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Hsu LL, Culhane AC. Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data. Front Oncol 2020; 10:973. [PMID: 32656082 PMCID: PMC7324639 DOI: 10.3389/fonc.2020.00973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/18/2020] [Indexed: 01/04/2023] Open
Abstract
Integrative, single-cell analyses may provide unprecedented insights into cellular and spatial diversity of the tumor microenvironment. The sparsity, noise, and high dimensionality of these data present unique challenges. Whilst approaches for integrating single-cell data are emerging and are far from being standardized, most data integration, cell clustering, cell trajectory, and analysis pipelines employ a dimension reduction step, frequently principal component analysis (PCA), a matrix factorization method that is relatively fast, and can easily scale to large datasets when used with sparse-matrix representations. In this review, we provide a guide to PCA and related methods. We describe the relationship between PCA and singular value decomposition, the difference between PCA of a correlation and covariance matrix, the impact of scaling, log-transforming, and standardization, and how to recognize a horseshoe or arch effect in a PCA. We describe canonical correlation analysis (CCA), a popular matrix factorization approach for the integration of single-cell data from different platforms or studies. We discuss alternatives to CCA and why additional preprocessing or weighting datasets within the joint decomposition should be considered.
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Affiliation(s)
- Lauren L Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Division of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Aedin C Culhane
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Division of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
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52
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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53
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Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes. Front Oncol 2020; 10:845. [PMID: 32528899 PMCID: PMC7259379 DOI: 10.3389/fonc.2020.00845] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is a disease that exhibits heterogeneity that goes from the genomic to the clinical levels. This heterogeneity is thought to be captured (at least partially) by the so-called breast cancer molecular subtypes. These molecular subtypes were initially defined based on the unsupervised clustering of gene expression and its correlate with histological, morphological, phenotypic and clinical features already known. Later, a 50-gene signature, PAM50, was defined in order to identify the biological subtype of a given sample within the clinical setting. The PAM50 signature was obtained by the use of unsupervised statistical methods, and therefore no limitation was set on the biological relevance (or lack of) of the selected genes beyond its predictive capacity. An open question that remains is what are the regulatory elements that drive the various expression behaviors of this set of genes in the different molecular subtypes. This question becomes more relevant as the measurement of more biological layers of regulation becomes accessible. In this work, we analyzed the gene expression regulation of the 50 genes in the PAM50 signature, in terms of (a) gene co-expression, (b) transcription factors, (c) micro-RNAs, and (d) methylation. Using data from the Cancer Genome Atlas (TCGA) for the Luminal A and B, Basal, and HER2-enriched molecular subtypes as well as normal tumor adjacent tissue, we identified predictors for gene expression through the use of an elastic net model. We compare and contrast the sets of identified regulators for the gene signature in each molecular subtype, and systematically compare them to current literature. We also identified a unique set of predictors for the expression of genes in the PAM50 signature associated with each of the molecular subtypes. Most selected predictors are exclusive for a PAM50 gene and predictors are not shared across subtypes. There are only 13 coding transcripts and 2 miRNAs selected for the four subtypes. MiR-21 and miR-10b connect almost all the PAM50 genes in all the subtypes and normal tissue, but do it in an exclusive manner, suggesting a cancer switch from miR-10b coordination in normal tissue to miR-21. The PAM50 gene sets of selected predictors that enrich for a function across subtypes, support that different regulatory molecular mechanisms are taking place. With this study we aim to a wider understanding of the regulatory mechanisms that differentiate the expression of the PAM50 signature, which in turn could perhaps help understand the molecular basis of the differences between the molecular subtypes.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Graduate Program in Biomedical Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Cátedras Conacyt para Jóvenes Investigadores', National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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54
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Wang Y, Zhou Y, Xiao X, Zheng J, Zhou H. Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota. J Proteomics 2020; 219:103737. [DOI: 10.1016/j.jprot.2020.103737] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
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55
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Min EJ, Long Q. Sparse multiple co-Inertia analysis with application to integrative analysis of multi -Omics data. BMC Bioinformatics 2020; 21:141. [PMID: 32293260 PMCID: PMC7157996 DOI: 10.1186/s12859-020-3455-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/13/2020] [Indexed: 01/28/2023] Open
Abstract
Background Multiple co-inertia analysis (mCIA) is a multivariate analysis method that can assess relationships and trends in multiple datasets. Recently it has been used for integrative analysis of multiple high-dimensional -omics datasets. However, its estimated loading vectors are non-sparse, which presents challenges for identifying important features and interpreting analysis results. We propose two new mCIA methods: 1) a sparse mCIA method that produces sparse loading estimates and 2) a structured sparse mCIA method that further enables incorporation of structural information among variables such as those from functional genomics. Results Our extensive simulation studies demonstrate the superior performance of the sparse mCIA and structured sparse mCIA methods compared to the existing mCIA in terms of feature selection and estimation accuracy. Application to the integrative analysis of transcriptomics data and proteomics data from a cancer study identified biomarkers that are suggested in the literature related with cancer disease. Conclusion Proposed sparse mCIA achieves simultaneous model estimation and feature selection and yields analysis results that are more interpretable than the existing mCIA. Furthermore, proposed structured sparse mCIA can effectively incorporate prior network information among genes, resulting in improved feature selection and enhanced interpretability.
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Affiliation(s)
- Eun Jeong Min
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 423 Guardian Dr, Philadelphia, 19104, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 423 Guardian Dr, Philadelphia, 19104, USA.
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56
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Fan Z, Zhou Y, Ressom HW. MOTA: Network-Based Multi-Omic Data Integration for Biomarker Discovery. Metabolites 2020; 10:metabo10040144. [PMID: 32276350 PMCID: PMC7241240 DOI: 10.3390/metabo10040144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/26/2020] [Accepted: 04/05/2020] [Indexed: 01/03/2023] Open
Abstract
The recent advancement of omic technologies provides researchers with the possibility to search for disease-associated biomarkers at the system level. The integrative analysis of data from a large number of molecules involved at various layers of the biological system offers a great opportunity to rank disease biomarker candidates. In this paper, we propose MOTA, a network-based method that uses data acquired at multiple layers to rank candidate disease biomarkers. The networks constructed by MOTA allow users to investigate the biological significance of the top-ranked biomarker candidates. We evaluated the performance of MOTA in ranking disease-associated molecules from three sets of multi-omic data representing three cohorts of hepatocellular carcinoma (HCC) cases and controls with liver cirrhosis. The results demonstrate that MOTA allows the identification of more top-ranked metabolite biomarker candidates that are shared by two different cohorts compared to traditional statistical methods. Moreover, the mRNA candidates top-ranked by MOTA comprise more cancer driver genes compared to those ranked by traditional differential expression methods.
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Affiliation(s)
- Ziling Fan
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA;
| | - Yuan Zhou
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA;
| | - Habtom W. Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA;
- Correspondence:
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57
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Wu W, Zhang L, Xia B, Tang S, Xie J, Zhang H. Modulation of Pectin on Mucosal Innate Immune Function in Pigs Mediated by Gut Microbiota. Microorganisms 2020; 8:microorganisms8040535. [PMID: 32276396 PMCID: PMC7232157 DOI: 10.3390/microorganisms8040535] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/22/2020] [Accepted: 04/03/2020] [Indexed: 12/19/2022] Open
Abstract
The use of prebiotics to regulate gut microbiota is a promising strategy to improve gut health. Pectin (PEC) is a prebiotic carbohydrate that enhances the health of the gut by promoting the growth of beneficial microbes. These microbes produce metabolites that are known to improve mucosal immune responses. This study was conducted to better understand effects of PEC on the microbiome and mucosal immunity in pigs. Pigs were fed two diets, with or without 5% apple PEC, for 72 days. Effects of PEC on the microbiota, cytokine expression, short-chain fatty acids (SCFAs) concentration and barrier function were examined in the ileum and cecum of the pigs. An integrative analysis was used to determine interactions of PEC consumption with bacterial metabolites and microbiome composition and host mucosal responses. Consumption of PEC reduced expression of pro-inflammatory cytokines such as IFN-γ, IL-6, IL-8, IL-12 and IL-18, and the activation of the pro-inflammatory NF-κB signaling cascade. Expression of MUC2 and TFF and the sIgA content was upregulated in the mucosa of PEC-fed pigs. Network analysis revealed that PEC induced significant interactions between microbiome composition in the ileum and cecum on mucosal immune pathways. PEC-induced changes in bacterial genera and fermentation metabolites, such as Akkermansia, Faecalibacterium, Oscillibacter, Lawsonia and butyrate, correlated with the differentially expressed genes and cytokines in the mucosa. In summary, the results demonstrate the anti-inflammatory properties of PEC on mucosal immune status in the ileum and cecum effected through modulation of the host microbiome.
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Affiliation(s)
- Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.W.); (B.X.); (S.T.); (J.X.)
| | - Li Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang 330047, China;
| | - Bing Xia
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.W.); (B.X.); (S.T.); (J.X.)
| | - Shanlong Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.W.); (B.X.); (S.T.); (J.X.)
| | - Jingjing Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.W.); (B.X.); (S.T.); (J.X.)
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (W.W.); (B.X.); (S.T.); (J.X.)
- Correspondence: ; Tel.: +86-10-62816013
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58
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Mallik S, Zhao Z. Graph- and rule-based learning algorithms: a comprehensive review of their applications for cancer type classification and prognosis using genomic data. Brief Bioinform 2020; 21:368-394. [PMID: 30649169 PMCID: PMC7373185 DOI: 10.1093/bib/bby120] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/26/2018] [Accepted: 11/21/2018] [Indexed: 12/20/2022] Open
Abstract
Cancer is well recognized as a complex disease with dysregulated molecular networks or modules. Graph- and rule-based analytics have been applied extensively for cancer classification as well as prognosis using large genomic and other data over the past decade. This article provides a comprehensive review of various graph- and rule-based machine learning algorithms that have been applied to numerous genomics data to determine the cancer-specific gene modules, identify gene signature-based classifiers and carry out other related objectives of potential therapeutic value. This review focuses mainly on the methodological design and features of these algorithms to facilitate the application of these graph- and rule-based analytical approaches for cancer classification and prognosis. Based on the type of data integration, we divided all the algorithms into three categories: model-based integration, pre-processing integration and post-processing integration. Each category is further divided into four sub-categories (supervised, unsupervised, semi-supervised and survival-driven learning analyses) based on learning style. Therefore, a total of 11 categories of methods are summarized with their inputs, objectives and description, advantages and potential limitations. Next, we briefly demonstrate well-known and most recently developed algorithms for each sub-category along with salient information, such as data profiles, statistical or feature selection methods and outputs. Finally, we summarize the appropriate use and efficiency of all categories of graph- and rule mining-based learning methods when input data and specific objective are given. This review aims to help readers to select and use the appropriate algorithms for cancer classification and prognosis study.
