1
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Rubalcava-Gracia D, Bubb K, Levander F, Burr S, August A, Chinnery P, Koolmeister C, Larsson NG. LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation. Nucleic Acids Res 2024; 52:11266-11282. [PMID: 39087558 PMCID: PMC11472161 DOI: 10.1093/nar/gkae662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Bubb
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Levander
- Department en Immunotechnology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Amelie V August
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Camilla Koolmeister
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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2
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Hernández-Melgar AG, Guerrero A, Moreno-Ulloa A. Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study. J Proteome Res 2024; 23:4273-4285. [PMID: 39024464 DOI: 10.1021/acs.jproteome.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an intersubject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of oil-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.
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Affiliation(s)
- Alan G Hernández-Melgar
- MS2 Laboratory, Biomedical Innovation Department, Ensenada Center for Scientific Research and Higher Education, Baja California (CICESE), No. 3918, Zona Playitas, Ensenada 22860, Baja California, Mexico
- Posgrado en Ciencias de la Vida, CICESE, Ensenada 22860, Baja California, Mexico
| | - Abraham Guerrero
- CONAHCyT Research, Research Center in Food & Development A.C. (CIAD), Mazatlán 82112, Sinaloa, Mexico
| | - Aldo Moreno-Ulloa
- MS2 Laboratory, Biomedical Innovation Department, Ensenada Center for Scientific Research and Higher Education, Baja California (CICESE), No. 3918, Zona Playitas, Ensenada 22860, Baja California, Mexico
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3
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Sittisaree W, Yokthongwattana K, Aonbangkhen C, Yingchutrakul Y, Krobthong S. Effect of NH4Cl supplementation on growth, photosynthesis, and triacylglycerol content in Chlamydomonas reinhardtii under mixotrophic cultivation. J Appl Microbiol 2024; 135:lxae233. [PMID: 39257021 DOI: 10.1093/jambio/lxae233] [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: 01/24/2024] [Revised: 08/20/2024] [Accepted: 09/09/2024] [Indexed: 09/12/2024]
Abstract
AIM Ammonium chloride (NH4Cl) is one of the nitrogen sources for microalgal cultivation. An excessive amounts of NH4Cl are toxic for microalgae. However, combining mixotrophic conditions and excessive quantities of NH4Cl positively affects microalgal biomass and lipid production. In this study, we investigated the impact of NH4Cl on the growth, biomass, and triglyceride (TAG) content of the green microalga Chlamydomonas reinhardtii especially under mixotrophic conditions. METHODS AND RESULTS Under photoautotrophic conditions (without organic carbon supplementation), adding 25 mM NH4Cl had no significant effect on microalgal growth or TAG content. However, under mixotrophic condition (with acetate supplementation), NH4Cl interfered with microalgal growth while inducing TAG content. To explore these effects further, we conducted a two-step cultivation process and found that NH4Cl reduced microalgal growth, but induced total lipid and TAG content, especially after 4-day cultivation. The photosynthesis performances showed that NH4Cl completely inhibited oxygen evolution on day 4. However, NH4Cl slightly reduced the Fv/Fm ratio indicating that the NH4Cl supplementation directly affects microalgal photosynthesis. To investigate the TAG induction effect by NH4Cl, we compared the protein expression profiles of microalgae grown mixotrophically with and without 25 mM NH4Cl using a proteomics approach. This analysis identified 1782 proteins, with putative acetate uptake transporter GFY5 and acyl-coenzyme A oxidase being overexpressed in the NH4Cl-treated group. CONCLUSION These findings suggested that NH4Cl supplementation may stimulate acetate utilization and fatty acid synthesis pathways in microalgae cells. Our study indicated that NH4Cl supplementation can induce microalgal biomass and lipid production, particularly when combined with mixotrophic conditions.
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Affiliation(s)
- Wattanapong Sittisaree
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | | | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | | | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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4
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Resjö S, Willforss J, Large A, Siino V, Alexandersson E, Levander F, Andreasson E. Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109032. [PMID: 39181085 DOI: 10.1016/j.plaphy.2024.109032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/08/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
There are limited molecular data and few biomarkers available for studies of field-grown plants, especially for plants grown during extremely long days. In this study we present quantitative proteomics data from 3 years of field trials on potato, conducted in northern and southern Sweden and analyze over 3000 proteins per year of the study and complement the proteomic analysis with metabolomic and transcriptomic analyses. Small but consistent differences linked to the longer days (an average of four more hours of light per day) in northern Sweden (20 h light/day) compared to southern Sweden can be observed, with a high correlation between the mRNA determined by RNA-seq and protein abundances. The majority of the proteins with differential abundances between northern and southern Sweden could be divided into three groups: metabolic enzymes (especially GABA metabolism), proteins involved in redox metabolism, and hydrolytic enzymes. The observed differences in metabolic enzyme abundances corresponded well with untargeted metabolite data determined by GC and LC mass-spectrometry. We also analyzed differences in protein abundance between potato varieties that performed relatively well in northern Sweden in terms of yield with those that performed relatively less well. This comparison indicates that the proteins with higher abundance in the high-yield quotient group are more anabolic in their character, whereas the proteins with lower abundance are more catabolic. Our results create a base of information about potato "field-omics" for improved understanding of physiological and molecular processes in field-grown plants, and our data indicate that the potato plant is not generally stressed by extremely long days.
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Affiliation(s)
- Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden.
| | | | - Annabel Large
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden
| | | | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden
| | | | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden
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5
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da Silva Pescador G, Baia Amaral D, Varberg JM, Zhang Y, Hao Y, Florens L, Bazzini AA. Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis. Cell Rep 2024; 43:114769. [PMID: 39302832 DOI: 10.1016/j.celrep.2024.114769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/22/2024] [Accepted: 08/30/2024] [Indexed: 09/22/2024] Open
Abstract
The maternal-to-zygotic transition is crucial in embryonic development, marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However, the changes occurring at the protein level during this transition remain unclear. Here, we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry, integrating transcriptomics and translatomics datasets. Our data show that, unlike RNA changes, protein changes are less dynamic. Further, increases in protein levels correlate with mRNA translation, whereas declines in protein levels do not, suggesting active protein degradation processes. Interestingly, proteins from pure zygotic genes are present at fertilization, challenging existing mRNA-based gene classifications. As a proof of concept, we utilized CRISPR-Cas13d to target znf281b mRNA, a gene whose protein significantly accumulates within the first 2 h post-fertilization, demonstrating its crucial role in development. Consequently, our protein profiling, coupled with CRISPR-Cas13d, offers a complementary approach to unraveling maternal factor function during embryonic development.
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Affiliation(s)
| | | | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas School of Medicine, Kansas City, KS 66160, USA.
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6
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Thowfeequ S, Fiorentino J, Hu D, Solovey M, Ruane S, Whitehead M, Zhou F, Godwin J, Mateo-Otero Y, Vanhaesebroeck B, Scialdone A, Srinivas S. An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migration. Dev Cell 2024; 59:2347-2363.e9. [PMID: 38843837 DOI: 10.1016/j.devcel.2024.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/09/2023] [Accepted: 05/14/2024] [Indexed: 09/12/2024]
Abstract
The anterior visceral endoderm (AVE) differs from the surrounding visceral endoderm (VE) in its migratory behavior and ability to restrict primitive streak formation to the opposite side of the mouse embryo. To characterize the molecular bases for the unique properties of the AVE, we combined single-cell RNA sequencing of the VE prior to and during AVE migration with phosphoproteomics, high-resolution live-imaging, and short-term lineage labeling and intervention. This identified the transient nature of the AVE with attenuation of "anteriorizing" gene expression as cells migrate and the emergence of heterogeneities in transcriptional states relative to the AVE's position. Using cell communication analysis, we identified the requirement of semaphorin signaling for normal AVE migration. Lattice light-sheet microscopy showed that Sema6D mutants have abnormalities in basal projections and migration speed. These findings point to a tight coupling between transcriptional state and position of the AVE and identify molecular controllers of AVE migration.
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Affiliation(s)
- Shifaan Thowfeequ
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Jonathan Fiorentino
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 81377, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Rome 00161, Italy
| | - Di Hu
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Maria Solovey
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 81377, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Sharon Ruane
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Maria Whitehead
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Felix Zhou
- University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathan Godwin
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK
| | - Yentel Mateo-Otero
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK; Unit of Cell Biology, Department of Biology, University of Girona, Girona 17004, Spain
| | | | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich 81377, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany.
| | - Shankar Srinivas
- Institute for Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7TY, UK.
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7
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Flanagan SD, Hougland JR, Zeng X, Cantrell PS, Sun M, Jones-Laughner J, Canino MC, Hughes JM, Foulis SA, Taylor KM, Walker LA, Guerriere KI, Sterczala AJ, Connaboy C, Beckner ME, Matheny RW, Nindl BC. Urinary Proteomic Biomarkers of Trabecular Bone Volume Change during Army Basic Combat Training. Med Sci Sports Exerc 2024; 56:1644-1654. [PMID: 38758530 DOI: 10.1249/mss.0000000000003464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
PURPOSE The purpose of this study is to optimize a dMS-based urinary proteomic technique and evaluate the relationship between urinary proteome content and adaptive changes in bone microarchitecture during BCT. METHODS Urinary proteomes were analyzed with an optimized dMS technique in two groups of 13 recruits ( N = 26) at the beginning (Pre) and end (Post) of BCT. Matched by age (21 ± 4 yr), sex (16 W), and baseline tibial trabecular bone volume fractions (Tb.BV/TV), these groups were distinguished by the most substantial (High) and minimal (Low) improvements in Tb.BV/TV. Differential protein expression was analyzed with mixed permutation ANOVA and false discovery proportion-based adjustment for multiple comparisons. RESULTS Tibial Tb.BV/TV increased from pre- to post-BCT in High (3.30 ± 1.64%, P < 0.0001) but not Low (-0.35 ± 1.25%, P = 0.4707). The optimized dMS technique identified 10,431 peptides from 1368 protein groups that represented 165 integrative biological processes. Seventy-four urinary proteins changed from pre- to post-BCT ( P = 0.0019), and neutrophil-mediated immunity was the most prominent ontology. Two proteins (immunoglobulin heavy constant gamma 4 and C-type lectin domain family 4 member G) differed from pre- to post-BCT in High and Low ( P = 0.0006). CONCLUSIONS The dMS technique can identify more than 1000 urinary proteins. At least 74 proteins are responsive to BCT, and other principally immune system-related proteins show differential expression patterns that coincide with adaptive bone formation.
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Affiliation(s)
| | | | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA
| | - Pamela S Cantrell
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA
| | - Mai Sun
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA
| | | | - Maria C Canino
- Department of Sports Medicine and Nutrition, School of Health and Rehabilitation Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Julie M Hughes
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA
| | - Stephen A Foulis
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA
| | - Kathryn M Taylor
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA
| | - Leila A Walker
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA
| | - Katelyn I Guerriere
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA
| | - Adam J Sterczala
- Department of Sports Medicine and Nutrition, School of Health and Rehabilitation Sciences, University of Pittsburgh, Pittsburgh, PA
| | | | - Meaghan E Beckner
- Military Performance Division, United States Army Research Institute of Environmental Medicine, Natick, MA
| | - Ronald W Matheny
- Military Operational Medicine Research Program, Fort Detrick, MD
| | - Bradley C Nindl
- Department of Sports Medicine and Nutrition, School of Health and Rehabilitation Sciences, University of Pittsburgh, Pittsburgh, PA
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8
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Junior SM, Levander F. Automated multiplexed affinity-based enrichment of peptides for LC-MS/MS plasma proteomics. Proteomics 2024:e2400049. [PMID: 39192483 DOI: 10.1002/pmic.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 08/05/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
Plasma proteomics offers high potential for biomarker discovery, as plasma is collected through a minimally invasive procedure and constitutes the most complex human-derived proteome. However, the wide dynamic range poses a significant challenge. Here, we propose a semi-automated method based on the use of multiple single chain variable fragment antibodies, each enriching for peptides found in up to a few hundred proteins. This approach allows for the analysis of a complementary fraction compared to full proteome analysis. Proteins from pooled plasma were extracted and digested before testing the performance of 29 different antibodies with the aim of reproducibly maximizing peptide enrichment. Our results demonstrate the enrichment of 3662 peptides not detected in neat plasma or negative controls. Moreover, most antibodies were able to enrich for at least 155 peptides across different levels of abundance in plasma. To further reduce analysis time, a combination of antibodies was used in a multiplexed setting. Repeated sample analyses showed low coefficients of variation, and the method is flexible in terms of affinity binders. It does not impose drastic increases in instrument time, thus showing excellent potential for usage in large scale discovery projects.
