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Anbarci DN, McKey J, Levic DS, Bagnat M, Capel B. Rediscovering the rete ovarii, a secreting auxiliary structure to the ovary. eLife 2025; 13:RP96662. [PMID: 40105200 PMCID: PMC11922502 DOI: 10.7554/elife.96662] [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] [Indexed: 03/20/2025] Open
Abstract
The rete ovarii (RO) is an appendage of the ovary that has been given little attention. Although the RO appears in drawings of the ovary in early versions of Gray's Anatomy, it disappeared from recent textbooks, and is often dismissed as a functionless vestige in the adult ovary. Using PAX8 immunostaining and confocal microscopy, we characterized the fetal development of the RO in the context of the mouse ovary. The RO consists of three distinct regions that persist in adult life, the intraovarian rete (IOR), the extraovarian rete (EOR), and the connecting rete (CR). While the cells of the IOR appear to form solid cords within the ovary, the EOR rapidly develops into a convoluted tubular epithelium ending in a distal dilated tip. Cells of the EOR are ciliated and exhibit cellular trafficking capabilities. The CR, connecting the EOR to the IOR, gradually acquires tubular epithelial characteristics by birth. Using microinjections into the distal dilated tip of the EOR, we found that luminal contents flow toward the ovary. Mass spectrometry revealed that the EOR lumen contains secreted proteins potentially important for ovarian function. We show that the cells of the EOR are closely associated with vasculature and macrophages, and are contacted by neuronal projections, consistent with a role as a sensory appendage of the ovary. The direct proximity of the RO to the ovary and its integration with the extraovarian landscape suggest that it plays an important role in ovary development and homeostasis.
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Affiliation(s)
- Dilara N Anbarci
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
| | - Jennifer McKey
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Daniel S Levic
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
| | - Michel Bagnat
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical CenterDurhamUnited States
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2
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Anbarci DN, McKey1 J, Levic DS, Bagnat M, Capel B. Rediscovering the Rete Ovarii: a secreting auxiliary structure to the ovary. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.566085. [PMID: 37986754 PMCID: PMC10659334 DOI: 10.1101/2023.11.08.566085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The rete ovarii (RO) is an appendage of the ovary that has been given little attention. Although the RO appears in drawings of the ovary in early versions of Gray's Anatomy, it disappeared from recent textbooks, and is often dismissed as a functionless vestige in the adult ovary. Using PAX8 immunostaining and confocal microscopy, we characterized the fetal development of the RO in the context of the ovary. The RO consists of three distinct regions that persist in adult life, the intraovarian rete (IOR), the extraovarian rete (EOR), and the connecting rete (CR). While the cells of the IOR appear to form solid cords within the ovary, the EOR rapidly develops into a convoluted tubular epithelium ending in a distal dilated tip. Cells of the EOR are ciliated and exhibit cellular trafficking capabilities. The CR, connecting the EOR to the IOR, gradually acquires tubular epithelial characteristics by birth. Using microinjections into the distal dilated tip of the EOR, we found that luminal contents flow towards the ovary. Mass spectrometry revealed that the EOR lumen contains secreted proteins potentially important for ovarian function. We show that the cells of the EOR are closely associated with vasculature and macrophages, and are contacted by neuronal projections, consistent with a role as a sensory appendage of the ovary. The direct proximity of the RO to the ovary and its integration with the extraovarian landscape suggest that it plays an important role in ovary development and homeostasis.
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Affiliation(s)
- Dilara N. Anbarci
- Department of Cell Biology, Duke University Medical Center, Durham NC 27710
| | - Jennifer McKey1
- Department of Cell Biology, Duke University Medical Center, Durham NC 27710
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Daniel S. Levic
- Department of Cell Biology, Duke University Medical Center, Durham NC 27710
| | - Michel Bagnat
- Department of Cell Biology, Duke University Medical Center, Durham NC 27710
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham NC 27710
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3
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Paul D, Sinnarasan VSP, Das R, Sheikh MMR, Venkatesan A. Machine learning approach to predict blood-secretory proteins and potential biomarkers for liver cancer using omics data. J Proteomics 2024; 309:105298. [PMID: 39216516 DOI: 10.1016/j.jprot.2024.105298] [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: 06/12/2024] [Revised: 08/22/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Identifying non-invasive blood-based biomarkers is crucial for early detection and monitoring of liver cancer (LC), thereby improving patient outcomes. This study leveraged computational approaches to predict potential blood-based biomarkers for LC. Machine learning (ML) models were developed using selected features from blood-secretory proteins collected from the curated databases. The logistic regression (LR) model demonstrated the optimal performance. Transcriptome analysis across 7 LC cohorts revealed 231 common differentially expressed genes (DEGs). The encoded proteins of these DEGs were compared with the ML dataset, revealing 29 proteins overlapping with the blood-secretory dataset. The LR model also predicted 29 additional proteins as blood-secretory with the remaining protein-coding genes. As a result, 58 potential blood-secretory proteins were obtained. Among the top 20 genes, 13 common hub genes were identified. Further, area under the receiver operating characteristic curve (ROC AUC) analysis was performed to assess the genes as potential diagnostic blood biomarkers. Six genes, ESM1, FCN2, MDK, GPC3, CTHRC1 and COL6A6, exhibited an AUC value higher than 0.85 and were predicted as blood-secretory. This study highlights the potential of an integrative computational approach for discovering non-invasive blood-based biomarkers in LC, facilitating for further validation and clinical translation. SIGNIFICANCE: Liver cancer is one of the leading causes of premature death worldwide, with its prevalence and mortality rates projected to increase. Although current diagnostic methods are highly sensitive, they are invasive and unsuitable for repeated testing. Blood biomarkers offer a promising non-invasive alternative, but their wide dynamic range of protein concentration poses experimental challenges. Therefore, utilizing available omics data to develop a diagnostic model could provide a potential solution for accurate diagnosis. This study developed a computational method integrating machine learning and bioinformatics analysis to identify potential blood biomarkers. As a result, ESM1, FCN2, MDK, GPC3, CTHRC1 and COL6A6 biomarkers were identified, holding significant promise for improving diagnosis and understanding of liver cancer. The integrated method can be applied to other cancers, offering a possible solution for early detection and improved patient outcomes.
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Affiliation(s)
- Dahrii Paul
- Department of Bioinformatics, Pondicherry University, Puducherry 605014, India
| | | | - Rajesh Das
- Department of Bioinformatics, Pondicherry University, Puducherry 605014, India
| | | | - Amouda Venkatesan
- Department of Bioinformatics, Pondicherry University, Puducherry 605014, India.
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4
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Lee-Ødegård S, Hjorth M, Olsen T, Moen GH, Daubney E, Evans DM, Hevener AL, Lusis AJ, Zhou M, Seldin MM, Allayee H, Hilser J, Viken JK, Gulseth H, Norheim F, Drevon CA, Birkeland KI. Serum proteomic profiling of physical activity reveals CD300LG as a novel exerkine with a potential causal link to glucose homeostasis. eLife 2024; 13:RP96535. [PMID: 39190027 PMCID: PMC11349297 DOI: 10.7554/elife.96535] [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] [Indexed: 08/28/2024] Open
Abstract
Background Physical activity has been associated with preventing the development of type 2 diabetes and atherosclerotic cardiovascular disease. However, our understanding of the precise molecular mechanisms underlying these effects remains incomplete and good biomarkers to objectively assess physical activity are lacking. Methods We analyzed 3072 serum proteins in 26 men, normal weight or overweight, undergoing 12 weeks of a combined strength and endurance exercise intervention. We estimated insulin sensitivity with hyperinsulinemic euglycemic clamp, maximum oxygen uptake, muscle strength, and used MRI/MRS to evaluate body composition and organ fat depots. Muscle and subcutaneous adipose tissue biopsies were used for mRNA sequencing. Additional association analyses were performed in samples from up to 47,747 individuals in the UK Biobank, as well as using two-sample Mendelian randomization and mice models. Results Following 12 weeks of exercise intervention, we observed significant changes in 283 serum proteins. Notably, 66 of these proteins were elevated in overweight men and positively associated with liver fat before the exercise regimen, but were normalized after exercise. Furthermore, for 19.7 and 12.1% of the exercise-responsive proteins, corresponding changes in mRNA expression levels in muscle and fat, respectively, were shown. The protein CD300LG displayed consistent alterations in blood, muscle, and fat. Serum CD300LG exhibited positive associations with insulin sensitivity, and to angiogenesis-related gene expression in both muscle and fat. Furthermore, serum CD300LG was positively associated with physical activity and negatively associated with glucose levels in the UK Biobank. In this sample, the association between serum CD300LG and physical activity was significantly stronger in men than in women. Mendelian randomization analysis suggested potential causal relationships between levels of serum CD300LG and fasting glucose, 2 hr glucose after an oral glucose tolerance test, and HbA1c. Additionally, Cd300lg responded to exercise in a mouse model, and we observed signs of impaired glucose tolerance in male, but not female, Cd300lg knockout mice. Conclusions Our study identified several novel proteins in serum whose levels change in response to prolonged exercise and were significantly associated with body composition, liver fat, and glucose homeostasis. Serum CD300LG increased with physical activity and is a potential causal link to improved glucose levels. CD300LG may be a promising exercise biomarker and a therapeutic target in type 2 diabetes. Funding South-Eastern Norway Regional Health Authority, Simon Fougners Fund, Diabetesforbundet, Johan Selmer Kvanes' legat til forskning og bekjempelse av sukkersyke. The UK Biobank resource reference 53641. Australian National Health and Medical Research Council Investigator Grant (APP2017942). Australian Research Council Discovery Early Career Award (DE220101226). Research Council of Norway (Project grant: 325640 and Mobility grant: 287198). The Medical Student Research Program at the University of Oslo. Novo Nordisk Fonden Excellence Emerging Grant in Endocrinology and Metabolism 2023 (NNF23OC0082123). Clinical trial number clinicaltrials.gov: NCT01803568.
