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Sajulga R, Bolon YT, Maiers MJ, Petersdorf EW. Assessment of HLA-DPB1 genetic variation using an HLA-DP tool and its implications in clinical transplantation. Blood Adv 2023; 7:4809-4821. [PMID: 37126658 PMCID: PMC10469530 DOI: 10.1182/bloodadvances.2022009554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/06/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
HLA-DP is a classic transplantation antigen that mediates alloreactivity through T-cell epitope (TCE) diversity and expression levels. A current challenge is to integrate these functional features into the prospective selection of unrelated donor candidates for transplantation. Genetically, HLA-DPB1 exon 2 defines the permissive and nonpermissive TCE groups, and exons 2 and 3 (in linkage with rs9277534) indicate low- and high-expression allotypes. In this study, we analyzed 356 272 exon 2-exon 3-phased sequences from individuals across 5 self-identified race and ethnicity categories: White, Hispanic, Asian or Pacific Islander, Black or African American, and American Indian or Alaskan Native. This sequence data set revealed the complex relationship between TCE and expression models and the importance of exon 3 sequence data. We also studied archived donor search lists for 2545 patients who underwent transplantation from an HLA-11/12 unrelated donor mismatched for a single HLA-DPB1 allele. Depending on the order in which the TCE and expression criteria were considered, some patients had different TCE- and expression-favorable donors. In addition, this data set revealed that many expression-favorable alternatives existed in the search lists. To improve the selection of candidate donors, we provide, disseminate, and automate our findings through our multifaceted tool called Expression of HLA-DP Assessment Tool, consisting of a public web application, Python package, and analysis pipeline.
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Affiliation(s)
- Ray Sajulga
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Martin J. Maiers
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Effie W. Petersdorf
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
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2
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Sajulga R, Madbouly A, Fingerson S, Gragert L, Bashyal P, Bolon YT, Maiers M. Predicting HLA-DPB1 permissive probabilities through a DPB1 prediction service towards the optimization of HCT donor selection. Hum Immunol 2021; 82:903-911. [PMID: 34362573 DOI: 10.1016/j.humimm.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 12/01/2022]
Abstract
Despite its demonstrated importance in hematopoietic cell transplantation, the HLA-DPB1 locus is only typed in one in five unrelated donors in the United States. Addressing this issue, we developed a DPB1 Prediction Service that leverages seven-locus haplotype frequencies (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1 ∼ DPB1) to extend the imputation of six-locus HLA typing (HLA-A ∼ C ∼ B ∼ DRB3/4/5 ∼ DRB1 ∼ DQB1) to the HLA-DPB1 locus, including the novel prediction of HLA-DPB1 TCE groups to calculate donor-recipient TCE permissive match probabilities. Simulations of current-day patient searches reveal the service can fill in missing gaps for another four in five donors that appears on lists. To validate its performance, samples of 206,328 registered donors and 5,218 donor-recipient pairs with known high-resolution HLA-DPB1 typing were used for predicted-versus-observed comparisons. These comparisons demonstrated that the predictions were correct for 11.9-19.7% of HLA-DPB1 genotypes, 64.9-70.0% of TCE groups, and 61.0% of permissive match categories. Although HLA-DPB1 match predictions must be confirmed by additional typing, knowledge of TCE match probabilities facilitates rapid and improved identification of best donor options, especially for populations of color. Thus, we developed the TCE Prediction Tool user interface for a pilot program with several transplant centers to preview the accuracy and utility of this prediction framework, which provides valuable upfront optimization of donor selection.
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Affiliation(s)
- Ray Sajulga
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA.
| | - Abeer Madbouly
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Stephanie Fingerson
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Loren Gragert
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Pradeep Bashyal
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Yung-Tsi Bolon
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA; Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401, USA
| | - Martin Maiers
- National Marrow Donor Program/Be The Match®, Minneapolis, MN 55401, USA
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Mehta S, Kumar P, Crane M, Johnson JE, Sajulga R, Nguyen DDA, McGowan T, Arntzen MØ, Griffin TJ, Jagtap PD. Updates on metaQuantome Software for Quantitative Metaproteomics. J Proteome Res 2021; 20:2130-2137. [PMID: 33683127 DOI: 10.1021/acs.jproteome.0c00960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.