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Affiliation(s)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, Sweden
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9
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de Ávila RI, Ljungberg Silic L, Carreira-Santos S, Merényi G, Bergendorff O, Zeller KS. In vitro characterisation of a novel rubber contact allergen in protective gloves. Contact Dermatitis 2024. [PMID: 39183491 DOI: 10.1111/cod.14682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/30/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Allergic contact dermatitis (ACD) from protective gloves is often caused by rubber additives, such as accelerators. However, while accelerator-free rubber gloves are available, they still cause ACD in some individuals. OBJECTIVES A new allergen, 2-cyаnоethyl dimethyldithiocarbamate, (CEDMC), has recently been identified in accelerator-free gloves, and we here provide a first in vitro characterisation of CEDMC in a dendritic cell (DC)-like cell model along with three reference sensitizer rubber chemicals, consisting of tetraethylthiuram disulfide (TETD) and two xanthogenates. METHODS Cellular responses after the exposure to the rubber chemicals were assessed using a transcriptomic approach, multiplex cytokine secretion profiling, and flow cytometry to determine DC model activation marker expression and apoptosis induction. RESULTS CEDMC and all other sensitizers were classified as strong skin sensitizers with the transcriptomic approach. They all significantly increased IL-8 secretion and exposure to all except one increased CD86 DC activation marker expression. When tested, CEDMC induced apoptosis, however, delayed compared to TETD. CONCLUSIONS The in vitro data corroborate CEDMC, TETD, and investigated xanthogenates as skin sensitizers. Transcriptomic analyses further reveal unique cellular responses induced by CEDMC, which together with future study can contribute to better understanding of cellular mechanisms underlying the sensitising capacity of rubber chemicals.
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Affiliation(s)
| | - Linda Ljungberg Silic
- Department of Occupational and Environmental Dermatology (DOED), Lund University, Skåne University Hospital, Malmö, Sweden
| | | | - Gábor Merényi
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Ola Bergendorff
- Department of Occupational and Environmental Dermatology (DOED), Lund University, Skåne University Hospital, Malmö, Sweden
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10
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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11
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Humphries EM, Loudon C, Craft GE, Hains PG, Robinson PJ. Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics. Anal Chem 2024; 96:13358-13370. [PMID: 39102789 DOI: 10.1021/acs.analchem.3c04479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs). Using this, five extraction methods from the literature were modified and evaluated for their performance using kidney, leg muscle, lung, and testicular rat organs. All methods performed well, except for SP3 due to insufficient tissue lysis. Heat n' Beat was the fastest and most reproducible method with the highest digestion efficiency and lowest CVs. S-Trap produced the highest peptide yield, while TFE produced the best phosphopeptide enrichment efficiency. The quantitation of FFPE-derived peptides remains an ongoing challenge with bias in UV and fluorescence assays across methods, most notably in SPEED. Functional enrichment analysis demonstrated that each method favored extracting some gene ontology cellular components over others including chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, and nucleoplasm protein groups. The outcome is a set of recommendations for choosing the most appropriate method for different settings.
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Affiliation(s)
- Erin M Humphries
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Clare Loudon
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - George E Craft
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
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12
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Samutrtai P, Yingchutrakul Y, Faikhruea K, Vilaivan T, Chaikeeratisak V, Chatwichien J, Krobthong S, Aonbangkhen C. Vernonia amygdalina Leaf Extract Induces Apoptosis in HeLa Cells: A Metabolomics and Proteomics Study. Pharmaceuticals (Basel) 2024; 17:1079. [PMID: 39204184 PMCID: PMC11360076 DOI: 10.3390/ph17081079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
Medicinal plants produce various bioactive molecules with potential anti-cancer properties with favorable safety profiles. We aimed to investigate the comprehensive composition of Vernonia amygdalina leaf extract and its cytotoxic effects via apoptosis in HeLa cells. The metabolomics approach using LC-MS/MS was conducted to gather the metabolite profile of the extract. Proteomics was performed to understand the comprehensive mechanistic pathways of action. The apoptosis was visualized by cellular staining and the apoptotic proteins were evaluated. V. amygdalina leaf extract exhibited dose-dependent cytotoxic effects on both HeLa and Vero cells after 24 h of exposure in the MTT assay with the IC50 values of 0.767 ± 0.0334 and 4.043 ± 0.469 µg mL-1, respectively, which demonstrated a higher concentration required for Vero cell cytotoxicity. The metabolomic profile of 112 known metabolites specified that the majority of them were alkaloids, phenolic compounds, and steroids. Among these metabolites, deacetylvindoline and licochalcone B were suggested to implicate cytotoxicity. The cytotoxic pathways involved the response to stress and cell death which was similar to doxorubicin. The upstream regulatory proteins, phosphatase and tensin homolog deleted on chromosome ten (PTEN) and X-box binding protein 1 (XBP1), were significantly altered, supporting the regulation of apoptosis and cell death. The levels of apoptotic proteins, c-Jun N-terminal kinases (JNK), p53, and caspase-9 were significantly increased. The novel insights gained from the metabolomic profiling and proteomic pathway analysis of V. amygdalina leaf extract have identified crucial components related to apoptosis induction, highlighting its potential to develop future chemotherapy.
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Affiliation(s)
- Pawitrabhorn Samutrtai
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand;
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.F.); (T.V.)
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit (OSRU), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.F.); (T.V.)
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Jaruwan Chatwichien
- Program in Chemical Sciences, Chulabhorn Graduate Institute (CGI), Bangkok 10210, Thailand;
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (C.A.)
- Center of Excellence on Petrochemical and Materials Technology, Chulalongkorn University, Bangkok 10330, Thailand
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13
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Seiler S, Rudolf F, Gomes FR, Pavlovic A, Nebel J, Seidenbecher CI, Foo LC. Astrocyte-derived factors regulate CNS myelination. Glia 2024. [PMID: 39092473 DOI: 10.1002/glia.24596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 06/20/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024]
Abstract
The role that astrocytes play in central nervous system (CNS) myelination is poorly understood. We investigated the contribution of astrocyte-derived factors to myelination and revealed a substantial overlap in the secretomes of human and rat astrocytes. Using in vitro myelinating co-cultures of primary retinal ganglion cells and cortical oligodendrocyte precursor cells, we discovered that factors secreted by resting astrocytes, but not reactive astrocytes, facilitated myelination. Soluble brevican emerged as a new enhancer of developmental myelination in vivo, CNS and its absence was linked to remyelination deficits following an immune-mediated damage in an EAE mouse model. The observed reduction of brevican expression in reactive astrocytes and human MS lesions suggested a potential link to the compromised remyelination characteristic of neurodegenerative diseases. Our findings suggested brevican's role in myelination may be mediated through interactions with binding partners such as contactin-1 and tenascin-R. Proteomic analysis of resting versus reactive astrocytes highlighted a shift in protein expression profiles, pinpointing candidates that either facilitate or impede CNS repair, suggesting that depending on their reactivity state, astrocytes play a dual role during myelination.
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Affiliation(s)
- Sybille Seiler
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Franziska Rudolf
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
| | - Filipa Ramilo Gomes
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
| | - Anto Pavlovic
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
| | - Jana Nebel
- Department Neurochemistry & Molecular Biology, Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
| | - Constanze I Seidenbecher
- Department Neurochemistry & Molecular Biology, Leibniz Institute for Neurobiology (LIN), Magdeburg, Germany
- Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Lynette C Foo
- F. Hoffmann-La Roche, pRED, Neuroscience, Discovery & Translational Area (NRD), Basel, Switzerland
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14
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Al Sultan A, Rattray Z, Rattray NJW. Cytotoxicity and toxicoproteomics analysis of thiazolidinedione exposure in human-derived cardiomyocytes. J Appl Toxicol 2024; 44:1214-1235. [PMID: 38654465 DOI: 10.1002/jat.4613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/16/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
Thiazolidinediones (TZDs) (e.g. pioglitazone and rosiglitazone), known insulin sensitiser agents for type II diabetes mellitus, exhibit controversial effects on cardiac tissue. Despite consensus on their association with increased heart failure risk, limiting TZD use in diabetes management, the underlying mechanisms remain uncharacterised. Herein, we report a comprehensive in vitro investigation utilising a novel toxicoproteomics pipeline coupled with cytotoxicity assays in human adult cardiomyocytes to elucidate mechanistic insights into TZD cardiotoxicity. The cytotoxicity assay findings showed a significant loss of mitochondrial adenosine triphosphate production upon exposure to either TZD agents, which may underpin TZD cardiotoxicity. Our toxicoproteomics analysis revealed that mitochondrial dysfunction primarily stems from oxidative phosphorylation impairment, with distinct signalling mechanisms observed for both agents. The type of cell death differed strikingly between the two agents, with rosiglitazone exhibiting features of caspase-dependent apoptosis and pioglitazone implicating mitochondrial-mediated necroptosis, as evidenced by the protein upregulation in the phosphoglycerate mutase family 5-dynamin-related protein 1 axis. Furthermore, our analysis revealed additional mechanistic aspects of cardiotoxicity, showcasing drug specificity. The downregulation of various proteins involved in protein machinery and protein processing in the endoplasmic reticulum was observed in rosiglitazone-treated cells, implicating proteostasis in the rosiglitazone cardiotoxicity. Regarding pioglitazone, the findings suggested the potential activation of the interplay between the complement and coagulation systems and the disruption of the cytoskeletal architecture, which was primarily mediated through the integrin-signalling pathways responsible for pioglitazone-induced myocardial contractile failure. Collectively, this study unlocks substantial mechanistic insight into TZD cardiotoxicity, providing the rationale for future optimisation of antidiabetic therapies.
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Affiliation(s)
- Abdullah Al Sultan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
- Faculty of Pharmacy, Kuwait University, Safat, Kuwait
| | - Zahra Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Nicholas J W Rattray
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
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15
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Sanz-Martinez P, Tascher G, Cano-Franco S, Cabrerizo-Poveda P, Münch C, Homan EJ, Stolz A. GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention. J Mol Biol 2024; 436:168643. [PMID: 38848865 DOI: 10.1016/j.jmb.2024.168643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Autophagy facilitates the degradation of cellular content via the lysosome and is involved in cellular homeostasis and stress response pathways. As such, malfunction of autophagy is linked to a variety of diseases ranging from organ-specific illnesses like cardiomyopathy to systemic illnesses such as cancer or metabolic syndromes. Given the variety of autophagic functions within a cell and tissue, regulation of autophagy is complex and contains numerous positive and negative feedback loops. While our knowledge of mechanisms for cargo selectivity has significantly improved over the last decade, our understanding of signaling routes activating individual autophagy pathways remains rather sparse. In this resource study, we report on a well-characterized chemical library containing 77 GPCR-targeting ligands that was used to systematically analyze LC3B-based autophagy as well as ER-phagy flux upon compound treatment. Upon others, compounds TC-G 1004, BAY 60-6583, PSNCBAM-1, TC-G 1008, LPA2 Antagonist 1, ML-154, JTC-801 and ML-290 targeting adenosine receptor A2a (ADORA2A), adenosine receptor A2b (ADORA2B), cannabinoid receptor 1 (CNR1), G-protein coupled receptor 39 (GPR39), lysophosphatidic acid receptor 2 (LPAR2), neuropeptide S receptor 1 (NPSR1), opioid related nociceptin receptor 1 (OPRL1), and relaxin receptor 1 (RXFP1), respectively, were hit compounds for general autophagy flux. From these compounds, only JTC-801 markly increased ER-phagy flux. In addition, the global impact of these selected hit compounds were analyzed by TMT-based mass spectrometry and demonstrated the differential impact of targeting GPCRs on autophagy-associated proteins. This chemical screening exercise indicates to a significant cross-talk between GPCR signaling and regulation of autophagy pathways.
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Affiliation(s)
- Pablo Sanz-Martinez
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Sara Cano-Franco
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Paloma Cabrerizo-Poveda
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Solna, Sweden.
| | - Alexandra Stolz
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany.