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Affiliation(s)
- Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston
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59
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Li S, Cirillo P, Hu X, Tran V, Krigbaum N, Yu S, Jones DP, Cohn B. Understanding mixed environmental exposures using metabolomics via a hierarchical community network model in a cohort of California women in 1960's. Reprod Toxicol 2020; 92:57-65. [PMID: 31299210 PMCID: PMC6949431 DOI: 10.1016/j.reprotox.2019.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023]
Abstract
Even though the majority of population studies in environmental health focus on a single factor, environmental exposure in the real world is a mixture of many chemicals. The concept of "exposome" leads to an intellectual framework of measuring many exposures in humans, and the emerging metabolomics technology offers a means to read out both the biological activity and environmental impact in the same dataset. How to integrate exposome and metabolome in data analysis is still challenging. Here, we employ a hierarchical community network to investigate the global associations between the metabolome and mixed exposures including DDTs, PFASs and PCBs, in a women cohort with sera collected in California in the 1960s. Strikingly, this analysis revealed that the metabolite communities associated with the exposures were non-specific and shared among exposures. This suggests that a small number of metabolic phenotypes may account for the response to a large class of environmental chemicals.
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Affiliation(s)
- Shuzhao Li
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, 30303, USA.
| | - Piera Cirillo
- The Center for Research on Women and Children's Health, Child Health and Development Studies, Public Health Institute, 1683 Shattuck Avenue, Suite B, Berkeley, CA, 94709, USA
| | - Xin Hu
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, 30303, USA
| | - ViLinh Tran
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, 30303, USA
| | - Nickilou Krigbaum
- The Center for Research on Women and Children's Health, Child Health and Development Studies, Public Health Institute, 1683 Shattuck Avenue, Suite B, Berkeley, CA, 94709, USA
| | - Shaojun Yu
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, 30303, USA
| | - Dean P Jones
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, 30303, USA
| | - Barbara Cohn
- The Center for Research on Women and Children's Health, Child Health and Development Studies, Public Health Institute, 1683 Shattuck Avenue, Suite B, Berkeley, CA, 94709, USA.
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60
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Pucher BM, Zeleznik OA, Thallinger GG. Comparison and evaluation of integrative methods for the analysis of multilevel omics data: a study based on simulated and experimental cancer data. Brief Bioinform 2020; 20:671-681. [PMID: 29688321 DOI: 10.1093/bib/bby027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/02/2018] [Indexed: 12/12/2022] Open
Abstract
Integrative analysis aims to identify the driving factors of a biological process by the joint exploration of data from multiple cellular levels. The volume of omics data produced is constantly increasing, and so too does the collection of tools for its analysis. Comparative studies assessing performance and the biological value of results, however, are rare but in great demand. We present a comprehensive comparison of three integrative analysis approaches, sparse canonical correlation analysis (sCCA), non-negative matrix factorization (NMF) and logic data mining MicroArray Logic Analyzer (MALA), by applying them to simulated and experimental omics data. We find that sCCA and NMF are able to identify differential features in simulated data, while the Logic Data Mining method, MALA, falls short. Applied to experimental data, we show that MALA performs best in terms of sample classification accuracy, and in general, the classification power of prioritized feature sets is high (97.1-99.5% accuracy). The proportion of features identified by at least one of the other methods, however, is approximately 60% for sCCA and NMF and nearly 30% for MALA, and the proportion of features jointly identified by all methods is only around 16%. Similarly, the congruence on functional levels (Gene Ontology, Reactome) is low. Furthermore, the agreement of identified feature sets with curated gene signatures relevant to the investigated disease is modest. We discuss possible reasons for the moderate overlap of identified feature sets with each other and with curated cancer signatures. The R code to create simulated data, results and figures is provided at https://github.com/ThallingerLab/IamComparison.
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Affiliation(s)
- Bettina M Pucher
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Ave, Boston MA 02115, USA
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
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61
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Mihalik A, Ferreira FS, Moutoussis M, Ziegler G, Adams RA, Rosa MJ, Prabhu G, de Oliveira L, Pereira M, Bullmore ET, Fonagy P, Goodyer IM, Jones PB, Shawe-Taylor J, Dolan R, Mourão-Miranda J. Multiple Holdouts With Stability: Improving the Generalizability of Machine Learning Analyses of Brain-Behavior Relationships. Biol Psychiatry 2020; 87:368-376. [PMID: 32040421 PMCID: PMC6970221 DOI: 10.1016/j.biopsych.2019.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND In 2009, the National Institute of Mental Health launched the Research Domain Criteria, an attempt to move beyond diagnostic categories and ground psychiatry within neurobiological constructs that combine different levels of measures (e.g., brain imaging and behavior). Statistical methods that can integrate such multimodal data, however, are often vulnerable to overfitting, poor generalization, and difficulties in interpreting the results. METHODS We propose an innovative machine learning framework combining multiple holdouts and a stability criterion with regularized multivariate techniques, such as sparse partial least squares and kernel canonical correlation analysis, for identifying hidden dimensions of cross-modality relationships. To illustrate the approach, we investigated structural brain-behavior associations in an extensively phenotyped developmental sample of 345 participants (312 healthy and 33 with clinical depression). The brain data consisted of whole-brain voxel-based gray matter volumes, and the behavioral data included item-level self-report questionnaires and IQ and demographic measures. RESULTS Both sparse partial least squares and kernel canonical correlation analysis captured two hidden dimensions of brain-behavior relationships: one related to age and drinking and the other one related to depression. The applied machine learning framework indicates that these results are stable and generalize well to new data. Indeed, the identified brain-behavior associations are in agreement with previous findings in the literature concerning age, alcohol use, and depression-related changes in brain volume. CONCLUSIONS Multivariate techniques (such as sparse partial least squares and kernel canonical correlation analysis) embedded in our novel framework are promising tools to link behavior and/or symptoms to neurobiology and thus have great potential to contribute to a biologically grounded definition of psychiatric disorders.
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Affiliation(s)
- Agoston Mihalik
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom; Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom.
| | - Fabio S. Ferreira
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom,Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom
| | - Michael Moutoussis
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom,Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom
| | - Gabriel Ziegler
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom,Institute of Cognitive Neurology and Dementia Research, Otto von Guericke University, Magdeburg, Magdeburg, Germany,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Rick A. Adams
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom,Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom,Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom
| | - Maria J. Rosa
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom,Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom
| | - Gita Prabhu
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom,Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom
| | - Leticia de Oliveira
- Laboratory of Neurophysiology of Behaviour, Department of Physiology and Pharmacology, Biomedical Institute, Federal Fluminense University, Niterói, Brazil
| | - Mirtes Pereira
- Laboratory of Neurophysiology of Behaviour, Department of Physiology and Pharmacology, Biomedical Institute, Federal Fluminense University, Niterói, Brazil
| | - Edward T. Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom,Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge, United Kingdom,Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, United Kingdom,ImmunoPsychiatry, GlaxoSmithKline Research and Development, Stevenage, United Kingdom
| | - Peter Fonagy
- Research Department of Clinical, Educational, and Health Psychology, University College London, London, United Kingdom
| | - Ian M. Goodyer
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom,Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, United Kingdom
| | - Peter B. Jones
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom,Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, United Kingdom
| | | | - John Shawe-Taylor
- Department of Computer Science, University College London, London, United Kingdom
| | - Raymond Dolan
- Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom,Wellcome Centre for Human Neuroimaging, University College London, London, United Kingdom
| | - Janaina Mourão-Miranda
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, United Kingdom,Max Planck University College London Centre for Computational Psychiatry and Ageing Research, University College London, London, United Kingdom
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Fan Z, Zhou Y, Ressom HW. MOTA: Multi-omic integrative analysis for biomarker discovery. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:243-247. [PMID: 31945887 DOI: 10.1109/embc.2019.8857049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent advancement of omic technologies provides researchers with opportunities to search for disease biomarkers at the systems level. However, selection of biomarker candidates from a large number of molecules involved at various layers of the biological system is challenging. In this paper, we propose multi-omic integrative analysis (MOTA), a network-based method that uses information from multi-omic data to identify candidate disease biomarkers. We evaluated the performance of MOTA in selecting disease-associated molecules from four sets of multi-omic data representing three cohorts of hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. The results demonstrate that MOTA leads to selection of more biomarker candidates that shared by two different cohorts compared to traditional statistical methods. Also, the networks constructed by MOTA allow users to investigate biological significance of the selected biomarker candidates.
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63
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Moroldo M, Munyaka PM, Lecardonnel J, Lemonnier G, Venturi E, Chevaleyre C, Oswald IP, Estellé J, Rogel-Gaillard C. Integrative analysis of blood and gut microbiota data suggests a non-alcoholic fatty liver disease (NAFLD)-related disorder in French SLA dd minipigs. Sci Rep 2020; 10:234. [PMID: 31937803 PMCID: PMC6959234 DOI: 10.1038/s41598-019-57127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
Minipigs are a group of small-sized swine lines, which show a broad range of phenotype variation and which often tend to be obese. The SLAdd (DD) minipig line was created by the NIH and selected as homozygous at the SLA locus. It was brought to France more than 30 years ago and maintained inbred ever since. In this report, we characterized the physiological status of a herd of French DD pigs by measuring intermediate phenotypes from blood and faeces and by using Large White (LW) pigs as controls. Three datasets were produced, i.e. complete blood counts (CBCs), microarray-based blood transcriptome, and faecal microbiota obtained by 16S rRNA sequencing. CBCs and expression profiles suggested a non-alcoholic fatty liver disease (NAFLD)-related pathology associated to comorbid cardiac diseases. The characterization of 16S sequencing data was less straightforward, suggesting only a potential weak link to obesity. The integration of the datasets identified several fine-scale associations between CBCs, gene expression, and faecal microbiota composition. NAFLD is a common cause of chronic liver disease in Western countries and is linked to obesity, type 2 diabetes mellitus and cardiac pathologies. Here we show that the French DD herd is potentially affected by this syndrome.