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Affiliation(s)
- Sindre Lee-Ødegård
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University HospitalOsloNorway
- Institute of Clinical Medicine, Faculty of Medicine, University of OsloOsloNorway
| | - Marit Hjorth
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of OsloOsloNorway
| | - Thomas Olsen
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of OsloOsloNorway
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of OsloOsloNorway
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
- The Frazer Institute, The University of QueenslandWoolloongabbaAustralia
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU, Norwegian University of Science and TechnologyTrondheimNorway
| | - Emily Daubney
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - David M Evans
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
- Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, NTNU, Norwegian University of Science and TechnologyTrondheimNorway
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
| | - Andrea L Hevener
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Aldons J Lusis
- Department of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Division of Cardiology, Department of Medicine, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Mingqi Zhou
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Hooman Allayee
- Departments of Population and Public Health Sciences, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - James Hilser
- Departments of Population and Public Health Sciences, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Jonas Krag Viken
- Institute of Clinical Medicine, Faculty of Medicine, University of OsloOsloNorway
| | - Hanne Gulseth
- Department of Chronic Diseases and Ageing, Norwegian Institute of Public HealthOsloNorway
| | - Frode Norheim
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of OsloOsloNorway
| | | | - Kåre Inge Birkeland
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University HospitalOsloNorway
- Institute of Clinical Medicine, Faculty of Medicine, University of OsloOsloNorway
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Yadav P, Ortega JG, Tamaki W, Chien C, Chang KC, Biswas N, Pan S, Nilsson J, Yin X, Bhattacharyya A, Boostanpour K, Jujaray T, Wang J, Tsukui T, Sheppard D, Li B, Maishan M, Taenaka H, Matthay MA, Muramatsu R, Maliskova L, Ghosh A, Eckalbar WL, Molofsky AB, Wolters PJ, Tamaki SJ, Bivona T, Abate AR, Wagner A, Tharp KM, Bhattacharya M. Macrophage-fibroblast crosstalk drives Arg1-dependent lung fibrosis via ornithine loading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.06.556606. [PMID: 39211079 PMCID: PMC11360891 DOI: 10.1101/2023.09.06.556606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Monocyte-derived macrophages recruited to injured tissues induce a maladaptive fibrotic response characterized by excessive production of collagen by local fibroblasts. Macrophages initiate this programming via paracrine factors, but it is unknown whether reciprocal responses from fibroblasts enhance profibrotic polarization of macrophages. We identify macrophage-fibroblast crosstalk necessary for injury-associated fibrosis, in which macrophages induced interleukin 6 ( IL-6 ) expression in fibroblasts via purinergic receptor P2rx4 signaling, and IL-6, in turn, induced arginase 1 ( Arg1 ) expression in macrophages. Arg1 contributed to fibrotic responses by metabolizing arginine to ornithine, which fibroblasts used as a substrate to synthesize proline, a uniquely abundant constituent of collagen. Imaging of idiopathic pulmonary fibrosis (IPF) lung samples confirmed expression of ARG1 in myeloid cells, and arginase inhibition suppressed collagen expression in cultured precision-cut IPF lung slices. Taken together, we define a circuit between macrophages and fibroblasts that facilitates cross-feeding metabolism necessary for injury-associated fibrosis.
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Kubrak O, Jørgensen AF, Koyama T, Lassen M, Nagy S, Hald J, Mazzoni G, Madsen D, Hansen JB, Larsen MR, Texada MJ, Hansen JL, Halberg KV, Rewitz K. LGR signaling mediates muscle-adipose tissue crosstalk and protects against diet-induced insulin resistance. Nat Commun 2024; 15:6126. [PMID: 39033139 PMCID: PMC11271308 DOI: 10.1038/s41467-024-50468-w] [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: 09/04/2023] [Accepted: 07/04/2024] [Indexed: 07/23/2024] Open
Abstract
Obesity impairs tissue insulin sensitivity and signaling, promoting type-2 diabetes. Although improving insulin signaling is key to reversing diabetes, the multi-organ mechanisms regulating this process are poorly defined. Here, we screen the secretome and receptome in Drosophila to identify the hormonal crosstalk affecting diet-induced insulin resistance and obesity. We discover a complex interplay between muscle, neuronal, and adipose tissues, mediated by Bone Morphogenetic Protein (BMP) signaling and the hormone Bursicon, that enhances insulin signaling and sugar tolerance. Muscle-derived BMP signaling, induced by sugar, governs neuronal Bursicon signaling. Bursicon, through its receptor Rickets, a Leucine-rich-repeat-containing G-protein coupled receptor (LGR), improves insulin secretion and insulin sensitivity in adipose tissue, mitigating hyperglycemia. In mouse adipocytes, loss of the Rickets ortholog LGR4 blunts insulin responses, showing an essential role of LGR4 in adipocyte insulin sensitivity. Our findings reveal a muscle-neuronal-fat-tissue axis driving metabolic adaptation to high-sugar conditions, identifying LGR4 as a critical mediator in this regulatory network.
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Affiliation(s)
- Olga Kubrak
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Anne F Jørgensen
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
- Novo Nordisk, Novo Nordisk Park, 2760, Maaløv, Denmark
| | - Takashi Koyama
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Mette Lassen
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Stanislav Nagy
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Jacob Hald
- Novo Nordisk, Novo Nordisk Park, 2760, Maaløv, Denmark
| | | | - Dennis Madsen
- Novo Nordisk, Novo Nordisk Park, 2760, Maaløv, Denmark
| | - Jacob B Hansen
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense, Denmark
| | - Michael J Texada
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | | | - Kenneth V Halberg
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark
| | - Kim Rewitz
- Department of Biology, University of Copenhagen, 2100, Copenhagen O, Denmark.
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7
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Samiminemati A, Aprile D, Siniscalco D, Di Bernardo G. Methods to Investigate the Secretome of Senescent Cells. Methods Protoc 2024; 7:52. [PMID: 39051266 PMCID: PMC11270363 DOI: 10.3390/mps7040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/27/2024] Open
Abstract
The word "secretome" was first used to describe the proteins that cells secrete under different circumstances; however, recent studies have proven the existence of other molecules such as RNA and chemical compounds in the secretome. The study of secretome has significance for the diagnosis and treatment of disease as it provides insight into cellular functions, including immune responses, development, and homeostasis. By halting cell division, cellular senescence plays a role in both cancer defense and aging by secreting substances known as senescence-associated secretory phenotypes (SASP). A variety of techniques could be used to analyze the secretome: protein-based approaches like mass spectrometry and protein microarrays, nucleic acid-based methods like RNA sequencing, microarrays, and in silico prediction. Each method offers unique advantages and limitations in characterizing secreted molecules. Top-down and bottom-up strategies for thorough secretome analysis are became possible by mass spectrometry. Understanding cellular function, disease causes, and proper treatment targets is aided by these methodologies. Their approaches, benefits, and drawbacks will all be discussed in this review.
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Affiliation(s)
- Afshin Samiminemati
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
| | - Domenico Aprile
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
| | - Dario Siniscalco
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
| | - Giovanni Di Bernardo
- Department of Experimental Medicine, Biotechnology, and Molecular Biology Section, Luigi Vanvitelli Campania University, 80138 Naples, Italy; (A.S.); (D.A.); (D.S.)
- Sbarro Health Research Organization, Temple University, Philadelphia, PA 19122, USA
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8
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Xiao H, Zou Y, Wang J, Wan S. A Review for Artificial Intelligence Based Protein Subcellular Localization. Biomolecules 2024; 14:409. [PMID: 38672426 PMCID: PMC11048326 DOI: 10.3390/biom14040409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer's disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcellular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.
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Affiliation(s)
- Hanyu Xiao
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Yijin Zou
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Jieqiong Wang
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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Molinelli L, Drula E, Gaillard JC, Navarro D, Armengaud J, Berrin JG, Tron T, Tarrago L. Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay. Appl Environ Microbiol 2024; 90:e0193123. [PMID: 38376171 PMCID: PMC10952391 DOI: 10.1128/aem.01931-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H218O2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.
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Affiliation(s)
- Lise Molinelli
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Elodie Drula
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - David Navarro
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Jean-Guy Berrin
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Thierry Tron
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
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10
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Guo L, Quan M, Pang W, Yin Y, Li F. Cytokines and exosomal miRNAs in skeletal muscle-adipose crosstalk. Trends Endocrinol Metab 2023; 34:666-681. [PMID: 37599201 DOI: 10.1016/j.tem.2023.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 08/22/2023]
Abstract
Skeletal muscle and adipose tissues (ATs) are secretory organs that release secretory factors including cytokines and exosomes. These factors mediate muscle-adipose crosstalk to regulate systemic metabolism via paracrine and endocrine pathways. Myokines and adipokines are cytokines secreted by skeletal muscle and ATs, respectively. Exosomes loaded with nucleic acids, proteins, lipid droplets, and organelles can fuse with the cytoplasm of target cells to perform regulatory functions. A major regulatory component of exosomes is miRNA. In addition, numerous novel myokines and adipokines have been identified through technological innovations. These discoveries have identified new biomarkers and sparked new insights into the molecular regulation of skeletal muscle growth and adipose deposition. The knowledge may contribute to potential diagnostic and therapeutic targets in metabolic disease.
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Affiliation(s)
- Liu Guo
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China; University of Chinese Academy of Sciences, Beijing 101408, China
| | - Menchus Quan
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Weijun Pang
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yulong Yin
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Fengna Li
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Perpiñá-Clérigues C, Mellado S, Català-Senent JF, Ibáñez F, Costa P, Marcos M, Guerri C, García-García F, Pascual M. Lipidomic landscape of circulating extracellular vesicles isolated from adolescents exposed to ethanol intoxication: a sex difference study. Biol Sex Differ 2023; 14:22. [PMID: 37085905 PMCID: PMC10120207 DOI: 10.1186/s13293-023-00502-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Lipids represent essential components of extracellular vesicles (EVs), playing structural and regulatory functions during EV biogenesis, release, targeting, and cell uptake. Importantly, lipidic dysregulation has been linked to several disorders, including metabolic syndrome, inflammation, and neurological dysfunction. Our recent results demonstrated the involvement of plasma EV microRNAs as possible amplifiers and biomarkers of neuroinflammation and brain damage induced by ethanol intoxication during adolescence. Considering the possible role of plasma EV lipids as regulatory molecules and biomarkers, we evaluated how acute ethanol intoxication differentially affected the lipid composition of plasma EVs in male and female adolescents and explored the participation of the immune response. METHODS Plasma EVs were extracted from humans and wild-type (WT) and Toll-like receptor 4 deficient (TLR4-KO) mice. Preprocessing and exploratory analyses were conducted after the extraction of EV lipids and data acquisition by mass spectrometry. Comparisons between ethanol-intoxicated and control human female and male individuals and ethanol-treated and untreated WT and TLR4-KO female and male mice were used to analyze the differential abundance of lipids. Annotation of lipids into their corresponding classes and a lipid set enrichment analysis were carried out to evaluate biological functions. RESULTS We demonstrated, for the first time, that acute ethanol intoxication induced a higher enrichment of distinct plasma EV lipid species in human female adolescents than in males. We observed a higher content of the PA, LPC, unsaturated FA, and FAHFA lipid classes in females, whereas males showed enrichment in PI. These lipid classes participate in the formation, release, and uptake of EVs and the activation of the immune response. Moreover, we observed changes in EV lipid composition between ethanol-treated WT and TLR4-KO mice (e.g., enrichment of glycerophosphoinositols in ethanol-treated WT males), and the sex-based differences in lipid abundance are more notable in WT mice than in TLR4-KO mice. All data and results generated have been made openly available on a web-based platform ( http://bioinfo.cipf.es/sal ). CONCLUSIONS Our results suggest that binge ethanol drinking in human female adolescents leads to a higher content of plasma EV lipid species associated with EV biogenesis and the propagation of neuroinflammatory responses than in males. In addition, we discovered greater differences in lipid abundance between sexes in WT mice compared to TLR4-KO mice. Our findings also support the potential use of EV-enriched lipids as biomarkers of ethanol-induced neuroinflammation during adolescence.