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16
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Niksirat H, Siino V, Steinbach C, Levander F. The quantification of zebrafish ocular-associated proteins provides hints for sex-biased visual impairments and perception. Heliyon 2024; 10:e33057. [PMID: 38994070 PMCID: PMC11238053 DOI: 10.1016/j.heliyon.2024.e33057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
Biochemical differences between sexes can also be seen in non-sexual organs and may affect organ functions and susceptibility to diseases. It has been shown that there are sex-biased visual perceptions and impairments. Abundance differences of eye proteins could provide explanations for some of these. Exploration of the ocular proteome was performed to find sex-based protein abundance differences in zebrafish Danio rerio. A label-free protein quantification workflow using high-resolution mass spectrometry was employed to find proteins with significant differences between the sexes. In total, 3740 unique master proteins were identified and quantified, and 49 proteins showed significant abundance differences between the eyes of male and female zebrafish. Those proteins belong to lipoproteins, immune system, blood coagulation, antioxidants, iron and heme-binding proteins, ion channels, pumps and exchangers, neuronal and photoreceptor proteins, and the cytoskeleton. An extensive literature review provided clues for the possible links between the sex-biased level of proteins and visual perception and impairments. In conclusion, sexual dimorphism at the protein level was discovered for the first time in the eye of zebrafish and should be accounted for in ophthalmological studies. Data are available via ProteomeXchange with identifier PXD033338.
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Affiliation(s)
- Hamid Niksirat
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Christoph Steinbach
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Vodňany, Czech Republic
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, Sweden
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17
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Johansson E, Nazziwa J, Freyhult E, Hong MG, Lindman J, Neptin M, Karlson S, Rezeli M, Biague AJ, Medstrand P, Månsson F, Norrgren H, Esbjörnsson J, Jansson M. HIV-2 mediated effects on target and bystander cells induce plasma proteome remodeling. iScience 2024; 27:109344. [PMID: 38500818 PMCID: PMC10945182 DOI: 10.1016/j.isci.2024.109344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/23/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
Despite low or undetectable plasma viral load, people living with HIV-2 (PLWH2) typically progress toward AIDS. The driving forces behind HIV-2 disease progression and the role of viremia are still not known, but low-level replication in tissues is believed to play a role. To investigate the impact of viremic and aviremic HIV-2 infection on target and bystander cell pathology, we used data-independent acquisition mass spectrometry to determine plasma signatures of tissue and cell type engagement. Proteins derived from target and bystander cells in multiple tissues, such as the gastrointestinal tract and brain, were detected at elevated levels in plasma of PLWH2, compared with HIV negative controls. Moreover, viremic HIV-2 infection appeared to induce enhanced release of proteins from a broader range of tissues compared to aviremic HIV-2 infection. This study expands the knowledge on the link between plasma proteome remodeling and the pathological cell engagement in tissues during HIV-2 infection.
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Affiliation(s)
- Emil Johansson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Lund University Virus Centre, Lund, Sweden
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, Lund, Sweden
- Lund University Virus Centre, Lund, Sweden
| | - Eva Freyhult
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mun-Gwan Hong
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jacob Lindman
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Malin Neptin
- Department of Translational Medicine, Lund University, Lund, Sweden
- Lund University Virus Centre, Lund, Sweden
| | - Sara Karlson
- Lund University Virus Centre, Lund, Sweden
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Melinda Rezeli
- BioMS – Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, Lund, Sweden
| | | | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Lund, Sweden
- Lund University Virus Centre, Lund, Sweden
| | - Fredrik Månsson
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - Hans Norrgren
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Lund, Sweden
- Lund University Virus Centre, Lund, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marianne Jansson
- Lund University Virus Centre, Lund, Sweden
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - for the SWEGUB CORE group
- Department of Translational Medicine, Lund University, Lund, Sweden
- Lund University Virus Centre, Lund, Sweden
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Laboratory Medicine, Lund University, Lund, Sweden
- BioMS – Swedish National Infrastructure for Biological Mass Spectrometry, Lund University, Lund, Sweden
- National Public Health Laboratory, Bissau, Guinea-Bissau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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18
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Xue X, Demirci D, Lenze EJ, Reynolds Iii CF, Mulsant BH, Wetherell JL, Wu GF, Blumberger DM, Karp JF, Butters MA, Mendes-Silva AP, Vieira EL, Tseng G, Diniz BS. Sex differences in plasma proteomic markers in late-life depression. Psychiatry Res 2024; 334:115773. [PMID: 38350292 PMCID: PMC10947839 DOI: 10.1016/j.psychres.2024.115773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/15/2024]
Abstract
Previous studies have shown significant sex-specific differences in major depressive disorder (MDD) in multiple biological parameters. Most studies focused on young and middle-aged adults, and there is a paucity of information about sex-specific biological differences in older adults with depression (aka, late-life depression (LLD)). To address this gap, this study aimed to evaluate sex-specific biological abnormalities in a large group of individuals with LLD using an untargeted proteomic analysis. We quantified 344 plasma proteins using a multiplex assay in 430 individuals with LLD and 140 healthy comparisons (HC) (age range between 60 and 85 years old for both groups). Sixty-six signaling proteins were differentially expressed in LLD (both sexes). Thirty-three proteins were uniquely associated with LLD in females, while six proteins were uniquely associated with LLD in males. The main biological processes affected by these proteins in females were related to immunoinflammatory control. In contrast, despite the smaller number of associated proteins, males showed dysregulations in a broader range of biological pathways, including immune regulation pathways, cell cycle control, and metabolic control. Sex has a significant impact on biomarker changes in LLD. Despite some overlap in differentially expressed biomarkers, males and females show different patterns of biomarkers changes, and males with LLD exhibit abnormalities in a larger set of biological processes compared to females. Our findings can provide novel targets for sex-specific interventions in LLD.
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Affiliation(s)
- Xiangning Xue
- Department of Biostatistics, University of Pittsburgh School of Public Health, PA USA
| | - Derya Demirci
- UConn Center on Aging, University of Connecticut, Farmington, CT USA
| | - Eric J Lenze
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO USA
| | - Charles F Reynolds Iii
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Benoit H Mulsant
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, & Centre for Addiction and Mental Health, Toronto, ON Canada
| | - Julie Loebach Wetherell
- VA San Diego Healthcare System, Mental Health Impact Unit 3, University of California, San Diego Department of Psychiatry USA
| | - Gregory F Wu
- Department of Neurology, Washington University, St Louis, MO USA
| | - Daniel M Blumberger
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA USA; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, & Centre for Addiction and Mental Health, Toronto, ON Canada
| | - Jordan F Karp
- Department of Psychiatry, The University of Arizona College of Medicine, Tucson, AZ USA
| | - Meryl A Butters
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Ana Paula Mendes-Silva
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Erica L Vieira
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh School of Public Health, PA USA
| | - Breno S Diniz
- UConn Center on Aging, University of Connecticut, Farmington, CT USA; Department of Psychiatry, UConn School of Medicine, Farmington, CT USA.
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19
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Capendale PE, García-Rodríguez I, Ambikan AT, Mulder LA, Depla JA, Freeze E, Koen G, Calitz C, Sood V, Vieira de Sá R, Neogi U, Pajkrt D, Sridhar A, Wolthers KC. Parechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease. Nat Commun 2024; 15:2532. [PMID: 38514653 PMCID: PMC10958052 DOI: 10.1038/s41467-024-46634-9] [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: 11/16/2023] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Picornaviruses are a leading cause of central nervous system (CNS) infections. While genotypes such as parechovirus A3 (PeV-A3) and echovirus 11 (E11) can elicit severe neurological disease, the highly prevalent PeV-A1 is not associated with CNS disease. Here, we expand our current understanding of these differences in PeV-A CNS disease using human brain organoids and clinical isolates of the two PeV-A genotypes. Our data indicate that PeV-A1 and A3 specific differences in neurological disease are not due to infectivity of CNS cells as both viruses productively infect brain organoids with a similar cell tropism. Proteomic analysis shows that PeV-A infection significantly alters the host cell metabolism. The inflammatory response following PeV-A3 (and E11 infection) is significantly more potent than that upon PeV-A1 infection. Collectively, our findings align with clinical observations and suggest a role for neuroinflammation, rather than viral replication, in PeV-A3 (and E11) infection.
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Affiliation(s)
- Pamela E Capendale
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Inés García-Rodríguez
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Anoop T Ambikan
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Lance A Mulder
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Josse A Depla
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- UniQure Biopharma B.V., Department of Research & Development, Paasheuvelweg 25A, Amsterdam, The Netherlands
| | - Eline Freeze
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Gerrit Koen
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Carlemi Calitz
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Vikas Sood
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Renata Vieira de Sá
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Campus Flemingsberg, Stockholm, Sweden
| | - Dasja Pajkrt
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Adithya Sridhar
- OrganoVIR Labs, Emma Children's Hospital, Department of Pediatric Infectious Diseases, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Reproduction and Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands
| | - Katja C Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
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20
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Hu J, Wang SG, Hou Y, Chen Z, Liu L, Li R, Li N, Zhou L, Yang Y, Wang L, Wang L, Yang X, Lei Y, Deng C, Li Y, Deng Z, Ding Y, Kuang Y, Yao Z, Xun Y, Li F, Li H, Hu J, Liu Z, Wang T, Hao Y, Jiao X, Guan W, Tao Z, Ren S, Chen K. Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression. Nat Genet 2024; 56:442-457. [PMID: 38361033 PMCID: PMC10937392 DOI: 10.1038/s41588-024-01662-5] [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: 02/20/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic and spatial transcriptomic and metabolomic analyses on 100 patients with ccRCC from the Tongji Hospital RCC (TJ-RCC) cohort. Our analysis identifies four ccRCC subtypes including De-clear cell differentiated (DCCD)-ccRCC, a subtype with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, reduced metabolic activity, enhanced nutrient uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting that it cannot be cured by nephrectomy alone. Our study also suggests a treatment strategy based on subtype-specific immune cell infiltration that could guide the clinical management of ccRCC.
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Affiliation(s)
- Junyi Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao-Gang Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaxin Hou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lilong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhi Li
- Shanghai Luming Biotech, Shanghai, China
| | - Nisha Li
- Shanghai Luming Biotech, Shanghai, China
- Shanghai OE Biotech, Shanghai, China
| | - Lijie Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Yang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liping Wang
- Department of Pathology, Baylor Scott & White Medical Center, Temple, TX, USA
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiong Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yichen Lei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Changqi Deng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhong Ding
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingchun Kuang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhipeng Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Xun
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuanmao Jiao
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Philadelphia, PA, USA
| | - Wei Guan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Zhen Tao
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shancheng Ren
- Department of Urology, Second Affiliated Hospital of Naval Medical University, Shanghai, China.
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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21
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Tan TCJ, Spanos C, Tollervey D. Improved detection and consistency of RNA-interacting proteomes using DIA SILAC. Nucleic Acids Res 2024; 52:e21. [PMID: 38197237 PMCID: PMC10899761 DOI: 10.1093/nar/gkad1249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
The RNA-interacting proteome is commonly characterized by UV-crosslinking followed by RNA purification, with protein recovery quantified using SILAC labeling followed by data-dependent acquisition (DDA) of proteomic data. However, the low efficiency of UV-crosslinking, combined with limited sensitivity of the DDA approach often restricts detection to relatively abundant proteins, necessitating multiple mass spec injections of fractionated peptides for each biological sample. Here we report an application of data-independent acquisition (DIA) with SILAC in a total RNA-associated protein purification (TRAPP) UV-crosslinking experiment. This gave 15% greater protein detection and lower inter-replicate variation relative to the same biological materials analyzed using DDA, while allowing single-shot analysis of the sample. As proof of concept, we determined the effects of arsenite treatment on the RNA-bound proteome of HEK293T cells. The DIA dataset yielded similar GO term enrichment for RNA-binding proteins involved in cellular stress responses to the DDA dataset while detecting extra proteins unseen by DDA. Overall, the DIA SILAC approach improved detection of proteins over conventional DDA SILAC for generating RNA-interactome datasets, at a lower cost due to reduced machine time. Analyses are described for TRAPP data, but the approach is suitable for proteomic analyses following essentially any RNA-binding protein enrichment technique.
