1
|
LoPiccolo J, Gusev A, Christiani DC, Jänne PA. Lung cancer in patients who have never smoked - an emerging disease. Nat Rev Clin Oncol 2024; 21:121-146. [PMID: 38195910 PMCID: PMC11014425 DOI: 10.1038/s41571-023-00844-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Lung cancer is the most common cause of cancer-related deaths globally. Although smoking-related lung cancers continue to account for the majority of diagnoses, smoking rates have been decreasing for several decades. Lung cancer in individuals who have never smoked (LCINS) is estimated to be the fifth most common cause of cancer-related deaths worldwide in 2023, preferentially occurring in women and Asian populations. As smoking rates continue to decline, understanding the aetiology and features of this disease, which necessitate unique diagnostic and treatment paradigms, will be imperative. New data have provided important insights into the molecular and genomic characteristics of LCINS, which are distinct from those of smoking-associated lung cancers and directly affect treatment decisions and outcomes. Herein, we review the emerging data regarding the aetiology and features of LCINS, particularly the genetic and environmental underpinnings of this disease as well as their implications for treatment. In addition, we outline the unique diagnostic and therapeutic paradigms of LCINS and discuss future directions in identifying individuals at high risk of this disease for potential screening efforts.
Collapse
Affiliation(s)
- Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - David C Christiani
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| |
Collapse
|
2
|
Xu BB, Zheng ED, Sun HY, Huang Y, Zheng L, Lan QL, Zhou XL, Geng XG, Wang YN, Wang XY, Yu YC. Comprehensive analysis of circular RNA-associated competing endogenous RNA networks and immune infiltration in gastric cancer. Transpl Immunol 2023; 77:101793. [PMID: 36773765 DOI: 10.1016/j.trim.2023.101793] [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: 08/02/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND Circular RNA (circRNA) has been proved to be an important regulator of gastric cancer (GC). However, the role and regulatory mechanism of circrna related competitive endogenous RNA (ceRNA) in GC have not been established. METHODS CircRNA data and clinical data were obtained from the GEO and TCGA databases. The ceRNA networks were constructed and a function enrichment analysis was completed. Additionally, correlations between hub genes expression, immune cell infiltration, and clinical phenotypes were determined. The differentially expressed circRNAs and their downstream microRNAs (miRNAs) were validated by quantitative real-time polymerase chain reaction, and the hub genes were validated by western blot analysis. The migration and invasion ability of overexpressed hsa_circ_0002504 was determined by a transwell assay. RESULTS The ceRNA network contained 2 circRNAs, 3 miRNAs, and 55 messenger RNAs (mRNAs). 323 biological processes terms, 53 cellular components terms, 51 molecular functions terms, and 4 signaling pathways were revealed by the function enrichment analysis. The GSEA analysis revealed that the hub genes were positively correlated with the axon guidance and adhesion molecules pathways. The correlation analysis revealed that overexpressed EPHA4 and KCNA1 indicated poor tissue differentiation and were associated with clinically advanced stages of GC. The in vitro experiments showed that hsa_circ_0002504 was significantly down-regulated in GC cell lines. In addition, the overexpression of hsa_circ_0002504 led to a significant downregulation of hsa-miR-615-5p and hsa-miR-767-5p, as well as an upregulation of EPHA4, KCNA1, and NCAM1. Furthermore, it suppressed the migration and invasion ability of GC cells. CONCLUSIONS Hsa_circ_0002504 is a potential diagnostic biomarker for GC. High expression of EPHA4 and KCNA1 may indicate poor prognosis.
Collapse
Affiliation(s)
- Bei-Bei Xu
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China; Soochow University, Suzhou 215000, Jiangsu, China; Department of Gastroenterology, Zhejiang Provincial People's Hospital, Hangzhou 310000, Zhejiang, China
| | - En-Dian Zheng
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Hao-Yue Sun
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Yi Huang
- Department of General Surgery, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou 325000, Zhejiang, China
| | - Liang Zheng
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Qiao-Li Lan
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Xiao-Lu Zhou
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, Hangzhou 310000, Zhejiang, China
| | - Xiao-Ge Geng
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, Hangzhou 310000, Zhejiang, China
| | - Ya-Nan Wang
- Zhejiang University of Technology, Hangzhou 310000, Zhejiang, China
| | - Xiu-Yan Wang
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
| | - Ying-Cong Yu
- Department of Gastroenterology, The Third Affiliated Hospital of Shanghai University, Wenzhou People's Hospital, Wenzhou Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| |
Collapse
|
3
|
Qi H, Grace Wright RH, Beato M, Price BD. The ADP-ribose hydrolase NUDT5 is important for DNA repair. Cell Rep 2022; 41:111866. [PMID: 36543120 DOI: 10.1016/j.celrep.2022.111866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
DNA damage leads to rapid synthesis of poly(ADP-ribose) (pADPr), which is important for damage signaling and repair. pADPr chains are removed by poly(ADP-ribose) glycohydrolase (PARG), releasing free mono(ADP-ribose) (mADPr). Here, we show that the NUDIX hydrolase NUDT5, which can hydrolyze mADPr to ribose-5-phosphate and either AMP or ATP, is recruited to damage sites through interaction with PARG. NUDT5 does not regulate PARP or PARG activity. Instead, loss of NUDT5 reduces basal cellular ATP levels and exacerbates the decrease in cellular ATP that occurs during DNA repair. Further, loss of NUDT5 activity impairs RAD51 recruitment, attenuates the phosphorylation of key DNA-repair proteins, and reduces both H2A.Z exchange at damage sites and repair by homologous recombination. The ability of NUDT5 to hydrolyze mADPr, and/or regulate cellular ATP, may therefore be important for efficient DNA repair. Targeting NUDT5 to disrupt PAR/mADPr and energy metabolism may be an effective anti-cancer strategy.
Collapse
Affiliation(s)
- Hongyun Qi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA
| | - Roni Helene Grace Wright
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Miguel Beato
- Centro de Regulación Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA.
| |
Collapse
|
4
|
Qin Q, Gomez-Salazar M, Tower RJ, Chang L, Morris CD, McCarthy EF, Ting K, Zhang X, James AW. NELL1 Regulates the Matrisome to Promote Osteosarcoma Progression. Cancer Res 2022; 82:2734-2747. [PMID: 35700263 PMCID: PMC9357190 DOI: 10.1158/0008-5472.can-22-0732] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/22/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023]
Abstract
Sarcomas produce an abnormal extracellular matrix (ECM), which in turn provides instructive cues for cell growth and invasion. Neural EGF like-like molecule 1 (NELL1) is a secreted glycoprotein characterized by its nonneoplastic osteoinductive effects, yet it is highly expressed in skeletal sarcomas. Here, we show that genetic deletion of NELL1 markedly reduces invasive behavior across human osteosarcoma (OS) cell lines. NELL1 deletion resulted in reduced OS disease progression, inhibiting metastasis and improving survival in a xenograft mouse model. These observations were recapitulated with Nell1 conditional knockout in mouse models of p53/Rb-driven sarcomagenesis, which reduced tumor frequency and extended tumor-free survival. Transcriptomic and phosphoproteomic analyses demonstrated that NELL1 loss skews the expression of matricellular proteins associated with reduced FAK signaling. Culturing NELL1 knockout sarcoma cells on wild-type OS-enriched matricellular proteins reversed the phenotypic and signaling changes induced by NELL1 deficiency. In sarcoma patients, high expression of NELL1 correlated with decreased overall survival. These findings in mouse and human models suggest that NELL1 expression alters the sarcoma ECM, thereby modulating cellular invasive potential and prognosis. Disruption of NELL1 signaling may represent a novel therapeutic approach to short-circuit sarcoma disease progression. SIGNIFICANCE NELL1 modulates the sarcoma matrisome to promote tumor growth, invasion, and metastasis, identifying the matrix-associated protein as an orchestrator of cell-ECM interactions in sarcomagenesis and disease progression.