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Affiliation(s)
- Marco Moroldo
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Peris Mumbi Munyaka
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Jérôme Lecardonnel
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gaëtan Lemonnier
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | | | - Isabelle P Oswald
- Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toxalim, 31027, Toulouse, France
| | - Jordi Estellé
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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Min EJ, Safo SE, Long Q. Penalized co-inertia analysis with applications to -omics data. Bioinformatics 2019; 35:1018-1025. [PMID: 30165424 DOI: 10.1093/bioinformatics/bty726] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/01/2018] [Accepted: 08/23/2018] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Co-inertia analysis (CIA) is a multivariate statistical analysis method that can assess relationships and trends in two sets of data. Recently CIA has been used for an integrative analysis of multiple high-dimensional omics data. However, for classical CIA, all elements in the loading vectors are nonzero, presenting a challenge for the interpretation when analyzing omics data. For other multivariate statistical methods such as canonical correlation analysis (CCA), penalized least squares (PLS), various approaches have been proposed to produce sparse loading vectors via l1-penalization/constraint. We propose a novel CIA method that uses l1-penalization to induce sparsity in estimators of loading vectors. Our method simultaneously conducts model fitting and variable selection. Also, we propose another CIA method that incorporates structure/network information such as those from functional genomics, besides using sparsity penalty so that one can get biologically meaningful and interpretable results. RESULTS Extensive simulations demonstrate that our proposed penalized CIA methods achieve the best or close to the best performance compared to the existing CIA method in terms of feature selection and recovery of true loading vectors. Also, we apply our methods to the integrative analysis of gene expression data and protein abundance data from the NCI-60 cancer cell lines. Our analysis of the NCI-60 cancer cell line data reveals meaningful variables for cancer diseases and biologically meaningful results that are consistent with previous studies. AVAILABILITY AND IMPLEMENTATION Our algorithms are implemented as an R package which is freely available at: https://www.med.upenn.edu/long-lab/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Eun Jeong Min
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sandra E Safo
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
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Bruffaerts R, Schaeverbeke J, De Weer AS, Nelissen N, Dries E, Van Bouwel K, Sieben A, Bergmans B, Swinnen C, Pijnenburg Y, Sunaert S, Vandenbulcke M, Vandenberghe R. Multivariate analysis reveals anatomical correlates of naming errors in primary progressive aphasia. Neurobiol Aging 2019; 88:71-82. [PMID: 31955981 DOI: 10.1016/j.neurobiolaging.2019.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/10/2019] [Accepted: 12/15/2019] [Indexed: 12/30/2022]
Abstract
Primary progressive aphasia (PPA) is an overarching term for a heterogeneous group of neurodegenerative diseases which affect language processing. Impaired picture naming has been linked to atrophy of the anterior temporal lobe in the semantic variant of PPA. Although atrophy of the anterior temporal lobe proposedly impairs picture naming by undermining access to semantic knowledge, picture naming also entails object recognition and lexical retrieval. Using multivariate analysis, we investigated whether cortical atrophy relates to different types of naming errors generated during picture naming in 43 PPA patients (13 semantic, 9 logopenic, 11 nonfluent, and 10 mixed variant). Omissions were associated with atrophy of the anterior temporal lobes. Semantic errors, for example, mistaking a rhinoceros for a hippopotamus, were associated with atrophy of the left mid and posterior fusiform cortex and the posterior middle and inferior temporal gyrus. Semantic errors and atrophy in these regions occurred in each PPA subtype, without major between-subtype differences. We propose that pathological changes to neural mechanisms associated with semantic errors occur across the PPA spectrum.
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Affiliation(s)
- Rose Bruffaerts
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium; Neurology Department, University Hospitals Leuven, Leuven, Belgium.
| | - Jolien Schaeverbeke
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - An-Sofie De Weer
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Natalie Nelissen
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Eva Dries
- Neurology Department, University Hospitals Leuven, Leuven, Belgium
| | - Karen Van Bouwel
- Neurology Department, University Hospitals Leuven, Leuven, Belgium
| | - Anne Sieben
- Neurology Department, University Hospital Ghent, Ghent, Belgium
| | - Bruno Bergmans
- Neurology Department, University Hospital Ghent, Ghent, Belgium; Neurology Department, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | | | - Yolande Pijnenburg
- Neurology Department, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Stefan Sunaert
- Radiology Department, University Hospitals Leuven, Leuven, Belgium
| | | | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, KU Leuven, Leuven, Belgium; Neurology Department, University Hospitals Leuven, Leuven, Belgium
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Chamcha V, Reddy PBJ, Kannanganat S, Wilkins C, Gangadhara S, Velu V, Green R, Law GL, Chang J, Bowen JR, Kozlowski PA, Lifton M, Santra S, Legere T, Chea LS, Chennareddi L, Yu T, Suthar MS, Silvestri G, Derdeyn CA, Gale M, Villinger F, Hunter E, Amara RR. Strong T H1-biased CD4 T cell responses are associated with diminished SIV vaccine efficacy. Sci Transl Med 2019; 11:eaav1800. [PMID: 31748228 PMCID: PMC7227795 DOI: 10.1126/scitranslmed.aav1800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/07/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022]
Abstract
Activated CD4 T cells are a major target of HIV infection. Results from the STEP HIV vaccine trial highlighted a potential role for total activated CD4 T cells in promoting HIV acquisition. However, the influence of vaccine insert-specific CD4 T cell responses on HIV acquisition is not known. Here, using the data obtained from four macaque studies, we show that the DNA prime/modified vaccinia Ankara boost vaccine induced interferon γ (IFNγ+) CD4 T cells [T helper 1 (TH1) cells] rapidly migrate to multiple tissues including colon, cervix, and vaginal mucosa. These mucosal TH1 cells persisted at higher frequencies and expressed higher density of CCR5, a viral coreceptor, compared to cells in blood. After intravaginal or intrarectal simian immunodeficiency virus (SIV)/simian-human immunodeficiency virus (SHIV) challenges, strong vaccine protection was evident only in animals that had lower frequencies of vaccine-specific TH1 cells but not in animals that had higher frequencies of TH1 cells, despite comparable vaccine-induced humoral and CD8 T cell immunity in both groups. An RNA transcriptome signature in blood at 7 days after priming immunization from one study was associated with induction of fewer TH1-type CD4 cells and enhanced protection. These results demonstrate that high and persisting frequencies of HIV vaccine-induced TH1-biased CD4 T cells in the intestinal and genital mucosa can mitigate beneficial effects of protective antibodies and CD8 T cells, highlighting a critical role of priming immunization and vaccine adjuvants in modulating HIV vaccine efficacy.
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Affiliation(s)
- Venkateswarlu Chamcha
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Pradeep B J Reddy
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sunil Kannanganat
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Courtney Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Vijayakumar Velu
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - G Lynn Law
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Jean Chang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - James R Bowen
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lifton
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Sampa Santra
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Traci Legere
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Lynette S Chea
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Lakshmi Chennareddi
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Francois Villinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
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Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. AN INTERNATIONAL JOURNAL ON INFORMATION FUSION 2019; 50:71-91. [PMID: 30467459 PMCID: PMC6242341 DOI: 10.1016/j.inffus.2018.09.012] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include myriad properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of all the factors relevant to understanding a phenomenon such as a disease. Integrative methods that combine data from multiple technologies have thus emerged as critical statistical and computational approaches. The key challenge in developing such approaches is the identification of effective models to provide a comprehensive and relevant systems view. An ideal method can answer a biological or medical question, identifying important features and predicting outcomes, by harnessing heterogeneous data across several dimensions of biological variation. In this Review, we describe the principles of data integration and discuss current methods and available implementations. We provide examples of successful data integration in biology and medicine. Finally, we discuss current challenges in biomedical integrative methods and our perspective on the future development of the field.
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Affiliation(s)
- Marinka Zitnik
- Department of Computer Science, Stanford University,
Stanford, CA, USA
| | - Francis Nguyen
- Department of Medical Biophysics, University of Toronto,
Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Bo Wang
- Hikvision Research Institute, Santa Clara, CA, USA
| | - Jure Leskovec
- Department of Computer Science, Stanford University,
Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Anna Goldenberg
- Genetics & Genome Biology, SickKids Research Institute,
Toronto, ON, Canada
- Department of Computer Science, University of Toronto,
Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Michael M. Hoffman
- Department of Medical Biophysics, University of Toronto,
Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Computer Science, University of Toronto,
Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
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68
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Wani N, Raza K. Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods. Comput Biol Chem 2019; 83:107120. [PMID: 31499298 DOI: 10.1016/j.compbiolchem.2019.107120] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/22/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data. These data have different types (discrete, real, string, etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data (copy number variation, single nucleotide polymorphisms), annotations, interactions, and association data are some of the commonly used biological datasets to study various cellular mechanisms of living organisms. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about the regulatory mechanisms of genes and their products. Therefore, integrating these data and inferring regulatory interactions from them offer a system level of biological insight in predicting gene functions and their phenotypic outcomes. To study genome functionality through regulatory networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here integration methods that reconstruct regulatory networks using state-of-the-art techniques to handle multi-omics (i.e., genomic, transcriptomic, proteomic) and other biological datasets.
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Affiliation(s)
- Nisar Wani
- Govt. Degree College Baramulla, J & K, India; Department of Computer Science, jamia Milia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, jamia Milia Islamia, New Delhi, India.
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69
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Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CAD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest 2019; 129:3792-3806. [PMID: 31403473 DOI: 10.1172/jci126905] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.
