1
|
Piana D, Iavarone F, De Paolis E, Daniele G, Parisella F, Minucci A, Greco V, Urbani A. Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges. Int J Mol Sci 2024; 25:8830. [PMID: 39201516 PMCID: PMC11354793 DOI: 10.3390/ijms25168830] [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: 06/23/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Tumor heterogeneity refers to the diversity observed among tumor cells: both between different tumors (inter-tumor heterogeneity) and within a single tumor (intra-tumor heterogeneity). These cells can display distinct morphological and phenotypic characteristics, including variations in cellular morphology, metastatic potential and variability treatment responses among patients. Therefore, a comprehensive understanding of such heterogeneity is necessary for deciphering tumor-specific mechanisms that may be diagnostically and therapeutically valuable. Innovative and multidisciplinary approaches are needed to understand this complex feature. In this context, proteogenomics has been emerging as a significant resource for integrating omics fields such as genomics and proteomics. By combining data obtained from both Next-Generation Sequencing (NGS) technologies and mass spectrometry (MS) analyses, proteogenomics aims to provide a comprehensive view of tumor heterogeneity. This approach reveals molecular alterations and phenotypic features related to tumor subtypes, potentially identifying therapeutic biomarkers. Many achievements have been made; however, despite continuous advances in proteogenomics-based methodologies, several challenges remain: in particular the limitations in sensitivity and specificity and the lack of optimal study models. This review highlights the impact of proteogenomics on characterizing tumor phenotypes, focusing on the critical challenges and current limitations of its use in different clinical and preclinical models for tumor phenotypic characterization.
Collapse
Affiliation(s)
- Diletta Piana
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| | - Elisa De Paolis
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
- Departmental Unit of Molecular and Genomic Diagnostics, Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Gennaro Daniele
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Federico Parisella
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
| | - Angelo Minucci
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
- Departmental Unit of Molecular and Genomic Diagnostics, Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| |
Collapse
|
2
|
Yan T, Cai B, Li F, Guo D, Xia C, Lv H, Lin B, Gao H, Geng Z. Proteomic and metabolomic revealed the effect of shading treatment on cigar tobacco. FRONTIERS IN PLANT SCIENCE 2024; 15:1433575. [PMID: 39100083 PMCID: PMC11294240 DOI: 10.3389/fpls.2024.1433575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024]
Abstract
Shading or low light conditions are essential cultivation techniques for cigar wrapper tobacco leaves production, yet their impact on protein and metabolic regulatory networks is not well understood. In this study, we integrated proteomic and metabolomic analyses to uncover the potential molecular mechanisms affecting cigar tobacco leaves under shading treatment. Our findings include: (1) Identification of 780 significantly differentially expressed proteins (DEPs) in the cigar wrapper tobacco leaves, comprising 560 up-regulated and 220 down-regulated proteins, predominantly located in the chloroplast, cytoplasm, and nucleus, collectively accounting for 50.01%. (2) Discovery of 254 significantly differentially expressed metabolites (DEMs), including 148 up-regulated and 106 down-regulated metabolites. (3) KEGG pathway enrichment analysis revealed that the mevalonate (MVA) pathway within 'Terpenoid backbone biosynthesis' was inhibited, leading to a down-regulation of 'Sesquiterpenoid and triterpenoid biosynthesis'. Conversely, the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was enhanced, resulting in an up-regulation of 'Monoterpenoid biosynthesis', 'Diterpenoid biosynthesis', and 'Carotenoid biosynthesis', thereby promoting the synthesis of terpenoids such as carotenoids and chlorophylls. Simultaneously, the Calvin cycle in 'Carbon fixation in photosynthetic organisms' was amplified, increasing photosynthetic efficiency. These results suggest that under low light conditions, cigar tobacco optimizes photosynthetic efficiency by reconfiguring its energy metabolism and terpenoid biosynthesis. This study contributes valuable insights into protein and metabolic analyses, paving the way for future functional studies on plant responses to low light.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Huajun Gao
- Haikou cigar Research Institute, Hainan Provincial Branch of China National Tobacco Corporation, Haikou, China
| | - Zhaoliang Geng
- Haikou cigar Research Institute, Hainan Provincial Branch of China National Tobacco Corporation, Haikou, China
| |
Collapse
|
3
|
Kratzl F, Urban M, Pandhal J, Shi M, Meng C, Kleigrewe K, Kremling A, Pflüger-Grau K. Pseudomonas putida as saviour for troubled Synechococcus elongatus in a synthetic co-culture - interaction studies based on a multi-OMICs approach. Commun Biol 2024; 7:452. [PMID: 38609451 PMCID: PMC11014904 DOI: 10.1038/s42003-024-06098-5] [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: 08/20/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
In their natural habitats, microbes rarely exist in isolation; instead, they thrive in consortia, where various interactions occur. In this study, a defined synthetic co-culture of the cyanobacterium S. elongatus cscB, which supplies sucrose to the heterotrophic P. putida cscRABY, is investigated to identify potential interactions. Initial experiments reveal a remarkable growth-promoting effect of the heterotrophic partner on the cyanobacterium, resulting in an up to 80% increase in the growth rate and enhanced photosynthetic capacity. Vice versa, the presence of the cyanobacterium has a neutral effect on P. putida cscRABY, highlighting the resilience of pseudomonads against stress and their potential as co-culture partners. Next, a suitable reference process reinforcing the growth-promoting effect is established in a parallel photobioreactor system, which sets the basis for the analysis of the co-culture at the transcriptome, proteome, and metabolome levels. In addition to several moderate changes, including alterations in the metabolism and stress response in both microbes, this comprehensive multi-OMICs approach strongly hints towards the exchange of further molecules beyond the unidirectional feeding with sucrose. Taken together, these findings provide valuable insights into the complex dynamics between both co-culture partners, indicating multi-level interactions, which can be employed for further streamlining of the co-cultivation system.
Collapse
Affiliation(s)
- Franziska Kratzl
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Marlene Urban
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Mengxun Shi
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, TUM School of Engineering and Design, Technical University of Munich, Garching, Germany.
| |
Collapse
|
4
|
Berthelier TH, Cabanac SC, Callot C, Bellec A, Mathé C, Jamet E, Dunand C. Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species. Int J Mol Sci 2024; 25:1938. [PMID: 38339216 PMCID: PMC10856686 DOI: 10.3390/ijms25031938] [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: 12/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Climate change is expected to intensify the occurrence of abiotic stress in plants, such as hypoxia and salt stresses, leading to the production of reactive oxygen species (ROS), which need to be effectively managed by various oxido-reductases encoded by the so-called ROS gene network. Here, we studied six oxido-reductases families in three Brassicaceae species, Arabidopsis thaliana as well as Nasturtium officinale and Eutrema salsugineum, which are adapted to hypoxia and salt stress, respectively. Using available and new genomic data, we performed a phylogenomic analysis and compared RNA-seq data to study genomic and transcriptomic adaptations. This comprehensive approach allowed for the gaining of insights into the impact of the adaptation to saline or hypoxia conditions on genome organization (gene gains and losses) and transcriptional regulation. Notably, the comparison of the N. officinale and E. salsugineum genomes to that of A. thaliana highlighted changes in the distribution of ohnologs and homologs, particularly affecting class III peroxidase genes (CIII Prxs). These changes were specific to each gene, to gene families subjected to duplication events and to each species, suggesting distinct evolutionary responses. The analysis of transcriptomic data has allowed for the identification of genes related to stress responses in A. thaliana, and, conversely, to adaptation in N. officinale and E. salsugineum.