Collapse
Affiliation(s)
- Qizhi Qin
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21205
| | | | - Robert J. Tower
- Department of Orthopaedics, Johns Hopkins University, Baltimore, MD 21205
| | - Leslie Chang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21205
| | - Carol D. Morris
- Department of Orthopaedics, Johns Hopkins University, Baltimore, MD 21205
| | | | - Kang Ting
- Forsyth Institute, Cambridge, MA 02142
| | - Xinli Zhang
- Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095
| | - Aaron W. James
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21205,Corresponding Author: Aaron W. James, M.D., Ph.D., 720 Rutland Avenue, Room 524A, Baltimore, MD 21205, Phone: (410) 502-4143,
| |
Collapse
|
5
|
Cheng X, Shi J, Jia Z, Ha P, Soo C, Ting K, James AW, Shi B, Zhang X. NELL-1 in Genome-Wide Association Studies across Human Diseases. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:395-405. [PMID: 34890556 PMCID: PMC8895422 DOI: 10.1016/j.ajpath.2021.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 02/08/2023]
Abstract
Neural epidermal growth factor-like (EGFL)-like protein (NELL)-1 is a potent and key osteogenic factor in the development and regeneration of skeletal tissues. Intriguingly, accumulative data from genome-wide association studies (GWASs) have started unveiling potential broader roles of NELL-1 beyond its functions in bone and cartilage. With exploration of the genetic variants of the entire genome in large-scale disease cohorts, GWASs have been used for establishing the connection between specific single-nucleotide polymorphisms of NELL1, in addition to osteoporosis, metabolic diseases, inflammatory conditions, neuropsychiatric diseases, neurodegenerative disorders, and malignant tumors. This review summarizes the findings from GWASs on the manifestation, significance level, implications on function, and correlation of specific NELL1 single-nucleotide polymorphisms in various disorders in humans. By offering a unique and comprehensive correlation between genetic variants and plausible functions of NELL1 in GWASs, this review illustrates the wide range of potential effects of a single gene on the pathogenesis of multiple disorders in humans.
Collapse
Affiliation(s)
- Xu Cheng
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, and the Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China,Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
| | - Jiayu Shi
- Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, and the Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Pin Ha
- Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California–Los Angeles, Los Angeles, California
| | - Chia Soo
- Division of Plastic and Reconstructive Surgery, Department of Orthopaedic Surgery, Orthopaedic Hospital Research Center, University of California–Los Angeles, Los Angeles, California
| | - Kang Ting
- Forsyth Institute, affiliate of the Harvard School of Dental Medicine, Boston, Massachusetts
| | - Aaron W. James
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bing Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, and the Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Xinli Zhang
- Section of Orthodontics, Division of Growth and Development, School of Dentistry, University of California-Los Angeles, Los Angeles, California.
| |
Collapse
|
6
|
Shen S, Wei Y, Li Y, Duan W, Dong X, Lin L, You D, Tardon A, Chen C, Field JK, Hung RJ, Liu G, Zhu D, Amos CI, Su L, Zhao Y, Hu Z, Shen H, Zhang R, Chen F, Christiani DC. A multi-omics study links TNS3 and SEPT7 to long-term former smoking NSCLC survival. NPJ Precis Oncol 2021; 5:39. [PMID: 34002017 PMCID: PMC8128887 DOI: 10.1038/s41698-021-00182-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/19/2021] [Indexed: 11/15/2022] Open
Abstract
The genetic architecture of non-small cell lung cancer (NSCLC) is relevant to smoking status. However, the genetic contribution of long-term smoking cessation to the prognosis of NSCLC patients remains largely unknown. We conducted a genome-wide association study primarily on the prognosis of 1299 NSCLC patients of long-term former smokers from independent discovery (n = 566) and validation (n = 733) sets, and used in-silico function prediction and multi-omics analysis to identify single nucleotide polymorphisms (SNPs) on prognostics with NSCLC. We further detected SNPs with at least moderate association strength on survival within each group of never, short-term former, long-term former, and current smokers, and compared their genetic similarity at the SNP, gene, expression quantitative trait loci (eQTL), enhancer, and pathway levels. We identified two SNPs, rs34211819TNS3 at 7p12.3 (P = 3.90 × 10-9) and rs1143149SEPT7 at 7p14.2 (P = 9.75 × 10-9), were significantly associated with survival of NSCLC patients who were long-term former smokers. Both SNPs had significant interaction effects with years of smoking cessation (rs34211819TNS3: Pinteraction = 8.0 × 10-4; rs1143149SEPT7: Pinteraction = 0.003). In addition, in silico function prediction and multi-omics analysis provided evidence that these QTLs were associated with survival. Moreover, comparison analysis found higher genetic similarity between long-term former smokers and never-smokers, compared to short-term former smokers or current smokers. Pathway enrichment analysis indicated a unique pattern among long-term former smokers that was related to immune pathways. This study provides important insights into the genetic architecture associated with long-term former smoking NSCLC.
Collapse
Affiliation(s)
- Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yongyue Wei
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Weiwei Duan
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Xuesi Dong
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Lijuan Lin
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Dongfang You
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Adonina Tardon
- University of Oviedo and CIBERESP, Faculty of Medicine, Oviedo, 33003, Spain
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, ON, M5T 3L9, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Dakai Zhu
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, TX, 77030, USA
| | - Christopher I Amos
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, TX, 77030, USA
| | - Li Su
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Hongbing Shen
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, Jiangsu, China.
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA.
- Pulmonary and Critical Care Division, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Boston, MA, 02114, USA.
| |
Collapse
|
7
|
Yang S, Tang D, Zhao YC, Liu H, Luo S, Stinchcombe TE, Glass C, Su L, Shen S, Christiani DC, Wang Q, Wei Q. Potentially functional variants of ERAP1, PSMF1 and NCF2 in the MHC-I-related pathway predict non-small cell lung cancer survival. Cancer Immunol Immunother 2021; 70:2819-2833. [PMID: 33651148 DOI: 10.1007/s00262-021-02877-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/01/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Cellular immunity against tumor cells is highly dependent on antigen presentation by major histocompatibility complex class I (MHC-I) molecules. However, few published studies have investigated associations between functional variants of MHC-I-related genes and clinical outcomes of lung cancer patients. METHODS We performed a two-phase Cox proportional hazards regression analysis by using two previously published genome-wide association studies to evaluate associations between genetic variants in the MHC-I-related gene set and the survival of non-small cell lung cancer (NSCLC) patients, followed by expression quantitative trait loci analysis. RESULTS Of the 7811 single-nucleotide polymorphisms (SNPs) in 89 genes of 1185 NSCLC patients in the discovery dataset of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial, 24 SNPs remained statistically significant after validation in additional 984 NSCLC patients from the Harvard Lung Cancer Susceptibility Study. In a multivariate stepwise Cox model, three independent functional SNPs (ERAP1 rs469783 T > C, PSMF1 rs13040574 C > A and NCF2 rs36071574 G > A) remained significant with an adjusted hazards ratio (HR) of 0.83 [95% confidence interval (CI) = 0.77-0.89, P = 8.0 × 10-7], 0.86 (0.80-0.93, P = 9.4 × 10-5) and 1.31 (1.11-1.54, P = 0.001) for overall survival (OS), respectively. Further combined genotypes revealed a poor survival in a dose-response manner in association with the number of unfavorable genotypes (Ptrend < 0.0001 and 0.0002 for OS and disease-specific survival, respectively). Also, ERAP1 rs469783C and PSMF1 rs13040574A alleles were associated with higher mRNA expression levels of their genes. CONCLUSION These potentially functional SNPs of the MHC-I-related genes may be biomarkers for NSCLC survival, possibly through modulating the expression of corresponding genes.
Collapse
Affiliation(s)
- Sen Yang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Dongfang Tang
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yu Chen Zhao
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Hongliang Liu
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Thomas E Stinchcombe
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Carolyn Glass
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA
- Department of Pathology, Duke ©University School of Medicine, Durham, NC, 27710, USA
| | - Li Su
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Sipeng Shen
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - David C Christiani
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.
| | - Qingyi Wei
- Duke University Medical Center and Department of Population Health Sciences, Duke Cancer Institute, Duke University School of Medicine, 905 S LaSalle Street, Durham, NC, 27710, USA.
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
| |
Collapse
|
8
|
Wu MF, Wang YC, Shen TC, Chang WS, Li HT, Liao CH, Gong CL, Wang ZH, Tsai CW, Hsia TC, Bau DAT. Significant Association of Interleukin-16 Genetic Variations to Taiwanese Lung Cancer. In Vivo 2021; 34:1117-1123. [PMID: 32354900 DOI: 10.21873/invivo.11883] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND/AIM Interleukin-16 has been reported to exhibit tumoricidal effects, however, the contribution of IL-16 genotypes to lung cancer is still largely unrevealed. This study aimed at investigating whether IL-16 genotypes contribute to lung cancer susceptibility. MATERIALS AND METHODS IL-16 rs4778889, rs11556218, and rs4072111 genotypic characteristics were determined among 358 lung cancer patients and 716 controls via the polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) methodology. RESULTS The highlight finding is that the distributions of genotypic (p=8.6E-10) and allelic (p=0.0001) frequencies of IL-16 rs11556218 was significantly different between cases and controls. In detail, the frequencies of IL-16 rs11556218 heterozygous variant TG and homozygous variant GG were 36.6 and 7.3% among the lung cancer patients, significantly higher than those among the controls (22.5% and 2.6%). On the other way, no difference was observed regarding IL-16 rs4778889 or IL-16 rs4072111. CONCLUSION The present study indicates IL-16 rs11556218 G allele is significantly associated with increased Taiwan lung cancer risk.