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Affiliation(s)
- Carla Perpiñá-Clérigues
- Bioinformatics and Biostatistics Unit, Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain
| | - Susana Mellado
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, 46012, Valencia, Spain
| | - José F Català-Senent
- Bioinformatics and Biostatistics Unit, Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
| | - Francesc Ibáñez
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, 46012, Valencia, Spain
| | - Pilar Costa
- Emergency Department, University Hospital of Salamanca-IBSAL, University of Salamanca, 37007, Salamanca, Spain
| | - Miguel Marcos
- Department of Internal Medicine, University Hospital of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, 37007, Salamanca, Spain
| | - Consuelo Guerri
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, 46012, Valencia, Spain
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Príncipe Felipe Research Center, C/ Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
| | - María Pascual
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain.
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, 46012, Valencia, Spain.
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12
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Glashauser J, Camelo C, Hollmann M, Backer W, Jacobs T, Sanchez JI, Schleutker R, Förster D, Berns N, Riechmann V, Luschnig S. Acute manipulation and real-time visualization of membrane trafficking and exocytosis in Drosophila. Dev Cell 2023; 58:709-723.e7. [PMID: 37023749 DOI: 10.1016/j.devcel.2023.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 01/05/2023] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
Intracellular trafficking of secretory proteins plays key roles in animal development and physiology, but so far, tools for investigating the dynamics of membrane trafficking have been limited to cultured cells. Here, we present a system that enables acute manipulation and real-time visualization of membrane trafficking through the reversible retention of proteins in the endoplasmic reticulum (ER) in living multicellular organisms. By adapting the "retention using selective hooks" (RUSH) approach to Drosophila, we show that trafficking of GPI-linked, secreted, and transmembrane proteins can be controlled with high temporal precision in intact animals and cultured organs. We demonstrate the potential of this approach by analyzing the kinetics of ER exit and apical secretion and the spatiotemporal dynamics of tricellular junction assembly in epithelia of living embryos. Furthermore, we show that controllable ER retention enables tissue-specific depletion of secretory protein function. The system is broadly applicable to visualizing and manipulating membrane trafficking in diverse cell types in vivo.
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Affiliation(s)
- Jade Glashauser
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Carolina Camelo
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Manuel Hollmann
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Wilko Backer
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Thea Jacobs
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Jone Isasti Sanchez
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Raphael Schleutker
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Dominique Förster
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany
| | - Nicola Berns
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Veit Riechmann
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Stefan Luschnig
- Institute of Integrative Cell Biology and Physiology, Faculty of Biology and Cells in Motion (CiM) Interfaculty Center, University of Münster, 48149 Münster, Germany.
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13
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Whole Transcriptome Analysis of Hypothalamus in Mice during Short-Term Starvation. Int J Mol Sci 2023; 24:ijms24043204. [PMID: 36834616 PMCID: PMC9968171 DOI: 10.3390/ijms24043204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Molecular profiling of the hypothalamus in response to metabolic shifts is a critical cue to better understand the principle of the central control of whole-body energy metabolism. The transcriptional responses of the rodent hypothalamus to short-term calorie restriction have been documented. However, studies on the identification of hypothalamic secretory factors that potentially contribute to the control of appetite are lacking. In this study, we analyzed the differential expression of hypothalamic genes and compared the selected secretory factors from the fasted mice with those of fed control mice using bulk RNA-sequencing. We verified seven secretory genes that were significantly altered in the hypothalamus of fasted mice. In addition, we determined the response of secretory genes in cultured hypothalamic cells to treatment with ghrelin and leptin. The current study provides further insights into the neuronal response to food restriction at the molecular level and may be useful for understanding the hypothalamic control of appetite.
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14
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Nesterenko M, Miroliubov A. From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala). F1000Res 2023; 11:583. [PMID: 36447930 PMCID: PMC9664023 DOI: 10.12688/f1000research.110492.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into "zombies". Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: the externa, and the main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite's body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for any rhizocephalan. Based on the results obtained, the spatial heterogeneity of protein-coding gene expression in different regions of the adult female body of P. reticulata was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans "got stuck in their metamorphosis", even at the reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of these extraordinary parasites.
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Affiliation(s)
- Maksim Nesterenko
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, 199034, Russian Federation,Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation,
| | - Aleksei Miroliubov
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
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15
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Li Z, Bagchi DP, Zhu J, Bowers E, Yu H, Hardij J, Mori H, Granger K, Skjaerlund J, Mandair G, Abrishami S, Singer K, Hankenson KD, Rosen CJ, MacDougald OA. Constitutive bone marrow adipocytes suppress local bone formation. JCI Insight 2022; 7:160915. [PMID: 36048537 PMCID: PMC9675472 DOI: 10.1172/jci.insight.160915] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/31/2022] [Indexed: 12/15/2022] Open
Abstract
BM adipocytes (BMAd) are a unique cell population derived from BM mesenchymal progenitors and marrow adipogenic lineage precursors. Although they have long been considered to be a space filler within bone cavities, recent studies have revealed important physiological roles in hematopoiesis and bone metabolism. To date, the approaches used to study BMAd function have been confounded by contributions by nonmarrow adipocytes or by BM stromal cells. To address this gap in the field, we have developed a BMAd-specific Cre mouse model to deplete BMAds by expression of diphtheria toxin A (DTA) or by deletion of peroxisome proliferator-activated receptor gamma (Pparg). We found that DTA-induced loss of BMAds results in decreased hematopoietic stem and progenitor cell numbers and increased bone mass in BMAd-enriched locations, including the distal tibiae and caudal vertebrae. Elevated bone mass appears to be secondary to enhanced endosteal bone formation, suggesting a local effect caused by depletion of BMAd. Augmented bone formation with BMAd depletion protects mice from bone loss induced by caloric restriction or ovariectomy, and it facilitates the bone-healing process after fracture. Finally, ablation of Pparg also reduces BMAd numbers and largely recapitulates high-bone mass phenotypes observed with DTA-induced BMAd depletion.
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Affiliation(s)
- Ziru Li
- Department of Molecular & Integrative Physiology and
| | | | - Junxiong Zhu
- Department of Orthopedic Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Emily Bowers
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Hui Yu
- Department of Molecular & Integrative Physiology and
| | - Julie Hardij
- Department of Molecular & Integrative Physiology and
| | - Hiroyuki Mori
- Department of Molecular & Integrative Physiology and
| | | | - Jon Skjaerlund
- Department of Orthopedic Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gurjit Mandair
- Department of Biologic and Materials Sciences, School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Simin Abrishami
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kanakadurga Singer
- Department of Molecular & Integrative Physiology and
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kurt D. Hankenson
- Department of Orthopedic Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Ormond A. MacDougald
- Department of Molecular & Integrative Physiology and
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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16
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Szeitz B, Megyesfalvi Z, Woldmar N, Valkó Z, Schwendenwein A, Bárány N, Paku S, László V, Kiss H, Bugyik E, Lang C, Szász AM, Pizzatti L, Bogos K, Hoda MA, Hoetzenecker K, Marko-Varga G, Horvatovich P, Döme B, Schelch K, Rezeli M. In-depth proteomic analysis reveals unique subtype-specific signatures in human small-cell lung cancer. Clin Transl Med 2022; 12:e1060. [PMID: 36149789 PMCID: PMC9506422 DOI: 10.1002/ctm2.1060] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
Background Small‐cell lung cancer (SCLC) molecular subtypes have been primarily characterized based on the expression pattern of the following key transcription regulators: ASCL1 (SCLC‐A), NEUROD1 (SCLC‐N), POU2F3 (SCLC‐P) and YAP1 (SCLC‐Y). Here, we investigated the proteomic landscape of these molecular subsets with the aim to identify novel subtype‐specific proteins of diagnostic and therapeutic relevance. Methods Pellets and cell media of 26 human SCLC cell lines were subjected to label‐free shotgun proteomics for large‐scale protein identification and quantitation, followed by in‐depth bioinformatic analyses. Proteomic data were correlated with the cell lines’ phenotypic characteristics and with public transcriptomic data of SCLC cell lines and tissues. Results Our quantitative proteomic data highlighted that four molecular subtypes are clearly distinguishable at the protein level. The cell lines exhibited diverse neuroendocrine and epithelial–mesenchymal characteristics that varied by subtype. A total of 367 proteins were identified in the cell pellet and 34 in the culture media that showed significant up‐ or downregulation in one subtype, including known druggable proteins and potential blood‐based markers. Pathway enrichment analysis and parallel investigation of transcriptomics from SCLC cell lines outlined unique signatures for each subtype, such as upregulated oxidative phosphorylation in SCLC‐A, DNA replication in SCLC‐N, neurotrophin signalling in SCLC‐P and epithelial–mesenchymal transition in SCLC‐Y. Importantly, we identified the YAP1‐driven subtype as the most distinct SCLC subgroup. Using sparse partial least squares discriminant analysis, we identified proteins that clearly distinguish four SCLC subtypes based on their expression pattern, including potential diagnostic markers for SCLC‐Y (e.g. GPX8, PKD2 and UFO). Conclusions We report for the first time, the protein expression differences among SCLC subtypes. By shedding light on potential subtype‐specific therapeutic vulnerabilities and diagnostic biomarkers, our results may contribute to a better understanding of SCLC biology and the development of novel therapies.
