1
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Zhang C, Nie C, Su W, Balezentis T. Are digital technologies an effective inhibitor of depression among middle-aged and older adults? Micro-level evidence from a panel study. Soc Sci Med 2024; 348:116853. [PMID: 38598985 DOI: 10.1016/j.socscimed.2024.116853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/07/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
The increased number of middle-aged and older adults leads to depression in this stratum of the population as a topical social and public health issue. However, the new generation of information technologies has exerted a profound impact on the lives of middle-aged and older adults, and offers potential solutions for alleviating their depression. This study utilizes data from the China Health and Retirement Longitudinal Study (CHARLS) collected between 2011 and 2018 and combines them with city-level traits. The results demonstrate that digital technology can reduce depression levels effectively in this group. Mechanism analysis reveals that digital technology could improve life satisfaction and subjective health status levels, which, in turn, reduces depression levels. Heterogeneity analysis shows that the positive effects of digital technology on depression were more pronounced among middle-aged and older adults with urban household registration compared to the rural population. Finally, recommendations are provided for reducing depression levels among middle-aged and older adults.
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Affiliation(s)
- Chonghui Zhang
- College of Statistics and Mathematics, Zhejiang Gongshang University, Hangzhou, 310018, China.
| | - Chenying Nie
- College of Statistics and Mathematics, Zhejiang Gongshang University, Hangzhou, 310018, China.
| | - Weihua Su
- College of Statistics and Mathematics, Zhejiang Gongshang University, Hangzhou, 310018, China.
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2
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Wang P, Lin Z, Xue H, Pan W. Collider bias correction for multiple covariates in GWAS using robust multivariable Mendelian randomization. PLoS Genet 2024; 20:e1011246. [PMID: 38648211 PMCID: PMC11065275 DOI: 10.1371/journal.pgen.1011246] [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] [Received: 12/05/2023] [Revised: 05/02/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified many genetic loci associated with complex traits and diseases in the past 20 years. Multiple heritable covariates may be added into GWAS regression models to estimate direct effects of genetic variants on a focal trait, or to improve the power by accounting for environmental effects and other sources of trait variations. When one or more covariates are causally affected by both genetic variants and hidden confounders, adjusting for them in GWAS will produce biased estimation of SNP effects, known as collider bias. Several approaches have been developed to correct collider bias through estimating the bias by Mendelian randomization (MR). However, these methods work for only one covariate, some of which utilize MR methods with relatively strong assumptions, both of which may not hold in practice. In this paper, we extend the bias-correction approaches in two aspects: first we derive an analytical expression for the collider bias in the presence of multiple covariates, then we propose estimating the bias using a robust multivariable MR (MVMR) method based on constrained maximum likelihood (called MVMR-cML), allowing the presence of invalid instrumental variables (IVs) and correlated pleiotropy. We also established the estimation consistency and asymptotic normality of the new bias-corrected estimator. We conducted simulations to show that all methods mitigated collider bias under various scenarios. In real data analyses, we applied the methods to two GWAS examples, the first a GWAS of waist-hip ratio with adjustment for only one covariate, body-mass index (BMI), and the second a GWAS of BMI adjusting metabolomic principle components as multiple covariates, illustrating the effectiveness of bias correction.
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Affiliation(s)
- Peiyao Wang
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Zhaotong Lin
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Haoran Xue
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Biostatistics, City University of Hong Kong, Hong Kong, China
| | - Wei Pan
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, United States of America
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3
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Zhang H, Hong X, Zheng Y, Hou L, Zheng C, Wang X, Liu L. High-dimensional quantile mediation analysis with application to a birth cohort study of mother-newborn pairs. Bioinformatics 2024; 40:btae055. [PMID: 38290773 PMCID: PMC10873903 DOI: 10.1093/bioinformatics/btae055] [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] [Received: 02/16/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/01/2024] Open
Abstract
MOTIVATION There has been substantial recent interest in developing methodology for high-dimensional mediation analysis. Yet, the majority of mediation statistical methods lean heavily on mean regression, which limits their ability to fully capture the complex mediating effects across the outcome distribution. To bridge this gap, we propose a novel approach for selecting and testing mediators throughout the full range of the outcome distribution spectrum. RESULTS The proposed high-dimensional quantile mediation model provides a comprehensive insight into how potential mediators impact outcomes via their mediation pathways. This method's efficacy is demonstrated through extensive simulations. The study presents a real-world data application examining the mediating effects of DNA methylation on the relationship between maternal smoking and offspring birthweight. AVAILABILITY AND IMPLEMENTATION Our method offers a publicly available and user-friendly function qHIMA(), which can be accessed through the R package HIMA at https://CRAN.R-project.org/package=HIMA.