Collapse
Affiliation(s)
- Meng-Feng Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C.,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C.,Division of Chest Surgery, Department of Surgery, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan, R.O.C
| | - Yun-Chi Wang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C.,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Te-Chun Shen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C.,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Wen-Shin Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C.,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Hsin-Ting Li
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Cheng-Hsi Liao
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C.,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Chi-Li Gong
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Zhi-Hong Wang
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung, Taiwan, R.O.C
| | - Chia-Wen Tsai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C. .,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - Te-Chun Hsia
- Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C. .,Department of Respiratory Therapy, China Medical University, Taichung, Taiwan, R.O.C.,Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan, R.O.C
| | - DA-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, R.O.C. .,Terry Fox Cancer Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan, R.O.C.,Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan, R.O.C
| |
Collapse
|
9
|
Construction of a Novel Multigene Panel Potently Predicting Poor Prognosis in Patients with Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2020; 12:cancers12113471. [PMID: 33266355 PMCID: PMC7700485 DOI: 10.3390/cancers12113471] [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: 09/18/2020] [Revised: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Clear cell renal cell carcinoma (ccRCC) is the predominant cause of kidney cancer death attributed to its prevalence (70%) and its nature being the most aggressive form of kidney cancer. Most ccRCC deaths are resulted from metastasis. It is essential to know which ccRCCs are at risk of metastasis and the development to lethal disease; however, our capacity for such analysis remains poor. To improve this diagnostic capacity, we have examined a comprehensive ccRCC dataset containing 512 patients and have produced a 9-gene signature. This signature is novel; all its 9 components genes are unknown to be related to ccRCC. Importantly, all 9 individual genes possess significant ability in diagnosis of ccRCC metastasis and fatality; the combination of these genes or this signature predicts deadly ccRCCs at an impressive efficiency. This research will open new avenues in ccRCC research and will have a major impact in reducing ccRCC-associated deaths. Abstract We observed associations of IQGAP1 downregulation with poor overall survival (OS) in clear cell renal cell carcinoma (ccRCC). Differentially expressed genes (DEGs, n = 611) were derived from ccRCCs with (n = 111) and without IQGAP1 (n = 397) reduction using the TCGA PanCancer Atlas ccRCC dataset. These DEGs exhibit downregulations of immune response and upregulations of DNA damage repair pathways. Through randomization of the TCGA dataset into a training and testing subpopulation, a 9-gene panel (SigIQGAP1NW) was derived; it predicts poor OS in training, testing, and the full population at a hazard ratio (HR) 2.718, p < 2 × 10−16, p = 1.08 × 10−5, and p < 2 × 10−16, respectively. SigIQGAP1NW independently associates with poor OS (HR 1.80, p = 2.85 × 10−6) after adjusting for a set of clinical features, and it discriminates ccRCC mortality at time-dependent AUC values of 70% at 13.8 months, 69%/31M, 69%/49M, and 75.3%/71M. All nine component genes of SigIQGAP1NW are novel to ccRCC. The inclusion of RECQL4 (a DNA helicase) in SigIQGAP1NW agrees with IQGAP1 DEGs enhancing DNA repair. THSD7A affects kidney function; its presence in SigIQGAP1NW is consistent with our observed THSD7A downregulation in ccRCC (n = 523) compared to non-tumor kidney tissues (n = 100). Collectively, we report a novel multigene panel that robustly predicts poor OS in ccRCC.
Collapse
|
10
|
Li DN, Yang CC, Li J, Ou Yang QG, Zeng LT, Fan GQ, Liu TH, Tian XY, Wang JJ, Zhang H, Dai DP, Cui J, Cai JP. The high expression of MTH1 and NUDT5 promotes tumor metastasis and indicates a poor prognosis in patients with non-small-cell lung cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118895. [PMID: 33096144 DOI: 10.1016/j.bbamcr.2020.118895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/03/2020] [Accepted: 10/15/2020] [Indexed: 12/25/2022]
Abstract
MutT Homolog 1 (MTH1) is a mammalian 8-oxodGTPase for sanitizing oxidative damage to the nucleotide pool. Nudix type 5 (NUDT5) also sanitizes 8-oxodGDP in the nucleotide pool. The role of MTH1 and NUDT5 in non-small-cell lung cancer (NSCLC) progression and metastasis remains unclear. In the present study, we reported that MTH1 and NUDT5 were upregulated in NSCLC cell lines and tissues, and higher levels of MTH1 or NUDT5 were associated with tumor metastasis and a poor prognosis in patients with NSCLC. Their suppression also restrained tumor growth and lung metastasis in vivo and significantly inhibited NSCLC cell migration, invasion, cell proliferation and cell cycle progression while promoting apoptosis in vitro. The opposite effects were observed in vitro following MTH1 or NUDT5 rescue. In addition, the upregulation of MTH1 or NUDT5 enhanced the MAPK pathway and PI3K/AKT activity. Furthermore, MTH1 and NUDT5 induce epithelial-mesenchymal transition both in vitro and in vivo. These results highlight the essential role of MTH1 and NUDT5 in NSCLC tumor tumorigenesis and metastasis as well as their functions as valuable markers of the NSCLC prognosis and potential therapeutic targets.
Collapse
Affiliation(s)
- Dan-Ni Li
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, PR China
| | - Cheng-Cheng Yang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China
| | - Qiu-Geng Ou Yang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Lv-Tao Zeng
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China
| | - Guo-Qing Fan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China
| | - Teng-Hui Liu
- School of Pharmacy, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xin-Yuan Tian
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, PR China
| | - Jing-Jing Wang
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, PR China
| | - He Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China
| | - Ju Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China
| | - Jian-Ping Cai
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, PR China; The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, NO.1 DaHua Road, Dong Dan, Beijing 100730, PR China.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Tang D, Zhao YC, Liu H, Luo S, Clarke JM, Glass C, Su L, Shen S, Christiani DC, Gao W, Wei Q. Potentially functional genetic variants in PLIN2, SULT2A1 and UGT1A9 genes of the ketone pathway and survival of nonsmall cell lung cancer. Int J Cancer 2020; 147:1559-1570. [PMID: 32072637 DOI: 10.1002/ijc.32932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/18/2020] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
The ketone metabolism pathway is a principle procedure in physiological homeostasis and induces cancer cells to switch between glycolysis and oxidative phosphorylation for energy production. We conducted a two-phase analysis for associations between genetic variants in the ketone metabolism pathway genes and survival of nonsmall cell lung cancer (NSCLC) by analyzing genotyping data from two published genome-wide association studies (GWASs). In the discovery, we used a genotyping dataset from the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial in the multivariable Cox proportional hazards regression analysis. We used Bayesian false discovery probability (≤0.80) for multiple testing correction to evaluate associations between 25,819 (2,176 genotyped and 23,643 imputed) single-nucleotide polymorphisms (SNPs) in 162 genes and survival of 1,185 NSCLC patients. Subsequently, we validated the identified significant SNPs with an additional 984 NSCLC patients from the Harvard Lung Cancer Susceptibility GWAS study. Finally, we found that three independent and potentially functional SNPs in three different genes (i.e., PLIN2 rs7867814 G>A, SULT2A1 rs2547235 C>T and UGT1A9 rs2011404 C>T) were independently associated with risk of death from NSCLC, with a combined hazards ratio of 1.22 [95% confidence interval = 1.09-1.36 and p = 0.0003], 0.82 (0.74-0.91 and p = 0.0002) and 1.21 (1.10-1.33 and p = 0.0001), respectively. Additional expression quantitative trait loci analysis found that the survival-associated PLIN2 rs7867814 GA + AA genotypes, but not the genotypes of other two SNPs, were significantly associated with increased mRNA expression levels (p = 0.005). These results indicated that PLIN2 variants may be potential predictors of NSCLC survival through regulating the PLIN2 expression.