Collapse
Affiliation(s)
- Thomas Horst Berthelier
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Sébastien Christophe Cabanac
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, France; (C.C.); (A.B.)
| | - Arnaud Bellec
- Centre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, France; (C.C.); (A.B.)
| | - Catherine Mathé
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France; (T.H.B.); (S.C.C.); (C.M.)
| |
Collapse
|
5
|
Linkner TR, Ambrus V, Kunkli B, Szojka ZI, Kalló G, Csősz É, Kumar A, Emri M, Tőzsér J, Mahdi M. Comparative Analysis of Differential Cellular Transcriptome and Proteome Regulation by HIV-1 and HIV-2 Pseudovirions in the Early Phase of Infection. Int J Mol Sci 2023; 25:380. [PMID: 38203551 PMCID: PMC10779251 DOI: 10.3390/ijms25010380] [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: 10/30/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
In spite of the similar structural and genomic organization of human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2), striking differences exist between them in terms of replication dynamics and clinical manifestation of infection. Although the pathomechanism of HIV-1 infection is well characterized, relatively few data are available regarding HIV-2 viral replication and its interaction with host-cell proteins during the early phase of infection. We utilized proteo-transcriptomic analyses to determine differential genome expression and proteomic changes induced by transduction with HIV-1/2 pseudovirions during 8, 12 and 26 h time-points in HEK-293T cells. We show that alteration in the cellular milieu was indeed different between the two pseudovirions. The significantly higher number of genes altered by HIV-2 in the first two time-points suggests a more diverse yet subtle effect on the host cell, preparing the infected cell for integration and latency. On the other hand, GO analysis showed that, while HIV-1 induced cellular oxidative stress and had a greater effect on cellular metabolism, HIV-2 mostly affected genes involved in cell adhesion, extracellular matrix organization or cellular differentiation. Proteomics analysis revealed that HIV-2 significantly downregulated the expression of proteins involved in mRNA processing and translation. Meanwhile, HIV-1 influenced the cellular level of translation initiation factors and chaperones. Our study provides insight into the understudied replication cycle of HIV-2 and enriches our knowledge about the use of HIV-based lentiviral vectors in general.
Collapse
Affiliation(s)
- Tamás Richárd Linkner
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.R.L.); (V.A.); (B.K.); (Z.I.S.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary;
| | - Viktor Ambrus
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.R.L.); (V.A.); (B.K.); (Z.I.S.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary;
| | - Balázs Kunkli
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.R.L.); (V.A.); (B.K.); (Z.I.S.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary;
| | - Zsófia Ilona Szojka
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.R.L.); (V.A.); (B.K.); (Z.I.S.)
- Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, 22100 Lund, Sweden
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Ajneesh Kumar
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary;
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Miklós Emri
- Department of Medical Imaging, Division of Nuclear Medicine and Translational Imaging, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - József Tőzsér
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.R.L.); (V.A.); (B.K.); (Z.I.S.)
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.K.); (É.C.)
| | - Mohamed Mahdi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (T.R.L.); (V.A.); (B.K.); (Z.I.S.)
| |
Collapse
|
6
|
Gauvrit T, Benderradji H, Pelletier A, Aboulouard S, Faivre E, Carvalho K, Deleau A, Vallez E, Launay A, Bogdanova A, Besegher M, Le Gras S, Tailleux A, Salzet M, Buée L, Delahaye F, Blum D, Vieau D. Multi-Omics Data Integration Reveals Sex-Dependent Hippocampal Programming by Maternal High-Fat Diet during Lactation in Adult Mouse Offspring. Nutrients 2023; 15:4691. [PMID: 37960344 PMCID: PMC10649590 DOI: 10.3390/nu15214691] [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: 10/05/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
Early-life exposure to high-fat diets (HF) can program metabolic and cognitive alterations in adult offspring. Although the hippocampus plays a crucial role in memory and metabolic homeostasis, few studies have reported the impact of maternal HF on this structure. We assessed the effects of maternal HF during lactation on physiological, metabolic, and cognitive parameters in young adult offspring mice. To identify early-programming mechanisms in the hippocampus, we developed a multi-omics strategy in male and female offspring. Maternal HF induced a transient increased body weight at weaning, and a mild glucose intolerance only in 3-month-old male mice with no change in plasma metabolic parameters in adult male and female offspring. Behavioral alterations revealed by a Barnes maze test were observed both in 6-month-old male and female mice. The multi-omics strategy unveiled sex-specific transcriptomic and proteomic modifications in the hippocampus of adult offspring. These studies that were confirmed by regulon analysis show that, although genes whose expression was modified by maternal HF were different between sexes, the main pathways affected were similar with mitochondria and synapses as main hippocampal targets of maternal HF. The effects of maternal HF reported here may help to better characterize sex-dependent molecular pathways involved in cognitive disorders and neurodegenerative diseases.
Collapse
Affiliation(s)
- Thibaut Gauvrit
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Hamza Benderradji
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Alexandre Pelletier
- The Department of Pharmacology & Biophysics, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Soulaimane Aboulouard
- U1192—Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), University of Lille, INSERM, 59000 Lille, France; (S.A.); (M.S.)
| | - Emilie Faivre
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Kévin Carvalho
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Aude Deleau
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Emmanuelle Vallez
- Institut Pasteur de Lille, U1011-EGID, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (E.V.); (A.T.)
| | - Agathe Launay
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Anna Bogdanova
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Mélanie Besegher
- US 41-UMS 2014-PLBS, Animal Facility, University of Lille, CNRS, INSERM, CHU Lille, 59000 Lille, France;
| | - Stéphanie Le Gras
- CNRS U7104, INSERM U1258, GenomEast Platform, IGBMC, University of Strasbourg, 67412 Illkirch, France;
| | - Anne Tailleux
- Institut Pasteur de Lille, U1011-EGID, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (E.V.); (A.T.)
| | - Michel Salzet
- U1192—Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), University of Lille, INSERM, 59000 Lille, France; (S.A.); (M.S.)
| | - Luc Buée
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Fabien Delahaye
- Sanofi Precision Medicine and Computational Biology, 94081 Vitry-sur-Seine, France;
| | - David Blum
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| | - Didier Vieau
- UMR-S1172, Lille Neurosciences & Cognition, University of Lille, INSERM, CHU Lille, 59000 Lille, France; (T.G.); (H.B.); (E.F.); (K.C.); (A.D.); (A.L.); (A.B.); (L.B.); (D.B.)
- Alzheimer & Tauopathies, LabEX DISTALZ, 59045 Lille, France
| |
Collapse
|
7
|
Campesi I, Capobianco G, Cano A, Lodde V, Cruciani S, Maioli M, Sotgiu G, Idda ML, Puci MV, Ruoppolo M, Costanzo M, Caterino M, Cambosu F, Montella A, Franconi F. Stratification of Amniotic Fluid Cells and Amniotic Fluid by Sex Opens Up New Perspectives on Fetal Health. Biomedicines 2023; 11:2830. [PMID: 37893203 PMCID: PMC10604128 DOI: 10.3390/biomedicines11102830] [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: 08/28/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Amniotic fluid is essential for fetus wellbeing and is used to monitor pregnancy and predict fetal outcomes. Sex affects health and medicine from the beginning of life, but knowledge of its influence on cell-depleted amniotic fluid (AF) and amniotic fluid cells (AFCs) is still neglected. We evaluated sex-related differences in AF and in AFCs to extend personalized medicine to prenatal life. AFCs and AF were obtained from healthy Caucasian pregnant women who underwent amniocentesis at the 16th-18th week of gestation for advanced maternal age. In the AF, inflammation biomarkers (TNFα, IL6, IL8, and IL4), malondialdehyde, nitrites, amino acids, and acylcarnitines were measured. Estrogen receptors and cell fate (autophagy, apoptosis, senescence) were measured in AFCs. TNFα, IL8, and IL4 were higher in female AF, whereas IL6, nitrites, and MDA were similar. Valine was higher in male AF, whereas several acylcarnitines were sexually different, suggesting a mitochondrial involvement in establishing sex differences. Female AFCs displayed higher expression of ERα protein and a higher ERα/ERβ ratio. The ratio of LC3II/I, an index of autophagy, was higher in female AFCs, while LC3 gene was similar in both sexes. No significant sex differences were found in the expression of the lysosomal protein LAMP1, while p62 was higher in male AFCs. LAMP1 gene was upregulated in male AFCs, while p62 gene was upregulated in female ones. Finally, caspase 9 activity and senescence linked to telomeres were higher in female AFCs, while caspase 3 and β-galactosidase activities were similar. This study supports the idea that sex differences start very early in prenatal life and influence specific parameters, suggesting that it may be relevant to appreciate sex differences to cover knowledge gaps. This might lead to improving the diagnosis of risk prediction for pregnancy complications and achieving a more satisfactory monitoring of fetus health, even preventing future diseases in adulthood.