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Affiliation(s)
- Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin 300072, China
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center On the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, United States
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Cheng Zheng
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center On the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, United States
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO 63110, United States
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4
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Li J, Yang L, Yu S, Ding A, Zuo R, Yang J, Li X, Wang J. Environmental stressors altered the groundwater microbiome and nitrogen cycling: A focus on influencing mechanisms and pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167004. [PMID: 37704146 DOI: 10.1016/j.scitotenv.2023.167004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/10/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023]
Abstract
Nitrogen cycling, as an important biogeochemical process in groundwater, strongly impacts the energy and matter flow of groundwater ecology. Phthalate esters (PAEs) were screened as key environmental stressors in the groundwater of Beijing, contributing to the alteration of microbial community structure and functions; thus, it could be deduced that these stressors might influence nitrogen cycling that is almost exclusively mediated by microorganisms. Identification of the influences of PAEs on groundwater nitrogen cycling and exploration of the potential influence mechanisms and pathways are vital but still challenging. This study explored the influence mechanisms and pathways of the environmental stressor PAE on nitrogen cycling in groundwater collected from a typical monitoring station in Beijing based on high-throughput sequencing and bioinformatics analysis combined with mediation analysis methods. The results suggested that among the 5 detected PAEs, dimethyl phthalate and diethyl phthalate significantly negatively impacted nitrogen cycling processes, especially nitrogen fixation and denitrification processes (p < 0.05), in groundwater. Their influences were fully or partially mediated by functional microorganisms, particularly assigned keystone genera (such as Dechloromonas, Aeromonas and Noviherbaspirillum), whose abundance was significantly inhibited by these PAEs via dysregulation of carbohydrate metabolism and activation of defense mechanisms. These findings confirmed that the influences of environmental stressors PAEs on nitrogen cycling in groundwater might be mediated by the "PAE stress-groundwater microbiome-nitrogen cycling alteration" pathway. This study may advance the understanding of the consequences of environmental stressors on groundwater ecology and support the ecological hazard assessment of groundwater stressors.
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Affiliation(s)
- Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Lei Yang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Aizhong Ding
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Jie Yang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiaofei Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China; Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai 519087, China.
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5
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Montenegro J, Armet AM, Willing BP, Deehan EC, Fassini PG, Mota JF, Walter J, Prado CM. Exploring the Influence of Gut Microbiome on Energy Metabolism in Humans. Adv Nutr 2023; 14:840-857. [PMID: 37031749 PMCID: PMC10334151 DOI: 10.1016/j.advnut.2023.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/13/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
The gut microbiome has a profound influence on host physiology, including energy metabolism, which is the process by which energy from nutrients is transformed into other forms of energy to be used by the body. However, mechanistic evidence for how the microbiome influences energy metabolism is derived from animal models. In this narrative review, we included human studies investigating the relationship between gut microbiome and energy metabolism -i.e., energy expenditure in humans and energy harvest by the gut microbiome. Studies have found no consistent gut microbiome patterns associated with energy metabolism, and most interventions were not effective in modulating the gut microbiome to influence energy metabolism. To date, cause-and-effect relationships and mechanistic evidence on the impact of the gut microbiome on energy expenditure have not been established in humans. Future longitudinal observational studies and randomized controlled trials utilizing robust methodologies and advanced statistical analysis are needed. Such knowledge would potentially inform the design of therapeutic avenues and specific dietary recommendations to improve energy metabolism through gut microbiome modulation.