Collapse
Affiliation(s)
- Dongfang Tang
- Department of Thoracic Oncology, Huadong Hospital, Fudan University, Shanghai, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Yu C Zhao
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC
| | - Jeffrey M Clarke
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Medicine, Duke University School of Medicine, Durham, NC
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Li Su
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Sipeng Shen
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - David C Christiani
- Department of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA.,Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Wen Gao
- Department of Thoracic Oncology, Huadong Hospital, Fudan University, Shanghai, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC.,Department of Medicine, Duke University School of Medicine, Durham, NC
| |
Collapse
|
13
|
Yu S, Li Y, Liao Z, Wang Z, Wang Z, Li Y, Qian L, Zhao J, Zong H, Kang B, Zou WB, Chen K, He X, Meng Z, Chen Z, Huang S, Wang P. Plasma extracellular vesicle long RNA profiling identifies a diagnostic signature for the detection of pancreatic ductal adenocarcinoma. Gut 2020; 69:540-550. [PMID: 31562239 DOI: 10.1136/gutjnl-2019-318860] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is difficult to diagnose at resectable stage. Recent studies have suggested that extracellular vesicles (EVs) contain long RNAs. The aim of this study was to develop a diagnostic (d-)signature for the detection of PDAC based on EV long RNA (exLR) profiling. DESIGN We conducted a case-control study with 501 participants, including 284 patients with PDAC, 100 patients with chronic pancreatitis (CP) and 117 healthy subjects. The exLR profile of plasma samples was analysed by exLR sequencing. The d-signature was identified using a support vector machine algorithm and a training cohort (n=188) and was validated using an internal validation cohort (n=135) and an external validation cohort (n=178). RESULTS We developed a d-signature that comprised eight exLRs, including FGA, KRT19, HIST1H2BK, ITIH2, MARCH2, CLDN1, MAL2 and TIMP1, for PDAC detection. The d-signature showed high accuracy, with an area under the receiver operating characteristic curve (AUC) of 0.960, 0.950 and 0.936 in the training, internal validation and external validation cohort, respectively. The d-signature was able to identify resectable stage I/II cancer with an AUC of 0.949 in the combined three cohorts. In addition, the d-signature showed superior performance to carbohydrate antigen 19-9 in distinguishing PDAC from CP (AUC 0.931 vs 0.873, p=0.028). CONCLUSION This study is the first to characterise the plasma exLR profile in PDAC and to report an exLR signature for the detection of pancreatic cancer. This signature may improve the prognosis of patients who would have otherwise missed the curative treatment window.
Collapse
Affiliation(s)
- Shulin Yu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuchen Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhuan Liao
- Department of Gastroenterology, Digestive Endoscopy Center, Changhai Hospital, the Second Military Medical University, Shanghai, China
| | - Zheng Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Zhen Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ling Qian
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingjing Zhao
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Huajie Zong
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of General Surgery, Huashan Hospital, Fudan University, Fudan University, Shanghai, China
| | - Bin Kang
- Fudan University Shanghai Cancer Center - InstitutMerieux Laboratory, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wen-Bin Zou
- Department of Gastroenterology, Digestive Endoscopy Center, Changhai Hospital, the Second Military Medical University, Shanghai, China
| | - Kun Chen
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhen Chen
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China .,Fudan University Shanghai Cancer Center, Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng Wang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
14
|
Shen TC, Chang WS, Hsia TC, Li HT, Chen WC, Tsai CW, Bau DT. Contribution of programmed cell death 6 genetic variations, gender, and smoking status to lung cancer. Onco Targets Ther 2019; 12:6237-6244. [PMID: 31496727 PMCID: PMC6693085 DOI: 10.2147/ott.s205544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/16/2019] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Programmed cell death 6 (PDCD6) is a calcium sensor participating in T-cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. At the sites of lung tumors, the expression of PDCD6 is higher than that in non-tumor tissues. However, the contribution of variant PDCD6 genotypes to lung cancer is largely unknown. The current study aimed to evaluate the contributions of the PDCD6 rs4957014 and rs3756712 genotypes to the risk of lung cancer. PATIENTS AND METHODS The contributions of PDCD6 genotypes to lung cancer risk were examined among 358 patients with lung cancer and 716 age- and gender-matched healthy controls by typical polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology. RESULTS The results showed that the GG but not the GT genotype of PDCD6 rs4957014 was associated with a decreased risk of lung cancer (odds ratio (OR) =0.41, 95% confidence interval (CI) =0.23-0.72, p=0.0013). The analysis of allelic frequency distributions showed that the G allele of PDCD6 rs4957014 decreased lung cancer susceptibility (p=0.0090). There was no association between PDCD6 rs3756712 genotypes and lung cancer risk. Interestingly, the GG genotype at PDCD6 rs4957014 significantly decreased the risk of lung cancer among males (adjusted OR =0.29, 95% CI =0.14-0.57) and smokers (adjusted OR =0.34, 95% CI =0.18-0.61) but not among females and non-smokers. CONCLUSION The GG genotype of PDCD6 rs4957014 may decrease lung cancer risk in males and smokers and may serve as a practical marker for early detection and the incidence of lung cancer in Taiwan.
Collapse
Affiliation(s)
- Te-Chun Shen
- Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
- Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Shin Chang
- Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Te-Chun Hsia
- Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
- Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Respiratory Therapy, China Medical University, Taichung, Taiwan
| | - Hsin-Ting Li
- Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Wei-Chun Chen
- Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Respiratory Therapy, China Medical University, Taichung, Taiwan
| | - Chia-Wen Tsai
- Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Da-Tian Bau
- Terry Fox Cancer Research Laboratory, Translational Medicine Research Center, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| |
Collapse
|
15
|
Junjappa RP, Kim HK, Park SY, Bhattarai KR, Kim KW, Soh JW, Kim HR, Chae HJ. Expression of TMBIM6 in Cancers: The Involvement of Sp1 and PKC. Cancers (Basel) 2019; 11:cancers11070974. [PMID: 31336725 PMCID: PMC6678130 DOI: 10.3390/cancers11070974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/28/2019] [Accepted: 07/08/2019] [Indexed: 12/29/2022] Open
Abstract
Transmembrane Bax Inhibitor Motif-containing 6 (TMBIM6) is upregulated in several cancer types and involved in the metastasis. Specific downregulation of TMBIM6 results in cancer cell death. However, the TMBIM6 gene transcriptional regulation in normal and cancer cells is least studied. Here, we identified the core promoter region (−133/+30 bp) sufficient for promoter activity of TMBIM6 gene. Reporter gene expression with mutations at transcription factor binding sites, EMSA, supershift, and ChIP assays demonstrated that Sp1 is an essential transcription factor for basal promoter activity of TMBIM6. The TMBIM6 mRNA expression was increased with Sp1 levels in a concentration dependent manner. Ablation of Sp1 through siRNA or inhibition with mithramycin-A reduced the TMBIM6 mRNA expression. We also found that the protein kinase-C activation stimulates promoter activity and endogenous TMBIM6 mRNA by 2- to 2.5-fold. Additionally, overexpression of active mutants of PKCι, PKCε, and PKCδ increased TMBIM6 expression by enhancing nuclear translocation of Sp1. Immunohistochemistry analyses confirmed that the expression levels of PKCι, Sp1, and TMBIM6 were correlated with one another in samples from human breast, prostate, and liver cancer patients. Altogether, this study suggests the involvement of Sp1 in basal transcription and PKC in the enhanced expression of TMBIM6 in cancer.
Collapse
Affiliation(s)
- Raghu Patil Junjappa
- Department of Pharmacology and New Drug Development Research Institute, Chonbuk National University Medical School, Jeonju 54896, Korea
| | - Hyun-Kyoung Kim
- Department of Pharmacology and New Drug Development Research Institute, Chonbuk National University Medical School, Jeonju 54896, Korea
| | - Seong Yeol Park
- Department of Pharmacology and New Drug Development Research Institute, Chonbuk National University Medical School, Jeonju 54896, Korea
| | - Kashi Raj Bhattarai
- Department of Pharmacology and New Drug Development Research Institute, Chonbuk National University Medical School, Jeonju 54896, Korea
| | - Kyung-Woon Kim
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration (RDA), Wanju-gun, Chonbuk 54875, Korea
| | - Jae-Won Soh
- Department of Chemistry, Inha University, Incheon 402-751, Korea
| | - Hyung-Ryong Kim
- College of Dentistry, Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 31116, Korea.
| | - Han-Jung Chae
- Department of Pharmacology and New Drug Development Research Institute, Chonbuk National University Medical School, Jeonju 54896, Korea.
| |
Collapse
|
16
|
Wei J, Sheng Y, Li J, Gao X, Ren N, Dong Q, Qin L. Genome-Wide Association Study Identifies a Genetic Prediction Model for Postoperative Survival in Patients with Hepatocellular Carcinoma. Med Sci Monit 2019; 25:2452-2478. [PMID: 30945699 PMCID: PMC6461006 DOI: 10.12659/msm.915511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background As an important aspect of tumor heterogeneity, genetic variation may influence susceptibility and prognosis in different types of cancer. By exploring the prognostic value of genetic variation, this study aimed to establish a model for predicting postoperative survival and assessing the impact of variation on clinical outcomes in patients with hepatocellular carcinoma (HCC). Material/Methods A genome-wide association study of 367 patients with HCC was conducted to identify single nucleotide polymorphisms (SNPs) associated with prognosis. Identified predictors were further evaluated in 758 patients. Two prognostic models were established using Cox proportional hazards regression and Nomogram strategy, and validated in another 316 patients. The effect of the SNP rs2431 was analyzed in detail. Results A prognostic model including 5 SNPs (rs10893585, rs2431, rs34675408, rs6078460, and rs6766361) was established and exhibited high predictive accuracy for HCC prognosis. The panel combined with tumor node metastasis (TNM) stage resulted in a significantly higher c-index (0.723) than the individual c-index values. Stratified by the Nomogram prediction model, the median overall survival for the low-risk and high-risk groups were 100.1 versus 30.8 months (P<0.001) in the training set and 82.2 versus 22.5 months (P<0.001) in the validation set. A closer examination of rs2431 revealed that it may regulate the expression of FNDC3B by disrupting a microRNA-binding site. Conclusions This study established prediction models based on genetic factors alone or in combination with TNM stage for postoperative survival in patients with HCC, and identified FNDC3B as a potential therapeutic target for combating HCC metastasis.
