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Chi S, Flowers CR, Li Z, Huang X, Wei P. MASH: MEDIATION ANALYSIS OF SURVIVAL OUTCOME AND HIGH-DIMENSIONAL OMICS MEDIATORS WITH APPLICATION TO COMPLEX DISEASES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554286. [PMID: 37662296 PMCID: PMC10473652 DOI: 10.1101/2023.08.22.554286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Environmental exposures such as cigarette smoking influence health outcomes through intermediate molecular phenotypes, such as the methylome, transcriptome, and metabolome. Mediation analysis is a useful tool for investigating the role of potentially high-dimensional intermediate phenotypes in the relationship between environmental exposures and health outcomes. However, little work has been done on mediation analysis when the mediators are high-dimensional and the outcome is a survival endpoint, and none of it has provided a robust measure of total mediation effect. To this end, we propose an estimation procedure for Mediation Analysis of Survival outcome and High-dimensional omics mediators (MASH) based on sure independence screening for putative mediator variable selection and a second-moment-based measure of total mediation effect for survival data analogous to the R 2 measure in a linear model. Extensive simulations showed good performance of MASH in estimating the total mediation effect and identifying true mediators. By applying MASH to the metabolomics data of 1919 subjects in the Framingham Heart Study, we identified five metabolites as mediators of the effect of cigarette smoking on coronary heart disease risk (total mediation effect, 51.1%) and two metabolites as mediators between smoking and risk of cancer (total mediation effect, 50.7%). Application of MASH to a diffuse large B-cell lymphoma genomics data set identified copy-number variations for eight genes as mediators between the baseline International Prognostic Index score and overall survival.
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Affiliation(s)
- Sunyi Chi
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher R Flowers
- Department of Lymphoma, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Pang L, Ding Z, Chai H, Li F, Wu M, Shuang W. Causal relationship between smoking status, smoking frequency and bladder cancer: a Mendelian randomization study. Genes Genomics 2023; 45:203-213. [PMID: 36508086 DOI: 10.1007/s13258-022-01346-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Smoking is a well-established risk factor for bladder cancer. However, it remained unclear that whether smoke status and smoke frequency increase bladder cancer. OBJECTIVE We aim to explore the causal relationship between smoking status, smoking frequency and the risk of bladder cancer by Mendelian randomization. METHODS Large sample size of the genome-wide association(GWAS) database of smoking status, smoking frequency and bladder cancer were obtained. Smoking status included never, previous and current whereas smoking frequency included cigarettes smoked per day, number of cigarettes currently smoked daily and pack years of smoking. Six sets of instrumental variables and 78 related single nucleotide polymorphic(SNP) loci were identified (P < 5 × 10-8. Linkage disequilibrium R2 < 0.001). The causal relationship between smoking status and bladder tumor was studied by inverse variance weighted (IVW), weighted median and MR-Egger regression. Sensitivity analysis were also performed. RESULTS There is no causal effect from smoke status on bladder cancer risk while significantly positive relationship between smoking frequency on bladder cancer risk were found. IVW results showed that cigarettes smoked per day, number of cigarettes currently smoked daily and pack years of smoking increase bladder cancer (OR 1.001, 95% CI 1.000-1.002, P = 0.047; OR 1.003, 95% CI 1.000-1.005, P = 0.028; OR 1.004, 95% CI 1.001-1.006, P = 0.003). Sensitivity analysis showed that genetic pleiotropy did not bias the results. CONCLUSION The results of two sample Mendelian randomization analysis show that there is a positive causal relationship between smoking frequency and the risk of bladder cancer.
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Affiliation(s)
- Lei Pang
- Fifth hospital of Shanxi Medical University (Shanxi Provincial People's Hospital), Urology, Taiyuan, Shanxi, China.,First Clinical Medical College of Shanxi Medical University, Urology, Taiyuan, Shanxi, China
| | - Zijun Ding
- Shanxi children's Hospital, Neonatology, Taiyuan, Shanxi, China
| | - Hongqiang Chai
- Fifth hospital of Shanxi Medical University (Shanxi Provincial People's Hospital), Urology, Taiyuan, Shanxi, China
| | - Fei Li
- Fifth hospital of Shanxi Medical University (Shanxi Provincial People's Hospital), Urology, Taiyuan, Shanxi, China
| | - Ming Wu
- Fifth hospital of Shanxi Medical University (Shanxi Provincial People's Hospital), Urology, Taiyuan, Shanxi, China
| | - Weibing Shuang
- First Clinical Medical College of Shanxi Medical University, Urology, Taiyuan, Shanxi, China. .,First Hospital of Shanxi Medical University, Shanxi, China.
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Fantini D, Seiler R, Meeks JJ. Molecular footprints of muscle-invasive bladder cancer in smoking and nonsmoking patients. Urol Oncol 2019; 37:818-825. [PMID: 30446446 DOI: 10.1016/j.urolonc.2018.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/24/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Bladder cancer is the fifth most common cancer in the United States and smoking is the largest known risk factor. Tobacco-derived carcinogens may induce the accumulation of somatic mutations in urothelial cells, and likely promote tumorigenesis. However, it is still unknown whether smoking-induced bladder carcinogenesis results in tumors with distinctive molecular features that can be therapeutically exploited. METHODS We investigated the genomic alterations of human bladder cancer and examined their association with patient smoking history. We performed bioinformatic analyses and looked at differences in gene expression, somatic mutations, and DNA mutational signatures comparing nonsmokers, reformed smokers, and current smokers. RESULTS We detected a limited set of gene expression and gene mutation differences between smokers and nonsmokers. We also identified a specific mutational signature that is enriched in tumors from smokers. This mutational signature was described before and has been linked to specific DNA repair defects in human bladder tumors, as well as to the direct effect of nitrosamine carcinogens in the BBN murine model of bladder cancer. CONCLUSION We showed associations between smoking status and selected mutational signatures, which could provide insights in the biology of bladder carcinogenesis and tumor progression.