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Affiliation(s)
- Julia Montenegro
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Anissa M Armet
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Benjamin P Willing
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Edward C Deehan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, United States; Nebraska Food for Health Center, University of Nebraska, Lincoln, Nebraska, United States
| | - Priscila G Fassini
- Department of Internal Medicine, Division of Nutrology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João F Mota
- School of Nutrition, Federal University of Goiás, Goiânia, Goiás, Brazil; APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork - National University of Ireland, Cork, Ireland
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork - National University of Ireland, Cork, Ireland.
| | - Carla M Prado
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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6
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Fu J, Koslovsky MD, Neophytou AM, Vannucci M. A Bayesian joint model for compositional mediation effect selection in microbiome data. Stat Med 2023. [PMID: 37173609 DOI: 10.1002/sim.9764] [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: 09/22/2022] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Analyzing multivariate count data generated by high-throughput sequencing technology in microbiome research studies is challenging due to the high-dimensional and compositional structure of the data and overdispersion. In practice, researchers are often interested in investigating how the microbiome may mediate the relation between an assigned treatment and an observed phenotypic response. Existing approaches designed for compositional mediation analysis are unable to simultaneously determine the presence of direct effects, relative indirect effects, and overall indirect effects, while quantifying their uncertainty. We propose a formulation of a Bayesian joint model for compositional data that allows for the identification, estimation, and uncertainty quantification of various causal estimands in high-dimensional mediation analysis. We conduct simulation studies and compare our method's mediation effects selection performance with existing methods. Finally, we apply our method to a benchmark data set investigating the sub-therapeutic antibiotic treatment effect on body weight in early-life mice.
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Affiliation(s)
- Jingyan Fu
- Department of Statistics, Rice University, Houston, Texas, USA
| | - Matthew D Koslovsky
- Department of Statistics, Colorado State University, Fort Collins, Colorado, USA
| | - Andreas M Neophytou
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Marina Vannucci
- Department of Statistics, Rice University, Houston, Texas, USA
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7
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Hong Q, Chen G, Tang ZZ. PhyloMed: a phylogeny-based test of mediation effect in microbiome. Genome Biol 2023; 24:72. [PMID: 37041566 PMCID: PMC10088256 DOI: 10.1186/s13059-023-02902-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 03/15/2023] [Indexed: 04/13/2023] Open
Abstract
Microbiome data from sequencing experiments contain the relative abundance of a large number of microbial taxa with their evolutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the microbiome mediator challenges the validity of standard mediation analyses. We propose a phylogeny-based mediation analysis method called PhyloMed to address this challenge. Unlike existing methods that directly identify individual mediating taxa, PhyloMed discovers mediation signals by analyzing subcompositions defined on the phylogenic tree. PhyloMed produces well-calibrated mediation test p-values and yields substantially higher discovery power than existing methods.
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Affiliation(s)
- Qilin Hong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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8
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Perera C, Zhang H, Zheng Y, Hou L, Qu A, Zheng C, Xie K, Liu L. HIMA2: high-dimensional mediation analysis and its application in epigenome-wide DNA methylation data. BMC Bioinformatics 2022; 23:296. [PMID: 35879655 PMCID: PMC9310002 DOI: 10.1186/s12859-022-04748-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/23/2022] [Indexed: 11/28/2022] Open
Abstract
Mediation analysis plays a major role in identifying significant mediators in the pathway between environmental exposures and health outcomes. With advanced data collection technology for large-scale studies, there has been growing research interest in developing methodology for high-dimensional mediation analysis. In this paper we present HIMA2, an extension of the HIMA method (Zhang in Bioinformatics 32:3150-3154, 2016). First, the proposed HIMA2 reduces the dimension of mediators to a manageable level based on the sure independence screening (SIS) method (Fan in J R Stat Soc Ser B 70:849-911, 2008). Second, a de-biased Lasso procedure is implemented for estimating regression parameters. Third, we use a multiple-testing procedure to accurately control the false discovery rate (FDR) when testing high-dimensional mediation hypotheses. We demonstrate its practical performance using Monte Carlo simulation studies and apply our method to identify DNA methylation markers which mediate the pathway from smoking to reduced lung function in the Coronary Artery Risk Development in Young Adults (CARDIA) Study.