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Affiliation(s)
- Thomas C J Tan
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh. Edinburgh EH9 3BF, Scotland, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh. Edinburgh EH9 3BF, Scotland, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh. Edinburgh EH9 3BF, Scotland, UK
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22
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Matějková T, Dodoková A, Kreisinger J, Stopka P, Stopková R. Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice. Microbiol Spectr 2024; 12:e0203723. [PMID: 38171017 PMCID: PMC10846187 DOI: 10.1128/spectrum.02037-23] [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: 05/15/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by Firmicutes and Proteobacteria but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera Gemella and Streptococcus, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of Muribacter and Rodentibacter. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.IMPORTANCEOur data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.
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Affiliation(s)
- Tereza Matějková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Alica Dodoková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Romana Stopková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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23
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Bruszel B, Tóth-Molnár E, Janáky T, Szabó Z. Sources of Variance in Human Tear Proteomic Samples: Statistical Evaluation, Quality Control, Normalization, and Biological Insight. Int J Mol Sci 2024; 25:1559. [PMID: 38338841 PMCID: PMC10855525 DOI: 10.3390/ijms25031559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Human tear fluid contains numerous compounds, which are present in highly variable amounts owing to the dynamic and multipurpose functions of tears. A better understanding of the level and sources of variance is essential for determining the functions of the different tear components and the limitations of tear samples as a potential biomarker source. In this study, a quantitative proteomic method was used to analyze variations in the tear protein profiles of healthy volunteers. High day-to-day and inter-eye personal variances were observed in the tear volumes, protein content, and composition of the tear samples. Several normalization and outlier exclusion approaches were evaluated to decrease variances. Despite the intrapersonal variances, statistically significant differences and cluster analysis revealed that proteome profile and immunoglobulin composition of tear fluid present personal characteristics. Using correlation analysis, we could identify several correlating protein clusters, mainly related to the source of the proteins. Our study is the first attempt to achieve more insight into the biochemical background of human tears by statistical evaluation of the experimentally observed dynamic behavior of the tear proteome. As a pilot study for determination of personal protein profiles of the tear fluids of individual patients, it contributes to the application of this noninvasively collectible body fluid in personal medicine.
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Affiliation(s)
- Bella Bruszel
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (B.B.); (T.J.)
| | - Edit Tóth-Molnár
- Department of Ophtalmology, Albert Szent-Györgyi Health Centre, University of Szeged, Korányi Fasor 10-11, H-6720 Szeged, Hungary;
| | - Tamás Janáky
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (B.B.); (T.J.)
| | - Zoltán Szabó
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary; (B.B.); (T.J.)
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24
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Bett VK, Macon A, Vicoso B, Elkrewi M. Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation. Genome Biol Evol 2024; 16:evae006. [PMID: 38245839 PMCID: PMC10827361 DOI: 10.1093/gbe/evae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/27/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.
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Affiliation(s)
| | - Ariana Macon
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
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25
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Bouyssié D, Altıner P, Capella-Gutierrez S, Fernández JM, Hagemeijer YP, Horvatovich P, Hubálek M, Levander F, Mauri P, Palmblad M, Raffelsberger W, Rodríguez-Navas L, Di Silvestre D, Kunkli BT, Uszkoreit J, Vandenbrouck Y, Vizcaíno JA, Winkelhardt D, Schwämmle V. WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows. J Proteome Res 2024; 23:418-429. [PMID: 38038272 DOI: 10.1021/acs.jproteome.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.
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Affiliation(s)
- David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III─Paul Sabatier (UT3), 31062 Toulouse, France
- Proteomics French Infrastructure, ProFI, FR 2048 Toulouse, France
| | - Pınar Altıner
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III─Paul Sabatier (UT3), 31062 Toulouse, France
| | | | - José M Fernández
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Yanick Paco Hagemeijer
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, CAS, 160 00 Prague, Czech Republic
| | - Fredrik Levander
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, 22100 Lund, Sweden
| | - Pierluigi Mauri
- Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), Segrate, 20054 Milan, Italy
| | - Magnus Palmblad
- Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Wolfgang Raffelsberger
- Wolfgang Raffelsberger: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Laura Rodríguez-Navas
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Dario Di Silvestre
- Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), Segrate, 20054 Milan, Italy
| | - Balázs Tibor Kunkli
- Balázs Tibor Kunkli: Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Julian Uszkoreit
- Medical Faculty, Medical Bioinformatics, Ruhr University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany
- Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Yves Vandenbrouck
- Proteomics French Infrastructure, ProFI, FR 2048 Toulouse, France
- CEA, Fundamental Research Division, Proteomics French Infrastructure, 91191 Gif-sur-Yvette, France
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust, Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Dirk Winkelhardt
- Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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26
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Fleitas O, Fontes W, De Souza CM, Da Costa MC, Cardoso MH, Castro MS, Sousa MV, Ricart CAO, Ramada MHS, Duque HM, Porto WF, Silva ON, Franco OL. A proteomic perspective on the resistance response of Klebsiella pneumoniae to antimicrobial peptide PaDBS1R1. J Antimicrob Chemother 2024; 79:112-122. [PMID: 37966053 DOI: 10.1093/jac/dkad354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/31/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND The synthetic antimicrobial peptide, PaDBS1R1, has been reported as a powerful anti-Klebsiella pneumoniae antimicrobial. However, there is only scarce knowledge about whether K. pneumoniae could develop resistance against PaDBS1R1 and which resistance mechanisms could be involved. OBJECTIVES Identify via label-free shotgun proteomics the K. pneumoniae resistance mechanisms developed against PaDBS1R1. METHODS An adaptive laboratory evolution experiment was performed to obtain a PaDBS1R1-resistant K. pneumoniae lineage. Antimicrobial susceptibility was determined through microdilution assay. Modifications in protein abundances between the resistant and sensitive lineages were measured via label-free quantitative shotgun proteomics. Enriched Gene Ontology terms and KEGG pathways were identified through over-representation analysis. Data are available via ProteomeXchange with identifier PXD033020. RESULTS K. pneumoniae ATCC 13883 parental strain challenged with increased subinhibitory PaDBS1R1 concentrations allowed the PaDBS1R1-resistant K. pneumoniae lineage to emerge. Proteome comparisons between PaDBS1R1-resistant K. pneumoniae and PaDBS1R1-sensitive K. pneumoniae under PaDBS1R1-induced stress conditions enabled the identification and quantification of 1702 proteins, out of which 201 were differentially abundant proteins (DAPs). The profiled DAPs comprised 103 up-regulated proteins (adjusted P value < 0.05, fold change ≥ 2) and 98 down-regulated proteins (adjusted P value < 0.05, fold change ≤ 0.5). The enrichment analysis suggests that PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery could be relevant resistance mechanisms against PaDBS1R1. CONCLUSIONS Based on experimental evolution and a label-free quantitative shotgun proteomic approach, we showed that K. pneumoniae developed resistance against PaDBS1R1, whereas PhoPQ-guided LPS modifications and CpxRA-dependent folding machinery appear to be relevant resistance mechanisms against PaDBS1R1.
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Affiliation(s)
- Osmel Fleitas
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Wagner Fontes
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Camila M De Souza
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Mylena C Da Costa
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Marlon H Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Instituto de Biociências (INBIO), Universidade Federal de Mato Grosso do Sul, Cidade Universitária, 79070900, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mariana S Castro
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Marcelo V Sousa
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Carlos A O Ricart
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Laboratório de Bioquímica e Química de Proteínas, Universidade de Brasília, Brasília, Brazil
| | - Marcelo H S Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Harry M Duque
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - William F Porto
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
| | - Osmar N Silva
- Programa de Pós-graduação em Ciências Farmacêuticas, Universidade Evangélica de Anapólis, University City, 75083-515 Anápolis-GO, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, Brazil
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
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27
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Chua AE, Pfeifer L, Sekera ER, Hummon AB, Desaire H. Workflow for Evaluating Normalization Tools for Omics Data Using Supervised and Unsupervised Machine Learning. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2775-2784. [PMID: 37897440 PMCID: PMC10919320 DOI: 10.1021/jasms.3c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
To achieve high quality omics results, systematic variability in mass spectrometry (MS) data must be adequately addressed. Effective data normalization is essential for minimizing this variability. The abundance of approaches and the data-dependent nature of normalization have led some researchers to develop open-source academic software for choosing the best approach. While these tools are certainly beneficial to the community, none of them meet all of the needs of all users, particularly users who want to test new strategies that are not available in these products. Herein, we present a simple and straightforward workflow that facilitates the identification of optimal normalization strategies using straightforward evaluation metrics, employing both supervised and unsupervised machine learning. The workflow offers a "DIY" aspect, where the performance of any normalization strategy can be evaluated for any type of MS data. As a demonstration of its utility, we apply this workflow on two distinct datasets, an ESI-MS dataset of extracted lipids from latent fingerprints and a cancer spheroid dataset of metabolites ionized by MALDI-MSI, for which we identified the best-performing normalization strategies.
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Affiliation(s)
- Aleesa E. Chua
- Department of Chemistry, University of Kansas, Lawrence, Kansas, United States, 66045
| | - Leah Pfeifer
- Department of Chemistry, University of Kansas, Lawrence, Kansas, United States, 66045
| | - Emily R. Sekera
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, United States, 66045
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28
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Lasne C, Elkrewi M, Toups MA, Layana L, Macon A, Vicoso B. The Scorpionfly (Panorpa cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Mol Biol Evol 2023; 40:msad245. [PMID: 37988296 PMCID: PMC10715201 DOI: 10.1093/molbev/msad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Many insects carry an ancient X chromosome-the Drosophila Muller element F-that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure to that of several dipteran species as well as more distantly related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.
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Affiliation(s)
- Clementine Lasne
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Melissa A Toups
- Department of Life and Environmental Sciences, Bournemouth University, Poole, UK
| | - Lorena Layana
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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29
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Reisbeck L, Linder B, Tascher G, Bozkurt S, Weber KJ, Herold-Mende C, van Wijk SJL, Marschalek R, Schaefer L, Münch C, Kögel D. The iron chelator and OXPHOS inhibitor VLX600 induces mitophagy and an autophagy-dependent type of cell death in glioblastoma cells. Am J Physiol Cell Physiol 2023; 325:C1451-C1469. [PMID: 37899749 DOI: 10.1152/ajpcell.00293.2023] [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: 07/03/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
Abstract
Induction of alternative, non-apoptotic cell death programs such as cell-lethal autophagy and mitophagy represent possible strategies to combat glioblastoma (GBM). Here we report that VLX600, a novel iron chelator and oxidative phosphorylation (OXPHOS) inhibitor, induces a caspase-independent type of cell death that is partially rescued in adherent U251 ATG5/7 (autophagy related 5/7) knockout (KO) GBM cells and NCH644 ATG5/7 knockdown (KD) glioma stem-like cells (GSCs), suggesting that VLX600 induces an autophagy-dependent cell death (ADCD) in GBM. This ADCD is accompanied by decreased oxygen consumption, increased expression/mitochondrial localization of BNIP3 (BCL2 interacting protein 3) and BNIP3L (BCL2 interacting protein 3 like), the induction of mitophagy as demonstrated by diminished levels of mitochondrial marker proteins [e.g., COX4I1 (cytochrome c oxidase subunit 4I1)] and the mitoKeima assay as well as increased histone H3 and H4 lysine tri-methylation. Furthermore, the extracellular addition of iron is able to significantly rescue VLX600-induced cell death and mitophagy, pointing out an important role of iron metabolism for GBM cell homeostasis. Interestingly, VLX600 is also able to completely eliminate NCH644 GSC tumors in an organotypic brain slice transplantation model. Our data support the therapeutic concept of ADCD induction in GBM and suggest that VLX600 may be an interesting novel drug candidate for the treatment of this tumor.NEW & NOTEWORTHY Induction of cell-lethal autophagy represents a possible strategy to combat glioblastoma (GBM). Here, we demonstrate that the novel iron chelator and OXPHOS inhibitor VLX600 exerts pronounced tumor cell-killing effects in adherently cultured GBM cells and glioblastoma stem-like cell (GSC) spheroid cultures that depend on the iron-chelating function of VLX600 and on autophagy activation, underscoring the context-dependent role of autophagy in therapy responses. VLX600 represents an interesting novel drug candidate for the treatment of this tumor.