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Affiliation(s)
- John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William H Weir
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jan R Crowley
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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Meng C, Basunia A, Peters B, Gholami AM, Kuster B, Culhane AC. MOGSA: Integrative Single Sample Gene-set Analysis of Multiple Omics Data. Mol Cell Proteomics 2019; 18:S153-S168. [PMID: 31243065 PMCID: PMC6692785 DOI: 10.1074/mcp.tir118.001251] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/26/2019] [Indexed: 11/15/2022] Open
Abstract
Gene-set analysis (GSA) summarizes individual molecular measurements to more interpretable pathways or gene-sets and has become an indispensable step in the interpretation of large-scale omics data. However, GSA methods are limited to the analysis of single omics data. Here, we introduce a new computation method termed multi-omics gene-set analysis (MOGSA), a multivariate single sample gene-set analysis method that integrates multiple experimental and molecular data types measured over the same set of samples. The method learns a low dimensional representation of most variant correlated features (genes, proteins, etc.) across multiple omics data sets, transforms the features onto the same scale and calculates an integrated gene-set score from the most informative features in each data type. MOGSA does not require filtering data to the intersection of features (gene IDs), therefore, all molecular features, including those that lack annotation may be included in the analysis. Using simulated data, we demonstrate that integrating multiple diverse sources of molecular data increases the power to discover subtle changes in gene-sets and may reduce the impact of unreliable information in any single data type. Using real experimental data, we demonstrate three use-cases of MOGSA. First, we show how to remove a source of noise (technical or biological) in integrative MOGSA of NCI60 transcriptome and proteome data. Second, we apply MOGSA to discover similarities and differences in mRNA, protein and phosphorylation profiles of a small study of stem cell lines and assess the influence of each data type or feature on the total gene-set score. Finally, we apply MOGSA to cluster analysis and show that three molecular subtypes are robustly discovered when copy number variation and mRNA data of 308 bladder cancers from The Cancer Genome Atlas are integrated using MOGSA. MOGSA is available in the Bioconductor R package "mogsa."
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Affiliation(s)
- Chen Meng
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany
| | - Azfar Basunia
- Department of Data Science, Division of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California 92037
| | - Amin Moghaddas Gholami
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany.
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany.
| | - Aedín C Culhane
- Department of Data Science, Division of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215.
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Kiros TG, Luise D, Derakhshani H, Petri R, Trevisi P, D’Inca R, Auclair E, van Kessel AG. Effect of live yeast Saccharomyces cerevisiae supplementation on the performance and cecum microbial profile of suckling piglets. PLoS One 2019; 14:e0219557. [PMID: 31329605 PMCID: PMC6645501 DOI: 10.1371/journal.pone.0219557] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/26/2019] [Indexed: 12/13/2022] Open
Abstract
One mechanism through which S. cerevisiae may improve the performance of pigs is by altering the composition of the gut microbiota, a response that may be enhanced by early postnatal supplementation of probiotics. To test this hypothesis, newborn piglets (16 piglets/group) were treated with either S. cerevisiae yeast (5 x 109 cfu/pig: Low) or (2.5 x 1010 cfu/piglet: High) or equivalent volume of sterile water (Control) by oral gavage every other day starting from day 1 of age until weaning (28±1 days of age). Piglet body weight was recorded on days 1, 3, 7, 10, 17, 24 and 28 and average daily gain (ADG) calculated for the total period. At weaning, piglets were euthanized to collect cecum content for microbial profiling by sequencing of the 16S rRNA gene. ADG was higher in both Low and High yeast groups than in Control group (P<0.05). Alpha diversity analyses indicated a more diverse microbiota in the Control group compared with Low yeast group; the High yeast being intermediate (P < 0.01). Similarly, Beta diversity analyses indicated differences among treatments (P = 0.03), mainly between Low yeast and Control groups (P = 0.02). The sparse Partial Least Squares Discriminant Analysis (sPLS-DA) indicated that Control group was discriminated by a higher abundance of Veillonella, Dorea, Oscillospira and Clostridium; Low yeast treated pigs by higher Blautia, Collinsella and Eubacterium; and High yeast treated pigs by higher Eubacterium, Anaerostipes, Parabacteroides, Mogibacterium and Phascolarctobacterium. Partial Least Squares (PLS) analysis showed that piglet ADG was positively correlated with genus Prevotella in High yeast group. Yeast supplementation significantly affected microbial diversity in cecal contents of suckling piglets associated with an improvement of short chain fatty acid producing bacteria in a dose-dependent manner. In conclusion, yeast treatment improved piglet performance and shaped the piglet cecum microbiota composition in a dose dependent way.
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Affiliation(s)
- Tadele G. Kiros
- University of Saskatchewan, Department of Animal and Poultry Science, Saskatoon, Saskatchewan, Canada
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Hooman Derakhshani
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Renee Petri
- University of Saskatchewan, Department of Animal and Poultry Science, Saskatoon, Saskatchewan, Canada
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Romain D’Inca
- Phileo-Lesaffre Animal Care, Marcq-en-Baroeul, France
| | - Eric Auclair
- Phileo-Lesaffre Animal Care, Marcq-en-Baroeul, France
| | - Andrew G. van Kessel
- University of Saskatchewan, Department of Animal and Poultry Science, Saskatoon, Saskatchewan, Canada
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Rappoport N, Shamir R. Multi-omic and multi-view clustering algorithms: review and cancer benchmark. Nucleic Acids Res 2019; 46:10546-10562. [PMID: 30295871 PMCID: PMC6237755 DOI: 10.1093/nar/gky889] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022] Open
Abstract
Recent high throughput experimental methods have been used to collect large biomedical omics datasets. Clustering of single omic datasets has proven invaluable for biological and medical research. The decreasing cost and development of additional high throughput methods now enable measurement of multi-omic data. Clustering multi-omic data has the potential to reveal further systems-level insights, but raises computational and biological challenges. Here, we review algorithms for multi-omics clustering, and discuss key issues in applying these algorithms. Our review covers methods developed specifically for omic data as well as generic multi-view methods developed in the machine learning community for joint clustering of multiple data types. In addition, using cancer data from TCGA, we perform an extensive benchmark spanning ten different cancer types, providing the first systematic comparison of leading multi-omics and multi-view clustering algorithms. The results highlight key issues regarding the use of single- versus multi-omics, the choice of clustering strategy, the power of generic multi-view methods and the use of approximated p-values for gauging solution quality. Due to the growing use of multi-omics data, we expect these issues to be important for future progress in the field.
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Affiliation(s)
- Nimrod Rappoport
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
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73
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Bancel E, Bonnot T, Davanture M, Alvarez D, Zivy M, Martre P, Déjean S, Ravel C. Proteomic Data Integration Highlights Central Actors Involved in Einkorn ( Triticum monococcum ssp. monococcum) Grain Filling in Relation to Grain Storage Protein Composition. FRONTIERS IN PLANT SCIENCE 2019; 10:832. [PMID: 31333693 PMCID: PMC6620720 DOI: 10.3389/fpls.2019.00832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/07/2019] [Indexed: 06/10/2023]
Abstract
Albumins and globulins (AGs) of wheat endosperm represent about 20% of total grain proteins. Some of these physiologically active proteins can influence the synthesis of storage proteins (SPs) (gliadins and glutenins) and consequently, rheological properties of wheat flour and processing. To identify such AGs, data, (published by Bonnot et al., 2017) concerning abundance in 352 AGs and in the different seed SPs during grain filling and in response to different nitrogen (N) and sulfur (S) supply, were integrated with mixOmics R package. Relationships between AGs and SPs were first unraveled using the unsupervised method sparse Partial Least Square, also known as Projection to Latent Structure (sPLS). Then, data were integrated using a supervised approach taking into account the nutrition and the grain developmental stage. We used the block.splda procedure also referred to as DIABLO (Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies). These approaches led to the identification of discriminant and highly correlated features from the two datasets (AGs and SPs) which are not necessarily differentially expressed during seed development or in response to N or S supply. Eighteen AGs were correlated with the quantity of SPs per grain. A statistical validation of these proteins by genetic association analysis confirmed that 5 out of this AG set were robust candidate proteins able to modulate the seed SP synthesis. In conclusion, this latter result confirmed that the integrative strategy is an adequate way to reduce the number of potentially relevant AGs for further functional validation.
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Affiliation(s)
- Emmanuelle Bancel
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Titouan Bonnot
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Marlène Davanture
- UMR GQE, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Agro ParisTech, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, France
| | - David Alvarez
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Michel Zivy
- UMR GQE, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Agro ParisTech, Université Paris-Sud – Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Martre
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219 Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Toulouse, France
| | - Catherine Ravel
- UMR GDEC, Institut National de la Recherche Agronomique (INRA), Université Clermont Auvergne, Clermont-Ferrand, France
- UMR1095, Genetics Diversity and Ecophysiology of Cereals, Clermont Auvergne University, Clermont-Ferrand, France
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74
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Consumption of transglycosylated starch down-regulates expression of mucosal innate immune response genes in the large intestine using a pig model. Br J Nutr 2019; 119:1366-1377. [PMID: 29845906 DOI: 10.1017/s0007114518001113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Benefits of resistant starch (RS) consumption on host physiology encompass microbial activity-derived attenuation of intestinal inflammation. However, little is known about anti-inflammatory properties of RS of type 4. This study compared the effects of transglycosylated starch (TGS) consumption on the jejunal barrier function and expression of genes related to inflammation, barrier function and the mucosal defence in jejunum, ileum, caecum and colon of pigs. Moreover, interactions of TGS-induced alterations in bacterial metabolites and composition with host mucosal responses were assessed using sparse partial least squares regression and relevance network analysis. Intestinal samples were collected after pigs (n 8/diet; 4 months of age) were fed the experimental diets for 10 d. Consumption of TGS did not modify jejunal barrier function and gene expression. By contrast, TGS down-regulated the caecal expression of zonula occludens-1 and mucin 2 and of genes within the toll-like receptor 4 and NF-κB pro-inflammatory signalling cascade. Relevance networks revealed a microbiome signature on ileal, caecal and colonic mucosal signalling as TGS-derived changes in bacterial genera and fermentation acids, such as propionic acid, correlated with the differently expressed genes in ileum, caecum and colon of pigs. In conclusion, the present findings suggest certain anti-inflammatory capabilities of TGS by down-regulating the expression of pro-inflammatory pathways in the caecal mucosa, which seems to be mediated, at least in part, by TGS-induced changes in microbial action in the large intestine.