Collapse
Affiliation(s)
- Jinwang Wei
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Yuanyuan Sheng
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Jianhua Li
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Xiaomei Gao
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Ning Ren
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, Shanghai, China (mainland)
| | - Qiongzhu Dong
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| | - Lunxiu Qin
- Department of General Surgery, Huashan Hospital; Cancer Metastasis Institute; Institutes of Biomedical Sciences, Fudan University, Shanghai, China (mainland)
| |
Collapse
|
17
|
Lung cancer survival among never smokers. Cancer Lett 2019; 451:142-149. [PMID: 30851418 DOI: 10.1016/j.canlet.2019.02.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/13/2019] [Accepted: 02/28/2019] [Indexed: 11/22/2022]
Abstract
Lung cancer incidence among never smokers has increased in recent decades with 10-30% of all lung cancers occurring in never smokers, where exposure to residential radon is the leading cause of this disease. Lung cancer survival is low, ranging from 12% to 16% at 5 years of diagnosis. There is scant evidence to date on survival from this disease in never smokers. We aim to evaluate lung cancer survival in never smokers and ascertain whether there might be differences regarding smokers, through a systematic review applying predefined inclusion and exclusion criteria. 17 Studies were included. Never-smoker lung cancer patients seem to experience longer survival times than do smokers or ex-smokers. Lung cancer in never smokers displays distinctive clinical characteristics, is more frequent among women, is diagnosed at more advanced stages, and the predominant histologic type is adenocarcinoma. Further studies are necessary to ascertain lung cancer survival among never smokers.
Collapse
|
18
|
Abstract
While lung cancer has been the leading cause of cancer-related deaths for many years in the United States, incidence and mortality statistics - among other measures - vary widely worldwide. The aim of this study was to review the evidence on lung cancer epidemiology, including data of international scope with comparisons of economically, socially, and biologically different patient groups. In industrialized nations, evolving social and cultural smoking patterns have led to rising or plateauing rates of lung cancer in women, lagging the long-declining smoking and cancer incidence rates in men. In contrast, emerging economies vary widely in smoking practices and cancer incidence but commonly also harbor risks from environmental exposures, particularly widespread air pollution. Recent research has also revealed clinical, radiologic, and pathologic correlates, leading to greater knowledge in molecular profiling and targeted therapeutics, as well as an emphasis on the rising incidence of adenocarcinoma histology. Furthermore, emergent evidence about the benefits of lung cancer screening has led to efforts to identify high-risk smokers and development of prediction tools. This review also includes a discussion on the epidemiologic characteristics of special groups including women and nonsmokers. Varying trends in smoking largely dictate international patterns in lung cancer incidence and mortality. With declining smoking rates in developed countries and knowledge gains made through molecular profiling of tumors, the emergence of new risk factors and disease features will lead to changes in the landscape of lung cancer epidemiology.
Collapse
Affiliation(s)
- Julie A. Barta
- Division of Pulmonary and Critical Care Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, US
| | - Charles A. Powell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, US
| | - Juan P. Wisnivesky
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, US
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, US
| |
Collapse
|
19
|
The KIF5B-RET Fusion Gene Mutation as a Novel Mechanism of Acquired EGFR Tyrosine Kinase Inhibitor Resistance in Lung Adenocarcinoma. Clin Lung Cancer 2019; 20:e73-e76. [DOI: 10.1016/j.cllc.2018.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/11/2018] [Accepted: 09/15/2018] [Indexed: 11/18/2022]
|
20
|
Transmembrane protein GRINA modulates aerobic glycolysis and promotes tumor progression in gastric cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:308. [PMID: 30541591 PMCID: PMC6292005 DOI: 10.1186/s13046-018-0974-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Recent observations indicate a decreased cancer risk in patients with Alzheimer's disease (AD). AD is a severe neurodegenerative disorder characterized by progressive cognitive decline. The 8q24 region has been shown to be involved in AD aetiology. We aimed to identify and explore the potential oncogenes or antioncogenes on chromosome 8q24. METHODS We compared expression of genes on Chromosome 8q24 in 32 pairs of samples from The Cancer Genome Atlas (TCGA) database. We conducted bioinformatics analysis of the commonly used gastric cancer databases and performed clinical verification of gastric cancer samples, combined with assessment of biological function both in vitro and in vivo to determine the relationship between upregulated expression of GRINA and gastric cancer progression. We also explored the molecular mechanism of GRINA upregulation and its function in gastric cancer development and progression. RESULTS The expression of GRINA in cancer tissues was significantly higher than that in normal tissues. GRINA indicated poor prognosis in gastric cancer. GRINA promoted the proliferation, migration and invasion capacity of gastric cancer cells. GRINA was transcriptionally mediated by c-Myc and promotes cell cycle transition. GRINA knockdown decreased PI3K/Akt/mTOR signaling and glycolytic metabolism in gastric cancer cells. The apoptosis rate was significantly increased in gastric cancer cell lines after knockdown of GRINA. The expression of pro-apoptotic protein Bax was significantly upregulated, whereas the anti-apoptotic protein Bcl-2 was significantly downregulated in GRINA silenced cells. CONCLUSIONS Human gastric cancers have increased levels of GRINA, which promotes growth of gastric cancer and inhibits tumor cells apoptosis.
Collapse
|
21
|
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: 143] [Impact Index Per Article: 23.8] [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."
Collapse
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
| |
Collapse
|
22
|
Carrara G, Parsons M, Saraiva N, Smith GL. Golgi anti-apoptotic protein: a tale of camels, calcium, channels and cancer. Open Biol 2018; 7:rsob.170045. [PMID: 28469007 PMCID: PMC5451544 DOI: 10.1098/rsob.170045] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
Golgi anti-apoptotic protein (GAAP), also known as transmembrane Bax inhibitor-1 motif-containing 4 (TMBIM4) or Lifeguard 4 (Lfg4), shares remarkable amino acid conservation with orthologues throughout eukaryotes, prokaryotes and some orthopoxviruses, suggesting a highly conserved function. GAAPs regulate Ca2+ levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store-operated Ca2+ entry, are essential for the viability of human cells, and affect orthopoxvirus virulence. GAAPs are oligomeric, multi-transmembrane proteins that are resident in Golgi membranes and form cation-selective ion channels that may explain the multiple functions of these proteins. Residues contributing to the ion-conducting pore have been defined and provide the first clues about the mechanistic link between these very different functions of GAAP. Although GAAPs are naturally oligomeric, they can also function as monomers, a feature that distinguishes them from other virus-encoded ion channels that must oligomerize for function. This review summarizes the known functions of GAAPs and discusses their potential importance in disease.
Collapse
Affiliation(s)
- Guia Carrara
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Nuno Saraiva
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK .,CBIOS, Universidade Lusófona Research Centre for Biosciences and Health Technologies, Campo Grande 376, Lisbon 1749-024, Portugal
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| |
Collapse
|
23
|
Sepesi B, Ye Y, Mitchell KG, Zhang L, Gu J, Ji L, Antonoff MB, Hofstetter WL, Rice DC, Mehran RJ, Walsh GL, Vaporciyan AA, Swisher SG, Roth JA, Wu X. Genetic variants in cytokine signaling pathways and clinical outcomes in early-stage lung cancer patients. J Thorac Cardiovasc Surg 2018; 155:2635-2645.e15. [PMID: 29548588 DOI: 10.1016/j.jtcvs.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 01/20/2018] [Accepted: 02/05/2018] [Indexed: 01/09/2023]
Abstract
OBJECTIVES The purpose of this study was to explore the role of single nucleotide polymorphisms (SNPs) in cytokine signaling genes and to compare them with clinical outcomes in surgical patients with non-small cell lung cancer (NSCLC). METHODS SNPs of the cytokine signaling pathway were analyzed using peripheral blood of 722 patients who underwent resection of stage I to III NSCLC between 1995 and 2009. Cox proportional hazard analyses were performed to identify SNPs associated with overall survival (OS) and risk of recurrence. Internal validation using bootstrap analysis selected SNPs for unfavorable genotype and survival tree analysis. RESULTS Seventeen and 9 SNPs were independently associated with OS and recurrence, respectively. Patients with ≥9 unfavorable genotypes experienced worse OS (median, 41 months) than patients with 7 to 8 (89 months) and ≤6 (153 months) after median follow-up of 71 months (P = 2.86 × 10-23). Patients with ≤3 unfavorable genotypes had greater time to recurrence (median not reached) than those with 4 to 6 (114 months) and ≥7 (44 months; P = 1.3 × 10-5). Survival tree analysis classified patients into 3 risk groups. Patients in the intermediate- (median OS, 82 months) and high-risk groups (43 months) had worse survival than the low-risk group (176 months; P = 5.51 × 10-20). Median time to recurrence was worse in the intermediate- (114 months) and high-risk groups (58 months) than the low-risk group (median not reached; P = 2.52 × 10-9). CONCLUSIONS Genetic variants in cytokine signaling pathways were associated with clinical outcomes in NSCLC patients treated with surgery individually and cumulatively. Further studies are necessary to elucidate our findings and translate them into the clinical setting.
