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Panyard DJ, Yu B, Snyder MP. The metabolomics of human aging: Advances, challenges, and opportunities. SCIENCE ADVANCES 2022; 8:eadd6155. [PMID: 36260671 PMCID: PMC9581477 DOI: 10.1126/sciadv.add6155] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
As the global population becomes older, understanding the impact of aging on health and disease becomes paramount. Recent advancements in multiomic technology have allowed for the high-throughput molecular characterization of aging at the population level. Metabolomics studies that analyze the small molecules in the body can provide biological information across a diversity of aging processes. Here, we review the growing body of population-scale metabolomics research on aging in humans, identifying the major trends in the field, implicated biological pathways, and how these pathways relate to health and aging. We conclude by assessing the main challenges in the research to date, opportunities for advancing the field, and the outlook for precision health applications.
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Affiliation(s)
- Daniel J. Panyard
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
- Corresponding author. (D.J.P.); (M.P.S.)
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
- Corresponding author. (D.J.P.); (M.P.S.)
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de Oliveira VM, Dias MMG, Avelino TM, Videira NB, da Silva FB, Doratioto TR, Whitford PC, Leite VBP, Figueira ACM. pH and the Breast Cancer Recurrent Mutation D538G Affect the Process of Activation of Estrogen Receptor α. Biochemistry 2022; 61:455-463. [PMID: 35238537 DOI: 10.1021/acs.biochem.1c00806] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Estrogen receptor α (ERα) is a regulatory protein that can access a set of distinct structural configurations. ERα undergoes extensive remodeling as it interacts with different agonists and antagonists, as well as transcription activation and repression factors. Moreover, breast cancer tumors resistant to hormone therapy have been associated with the imbalance between the active and inactive ERα states. Cancer-activating mutations in ERα play a crucial role in this imbalance and can promote the progression of cancer. However, the rate of this progression can also be increased by dysregulated pH in the tumor microenvironment. Many molecular aspects of the process of activation of ERα that can be affected by these pH changes and mutations are still unclear. Thus, we applied computational and experimental techniques to explore the activation process dynamics of ER for environments with different pHs and in the presence of one of the most recurrent cancer-activating mutations, D538G. Our results indicated that the effect of the pH increase associated with the D538G mutation promoted a robust stabilization of the active state of ER. We were also able to determine the main protein regions that have the most potential to influence the activation process under different pH conditions, which may provide targets of future therapeutics for the treatment of hormone-resistant breast cancer tumors. Finally, the approach used here can be applied for proteins associated with the proliferation of other cancer types, which can also have their function affected by small pH changes.
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Affiliation(s)
- Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM, Campinas 13083-970, SP, Brazil
| | - Marieli M G Dias
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM, Campinas 13083-970, SP, Brazil
| | - Thayná M Avelino
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM, Campinas 13083-970, SP, Brazil
| | - Natália B Videira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM, Campinas 13083-970, SP, Brazil
| | - Fernando B da Silva
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto 01140-070, SP, Brazil
| | - Tábata R Doratioto
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM, Campinas 13083-970, SP, Brazil
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Vitor B P Leite
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto 01140-070, SP, Brazil
| | - Ana Carolina M Figueira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM, Campinas 13083-970, SP, Brazil
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Loveland JL, Lank DB, Küpper C. Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs. Front Genet 2021; 12:641620. [PMID: 34149796 PMCID: PMC8213371 DOI: 10.3389/fgene.2021.641620] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/22/2021] [Indexed: 11/22/2022] Open
Abstract