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75
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Mai Q, Zhang X. An iterative penalized least squares approach to sparse canonical correlation analysis. Biometrics 2019; 75:734-744. [PMID: 30714093 DOI: 10.1111/biom.13043] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/29/2019] [Indexed: 11/30/2022]
Abstract
It is increasingly interesting to model the relationship between two sets of high-dimensional measurements with potentially high correlations. Canonical correlation analysis (CCA) is a classical tool that explores the dependency of two multivariate random variables and extracts canonical pairs of highly correlated linear combinations. Driven by applications in genomics, text mining, and imaging research, among others, many recent studies generalize CCA to high-dimensional settings. However, most of them either rely on strong assumptions on covariance matrices, or do not produce nested solutions. We propose a new sparse CCA (SCCA) method that recasts high-dimensional CCA as an iterative penalized least squares problem. Thanks to the new iterative penalized least squares formulation, our method directly estimates the sparse CCA directions with efficient algorithms. Therefore, in contrast to some existing methods, the new SCCA does not impose any sparsity assumptions on the covariance matrices. The proposed SCCA is also very flexible in the sense that it can be easily combined with properly chosen penalty functions to perform structured variable selection and incorporate prior information. Moreover, our proposal of SCCA produces nested solutions and thus provides great convenient in practice. Theoretical results show that SCCA can consistently estimate the true canonical pairs with an overwhelming probability in ultra-high dimensions. Numerical results also demonstrate the competitive performance of SCCA.
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Affiliation(s)
- Qing Mai
- Department of Statistics, Florida State University, Tallahassee, Florida
| | - Xin Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida
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76
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Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae. Vaccine 2019; 37:1743-1755. [PMID: 30808565 DOI: 10.1016/j.vaccine.2019.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
We investigated gene expression patterns in whole blood and fecal microbiota profile as potential predictors of immune response to vaccination, using healthy M. hyopneumoniae infection free piglets (n = 120). Eighty piglets received a dose of prophylactic antibiotics during the first two days of life, whereas the remaining 40 did not. Blood samples for RNA-Seq analysis were collected on experimental Day 0 (D0; 28 days of age) just prior to vaccination, D2, and D6 post-vaccination. A booster vaccine was given at D24. Fecal samples for microbial 16SrRNA sequencing were collected at 7 days of age, and at D0 and D35 post-vaccination. Pigs were ranked based on the levels of M. hyopneumoniae-specific antibodies in serum samples collected at D35, and groups of 'high' (HR) and 'low' (LR) responder pigs (n = 15 each) were selected. Prophylactic antibiotics did not influence antibody titer levels and differential expression analysis did not reveal differences between HR and LR at any time-point (FDR > 0.05); however, based on functional annotation with Ingenuity Pathway Analysis, D2 post-vaccination, HR pigs were enriched for biological terms relating to increased activation of immune cells. In contrast, the immune activation decreased in HR, 6 days post-vaccination. No significant differences were observed prior to vaccination (D0). Two days post-vaccination, multivariate analysis revealed that ADAM8, PROSER3, B4GALNT1, MAP7D1, SPP1, HTRA4, and ENO3 genes were the most promising potential biomarkers. At D0, OTUs annotated to Prevotella, CF21, Bacteroidales and S24-7 were more abundant in HR, whereas Fibrobacter, Paraprevotella, Anaerovibrio, [Prevotella], YRC22, and Helicobacter positively correlated with the antibody titer as well as MYL1, SPP1, and ENO3 genes. Our study integrates gene differential expression and gut microbiota to predict vaccine response in pigs. The results indicate that post-vaccination gene-expression and early-life gut microbiota profile could potentially predict vaccine response in pigs, and inform a direction for future research.
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77
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Sovran B, Hugenholtz F, Elderman M, Van Beek AA, Graversen K, Huijskes M, Boekschoten MV, Savelkoul HFJ, De Vos P, Dekker J, Wells JM. Age-associated Impairment of the Mucus Barrier Function is Associated with Profound Changes in Microbiota and Immunity. Sci Rep 2019; 9:1437. [PMID: 30723224 PMCID: PMC6363726 DOI: 10.1038/s41598-018-35228-3] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Aging significantly increases the vulnerability to gastrointestinal (GI) disorders but there are few studies investigating the key factors in aging that affect the GI tract. To address this knowledge gap, we used 10-week- and 19-month-old litter-mate mice to investigate microbiota and host gene expression changes in association with ageing. In aged mice the thickness of the colonic mucus layer was reduced about 6-fold relative to young mice, and more easily penetrable by luminal bacteria. This was linked to increased apoptosis of goblet cells in the upper part of the crypts. The barrier function of the small intestinal mucus was also compromised and the microbiota were frequently observed in contact with the villus epithelium. Antimicrobial Paneth cell factors Ang4 and lysozyme were expressed in significantly reduced amounts. These barrier defects were accompanied by major changes in the faecal microbiota and significantly decreased abundance of Akkermansia muciniphila which is strongly and negatively affected by old age in humans. Transcriptomics revealed age-associated decreases in the expression of immunity and other genes in intestinal mucosal tissue, including decreased T cell-specific transcripts and T cell signalling pathways. The physiological and immunological changes we observed in the intestine in old age, could have major consequences beyond the gut.
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Affiliation(s)
- Bruno Sovran
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Cell Biology and Immunology Group, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Marlies Elderman
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Adriaan A Van Beek
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Cell Biology and Immunology Group, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Katrine Graversen
- Host-Microbe Interactomics Group, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Myrte Huijskes
- Host-Microbe Interactomics Group, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Mark V Boekschoten
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Division of Human Nutrition, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Huub F J Savelkoul
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Cell Biology and Immunology Group, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Paul De Vos
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Dekker
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Host-Microbe Interactomics Group, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Jerry M Wells
- Top Institute Food and Nutrition, Wageningen, The Netherlands. .,Host-Microbe Interactomics Group, Wageningen University and Research Center, Wageningen, The Netherlands.
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78
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Wu C, Zhou F, Ren J, Li X, Jiang Y, Ma S. A Selective Review of Multi-Level Omics Data Integration Using Variable Selection. High Throughput 2019; 8:E4. [PMID: 30669303 PMCID: PMC6473252 DOI: 10.3390/ht8010004] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 01/02/2023] Open
Abstract
High-throughput technologies have been used to generate a large amount of omics data. In the past, single-level analysis has been extensively conducted where the omics measurements at different levels, including mRNA, microRNA, CNV and DNA methylation, are analyzed separately. As the molecular complexity of disease etiology exists at all different levels, integrative analysis offers an effective way to borrow strength across multi-level omics data and can be more powerful than single level analysis. In this article, we focus on reviewing existing multi-omics integration studies by paying special attention to variable selection methods. We first summarize published reviews on integrating multi-level omics data. Next, after a brief overview on variable selection methods, we review existing supervised, semi-supervised and unsupervised integrative analyses within parallel and hierarchical integration studies, respectively. The strength and limitations of the methods are discussed in detail. No existing integration method can dominate the rest. The computation aspects are also investigated. The review concludes with possible limitations and future directions for multi-level omics data integration.
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Affiliation(s)
- Cen Wu
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA.
| | - Fei Zhou
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA.
| | - Jie Ren
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA.
| | - Xiaoxi Li
- Department of Statistics, Kansas State University, Manhattan, KS 66506, USA.
| | - Yu Jiang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA.
| | - Shuangge Ma
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT 06510, USA.
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79
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Perakakis N, Yazdani A, Karniadakis GE, Mantzoros C. Omics, big data and machine learning as tools to propel understanding of biological mechanisms and to discover novel diagnostics and therapeutics. Metabolism 2018; 87:A1-A9. [PMID: 30098323 PMCID: PMC6325641 DOI: 10.1016/j.metabol.2018.08.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Nikolaos Perakakis
- Department of Endocrinology, VA Boston Healthcare System, Jamaica Plain, Boston, MA 02130, USA; Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Alireza Yazdani
- Division of Applied Mathematics, Brown University, Providence, RI 02906, USA
| | | | - Christos Mantzoros
- Department of Endocrinology, VA Boston Healthcare System, Jamaica Plain, Boston, MA 02130, USA; Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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80
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Kang K, Kwak K, Yoon U, Lee JM. Lateral Ventricle Enlargement and Cortical Thinning in Idiopathic Normal-pressure Hydrocephalus Patients. Sci Rep 2018; 8:13306. [PMID: 30190599 PMCID: PMC6127145 DOI: 10.1038/s41598-018-31399-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/14/2018] [Indexed: 01/26/2023] Open
Abstract
We utilized three-dimensional, surface-based, morphometric analysis to investigate ventricle shape between 2 groups: (1) idiopathic normal-pressure hydrocephalus (INPH) patients who had a positive response to the cerebrospinal fluid tap test (CSFTT) and (2) healthy controls. The aims were (1) to evaluate the location of INPH-related structural abnormalities of the lateral ventricles and (2) to investigate relationships between lateral ventricular enlargement and cortical thinning in INPH patients. Thirty-three INPH patients and 23 healthy controls were included in this study. We used sparse canonical correlation analysis to show correlated regions of ventricular surface expansion and cortical thinning. Significant surface expansion in the INPH group was observed mainly in clusters bilaterally located in the superior portion of the lateral ventricles, adjacent to the high convexity of the frontal and parietal regions. INPH patients showed a significant bilateral expansion of both the temporal horns of the lateral ventricles and the medial aspects of the frontal horns of the lateral ventricles to surrounding brain regions, including the medial frontal lobe. Ventricular surface expansion was associated with cortical thinning in the bilateral orbitofrontal cortex, bilateral rostral anterior cingulate cortex, left parahippocampal cortex, left temporal pole, right insula, right inferior temporal cortex, and right fusiform gyrus. These results suggest that patients with INPH have unique patterns of ventricular surface expansion. Our findings encourage future studies to elucidate the underlying mechanism of lateral ventricular morphometric abnormalities in INPH patients.
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Affiliation(s)
- Kyunghun Kang
- Department of Biomedical Engineering, Hanyang University, Seoul, South Korea.,Department of Neurology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Kichang Kwak
- McGill Centre for Integrative Neuroscience, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Uicheul Yoon
- Department of Biomedical Engineering, Daegu Catholic University, Gyeongsan-si, South Korea
| | - Jong-Min Lee
- Department of Biomedical Engineering, Hanyang University, Seoul, South Korea.