Collapse
Affiliation(s)
- Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex.
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Kyle G Mitchell
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Liren Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Jianchun Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Lin Ji
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - David C Rice
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Reza J Mehran
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Tex.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Zhang Y, Wei Y, Jiang B, Chen L, Bai H, Zhu X, Li X, Zhang H, Yang Q, Ma J, Xu Y, Ben J, Christiani DC, Chen Q. Scavenger Receptor A1 Prevents Metastasis of Non-Small Cell Lung Cancer via Suppression of Macrophage Serum Amyloid A1. Cancer Res 2017; 77:1586-1598. [PMID: 28202524 DOI: 10.1158/0008-5472.can-16-1569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 12/27/2016] [Accepted: 01/03/2017] [Indexed: 11/16/2022]
Abstract
Mechanisms of cross-talk between tumor cells and tumor-associated macrophages (TAM), which drive metastasis, are not fully understood. Scavenger receptor A1 (SR-A1) expressed primarily in macrophages has been associated with lung tumorigenesis. In this study, we used population genetics, transcriptomics, and functional analyses to uncover how SR-A1 is involved in lung cancer and its prognosis. SR-A1 genetic variants were investigated for possible association with survival of advanced stage NSCLC patients in the Harvard Lung Cancer Study cohort. Two SNPs (rs17484273, rs1484751) in SR-A1 were associated significantly with poor overall survival in this cohort. Data from The Cancer Genome Atlas showed considerable downregulation of SR-A1 in lung tumor tissues. The association of SR-A1 with prognosis was validated in animal models in the context of lung cancer metastasis. Macrophages derived from mice genetically deficient for SR-A1 exhibited accelerated metastasis in a model of lung cancer. On the other hand, tumor cell seeding, migration, and invasion, as well as macrophage accumulation in lung cancer tissue, were enhanced in SR-A1-deficient mice. SR-A1 deletion upregulated serum amyloid A1 (SAA1) in macrophages via MAPK/IκB/NFκB signaling. SAA1 promoted tumor cell invasion and macrophage migration in vitro and in vivo, but these effects were blocked by administration of an anti-SAA1 antibody. Overall, our findings show how SR-A1 suppresses lung cancer metastasis by downregulating SAA1 production in TAMs. Cancer Res; 77(7); 1586-98. ©2017 AACR.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Yongyue Wei
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Bin Jiang
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Lili Chen
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Hui Bai
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Xudong Zhu
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Xiaoyu Li
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Hanwen Zhang
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Qing Yang
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Junqing Ma
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Yong Xu
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China
| | - Jingjing Ben
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China.
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Pulmonary and Critical Care Division, Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Qi Chen
- Department of Pathophysiology, Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, China.
| |
Collapse
|
26
|
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.
Collapse
|
27
|
Zhu M, Geng L, Shen W, Wang Y, Liu J, Cheng Y, Wang C, Dai J, Jin G, Hu Z, Ma H, Shen H. Exome-Wide Association Study Identifies Low-Frequency Coding Variants in 2p23.2 and 7p11.2 Associated with Survival of Non-Small Cell Lung Cancer Patients. J Thorac Oncol 2017; 12:644-656. [PMID: 28104536 DOI: 10.1016/j.jtho.2016.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/23/2016] [Accepted: 12/15/2016] [Indexed: 01/10/2023]
Abstract
INTRODUCTION A growing body of evidence has suggested that low-frequency or rare coding variants might have strong effects on the development and prognosis of cancer. Here, we aim to assess the role of low-frequency and rare coding variants in the survival of NSCLC in Chinese populations. METHODS We performed an exome-wide scan of 247,870 variants in 1008 patients with NSCLC and replicated the promising variants by using imputed genotype data of The Cancer Genome Atlas (TCGA) with a Cox regression model. Gene-based and pathway-based analysis were also performed for nonsynonymous or splice site variants. Additionally, analysis of gene expression data in the TCGA was used to increase the reliability of candidate loci and genes. RESULTS A low-frequency missense variant in chaperonin containing TCP1 subunit 6A gene (CCT6A) (rs33922584: adjusted hazard ratio [HRadjusted] = 1.75, p = 6.06 × 10-4) was significantly related to the survival of patients with NSCLC, which was further replicated by the TCGA samples (HRadjusted = 4.19, p = 0.015). Interestingly, the G allele of rs33922584 was significantly associated with high expression of CCT6A (p = 0.019) that might induce the worse survival in the TCGA samples (HRadjusted = 1.15, p = 0.047). Besides, rs117512489 in gene phospholipase B1 gene (PLB1) (HR = 2.02, p = 7.28 × 10-4) was also associated with survival of the patients with NSCLC in our samples, but it was supported only by gene expression analysis in the TCGA (HRadjusted = 1.15, p = 0.023). Gene-based and pathway-based analysis revealed a total of 32 genes, including CCT6A and 34 potential pathways might account for the survival of NSCLC, respectively. CONCLUSION These results provided more evidence for the important role of low-frequency or rare variants in the survival of patients with NSCLC.
Collapse
Affiliation(s)
- Meng Zhu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Liguo Geng
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yuzhuo Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yang Cheng
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China.
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| |
Collapse
|
28
|
|
29
|
Liu WB, Han F, Jiang X, Chen HQ, Zhao H, Liu Y, Li YH, Huang C, Cao J, Liu JY. TMEM196 acts as a novel functional tumour suppressor inactivated by DNA methylation and is a potential prognostic biomarker in lung cancer. Oncotarget 2016; 6:21225-39. [PMID: 26056045 PMCID: PMC4673261 DOI: 10.18632/oncotarget.4237] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/12/2015] [Indexed: 12/31/2022] Open
Abstract
Epigenetic silencing of tumour suppressors contributes to the development and progression of lung cancer. We recently found that TMEM196 was hypermethylated in lung cancer. This study aimed to clarify its epigenetic regulation, possible roles and clinical significance. TMEM196 methylation correlated with loss of protein expression in chemical-induced rat lung pathologic lesions and human lung cancer tissues and cell lines. 5-aza-2′-deoxycytidine restored TMEM196 expression. Moreover, TMEM196 hypermethylation was detected in 61.2% of primary lung tumours and found to be associated with poor differentiation and pathological stage of lung cancer. Functional studies showed that ectopic re-expression of TMEM196 in lung cancer cells inhibited cell proliferation, clonogenicity, cell motility and tumour formation. However, TMEM196 knockdown increased cell proliferation and inhibited apoptosis and cell-cycle arrest. These effects were associated with upregulation of p21 and Bax, and downregulation of cyclin D1, c-myc, CD44 and β-catenin. Kaplan–Meier survival curves showed that TMEM196 downregulation was significantly associated with shortened survival in lung cancer patients. Multivariate analysis showed that patients with TMEM196 expression had a better overall survival. Our results revealed for the first time that TMEM196 acts as a novel functional tumour suppressor inactivated by DNA methylation and is an independent prognostic factor of lung cancer.
Collapse
Affiliation(s)
- Wen-bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Hong-qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Huan Zhao
- Department of Internal Neurology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Yong Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Yong-hong Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Chuanshu Huang
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York, USA
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| | - Jin-yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, P. R. China
| |
Collapse
|
30
|
Choi JR, Park SY, Noh OK, Koh YW, Kang DR. Gene mutation discovery research of non-smoking lung cancer patients due to indoor radon exposure. Ann Occup Environ Med 2016; 28:13. [PMID: 26985396 PMCID: PMC4793700 DOI: 10.1186/s40557-016-0095-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/18/2016] [Indexed: 11/10/2022] Open
Abstract
Although the incidence and mortality for most cancers such as lung and colon are decreasing in several countries, they are increasing in several developed countries because of an unhealthy western lifestyles including smoking, physical inactivity and consumption of calorie-dense food. The incidences for lung and colon cancers in a few of these countries have already exceeded those in the United States and other western countries. Among them, lung cancer is the main cause of cancer death in worldwide. The cumulative survival rate at five years differs between 13 and 21 % in several countries. Although the most important risk factors are smoking for lung cancer, however, the increased incidence of lung cancer in never smokers(LCINS) is necessary to improve knowledge concerning other risk factors. Environmental factors and genetic susceptibility are also thought to contribute to lung cancer risk. Patients with lung adenocarcinoma who have never smoking frequently contain mutation within tyrosine kinase domain of the epidermal growth factor receptor(EGFR) gene. Also, K-ras mutations are more common in individuals with a history of smoking use and are related with resistance to EFGR-tyrosine kinase inhibitors. Recently, radon(Rn), natural and noble gas, has been recognized as second common reason of lung cancer. In this review, we aim to know whether residential radon is associated with an increased risk for developing lung cancer and regulated by several genetic polymorphisms.