Chromosomal inversions are structural rearrangements that frequently provide genomic substrate for phenotypic diversity. In the ruff Philomachus pugnax, three distinct male reproductive morphs (Independents, Satellites and Faeders) are genetically determined by a 4.5 Mb autosomal inversion. Here we test how this stable inversion polymorphism affects gene expression in males during the lekking season. Gene expression may be altered through disruptions at the breakpoints and the accumulation of mutations due to suppressed recombination. We used quantitative PCR to measure expression of 11 candidate inversion genes across three different tissues (liver, adrenal glands and gonads) and tested for allelic imbalance in four inversion genes across 12 males of all three morphs (8 Independents, 2 Satellites, 2 Faeders). We quantified transcripts of CENPN, an essential gene disrupted by the inversion at the proximal breakpoint, at different exons distributed near and across the breakpoint region. Consistent with dosage dependent gene expression for the breakpoint gene CENPN, we found that expression in Independents was broadly similar for transcripts segments from inside and outside the inversion regions, whereas for Satellites and Faeders, transcript segments outside of the inversion showed at least twofold higher expression than those spanning over the breakpoint. Within the inversion, observed expression differences for inversion males across all four genes with allele-specific primers were consistent with allelic imbalance. We further analyzed gonadal expression of two inversion genes, HSD17B2 and SDR42E1, along with 12 non-inversion genes related to steroid metabolism and signaling in 25 males (13 Independents, 7 Satellites, 5 Faeders). Although we did not find clear morph differentiation for many individual genes, all three morphs could be separated based on gene expression differences when using linear discriminant analysis (LDA), regardless of genomic location (i.e., inside or outside of the inversion). This was robust to the removal of genes with the highest loadings. Pairwise correlations in the expression of genes showed significant correlations for 9–18 pairs of genes within morphs. However, between morphs, we only found a single association between genes SDR42E1 and AROM for Independents and Satellites. Our results suggest complex and wide-ranging changes in gene expression caused by structural variants.
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Affiliation(s)
- Jasmine L Loveland
- Research Group for Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - David B Lank
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Clemens Küpper
- Research Group for Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Seewiesen, Germany
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Nugent BM, Stiver KA, Alonzo SH, Hofmann HA. Neuroendocrine profiles associated with discrete behavioural variation in
Symphodus ocellatus
, a species with male alternative reproductive tactics. Mol Ecol 2016; 25:5212-5227. [DOI: 10.1111/mec.13828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/21/2022]
Affiliation(s)
- B. M. Nugent
- Department of Ecology and Evolutionary Biology Yale University 165 Prospect St. New Haven CT 06520 USA
- Department of Integrative Biology Center for Computational Biology and Bioinformatics The University of Texas at Austin 2415 Speedway Austin TX 78712 USA
| | - K. A. Stiver
- Department of Ecology and Evolutionary Biology Yale University 165 Prospect St. New Haven CT 06520 USA
- Department of Psychology Southern Connecticut State University 501 Crescent St. New Haven CT 06515 USA
| | - S. H. Alonzo
- Department of Ecology and Evolutionary Biology Yale University 165 Prospect St. New Haven CT 06520 USA
- Department of Ecology and Evolutionary Biology University of California Santa Cruz 1156 High St. Santa Cruz CA 95064 USA
| | - H. A. Hofmann
- Department of Integrative Biology Center for Computational Biology and Bioinformatics The University of Texas at Austin 2415 Speedway Austin TX 78712 USA
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Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Sci 2014; 12:23. [PMID: 24987309 PMCID: PMC4077045 DOI: 10.1186/1477-5956-12-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/25/2014] [Indexed: 01/01/2023] Open
Abstract
Background Tight spatio-temporal signaling of cytoskeletal and adhesion dynamics is required for localized membrane protrusion that drives directed cell migration. Different ensembles of proteins are therefore likely to get recruited and phosphorylated in membrane protrusions in response to specific cues. Results Here, we use an assay that allows to biochemically purify extending protrusions of cells migrating in response to three prototypical receptors: integrins, recepor tyrosine kinases and G-coupled protein receptors. Using quantitative proteomics and phospho-proteomics approaches, we provide evidence for the existence of cue-specific, spatially distinct protein networks in the different cell migration modes. Conclusions The integrated analysis of the large-scale experimental data with protein information from databases allows us to understand some emergent properties of spatial regulation of signaling during cell migration. This provides the cell migration community with a large-scale view of the distribution of proteins and phospho-proteins regulating directed cell migration.
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