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Affiliation(s)
- Subina Mehta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Marie Crane
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ray Sajulga
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
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4
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Mehta S, Crane M, Leith E, Batut B, Hiltemann S, Arntzen MØ, Kunath BJ, Pope PB, Delogu F, Sajulga R, Kumar P, Johnson JE, Griffin TJ, Jagtap PD. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Res 2021; 10:103. [PMID: 34484688 PMCID: PMC8383124 DOI: 10.12688/f1000research.28608.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.
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Affiliation(s)
- Subina Mehta
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Marie Crane
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Emma Leith
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Bérénice Batut
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Saskia Hiltemann
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | - Ray Sajulga
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Praveen Kumar
- University of Minnesota, Twin Cities, MN, 55455, USA
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5
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Mehta S, Crane M, Leith E, Batut B, Hiltemann S, Arntzen MØ, Kunath BJ, Pope PB, Delogu F, Sajulga R, Kumar P, Johnson JE, Griffin TJ, Jagtap PD. ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework. F1000Res 2021; 10:103. [PMID: 34484688 PMCID: PMC8383124 DOI: 10.12688/f1000research.28608.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.
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Affiliation(s)
- Subina Mehta
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Marie Crane
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Emma Leith
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Bérénice Batut
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, Germany
| | - Saskia Hiltemann
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | | | | | - Ray Sajulga
- University of Minnesota, Twin Cities, MN, 55455, USA
| | - Praveen Kumar
- University of Minnesota, Twin Cities, MN, 55455, USA
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6
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Sajulga R, Easterly C, Riffle M, Mesuere B, Muth T, Mehta S, Kumar P, Johnson J, Gruening BA, Schiebenhoefer H, Kolmeder CA, Fuchs S, Nunn BL, Rudney J, Griffin TJ, Jagtap PD. Survey of metaproteomics software tools for functional microbiome analysis. PLoS One 2020; 15:e0241503. [PMID: 33170893 PMCID: PMC7654790 DOI: 10.1371/journal.pone.0241503] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022] Open
Abstract
To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.
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Affiliation(s)
- Ray Sajulga
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Caleb Easterly
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michael Riffle
- University of Washington, Seattle, Washington, United States of America
| | | | - Thilo Muth
- Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Subina Mehta
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Praveen Kumar
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - James Johnson
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | | | | | | | - Brook L. Nunn
- University of Washington, Seattle, Washington, United States of America
| | - Joel Rudney
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Timothy J. Griffin
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Pratik D. Jagtap
- University of Minnesota, Minneapolis, Minnesota, United States of America
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7
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Bhargava M, Viken KJ, Barkes B, Griffin TJ, Gillespie M, Jagtap PD, Sajulga R, Peterson EJ, Dincer HE, Li L, Restrepo CI, O'Connor BP, Fingerlin TE, Perlman DM, Maier LA. Novel protein pathways in development and progression of pulmonary sarcoidosis. Sci Rep 2020; 10:13282. [PMID: 32764642 PMCID: PMC7413390 DOI: 10.1038/s41598-020-69281-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pulmonary involvement occurs in up to 95% of sarcoidosis cases. In this pilot study, we examine lung compartment-specific protein expression to identify pathways linked to development and progression of pulmonary sarcoidosis. We characterized bronchoalveolar lavage (BAL) cells and fluid (BALF) proteins in recently diagnosed sarcoidosis cases. We identified 4,306 proteins in BAL cells, of which 272 proteins were differentially expressed in sarcoidosis compared to controls. These proteins map to novel pathways such as integrin-linked kinase and IL-8 signaling and previously implicated pathways in sarcoidosis, including phagosome maturation, clathrin-mediated endocytic signaling and redox balance. In the BALF, the differentially expressed proteins map to several pathways identified in the BAL cells. The differentially expressed BALF proteins also map to aryl hydrocarbon signaling, communication between innate and adaptive immune response, integrin, PTEN and phospholipase C signaling, serotonin and tryptophan metabolism, autophagy, and B cell receptor signaling. Additional pathways that were different between progressive and non-progressive sarcoidosis in the BALF included CD28 signaling and PFKFB4 signaling. Our studies demonstrate the power of contemporary proteomics to reveal novel mechanisms operational in sarcoidosis. Application of our workflows in well-phenotyped large cohorts maybe beneficial to identify biomarkers for diagnosis and prognosis and therapeutically tenable molecular mechanisms.