Collapse
Affiliation(s)
- Jung Ran Choi
- Department of Bio-resource engineering, College of Life Sciences, Sejong University, Seoul, Republic of Korea
| | - Seong Yong Park
- Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - O Kyu Noh
- Department of Radiation Oncology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Young Wha Koh
- Department of Pathology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Dae Ryong Kang
- Department of Humanities and Social Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Nikooienejad A, Wang W, Johnson VE. Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors. Bioinformatics 2016; 32:1338-45. [PMID: 26740524 PMCID: PMC4848399 DOI: 10.1093/bioinformatics/btv764] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 12/28/2015] [Indexed: 01/10/2023] Open
Abstract
Motivation: The advent of new genomic technologies has resulted in the production of massive data sets. Analyses of these data require new statistical and computational methods. In this article, we propose one such method that is useful in selecting explanatory variables for prediction of a binary response. Although this problem has recently been addressed using penalized likelihood methods, we adopt a Bayesian approach that utilizes a mixture of non-local prior densities and point masses on the binary regression coefficient vectors. Results: The resulting method, which we call iMOMLogit, provides improved performance in identifying true models and reducing estimation and prediction error in a number of simulation studies. More importantly, its application to several genomic datasets produces predictions that have high accuracy using far fewer explanatory variables than competing methods. We also describe a novel approach for setting prior hyperparameters by examining the total variation distance between the prior distributions on the regression parameters and the distribution of the maximum likelihood estimator under the null distribution. Finally, we describe a computational algorithm that can be used to implement iMOMLogit in ultrahigh-dimensional settings (p>>n) and provide diagnostics to assess the probability that this algorithm has identified the highest posterior probability model. Availability and implementation: Software to implement this method can be downloaded at: http://www.stat.tamu.edu/∼amir/code.html. Contact:wwang7@mdanderson.org or vjohnson@stat.tamu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Amir Nikooienejad
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA and
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Valen E Johnson
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA and
| |
Collapse
|
33
|
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.
Collapse
|
34
|
Carrara G, Saraiva N, Parsons M, Byrne B, Prole DL, Taylor CW, Smith GL. Golgi anti-apoptotic proteins are highly conserved ion channels that affect apoptosis and cell migration. J Biol Chem 2015; 290:11785-801. [PMID: 25713081 PMCID: PMC4416878 DOI: 10.1074/jbc.m115.637306] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 12/03/2022] Open
Abstract
Golgi anti-apoptotic proteins (GAAPs) are multitransmembrane proteins that are expressed in the Golgi apparatus and are able to homo-oligomerize. They are highly conserved throughout eukaryotes and are present in some prokaryotes and orthopoxviruses. Within eukaryotes, GAAPs regulate the Ca2+ content of intracellular stores, inhibit apoptosis, and promote cell adhesion and migration. Data presented here demonstrate that purified viral GAAPs (vGAAPs) and human Bax inhibitor 1 form ion channels and that vGAAP from camelpox virus is selective for cations. Mutagenesis of vGAAP, including some residues conserved in the recently solved structure of a related bacterial protein, BsYetJ, altered the conductance (E207Q and D219N) and ion selectivity (E207Q) of the channel. Mutation of residue Glu-207 or -178 reduced the effects of GAAP on cell migration and adhesion without affecting protection from apoptosis. In contrast, mutation of Asp-219 abrogated the anti-apoptotic activity of GAAP but not its effects on cell migration and adhesion. These results demonstrate that GAAPs are ion channels and define residues that contribute to the ion-conducting pore and affect apoptosis, cell adhesion, and migration independently.
Collapse
Affiliation(s)
- Guia Carrara
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nuno Saraiva
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Maddy Parsons
- the Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom
| | - Bernadette Byrne
- the Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom, and
| | - David L Prole
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom,
| | - Colin W Taylor
- the Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom,
| | - Geoffrey L Smith
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
| |
Collapse
|
35
|
Qian J, Liu H, Gu S, Wu Q, Zhao X, Wu W, Wang H, Wang J, Chen H, Zhang W, Wei Q, Jin L, Lu D. Genetic Variants of the MDM2 Gene Are Predictive of Treatment-Related Toxicities and Overall Survival in Patients With Advanced NSCLC. Clin Lung Cancer 2015; 16:e37-53. [PMID: 25818095 DOI: 10.1016/j.cllc.2015.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Platinum agents can cause the formation of DNA adducts and induce apoptosis to eliminate tumor cells. The aim of the present study was to investigate the influence of genetic variants of MDM2 on chemotherapy-related toxicities and clinical outcomes in patients with advanced non-small-cell lung cancer (NSCLC). MATERIALS AND METHODS We recruited 663 patients with advanced NSCLC who had been treated with first-line platinum-based chemotherapy. Five tagging single nucleotide polymorphisms (SNPs) in MDM2 were genotyped in these patients. The associations of these SNPs with clinical toxicities and outcomes were evaluated using logistic regression and Cox regression analyses. RESULTS Two SNPs (rs1470383 and rs1690924) showed significant associations with chemotherapy-related toxicities (ie, overall, hematologic, and gastrointestinal toxicity). Compared with the wild genotype AA carriers, patients with the GG genotype of rs1470383 had an increased risk of overall toxicity (odds ratio [OR], 3.28; 95% confidence interval [CI], 1.34-8.02; P = .009) and hematologic toxicity (OR, 4.10; 95% CI, 1.73-9.71; P = .001). Likewise, patients with the AG genotype of rs1690924 showed more sensitivity to gastrointestinal toxicity than did those with the wild-type homozygote GG (OR, 2.32; 95% CI, 1.30-4.14; P = .004). Stratified survival analysis revealed significant associations between rs1470383 genotypes and overall survival in patients without overall or hematologic toxicity (P = .007 and P = .0009, respectively). CONCLUSION The results of our study suggest that SNPs in MDM2 might be used to predict the toxicities of platinum-based chemotherapy and overall survival in patients with advanced NSCLC. Additional validations of the association are warranted.
Collapse
Affiliation(s)
- Ji Qian
- Cancer Institute, Fudan University Shanghai Cancer Center, and Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China.
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Shaohua Gu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China
| | - Qihan Wu
- East China Normal University School of Life Science, Shanghai, China
| | - Xueying Zhao
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China
| | - Wenting Wu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China; Beyster Center for Genomics of Psychiatric Diseases, Department of Psychiatry, University of California, San Diego, La Jolla, CA
| | - Haijian Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China
| | - Hongyan Chen
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China
| | - Wei Zhang
- Department of Respiratory Disease, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, and Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China; Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Li Jin
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Fudan University School of Life Sciences and Fudan Taizhou Institute of Health Sciences, Shanghai, China.
| |
Collapse
|
36
|
Woods NT, Monteiro AN, Thompson ZJ, Amankwah EK, Naas N, Haura EB, Beg AA, Schabath MB. Interleukin polymorphisms associated with overall survival, disease-free survival, and recurrence in non-small cell lung cancer patients. Mol Carcinog 2015; 54 Suppl 1:E172-84. [PMID: 25597281 DOI: 10.1002/mc.22275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 11/24/2014] [Accepted: 12/01/2014] [Indexed: 01/15/2023]
Abstract
Biomarkers based on germline DNA variations could have translational implications by identifying prognostic factors and sub-classifying patients to tailored, patient-specific treatment. To investigate the association between germline variations in interleukin (IL) genes and lung cancer outcomes, we genotyped 251 single nucleotide polymorphisms (SNPs) from 33 different IL genes in 651 non-small cell lung cancer (NSCLC) patients. Analyses were performed to investigate overall survival, disease-free survival, and recurrence. Our analyses revealed 24 different IL SNPs significantly associated with one or more of the lung cancer outcomes of interest. The GG genotype of IL16:rs7170924 was significantly associated with disease-free survival (HR = 0.65; 95% CI 0.50-0.83) and was the only SNP that produced a false discovery rate (FDR) of modest confidence that the association is unlikely to represent a false-positive result (FDR = 0.142). Classification and regression tree (CART) analyses were used to identify potential higher-order interactions. We restricted the CART analyses to the five SNPs that were significantly associated with multiple endpoints (IL1A:rs1800587, IL1B:rs1143634, IL8:s12506479, IL12A:rs662959, and IL13:rs1881457) and IL16:rs7170924 which had the lowest FDR. CART analyses did not yield a tree structure for overall survival; separate CART tree structures were identified for recurrence, based on three SNPs (IL13:rs1881457, IL1B:rs1143634, and IL12A:rs662959), and for disease-free survival, based on two SNPs (IL12A:rs662959 and IL16:rs7170924), which may suggest that these candidate IL SNPs have a specific impact on lung cancer progression and recurrence. These data suggest that germline variations in IL genes are associated with clinical outcomes in NSCLC patients.