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Affiliation(s)
- Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Zsolt Megyesfalvi
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary
| | - Nicole Woldmar
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden.,Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zsuzsanna Valkó
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Anna Schwendenwein
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Nándor Bárány
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sándor Paku
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória László
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Helga Kiss
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary.,University of Pécs, Pécs, Hungary
| | - Edina Bugyik
- National Korányi Institute of Pulmonology, Budapest, Hungary.,First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Christian Lang
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Attila Marcell Szász
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Luciana Pizzatti
- Laboratory of Molecular Biology and Proteomics of Blood/LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Krisztina Bogos
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Mir Alireza Hoda
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - György Marko-Varga
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Balázs Döme
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, Budapest, Hungary.,Department of Translational Medicine, Lund University, Lund, Sweden
| | - Karin Schelch
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Melinda Rezeli
- Division of Clinical Protein Science, & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, Lund, Sweden
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17
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Deficiency of WTAP in hepatocytes induces lipoatrophy and non-alcoholic steatohepatitis (NASH). Nat Commun 2022; 13:4549. [PMID: 35927268 PMCID: PMC9352699 DOI: 10.1038/s41467-022-32163-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/18/2022] [Indexed: 01/18/2023] Open
Abstract
Ectopic lipid accumulation and inflammation are the essential signs of NASH. However, the molecular mechanisms of ectopic lipid accumulation and inflammation during NASH progression are not fully understood. Here we reported that hepatic Wilms' tumor 1-associating protein (WTAP) is a key integrative regulator of ectopic lipid accumulation and inflammation during NASH progression. Hepatic deletion of Wtap leads to NASH due to the increased lipolysis in white adipose tissue, enhanced hepatic free fatty acids uptake and induced inflammation, all of which are mediated by IGFBP1, CD36 and cytochemokines such as CCL2, respectively. WTAP binds to specific DNA motifs which are enriched in the promoters and suppresses gene expression (e.g., Igfbp1, Cd36 and Ccl2) with the involvement of HDAC1. In NASH, WTAP is tranlocated from nucleus to cytosol, which is related to CDK9-mediated phosphorylation. These data uncover a mechanism by which hepatic WTAP regulates ectopic lipid accumulation and inflammation during NASH progression. Ectopic lipid accumulation and inflammation are the essential signs of NASH. Here, the authors show that hepatic WTAP is a key integrative repressor of ectopic lipid accumulation and inflammation during NASH progression, and hepatic deletion of Wtap promotes both of them, leading to NASH
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18
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Nesterenko M, Miroliubov A. From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala). F1000Res 2022; 11:583. [PMID: 36447930 PMCID: PMC9664023 DOI: 10.12688/f1000research.110492.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 09/16/2023] Open
Abstract
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into "zombies". Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: the externa, and the main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite's body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for any rhizocephalan. Based on the results obtained, the spatial heterogeneity of protein-coding gene expression in different regions of the adult female body of P. reticulata was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans "got stuck in their metamorphosis", even at the reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of these extraordinary parasites.
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Affiliation(s)
- Maksim Nesterenko
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, 199034, Russian Federation
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
| | - Aleksei Miroliubov
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
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19
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Park A, Choi SJ, Park S, Kim SM, Lee HE, Joo M, Kim KK, Kim D, Chung DH, Im JB, Jung J, Shin SK, Oh BC, Choi C, Nam S, Lee DH. Plasma Aldo-Keto Reductase Family 1 Member B10 as a Biomarker Performs Well in the Diagnosis of Nonalcoholic Steatohepatitis and Fibrosis. Int J Mol Sci 2022; 23:ijms23095035. [PMID: 35563425 PMCID: PMC9101253 DOI: 10.3390/ijms23095035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023] Open
Abstract
We found several blood biomarkers through computational secretome analyses, including aldo-keto reductase family 1 member B10 (AKR1B10), which reflected the progression of nonalcoholic fatty liver disease (NAFLD). After confirming that hepatic AKR1B10 reflected the progression of NAFLD in a subgroup with NAFLD, we evaluated the diagnostic accuracy of plasma AKR1B10 and other biomarkers for the diagnosis of nonalcoholic steatohepatitis (NASH) and fibrosis in replication cohort. We enrolled healthy control subjects and patients with biopsy-proven NAFLD (n = 102) and evaluated the performance of various diagnostic markers. Plasma AKR1B10 performed well in the diagnosis of NASH with an area under the receiver operating characteristic (AUROC) curve of 0.834 and a cutoff value of 1078.2 pg/mL, as well as advanced fibrosis (AUROC curve value of 0.914 and cutoff level 1078.2 pg/mL), with further improvement in combination with C3. When we monitored a subgroup of obese patients who underwent bariatric surgery (n = 35), plasma AKR1B10 decreased dramatically, and 40.0% of patients with NASH at baseline showed a decrease in plasma AKR1B10 levels to below the cutoff level after the surgery. In an independent validation study, we proved that plasma AKR1B10 was a specific biomarker of NAFLD progression across varying degrees of renal dysfunction. Despite perfect correlation between plasma and serum levels of AKR1B10 in paired sample analysis, its serum level was 1.4-fold higher than that in plasma. Plasma AKR1B10 alone and in combination with C3 could be a useful noninvasive biomarker for the diagnosis of NASH and hepatic fibrosis.
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Affiliation(s)
- Aron Park
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea; (A.P.); (M.J.); (J.B.I.)
| | - Seung Joon Choi
- Department of Radiology, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea;
| | - Sungjin Park
- Department of Genome Medicine and Science, AI Convergence Center for Genome Medicine, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea;
| | - Seong Min Kim
- Department of Surgery, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (S.M.K.); (D.K.)
| | - Hye Eun Lee
- Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (H.E.L.); (S.K.S.); (C.C.)
| | - Minjae Joo
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea; (A.P.); (M.J.); (J.B.I.)
| | - Kyoung Kon Kim
- Department of Family Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea;
| | - Doojin Kim
- Department of Surgery, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (S.M.K.); (D.K.)
| | - Dong Hae Chung
- Department of Pathology, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea;
| | - Jae Been Im
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea; (A.P.); (M.J.); (J.B.I.)
- Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (H.E.L.); (S.K.S.); (C.C.)
| | - Jaehun Jung
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon 21565, Korea;
| | - Seung Kak Shin
- Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (H.E.L.); (S.K.S.); (C.C.)
| | - Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999, Korea;
| | - Cheolsoo Choi
- Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (H.E.L.); (S.K.S.); (C.C.)
| | - Seungyoon Nam
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Korea; (A.P.); (M.J.); (J.B.I.)
- Department of Genome Medicine and Science, AI Convergence Center for Genome Medicine, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea;
- Correspondence: (S.N.); (D.H.L.); Tel.: +82-32-458-2737 (S.N.); +82-32-458-2733 (D.H.L.); Fax: +82-32-458-2875 (S.N.); +82-32-468-5836 (D.H.L.)
| | - Dae Ho Lee
- Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon 21565, Korea; (H.E.L.); (S.K.S.); (C.C.)
- Correspondence: (S.N.); (D.H.L.); Tel.: +82-32-458-2737 (S.N.); +82-32-458-2733 (D.H.L.); Fax: +82-32-458-2875 (S.N.); +82-32-468-5836 (D.H.L.)
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20
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Pastrello C, Abovsky M, Lu R, Ahmed Z, Kotlyar M, Veillette C, Jurisica I. Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database. OSTEOARTHRITIS AND CARTILAGE OPEN 2022; 4:100237. [DOI: 10.1016/j.ocarto.2022.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022] Open
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21
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Termini CM, Pang A, Fang T, Roos M, Chang VY, Zhang Y, Setiawan NJ, Signaevskaia L, Li M, Kim MM, Tabibi O, Lin PK, Sasine JP, Chatterjee A, Murali R, Himburg HA, Chute JP. Neuropilin 1 regulates bone marrow vascular regeneration and hematopoietic reconstitution. Nat Commun 2021; 12:6990. [PMID: 34848712 PMCID: PMC8635308 DOI: 10.1038/s41467-021-27263-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/07/2021] [Indexed: 12/27/2022] Open
Abstract
Ionizing radiation and chemotherapy deplete hematopoietic stem cells and damage the vascular niche wherein hematopoietic stem cells reside. Hematopoietic stem cell regeneration requires signaling from an intact bone marrow (BM) vascular niche, but the mechanisms that control BM vascular niche regeneration are poorly understood. We report that BM vascular endothelial cells secrete semaphorin 3 A (SEMA3A) in response to myeloablation and SEMA3A induces p53 - mediated apoptosis in BM endothelial cells via signaling through its receptor, Neuropilin 1 (NRP1), and activation of cyclin dependent kinase 5. Endothelial cell - specific deletion of Nrp1 or Sema3a or administration of anti-NRP1 antibody suppresses BM endothelial cell apoptosis, accelerates BM vascular regeneration and concordantly drives hematopoietic reconstitution in irradiated mice. In response to NRP1 inhibition, BM endothelial cells increase expression and secretion of the Wnt signal amplifying protein, R spondin 2. Systemic administration of anti - R spondin 2 blocks HSC regeneration and hematopoietic reconstitution which otherwise occurrs in response to NRP1 inhibition. SEMA3A - NRP1 signaling promotes BM vascular regression following myelosuppression and therapeutic blockade of SEMA3A - NRP1 signaling in BM endothelial cells accelerates vascular and hematopoietic regeneration in vivo.
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Affiliation(s)
- Christina M Termini
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
- Division of Hematology & Cellular Therapy, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Department of Orthopedic Surgery, UCLA, Los Angeles, CA, USA
| | - Amara Pang
- Division of Hematology & Cellular Therapy, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Tiancheng Fang
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, USA
| | - Martina Roos
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
- Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Vivian Y Chang
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
- Pediatric Hematology/Oncology, UCLA, Los Angeles, CA, USA
| | - Yurun Zhang
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Nicollette J Setiawan
- Division of Hematology & Cellular Therapy, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Lia Signaevskaia
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Michelle Li
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Mindy M Kim
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Orel Tabibi
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Paulina K Lin
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Joshua P Sasine
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, CA, USA
- Division of Hematology & Cellular Therapy, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Avradip Chatterjee
- Department of Biomedical Sciences, Research Division of Immunology, Los Angeles, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Research Division of Immunology, Los Angeles, USA
| | - Heather A Himburg
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - John P Chute
- Division of Hematology & Cellular Therapy, Cedars Sinai Medical Center, Los Angeles, CA, USA.
- Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
- Samuel Oschin Cancer Center, Cedars Sinai Medical Center, Los Angeles, CA, USA.