Collapse
Affiliation(s)
- Ilaria Campesi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (V.L.); (S.C.); (M.M.); (A.M.)
- Laboratory of Sex-Gender Medicine, National Institute of Biostructures and Biosystems, 07100 Sassari, Italy;
| | - Giampiero Capobianco
- Gynecologic and Obstetric Clinic, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Antonella Cano
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (V.L.); (S.C.); (M.M.); (A.M.)
| | - Valeria Lodde
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (V.L.); (S.C.); (M.M.); (A.M.)
| | - Sara Cruciani
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (V.L.); (S.C.); (M.M.); (A.M.)
| | - Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (V.L.); (S.C.); (M.M.); (A.M.)
| | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (G.S.); (M.V.P.)
| | - Maria Laura Idda
- Institute of Genetics and Biomedical Research, 07100 Sassari, Italy;
| | - Mariangela Valentina Puci
- Clinical Epidemiology and Medical Statistics Unit, Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy; (G.S.); (M.V.P.)
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (M.R.); (M.C.); (M.C.)
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (M.R.); (M.C.); (M.C.)
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (M.R.); (M.C.); (M.C.)
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy
| | - Francesca Cambosu
- Genetics and Developmental Biology Unit, Azienda Ospedaliera Universitaria Sassari, 07100 Sassari, Italy;
| | - Andrea Montella
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (A.C.); (V.L.); (S.C.); (M.M.); (A.M.)
| | - Flavia Franconi
- Laboratory of Sex-Gender Medicine, National Institute of Biostructures and Biosystems, 07100 Sassari, Italy;
| |
Collapse
|
8
|
Olanrewaju GO, Kruse CPS, Wyatt SE. Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments. Int J Mol Sci 2023; 24:14425. [PMID: 37833871 PMCID: PMC10573023 DOI: 10.3390/ijms241914425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.
Collapse
Affiliation(s)
- Gbolaga O. Olanrewaju
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Colin P. S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA;
| | - Sarah E. Wyatt
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| |
Collapse
|
9
|
Espineira S, Flores-Piñas M, Chafino S, Viladés C, Negredo E, Fernández-Arroyo S, Mallolas J, Villar B, Moreno S, Vidal F, Rull A, Peraire J. Multi-omics in HIV: searching insights to understand immunological non-response in PLHIV. Front Immunol 2023; 14:1228795. [PMID: 37649488 PMCID: PMC10465175 DOI: 10.3389/fimmu.2023.1228795] [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: 05/25/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023] Open
Abstract
Antiretroviral therapy (ART) induces persistent suppression of HIV-1 replication and gradual recovery of T-cell counts, and consequently, morbidity and mortality from HIV-related illnesses have been significantly reduced. However, in approximately 30% of people living with HIV (PLHIV) on ART, CD4+ T-cell counts fail to normalize despite ART and complete suppression of HIV viral load, resulting in severe immune dysfunction, which may represent an increased risk of clinical progression to AIDS and non-AIDS events as well as increased mortality. These patients are referred to as "immune inadequate responders", "immunodiscordant responders" or "immune nonresponders (INR)". The molecular mechanisms underlying poor CD4+ T-cell recovery are still unclear. In this sense, the use of omics sciences has shed light on possible factors involved in the activity and metabolic dysregulation of immune cells during the failure of CD4+ T-cell recovery in INR. Moreover, identification of key molecules by omics approaches allows for the proposal of potential biomarkers or therapeutic targets to improve CD4+ T-cell recovery and the quality of life of these patients. Hence, this review aimed to summarize the information obtained through different omics concerning the molecular factors and pathways associated with the INR phenotype to better understand the complexity of this immunological status in HIV infection.
Collapse
Affiliation(s)
- Sonia Espineira
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Marina Flores-Piñas
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
| | - Silvia Chafino
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Consuelo Viladés
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Eugenia Negredo
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Lluita contra les Infeccions, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat de Vic - Universitat Central de Catalunya, Vic, Spain
| | - Salvador Fernández-Arroyo
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences, Joint Unit Eurecat-Universitat Rovira i Virgili, Unique Scientific and Technical Infrastructure (ICTS), Reus, Spain
| | - Josep Mallolas
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- HIV Unit, Hospital Clínic-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Beatriz Villar
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
| | - Santiago Moreno
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Infectious Diseases, University Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Universidad de Alcalá (UAH), Madrid, Spain
| | - Francesc Vidal
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Rull
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Joaquim Peraire
- Infection and Immunity Research Group (INIM), Institut Investigació Sanitària Pere Virgili (IISPV), Tarragona, Spain
- Infection and Immunity Research Group (INIM), Hospital Universitari de Tarragona Joan XXIII (HJ23), Tarragona, Spain
- Universitat Rovira i Virgili (URV), Tarragona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
10
|
Han W, Wu Z, Zhong Z, Williams J, Jacobsen SE, Sun Z, Tang Y. Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37471583 DOI: 10.1021/acs.jafc.3c03240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Natural products biosynthesized from biocontrol fungi in the rhizosphere can have both beneficial and deleterious effects on plants. Herein, we performed a comprehensive analysis of natural product biosynthetic gene clusters (BGCs) from the widely used biocontrol fungus Trichoderma afroharzianum T22 (ThT22). This fungus encodes at least 64 BGCs, yet only seven compounds and four BGCs were previously characterized or mined. We correlated 21 BGCs of ThT22 with known primary and secondary metabolites through homologous BGC comparison and characterized one unknown BGC involved in the biosynthesis of eujavanicol A using heterologous expression. In addition, we performed untargeted transcriptomics and metabolic analysis to demonstrate the activation of silent ThT22 BGCs via the "one strain many compound" (OSMAC) approach. Collectively, our analysis showcases the biosynthetic capacity of ThT22 and paves the way for fully exploring the roles of natural products of ThT22.
