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Liu C, Li L, Yang S, Wang M, Zhang H, Li S. Multi-omic insights into the cellular response of Phaeodactylum tricornutum (Bacillariophyta) strains under grazing pressure. FRONTIERS IN PLANT SCIENCE 2024; 14:1308085. [PMID: 38259919 PMCID: PMC10801743 DOI: 10.3389/fpls.2023.1308085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Background/Aims Phaeodactylum tricornutum, a model organism of diatoms, plays a crucial role in Earth's primary productivity. Investigating its cellular response to grazing pressure is highly significant for the marine ecological environment. Furthermore, the integration of multi-omics approaches has enhanced the understanding of its response mechanism. Methods To assess the molecular and cellular responses of P.tricornutum to grazer presence, we conducted transcriptomic, proteomic, and metabolomic analyses, combined with phenotypic data from previous studies. Sequencing data were obtained by Illumina RNA sequencing, TMT Labeled Quantitative Proteomics and Non-targeted Metabolomics, and WGCNA analysis and statistical analysis were performed. Results Among the differentially expressed genes, we observed complex expression patterns of the core genes involved in the phenotypic changes of P.tricornutum under grazing pressure across different strains and multi-omics datasets. These core genes primarily regulate the levels of various proteins and fatty acids, as well as the cellular response to diverse signals. Conclusion Our research reveals the association of multi-omics in four strains responses to grazing effects in P.tricornutum. Grazing pressure significantly impacted cell growth, fatty acid composition, stress response, and the core genes involved in phenotype transformation.
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Affiliation(s)
| | | | | | | | | | - Si Li
- School of Chemical Engineering, Hebei University of Technology, Tianjin, China
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Moore J, Ewoldt J, Venturini G, Pereira AC, Padilha K, Lawton M, Lin W, Goel R, Luptak I, Perissi V, Seidman CE, Seidman J, Chin MT, Chen C, Emili A. Multi-Omics Profiling of Hypertrophic Cardiomyopathy Reveals Altered Mechanisms in Mitochondrial Dynamics and Excitation-Contraction Coupling. Int J Mol Sci 2023; 24:4724. [PMID: 36902152 PMCID: PMC10002553 DOI: 10.3390/ijms24054724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Hypertrophic cardiomyopathy is one of the most common inherited cardiomyopathies and a leading cause of sudden cardiac death in young adults. Despite profound insights into the genetics, there is imperfect correlation between mutation and clinical prognosis, suggesting complex molecular cascades driving pathogenesis. To investigate this, we performed an integrated quantitative multi-omics (proteomic, phosphoproteomic, and metabolomic) analysis to illuminate the early and direct consequences of mutations in myosin heavy chain in engineered human induced pluripotent stem-cell-derived cardiomyocytes relative to late-stage disease using patient myectomies. We captured hundreds of differential features, which map to distinct molecular mechanisms modulating mitochondrial homeostasis at the earliest stages of pathobiology, as well as stage-specific metabolic and excitation-coupling maladaptation. Collectively, this study fills in gaps from previous studies by expanding knowledge of the initial responses to mutations that protect cells against the early stress prior to contractile dysfunction and overt disease.
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Affiliation(s)
- Jarrod Moore
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jourdan Ewoldt
- Department of Biomedical Engineering, Boston University, Boston, MA 02218, USA
| | | | | | - Kallyandra Padilha
- Laboratory of Genetics and Molecular Cardiology, Clinical Hospital, Faculty of Medicine, University of São Paulo, Sao Paulo 05508-000, Brazil
| | - Matthew Lawton
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Weiwei Lin
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Raghuveera Goel
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ivan Luptak
- Myocardial Biology Unit, Boston University School of Medicine, Boston, MA 02118, USA
| | - Valentina Perissi
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jonathan Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Michael T. Chin
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02145, USA
| | - Christopher Chen
- Department of Biomedical Engineering, Boston University, Boston, MA 02218, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Andrew Emili
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
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Kurbatov I, Dolgalev G, Arzumanian V, Kiseleva O, Poverennaya E. The Knowns and Unknowns in Protein-Metabolite Interactions. Int J Mol Sci 2023; 24:4155. [PMID: 36835565 PMCID: PMC9964805 DOI: 10.3390/ijms24044155] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Increasing attention has been focused on the study of protein-metabolite interactions (PMI), which play a key role in regulating protein functions and directing an orchestra of cellular processes. The investigation of PMIs is complicated by the fact that many such interactions are extremely short-lived, which requires very high resolution in order to detect them. As in the case of protein-protein interactions, protein-metabolite interactions are still not clearly defined. Existing assays for detecting protein-metabolite interactions have an additional limitation in the form of a limited capacity to identify interacting metabolites. Thus, although recent advances in mass spectrometry allow the routine identification and quantification of thousands of proteins and metabolites today, they still need to be improved to provide a complete inventory of biological molecules, as well as all interactions between them. Multiomic studies aimed at deciphering the implementation of genetic information often end with the analysis of changes in metabolic pathways, as they constitute one of the most informative phenotypic layers. In this approach, the quantity and quality of knowledge about PMIs become vital to establishing the full scope of crosstalk between the proteome and the metabolome in a biological object of interest. In this review, we analyze the current state of investigation into the detection and annotation of protein-metabolite interactions, describe the recent progress in developing associated research methods, and attempt to deconstruct the very term "interaction" to advance the field of interactomics further.
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Affiliation(s)
| | | | | | - Olga Kiseleva
- Institute of Biomedical Chemistry, Moscow 119121, Russia
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Heckendorf C, Blum BC, Lin W, Lawton ML, Emili A. Integration of Metabolomic and Proteomic Data to Uncover Actionable Metabolic Pathways. Methods Mol Biol 2023; 2660:137-148. [PMID: 37191795 DOI: 10.1007/978-1-0716-3163-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Mass spectrometry (MS) is an important tool for biological studies because it is capable of interrogating a diversity of biomolecules (proteins, drugs, metabolites) not captured via alternate genomic platforms. Unfortunately, downstream data analysis becomes complicated when attempting to evaluate and integrate measurements of different molecular classes and requires the aggregation of expertise from different relevant disciplines. This complexity represents a significant bottleneck that limits the routine deployment of MS-based multi-omic methods, despite the unmatched biological and functional insight the data can provide. To address this unmet need, our group introduced Omics Notebook as an open-source framework for facilitating exploratory analysis, reporting and integrating MS-based multi-omic data in a way that is automated, reproducible and customizable. By deploying this pipeline, we have devised a framework for researchers to more rapidly identify functional patterns across complex data types and focus on statistically significant and biologically interesting aspects of their multi-omic profiling experiments. This chapter aims to describe a protocol which leverages our publicly accessible tools to analyze and integrate data from high-throughput proteomics and metabolomics experiments and produce reports that will facilitate more impactful research, cross-institutional collaborations, and wider data dissemination.
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Affiliation(s)
- Christian Heckendorf
- Center for Network Systems Biology, Boston University, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Weiwei Lin
- Center for Network Systems Biology, Boston University, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Matthew L Lawton
- Center for Network Systems Biology, Boston University, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA.
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
- Division of Oncological Sciences, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
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