Collapse
Affiliation(s)
- Nicholas T Woods
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida.,Department of Oncologic Sciences, University of South Florida College of Medicine, Tampa, Florida
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida.,Department of Oncologic Sciences, University of South Florida College of Medicine, Tampa, Florida
| | - Zachary J Thompson
- Department of Biostatistics Bioinformatics, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida
| | - Ernest K Amankwah
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida
| | - Nina Naas
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida
| | - Eric B Haura
- Department of Oncologic Sciences, University of South Florida College of Medicine, Tampa, Florida.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida
| | - Amer A Beg
- Department of Oncologic Sciences, University of South Florida College of Medicine, Tampa, Florida.,Department of Immunology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center Research Institute, Tampa, Florida.,Department of Oncologic Sciences, University of South Florida College of Medicine, Tampa, Florida
| |
Collapse
|
37
|
Vucic EA, Thu KL, Pikor LA, Enfield KSS, Yee J, English JC, MacAulay CE, Lam S, Jurisica I, Lam WL. Smoking status impacts microRNA mediated prognosis and lung adenocarcinoma biology. BMC Cancer 2014; 14:778. [PMID: 25342220 PMCID: PMC4216369 DOI: 10.1186/1471-2407-14-778] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/13/2014] [Indexed: 01/08/2023] Open
Abstract
Background Cigarette smoke is associated with the majority of lung cancers: however, 25% of lung cancer patients are non-smokers, and half of all newly diagnosed lung cancer patients are former smokers. Lung tumors exhibit distinct epidemiological, clinical, pathological, and molecular features depending on smoking status, suggesting divergent mechanisms underlie tumorigenesis in smokers and non-smokers. MicroRNAs (miRNAs) are integral contributors to tumorigenesis and mediate biological responses to smoking. Based on the hypothesis that smoking-specific miRNA differences in lung adenocarcinomas reflect distinct tumorigenic processes selected by different smoking and non-smoking environments, we investigated the contribution of miRNA disruption to lung tumor biology and patient outcome in the context of smoking status. Methods We applied a whole transcriptome sequencing based approach to interrogate miRNA levels in 94 patient-matched lung adenocarcinoma and non-malignant lung parenchymal tissue pairs from current, former and never smokers. Results We discovered novel and distinct smoking status-specific patterns of miRNA and miRNA-mediated gene networks, and identified miRNAs that were prognostically significant in a smoking dependent manner. Conclusions We conclude that miRNAs disrupted in a smoking status-dependent manner affect distinct cellular pathways and differentially influence lung cancer patient prognosis in current, former and never smokers. Our findings may represent promising biologically relevant markers for lung cancer prognosis or therapeutic intervention. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-778) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Qian Y, Chai S, Liang Z, Wang Y, Zhou Y, Xu X, Zhang C, Zhang M, Si J, Huang F, Huang Z, Hong W, Wang K. KIF5B-RET fusion kinase promotes cell growth by multilevel activation of STAT3 in lung cancer. Mol Cancer 2014; 13:176. [PMID: 25047660 PMCID: PMC4114102 DOI: 10.1186/1476-4598-13-176] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/10/2014] [Indexed: 11/18/2022] Open
Abstract
Background Lung cancer in nonsmokers tends to be driven by a single somatic mutation or a gene fusion. KIF5B-RET fusion is an oncogene identified in non-small cell lung cancers. In this study, we verified the oncogenic activity of KIF5B-RET fusion and investigated how KIF5B-RET activates the specific signaling pathways for cellular transformation. We aimed to provide a basis for the further development of the therapy for KIF5B-RET positive lung cancer patients. Methods RT-PCR was used to screen for KIF5B-RET fusions in Chinese lung cancer patients. To verify the oncogenic activity of KIF5B-RET kinase in lung cancer cells, we manipulated its expression genetically followed by colony formation and tumor formation assays. The mechanism by which KIF5B-RET kinase induces proliferation was investigated by western blot, coimmunoprecipitation, and administration of RET, MAPK and STAT3 inhibitors. Results Our study identified a KIF5B-RET fusion in Chinese NSCLC patients and demonstrated that KIF5B-RET transfected cells showed a significantly increased proliferation rate and colony-forming ability. Furthermore, we found that KIF5B-RET fusion kinase induced multilevel activation of STAT3 at both Tyr705 and Ser727, and KIF5B-RET-STAT3 signaling related inhibitors repressed the proliferation and tumorigenicity of lung cancer cells significantly. Conclusions Our data suggest that KIF5B-RET promotes the cell growth and tumorigenicity of non-small cell lung cancers through multilevel activation of STAT3 signaling, providing possible strategies for the treatment of KIF5B-RET positive lung cancers.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Kai Wang
- Department of Respiratory Medicine, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.
| |
Collapse
|
39
|
Wnt signaling pathway pharmacogenetics in non-small cell lung cancer. THE PHARMACOGENOMICS JOURNAL 2014; 14:509-22. [PMID: 24980784 PMCID: PMC4237616 DOI: 10.1038/tpj.2014.21] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 04/02/2014] [Accepted: 04/15/2014] [Indexed: 12/27/2022]
Abstract
Wnt/β-catenin pathway alterations in non-small cell lung cancer (NSCLC) are associated with poor prognosis and resistance. In 598 stage III-IV NSCLC patients receiving platinum-based chemotherapy at MD Anderson Cancer Center (MDACC), we correlated survival with 441 host SNPs in 50 Wnt pathway genes. We then assessed the most significant SNPs in 240 Mayo Clinic patients receiving platinum-based chemotherapy for advanced NSCLC, 127 MDACC patients receiving platinum-based adjuvant chemotherapy and 340 early stage MDACC patients undergoing surgery alone (cohorts 2–4). In multivariate analysis, survival correlates with SNPs for AXIN2 (rs11868547 and rs4541111, of which rs11868547 was assessed in cohorts 2–4), Wnt-5B (rs12819505), CXXC4 (rs4413407) and WIF-1 (rs10878232). Median survival was 19.7, 15.6, and 10.7 months for patients with 1, 2, and 3–5 unfavorable genotypes, respectively (p= 3.8×10−9). Survival tree analysis classified patients into two groups (MST 11.3 vs 17.3 months, p=4.7×10−8). None of the SNPs achieved significance in cohorts 2–4; however, there was a trend in the same direction as cohort 1 for 3 of the SNPs. Using online databases, we found rs10878232 displayed expression quantitative trait loci (eQTL) correlation with the expression of LEMD3, a neighboring gene previously associated with NSCLC survival. In conclusion, results from cohort 1 provide further evidence for an important role for Wnt in NSCLC. Investigation of Wnt inhibitors in advanced NSCLC would be reasonable. Lack of a SNP association with outcome in cohorts 2–4 could be due to low statistical power, impact of patient heterogeneity, or false positive observations in cohort 1.
Collapse
|
40
|
TMBIM protein family: ancestral regulators of cell death. Oncogene 2014; 34:269-80. [DOI: 10.1038/onc.2014.6] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/27/2013] [Accepted: 01/02/2014] [Indexed: 12/13/2022]
|
41
|
Vavalà T, Giaj Levra M, Novello S. Lung cancer in never smokers: a different disease. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13665-013-0071-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
42
|
Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell 2013; 155:27-38. [PMID: 24074859 DOI: 10.1016/j.cell.2013.09.006] [Citation(s) in RCA: 595] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Indexed: 02/07/2023]
Abstract
Genomics is a relatively new scientific discipline, having DNA sequencing as its core technology. As technology has improved the cost and scale of genome characterization over sequencing's 40-year history, the scope of inquiry has commensurately broadened. Massively parallel sequencing has proven revolutionary, shifting the paradigm of genomics to address biological questions at a genome-wide scale. Sequencing now empowers clinical diagnostics and other aspects of medical care, including disease risk, therapeutic identification, and prenatal testing. This Review explores the current state of genomics in the massively parallel sequencing era.
Collapse
Affiliation(s)
- Daniel C Koboldt
- The Genome Institute, School of Medicine, Washington University, St. Louis, MO 63108, USA
| | | | | | | | | |
Collapse
|