Collapse
Affiliation(s)
- Wenyu Han
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Zhongshou Wu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, United States
| | - Zhenhui Zhong
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, United States
| | - Jason Williams
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Steven E Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, United States
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, California 90095, United States
- Department of Biological Chemistry, University of California, Los Angeles, California 90095, United States
| | - Zuodong Sun
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| |
Collapse
|
11
|
Rocha RO, Hussey RS, Pepi LE, Azadi P, Mitchum MG. Discovery of Novel Effector Protein Candidates Produced in the Dorsal Gland of Adult Female Root-Knot Nematodes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:372-380. [PMID: 36847650 PMCID: PMC11321544 DOI: 10.1094/mpmi-11-22-0232-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Root-knot nematodes (RKN) (Meloidogyne spp.) represent one of the most damaging groups of plant-parasitic nematodes. They secrete effector proteins through a protrusible stylet to manipulate host cells for their benefit. Stylet-secreted effector proteins are produced within specialized secretory esophageal gland cells, one dorsal gland (DG) and two subventral glands (SvG), whose activity differ throughout the nematode life cycle. Previous gland transcriptomic profiling studies identified dozens of candidate RKN effectors but were focused on the juvenile stages of the nematode, when the SvGs are most active. We developed a new approach to enrich for the active DGs of M. incognita adult female RKN for RNA and protein extraction. Female heads were manually cut from the body, and a combination of sonication and vortexing was used to dislodge contents inside the heads. DG-enriched fractions were collected by filtering, using cell strainers. Comparative transcriptome profiling of pre-parasitic second-stage juveniles, female heads, and DG-enriched samples was conducted using RNA sequencing. Application of an established effector mining pipeline led to the identification of 83 candidate effector genes upregulated in DG-enriched samples of adult females that code for proteins with a predicted signal peptide but lack transmembrane domains or homology to proteins in the free-living nematode Caenorhabditis elegans. In situ hybridization resulted in the identification of 14 new DG-specific candidate effectors expressed in adult females. Taken together, we have identified novel candidate Meloidogyne effector genes that may have essential roles during later stages of parasitism. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Raquel O. Rocha
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, U.S.A
| | - Richard S. Hussey
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, U.S.A
| | - Lauren E. Pepi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, U.S.A
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, U.S.A
| | - Melissa G. Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, U.S.A
| |
Collapse
|
12
|
Zuluaga-Vélez A, Toro-Acevedo CA, Quintero-Martinez A, Melchor-Moncada JJ, Pedraza-Ordoñez F, Aguilar-Fernández E, Sepúlveda-Arias JC. Performance of Colombian Silk Fibroin Hydrogels for Hyaline Cartilage Tissue Engineering. J Funct Biomater 2022; 13:297. [PMID: 36547557 PMCID: PMC9788426 DOI: 10.3390/jfb13040297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The development and evaluation of scaffolds play a crucial role in the engineering of hyaline cartilage tissue. This work aims to evaluate the performance of silk fibroin hydrogels fabricated from the cocoons of the Colombian hybrid in the in vitro regeneration of hyaline cartilage. The scaffolds were physicochemically characterized, and their performance was evaluated in a cellular model. The results showed that the scaffolds were rich in random coils and β-sheets in their structure and susceptible to various serine proteases with different degradation profiles. Furthermore, they showed a significant increase in ACAN, COL10A1, and COL2A1 expression compared to pellet culture alone and allowed GAG deposition. The soluble portion of the scaffold did not affect chondrogenesis. Furthermore, they promoted the increase in COL1A2, showing a slight tendency to differentiate towards fibrous cartilage. The results also showed that Colombian silk could be used as a source of biomedical devices, paving the way for sericulture to become a more diverse economic activity in emerging countries.
Collapse
Affiliation(s)
- Augusto Zuluaga-Vélez
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
| | - Carlos Andrés Toro-Acevedo
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
| | - Adrián Quintero-Martinez
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, México City 04510, Mexico
| | - Jhon Jairo Melchor-Moncada
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
| | | | - Enrique Aguilar-Fernández
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
| | - Juan Carlos Sepúlveda-Arias
- Grupo Infección e Inmunidad, Facultad de Ciencias de la Salud, Universidad Tecnológica de Pereira, Pereira 660003, Colombia
| |
Collapse
|
13
|
Agamah FE, Bayjanov JR, Niehues A, Njoku KF, Skelton M, Mazandu GK, Ederveen THA, Mulder N, Chimusa ER, 't Hoen PAC. Computational approaches for network-based integrative multi-omics analysis. Front Mol Biosci 2022; 9:967205. [PMID: 36452456 PMCID: PMC9703081 DOI: 10.3389/fmolb.2022.967205] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/20/2022] [Indexed: 08/27/2023] Open
Abstract
Advances in omics technologies allow for holistic studies into biological systems. These studies rely on integrative data analysis techniques to obtain a comprehensive view of the dynamics of cellular processes, and molecular mechanisms. Network-based integrative approaches have revolutionized multi-omics analysis by providing the framework to represent interactions between multiple different omics-layers in a graph, which may faithfully reflect the molecular wiring in a cell. Here we review network-based multi-omics/multi-modal integrative analytical approaches. We classify these approaches according to the type of omics data supported, the methods and/or algorithms implemented, their node and/or edge weighting components, and their ability to identify key nodes and subnetworks. We show how these approaches can be used to identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers of physiological and pathological mechanisms. We provide insight into the most appropriate methods and tools for research questions as showcased around the aetiology and treatment of COVID-19 that can be informed by multi-omics data integration. We conclude with an overview of challenges associated with multi-omics network-based analysis, such as reproducibility, heterogeneity, (biological) interpretability of the results, and we highlight some future directions for network-based integration.
Collapse
Affiliation(s)
- Francis E. Agamah
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jumamurat R. Bayjanov
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anna Niehues
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kelechi F. Njoku
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K. Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. 't Hoen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
14
|
Gjorgjieva M, Ay AS, Correia de Sousa M, Delangre E, Dolicka D, Sobolewski C, Maeder C, Fournier M, Sempoux C, Foti M. MiR-22 Deficiency Fosters Hepatocellular Carcinoma Development in Fatty Liver. Cells 2022; 11:cells11182860. [PMID: 36139435 PMCID: PMC9496902 DOI: 10.3390/cells11182860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 12/24/2022] Open
Abstract
MiR-22 is mostly considered as a hepatic tumor-suppressor microRNA based on in vitro analyses. Yet, whether miR-22 exerts a tumor-suppressive function in the liver has not been investigated in vivo. Herein, in silico analyses of miR-22 expression were performed in hepatocellular carcinomas from human patient cohorts and different mouse models. Diethylnitrosamine-induced hepatocellular carcinomas were then investigated in lean and diet-induced obese miR-22-deficient mice. The proteome of liver tissues from miR-22-deficient mice prior to hepatocellular carcinoma development was further analyzed to uncover miR-22 regulated factors that impact hepatocarcinogenesis with miR-22 deficiency. MiR-22 downregulation was consistently observed in hepatocellular carcinomas from all human cohorts and mouse models investigated. The time of appearance of the first tumors was decreased and the number of tumoral foci induced by diethylnitrosamine was significantly increased by miR-22-deficiency in vivo, two features which were further drastically exacerbated with diet-induced obesity. At the molecular level, we provide evidence that the loss of miR-22 significantly affects the energetic metabolism and mitochondrial functions of hepatocytes, and the expression of tumor-promoting factors such as thrombospondin-1. Our study demonstrates that miR-22 acts as a hepatic tumor suppressor in vivo by restraining pro-carcinogenic metabolic deregulations through pleiotropic mechanisms and the overexpression of relevant oncogenes.
Collapse
Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Anne-Sophie Ay
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Etienne Delangre
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital, University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Translational Research Centre in Onco-Haematology, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Correspondence:
| |
Collapse
|
15
|
Ferrocino I, Rantsiou K, Cocolin L. Microbiome and -omics application in food industry. Int J Food Microbiol 2022; 377:109781. [DOI: 10.1016/j.ijfoodmicro.2022.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
|
16
|
Lombardo SD, Wangsaputra IF, Menche J, Stevens A. Network Approaches for Charting the Transcriptomic and Epigenetic Landscape of the Developmental Origins of Health and Disease. Genes (Basel) 2022; 13:764. [PMID: 35627149 PMCID: PMC9141211 DOI: 10.3390/genes13050764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/04/2022] [Accepted: 04/13/2022] [Indexed: 02/04/2023] Open
Abstract
The early developmental phase is of critical importance for human health and disease later in life. To decipher the molecular mechanisms at play, current biomedical research is increasingly relying on large quantities of diverse omics data. The integration and interpretation of the different datasets pose a critical challenge towards the holistic understanding of the complex biological processes that are involved in early development. In this review, we outline the major transcriptomic and epigenetic processes and the respective datasets that are most relevant for studying the periconceptional period. We cover both basic data processing and analysis steps, as well as more advanced data integration methods. A particular focus is given to network-based methods. Finally, we review the medical applications of such integrative analyses.