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Affiliation(s)
- Lisa Reisbeck
- Experimental Neurosurgery, Department of Neurosurgery, Neuroscience Center, Goethe University Hospital, Frankfurt am Main, Germany
| | - Benedikt Linder
- Experimental Neurosurgery, Department of Neurosurgery, Neuroscience Center, Goethe University Hospital, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Süleyman Bozkurt
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), Goethe University Hospital, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Main, a partnership between DKFZ and University Hospital, Frankfurt, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Sjoerd J L van Wijk
- Institute for Pediatric Hematology and Oncology, Goethe University Hospital Frankfurt/Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Main, a partnership between DKFZ and University Hospital, Frankfurt, Germany
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Diagnostic Center of Acute Leukemia, University of Frankfurt, Frankfurt/Main, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany
| | - Donat Kögel
- Experimental Neurosurgery, Department of Neurosurgery, Neuroscience Center, Goethe University Hospital, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Main, a partnership between DKFZ and University Hospital, Frankfurt, Germany
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Chomchoei N, Leelapornpisid P, Tipduangta P, Sangthong P, Papan P, Sirithunyalug B, Samutrtai P. Potential of electro-sprayed purified mangiferin nanoparticles for anti-aging cosmetic applications. RSC Adv 2023; 13:34987-35002. [PMID: 38046636 PMCID: PMC10690135 DOI: 10.1039/d3ra06308a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/23/2023] [Indexed: 12/05/2023] Open
Abstract
The fabrication of mangiferin nanoparticles using an electrospraying technique is a new and promising method for developing nanoparticles with higher efficiency and safety. This study aimed to fabricate mangiferin nanoparticles (MNPs) using cellulose acetate (CA) as a polymer at various parameters using electrospraying. Commercial mangiferin (CM) was purified from 88.46 to 95.71% by a recrystallization method to improve its purity and biological activities and remove any residue. The properties of recrystallized mangiferin (RM) were characterized using DSC, FTIR, X-ray diffraction (XRD) and HPLC. Then its biological activity and proteomics were determined. Proteomics analysis of RM showed that up-regulated proteins were involved in more biological processes than CM. MNPs were fabricated by varying the electrospraying parameters including voltage, the distance between the needle-tip-collector and flow rate. Skin permeation, release and irritation were also evaluated. The results revealed that the average particle size of the MNPs ranged between 295.47 ± 5.58 and 448.87 ± 3.00 nm, and had a smooth spherical morphology in SEM images. The MNPs also showed good potential in antioxidant and anti-aging properties. The encapsulation efficiency of MNPs was determined to be 85.31%. From skin permeation studies of CM, RM, and MNPs, the mangiferin content was found in the stratum corneum and dermis skin layers. Moreover, the MNPs solution had 23.68 ± 0.27% and 11.98 ± 0.13% of mangiferin in the stratum corneum and viable epidermis and dermis, respectively. Additionally, the irritation test by HET-CAM was mild and safe. Therefore, MNPs produced by electrospraying are a promising delivery system for cosmetic/cosmeceutical applications.
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Affiliation(s)
- Neungreuthai Chomchoei
- PhD Degree Program in Pharmacy, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
| | - Pimporn Leelapornpisid
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
- Innovation Center for Holistic Health, Nutraceuticals and Cosmeceuticals, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
| | - Pratchaya Tipduangta
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
| | - Padchanee Sangthong
- Department of Chemistry, Faculty of Science, Chiang Mai University Chiang Mai 50200 Thailand
| | - Phakorn Papan
- Department of Chemistry, Faculty of Science, Chiang Mai University Chiang Mai 50200 Thailand
| | - Busaban Sirithunyalug
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
| | - Pawitrabhorn Samutrtai
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University Chiang Mai 50200 Thailand
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31
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Ashraf MZ, Mogilicherla K, Sellamuthu G, Siino V, Levander F, Roy A. Comparative gut proteomics study revealing adaptive physiology of Eurasian spruce bark beetle, Ips typographus (Coleoptera: Scolytinae). FRONTIERS IN PLANT SCIENCE 2023; 14:1157455. [PMID: 38078109 PMCID: PMC10703158 DOI: 10.3389/fpls.2023.1157455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/01/2023] [Indexed: 01/23/2024]
Abstract
The bark beetle, Ips typographus (L.), is a major pest of Norway spruce, Picea abies (L.), causing enormous economic losses globally. The adult stage of the I. typographus has a complex life cycle (callow and sclerotized); the callow beetles feed ferociously, whereas sclerotized male beetles are more aggressive and pioneers in establishing new colonies. We conducted a comparative proteomics study to understand male and female digestion and detoxification processes in callow and sclerotized beetles. Proteome profiling was performed using high-throughput liquid chromatography-mass spectrometry. A total of >3000 proteins were identified from the bark beetle gut, and among them, 539 were differentially abundant (fold change ±2, FDR <0.05) between callow and sclerotized beetles. The differentially abundant proteins (DAPs) mainly engage with binding, catalytic activity, anatomical activity, hydrolase activity, metabolic process, and carbohydrate metabolism, and hence may be crucial for growth, digestion, detoxification, and signalling. We validated selected DAPs with RT-qPCR. Gut enzymes such as NADPH-cytochrome P450 reductase (CYC), glutathione S-transferase (GST), and esterase (EST) play a crucial role in the I. typographus for detoxification and digesting of host allelochemicals. We conducted enzyme activity assays with them and observed a positive correlation of CYC and GST activities with the proteomic results, whereas EST activity was not fully correlated. Furthermore, our investigation revealed that callow beetles had an upregulation of proteins associated with juvenile hormone (JH) biosynthesis and chitin metabolism, whereas sclerotized beetles exhibited an upregulation of proteins linked to fatty acid metabolism and the TCA cycle. These distinctive patterns of protein regulation in metabolic and functional processes are specific to each developmental stage, underscoring the adaptive responses of I. typographicus in overcoming conifer defences and facilitating their survival. Taken together, it is the first gut proteomic study comparing males and females of callow and sclerotized I. typographus, shedding light on the adaptive ecology at the molecular level. Furthermore, the information about bark beetle handling of nutritionally limiting and defence-rich spruce phloem diet can be utilized to formulate RNAi-mediated beetle management.
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Affiliation(s)
- Muhammad Zubair Ashraf
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Kanakachari Mogilicherla
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Gothandapani Sellamuthu
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, Sweden
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
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32
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Hutchings C, Dawson CS, Krueger T, Lilley KS, Breckels LM. A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data. F1000Res 2023; 12:1402. [PMID: 38021401 PMCID: PMC10683783 DOI: 10.12688/f1000research.139116.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Expression proteomics involves the global evaluation of protein abundances within a system. In turn, differential expression analysis can be used to investigate changes in protein abundance upon perturbation to such a system. Methods: Here, we provide a workflow for the processing, analysis and interpretation of quantitative mass spectrometry-based expression proteomics data. This workflow utilizes open-source R software packages from the Bioconductor project and guides users end-to-end and step-by-step through every stage of the analyses. As a use-case we generated expression proteomics data from HEK293 cells with and without a treatment. Of note, the experiment included cellular proteins labelled using tandem mass tag (TMT) technology and secreted proteins quantified using label-free quantitation (LFQ). Results: The workflow explains the software infrastructure before focusing on data import, pre-processing and quality control. This is done individually for TMT and LFQ datasets. The application of statistical differential expression analysis is demonstrated, followed by interpretation via gene ontology enrichment analysis. Conclusions: A comprehensive workflow for the processing, analysis and interpretation of expression proteomics is presented. The workflow is a valuable resource for the proteomics community and specifically beginners who are at least familiar with R who wish to understand and make data-driven decisions with regards to their analyses.
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Affiliation(s)
- Charlotte Hutchings
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Charlotte S. Dawson
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Thomas Krueger
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Lisa M. Breckels
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, CB2 1QR, UK
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33
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Toledo AG, Bratanis E, Velásquez E, Chowdhury S, Olofsson B, Sorrentino JT, Karlsson C, Lewis NE, Esko JD, Collin M, Shannon O, Malmström J. Pathogen-driven degradation of endogenous and therapeutic antibodies during streptococcal infections. Nat Commun 2023; 14:6693. [PMID: 37872209 PMCID: PMC10593946 DOI: 10.1038/s41467-023-42572-0] [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: 03/16/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023] Open
Abstract
Group A streptococcus (GAS) is a major bacterial pathogen responsible for both local and systemic infections in humans. The molecular mechanisms that contribute to disease heterogeneity remain poorly understood. Here we show that the transition from a local to a systemic GAS infection is paralleled by pathogen-driven alterations in IgG homeostasis. Using animal models and a combination of sensitive proteomics and glycoproteomics readouts, we documented the progressive accumulation of IgG cleavage products in plasma, due to extensive enzymatic degradation triggered by GAS infection in vivo. The level of IgG degradation was modulated by the route of pathogen inoculation, and mechanistically linked to the combined activities of the bacterial protease IdeS and the endoglycosidase EndoS, upregulated during infection. Importantly, we show that these virulence factors can alter the structure and function of exogenous therapeutic IgG in vivo. These results shed light on the role of bacterial virulence factors in shaping GAS pathogenesis, and potentially blunting the efficacy of antimicrobial therapies.
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Affiliation(s)
- Alejandro Gomez Toledo
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Eleni Bratanis
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Erika Velásquez
- IPSC Laboratory for CNS Disease Modeling, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Sounak Chowdhury
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Berit Olofsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - James T Sorrentino
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Christofer Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Nathan E Lewis
- Departments of Pediatrics and Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mattias Collin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Oonagh Shannon
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
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34
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Jin L, Wang F, Wang X, Harvey BP, Bi Y, Hu C, Cui B, Darcy AT, Maull JW, Phillips BR, Kim Y, Jenkins GJ, Sornasse TR, Tian Y. Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow. Proteomes 2023; 11:32. [PMID: 37873874 PMCID: PMC10594463 DOI: 10.3390/proteomes11040032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease. Plasma biomarkers are critical for understanding disease mechanisms, treatment effects, and diagnosis. Mass spectrometry-based proteomics is a powerful tool for unbiased biomarker discovery. However, plasma proteomics is significantly hampered by signal interference from high-abundance proteins, low overall protein coverage, and high levels of missing data from data-dependent acquisition (DDA). To achieve quantitative proteomics analysis for plasma samples with a balance of throughput, performance, and cost, we developed a workflow incorporating plate-based high abundance protein depletion and sample preparation, comprehensive peptide spectral library building, and data-independent acquisition (DIA) SWATH mass spectrometry-based methodology. In this study, we analyzed plasma samples from both RA patients and healthy donors. The results showed that the new workflow performance exceeded that of the current state-of-the-art depletion-based plasma proteomic platforms in terms of both data quality and proteome coverage. Proteins from biological processes related to the activation of systemic inflammation, suppression of platelet function, and loss of muscle mass were enriched and differentially expressed in RA. Some plasma proteins, particularly acute-phase reactant proteins, showed great power to distinguish between RA patients and healthy donors. Moreover, protein isoforms in the plasma were also analyzed, providing even deeper proteome coverage. This workflow can serve as a basis for further application in discovering plasma biomarkers of other diseases.
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Affiliation(s)
- Liang Jin
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Fei Wang
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Xue Wang
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Bohdan P. Harvey
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Yingtao Bi
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Chenqi Hu
- DMPK, Takeda Development Center Americas Inc., Cambridge, MA 02142, USA; (C.H.)
| | - Baoliang Cui
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Anhdao T. Darcy
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - John W. Maull
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Ben R. Phillips
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Youngjae Kim
- DMPK, Takeda Development Center Americas Inc., Cambridge, MA 02142, USA; (C.H.)
| | - Gary J. Jenkins
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Thierry R. Sornasse
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Yu Tian
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
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35
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Anderson JR, Johnson E, Jenkins R, Jacobsen S, Green D, Walters M, Bundgaard L, Hausmans BAC, van den Akker G, Welting TJM, Chabronova A, Kharaz YA, Clarke EJ, James V, Peffers MJ. Multi-Omic Temporal Landscape of Plasma and Synovial Fluid-Derived Extracellular Vesicles Using an Experimental Model of Equine Osteoarthritis. Int J Mol Sci 2023; 24:14888. [PMID: 37834337 PMCID: PMC10573509 DOI: 10.3390/ijms241914888] [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: 08/03/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Extracellular vesicles (EVs) contribute to osteoarthritis pathogenesis through their release into joint tissues and synovial fluid. Synovial fluid-derived EVs have the potential to be direct biomarkers in the causal pathway of disease but also enable understanding of their role in disease progression. Utilizing a temporal model of osteoarthritis, we defined the changes in matched synovial fluid and plasma-derived EV small non-coding RNA and protein cargo using sequencing and mass spectrometry. Data exploration included time series clustering, factor analysis and gene enrichment interrogation. Chondrocyte signalling was analysed using luciferase-based transcription factor activity assays. EV protein cargo appears to be more important during osteoarthritis progression than small non-coding RNAs. Cluster analysis revealed plasma-EVs represented a time-dependent response to osteoarthritis induction associated with supramolecular complexes. Clusters for synovial fluid-derived EVs were associated with initial osteoarthritis response and represented immune/inflammatory pathways. Factor analysis for plasma-derived EVs correlated with day post-induction and were primarily composed of proteins modulating lipid metabolism. Synovial fluid-derived EVs factors represented intermediate filament and supramolecular complexes reflecting tissue repair. There was a significant interaction between time and osteoarthritis for CRE, NFkB, SRE, SRF with a trend for osteoarthritis synovial fluid-derived EVs at later time points to have a more pronounced effect.