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Affiliation(s)
- Maneesh Bhargava
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Minnesota, MMC 276, 420 Delaware St SE, Minneapolis, MN, USA.
| | - K J Viken
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Minnesota, MMC 276, 420 Delaware St SE, Minneapolis, MN, USA
| | - B Barkes
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
| | - T J Griffin
- Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - M Gillespie
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
| | - P D Jagtap
- Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - R Sajulga
- Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - E J Peterson
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - H E Dincer
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Minnesota, MMC 276, 420 Delaware St SE, Minneapolis, MN, USA
| | - L Li
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
| | - C I Restrepo
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
| | - B P O'Connor
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - T E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - D M Perlman
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Minnesota, MMC 276, 420 Delaware St SE, Minneapolis, MN, USA
| | - L A Maier
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
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8
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Kumar P, Johnson JE, Easterly C, Mehta S, Sajulga R, Nunn B, Jagtap PD, Griffin TJ. A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases. J Proteome Res 2020; 19:2772-2785. [DOI: 10.1021/acs.jproteome.0c00260] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Praveen Kumar
- Bioinformatics and Computational Biology, University of Minnesota−Rochester, Rochester, Minnesota 55904, United States
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Caleb Easterly
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Subina Mehta
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ray Sajulga
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Brook Nunn
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Pratik D. Jagtap
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Timothy J. Griffin
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
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9
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McGowan T, Johnson JE, Kumar P, Sajulga R, Mehta S, Jagtap PD, Griffin TJ. Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. Gigascience 2020; 9:giaa025. [PMID: 32236523 PMCID: PMC7102281 DOI: 10.1093/gigascience/giaa025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Proteogenomics integrates genomics, transcriptomics, and mass spectrometry (MS)-based proteomics data to identify novel protein sequences arising from gene and transcript sequence variants. Proteogenomic data analysis requires integration of disparate 'omic software tools, as well as customized tools to view and interpret results. The flexible Galaxy platform has proven valuable for proteogenomic data analysis. Here, we describe a novel Multi-omics Visualization Platform (MVP) for organizing, visualizing, and exploring proteogenomic results, adding a critically needed tool for data exploration and interpretation. FINDINGS MVP is built as an HTML Galaxy plug-in, primarily based on JavaScript. Via the Galaxy API, MVP uses SQLite databases as input-a custom data type (mzSQLite) containing MS-based peptide identification information, a variant annotation table, and a coding sequence table. Users can interactively filter identified peptides based on sequence and data quality metrics, view annotated peptide MS data, and visualize protein-level information, along with genomic coordinates. Peptides that pass the user-defined thresholds can be sent back to Galaxy via the API for further analysis; processed data and visualizations can also be saved and shared. MVP leverages the Integrated Genomics Viewer JavaScript framework, enabling interactive visualization of peptides and corresponding transcript and genomic coding information within the MVP interface. CONCLUSIONS MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomic results within the Galaxy environment, adding a unique and critically needed tool for empowering exploration and interpretation of results. The platform is extensible, providing a basis for further development of new functionalities for proteogenomic data visualization.