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22
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Bruno NE, Nwachukwu JC, Hughes DC, Srinivasan S, Hawkins R, Sturgill D, Hager GL, Hurst S, Sheu SS, Bodine SC, Conkright MD, Nettles KW. Activation of Crtc2/Creb1 in skeletal muscle enhances weight loss during intermittent fasting. FASEB J 2021; 35:e21999. [PMID: 34748223 DOI: 10.1096/fj.202100171r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/11/2022]
Abstract
The Creb-Regulated Transcriptional Coactivator (Crtc) family of transcriptional coregulators drive Creb1-mediated transcription effects on metabolism in many tissues, but the in vivo effects of Crtc2/Creb1 transcription on skeletal muscle metabolism are not known. Skeletal muscle-specific overexpression of Crtc2 (Crtc2 mice) induced greater mitochondrial activity, metabolic flux capacity for both carbohydrates and fats, improved glucose tolerance and insulin sensitivity, and increased oxidative capacity, supported by upregulation of key metabolic genes. Crtc2 overexpression led to greater weight loss during alternate day fasting (ADF), selective loss of fat rather than lean mass, maintenance of higher energy expenditure during the fast and reduced binge-eating during the feeding period. ADF downregulated most of the mitochondrial electron transport genes, and other regulators of mitochondrial function, that were substantially reversed by Crtc2-driven transcription. Glucocorticoids acted with AMPK to drive atrophy and mitophagy, which was reversed by Crtc2/Creb1 signaling. Crtc2/Creb1-mediated signaling coordinates metabolic adaptations in skeletal muscle that explain how Crtc2/Creb1 regulates metabolism and weight loss.
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Affiliation(s)
- Nelson E Bruno
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David C Hughes
- Section for Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Sathish Srinivasan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Richard Hawkins
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Stephen Hurst
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Shey-Shing Sheu
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sue C Bodine
- Section for Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Michael D Conkright
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
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23
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Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling. Proc Natl Acad Sci U S A 2021; 118:2103087118. [PMID: 34663698 DOI: 10.1073/pnas.2103087118] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 12/26/2022] Open
Abstract
The patterning and ossification of the mammalian skeleton requires the coordinated actions of both intrinsic bone morphogens and extrinsic neurovascular signals, which function in a temporal and spatial fashion to control mesenchymal progenitor cell (MPC) fate. Here, we show the genetic inhibition of tropomyosin receptor kinase A (TrkA) sensory nerve innervation of the developing cranium results in premature calvarial suture closure, associated with a decrease in suture MPC proliferation and increased mineralization. In vitro, axons from peripheral afferent neurons derived from dorsal root ganglions (DRGs) of wild-type mice induce MPC proliferation in a spatially restricted manner via a soluble factor when cocultured in microfluidic chambers. Comparative spatial transcriptomic analysis of the cranial sutures in vivo confirmed a positive association between sensory axons and proliferative MPCs. SpatialTime analysis across the developing suture revealed regional-specific alterations in bone morphogenetic protein (BMP) and TGF-β signaling pathway transcripts in response to TrkA inhibition. RNA sequencing of DRG cell bodies, following direct, axonal coculture with MPCs, confirmed the alterations in BMP/TGF-β signaling pathway transcripts. Among these, the BMP inhibitor follistatin-like 1 (FSTL1) replicated key features of the neural-to-bone influence, including mitogenic and anti-osteogenic effects via the inhibition of BMP/TGF-β signaling. Taken together, our results demonstrate that sensory nerve-derived signals, including FSTL1, function to coordinate cranial bone patterning by regulating MPC proliferation and differentiation in the suture mesenchyme.
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24
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Bacolod MD, Barany F. A Unified Transcriptional, Pharmacogenomic, and Gene Dependency Approach to Decipher the Biology, Diagnostic Markers, and Therapeutic Targets Associated with Prostate Cancer Metastasis. Cancers (Basel) 2021; 13:cancers13205158. [PMID: 34680307 PMCID: PMC8534121 DOI: 10.3390/cancers13205158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/18/2023] Open
Abstract
Simple Summary This manuscript demonstrates how integrated bioinformatic and statistical reanalysis of publicly available genomic datasets can be utilized to identify molecular pathways and biomarkers that may be clinically relevant to metastatic prostate cancer (mPrCa) progression. The most notable observation is that the transition from primary prostate cancer to mPrCa is characterized by upregulation of processes associated with DNA replication, metastasis, and events regulated by the serine/threonine kinase PLK1. Moreover, our analysis also identified over-expressed genes that may be exploited for potential targeted therapeutics and minimally invasive diagnostics and monitoring of mPrCa. The primary data analyzed were two transcriptional datasets for tissues derived from normal prostate, primary prostate cancer, and mPrCa. Also incorporated in the analysis were the transcriptional, gene dependency, and drug response data for hundreds of cell lines, including those derived from prostate cancer tissues. Abstract Our understanding of metastatic prostate cancer (mPrCa) has dramatically advanced during the genomics era. Nonetheless, many aspects of the disease may still be uncovered through reanalysis of public datasets. We integrated the expression datasets for 209 PrCa tissues (metastasis, primary, normal) with expression, gene dependency (GD) (from CRISPR/cas9 screen), and drug viability data for hundreds of cancer lines (including PrCa). Comparative statistical and pathways analyses and functional annotations (available inhibitors, protein localization) revealed relevant pathways and potential (and previously reported) protein markers for minimally invasive mPrCa diagnostics. The transition from localized to mPrCa involved the upregulation of DNA replication, mitosis, and PLK1-mediated events. Genes highly upregulated in mPrCa and with very high average GD (~1) are potential therapeutic targets. We showed that fostamatinib (which can target PLK1 and other over-expressed serine/threonine kinases such as AURKA, MELK, NEK2, and TTK) is more active against cancer lines with more pronounced signatures of invasion (e.g., extracellular matrix organization/degradation). Furthermore, we identified surface-bound (e.g., ADAM15, CD276, ABCC5, CD36, NRP1, SCARB1) and likely secreted proteins (e.g., APLN, ANGPT2, CTHRC1, ADAM12) that are potential mPrCa diagnostic markers. Overall, we demonstrated that comprehensive analyses of public genomics data could reveal potentially clinically relevant information regarding mPrCa.
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25
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SecProCT: In Silico Prediction of Human Secretory Proteins Based on Capsule Network and Transformer. Int J Mol Sci 2021; 22:ijms22169054. [PMID: 34445760 PMCID: PMC8396571 DOI: 10.3390/ijms22169054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/12/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
Identifying secretory proteins from blood, saliva or other body fluids has become an effective method of diagnosing diseases. Existing secretory protein prediction methods are mainly based on conventional machine learning algorithms and are highly dependent on the feature set from the protein. In this article, we propose a deep learning model based on the capsule network and transformer architecture, SecProCT, to predict secretory proteins using only amino acid sequences. The proposed model was validated using cross-validation and achieved 0.921 and 0.892 accuracy for predicting blood-secretory proteins and saliva-secretory proteins, respectively. Meanwhile, the proposed model was validated on an independent test set and achieved 0.917 and 0.905 accuracy for predicting blood-secretory proteins and saliva-secretory proteins, respectively, which are better than conventional machine learning methods and other deep learning methods for biological sequence analysis. The main contributions of this article are as follows: (1) a deep learning model based on a capsule network and transformer architecture is proposed for predicting secretory proteins. The results of this model are better than the those of existing conventional machine learning methods and deep learning methods for biological sequence analysis; (2) only amino acid sequences are used in the proposed model, which overcomes the high dependence of existing methods on the annotated protein features; (3) the proposed model can accurately predict most experimentally verified secretory proteins and cancer protein biomarkers in blood and saliva.
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26
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Characterization of the Skeletal Muscle Secretome Reveals a Role for Extracellular Vesicles and IL1α/IL1β in Restricting Fibro/Adipogenic Progenitor Adipogenesis. Biomolecules 2021; 11:biom11081171. [PMID: 34439837 PMCID: PMC8392554 DOI: 10.3390/biom11081171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/01/2021] [Accepted: 08/05/2021] [Indexed: 12/31/2022] Open
Abstract
Repeated mechanical stress causes injuries in the adult skeletal muscle that need to be repaired. Although muscle regeneration is a highly efficient process, it fails in some pathological conditions, compromising tissue functionality. This may be caused by aberrant cell-cell communication, resulting in the deposition of fibrotic and adipose infiltrates. Here, we investigate in vivo changes in the profile of skeletal muscle secretome during the regeneration process to suggest new targetable regulatory circuits whose failure may lead to tissue degeneration in pathological conditions. We describe the kinetic variation of expression levels of 76 secreted proteins during the regeneration process. In addition, we profile the gene expression of immune cells, endothelial cells, satellite cells, and fibro-adipogenic progenitors. This analysis allowed us to annotate each cell-type with the cytokines and receptors they have the potential to synthetize, thus making it possible to draw a cell-cell interaction map. We next selected 12 cytokines whose receptors are expressed in FAPs and tested their ability to modulate FAP adipogenesis and proliferation. We observed that IL1α and IL1β potently inhibit FAP adipogenesis, while EGF and BTC notably promote FAP proliferation. In addition, we characterized the cross-talk mediated by extracellular vesicles (EVs). We first monitored the modulation of muscle EV cargo during tissue regeneration. Using a single-vesicle flow cytometry approach, we observed that EVs differentially affect the uptake of RNA and proteins into their lumen. We also investigated the EV capability to interact with SCs and FAPs and to modulate their proliferation and differentiation. We conclude that both cytokines and EVs secreted during muscle regeneration have the potential to modulate adipogenic differentiation of FAPs. The results of our approach provide a system-wide picture of mechanisms that control cell fate during the regeneration process in the muscle niche.
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27
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Cheng LC, Zheng D, Zhang Q, Guvenek A, Cheng H, Tian B. Alternative 3' UTRs play a widespread role in translation-independent mRNA association with the endoplasmic reticulum. Cell Rep 2021; 36:109407. [PMID: 34289366 PMCID: PMC8501909 DOI: 10.1016/j.celrep.2021.109407] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/17/2021] [Accepted: 06/23/2021] [Indexed: 12/28/2022] Open
Abstract
Transcripts encoding membrane and secreted proteins are known to associate with the endoplasmic reticulum (ER) through translation. Here, using cell fractionation, polysome profiling, and 3' end sequencing, we show that transcripts differ substantially in translation-independent ER association (TiERA). Genes in certain functional groups, such as cell signaling, tend to have significantly higher TiERA potentials than others, suggesting the importance of ER association for their mRNA metabolism, such as localized translation. The TiERA potential of a transcript is determined largely by size, sequence content, and RNA structures. Alternative polyadenylation (APA) isoforms can have distinct TiERA potentials because of changes in transcript features. The widespread 3' UTR lengthening in cell differentiation leads to greater transcript association with the ER, especially for genes that are capable of expressing very long 3' UTRs. Our data also indicate that TiERA is in dynamic competition with translation-dependent ER association, suggesting limited space on the ER for mRNA association.