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Affiliation(s)
- Damiano Fantini
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Roland Seiler
- Department of Urology, University Hospital Bern, Bern, Switzerland
| | - Joshua J Meeks
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL.
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Akinboro O, Nwabudike S, Elias R, Balasire O, Ola O, Ostroff JS. Electronic Cigarette Use among Survivors of Smoking-Related Cancers in the United States. Cancer Epidemiol Biomarkers Prev 2019; 28:2087-2094. [PMID: 31501150 DOI: 10.1158/1055-9965.epi-19-0105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/02/2019] [Accepted: 09/03/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The prevalence of electronic cigarette (e-cigarette) use and its impact on smoking cessation among cancer survivors in the United States is largely unknown. We sought to estimate the prevalence of e-cigarette use and examine its associations with cigarette smoking and smoking quit attempts among smoking-related cancer survivors in the United States. METHODS We obtained data from the 2014-2017 annual cycles of the National Health Interview Survey for participants with self-reported history of smoking-related cancer(s). We calculated the prevalence of current e-cigarette use and utilized multinomial logistic regression in examining the independent association between e-cigarette use and cigarette smoking. Appropriate survey weights were applied in estimating the prevalence rates, relative risk ratios (RRR), ORs, and confidence intervals (CI). RESULTS Our sample comprised 3,162 smoking-related cancer survivors. The prevalence of current e-cigarette use was 3.18% (95% CI, 2.40-3.96). Current e-cigarette users were 83 times as likely as never users to be current cigarette smokers (RRR, 82.89; 95% CI, 16.54-415.37). Among those with a history of cigarette smoking, current e-cigarette users were 90% less likely to be former smokers (OR, 0.10; 95% CI, 0.05-0.18). No association was seen between current e-cigarette use and a smoking quit attempt in the prior year. CONCLUSIONS E-cigarette use among cigarette ever smokers was associated with a lower likelihood of being a former smoker/having quit smoking, and e-cigarette use was not associated with smoking quit attempts. IMPACT Our findings do not provide evidence that e-cigarette use facilitates smoking cessation among smoking-related cancer survivors.
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Affiliation(s)
| | | | - Rawad Elias
- Hartford Hospital Cancer Center, Hartford, Connecticut
| | | | - Olatunde Ola
- Mayo Clinic Health System Franciscan Medical Center, LaCrosse, Wisconsin
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van Osch FHM, Jochems SHJ, Reulen RC, Pirrie SJ, Nekeman D, Wesselius A, James ND, Wallace DMA, Cheng KK, van Schooten FJ, Bryan RT, Zeegers MP. The association between smoking cessation before and after diagnosis and non-muscle-invasive bladder cancer recurrence: a prospective cohort study. Cancer Causes Control 2018; 29:675-683. [PMID: 29846846 PMCID: PMC5999150 DOI: 10.1007/s10552-018-1046-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/28/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Smoking is a major risk factor for bladder cancer, but the relationship between smoking cessation after initial treatment and bladder cancer recurrence has been investigated less frequently and not prospectively yet. METHODS 722 non-muscle-invasive bladder cancer (NMIBC) patients (pTa, pT1, and CIS) from the prospective Bladder Cancer Prognosis Programme (BCPP) cohort, selected in the UK between 2005 and 2011, provided complete data on smoking behavior before and up to 5 years after diagnosis. The impact of smoking behavior on NMIBC recurrence was explored by multivariable Cox regression models investigating time-to-first NMIBC recurrence. RESULTS Over a median follow-up period of 4.21 years, 403 pathologically confirmed NMIBC recurrences occurred in 210 patients. Only 25 current smokers at diagnosis quit smoking (14%) during follow-up and smoking cessation after diagnosis did not decrease risk of recurrence compared to continuing smokers (p = 0.352). CONCLUSIONS Although quitting smoking after diagnosis might reduce the risk of recurrence based on retrospective evidence, this is not confirmed in this prospective study because the number of NMIBC patients quitting smoking before their first recurrence was too low. Nevertheless, this indicates an important role for urologists and other health care professionals in promoting smoking cessation in NMIBC.
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Affiliation(s)
- Frits H M van Osch
- Unit of Nutritional and Cancer Epidemiology, Chairgroup of Complex Genetics and Epidemiology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands.
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Sylvia H J Jochems
- Unit of Nutritional and Cancer Epidemiology, Chairgroup of Complex Genetics and Epidemiology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Raoul C Reulen
- Department of Public Health and Epidemiology, University of Birmingham, Birmingham, UK
| | - Sarah J Pirrie
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Duncan Nekeman
- Unit of Nutritional and Cancer Epidemiology, Chairgroup of Complex Genetics and Epidemiology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anke Wesselius
- Unit of Nutritional and Cancer Epidemiology, Chairgroup of Complex Genetics and Epidemiology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Nicholas D James
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- University Hospital Birmingham, NHS Foundation Trust, Birmingham, UK
| | - D Michael A Wallace
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- University Hospital Birmingham, NHS Foundation Trust, Birmingham, UK
| | - K K Cheng
- Department of Public Health and Epidemiology, University of Birmingham, Birmingham, UK
| | - Frederik J van Schooten
- Department of Pharmacology and Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Maurice P Zeegers
- Unit of Nutritional and Cancer Epidemiology, Chairgroup of Complex Genetics and Epidemiology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
- Chairgroup of Complex Genetics and Epidemiology, Care and Public Health Research Institute (CAPRHI), Maastricht University, Maastricht, The Netherlands
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