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Affiliation(s)
- Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, 599 Walter Library, 117 Pleasant Street SE, Minneapolis, MN 55455, USA
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
- Bioinformatics and Computational Biology program, University of Minnesota-Rochester, 111 South Broadway, Suite 300, Rochester, MN 55904, USA
| | - Ray Sajulga
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6–155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
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10
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Easterly CW, Sajulga R, Mehta S, Johnson J, Kumar P, Hubler S, Mesuere B, Rudney J, Griffin TJ, Jagtap PD. metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex Microbiomes. Mol Cell Proteomics 2019; 18:S82-S91. [PMID: 31235611 PMCID: PMC6692774 DOI: 10.1074/mcp.ra118.001240] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/21/2019] [Indexed: 01/15/2023] Open
Abstract
Microbiome research offers promising insights into the impact of microorganisms on biological systems. Metaproteomics, the study of microbial proteins at the community level, integrates genomic, transcriptomic, and proteomic data to determine the taxonomic and functional state of a microbiome. However, standard metaproteomics software is subject to several limitations, commonly supporting only spectral counts, emphasizing exploratory analysis rather than hypothesis testing and rarely offering the ability to analyze the interaction of function and taxonomy - that is, which taxa are responsible for different processes.Here we present metaQuantome, a novel, multifaceted software suite that analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information, emphasizing label-free intensity-based methods. For experiments with multiple experimental conditions, metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition. We benchmark metaQuantome analysis against standard methods, using two previously published datasets: (1) an artificially assembled microbial community dataset (taxonomy benchmarking) and (2) a dataset with a range of recombinant human proteins spiked into an Escherichia coli background (functional benchmarking). Furthermore, we demonstrate the use of metaQuantome on a previously published human oral microbiome dataset.In both the taxonomic and functional benchmarking analyses, metaQuantome quantified taxonomic and functional terms more accurately than standard summarization-based methods. We use the oral microbiome dataset to demonstrate metaQuantome's ability to produce publication-quality figures and elucidate biological processes of the oral microbiome. metaQuantome enables advanced investigation of metaproteomic datasets, which should be broadly applicable to microbiome-related research. In the interest of accessible, flexible, and reproducible analysis, metaQuantome is open source and available on the command line and in Galaxy.
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Affiliation(s)
- Caleb W Easterly
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Ray Sajulga
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Subina Mehta
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
| | - Praveen Kumar
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN; Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN
| | - Shane Hubler
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Joel Rudney
- ‡School of Dentistry, University of Minnesota, Minneapolis, MN
| | - Timothy J Griffin
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN
| | - Pratik D Jagtap
- Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN.
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Kumar P, Panigrahi P, Johnson J, Weber WJ, Mehta S, Sajulga R, Easterly C, Crooker BA, Heydarian M, Anamika K, Griffin TJ, Jagtap PD. QuanTP: A Software Resource for Quantitative Proteo-Transcriptomic Comparative Data Analysis and Informatics. J Proteome Res 2018; 18:782-790. [DOI: 10.1021/acs.jproteome.8b00727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Praveen Kumar
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, Minnesota 55904, United States
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | - James Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Wanda J. Weber
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ray Sajulga
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Caleb Easterly
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brian A. Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Mohammad Heydarian
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Krishanpal Anamika
- LABS, Persistent Systems, Aryabhata-Pingala, Erandwane, Pune 411004, India
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Sajulga R, Mehta S, Kumar P, Johnson JE, Guerrero CR, Ryan MC, Karchin R, Jagtap PD, Griffin TJ. Bridging the Chromosome-centric and Biology/Disease-driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics. J Proteome Res 2018; 17:4329-4336. [DOI: 10.1021/acs.jproteome.8b00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ray Sajulga
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, Minnesota 55904, United States
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Candace R. Guerrero
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael C. Ryan
- In-Silico Solutions, Falls Church, Virginia 22043, United States
| | - Rachel Karchin
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- The Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21217, United States
| | - Pratik D. Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Timothy J. Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Jeong LN, Sajulga R, Forte SG, Stoll DR, Rutan SC. Erratum to “Simulation of elution profiles in liquid chromatography—I: Gradient elution conditions, and with mismatched injection and mobile phases solvents’’ [J. Chromatogr. A 1457 (2016) 41–49]. J Chromatogr A 2016; 1478:84. [DOI: 10.1016/j.chroma.2016.11.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Jeong LN, Sajulga R, Forte SG, Stoll DR, Rutan SC. Simulation of elution profiles in liquid chromatographyI: Gradient elution conditions, and with mismatched injection and mobile phase solvents. J Chromatogr A 2016; 1457:41-9. [DOI: 10.1016/j.chroma.2016.06.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 05/19/2016] [Accepted: 06/05/2016] [Indexed: 11/25/2022]
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