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Affiliation(s)
- James R. Anderson
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK (Y.A.K.)
| | - Emily Johnson
- Computational Biology Facility, Liverpool Shared Research Facilities, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Rosalind Jenkins
- CDSS Bioanalytical Facility, Liverpool Shared Research Facilities, Department Pharmacology and Therapeutics, University of Liverpool, Liverpool L7 8TX, UK
| | - Stine Jacobsen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Taastrup, DK-1870 Copenhagen, Denmark
| | - Daniel Green
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK (Y.A.K.)
| | - Marie Walters
- Department of Veterinary Clinical Sciences, University of Copenhagen, Taastrup, DK-1870 Copenhagen, Denmark
| | - Louise Bundgaard
- Department of Veterinary Clinical Sciences, University of Copenhagen, Taastrup, DK-1870 Copenhagen, Denmark
| | - Bas A. C. Hausmans
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 Maastricht, The Netherlands; (B.A.C.H.)
| | - Guus van den Akker
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 Maastricht, The Netherlands; (B.A.C.H.)
| | - Tim J. M. Welting
- Laboratory for Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University, 6229 Maastricht, The Netherlands; (B.A.C.H.)
| | - Alzbeta Chabronova
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK (Y.A.K.)
| | - Yalda A. Kharaz
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK (Y.A.K.)
| | - Emily J. Clarke
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK (Y.A.K.)
| | - Victoria James
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Loughborough, Nottingham LE12 5RD, UK
| | - Mandy J. Peffers
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK (Y.A.K.)
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Mengal K, Kor G, Siino V, Buřič M, Kozák P, Levander F, Niksirat H. Quantification of proteomic profile changes in the hemolymph of crayfish during in vitro coagulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104760. [PMID: 37331675 DOI: 10.1016/j.dci.2023.104760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
Hemolymph is the circulatory fluid that fills the body cavity of crustaceans, analogous to blood in vertebrates. Hemolymph coagulation, similar to blood clotting in vertebrates, plays a crucial role in wound healing and innate immune responses. Despite extensive studies on the clotting process in crustaceans, no comparative quantitative analysis of the protein composition of non-clotted and clotted hemolymph in any decapod has been reported. In this study, we used label-free protein quantification with high-resolution mass spectrometry to identify the proteomic profile of hemolymph in crayfish and quantify significant changes in protein abundances between non-clotted and clotted hemolymph. Our analysis identified a total of two-hundred and nineteen proteins in both hemolymph groups. Furthermore, we discussed the potential functions of the top most high and low-abundant proteins in hemolymph proteomic profile. The quantity of most of the proteins was not significantly changed during coagulation between non-clotted and clotted hemolymph, which may indicate that clotting proteins are likely pre-synthesized, allowing for a swift coagulation response to injury. Four proteins still showed abundance differences (p < 0.05, fold change>2), including C-type lectin domain-containing proteins, Laminin A chain, Tropomyosin, and Reverse transcriptase domain-containing proteins. While the first three proteins were down-regulated, the last one was up-regulated. The down-regulation of structural and cytoskeletal proteins may affect the process of hemocyte degranulation needed for coagulation, while the up-regulation of an immune-related protein might be attributed to the phagocytosis ability of viable hemocytes during coagulation.
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Affiliation(s)
- Kifayatullah Mengal
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
| | - Golara Kor
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Valentina Siino
- Lund University, Department of Immunotechnology, Medicon Village, House 406, 22387, Lund, Sweden
| | - Miloš Buřič
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Pavel Kozák
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Fredrik Levander
- Lund University, Department of Immunotechnology, Medicon Village, House 406, 22387, Lund, Sweden; National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, Lund, 223 87, Sweden
| | - Hamid Niksirat
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic.
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Yang Y, García-Cruzado M, Zeng H, Camprubí-Ferrer L, Bahatyrevich-Kharitonik B, Bachiller S, Deierborg T. LPS priming before plaque deposition impedes microglial activation and restrains Aβ pathology in the 5xFAD mouse model of Alzheimer's disease. Brain Behav Immun 2023; 113:228-247. [PMID: 37437821 DOI: 10.1016/j.bbi.2023.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Microglia have an innate immunity memory (IIM) with divergent functions in different animal models of neurodegenerative diseases, including Alzheimer's disease (AD). AD is characterized by chronic neuroinflammation, neurodegeneration, tau tangles and β-amyloid (Aβ) deposition. Systemic inflammation has been implicated in contributing to the progression of AD. Multiple reports have demonstrated unique microglial signatures in AD mouse models and patients. However, the proteomic profiles of microglia modified by IIM have not been well-documented in an AD model. Therefore, in the present study, we investigate whether lipopolysaccharide (LPS)-induced IIM in the pre-clinical stage of AD alters the microglial responses and shapes the neuropathology. We accomplished this by priming 5xFAD and wild-type (WT) mice with an LPS injection at 6 weeks (before the robust development of plaques). 140 days later, we evaluated microglial morphology, activation, the microglial barrier around Aβ, and Aβ deposition in both 5xFAD primed and unprimed mice. Priming induced decreased soma size of microglia and reduced colocalization of PSD95 and Synaptophysin in the retrosplenial cortex. Priming appeared to increase phagocytosis of Aβ, resulting in fewer Thioflavin S+ Aβ fibrils in the dentate gyrus. RIPA-soluble Aβ 40 and 42 were significantly reduced in Primed-5xFAD mice leading to a smaller size of MOAB2+ Aβ plaques in the prefrontal cortex. We also found that Aβ-associated microglia in the Primed-5xFAD mice were less activated and fewer in number. After priming, we also observed improved memory performance in 5xFAD. To further elucidate the molecular mechanism underlying these changes, we performed quantitative proteomic analysis of microglia and bone marrow monocytes. A specific pattern in the microglial proteome was revealed in primed 5xFAD mice. These results suggest that the imprint signatures of primed microglia display a distinctive phenotype and highlight the potential for a beneficial adaption of microglia when intervention occurs in the pre-clinical stage of AD.
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Affiliation(s)
- Yiyi Yang
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden.
| | - Marta García-Cruzado
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden
| | - Hairuo Zeng
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden
| | - Lluís Camprubí-Ferrer
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden
| | - Bazhena Bahatyrevich-Kharitonik
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, CSIC, Spain; Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of Seville, Seville, Spain
| | - Sara Bachiller
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden; Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, CSIC, Spain; Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Tomas Deierborg
- Department of Experimental Medical Science, Experimental Neuroinflammation Laboratory, Lund University, Sweden.
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Lin LC, Chang HY, Kuo TT, Chen HY, Liu WS, Lo YJ, Hsia SM, Huang TC. Oxidative stress mediates the inhibitory effects of Manzamine A on uterine leiomyoma cell proliferation and extracellular matrix deposition via SOAT inhibition. Redox Biol 2023; 66:102861. [PMID: 37666118 PMCID: PMC10491796 DOI: 10.1016/j.redox.2023.102861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023] Open
Abstract
Uterine fibroids, the most common benign tumors of the myometrium in women, are characterized by abnormal extracellular matrix deposition and uterine smooth muscle cell neoplasia, with high recurrence rates. Here, we investigated the potential of the marine natural product manzamine A (Manz A), which has potent anti-cancer effects, as a treatment for uterine fibroids. Manz A inhibited leiomyoma cell proliferation in vitro and in vivo by arresting cell cycle progression and inducing caspase-mediated apoptosis. We performed target prediction analysis and identified sterol o-acyltransferases (SOATs) as potential targets of Manz A. Cholesterol esterification and lipid droplet formation were reduced by Manz A, in line with reduced SOAT expression. As a downstream target of SOAT, Manz A also prevented extracellular matrix deposition by inhibiting the β-catenin/fibronectin/metalloproteinases axis and enhanced autophagy turnover. Excessive free fatty acid accumulation by SOAT inhibition led to reactive oxygen species to impair mitochondrial oxidative phosphorylation and trigger endoplasmic reticulum stress via PERK/eIF2α/CHOP signaling. The inhibitory effect of ManzA on cell proliferation was partially restored by PERK knockdown and eliminated by tauroursodeoxycholic acid, suggesting oxidative stress plays a critical role in the mechanism of action of Manz A. These findings suggest that targeting SOATs by Manz A may be a promising therapeutic approach for uterine fibroids.
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Affiliation(s)
- Li-Chun Lin
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan; School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei, 11031, Taiwan
| | - Hsin-Yi Chang
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, 11031, Taiwan; Department of Research and Development, National Defense Medical Center, Taipei, Taiwan
| | - Tzu-Ting Kuo
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Hsin-Yuan Chen
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei, 11031, Taiwan
| | - Wen-Shan Liu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Yii-Jwu Lo
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei, 11031, Taiwan
| | - Shih-Min Hsia
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei, 11031, Taiwan; Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei, 11031, Taiwan; School of Food Safety, College of Nutrition, Taipei Medical University, Taipei, 11031, Taiwan
| | - Tsui-Chin Huang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan; Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, 11031, Taiwan; Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, 11031, Taiwan.
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Tran HC, Schmitt V, Lama S, Wang C, Launay-Avon A, Bernfur K, Sultan K, Khan K, Brunaud V, Liehrmann A, Castandet B, Levander F, Rasmusson AG, Mireau H, Delannoy E, Van Aken O. An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants. Science 2023; 381:eadg0995. [PMID: 37651534 DOI: 10.1126/science.adg0995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that "mitochondrial translation factors" mTRAN1 and mTRAN2 are land plant-specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)-like RNA binding proteins of the mitoribosomal "small" subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5' regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria.
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Affiliation(s)
| | | | - Sbatie Lama
- Department of Biology, Lund University, Lund, Sweden
| | - Chuande Wang
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Katja Bernfur
- Department of Chemistry, Lund University, Lund, Sweden
| | - Kristin Sultan
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Arnaud Liehrmann
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
- Université Paris-Saclay, CNRS, Université d'Évry, Laboratoire de Mathématiques et Modélisation d'Évry, 91037 Évry-Courcouronnes, France
| | - Benoît Castandet
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | | | - Hakim Mireau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
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40
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Jiang L, Xiao M, Liao QQ, Zheng L, Li C, Liu Y, Yang B, Ren A, Jiang C, Feng XH. High-sensitivity profiling of SARS-CoV-2 noncoding region-host protein interactome reveals the potential regulatory role of negative-sense viral RNA. mSystems 2023; 8:e0013523. [PMID: 37314180 PMCID: PMC10469612 DOI: 10.1128/msystems.00135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/11/2023] [Indexed: 06/15/2023] Open
Abstract
A deep understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-host interactions is crucial to developing effective therapeutics and addressing the threat of emerging coronaviruses. The role of noncoding regions of viral RNA (ncrRNAs) has yet to be systematically scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry and designed a diverse set of bait ncrRNAs to systematically map the interactome of SARS-CoV-2 ncrRNA in Calu-3, Huh7, and HEK293T cells. Integration of the results defined the core ncrRNA-host protein interactomes among cell lines. The 5' UTR interactome is enriched with proteins in the small nuclear ribonucleoproteins family and is a target for the regulation of viral replication and transcription. The 3' UTR interactome is enriched with proteins involved in the stress granules and heterogeneous nuclear ribonucleoproteins family. Intriguingly, compared with the positive-sense ncrRNAs, the negative-sense ncrRNAs, especially the negative-sense of 3' UTR, interacted with a large array of host proteins across all cell lines. These proteins are involved in the regulation of the viral production process, host cell apoptosis, and immune response. Taken together, our study depicts the comprehensive landscape of the SARS-CoV-2 ncrRNA-host protein interactome and unveils the potential regulatory role of the negative-sense ncrRNAs, providing a new perspective on virus-host interactions and the design of future therapeutics. Given the highly conserved nature of UTRs in positive-strand viruses, the regulatory role of negative-sense ncrRNAs should not be exclusive to SARS-CoV-2. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic affecting millions of lives. During replication and transcription, noncoding regions of the viral RNA (ncrRNAs) may play an important role in the virus-host interactions. Understanding which and how these ncrRNAs interact with host proteins is crucial for understanding the mechanism of SARS-CoV-2 pathogenesis. We developed the MS2 affinity purification coupled with liquid chromatography-mass spectrometry method and designed a diverse set of ncrRNAs to identify the SARS-CoV-2 ncrRNA interactome comprehensively in different cell lines and found that the 5' UTR binds to proteins involved in U1 small nuclear ribonucleoprotein, while the 3' UTR interacts with proteins involved in stress granules and the heterogeneous nuclear ribonucleoprotein family. Interestingly, negative-sense ncrRNAs showed interactions with a large number of diverse host proteins, indicating a crucial role in infection. The results demonstrate that ncrRNAs could serve diverse regulatory functions.