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81
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Gossmann A, Zille P, Calhoun V, Wang YP. FDR-Corrected Sparse Canonical Correlation Analysis With Applications to Imaging Genomics. IEEE TRANSACTIONS ON MEDICAL IMAGING 2018; 37:1761-1774. [PMID: 29993802 DOI: 10.1109/tmi.2018.2815583] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Reducing the number of false discoveries is presently one of the most pressing issues in the life sciences. It is of especially great importance for many applications in neuroimaging and genomics, where data sets are typically high-dimensional, which means that the number of explanatory variables exceeds the sample size. The false discovery rate (FDR) is a criterion that can be employed to address that issue. Thus it has gained great popularity as a tool for testing multiple hypotheses. Canonical correlation analysis (CCA) is a statistical technique that is used to make sense of the cross-correlation of two sets of measurements collected on the same set of samples (e.g., brain imaging and genomic data for the same mental illness patients), and sparse CCA extends the classical method to high-dimensional settings. Here, we propose a way of applying the FDR concept to sparse CCA, and a method to control the FDR. The proposed FDR correction directly influences the sparsity of the solution, adapting it to the unknown true sparsity level. Theoretical derivation as well as simulation studies show that our procedure indeed keeps the FDR of the canonical vectors below a user-specified target level. We apply the proposed method to an imaging genomics data set from the Philadelphia Neurodevelopmental Cohort. Our results link the brain connectivity profiles derived from brain activity during an emotion identification task, as measured by functional magnetic resonance imaging, to the corresponding subjects' genomic data.
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82
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Kellingray L, Gall GL, Defernez M, Beales ILP, Franslem-Elumogo N, Narbad A. Microbial taxonomic and metabolic alterations during faecal microbiota transplantation to treat Clostridium difficile infection. J Infect 2018; 77:107-118. [PMID: 29746938 DOI: 10.1016/j.jinf.2018.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 02/08/2023]
Abstract
OBJECTIVES This study aimed to examine changes to the microbiota composition and metabolic profiles of seven patients with recurrent Clostridium difficile infection (rCDI), following treatment with faecal microbiota transplant (FMT). METHODS 16S rDNA sequencing and 1H NMR were performed on faecal samples from the patients (pre-, post-FMT, and follow-up) and the associated donor samples. Sparse partial-least-square analysis was used to identify correlations between the two datasets. RESULTS The patients' microbiota post-FMT tended to shift towards the donor microbiota, specifically through proportional increases of Bacteroides, Blautia, and Ruminococcus, and proportional decreases of Enterococcus, Escherichia, and Klebsiella. However, although cured of infection, one patient, who suffers from chronic alcohol abuse, retained the compositional characteristics of the pre-FMT microbiota. Following FMT, increased levels of short-chain fatty acids, particularly butyrate and acetate, were observed in all patients. Sparse partial-least-square analysis confirmed a positive correlation between butyrate and Bacteroides, Blautia, and Ruminococcus, with a negative correlation between butyrate and Klebsiella and Enterococcus. CONCLUSIONS Clear differences were observed in the microbiota composition and metabolic profiles between donors and rCDI patients, which were largely resolved in patients following FMT. Increased levels of butyrate appear to be a factor associated with resolution of rCDI.
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Affiliation(s)
- Lee Kellingray
- Gut Health and Microbiome Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK; NIHR Health Protection Research Unit in Gastrointestinal Infections, UK.
| | - Gwénaëlle Le Gall
- Analytical Sciences Unit, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK.
| | - Marianne Defernez
- Analytical Sciences Unit, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UA, UK.
| | - Ian L P Beales
- Gastroenterology, Norfolk and Norwich University Hospital, Norwich NR4 7UY, UK.
| | | | - Arjan Narbad
- Gut Health and Microbiome Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UA, UK; NIHR Health Protection Research Unit in Gastrointestinal Infections, UK.
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83
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Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife 2018; 7:37816. [PMID: 30039798 PMCID: PMC6085123 DOI: 10.7554/elife.37816] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 12/18/2022] Open
Abstract
The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated type 1 diabetes (T1D) development in male NOD mice. The single course had deep and persistent effects on the intestinal microbiome, leading to altered cecal, hepatic, and serum metabolites. The exposure elicited sex-specific effects on chromatin states in the ileum and liver and perturbed ileal gene expression, altering normal maturational patterns. The global signature changes included specific genes controlling both innate and adaptive immunity. Microbiome analysis revealed four taxa each that potentially protect against or accelerate T1D onset, that were linked in a network model to specific differences in ileal gene expression. This simplified animal model reveals multiple potential pathways to understand pathogenesis by which early-life gut microbiome perturbations alter a global suite of intestinal responses, contributing to the accelerated and enhanced T1D development.
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Affiliation(s)
- Xue-Song Zhang
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Jackie Li
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Kimberly A Krautkramer
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Michelle Badri
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Center for Data Science, New York University, New York, United States
| | - Thomas Battaglia
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Timothy C Borbet
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Hyunwook Koh
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Sandy Ng
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Rachel A Sibley
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Yuanyuan Li
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Wimal Pathmasiri
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Shawn Jindal
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Robin R Shields-Cutler
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Ben Hillmann
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Gabriel A Al-Ghalith
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Victoria E Ruiz
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Alexandra Livanos
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Angélique B van 't Wout
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Nabeetha Nagalingam
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Arlin B Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, United States
| | - Susan Jenkins Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Dan Knights
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - John M Denu
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Kelly V Ruggles
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, United States
| | - R Anthony Williamson
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Marcus Rauch
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Department of Microbiology, New York Uniersity Langone Medical Center, New York, United States
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84
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Changes in intestinal gene expression and microbiota composition during late pregnancy are mouse strain dependent. Sci Rep 2018; 8:10001. [PMID: 29968760 PMCID: PMC6030191 DOI: 10.1038/s41598-018-28292-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/20/2018] [Indexed: 12/12/2022] Open
Abstract
Hormones and placental factors are thought to underlie the maternal immunological changes during pregnancy. However, as several intestinal microbiota are linked to immune modulations, we hypothesized that the intestinal microbiota are altered during pregnancy in favor of species associated with pregnancy associated immune modulations. We studied the fecal microbiota composition (MITchip) and intestinal and peripheral immune cells (microarray and flow cytometry) in pregnant and non-pregnant C57BL/6 and BALB/c mice. Pregnancy influenced intestinal microbiota diversity and composition, however in a mouse strain dependent way. Pregnant BALB/c mice had, among others, a relative higher abundance of Lactobacillus paracasei et rel., Roseburia intestinalis et rel. and Eubacterium hallii et rel., as compared to non-pregnant BALB/c mice, while the microbiota composition in B6 mice hardly changed during pregnancy. Additionally, intestinal immunological pathways were changed during pregnancy, however again in a mouse strain dependent way. Correlations between various bacteria and immunological genes were observed. Our data do support a role for the microbiome in changing immune responses in pregnancy. However, other factors are also involved, such as for instance changes in SCFA or changes in sensitivity to bacteria, since although immunological changes are observed in B6 mice, hardly any changes in microbiota were found in this strain. Follow up studies are needed to study the exact relationship between these parameters.
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85
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Feng Q, Jiang M, Hannig J, Marron J. Angle-based joint and individual variation explained. J MULTIVARIATE ANAL 2018. [DOI: 10.1016/j.jmva.2018.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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86
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Elderman M, Hugenholtz F, Belzer C, Boekschoten M, van Beek A, de Haan B, Savelkoul H, de Vos P, Faas M. Sex and strain dependent differences in mucosal immunology and microbiota composition in mice. Biol Sex Differ 2018; 9:26. [PMID: 29914546 PMCID: PMC6006852 DOI: 10.1186/s13293-018-0186-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Abstract
Background A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a sex bias, suggesting sex differences in immune responses and in the intestinal microbiome. We hypothesized that sex differences in immune responses are associated with sex differences in microbiota composition. Methods Fecal microbiota composition (MITchip), mRNA expression in intestinal tissue (microarray), and immune cell populations in mesenteric lymph nodes (MLNs) were studied in male and female mice of two mouse strains (C57B1/6OlaHsd and Balb/cOlaHsd). Transcriptomics and microbiota data were combined to identify bacterial species which may potentially be related to sex-specific differences in intestinal immune related genes. Results We found clear sex differences in intestinal microbiota species, diversity, and richness in healthy mice. However, the nature of the sex effects appeared to be determined by the mouse strain as different bacterial species were enriched in males and females of the two strains. For example, Lactobacillus plantarum and Bacteroides distasonis were enriched in B6 females as compared to B6 males, while Bifidobacterium was enriched BALB/c females as compared to BALB/c males. The strain-dependent sex effects were also observed in the expression of immunological genes in the colon. We found that the abundance of various bacteria (e.g., Clostridium leptum et rel.) which were enriched in B6 females positively correlated with the expression of several genes (e.g., Il-2rb, Ccr3, and Cd80) which could be related to immunological functions, such as inflammatory responses and migration of leukocytes. The abundance of several bacteria (e.g., Faecalibacterium prausnitzii et rel. and Coprobacillus et rel.- Clostridium ramosum et rel.) which were enriched in BALB/c males positively correlated to the expression of several genes (e.g., Apoe, Il-1b, and Stat4) related to several immunological functions, such as proliferation and quantity of lymphocytes. The net result was the same, since both mouse strains showed similar sex induced differences in immune cell populations in the MLNs. Conclusions Our data suggests a correlation between microbiota and intestinal immune populations in a sex and strain-specific way. These findings may contribute to the development of more sex and genetic specific treatments for intestinal-related disorders. Electronic supplementary material The online version of this article (10.1186/s13293-018-0186-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marlies Elderman
- Top Institute Food and Nutrition, Wageningen, the Netherlands. .,Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, 9713, GZ, Groningen, the Netherlands.