Collapse
Affiliation(s)
- Salvo Danilo Lombardo
- Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, 1030 Vienna, Austria;
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Ivan Fernando Wangsaputra
- Maternal and Fetal Health Research Group, Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK;
| | - Jörg Menche
- Max Perutz Labs, Department of Structural and Computational Biology, University of Vienna, 1030 Vienna, Austria;
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1030 Vienna, Austria
- Faculty of Mathematics, University of Vienna, 1030 Vienna, Austria
| | - Adam Stevens
- Maternal and Fetal Health Research Group, Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK;
| |
Collapse
|
17
|
Van Simaeys D, De La Fuente A, Zilio S, Zoso A, Kuznetsova V, Alcazar O, Buchwald P, Grilli A, Caroli J, Bicciato S, Serafini P. RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells. Nat Commun 2022; 13:1815. [PMID: 35383192 PMCID: PMC8983715 DOI: 10.1038/s41467-022-29377-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to detect and target β cells in vivo can substantially refine how diabetes is studied and treated. However, the lack of specific probes still hampers a precise characterization of human β cell mass and the delivery of therapeutics in clinical settings. Here, we report the identification of two RNA aptamers that specifically and selectively recognize mouse and human β cells. The putative targets of the two aptamers are transmembrane p24 trafficking protein 6 (TMED6) and clusterin (CLUS). When given systemically in immune deficient mice, these aptamers recognize the human islet graft producing a fluorescent signal proportional to the number of human islets transplanted. These aptamers cross-react with endogenous mouse β cells and allow monitoring the rejection of mouse islet allografts. Finally, once conjugated to saRNA specific for X-linked inhibitor of apoptosis (XIAP), they can efficiently transfect non-dissociated human islets, prevent early graft loss, and improve the efficacy of human islet transplantation in immunodeficient in mice.
Collapse
Affiliation(s)
- Dimitri Van Simaeys
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Adriana De La Fuente
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Serena Zilio
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Alessia Zoso
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Victoria Kuznetsova
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Oscar Alcazar
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Andrea Grilli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jimmy Caroli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Serafini
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
| |
Collapse
|
18
|
Szajko K, Sołtys-Kalina D, Heidorn-Czarna M, Smyda-Dajmund P, Wasilewicz-Flis I, Jańska H, Marczewski W. Transcriptomic and proteomic data provide new insights into cold-treated potato tubers with T- and D-type cytoplasm. PLANTA 2022; 255:97. [PMID: 35380306 PMCID: PMC8983635 DOI: 10.1007/s00425-022-03879-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Tuber-omics in potato with the T- and D-types of cytoplasm showed different sets of differentially expressed genes and proteins in response to cold storage. For the first time, we report differences in gene and protein expression in potato (Solanum tuberosum L.) tubers possessing the T- or D-type cytoplasm. Two F1 diploid reciprocal populations, referred to as T and D, were used. The pooling strategy was applied for detection of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in tubers consisting of extreme chip colour after cold storage. RNA and protein bulks were constructed from contrasting phenotypes. We recognized 48 and 15 DEGs for the T and D progenies, respectively. DEPs were identified in the amyloplast and mitochondrial fractions. In the T-type cytoplasm, only 2 amyloplast-associated and 5 mitochondria-associated DEPs were detected. Of 37 mitochondria-associated DEPs in the D-type cytoplasm, there were 36 downregulated DEPs in the dark chip colour bulks. These findings suggest that T- and D-type of cytoplasm might influence sugar accumulation in cold-stored potato tubers in different ways. We showed that the mt/nucDNA ratio was higher in D-possessing tubers after cold storage than in T progeny. For the D-type cytoplasm, the pt/nucDNA ratio was higher for tubers characterized by dark chip colour than for those with light chip colour. Our findings suggest that T- and D-type cytoplasm might influence sugar accumulation in cold-stored potato tubers in different ways.
Collapse
Affiliation(s)
- Katarzyna Szajko
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| | - Dorota Sołtys-Kalina
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | | | - Paulina Smyda-Dajmund
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Iwona Wasilewicz-Flis
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland
| | - Hanna Jańska
- Faculty of Biotechnology, University of Wroclaw, 50-383, Wrocław, Poland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute-National Research Institute, Platanowa 19, 05-831, Młochów, Poland.
| |
Collapse
|
19
|
Trapotsi MA, Hosseini-Gerami L, Bender A. Computational analyses of mechanism of action (MoA): data, methods and integration. RSC Chem Biol 2022; 3:170-200. [PMID: 35360890 PMCID: PMC8827085 DOI: 10.1039/d1cb00069a] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
The elucidation of a compound's Mechanism of Action (MoA) is a challenging task in the drug discovery process, but it is important in order to rationalise phenotypic findings and to anticipate potential side-effects. Bioinformatic approaches, advances in machine learning techniques and the increasing deposition of high-throughput data in public databases have significantly contributed to recent advances in the field, but it is not straightforward to decide which data and methods are most suitable to use in a given case. In this review, we focus on these methods and data and their applications in generating MoA hypotheses for subsequent experimental validation. We discuss compound-specific data such as -omics, cell morphology and bioactivity data, as well as commonly used supplementary prior knowledge such as network and pathway data, and provide information on databases where this data can be accessed. In terms of methodologies, we discuss both well-established methods (connectivity mapping, pathway enrichment) as well as more developing methods (neural networks and multi-omics integration). Finally, we review case studies where the MoA of a compound was successfully suggested from computational analysis by incorporating multiple data modalities and/or methodologies. Our aim for this review is to provide researchers with insights into the benefits and drawbacks of both the data and methods in terms of level of understanding, biases and interpretation - and to highlight future avenues of investigation which we foresee will improve the field of MoA elucidation, including greater public access to -omics data and methodologies which are capable of data integration.
Collapse
Affiliation(s)
- Maria-Anna Trapotsi
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge UK
| | - Layla Hosseini-Gerami
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge UK
| | - Andreas Bender
- Centre for Molecular Informatics, Yusuf Hamied Department of Chemistry, University of Cambridge UK
| |
Collapse
|
20
|
Loric S, Conti M. Versatile Functional Energy Metabolism Platform Working From Research to Patient: An Integrated View of Cell Bioenergetics. FRONTIERS IN TOXICOLOGY 2022; 3:750431. [PMID: 35295105 PMCID: PMC8915814 DOI: 10.3389/ftox.2021.750431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/08/2021] [Indexed: 12/06/2022] Open
Abstract
Mitochondrial dysfunctions that were not discovered during preclinical and clinical testing have been responsible for at least restriction of use as far as withdrawal of many drugs. To solve mitochondrial machinery complexity, integrative methodologies combining different data, coupled or not to mathematic modelling into systems biology, could represent a strategic way but are still very hard to implement. These technologies should be accurate and precise to avoid accumulation of errors that can lead to misinterpretations, and then alter prediction efficiency. To address such issue, we have developed a versatile functional energy metabolism platform that can measure quantitatively, in parallel, with a very high precision and accuracy, a high number of biological parameters like substrates or enzyme cascade activities in essential metabolism units (glycolysis, respiratory chain ATP production, oxidative stress...) Its versatility (our platform works on either cell lines or small animals and human samples) allows cell metabolism pathways fine tuning comparison from preclinical to clinical studies. Applied here to OXPHOS and/or oxidative stress as an example, it allows discriminating compounds with acute toxic effects but, most importantly, those inducing low noise chronic ones.