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Affiliation(s)
- Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mu Xiao
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qing-Qing Liao
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luqian Zheng
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuemei Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xin-Hua Feng
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
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Hardt R, Dehghani A, Schoor C, Gödderz M, Cengiz Winter N, Ahmadi S, Sharma R, Schork K, Eisenacher M, Gieselmann V, Winter D. Proteomic investigation of neural stem cell to oligodendrocyte precursor cell differentiation reveals phosphorylation-dependent Dclk1 processing. Cell Mol Life Sci 2023; 80:260. [PMID: 37594553 PMCID: PMC10439241 DOI: 10.1007/s00018-023-04892-8] [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: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Oligodendrocytes are generated via a two-step mechanism from pluripotent neural stem cells (NSCs): after differentiation of NSCs to oligodendrocyte precursor/NG2 cells (OPCs), they further develop into mature oligodendrocytes. The first step of this differentiation process is only incompletely understood. In this study, we utilized the neurosphere assay to investigate NSC to OPC differentiation in a time course-dependent manner by mass spectrometry-based (phospho-) proteomics. We identify doublecortin-like kinase 1 (Dclk1) as one of the most prominently regulated proteins in both datasets, and show that it undergoes a gradual transition between its short/long isoform during NSC to OPC differentiation. This is regulated by phosphorylation of its SP-rich region, resulting in inhibition of proteolytic Dclk1 long cleavage, and therefore Dclk1 short generation. Through interactome analyses of different Dclk1 isoforms by proximity biotinylation, we characterize their individual putative interaction partners and substrates. All data are available via ProteomeXchange with identifier PXD040652.
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Affiliation(s)
- Robert Hardt
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Alireza Dehghani
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Carmen Schoor
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Markus Gödderz
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Nur Cengiz Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Institute of Human Genetics, University Hospital Cologne, 50931, Cologne, Germany
| | - Shiva Ahmadi
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
- Bayer Pharmaceuticals, 42113, Wuppertal, Germany
| | - Ramesh Sharma
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Karin Schork
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom-Center, Medical Faculty, Ruhr-University Bochum, 44801, Bochum, Germany
- Medical Proteome Analysis, Center for Protein Diagnostics, Ruhr-University Bochum, 44801, Bochum, Germany
| | - Volkmar Gieselmann
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, Nussallee 11, 53115, Bonn, Germany.
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42
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Ortenlöf N, Vallius S, Karlsson H, Ekström C, Kristiansson A, Holmqvist B, Göransson O, Vaváková M, Rydén M, Carey G, Barton N, Ley D, Gram M. Characterization of choroid plexus in the preterm rabbit pup following subcutaneous administration of recombinant human IGF-1/IGFBP-3. Fluids Barriers CNS 2023; 20:59. [PMID: 37582792 PMCID: PMC10426218 DOI: 10.1186/s12987-023-00460-1] [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: 04/27/2023] [Accepted: 07/27/2023] [Indexed: 08/17/2023] Open
Abstract
Insulin-like growth factor-1 (IGF-1) is essential for normal brain development and regulates essential processes of vascular maturation and stabilization. Importantly, preterm birth is associated with reduced serum levels of IGF-1 as compared to in utero levels. Using a preterm rabbit pup model, we investigated the uptake of systemic recombinant human (rh) IGF-1 in complex with its main binding protein IGF-binding protein 3 (BP-3) to the brain parenchyma via the choroid plexus. Five hours after subcutaneous administration, labeled rhIGF-1/rhIGFBP-3 displayed a widespread presence in the choroid plexus of the lateral and third ventricle, however, to a less degree in the fourth, as well as in the perivascular and subarachnoid space. We found a time-dependent uptake of IGF-1 in cerebrospinal fluid, decreasing with postnatal age, and a translocation of IGF-1 through the choroid plexus. The impact of systemic rhIGF-1/rhIGFBP-3 on IGF-1 receptor activation in the choroid plexus decreased with postnatal age, correlating with IGF-1 uptake in cerebrospinal fluid. In addition, choroid plexus gene expression was observed to increase with postnatal age. Moreover, using choroid plexus in vitro cell cultures, gene expression and protein synthesis were further investigated upon rhIGF-1/rhIGFBP-3 stimulation as compared to rhIGF-1 alone, and found not to be differently altered. Here, we characterize the uptake of systemic rhIGF-1/rhIGFBP-3 to the preterm brain, and show that the interaction between systemic rhIGF-1/rhIGFBP-3 and choroid plexus varies over time.
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Affiliation(s)
- Niklas Ortenlöf
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Suvi Vallius
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Helena Karlsson
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Claes Ekström
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Amanda Kristiansson
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | | | - Olga Göransson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Magdaléna Vaváková
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Martin Rydén
- Orthopaedics, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | | | - Norman Barton
- Oak Hill Bio, Scientific Advisory Board, Boston, MA, USA
| | - David Ley
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Magnus Gram
- Pediatrics, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden.
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Faravelli I, Gagliardi D, Abati E, Meneri M, Ongaro J, Magri F, Parente V, Petrozzi L, Ricci G, Farè F, Garrone G, Fontana M, Caruso D, Siciliano G, Comi GP, Govoni A, Corti S, Ottoboni L. Multi-omics profiling of CSF from spinal muscular atrophy type 3 patients after nusinersen treatment: a 2-year follow-up multicenter retrospective study. Cell Mol Life Sci 2023; 80:241. [PMID: 37543540 PMCID: PMC10404194 DOI: 10.1007/s00018-023-04885-7] [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: 04/02/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 08/07/2023]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disorder caused by mutations in the SMN1 gene resulting in reduced levels of the SMN protein. Nusinersen, the first antisense oligonucleotide (ASO) approved for SMA treatment, binds to the SMN2 gene, paralogue to SMN1, and mediates the translation of a functional SMN protein. Here, we used longitudinal high-resolution mass spectrometry (MS) to assess both global proteome and metabolome in cerebrospinal fluid (CSF) from ten SMA type 3 patients, with the aim of identifying novel readouts of pharmacodynamic/response to treatment and predictive markers of treatment response. Patients had a median age of 33.5 [29.5; 38.25] years, and 80% of them were ambulant at time of the enrolment, with a median HFMSE score of 37.5 [25.75; 50.75]. Untargeted CSF proteome and metabolome were measured using high-resolution MS (nLC-HRMS) on CSF samples obtained before treatment (T0) and after 2 years of follow-up (T22). A total of 26 proteins were found to be differentially expressed between T0 and T22 upon VSN normalization and LIMMA differential analysis, accounting for paired replica. Notably, key markers of the insulin-growth factor signaling pathway were upregulated after treatment together with selective modulation of key transcription regulators. Using CombiROC multimarker signature analysis, we suggest that detecting a reduction of SEMA6A and an increase of COL1A2 and GRIA4 might reflect therapeutic efficacy of nusinersen. Longitudinal metabolome profiling, analyzed with paired t-Test, showed a significant shift for some aminoacid utilization induced by treatment, whereas other metabolites were largely unchanged. Together, these data suggest perturbation upon nusinersen treatment still sustained after 22 months of follow-up and confirm the utility of CSF multi-omic profiling as pharmacodynamic biomarker for SMA type 3. Nonetheless, validation studies are needed to confirm this evidence in a larger sample size and to further dissect combined markers of response to treatment.
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Affiliation(s)
- Irene Faravelli
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elena Abati
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Megi Meneri
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Jessica Ongaro
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesca Magri
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valeria Parente
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lucia Petrozzi
- Department of Clinical and Experimental Medicine, Neurological Clinics, University of Pisa, Pisa, Italy
| | - Giulia Ricci
- Department of Clinical and Experimental Medicine, Neurological Clinics, University of Pisa, Pisa, Italy
| | | | | | | | - Donatella Caruso
- Unitech OMICs, University of Milan, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinics, University of Pisa, Pisa, Italy
| | - Giacomo Pietro Comi
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Govoni
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy.
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Milan, Italy.
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Awoniyi LO, Cunha DM, Sarapulov AV, Hernández-Pérez S, Runsala M, Tejeda-González B, Šuštar V, Balci MÖ, Petrov P, Mattila PK. B cell receptor-induced protein dynamics and the emerging role of SUMOylation revealed by proximity proteomics. J Cell Sci 2023; 136:jcs261119. [PMID: 37417469 PMCID: PMC10445728 DOI: 10.1242/jcs.261119] [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: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
Successful B cell activation, which is critical for high-affinity antibody production, is controlled by the B cell antigen receptor (BCR). However, we still lack a comprehensive protein-level view of the very dynamic multi-branched cellular events triggered by antigen binding. Here, we employed APEX2 proximity biotinylation to study antigen-induced changes, 5-15 min after receptor activation, at the vicinity of the plasma membrane lipid rafts, wherein BCR enriches upon activation. The data reveals dynamics of signaling proteins, as well as various players linked to the subsequent processes, such as actin cytoskeleton remodeling and endocytosis. Interestingly, our differential expression analysis identified dynamic responses in various proteins previously not linked to early B cell activation. We demonstrate active SUMOylation at the sites of BCR activation in various conditions and report its functional role in BCR signaling through the AKT and ERK1/2 axes.
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Affiliation(s)
- Luqman O. Awoniyi
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Diogo M. Cunha
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Alexey V. Sarapulov
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Sara Hernández-Pérez
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Marika Runsala
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Blanca Tejeda-González
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Vid Šuštar
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
| | - M. Özge Balci
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Petar Petrov
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
| | - Pieta K. Mattila
- Institute of Biomedicine and MediCity Research Laboratories, University of Turku, 20014 Turku, Finland
- Turku Bioscience, University of Turku and Åbo Akademi University, 20520 Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, 20014 Turku, Finland
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Siriwaseree J, Yingchutrakul Y, Samutrtai P, Aonbangkhen C, Srathong P, Krobthong S, Choowongkomon K. Exploring the Apoptotic-Induced Biochemical Mechanism of Traditional Thai Herb (Kerra™) Extract in HCT116 Cells Using a Label-Free Proteomics Approach. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1376. [PMID: 37629666 PMCID: PMC10456832 DOI: 10.3390/medicina59081376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Background and Objectives: Natural products have proven to be a valuable source for the discovery of new candidate drugs for cancer treatment. This study aims to investigate the potential therapeutic effects of "Kerra™", a natural extract derived from a mixture of nine medicinal plants mentioned in the ancient Thai scripture named the Takxila Scripture, on HCT116 cells. Materials and Methods: In this study, the effect of the Kerra™ extract on cancer cells was assessed through cell viability assays. Apoptotic activity was evaluated by examining the apoptosis characteristic features. A proteomics analysis was conducted to identify proteins and pathways associated with the extract's mechanism of action. The expression levels of apoptotic protein markers were measured to validate the extract's efficacy. Results: The Kerra™ extract demonstrated a dose-dependent inhibitory effect on the cells, with higher concentrations leading to decreased cell viability. Treatment with the extract for 72 h induced characteristic features of early and late apoptosis, as well as cell death. An LC-MS/MS analysis identified a total of 3406 proteins. The pathway analysis revealed that the Kerra™ extract stimulated apoptosis and cell death in colorectal cancer cell lines and suppressed cell proliferation in adenocarcinoma cell lines through the EIF2 signaling pathway. Upstream regulatory proteins, including cyclin-dependent kinase inhibitor 1A (CDKN1A) and MYC proto-oncogene, bHLH transcription factor (MYC), were identified. The expressions of caspase-8 and caspase-9 were significantly elevated by the Kerra™ extract compared to the chemotherapy drug Doxorubicin (Dox). Conclusions: These findings provide strong evidence for the ability of the Kerra™ extract to induce apoptosis in HCT116 colon cancer cells. The extract's efficacy was demonstrated by its dose-dependent inhibitory effect, induction of apoptotic activity, and modulation of key proteins involved in cell death and proliferation pathways. This study highlights the potential of Kerra™ as a promising therapeutic agent in cancer treatment.