| | - Floor Hugenholtz
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Laboratory of Microbiology, Wageningen University and Research, 6703, WE, Wageningen, the Netherlands
| | - Clara Belzer
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Laboratory of Microbiology, Wageningen University and Research, 6703, WE, Wageningen, the Netherlands
| | - Mark Boekschoten
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Division of Human Nutrition, Wageningen University and Research, 6703, WE, Wageningen, the Netherlands
| | - Adriaan van Beek
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Cell Biology and Immunology, Wageningen University and Research, 6708 WD, Wageningen, the Netherlands
| | - Bart de Haan
- Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, 9713, GZ, Groningen, the Netherlands
| | - Huub Savelkoul
- Cell Biology and Immunology, Wageningen University and Research, 6708 WD, Wageningen, the Netherlands
| | - Paul de Vos
- Top Institute Food and Nutrition, Wageningen, the Netherlands.,Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, 9713, GZ, Groningen, the Netherlands
| | - Marijke Faas
- Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Centre Groningen, 9713, GZ, Groningen, the Netherlands.,Department of Obstetrics and Gynecology, University of Groningen and University Medical Centre Groningen, 9713, GZ, Groningen, the Netherlands
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87
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Metzler-Zebeli BU, Lawlor PG, Magowan E, Zebeli Q. Interactions between metabolically active bacteria and host gene expression at the cecal mucosa in pigs of diverging feed efficiency. J Anim Sci 2018; 96:2249-2264. [PMID: 29746643 PMCID: PMC6095344 DOI: 10.1093/jas/sky118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/27/2018] [Indexed: 12/12/2022] Open
Abstract
Little is known about the role of the gut mucosal microbiota and microbe-host signaling in the variation of pig's feed efficiency (FE). This study therefore aimed to investigate the FE-related differences in the metabolically active mucosal bacterial microbiota and expression of genes for innate immune response, barrier function, nutrient uptake, and incretins in the cecum of finishing pigs. Pigs (n = 72) were ranked for their residual feed intake (RFI; metric for FE) between days 42 and 91 postweaning and were stratified within litter and sex into high (HRFI; n = 8) and low RFI (LRFI; n = 8). Cecal mucosa and digesta were collected on day 137-141 of life. After isolating total RNA from the mucosa, the RNA was transcribed into cDNA which was used for gene expression analysis, total bacterial quantification, and high-throughput sequencing (Illumina MiSeq) of the hypervariable V3-V4 region of the 16S rRNA gene. The RFI differed by 2.1 kg between low RFI (LRFI; good FE) and high RFI (HRFI; poor FE) pigs (P < 0.001). The cecal mucosa was mainly colonized by Helicobacteraceae, Campylobacteraceae, Veillonellaceae, Lachnospiraceae, and Prevotellaceae. Despite the lack of differences in microbial diversity and absolute abundance, RFI-associated compositional differences were found. The predominant genus Campylobacter tended (P < 0.10) to be 0.4-fold more abundant in LRFI pigs, whereas low abundant Escherichia/Shigella (P < 0.05), Ruminobacter (P < 0.05), and Veillonella (P < 0.10) were 3.4-, 6.6-, and 4.4-fold less abundant at the cecal mucosa of LRFI compared to HRFI pigs. Moreover, mucin 2 and zona occludens-1 were less expressed (P < 0.05) in the cecal mucosa of LRFI compared to HRFI pigs. Cecal mucosal expression of monocarboxylate transporter-1, glucagon-like peptide-1, and peptide YY further tended (P < 0.10) to be downregulated in LRFI compared to HRFI pigs, indicating an enhanced VFA uptake and signaling in HRFI pigs. Sparse partial least square regression and relevance networking support the hypothesis that certain mucosal bacteria and luminal microbial metabolites were more associated than others with differences in RFI and cecal gene expression. However, present results do not allow the determination of whether mucosal bacterial changes contributed to variation in FE or were rather a consequence of FE-related changes in the pig's physiology or feeding behavior.
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Affiliation(s)
- Barbara U Metzler-Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz, Vienna, Austria
| | - Peadar G Lawlor
- Teagasc Pig Development Department, Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Elizabeth Magowan
- Agri-Food and Biosciences Institute, Agriculture Branch, Large Park, Co. Down BT26 6DR, Hillsborough, Northern Ireland, UK
| | - Qendrim Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz, Vienna, Austria
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88
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Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 2018; 36:411-420. [PMID: 29608179 PMCID: PMC6700744 DOI: 10.1038/nbt.4096] [Citation(s) in RCA: 6711] [Impact Index Per Article: 1118.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 02/09/2018] [Indexed: 02/06/2023]
Abstract
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.
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Affiliation(s)
- Andrew Butler
- New York Genome Center, New York, NY 10013, USA
- Center for Genomics and Systems Biology, New York University, New York, NY 10003-6688, USA
| | | | | | - Efthymia Papalexi
- New York Genome Center, New York, NY 10013, USA
- Center for Genomics and Systems Biology, New York University, New York, NY 10003-6688, USA
| | - Rahul Satija
- New York Genome Center, New York, NY 10013, USA
- Center for Genomics and Systems Biology, New York University, New York, NY 10003-6688, USA
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89
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Beauclercq S, Nadal-Desbarats L, Hennequet-Antier C, Gabriel I, Tesseraud S, Calenge F, Le Bihan-Duval E, Mignon-Grasteau S. Relationships between digestive efficiency and metabolomic profiles of serum and intestinal contents in chickens. Sci Rep 2018; 8:6678. [PMID: 29703927 PMCID: PMC5923279 DOI: 10.1038/s41598-018-24978-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/12/2018] [Indexed: 01/26/2023] Open
Abstract
The increasing cost of conventional feedstuffs has bolstered interest in genetic selection for digestive efficiency (DE), a component of feed efficiency, assessed by apparent metabolisable energy corrected to zero nitrogen retention (AMEn). However, its measurement is time-consuming and constraining, and its relationship with metabolic efficiency poorly understood. To simplify selection for this trait, we searched for indirect metabolic biomarkers through an analysis of the serum metabolome using nuclear magnetic resonance (1H NMR). A partial least squares (PLS) model including six amino acids and two derivatives from butyrate predicted 59% of AMEn variability. Moreover, to increase our knowledge of the molecular mechanisms controlling DE, we investigated 1H NMR metabolomes of ileal, caecal, and serum contents by fitting canonical sparse PLS. This analysis revealed strong associations between metabolites and DE. Models based on the ileal, caecal, and serum metabolome respectively explained 77%, 78%, and 74% of the variability of AMEn and its constitutive components (utilisation of starch, lipids, and nitrogen). In our conditions, the metabolites presenting the strongest associations with AMEn were proline in the serum, fumarate in the ileum and glucose in caeca. This study shows that serum metabolomics offers new opportunities to predict chicken DE.
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Affiliation(s)
| | - Lydie Nadal-Desbarats
- Département d'analyse chimique biologique et médicale, PPF Analyse des systèmes biologiques, Université de Tours, 37032, Tours, France
| | | | - Irène Gabriel
- BOA, INRA, Université de Tours, 37380, Nouzilly, France
| | | | - Fanny Calenge
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78352, Jouy-en-Josas, France
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90
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Jain P, Vineis P, Liquet B, Vlaanderen J, Bodinier B, van Veldhoven K, Kogevinas M, Athersuch TJ, Font-Ribera L, Villanueva CM, Vermeulen R, Chadeau-Hyam M. A multivariate approach to investigate the combined biological effects of multiple exposures. J Epidemiol Community Health 2018; 72:564-571. [PMID: 29563153 PMCID: PMC6031275 DOI: 10.1136/jech-2017-210061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/17/2018] [Accepted: 02/19/2018] [Indexed: 12/18/2022]
Abstract
Epidemiological studies provide evidence that environmental exposures may affect health through complex mixtures. Formal investigation of the effect of exposure mixtures is usually achieved by modelling interactions, which relies on strong assumptions relating to the identity and the number of the exposures involved in such interactions, and on the order and parametric form of these interactions. These hypotheses become difficult to formulate and justify in an exposome context, where influential exposures are numerous and heterogeneous. To capture both the complexity of the exposome and its possibly pleiotropic effects, models handling multivariate predictors and responses, such as partial least squares (PLS) algorithms, can prove useful. As an illustrative example, we applied PLS models to data from a study investigating the inflammatory response (blood concentration of 13 immune markers) to the exposure to four disinfection by-products (one brominated and three chlorinated compounds), while swimming in a pool. To accommodate the multiple observations per participant (n=60; before and after the swim), we adopted a multilevel extension of PLS algorithms, including sparse PLS models shrinking loadings coefficients of unimportant predictors (exposures) and/or responses (protein levels). Despite the strong correlation among co-occurring exposures, our approach identified a subset of exposures (n=3/4) affecting the exhaled levels of 8 (out of 13) immune markers. PLS algorithms can easily scale to high-dimensional exposures and responses, and prove useful for exposome research to identify sparse sets of exposures jointly affecting a set of (selected) biological markers. Our descriptive work may guide these extensions for higher dimensional data.
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Affiliation(s)
- Pooja Jain
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Molecular and Genetic Epidemiology Unit, Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Benoît Liquet
- UMR CNRS 5142, Laboratoire de Mathématiques et de leurs Applications, Université de Pau et des Pays de l'Adour, Anglet, France.,School of Mathematics, ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Australia
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Karin van Veldhoven
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Toby J Athersuch
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Laia Font-Ribera
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Cristina M Villanueva
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Roel Vermeulen
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.,Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, Utrecht, Netherlands
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91
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92
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Seiler C, Green T, Hong D, Chromik L, Huffman L, Holmes S, Reiss AL. Multi-Table Differential Correlation Analysis of Neuroanatomical and Cognitive Interactions in Turner Syndrome. Neuroinformatics 2017; 16:81-93. [PMID: 29270892 DOI: 10.1007/s12021-017-9351-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Girls and women with Turner syndrome (TS) have a completely or partially missing X chromosome. Extensive studies on the impact of TS on neuroanatomy and cognition have been conducted. The integration of neuroanatomical and cognitive information into one consistent analysis through multi-table methods is difficult and most standard tests are underpowered. We propose a new two-sample testing procedure that compares associations between two tables in two groups. The procedure combines multi-table methods with permutation tests. In particular, we construct cluster size test statistics that incorporate spatial dependencies. We apply our new procedure to a newly collected dataset comprising of structural brain scans and cognitive test scores from girls with TS and healthy control participants (age and sex matched). We measure neuroanatomy with Tensor-Based Morphometry (TBM) and cognitive function with Wechsler IQ and NEuroPSYchological tests (NEPSY-II). We compare our multi-table testing procedure to a single-table analysis. Our new procedure reports differential correlations between two voxel clusters and a wide range of cognitive tests whereas the single-table analysis reports no differences. Our findings are consistent with the hypothesis that girls with TS have a different brain-cognition association structure than healthy controls.