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Affiliation(s)
- Chamila Perera
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Annie Qu
- Department of Statistics, University of California, Irvine, CA, 92697, USA
| | - Cheng Zheng
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ke Xie
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, 63110, USA.
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9
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Kodikara S, Ellul S, Lê Cao KA. Statistical challenges in longitudinal microbiome data analysis. Brief Bioinform 2022; 23:bbac273. [PMID: 35830875 PMCID: PMC9294433 DOI: 10.1093/bib/bbac273] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/28/2022] [Accepted: 06/12/2022] [Indexed: 11/13/2022] Open
Abstract
The microbiome is a complex and dynamic community of microorganisms that co-exist interdependently within an ecosystem, and interact with its host or environment. Longitudinal studies can capture temporal variation within the microbiome to gain mechanistic insights into microbial systems; however, current statistical methods are limited due to the complex and inherent features of the data. We have identified three analytical objectives in longitudinal microbial studies: (1) differential abundance over time and between sample groups, demographic factors or clinical variables of interest; (2) clustering of microorganisms evolving concomitantly across time and (3) network modelling to identify temporal relationships between microorganisms. This review explores the strengths and limitations of current methods to fulfill these objectives, compares different methods in simulation and case studies for objectives (1) and (2), and highlights opportunities for further methodological developments. R tutorials are provided to reproduce the analyses conducted in this review.
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Affiliation(s)
- Saritha Kodikara
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Royal Parade, 3052, Victoria, Australia
| | - Susan Ellul
- Murdoch Children’s Research Institute and Department of Paediatrics, University of Melbourne, Bouverie Street, 3052, Victoria, Australia
| | - Kim-Anh Lê Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Royal Parade, 3052, Victoria, Australia
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10
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Yue Y, Hu YJ. A new approach to testing mediation of the microbiome at both the community and individual taxon levels. Bioinformatics 2022; 38:3173-3180. [PMID: 35512399 PMCID: PMC9191207 DOI: 10.1093/bioinformatics/btac310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
MOTIVATION Understanding whether and which microbes played a mediating role between an exposure and a disease outcome are essential for researchers to develop clinical interventions to treat the disease by modulating the microbes. Existing methods for mediation analysis of the microbiome are often limited to a global test of community-level mediation or selection of mediating microbes without control of the false discovery rate (FDR). Further, while the null hypothesis of no mediation at each microbe is a composite null that consists of three types of null, most existing methods treat the microbes as if they were all under the same type of null, leading to excessive false positive results. RESULTS We propose a new approach based on inverse regression that regresses the microbiome data at each taxon on the exposure and the exposure-adjusted outcome. Then, the P-values for testing the coefficients are used to test mediation at both the community and individual taxon levels. This approach fits nicely into our Linear Decomposition Model (LDM) framework, so our new method LDM-med, implemented in the LDM framework, enjoys all the features of the LDM, e.g. allowing an arbitrary number of taxa to be tested simultaneously, supporting continuous, discrete, or multivariate exposures and outcomes (including survival outcomes), and so on. Using extensive simulations, we showed that LDM-med always preserved the FDR of testing individual taxa and had adequate sensitivity; LDM-med always controlled the type I error of the global test and had compelling power over existing methods. The flexibility of LDM-med for a variety of mediation analyses is illustrated by an application to a murine microbiome dataset, which identified several plausible mediating taxa. AVAILABILITY AND IMPLEMENTATION Our new method has been added to our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ye Yue
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Yi-Juan Hu
- To whom correspondence should be addressed.