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Affiliation(s)
- Jeeraprapa Siriwaseree
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
| | - Yodying Yingchutrakul
- National Center for Genetic Engineering and Biotechnology, NSTDA, Pathum Thani 12120, Thailand;
| | - Pawitrabhorn Samutrtai
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Pussadee Srathong
- Faculty of Nursing, Praboromarajchanok Institute, Nonthaburi 11000, Thailand;
| | - Sucheewin Krobthong
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok 10900, Thailand
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46
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Mattoli L, Gianni M, Burico M. Mass spectrometry-based metabolomic analysis as a tool for quality control of natural complex products. MASS SPECTROMETRY REVIEWS 2023; 42:1358-1396. [PMID: 35238411 DOI: 10.1002/mas.21773] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/16/2021] [Accepted: 02/11/2022] [Indexed: 06/07/2023]
Abstract
Metabolomics is an area of intriguing and growing interest. Since the late 1990s, when the first Omic applications appeared to study metabolite's pool ("metabolome"), to understand new aspects of the global regulation of cellular metabolism in biology, there have been many evolutions. Currently, there are many applications in different fields such as clinical, medical, agricultural, and food. In our opinion, it is clear that developments in metabolomics analysis have also been driven by advances in mass spectrometry (MS) technology. As natural complex products (NCPs) are increasingly used around the world as medicines, food supplements, and substance-based medical devices, their analysis using metabolomic approaches will help to bring more and more rigor to scientific studies and industrial production monitoring. This review is intended to emphasize the importance of metabolomics as a powerful tool for studying NCPs, by which significant advantages can be obtained in terms of elucidation of their composition, biological effects, and quality control. The different approaches of metabolomic analysis, the main and basic techniques of multivariate statistical analysis are also briefly illustrated, to allow an overview of the workflow associated with the metabolomic studies of NCPs. Therefore, various articles and reviews are illustrated and commented as examples of the application of MS-based metabolomics to NCPs.
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Affiliation(s)
- Luisa Mattoli
- Department of Metabolomics & Analytical Sciences, Aboca SpA Società Agricola, Sansepolcro, AR, Italy
| | - Mattia Gianni
- Department of Metabolomics & Analytical Sciences, Aboca SpA Società Agricola, Sansepolcro, AR, Italy
| | - Michela Burico
- Department of Metabolomics & Analytical Sciences, Aboca SpA Società Agricola, Sansepolcro, AR, Italy
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47
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Scott AM, Karlsson C, Mohanty T, Hartman E, Vaara ST, Linder A, Malmström J, Malmström L. Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics. Commun Biol 2023; 6:628. [PMID: 37301900 PMCID: PMC10257694 DOI: 10.1038/s42003-023-04977-x] [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: 12/19/2022] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Data independent acquisition mass spectrometry (DIA-MS) has recently emerged as an important method for the identification of blood-based biomarkers. However, the large search space required to identify novel biomarkers from the plasma proteome can introduce a high rate of false positives that compromise the accuracy of false discovery rates (FDR) using existing validation methods. We developed a generalized precursor scoring (GPS) method trained on 2.75 million precursors that can confidently control FDR while increasing the number of identified proteins in DIA-MS independent of the search space. We demonstrate how GPS can generalize to new data, increase protein identification rates, and increase the overall quantitative accuracy. Finally, we apply GPS to the identification of blood-based biomarkers and identify a panel of proteins that are highly accurate in discriminating between subphenotypes of septic acute kidney injury from undepleted plasma to showcase the utility of GPS in discovery DIA-MS proteomics.
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Affiliation(s)
- Aaron M Scott
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
| | - Christofer Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Tirthankar Mohanty
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Erik Hartman
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Suvi T Vaara
- Division of Anaesthesia and Intensive Care Medicine Department of Surgery, Intensive Care Units, Helsinki University Central Hospital, Box 340, 00029 HUS, Helsinki, Finland
| | - Adam Linder
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lars Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
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48
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Jones J, MacKrell EJ, Wang TY, Lomenick B, Roukes ML, Chou TF. Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization. BMC Bioinformatics 2023; 24:239. [PMID: 37280522 DOI: 10.1186/s12859-023-05360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approachable standardized post-processing analyses such as sample group statistics, quantitative variation and even data filtering. We developed tidyproteomics to facilitate basic analysis, improve data interoperability and potentially ease the integration of new processing algorithms, mainly through the use of a simplified data-object. RESULTS The R package tidyproteomics was developed as both a framework for standardizing quantitative proteomics data and a platform for analysis workflows, containing discrete functions that can be connected end-to-end, thus making it easier to define complex analyses by breaking them into small stepwise units. Additionally, as with any analysis workflow, choices made during analysis can have large impacts on the results and as such, tidyproteomics allows researchers to string each function together in any order, select from a variety of options and in some cases develop and incorporate custom algorithms. CONCLUSIONS Tidyproteomics aims to simplify data exploration from multiple platforms, provide control over individual functions and analysis order, and serve as a tool to assemble complex repeatable processing workflows in a logical flow. Datasets in tidyproteomics are easy to work with, have a structure that allows for biological annotations to be added, and come with a framework for developing additional analysis tools. The consistent data structure and accessible analysis and plotting tools also offers a way for researchers to save time on mundane data manipulation tasks.
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Affiliation(s)
- Jeff Jones
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
| | - Elliot J MacKrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Ting-Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Michael L Roukes
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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49
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Brown RD, Hunter KS, Li M, Frid MG, Harral J, Krafsur GM, Holt TN, Williams J, Zhang H, Riddle SR, Edwards MG, Kumar S, Hu CJ, Graham BB, Walker LA, Garry FB, Buttrick PM, Lahm T, Kheyfets VO, Hansen KC, Stenmark KR. Functional and molecular determinants of right ventricular response to severe pulmonary hypertension in a large animal model. Am J Physiol Heart Circ Physiol 2023; 324:H804-H820. [PMID: 36961489 PMCID: PMC10190846 DOI: 10.1152/ajpheart.00614.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/01/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
Right ventricular (RV) failure is the major determinant of outcome in pulmonary hypertension (PH). Calves exposed to 2-wk hypoxia develop severe PH and unlike rodents, hypoxia-induced PH in this species can lead to right heart failure. We, therefore, sought to examine the molecular and structural changes in the RV in calves with hypoxia-induced PH, hypothesizing that we could identify mechanisms underlying compensated physiological function in the face of developing severe PH. Calves were exposed to 14 days of environmental hypoxia (equivalent to 4,570 m/15,000 ft elevation, n = 29) or ambient normoxia (1,525 m/5,000 ft, n = 25). Cardiopulmonary function was evaluated by right heart catheterization and pressure volume loops. Molecular and cellular determinants of RV remodeling were analyzed by cDNA microarrays, RealTime PCR, proteomics, and immunochemistry. Hypoxic exposure induced robust PH, with increased RV contractile performance and preserved cardiac output, yet evidence of dysregulated RV-pulmonary artery mechanical coupling as seen in advanced disease. Analysis of gene expression revealed cellular processes associated with structural remodeling, cell signaling, and survival. We further identified specific clusters of gene expression associated with 1) hypertrophic gene expression and prosurvival mechanotransduction through YAP-TAZ signaling, 2) extracellular matrix (ECM) remodeling, 3) inflammatory cell activation, and 4) angiogenesis. A potential transcriptomic signature of cardiac fibroblasts in RV remodeling was detected, enriched in functions related to cell movement, tissue differentiation, and angiogenesis. Proteomic and immunohistochemical analysis confirmed RV myocyte hypertrophy, together with localization of ECM remodeling, inflammatory cell activation, and endothelial cell proliferation within the RV interstitium. In conclusion, hypoxia and hemodynamic load initiate coordinated processes of protective and compensatory RV remodeling to withstand the progression of PH.NEW & NOTEWORTHY Using a large animal model and employing a comprehensive approach integrating hemodynamic, transcriptomic, proteomic, and immunohistochemical analyses, we examined the early (2 wk) effects of severe PH on the RV. We observed that RV remodeling during PH progression represents a continuum of transcriptionally driven processes whereby cardiac myocytes, fibroblasts, endothelial cells, and proremodeling macrophages act to coordinately maintain physiological homeostasis and protect myocyte survival during chronic, severe, and progressive pressure overload.
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Affiliation(s)
- R Dale Brown
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Kendall S Hunter
- Department of Bioengineering, University of Coloradoo Denver, Denver, Colorado, United States
| | - Min Li
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Maria G Frid
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Julie Harral
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Greta M Krafsur
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Timothy N Holt
- Department of Clinical Sciences, College of Veterinary Medicine and Biological Sciences, Colorado State University, Fort Collins, Colorado, United States
| | - Jason Williams
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Denver, Colorado, United States
| | - Hui Zhang
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Suzette R Riddle
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | | | - Sushil Kumar
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Cheng-Jun Hu
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Brian B Graham
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, California, United States
| | - Lori A Walker
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Franklyn B Garry
- Department of Clinical Sciences, College of Veterinary Medicine and Biological Sciences, Colorado State University, Fort Collins, Colorado, United States
| | - Peter M Buttrick
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Tim Lahm
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, University of Colorado Denver, Denver, Colorado, United States
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Denver, Colorado, United States
| | - Vitaly O Kheyfets
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
- Department of Biomedical Informatics, University of Colorado Denver, Denver, Colorado, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Denver, Colorado, United States
| | - Kurt R Stenmark
- Cardiovascular Pulmonary Research Laboratories, Department of Pediatrics, University of Colorado Denver, Denver, Colorado, United States
- Department of Medicine, University of Colorado Denver, Denver, Colorado, United States
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50
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Bhattacharya A, Mukherjee R, Kuncha SK, Brunstein ME, Rathore R, Junek S, Münch C, Dikic I. A lysosome membrane regeneration pathway depends on TBC1D15 and autophagic lysosomal reformation proteins. Nat Cell Biol 2023; 25:685-698. [PMID: 37024685 DOI: 10.1038/s41556-023-01125-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Acute lysosomal membrane damage reduces the cellular population of functional lysosomes. However, these damaged lysosomes have a remarkable recovery potential independent of lysosomal biogenesis and remain unaffected in cells depleted in TFEB and TFE3. We combined proximity-labelling-based proteomics, biochemistry and high-resolution microscopy to unravel a lysosomal membrane regeneration pathway that depends on ATG8, the lysosomal membrane protein LIMP2, the RAB7 GTPase-activating protein TBC1D15 and proteins required for autophagic lysosomal reformation, including dynamin-2, kinesin-5B and clathrin. Following lysosomal damage, LIMP2 acts as a lysophagy receptor to bind ATG8, which in turn recruits TBC1D15 to damaged membranes. TBC1D15 interacts with ATG8 proteins on damaged lysosomes and provides a scaffold to assemble and stabilize the autophagic lysosomal reformation machinery. This potentiates the formation of lysosomal tubules and subsequent dynamin-2-dependent scission. TBC1D15-mediated lysosome regeneration was also observed in a cell culture model of oxalate nephropathy.
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Affiliation(s)
- Anshu Bhattacharya
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Santosh Kumar Kuncha
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | | | - Rajeshwari Rathore
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Stephan Junek
- Max Planck Institute of Biophysics, Frankfurt, Germany
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
- Max Planck Institute of Biophysics, Frankfurt, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Frankfurt, Germany.
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