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Yoo EJ, Kim JS, Stransky S, Spivack S, Sidoli S. Advances in proteomics methods for the analysis of exhaled breath condensate. MASS SPECTROMETRY REVIEWS 2024; 43:713-722. [PMID: 38149478 DOI: 10.1002/mas.21871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
The analysis of exhaled breath condensate (EBC) demonstrates a promising avenue of minimally invasive biopsies for diagnostics. EBC is obtained by cooling exhaled air and collecting the condensation to be utilized for downstream analysis using various analytical methods. The aqueous phase of breath contains a large variety of miscible small compounds including polar electrolytes, amino acids, cytokines, chemokines, peptides, small proteins, metabolites, nucleic acids, and lipids/eicosanoids-however, these analytes are typically present at minuscule levels in EBC, posing a considerable technical challenge. Along with recent improvements in devices for breath collection, the sensitivity and resolution of liquid chromatography coupled to online mass spectrometry-based proteomics has attained subfemtomole sensitivity, vastly enhancing the quality of EBC sample analysis. As a result, proteomics analysis of EBC has been expanding the field of breath biomarker research. We present an au courant overview of the achievements in proteomics of EBC, the advancement of EBC collection devices, and the current and future applications for EBC biomarker analysis.
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Affiliation(s)
- Edwin J Yoo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Simon Spivack
- Department of Medicine, Department of Epidemiology & Population Health, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
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Grigorev K, Nelson TM, Overbey EG, Houerbi N, Kim J, Najjar D, Damle N, Afshin EE, Ryon KA, Thierry-Mieg J, Thierry-Mieg D, Melnick AM, Mateus J, Mason CE. Direct RNA sequencing of astronaut blood reveals spaceflight-associated m6A increases and hematopoietic transcriptional responses. Nat Commun 2024; 15:4950. [PMID: 38862496 PMCID: PMC11166648 DOI: 10.1038/s41467-024-48929-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
The advent of civilian spaceflight challenges scientists to precisely describe the effects of spaceflight on human physiology, particularly at the molecular and cellular level. Newer, nanopore-based sequencing technologies can quantitatively map changes in chemical structure and expression at single molecule resolution across entire isoforms. We perform long-read, direct RNA nanopore sequencing, as well as Ultima high-coverage RNA-sequencing, of whole blood sampled longitudinally from four SpaceX Inspiration4 astronauts at seven timepoints, spanning pre-flight, day of return, and post-flight recovery. We report key genetic pathways, including changes in erythrocyte regulation, stress induction, and immune changes affected by spaceflight. We also present the first m6A methylation profiles for a human space mission, suggesting a significant spike in m6A levels immediately post-flight. These data and results represent the first longitudinal long-read RNA profiles and RNA modification maps for each gene for astronauts, improving our understanding of the human transcriptome's dynamic response to spaceflight.
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Affiliation(s)
- Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Theodore M Nelson
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eliah G Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Center for STEM, University of Austin, Austin, TX, USA
- BioAstra, Inc, New York, NY, USA
| | - Nadia Houerbi
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Deena Najjar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information (NCBI), National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information (NCBI), National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Jaime Mateus
- Space Exploration Technologies Corporation (SpaceX), Hawthorne, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, New York, NY, USA.