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11
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Wu Q, O’Malley J, Datta S, Gharaibeh RZ, Jobin C, Karagas MR, Coker MO, Hoen AG, Christensen BC, Madan JC, Li Z. MarZIC: A Marginal Mediation Model for Zero-Inflated Compositional Mediators with Applications to Microbiome Data. Genes (Basel) 2022; 13:1049. [PMID: 35741811 PMCID: PMC9223163 DOI: 10.3390/genes13061049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the excessive number of zero-valued sequencing reads in the data and that the relative abundances have to sum to one. The two main challenges raised by the zero-inflated data structure are: (a) disentangling the mediation effect induced by the point mass at zero; and (b) identifying the observed zero-valued data points that are not zero (i.e., false zeros). METHODS We develop a novel marginal mediation analysis method under the potential-outcomes framework to address the issues. We also show that the marginal model can account for the compositional structure of microbiome data. RESULTS The mediation effect can be decomposed into two components that are inherent to the two-part nature of zero-inflated distributions. With probabilistic models to account for observing zeros, we also address the challenge with false zeros. A comprehensive simulation study and the application in a real microbiome study showcase our approach in comparison with existing approaches. CONCLUSIONS When analyzing the zero-inflated microbiome composition as the mediators, MarZIC approach has better performance than standard causal mediation analysis approaches and existing competing approach.
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Affiliation(s)
- Quran Wu
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA; (Q.W.); (S.D.)
| | - James O’Malley
- The Dartmouth Institute, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA;
| | - Susmita Datta
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA; (Q.W.); (S.D.)
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL 32611, USA; (R.Z.G.); (C.J.)
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL 32611, USA; (R.Z.G.); (C.J.)
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (M.R.K.); (M.O.C.); (A.G.H.); (B.C.C.); (J.C.M.)
| | - Modupe O. Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (M.R.K.); (M.O.C.); (A.G.H.); (B.C.C.); (J.C.M.)
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (M.R.K.); (M.O.C.); (A.G.H.); (B.C.C.); (J.C.M.)
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (M.R.K.); (M.O.C.); (A.G.H.); (B.C.C.); (J.C.M.)
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (M.R.K.); (M.O.C.); (A.G.H.); (B.C.C.); (J.C.M.)
| | - Zhigang Li
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA; (Q.W.); (S.D.)
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Srinivasan A, Xue L, Zhan X. Compositional knockoff filter for high-dimensional regression analysis of microbiome data. Biometrics 2021; 77:984-995. [PMID: 32683674 PMCID: PMC7831267 DOI: 10.1111/biom.13336] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 06/29/2020] [Accepted: 07/09/2020] [Indexed: 01/10/2023]
Abstract
A critical task in microbiome data analysis is to explore the association between a scalar response of interest and a large number of microbial taxa that are summarized as compositional data at different taxonomic levels. Motivated by fine-mapping of the microbiome, we propose a two-step compositional knockoff filter to provide the effective finite-sample false discovery rate (FDR) control in high-dimensional linear log-contrast regression analysis of microbiome compositional data. In the first step, we propose a new compositional screening procedure to remove insignificant microbial taxa while retaining the essential sum-to-zero constraint. In the second step, we extend the knockoff filter to identify the significant microbial taxa in the sparse regression model for compositional data. Thereby, a subset of the microbes is selected from the high-dimensional microbial taxa as related to the response under a prespecified FDR threshold. We study the theoretical properties of the proposed two-step procedure, including both sure screening and effective false discovery control. We demonstrate these properties in numerical simulation studies to compare our methods to some existing ones and show power gain of the new method while controlling the nominal FDR. The potential usefulness of the proposed method is also illustrated with application to an inflammatory bowel disease data set to identify microbial taxa that influence host gene expressions.