Collapse
|
21
|
JAK2/STAT3 inhibition attenuates intestinal ischemia-reperfusion injury via promoting autophagy: in vitro and in vivo study. Mol Biol Rep 2022; 49:2857-2867. [PMID: 35067814 DOI: 10.1007/s11033-021-07099-x] [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: 08/10/2021] [Accepted: 12/16/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Intestinal ischemia-reperfusion (I/R) causes severe injury to the intestine, leading to systemic inflammation and multiple organ failure. Autophagy is a stress-response mechanism that can protect against I/R injury by removing damaged organelles and toxic protein aggregates. Recent evidence has identified JAK-STAT signaling pathway as a new regulator of autophagy process, however, their regulatory relationship in intestinal I/R remains unknown. METHODS AND RESULTS We systematically analyzed intestinal transcriptome data and found that JAK-STAT pathway was largely activated in response to I/R with most significant upregulation observed for JAK2 and STAT3. ChIP-Seq and luciferase assays in an in vitro oxygen-glucose deprivation and reoxygenation model revealed that activated JAK2/STAT3 signaling directly inhibited the transcription of autophagy regulator Beclin-1, leading to the suppression of autophagy and the activation of intestinal cell death. These findings were further confirmed in an in vivo mouse model, in which, intestinal I/R injury was associated with the activation of JAK2/STAT3 pathway and the deactivation of Beclin-1-mediated autophagy, while inhibiting JAK2/STAT3 with AG490 reactivated autophagy and improved survival after intestinal I/R injury. CONCLUSIONS JAK2/STAT3 signaling suppresses autophagy process during intestinal I/R, while inhibiting JAK-STAT can be protective against intestinal I/R injury by activating autophagy. These findings expand our knowledge on intestinal I/R injury and provide therapeutic targets for clinical treatment.
Collapse
|
22
|
Wong DCS, Seinkmane E, Zeng A, Stangherlin A, Rzechorzek NM, Beale AD, Day J, Reed M, Peak‐Chew SY, Styles CT, Edgar RS, Putker M, O’Neill JS. CRYPTOCHROMES promote daily protein homeostasis. EMBO J 2022; 41:e108883. [PMID: 34842284 PMCID: PMC8724739 DOI: 10.15252/embj.2021108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
Collapse
Affiliation(s)
| | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | | | - Jason Day
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Martin Reed
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Rachel S Edgar
- Department of Infectious DiseasesImperial CollegeLondonUK
| | - Marrit Putker
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Crown BioscienceUtrechtthe Netherlands
| | | |
Collapse
|
23
|
Shashikadze B, Flenkenthaler F, Stöckl JB, Valla L, Renner S, Kemter E, Wolf E, Fröhlich T. Developmental Effects of (Pre-)Gestational Diabetes on Offspring: Systematic Screening Using Omics Approaches. Genes (Basel) 2021; 12:1991. [PMID: 34946940 PMCID: PMC8701487 DOI: 10.3390/genes12121991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/27/2022] Open
Abstract
Worldwide, gestational diabetes affects 2-25% of pregnancies. Due to related disturbances of the maternal metabolism during the periconceptional period and pregnancy, children bear an increased risk for future diseases. It is well known that an aberrant intrauterine environment caused by elevated maternal glucose levels is related to elevated risks for increased birth weights and metabolic disorders in later life, such as obesity or type 2 diabetes. The complexity of disturbances induced by maternal diabetes, with multiple underlying mechanisms, makes early diagnosis or prevention a challenging task. Omics technologies allowing holistic quantification of several classes of molecules from biological fluids, cells, or tissues are powerful tools to systematically investigate the effects of maternal diabetes on the offspring in an unbiased manner. Differentially abundant molecules or distinct molecular profiles may serve as diagnostic biomarkers, which may also support the development of preventive and therapeutic strategies. In this review, we summarize key findings from state-of-the-art Omics studies addressing the impact of maternal diabetes on offspring health.
Collapse
Affiliation(s)
- Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; (B.S.); (F.F.); (J.B.S.)
| | - Florian Flenkenthaler
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; (B.S.); (F.F.); (J.B.S.)
| | - Jan B. Stöckl
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; (B.S.); (F.F.); (J.B.S.)
| | - Libera Valla
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; (L.V.); (S.R.); (E.K.)
| | - Simone Renner
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; (L.V.); (S.R.); (E.K.)
- Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Elisabeth Kemter
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; (L.V.); (S.R.); (E.K.)
- Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; (B.S.); (F.F.); (J.B.S.)
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany; (L.V.); (S.R.); (E.K.)
- Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; (B.S.); (F.F.); (J.B.S.)
| |
Collapse
|
24
|
Abdelli N, Ramser A, Greene ES, Beer L, Tabler TW, Orlowski SK, Pérez JF, Solà-Oriol D, Anthony NB, Dridi S. Effects of Cyclic Chronic Heat Stress on the Expression of Nutrient Transporters in the Jejunum of Modern Broilers and Their Ancestor Wild Jungle Fowl. Front Physiol 2021; 12:733134. [PMID: 34744775 PMCID: PMC8566887 DOI: 10.3389/fphys.2021.733134] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 01/10/2023] Open
Abstract
Heat stress (HS) has been reported to disrupt nutrient digestion and absorption in broilers. These effects may be more prominent in fast-growing chickens due to their high metabolic activity. However, the underlying molecular mechanisms are not yet fully elucidated. Hence, the current study aimed to evaluate the effect of chronic HS on jejunal nutrient transport in slow- (Athens Canadian Random Bred, ACRB from 1950), moderate- (The 1995 random bred, 95RAN), rapid- (modern broilers, modern random bred, MRB) growing birds and their ancestor wild jungle fowl (JF). One-day male chicks (n = 150/line) were placed by line in environmentally controlled chambers and kept under the same industry-standard environmental conditions until d28. On d29, an 8-h daily cyclic HS (36°C) was applied to half of the chambers, which lasted until d55, while keeping the rest under thermal neutral (TN, 24°C) conditions. Jejunum tissues were collected for morphology assessment and molecular analysis of carbohydrate-, amino acid-, and fatty acid-transporters. MRB exhibited the highest body weight (BW) followed by 95RAN under both conditions. HS decreased feed intake (FI) in MRB and 95RAN, which resulted in lower BW compared to their TN counterparts; however, no effect was observed in ACRB and JF. MRB showed a greater villus height (VH) to crypt depth (CD) ratio under both environmental conditions. Molecular analyses showed that glucose transporter (GLUT) 2, 5, 10, and 11 were upregulated in MRB compared to some of the other populations under TN conditions. HS downregulated GLUT2, 10, 11, and 12 in MRB while it increased the expression of GLUT1, 5, 10, and 11 in JF. GLUT2 protein expression was higher in JF compared to ACRB and MRB under TN conditions. It also showed an increase in ACRB but no effect on 95RAN and MRB under HS conditions. ACRB exhibited greater expression of the EAAT3 gene as compared to the rest of the populations maintained under TN conditions. HS exposure did not alter the gene expression of amino acid transporters in MRB. Gene expression of CD36 and FABP2 was upregulated in HS JF birds. Protein expression of CD36 was downregulated in HS JF while no effect was observed in ACRB, 95RAN, and MRB. Taken together, these data are the first to show the effect of HS on jejunal expression of nutrient transporters in three broiler populations known to represent 70 years of genetic progress in the poultry industry and a Red Jungle Fowl population representative of the primary ancestor of domestic chickens.