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Affiliation(s)
- Larry C Cheng
- Program in Gene Expression and Regulation and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, Piscataway, NJ 08854, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Qiang Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Aysegul Guvenek
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Rutgers School of Graduate Studies, Newark, NJ 07103, USA
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Tian
- Program in Gene Expression and Regulation and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA; Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, Piscataway, NJ 08854, USA; Rutgers School of Graduate Studies, Newark, NJ 07103, USA.
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28
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Wang Y, Fu AKY, Ip NY. Instructive roles of astrocytes in hippocampal synaptic plasticity: neuronal activity-dependent regulatory mechanisms. FEBS J 2021; 289:2202-2218. [PMID: 33864430 PMCID: PMC9290076 DOI: 10.1111/febs.15878] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022]
Abstract
In the adult hippocampus, synaptic plasticity is important for information processing, learning, and memory encoding. Astrocytes, the most common glial cells, play a pivotal role in the regulation of hippocampal synaptic plasticity. While astrocytes were initially described as a homogenous cell population, emerging evidence indicates that in the adult hippocampus, astrocytes are highly heterogeneous and can differentially respond to changes in neuronal activity in a subregion‐dependent manner to actively modulate synaptic plasticity. In this review, we summarize how local neuronal activity changes regulate the interactions between astrocytes and synapses, either by modulating the secretion of gliotransmitters and synaptogenic proteins or via contact‐mediated signaling pathways. In turn, these specific responses induced in astrocytes mediate the interactions between astrocytes and neurons, thus shaping synaptic communication in the adult hippocampus. Importantly, the activation of astrocytic signaling is required for memory performance including memory acquisition and recall. Meanwhile, the dysregulation of this signaling can cause hippocampal circuit dysfunction in pathological conditions, resulting in cognitive impairment and neurodegeneration. Indeed, reactive astrocytes, which have dysregulated signaling associated with memory, are induced in the brains of patients with Alzheimer's disease (AD) and transgenic mouse model of AD. Emerging technologies that can precisely manipulate and monitor astrocytic signaling in vivo enable the examination of the specific actions of astrocytes in response to neuronal activity changes as well as how they modulate synaptic connections and circuit activity. Such findings will clarify the roles of astrocytes in hippocampal synaptic plasticity and memory in health and disease.
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Affiliation(s)
- Ye Wang
- Division of Life Science, The Hong Kong University of Science and Technology, China.,Molecular Neuroscience Center, The Hong Kong University of Science and Technology, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China.,Hong Kong Center for Neurodegenerative Diseases, China
| | - Amy K Y Fu
- Division of Life Science, The Hong Kong University of Science and Technology, China.,Molecular Neuroscience Center, The Hong Kong University of Science and Technology, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China.,Hong Kong Center for Neurodegenerative Diseases, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - Nancy Y Ip
- Division of Life Science, The Hong Kong University of Science and Technology, China.,Molecular Neuroscience Center, The Hong Kong University of Science and Technology, China.,State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, China.,Hong Kong Center for Neurodegenerative Diseases, China.,Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
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29
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Choi S, Zhang B, Ma S, Gonzalez-Celeiro M, Stein D, Jin X, Kim ST, Kang YL, Besnard A, Rezza A, Grisanti L, Buenrostro J, Rendl M, Nahrendorf M, Sahay A, Hsu YC. Corticosterone inhibits GAS6 to govern hair follicle stem-cell quiescence. Nature 2021; 592:428-432. [PMID: 33790465 PMCID: PMC8923613 DOI: 10.1038/s41586-021-03417-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/04/2021] [Indexed: 02/01/2023]
Abstract
Chronic, sustained exposure to stressors can profoundly affect tissue homeostasis, although the mechanisms by which these changes occur are largely unknown. Here we report that the stress hormone corticosterone-which is derived from the adrenal gland and is the rodent equivalent of cortisol in humans-regulates hair follicle stem cell (HFSC) quiescence and hair growth in mice. In the absence of systemic corticosterone, HFSCs enter substantially more rounds of the regeneration cycle throughout life. Conversely, under chronic stress, increased levels of corticosterone prolong HFSC quiescence and maintain hair follicles in an extended resting phase. Mechanistically, corticosterone acts on the dermal papillae to suppress the expression of Gas6, a gene that encodes the secreted factor growth arrest specific 6. Restoring Gas6 expression overcomes the stress-induced inhibition of HFSC activation and hair growth. Our work identifies corticosterone as a systemic inhibitor of HFSC activity through its effect on the niche, and demonstrates that the removal of such inhibition drives HFSCs into frequent regeneration cycles, with no observable defects in the long-term.
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Affiliation(s)
- Sekyu Choi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Bing Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Present address: School of Life Science, Westlake University, Hangzhou, Zhejiang, China
| | - Sai Ma
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biology and Koch Institute, MIT, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Meryem Gonzalez-Celeiro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Daniel Stein
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Xin Jin
- Society of Fellows, Harvard University, Cambridge MA, USA
| | - Seung Tea Kim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Yuan-Lin Kang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Antoine Besnard
- Harvard Stem Cell Institute, Cambridge, MA, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Present address: CNRS, Institut de Génomique Fonctionnelle, Montpellier, F-34094, France
| | - Amelie Rezza
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Present address: 4 genOway, Lyon, 69007, France
| | - Laura Grisanti
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Michael Rendl
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthias Nahrendorf
- Center for Systems Biology and Department of Radiology, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Amar Sahay
- Harvard Stem Cell Institute, Cambridge, MA, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ya-Chieh Hsu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Correspondence to: Correspondence and requests for materials should be addressed to Y-C.H. Ya-Chieh Hsu, PhD (Lead Contact),
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30
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Hemanthakumar KA, Fang S, Anisimov A, Mäyränpää MI, Mervaala E, Kivelä R. Cardiovascular disease risk factors induce mesenchymal features and senescence in mouse cardiac endothelial cells. eLife 2021; 10:62678. [PMID: 33661096 PMCID: PMC8043751 DOI: 10.7554/elife.62678] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/03/2021] [Indexed: 12/21/2022] Open
Abstract
Aging, obesity, hypertension, and physical inactivity are major risk factors for endothelial dysfunction and cardiovascular disease (CVD). We applied fluorescence-activated cell sorting (FACS), RNA sequencing, and bioinformatic methods to investigate the common effects of CVD risk factors in mouse cardiac endothelial cells (ECs). Aging, obesity, and pressure overload all upregulated pathways related to TGF-β signaling and mesenchymal gene expression, inflammation, vascular permeability, oxidative stress, collagen synthesis, and cellular senescence, whereas exercise training attenuated most of the same pathways. We identified collagen chaperone Serpinh1 (also called as Hsp47) to be significantly increased by aging and obesity and repressed by exercise training. Mechanistic studies demonstrated that increased SERPINH1 in human ECs induced mesenchymal properties, while its silencing inhibited collagen deposition. Our data demonstrate that CVD risk factors significantly remodel the transcriptomic landscape of cardiac ECs inducing inflammatory, senescence, and mesenchymal features. SERPINH1 was identified as a potential therapeutic target in ECs. Cardiovascular diseases are the number one cause of death in the western world. Endothelial cells that line the blood vessels of the heart play a central role in the development of these diseases. In addition to helping transport blood, these cells support the normal running of the heart, and help it to grow and regenerate. Over time as the body ages and experiences stress, endothelial cells start to deteriorate. This can cause the cells to undergo senescence and stop dividing, and lay down scar-like tissue via a process called fibrosis. As a result, the blood vessels start to stiffen and become less susceptible to repair. Ageing, obesity, high blood pressure, and inactivity all increase the risk of developing cardiovascular diseases, whereas regular exercise has a protective effect. But it was unclear how these different factors affect endothelial cells. To investigate this, Hemanthakumar et al. compared the gene activity of different sets of mice: old vs young, obese vs lean, heart problems vs healthy, and fit vs sedentary. All these risk factors – age, weight, inactivity and heart defects – caused the mice’s endothelial cells to activate mechanisms that lead to stress, senescence and fibrosis. Whereas exercise training had the opposite effect, and turned off the same genes and pathways. All of the at-risk groups also had high levels of a gene called SerpinH1, which helps produce tissue fiber and collagen. Experiments increasing the levels of SerpinH1 in human endothelial cells grown in the laboratory recreated the effects seen in mice, and switched on markers of stress, senescence and fibrosis. According to the World Health Organization, cardiovascular disease now accounts for 10% of the disease burden worldwide. Revealing the affects it has on gene activity could help identify new targets for drug development, such as SerpinH1. Understanding the molecular effects of exercise on blood vessels could also aid in the design of treatments that mimic exercise. This could help people who are unable to follow training programs to reduce their risk of cardiovascular disease.