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Affiliation(s)
- Arun Srinivasan
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Lingzhou Xue
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Xiang Zhan
- Department of Public Health Sciences, Pennsylvania State University, Hershey, PA 17033, U.S.A
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Zhang H, Zheng Y, Hou L, Zheng C, Liu L. Mediation analysis for survival data with High-Dimensional mediators. Bioinformatics 2021; 37:3815-3821. [PMID: 34343267 PMCID: PMC8570823 DOI: 10.1093/bioinformatics/btab564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/18/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Mediation analysis has become a prevalent method to identify causal pathway(s) between an independent variable and a dependent variable through intermediate variable(s). However, little work has been done when the intermediate variables (mediators) are high-dimensional and the outcome is a survival endpoint. In this paper, we introduce a novel method to identify potential mediators in a causal framework of high-dimensional Cox regression. RESULTS We first reduce the data dimension through a mediation-based sure independence screening (SIS) method. A de-biased Lasso inference procedure is used for Cox's regression parameters. We adopt a multiple-testing procedure to accurately control the false discovery rate (FDR) when testing high-dimensional mediation hypotheses. Simulation studies are conducted to demonstrate the performance of our method. We apply this approach to explore the mediation mechanisms of 379,330 DNA methylation markers between smoking and overall survival among lung cancer patients in the TCGA lung cancer cohort. Two methylation sites (cg08108679 and cg26478297) are identified as potential mediating epigenetic markers. AVAILABILITY Our proposed method is available with the R package HIMA at https://cran.r-project.org/web/packages/HIMA/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Cheng Zheng
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, 63110, USA
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Binder N, Lederer AK, Michels KB, Binder H. Assessing mediating effects of high-dimensional microbiome measurements in dietary intervention studies. Biom J 2021; 63:1366-1374. [PMID: 33960007 DOI: 10.1002/bimj.201900373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/12/2020] [Accepted: 03/24/2021] [Indexed: 11/08/2022]
Abstract
Habitual diet can influence health-related outcomes directly, but such effects may also be modulated indirectly by gut microbiota. We consider randomized trials and the question to what extent the effect of diet on an outcome of interest is mediated through the gut microbiome or whether there is a diet-microbiome interaction identifying subgroups of individuals who are more susceptible to specific dietary effects. The baseline microbiome by itself may be a modifier of the effects of diet on health. Yet, the high dimensionality of microbiome data requires innovative statistical approaches to identify potential mediating or moderating effects. To motivate our proposal for an appropriate analysis workflow, we consider a randomized trial that investigates the effect of a 4-week vegan diet on the diversity of gut microbiota and branched-chain amino acid metabolism in healthy omnivorous volunteers. To address the challenge of compositional microbiome data, we consider an adaptation of the lasso for penalized estimation of multivariable regression models with a large number of microbiotic taxa. This is plugged into a classical regression mediation effect analysis strategy. The interaction effects are obtained via an approach that can directly estimate them without having to deal with main effects. As a result we obtain signatures comprised of microbiotic taxa with potential mediating and moderating effects. Some taxa no longer show up as mediating, when taking moderating effects into account. Thus, the proposed analysis strategy allows to identify specific mediating effects, while avoiding potential erroneous conclusions, where moderating effects might have believed to be mediating effects.
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Affiliation(s)
- Nadine Binder
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.,Institute of Digitalization in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Ann-Kathrin Lederer
- Center for Complementary Medicine, Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Karin B Michels
- Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.,Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Harald Binder
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
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Zhang H, Chen J, Feng Y, Wang C, Li H, Liu L. Mediation effect selection in high-dimensional and compositional microbiome data. Stat Med 2021; 40:885-896. [PMID: 33205470 PMCID: PMC7855955 DOI: 10.1002/sim.8808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/31/2020] [Accepted: 10/16/2020] [Indexed: 01/08/2023]
Abstract
The microbiome plays an important role in human health by mediating the path from environmental exposures to health outcomes. The relative abundances of the high-dimensional microbiome data have an unit-sum restriction, rendering standard statistical methods in the Euclidean space invalid. To address this problem, we use the isometric log-ratio transformations of the relative abundances as the mediator variables. To select significant mediators, we consider a closed testing-based selection procedure with desirable confidence. Simulations are provided to verify the effectiveness of our method. As an illustrative example, we apply the proposed method to study the mediation effects of murine gut microbiome between subtherapeutic antibiotic treatment and body weight gain, and identify Coprobacillus and Adlercreutzia as two significant mediators.
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Affiliation(s)
- Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Yang Feng
- Department of Biostatistics, College of Global Public Health, New York University, New York, NY 10003, USA
| | - Chan Wang
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Huilin Li
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016, USA
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO 63110, USA
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