Collapse
Affiliation(s)
- Nedra Abdelli
- Animal Nutrition and Welfare Service, Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Alison Ramser
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Elizabeth S Greene
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Lesleigh Beer
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Travis W Tabler
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sara K Orlowski
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - José Francisco Pérez
- Animal Nutrition and Welfare Service, Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David Solà-Oriol
- Animal Nutrition and Welfare Service, Department of Animal and Food Sciences, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Nicholas B Anthony
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sami Dridi
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| |
Collapse
|
25
|
Cellular Proteo-Transcriptomic Changes in the Immediate Early-Phase of Lentiviral Transduction. Microorganisms 2021; 9:microorganisms9112207. [PMID: 34835333 PMCID: PMC8625573 DOI: 10.3390/microorganisms9112207] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/28/2022] Open
Abstract
Lentivirus-based vectors derived from human immunodeficiency viruses type 1 and 2 (HIV-1 and 2) are widely used tools in research and may also be utilized in clinical settings. Like their parental virions, they are known to depend on the cellular machinery for successful gene delivery and integration. While most of the studies on cellular proteomic and transcriptomic changes have focused on the late phase of the transduction, studies of those changes in early time-points, especially in the case of HIV-2 based vectors, are widely lacking. Using second generation HIV-1 and 2 vesicular stomatitis virus G protein (VSV-G) pseudotyped lentiviral vectors, we transduced HEK-293T human embryonic kidney cells and carried out transcriptomic profiling at 0 and 2 h time points, with accompanying proteomic analysis at 2 h following transduction. Significant variations were observed in gene expression profile between HIV-1 and HIV-2 transduced samples. Thrombospondin 1 (THBS1), collagens (COL1A2, COL3A1), and eukaryotic translation factors (EIF3CL) in addition to various genes coding for long non-coding RNA (lncRNA) were significantly upregulated 2 h after HIV-2 transduction compared to HIV-1. Label-free quantification mass spectrometry (MS) indicated that seven proteins involved in RNA binding, mRNA transport, and chaperoning were significantly downregulated. The identification of cellular protein targets of lentiviral vectors and their effect on the cellular transcriptome will undoubtedly shed more light on their complex life cycle and may be utilized against infection by their parental lentiviruses. Furthermore, characterizing the early phase of HIV-2 infection may aid in the understanding of its pathomechanism and long incubation period.
Collapse
|
26
|
Valenzuela A, Tardiveau C, Ayuso M, Buyssens L, Bars C, Van Ginneken C, Fant P, Leconte I, Braendli-Baiocco A, Parrott N, Schmitt G, Tessier Y, Barrow P, Van Cruchten S. Safety Testing of an Antisense Oligonucleotide Intended for Pediatric Indications in the Juvenile Göttingen Minipig, including an Evaluation of the Ontogeny of Key Nucleases. Pharmaceutics 2021; 13:1442. [PMID: 34575518 PMCID: PMC8470776 DOI: 10.3390/pharmaceutics13091442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
The adult Göttingen Minipig is an acknowledged model for safety assessment of antisense oligonucleotide (ASO) drugs developed for adult indications. To assess whether the juvenile Göttingen Minipig is also a suitable nonclinical model for pediatric safety assessment of ASOs, we performed an 8-week repeat-dose toxicity study in different age groups of minipigs ranging from 1 to 50 days of age. The animals received a weekly dose of a phosphorothioated locked-nucleic-acid-based ASO that was assessed previously for toxicity in adult minipigs. The endpoints included toxicokinetic parameters, in-life monitoring, clinical pathology, and histopathology. Additionally, the ontogeny of key nucleases involved in ASO metabolism and pharmacologic activity was investigated using quantitative polymerase chain reaction and nuclease activity assays. Similar clinical chemistry and toxicity findings were observed; however, differences in plasma and tissue exposures as well as pharmacologic activity were seen in the juvenile minipigs when compared with the adult data. The ontogeny study revealed a differential nuclease expression and activity, which could affect the metabolic pathway and pharmacologic effect of ASOs in different tissues and age groups. These data indicate that the juvenile Göttingen Minipig is a promising nonclinical model for safety assessment of ASOs intended to treat disease in the human pediatric population.
Collapse
Affiliation(s)
- Allan Valenzuela
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Claire Tardiveau
- Charles River Laboratories France Safety Assessment SAS, 69210 Saint-Germain-Nuelles, France; (C.T.); (P.F.); (I.L.)
| | - Miriam Ayuso
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Laura Buyssens
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Chloe Bars
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| | - Pierluigi Fant
- Charles River Laboratories France Safety Assessment SAS, 69210 Saint-Germain-Nuelles, France; (C.T.); (P.F.); (I.L.)
| | - Isabelle Leconte
- Charles River Laboratories France Safety Assessment SAS, 69210 Saint-Germain-Nuelles, France; (C.T.); (P.F.); (I.L.)
| | - Annamaria Braendli-Baiocco
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Neil Parrott
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Georg Schmitt
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Yann Tessier
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Paul Barrow
- Roche Pharmaceutical Research and Early Development, F. Hoffmann-La-Roche, Ltd., 4070 Basel, Switzerland; (A.B.-B.); (N.P.); (G.S.); (Y.T.); (P.B.)
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (A.V.); (M.A.); (L.B.); (C.B.); (C.V.G.)
| |
Collapse
|
27
|
Brauer M, Lassek C, Hinze C, Hoyer J, Becher D, Jahn D, Sievers S, Riedel K. What's a Biofilm?-How the Choice of the Biofilm Model Impacts the Protein Inventory of Clostridioides difficile. Front Microbiol 2021; 12:682111. [PMID: 34177868 PMCID: PMC8225356 DOI: 10.3389/fmicb.2021.682111] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The anaerobic pathogen Clostridioides difficile is perfectly equipped to survive and persist inside the mammalian intestine. When facing unfavorable conditions C. difficile is able to form highly resistant endospores. Likewise, biofilms are currently discussed as form of persistence. Here a comprehensive proteomics approach was applied to investigate the molecular processes of C. difficile strain 630Δerm underlying biofilm formation. The comparison of the proteome from two different forms of biofilm-like growth, namely aggregate biofilms and colonies on agar plates, revealed major differences in the formation of cell surface proteins, as well as enzymes of its energy and stress metabolism. For instance, while the obtained data suggest that aggregate biofilm cells express both flagella, type IV pili and enzymes required for biosynthesis of cell-surface polysaccharides, the S-layer protein SlpA and most cell wall proteins (CWPs) encoded adjacent to SlpA were detected in significantly lower amounts in aggregate biofilm cells than in colony biofilms. Moreover, the obtained data suggested that aggregate biofilm cells are rather actively growing cells while colony biofilm cells most likely severely suffer from a lack of reductive equivalents what requires induction of the Wood-Ljungdahl pathway and C. difficile’s V-type ATPase to maintain cell homeostasis. In agreement with this, aggregate biofilm cells, in contrast to colony biofilm cells, neither induced toxin nor spore production. Finally, the data revealed that the sigma factor SigL/RpoN and its dependent regulators are noticeably induced in aggregate biofilms suggesting an important role of SigL/RpoN in aggregate biofilm formation.
Collapse
Affiliation(s)
- Madita Brauer
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Lassek
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Juliane Hoyer
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Sievers
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| |
Collapse
|
28
|
Shukla SK, Sharma AK, Bajaj S, Yashavarddhan MH. Radiation proteome: a clue to protection, carcinogenesis, and drug development. Drug Discov Today 2020; 26:525-531. [PMID: 33137481 DOI: 10.1016/j.drudis.2020.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 09/29/2020] [Accepted: 10/26/2020] [Indexed: 02/04/2023]
Affiliation(s)
- Sandeep Kumar Shukla
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Lucknow road, Timarpur, Delhi, 110054, India.
| | - Ajay Kumar Sharma
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Lucknow road, Timarpur, Delhi, 110054, India
| | - Sania Bajaj
- Institute of Nuclear Medicine and Allied Sciences, Defence Research and Development Organization, Lucknow road, Timarpur, Delhi, 110054, India
| | - M H Yashavarddhan
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow road, Timarpur, Delhi, 110054, India
| |
Collapse
|
29
|
Liang X, Martyniuk CJ, Simmons DBD. Are we forgetting the "proteomics" in multi-omics ecotoxicology? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100751. [PMID: 33142247 DOI: 10.1016/j.cbd.2020.100751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 07/19/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Proteomics plays a significant role in discerning the effects of chemical exposures in animal taxa. Multi-omics applications have become more pervasive in toxicology, however questions remain about whether proteomics is being utilized by the community to its full potential - are we placing too much stock in transcriptomics and other omics approaches for developing adverse outcome pathways? Proteins are more relevant than transcripts because they are direct mediators of the resulting phenotype. There is also rarely perfect stoichiometry between transcript and protein abundance and transcript abundance may not accurately predict physiologic response. Proteins direct all levels of phenotype: structural proteins dictate physical form, enzymes catalyze biochemical reactions, and proteins act as signaling proteins, antibodies, transporters, ion pumps, and transcription factors to control gene expression. Molecular initiating events (MIEs) of AOPs predominantly occur at the level of the protein (e.g. ligand-receptor binding) and proteomics can elucidate novel MIEs and mapping KEs in AOPs. This critical review highlights the need for proteomics in multi-omics studies in environmental toxicology and outlines steps required for inclusion and wider acceptance in chemical risk assessment. We also present case studies of multi-omics approaches that utilize proteomics and discuss some of the challenges and opportunities for proteomics in comparative ecotoxicology. Our intention is not to minimize the importance of other omics technologies, as each has strengths and limitations, but rather to encourage researchers to consider proteomics-based methods in multi-omics studies and AOP development.