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Affiliation(s)
- Christof Seiler
- Department of Statistics, Stanford University, Stanford, CA, USA.
| | - Tamar Green
- Center for Interdisciplinary Brain Sciences Research, Stanford University School of Medicine, Stanford, CA, USA.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Hong
- Center for Interdisciplinary Brain Sciences Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Lindsay Chromik
- Center for Interdisciplinary Brain Sciences Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynne Huffman
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Allan L Reiss
- Center for Interdisciplinary Brain Sciences Research, Stanford University School of Medicine, Stanford, CA, USA.,Departments of Radiology, Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
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93
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Multiple-stressor effects in an apex predator: combined influence of pollutants and sea ice decline on lipid metabolism in polar bears. Sci Rep 2017; 7:16487. [PMID: 29184161 PMCID: PMC5705648 DOI: 10.1038/s41598-017-16820-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022] Open
Abstract
There is growing evidence from experimental and human epidemiological studies that many pollutants can disrupt lipid metabolism. In Arctic wildlife, the occurrence of such compounds could have serious consequences for seasonal feeders. We set out to study whether organohalogenated compounds (OHCs) could cause disruption of energy metabolism in female polar bears (Ursus maritimus) from Svalbard, Norway (n = 112). We analyzed biomarkers of energy metabolism including the abundance profiles of nine lipid-related genes, fatty acid (FA) synthesis and elongation indices in adipose tissue, and concentrations of lipid-related variables in plasma (cholesterol, high-density lipoprotein, triglycerides). Furthermore, the plasma metabolome and lipidome were characterized by low molecular weight metabolites and lipid fingerprinting, respectively. Polychlorinated biphenyls, chlordanes, brominated diphenyl ethers and perfluoroalkyl substances were significantly related to biomarkers involved in lipid accumulation, FA metabolism, insulin utilization, and cholesterol homeostasis. Moreover, the effects of pollutants were measurable at the metabolome and lipidome levels. Our results indicate that several OHCs affect lipid biosynthesis and catabolism in female polar bears. Furthermore, these effects were more pronounced when combined with reduced sea ice extent and thickness, suggesting that climate-driven sea ice decline and OHCs have synergistic negative effects on polar bears.
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94
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Alterations in gut microbiota associated with a cafeteria diet and the physiological consequences in the host. Int J Obes (Lond) 2017; 42:746-754. [PMID: 29167556 DOI: 10.1038/ijo.2017.284] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Gut microbiota have been described as key factors in the pathophysiology of obesity and different components of metabolic syndrome (MetS). The cafeteria diet (CAF)-fed rat is a preclinical model that reproduces most of the alterations found in human MetS by simulating a palatable human unbalanced diet. Our objective was to assess the effects of CAF on gut microbiota and their associations with different components of MetS in Wistar rats. METHODS Animals were fed a standard diet or CAF for 12 weeks. A partial least square-based methodology was used to reveal associations between gut microbiota, characterized by 16S ribosomal DNA gene sequencing, and biochemical, nutritional and physiological parameters. RESULTS CAF feeding resulted in obesity, dyslipidemia, insulin resistance and hepatic steatosis. These changes were accompanied by a significant decrease in gut bacterial diversity, decreased Firmicutes and an increase in Actinobacteria and Proteobacteria abundances, which were concomitant with increased endotoxemia. Associations of different genera with the intake of lipids and carbohydrates were opposed from those associated with the intake of fiber. Changes in gut microbiota were also associated with the different physiological effects of CAF, mainly increased adiposity and altered levels of plasma leptin and glycerol, consistent with altered adipose tissue metabolism. Also hepatic lipid accretion was associated with changes in microbiota, highlighting the relevance of gut microbiota homeostasis in the adipose-liver axis. CONCLUSIONS Overall, our results suggest that CAF feeding has a profound impact on the gut microbiome and, in turn, that these changes may be associated with important features of MetS.
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95
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Sanmiguel CP, Jacobs J, Gupta A, Ju T, Stains J, Coveleskie K, Lagishetty V, Balioukova A, Chen Y, Dutson E, Mayer EA, Labus JS. Surgically Induced Changes in Gut Microbiome and Hedonic Eating as Related to Weight Loss: Preliminary Findings in Obese Women Undergoing Bariatric Surgery. Psychosom Med 2017; 79:880-887. [PMID: 28570438 PMCID: PMC5628115 DOI: 10.1097/psy.0000000000000494] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Weight loss surgery results in significant changes in the anatomy, function, and intraluminal environment of the gastrointestinal tract affecting the gut microbiome. Although bariatric surgery results in sustained weight loss, decreased appetite, and hedonic eating, it is unknown whether the surgery-induced alterations in gut microbiota play a role in the observed changes in hedonic eating. We explored the following hypotheses: (1) laparoscopic sleeve gastrectomy (LSG) results in changes in gut microbial composition; (2) alterations in gut microbiota are related to weight loss; (3) alterations in gut microbiome are associated with changes in appetite and hedonic eating. METHODS Eight obese women underwent LSG. Their body mass index, body fat mass, food intake, hunger, hedonic eating scores, and stool samples were obtained at baseline and 1-month postsurgery. 16S ribosomal RNA gene sequencing was performed on stool samples. DESeq2 changes in microbial abundance. Multilevel-sparse partial least squares discriminant analysis was applied to genus-level abundance for discriminative microbial signatures. RESULTS LSG resulted in significant reductions in body mass index, food intake, and hedonic eating. A microbial signature composed of five bacterial genera discriminated between pre- and postsurgery status. Several bacterial genera were significantly associated with weight loss (Bilophila, q = 3E-05; Faecalibacterium q = 4E-05), lower appetite (Enterococcus, q = 3E-05), and reduced hedonic eating (Akkermansia, q = .037) after surgery. CONCLUSIONS In this preliminary analysis, changes in gut microbial abundance discriminated between pre- and postoperative status. Alterations in gut microbiome were significantly associated with weight loss and with reduced hedonic eating after surgery; however, a larger sample is needed to confirm these findings.
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Affiliation(s)
- Claudia P Sanmiguel
- From the Ingestive Behavior and Obesity Program (Sanmiguel, Gupta, Ju, Stains, Coveleskie, Mayer, Labus), Oppenheimer Center for Neurobiology of Stress & Resilience; Department of Surgery (Balioukova, Chen, Dutson), Center for Obesity and Metabolic Health; UCLA Microbiome Center (Sanmiguel, Jacobs, Lagishetty, Mayer, Labus); and David Geffen School of Medicine at UCLA (Sanmiguel, Jacobs, Gupta, Ju, Stains, Lagishetty, Balioukova, Chen, Dutson, Mayer, Labus), Los Angeles, California
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Abstract
OBJECTIVE Brain-gut-microbiota interactions may play an important role in human health and behavior. Although rodent models have demonstrated effects of the gut microbiota on emotional, nociceptive, and social behaviors, there is little translational human evidence to date. In this study, we identify brain and behavioral characteristics of healthy women clustered by gut microbiota profiles. METHODS Forty women supplied fecal samples for 16S rRNA profiling. Microbial clusters were identified using Partitioning Around Medoids. Functional magnetic resonance imaging was acquired. Microbiota-based group differences were analyzed in response to affective images. Structural and diffusion tensor imaging provided gray matter metrics (volume, cortical thickness, mean curvature, surface area) as well as fiber density between regions. A sparse Partial Least Square-Discrimination Analysis was applied to discriminate microbiota clusters using white and gray matter metrics. RESULTS Two bacterial genus-based clusters were identified, one with greater Bacteroides abundance (n = 33) and one with greater Prevotella abundance (n = 7). The Prevotella group showed less hippocampal activity viewing negative valences images. White and gray matter imaging discriminated the two clusters, with accuracy of 66.7% and 87.2%, respectively. The Prevotella cluster was associated with differences in emotional, attentional, and sensory processing regions. For gray matter, the Bacteroides cluster showed greater prominence in the cerebellum, frontal regions, and the hippocampus. CONCLUSIONS These results support the concept of brain-gut-microbiota interactions in healthy humans. Further examination of the interaction between gut microbes, brain, and affect in humans is needed to inform preclinical reports that microbial modulation may affect mood and behavior.
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98
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Schiavone M, Déjean S, Sieczkowski N, Castex M, Dague E, François JM. Integration of Biochemical, Biophysical and Transcriptomics Data for Investigating the Structural and Nanomechanical Properties of the Yeast Cell Wall. Front Microbiol 2017; 8:1806. [PMID: 29085340 PMCID: PMC5649194 DOI: 10.3389/fmicb.2017.01806] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022] Open
Abstract
The yeast cell is surrounded by a cell wall conferring protection and resistance to environmental conditions that can be harmful. Identify the molecular cues (genes) which shape the biochemical composition and the nanomechanical properties of the cell wall and the links between these two parameters represent a major issue in the understanding of the biogenesis and the molecular assembly of this essential cellular structure, which may have consequences in diverse biotechnological applications. We addressed this question in two ways. Firstly, we compared the biochemical and biophysical properties using atomic force microscopy (AFM) methods of 4 industrial strains with the laboratory sequenced strain BY4743 and used transcriptome data of these strains to infer biological hypothesis about differences of these properties between strains. This comparative approach showed a 4–6-fold higher hydrophobicity of industrial strains that was correlated to higher expression of genes encoding adhesin and adhesin-like proteins and not to their higher mannans content. The second approach was to employ a multivariate statistical analysis to identify highly correlated variables among biochemical, biophysical and genes expression data. Accordingly, we found a tight association between hydrophobicity and adhesion events that positively correlated with a set of 22 genes in which the main enriched GO function was the sterol metabolic process. We also identified a strong association of β-1,3-glucans with contour length that corresponds to the extension of mannans chains upon pulling the mannosyl units with the lectin-coated AFM tips. This association was positively correlated with a group of 27 genes in which the seripauperin multigene family was highly documented and negatively connected with a set of 23 genes whose main GO biological process was sulfur assimilation/cysteine biosynthetic process. On the other hand, the elasticity modulus was found weakly associated with levels of β-1,6-glucans, and this biophysical variable was positively correlated with a set of genes implicated in microtubules polymerization, tubulin folding and mitotic organization.
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Affiliation(s)
- Marion Schiavone
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, Institut National des Sciences Appliquées de Toulouse, UPS, INP, Université de ToulouseToulouse, France.,Lallemand SASBlagnac, France
| | | | | | | | - Etienne Dague
- Laboratoire D'analyse et D'architecture des Systèmes du-Centre National de la Recherche Scientifique, Université de ToulouseToulouse, France
| | - Jean M François
- Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, Institut National des Sciences Appliquées de Toulouse, UPS, INP, Université de ToulouseToulouse, France
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100
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Hugerth LW, Andersson AF. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol 2017; 8:1561. [PMID: 28928718 PMCID: PMC5591341 DOI: 10.3389/fmicb.2017.01561] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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Affiliation(s)
- Luisa W Hugerth
- Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska InstitutetSolna, Sweden.,Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
| | - Anders F Andersson
- Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
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