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Affiliation(s)
- Karthik Amudhala Hemanthakumar
- Wihuri Research Institute, Helsinki, Finland.,Stem cells and Metabolism Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Shentong Fang
- Wihuri Research Institute, Helsinki, Finland.,Translational Cancer Medicine Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Andrey Anisimov
- Wihuri Research Institute, Helsinki, Finland.,Translational Cancer Medicine Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikko I Mäyränpää
- Pathology, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Eero Mervaala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riikka Kivelä
- Wihuri Research Institute, Helsinki, Finland.,Stem cells and Metabolism Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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31
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Cheedipudi SM, Hu J, Fan S, Yuan P, Karmouch J, Czernuszewicz G, Robertson MJ, Coarfa C, Hong K, Yao Y, Campbell H, Wehrens X, Gurha P, Marian AJ. Exercise restores dysregulated gene expression in a mouse model of arrhythmogenic cardiomyopathy. Cardiovasc Res 2021; 116:1199-1213. [PMID: 31350552 DOI: 10.1093/cvr/cvz199] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022] Open
Abstract
AIMS Arrhythmogenic cardiomyopathy (ACM) is a myocardial disease caused mainly by mutations in genes encoding desmosome proteins ACM patients present with ventricular arrhythmias, cardiac dysfunction, sudden cardiac death, and a subset with fibro-fatty infiltration of the right ventricle predominantly. Endurance exercise is thought to exacerbate cardiac dysfunction and arrhythmias in ACM. The objective was to determine the effects of treadmill exercise on cardiac phenotype, including myocyte gene expression in myocyte-specific desmoplakin (Dsp) haplo-insufficient (Myh6-Cre:DspW/F) mice. METHODS AND RESULTS Three months old sex-matched wild-type (WT) and Myh6-Cre:DspW/F mice with normal cardiac function, as assessed by echocardiography, were randomized to regular activity or 60 min of daily treadmill exercise (5.5 kJ work per run). Cardiac myocyte gene expression, cardiac function, arrhythmias, and myocardial histology, including apoptosis, were analysed prior to and after 3 months of routine activity or treadmill exercise. Fifty-seven and 781 genes were differentially expressed in 3- and 6-month-old Myh6-Cre:DspW/F cardiac myocytes, compared to the corresponding WT myocytes, respectively. Genes encoding secreted proteins (secretome), including inhibitors of the canonical WNT pathway, were among the most up-regulated genes. The differentially expressed genes (DEGs) predicted activation of epithelial-mesenchymal transition (EMT) and inflammation, and suppression of oxidative phosphorylation pathways in the Myh6-Cre:DspW/F myocytes. Treadmill exercise restored transcript levels of two-third (492/781) of the DEGs and the corresponding dysregulated transcriptional and biological pathways, including EMT, inflammation, and secreted inhibitors of the canonical WNT. The changes were associated with reduced myocardial apoptosis and eccentric cardiac hypertrophy without changes in cardiac function. CONCLUSION Treadmill exercise restored transcript levels of the majority of dysregulated genes in cardiac myocytes, reduced myocardial apoptosis, and induced eccentric cardiac hypertrophy without affecting cardiac dysfunction in a mouse model of ACM. The findings suggest that treadmill exercise has potential beneficial effects in a subset of cardiac phenotypes in ACM.
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Affiliation(s)
- Sirisha M Cheedipudi
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Jinzhu Hu
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Siyang Fan
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Ping Yuan
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Jennifer Karmouch
- Department of Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Grace Czernuszewicz
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Matthew J Robertson
- Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kui Hong
- Department of Cardiovascular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, PR China
| | - Yan Yao
- Fuwai Hospital, Peking Union Medical College, Beijing, PR China
| | - Hanna Campbell
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xander Wehrens
- Cardiovascular Research Institute, Departments of Molecular Physiology & Biophysics, Medicine, Neuroscience, Pediatrics, and Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
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32
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Astrocyte-secreted IL-33 mediates homeostatic synaptic plasticity in the adult hippocampus. Proc Natl Acad Sci U S A 2020; 118:2020810118. [PMID: 33443211 PMCID: PMC7817131 DOI: 10.1073/pnas.2020810118] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Synaptic plasticity in the hippocampus is important for learning and memory formation. In particular, homeostatic synaptic plasticity enables neurons to restore their activity levels in response to chronic neuronal activity changes. While astrocytes modulate synaptic functions via the secretion of factors, the underlying molecular mechanisms remain unclear. Here, we show that suppression of hippocampal neuronal activity increases cytokine IL-33 release from astrocytes in the CA1 region. Activation of IL-33 and its neuronal ST2 receptor complex promotes functional excitatory synapse formation. Moreover, IL-33/ST2 signaling is important for the neuronal activity blockade-induced increase of CA1 excitatory synapses in vivo and spatial memory formation. This study suggests that astrocyte-secreted IL-33 acts as a negative feedback control signal to regulate hippocampal homeostatic synaptic plasticity. Hippocampal synaptic plasticity is important for learning and memory formation. Homeostatic synaptic plasticity is a specific form of synaptic plasticity that is induced upon prolonged changes in neuronal activity to maintain network homeostasis. While astrocytes are important regulators of synaptic transmission and plasticity, it is largely unclear how they interact with neurons to regulate synaptic plasticity at the circuit level. Here, we show that neuronal activity blockade selectively increases the expression and secretion of IL-33 (interleukin-33) by astrocytes in the hippocampal cornu ammonis 1 (CA1) subregion. This IL-33 stimulates an increase in excitatory synapses and neurotransmission through the activation of neuronal IL-33 receptor complex and synaptic recruitment of the scaffold protein PSD-95. We found that acute administration of tetrodotoxin in hippocampal slices or inhibition of hippocampal CA1 excitatory neurons by optogenetic manipulation increases IL-33 expression in CA1 astrocytes. Furthermore, IL-33 administration in vivo promotes the formation of functional excitatory synapses in hippocampal CA1 neurons, whereas conditional knockout of IL-33 in CA1 astrocytes decreases the number of excitatory synapses therein. Importantly, blockade of IL-33 and its receptor signaling in vivo by intracerebroventricular administration of its decoy receptor inhibits homeostatic synaptic plasticity in CA1 pyramidal neurons and impairs spatial memory formation in mice. These results collectively reveal an important role of astrocytic IL-33 in mediating the negative-feedback signaling mechanism in homeostatic synaptic plasticity, providing insights into how astrocytes maintain hippocampal network homeostasis.
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33
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Duan J, Zhang T, Gaffrey MJ, Weitz KK, Moore RJ, Li X, Xian M, Thrall BD, Qian WJ. Stochiometric quantification of the thiol redox proteome of macrophages reveals subcellular compartmentalization and susceptibility to oxidative perturbations. Redox Biol 2020; 36:101649. [PMID: 32750668 PMCID: PMC7397701 DOI: 10.1016/j.redox.2020.101649] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/24/2020] [Accepted: 07/17/2020] [Indexed: 12/12/2022] Open
Abstract
Posttranslational modifications of protein cysteine thiols play a significant role in redox regulation and the pathogenesis of human diseases. Herein, we report the characterization of the cellular redox landscape in terms of quantitative, site-specific occupancies of both S-glutathionylation (SSG) and total reversible thiol oxidation (total oxidation) in RAW 264.7 macrophage cells under basal conditions. The occupancies of thiol modifications for ~4000 cysteine sites were quantified, revealing a mean site occupancy of 4.0% for SSG and 11.9% for total oxidation, respectively. Correlations between site occupancies and structural features such as pKa, relative residue surface accessibility, and hydrophobicity were observed. Proteome-wide site occupancy analysis revealed that the average occupancies of SSG and total oxidation in specific cellular compartments correlate well with the expected redox potentials of respective organelles in macrophages, consistent with the notion of redox compartmentalization. The lowest average occupancies were observed in more reducing organelles such as the mitochondria (non-membrane) and nucleus, while the highest average occupancies were found in more oxidizing organelles such as endoplasmic reticulum (ER) and lysosome. Furthermore, a pattern of subcellular susceptibility to redox changes was observed under oxidative stress induced by exposure to engineered metal oxide nanoparticles. Peroxisome, ER, and mitochondria (membrane) are the organelles which exhibit the most significant redox changes; while mitochondria (non-membrane) and Golgi were observed as the organelles being most resistant to oxidative stress. Finally, it was observed that Cys residues at enzymatic active sites generally had a higher level of occupancy compared to non-active Cys residues within the same proteins, suggesting site occupancy as a potential indicator of protein functional sites. The raw data are available via ProteomeXchange with identifier PXD019913.
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Affiliation(s)
- Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xiaolu Li
- Department of Biological Systems Engineering, Washington State University, Richland, WA, USA
| | - Ming Xian
- Department of Chemistry, Washington State University, Pullman, WA, USA
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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34
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Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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Longmate WM, Varney S, Power D, Miskin RP, Anderson KE, DeFreest L, Van De Water L, DiPersio CM. Integrin α3β1 on Tumor Keratinocytes Is Essential to Maintain Tumor Growth and Promotes a Tumor-Supportive Keratinocyte Secretome. J Invest Dermatol 2020; 141:142-151.e6. [PMID: 32454065 DOI: 10.1016/j.jid.2020.05.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 05/01/2020] [Indexed: 02/01/2023]
Abstract
The development of integrin-targeted cancer therapies is hindered by incomplete understanding of integrin function in tumor cells and the tumor microenvironment. Previous studies showed that mice with epidermis-specific deletion of the α3 integrin subunit fail to form skin tumors during two-step chemical tumorigenesis, indicating a protumorigenic role for integrin α3β1. Here, we generated mice with tamoxifen-inducible, epidermis-specific α3 knockout to determine the role of α3β1 in the maintenance of established tumor cells and/or the associated stroma. Genetic ablation of α3 in established skin tumors caused their rapid regression, indicating that α3β1 is essential to maintain tumor growth. Although reduced proliferation and increased apoptosis were observed in α3β1-deficient tumor cells, these changes followed a robust increase in stromal apoptosis. Furthermore, macrophages and fibulin-2 levels were reduced in stroma following α3 deletion from tumor cells. Mass spectrometric analysis of conditioned medium from immortalized keratinocytes showed that α3β1 regulates a substantial fraction of the keratinocyte secretome, including fibulin-2 and macrophage CSF1; RNA in situ hybridization showed that expression of these two genes was reduced in tumor keratinocytes in vivo. Our findings identify α3β1 as a regulator of the keratinocyte secretome and skin tumor microenvironment and as a potential therapeutic target.
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Affiliation(s)
| | - Scott Varney
- Department of Surgery Albany Medical College, Albany, New York, USA
| | - Derek Power
- Department of Surgery Albany Medical College, Albany, New York, USA
| | | | - Karl E Anderson
- Department of Surgery Albany Medical College, Albany, New York, USA
| | - Lori DeFreest
- Department of Surgery Albany Medical College, Albany, New York, USA
| | - Livingston Van De Water
- Department of Surgery Albany Medical College, Albany, New York, USA; Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA
| | - C Michael DiPersio
- Department of Surgery Albany Medical College, Albany, New York, USA; Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, New York, USA.
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36
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Pascual M, Ibáñez F, Guerri C. Exosomes as mediators of neuron-glia communication in neuroinflammation. Neural Regen Res 2020; 15:796-801. [PMID: 31719239 PMCID: PMC6990780 DOI: 10.4103/1673-5374.268893] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/07/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
In recent years, a type of extracellular vesicles named exosomes has emerged that play an important role in intercellular communication under physiological and pathological conditions. These nanovesicles (30-150 nm) contain proteins, RNAs and lipids, and their internalization by bystander cells could alter their normal functions. This review focuses on recent knowledge about exosomes as messengers of neuron-glia communication and their participation in the physiological and pathological functions in the central nervous system. Special emphasis is placed on the role of exosomes under toxic or pathological stimuli within the brain, in which the glial exosomes containing inflammatory molecules are able to communicate with neurons and contribute to the pathogenesis of neuroinflammation and neurodegenerative disorders. Given the small size and characteristics of exosomes, they can cross the blood-brain barrier and be used as biomarkers and diagnosis for brain disorders and neuropathologies. Finally, although the application potential of exosome is still limited, current studies indicate that exosomes represent a promising strategy to gain pathogenic information to identify therapeutically targets and biomarkers for neurological disorders and neuroinflammation.