Collapse
Affiliation(s)
- Xuefang Liang
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | | |
Collapse
|
30
|
Gjorgjieva M, Sobolewski C, Ay AS, Abegg D, Correia de Sousa M, Portius D, Berthou F, Fournier M, Maeder C, Rantakari P, Zhang FP, Poutanen M, Picard D, Montet X, Nef S, Adibekian A, Foti M. Genetic Ablation of MiR-22 Fosters Diet-Induced Obesity and NAFLD Development. J Pers Med 2020; 10:jpm10040170. [PMID: 33066497 PMCID: PMC7711493 DOI: 10.3390/jpm10040170] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
miR-22 is one of the most abundant miRNAs in the liver and alterations of its hepatic expression have been associated with the development of hepatic steatosis and insulin resistance, as well as cancer. However, the pathophysiological roles of miR-22-3p in the deregulated hepatic metabolism with obesity and cancer remains poorly characterized. Herein, we observed that alterations of hepatic miR-22-3p expression with non-alcoholic fatty liver disease (NAFLD) in the context of obesity are not consistent in various human cohorts and animal models in contrast to the well-characterized miR-22-3p downregulation observed in hepatic cancers. To unravel the role of miR-22 in obesity-associated NAFLD, we generated constitutive Mir22 knockout (miR-22KO) mice, which were subsequently rendered obese by feeding with fat-enriched diet. Functional NAFLD- and obesity-associated metabolic parameters were then analyzed. Insights about the role of miR-22 in NAFLD associated with obesity were further obtained through an unbiased proteomic analysis of miR-22KO livers from obese mice. Metabolic processes governed by miR-22 were finally investigated in hepatic transformed cancer cells. Deletion of Mir22 was asymptomatic when mice were bred under standard conditions, except for an onset of glucose intolerance. However, when challenged with a high fat-containing diet, Mir22 deficiency dramatically exacerbated fat mass gain, hepatomegaly, and liver steatosis in mice. Analyses of explanted white adipose tissue revealed increased lipid synthesis, whereas mass spectrometry analysis of the liver proteome indicated that Mir22 deletion promotes hepatic upregulation of key enzymes in glycolysis and lipid uptake. Surprisingly, expression of miR-22-3p in Huh7 hepatic cancer cells triggers, in contrast to our in vivo observations, a clear induction of a Warburg effect with an increased glycolysis and an inhibited mitochondrial respiration. Together, our study indicates that miR-22-3p is a master regulator of the lipid and glucose metabolism with differential effects in specific organs and in transformed hepatic cancer cells, as compared to non-tumoral tissue.
Collapse
Affiliation(s)
- Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Anne-Sophie Ay
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Dorothea Portius
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
| | - Pia Rantakari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Fu-Ping Zhang
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Matti Poutanen
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, FI-20014 Turku, Finland; (P.R.); (F.-P.Z.); (M.P.)
| | - Didier Picard
- Department of Cell Biology, Faculty of Science, University of Geneva, 1205 Geneva, Switzerland;
| | - Xavier Montet
- Department of Radiology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland;
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA; (D.A.); (A.A.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (M.G.); (C.S.); (A.-S.A.); (M.C.d.S.); (D.P.); (F.B.); (M.F.); (C.M.)
- Diabetes Center, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Correspondence: ; Tel.: +41-22-37-95-204; Fax: +41-22-37-95-260
| |
Collapse
|
31
|
Martyniuk CJ. Perspectives on transcriptomics in animal physiology studies. Comp Biochem Physiol B Biochem Mol Biol 2020; 250:110490. [PMID: 32798690 DOI: 10.1016/j.cbpb.2020.110490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/05/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022]
Abstract
Reductionist approaches in physiology and biochemistry are essential for understanding how animals cope and adapt to their environments. Transcriptomics is no longer restricted to a select few, and accessibility and affordability continue to facilitate its rapid growth as a science. More than 6000 publications (a conservative estimate) over the past decade quantify the response of the transcriptome to a wide breadth of questions in animal physiology. Transcriptomes have been quantified under conditions of hypoxia, climate change, salinity, drought, environmental pollution, and ultraviolet radiation among others; these studies have greatly improved understanding of the molecular machinery required for organismal adaptation. These "snapshots in time" however are never complete as the transcriptome is exquisitely sensitive to an individual's current physiologic state. Animal physiologists new to the field must recognize limitations of transcriptome technologies and consider experimental designs that strengthen physiologic interpretation. Current estimates suggest that a sample size of 6 or more are required for RNA-seq experiments in order to capture the majority of differentially expressed genes confidently. "Outside-the-box" approaches for statistical analyses of data derived from RNA-seq should be explored, as studies continue to point out that high false discoveries rates are pervasive with RNA-seq studies, reminiscent of the early days of microarrays. Incorporating biological variability, rather than reducing it (i.e. pooling strategies), into experimental designs is essential. Moreover, real-time PCR must not be viewed as a "validation step" to justify low samples sizes, but rather an orthogonal method to strengthen biological interpretation. The use of proper experimental controls in transcriptomics studies (i.e. spike-in controls and technical replication) are recommended and there is a pressing need for inter-laboratory tests (round robin experiments) to quantify repeatability and to identify sources of transcriptome variation within the context of animal physiology. Testing the reproducibility of transcriptome experiments in light of physiology in non-model organisms would be a significant contribution to the community. Single cell transcriptomics and multiplexing barcoding strategies such as decode-seq are poised to further advance the reductionist view of animal physiology; researchers are encouraged to consult literature herein and elsewhere for guidance on best practices and limitations of transcriptome technologies when studying the physiology of animals.
Collapse
Affiliation(s)
- Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
32
|
Bonomo R, Cavaletti G, Skene DJ. Metabolomics markers in Neurology: current knowledge and future perspectives for therapeutic targeting. Expert Rev Neurother 2020; 20:725-738. [PMID: 32538242 DOI: 10.1080/14737175.2020.1782746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Metabolomics is an emerging approach providing new insights into the metabolic changes and underlying mechanisms involved in the pathogenesis of neurological disorders. AREAS COVERED Here, the authors present an overview of the current knowledge of metabolic profiling (metabolomics) to provide critical insight on the role of biochemical markers and metabolic alterations in neurological diseases. EXPERT OPINION Elucidation of characteristic metabolic alterations in neurological disorders is crucial for a better understanding of their pathogenesis, and for identifying potential biomarkers and drug targets. Nevertheless, discrepancies in diagnostic criteria, sample handling protocols, and analytical methods still affect the generalizability of current study results.
Collapse
Affiliation(s)
- Roberta Bonomo
- Experimental Neurology Unit, School of Medicine and Surgery, University of Milano-Bicocca , Monza, Italy.,Chronobiology, Faculty of Health and Medical Sciences, University of Surrey , Guildford, UK
| | - Guido Cavaletti
- Experimental Neurology Unit, School of Medicine and Surgery, University of Milano-Bicocca , Monza, Italy
| | - Debra J Skene
- Chronobiology, Faculty of Health and Medical Sciences, University of Surrey , Guildford, UK
| |
Collapse
|