyly and bilateral cryptorchidism as well as cerebellar atrophy, as previously reported. METHODS Sural biopsy was investigated by electron microscopy. PLA2G6 was screened for mutations by Sanger sequencing. In the mutation-free family, candidate disease loci were found via linkage analysis using data from single nucleotide polymorphism genome scans. Exome sequencing was applied to find the variants at the loci. RESULTS PLA2G6 mutations were identified in four families including the one with an unusually severe phenotype that led to death within the first 2 years of life. In the remaining family, seven candidate loci totalling 15.2 Mb were found and a homozygous truncating mutation p.Q642X was identified in NALCN at 13q32.3. The patients are around 20-years-old. CONCLUSIONS NALCN is the gene responsible for INAD with facial dysmorphism. The patients have lived to adulthood despite severe growth and neuromotor retardation. NALCN forms a voltage-independent ion channel with a role in the regulation of neuronal excitability. Our findings broaden the spectrum of genes associated with neuroaxonal dystrophy. Testing infants with idiopathic severe growth retardation and neurodegeneration for NALCN mutations could benefit families.
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Affiliation(s)
- Çiğdem Köroğlu
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
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