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Cope H, Willis CR, MacKay MJ, Rutter LA, Toh LS, Williams PM, Herranz R, Borg J, Bezdan D, Giacomello S, Muratani M, Mason CE, Etheridge T, Szewczyk NJ. Routine omics collection is a golden opportunity for European human research in space and analog environments. PATTERNS 2022; 3:100550. [PMID: 36277820 PMCID: PMC9583032 DOI: 10.1016/j.patter.2022.100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kanjanapruthipong T, Sukphopetch P, Reamtong O, Isarangkul D, Muangkaew W, Thiangtrongjit T, Sansurin N, Fongsodsri K, Ampawong S. Cytoskeletal Alteration Is an Early Cellular Response in Pulmonary Epithelium Infected with Aspergillus fumigatus Rather than Scedosporium apiospermum. MICROBIAL ECOLOGY 2022; 83:216-235. [PMID: 33890146 DOI: 10.1007/s00248-021-01750-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Invasive aspergillosis and scedosporiosis are life-threatening fungal infections with similar clinical manifestations in immunocompromised patients. Contrarily, Scedosporium apiospermum is susceptible to some azole derivative but often resistant to amphotericin B. Histopathological examination alone cannot diagnose these two fungal species. Pathogenesis studies could contribute to explore candidate protein markers for new diagnosis and treatment methods leading to a decrease in mortality. In the present study, proteomics was conducted to identify significantly altered proteins in A549 cells infected with or without Aspergillus fumigatus and S. apiospermum as measured at initial invasion. Protein validation was performed with immunogold labelling alongside immunohistochemical techniques in infected A549 cells and lungs from murine models. Further, cytokine production was measured, using the Bio-Plex-Multiplex immunoassay. The cytoskeletal proteins HSPA9, PA2G4, VAT1, PSMA2, PEX1, PTGES3, KRT1, KRT9, CLIP1 and CLEC20A were mainly changed during A. fumigatus infection, while the immunologically activated proteins WNT7A, GAPDH and ANXA2 were principally altered during S. apiospermum infection. These proteins are involved in fungal internalisation and structural destruction leading to pulmonary disorders. Interleukin (IL)-21, IL-1α, IL-22, IL-2, IL-8, IL-12, IL-17A, interferon-γ and tumour necrosis factor-α were upregulated in both aspergillosis and scedosporiosis, although more predominately in the latter, in accordance with chitin synthase-1 and matrix metalloproteinase levels. Our results demonstrated that during invasion, A. fumigatus primarily altered host cellular integrity, whereas S. apiospermum chiefly induced and extensively modulated host immune responses.
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Affiliation(s)
- Tapanee Kanjanapruthipong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Passanesh Sukphopetch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetic, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Duangnate Isarangkul
- Department of Microbiology, Faculty of Science, Mahidol University, 272, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Watcharamat Muangkaew
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetic, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Nichapa Sansurin
- Northeast Laboratory Animal Center, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kamonpan Fongsodsri
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand.
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Zakharova N, Kozyr A, Ryabokon AM, Indeykina M, Strelnikova P, Bugrova A, Nikolaev EN, Kononikhin AS. Mass spectrometry based proteome profiling of the exhaled breath condensate for lung cancer biomarkers search. Expert Rev Proteomics 2021; 18:637-642. [PMID: 34477466 DOI: 10.1080/14789450.2021.1976150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Lung cancer remains the most prevalent cause of cancer mortality worldwide mainly due to insufficient availability of early screening methods for wide-scale application. Exhaled breath condensate (EBC) is currently considered as one of the promising targets for early screening and is particularly attractive due to its absolutely noninvasive collection and possibility for long-term frozen storage. EBC proteome analysis can provide valuable information about the (patho)physiological changes in the respiratory system and may help to identify in time a high risk of lung cancer. Mass spectrometry (MS) profiling of EBC proteome seems to have no alternative in obtaining the most extensive data and characteristic marker panels for screening. AREAS COVERED This special report summarizes the data of several proteomic studies of EBC in normal and lung cancer (from 2012 to 2021, PubMed), focuses on the possible reasons for the significant discrepancy in the results, and discusses some aspects for special attention in further studies. EXPERT OPINION The significant discrepancy in the results of various studies primarily highlights the need to create standardized protocols for the collection and preparation of EBC for proteomic analysis. The application of quantitative and targeted LC-MS/MS based approaches seems to be the most promising in further EBC proteomic studies.
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Affiliation(s)
- Natalia Zakharova
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Anna Kozyr
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Anna M Ryabokon
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Maria Indeykina
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow.,Laboratory of ion and molecular physics, V.l. Talrose Institute for Energy Problems of Chemical Physics, N.n. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Polina Strelnikova
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Anna Bugrova
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow
| | - Eugene N Nikolaev
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexey S Kononikhin
- Laboratory of mass spectrometry of biomacromolecules Emanuel Institute for Biochemical Physics, Russian Academy of Science Moscow.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo, Russia
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Fan Y, Han Z, Lu X, Arbab AAI, Nazar M, Yang Y, Yang Z. Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process. Genes (Basel) 2021; 12:genes12060942. [PMID: 34203058 PMCID: PMC8235497 DOI: 10.3390/genes12060942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 12/29/2022] Open
Abstract
The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.
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Affiliation(s)
- Yongliang Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ziyin Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Abdelaziz Adam Idriss Arbab
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Mudasir Nazar
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Yi Yang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.F.); (Z.H.); (X.L.); (A.A.I.A.); (M.N.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-0514-87979269
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Ma L, Muscat JE, Sinha R, Sun D, Xiu G. Proteomics of exhaled breath condensate in lung cancer and controls using data-independent acquisition (DIA): a pilot study. J Breath Res 2021; 15. [DOI: 10.1088/1752-7163/abd07e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022]
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Proteome of exhaled breath condensate on exposure to high-temperature thermoheliox. Russ Chem Bull 2020; 69:1816-1818. [PMID: 33071535 PMCID: PMC7547291 DOI: 10.1007/s11172-020-2967-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/23/2020] [Indexed: 11/08/2022]
Abstract
The proteome of exhaled breath condensate was analyzed by mass spectrometry before and immediately after the thermoheliox procedure and after a 3 h relaxation. The major part of the proteome remained unchanged and there was no extensive cell destruction.
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Varfolomeev SD, Panin AA, Ryabokon AM, Kozyr AS, Kononikhin AS, Shogenova LV, Chuchalin AG. [Thermal heliox proteome. High-temperature heliox does not cause destruction of human respiratory system cells]. TERAPEVT ARKH 2020; 92:69-72. [PMID: 33346495 DOI: 10.26442/00403660.2020.06.000769] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Indexed: 12/26/2022]
Abstract
AIM Conducting a pilot study to assess the effect of thermal heliox on the state of the respiratory tract by studying of the exhaled breath condensate protein composition before the thermal heliox procedure, immediately after and after three hours of relaxation Materials and methods. A comparative study of the exhaled breath condensates (EBC) protein composition of five non-smoking healthy donors was carried out. The EBC was taken before the respiratory procedure, immediately after a 20-minute inhalation by mixture of He/O2 gases (70/30) heated to 70C and 3 hours later. The protein composition was determined by chromatography-mass spectrometric analysis after selective tryptic hydrolysis. The results were processed using the Mascot program and the UniProt database. RESULTS After the heliox procedure, the volume of the collected condensate (11.5 ml) decreases by an average of 32% and is practically restored after three hours of relaxation. Most proteins were consistent for all samples, regardless of the thermal heliox procedure. These are keratins, several proteins of the immune system (immunoglobulins, compliment proteins), tubulin. In samples after thermal heliox, the appearance of small amounts of additional proteins is observed. These are proteins of muscle metabolism (actin and calmodulin), fibrinogen, traces of hemoglobin, apolipoprotein, type B creatine kinase. After three hours of relaxation, tubulin disappears in the EBC. CONCLUSION Most exhaled proteins are the same before, after the procedure, and for three hours of relaxation. The results obtained demonstrate the relative safety of the use of high temperature heliox as a therapeutic agent.
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Affiliation(s)
- S D Varfolomeev
- Lomonosov Moscow State University.,Emanuel Institute of Biochemical Physics
| | | | - A M Ryabokon
- Lomonosov Moscow State University.,Emanuel Institute of Biochemical Physics
| | - A S Kozyr
- Emanuel Institute of Biochemical Physics
| | | | - L V Shogenova
- Pirogov Russian National Research Medical University.,Pletnev City Clinical Hospital
| | - A G Chuchalin
- Pirogov Russian National Research Medical University
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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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