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Affiliation(s)
- María Pascual
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Francesc Ibáñez
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, Valencia, Spain
| | - Consuelo Guerri
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center, Valencia, Spain
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37
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Li X, Li W, Zeng M, Zheng R, Li M. Network-based methods for predicting essential genes or proteins: a survey. Brief Bioinform 2020; 21:566-583. [PMID: 30776072 DOI: 10.1093/bib/bbz017] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/03/2025] Open
Abstract
Genes that are thought to be critical for the survival of organisms or cells are called essential genes. The prediction of essential genes and their products (essential proteins) is of great value in exploring the mechanism of complex diseases, the study of the minimal required genome for living cells and the development of new drug targets. As laboratory methods are often complicated, costly and time-consuming, a great many of computational methods have been proposed to identify essential genes/proteins from the perspective of the network level with the in-depth understanding of network biology and the rapid development of biotechnologies. Through analyzing the topological characteristics of essential genes/proteins in protein-protein interaction networks (PINs), integrating biological information and considering the dynamic features of PINs, network-based methods have been proved to be effective in the identification of essential genes/proteins. In this paper, we survey the advanced methods for network-based prediction of essential genes/proteins and present the challenges and directions for future research.
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Affiliation(s)
- Xingyi Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Wenkai Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Min Zeng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Ruiqing Zheng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
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38
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Lee J, Zhang J, Chung YJ, Kim JH, Kook CM, González-Navajas JM, Herdman DS, Nürnberg B, Insel PA, Corr M, Mo JH, Tao A, Yasuda K, Rifkin IR, Broide DH, Sciammas R, Webster NJG, Raz E. Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses. eLife 2020; 9:e49416. [PMID: 32014112 PMCID: PMC7000221 DOI: 10.7554/elife.49416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022] Open
Abstract
Cyclic AMP (cAMP) is involved in many biological processes but little is known regarding its role in shaping immunity. Here we show that cAMP-PKA-CREB signaling (a pattern recognition receptor [PRR]-independent mechanism) regulates conventional type-2 Dendritic Cells (cDC2s) in mice and reprograms their Th17-inducing properties via repression of IRF4 and KLF4, transcription factors essential for cDC2-mediated Th2 induction. In mice, genetic loss of IRF4 phenocopies the effects of cAMP on Th17 induction and restoration of IRF4 prevents the cAMP effect. Moreover, curdlan, a PRR-dependent microbial product, activates CREB and represses IRF4 and KLF4, resulting in a pro-Th17 phenotype of cDC2s. These in vitro and in vivo results define a novel signaling pathway by which cDC2s display plasticity and provide a new molecular basis for the classification of novel cDC2 and cDC17 subsets. The findings also reveal that repressing IRF4 and KLF4 pathway can be harnessed for immuno-regulation.
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Affiliation(s)
- Jihyung Lee
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
| | - Junyan Zhang
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
- The Second Affiliated Hospital of Guangzhou Medical University (GMU), The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical ImmunologyGuangzhouChina
- Center for Immunology, Inflammation and Immune-mediated disease, GMUGuangzhouChina
| | - Young-Jun Chung
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
- Department of Otorhinolaryngology-Head and Neck SurgeryDankook University College of MedicineChungnamRepublic of Korea
| | - Jun Hwan Kim
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
| | - Chae Min Kook
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
| | - José M González-Navajas
- Center for Immunology, Inflammation and Immune-mediated disease, GMUGuangzhouChina
- Alicante Institute for Health and Biomedical Research (ISABIAL - FISABIO)AlicanteSpain
- Networked Biomedical Research Center for Hepatic and Digestive Diseases (CIBERehd)Institute of Health Carlos IIIMadridSpain
| | - David S Herdman
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
| | - Bernd Nürnberg
- Department of Pharmacology and Experimental TherapyUniversity of TübingenTübingenGermany
| | - Paul A Insel
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
- Department of PharmacologyUniversity of California San DiegoSan DiegoUnited States
| | - Maripat Corr
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
| | - Ji-Hun Mo
- Department of Otorhinolaryngology-Head and Neck SurgeryDankook University College of MedicineChungnamRepublic of Korea
| | - Ailin Tao
- The Second Affiliated Hospital of Guangzhou Medical University (GMU), The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical ImmunologyGuangzhouChina
- Center for Immunology, Inflammation and Immune-mediated disease, GMUGuangzhouChina
| | - Kei Yasuda
- Boston University School of MedicineBostonUnited States
| | - Ian R Rifkin
- Boston University School of MedicineBostonUnited States
- VA Boston Healthcare SystemBostonUnited States
| | - David H Broide
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
| | - Roger Sciammas
- Center for Comparative MedicineUniversity of California, DavisDavisUnited States
| | - Nicholas JG Webster
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
- VA San Diego Healthcare SystemSan DiegoUnited States
| | - Eyal Raz
- Department of MedicineUniversity of California San DiegoSan DiegoUnited States
- Center for Immunology, Inflammation and Immune-mediated disease, GMUGuangzhouChina
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Kitakaze T, Yoshikawa M, Kobayashi Y, Kimura N, Goshima N, Ishikawa T, Ogata Y, Yamashita Y, Ashida H, Harada N, Yamaji R. Extracellular transglutaminase 2 induces myotube hypertrophy through G protein-coupled receptor 56. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2020; 1867:118563. [PMID: 31666191 DOI: 10.1016/j.bbamcr.2019.118563] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
Abstract
Skeletal muscle secretes biologically active proteins that contribute to muscle hypertrophy in response to either exercise or dietary intake. The identification of skeletal muscle-secreted proteins that induces hypertrophy can provide critical information regarding skeletal muscle health. Dietary provitamin A, β-carotene, induces hypertrophy of the soleus muscle in mice. Here, we hypothesized that skeletal muscle produces hypertrophy-inducible secretory proteins via dietary β-carotene. Knockdown of retinoic acid receptor (RAR) γ inhibited the β-carotene-induced increase soleus muscle mass in mice. Using RNA sequencing, bioinformatic analyses, and literature searching, we predicted transglutaminase 2 (TG2) to be an all-trans retinoic acid (ATRA)-induced secretory protein in cultured C2C12 myotubes. Tg2 mRNA expression increased in ATRA- or β-carotene-stimulated myotubes and in the soleus muscle of β-carotene-treated mice. Knockdown of RARγ inhibited β-carotene-increased mRNA expression of Tg2 in the soleus muscle. ATRA increased endogenous TG2 levels in conditioned medium from myotubes. Extracellular TG2 promoted the phosphorylation of Akt, mechanistic target of rapamycin (mTOR), and ribosomal p70 S6 kinase (p70S6K), and inhibitors of mTOR, phosphatidylinositol 3-kinase, and Src (rapamycin, LY294002, and Src I1, respectively) inhibited TG2-increased phosphorylation of mTOR and p70S6K. Furthermore, extracellular TG2 promoted protein synthesis and hypertrophy in myotubes. TG2 mutant lacking transglutaminase activity exerted the same effects as wild-type TG2. Knockdown of G protein-coupled receptor 56 (GPR56) inhibited the effects of TG2 on mTOR signaling, protein synthesis, and hypertrophy. These results indicated that TG2 expression was upregulated through ATRA-mediated RARγ and that extracellular TG2 induced myotube hypertrophy by activating mTOR signaling-mediated protein synthesis through GPR56, independent of transglutaminase activity.
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MESH Headings
- Animals
- Cell Enlargement/drug effects
- Cell Line
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Insulin-Like Growth Factor I/genetics
- Insulin-Like Growth Factor I/metabolism
- Mice
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Myoblasts/cytology
- Myoblasts/metabolism
- Phosphorylation/drug effects
- Protein Glutamine gamma Glutamyltransferase 2
- Proto-Oncogene Proteins c-akt/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Retinoic Acid/antagonists & inhibitors
- Receptors, Retinoic Acid/genetics
- Receptors, Retinoic Acid/metabolism
- Retinoic Acid Receptor alpha/antagonists & inhibitors
- Retinoic Acid Receptor alpha/genetics
- Retinoic Acid Receptor alpha/metabolism
- Ribosomal Protein S6 Kinases, 70-kDa/metabolism
- Signal Transduction/drug effects
- TOR Serine-Threonine Kinases/metabolism
- Transglutaminases/genetics
- Transglutaminases/metabolism
- Tretinoin/pharmacology
- beta Carotene/administration & dosage
- beta Carotene/pharmacology
- Retinoic Acid Receptor gamma
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Affiliation(s)
- Tomoya Kitakaze
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan; Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Miki Yoshikawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Yasuyuki Kobayashi
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Naohiro Kimura
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Naoki Goshima
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Shimane, Japan
| | - Yoshiyuki Ogata
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Yoko Yamashita
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Hitoshi Ashida
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Naoki Harada
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ryoichi Yamaji
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan.
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Zhang Y, Wu X, Kai Y, Lee CH, Cheng F, Li Y, Zhuang Y, Ghaemmaghami J, Chuang KH, Liu Z, Meng Y, Keswani M, Gough NR, Wu X, Zhu W, Tzatsos A, Peng W, Seto E, Sotomayor EM, Zheng X. Secretome profiling identifies neuron-derived neurotrophic factor as a tumor-suppressive factor in lung cancer. JCI Insight 2019; 4:129344. [PMID: 31852841 DOI: 10.1172/jci.insight.129344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022] Open
Abstract
Clinical and preclinical studies show tissue-specific differences in tumorigenesis. Tissue specificity is controlled by differential gene expression. We prioritized genes that encode secreted proteins according to their preferential expression in normal lungs to identify candidates associated with lung cancer. Indeed, most of the lung-enriched genes identified in our analysis have known or suspected roles in lung cancer. We focused on the gene encoding neuron-derived neurotrophic factor (NDNF), which had not yet been associated with lung cancer. We determined that NDNF was preferentially expressed in the normal adult lung and that its expression was decreased in human lung adenocarcinoma and a mouse model of this cancer. Higher expression of NDNF was associated with better clinical outcome of patients with lung adenocarcinoma. Purified NDNF inhibited proliferation of lung cancer cells, whereas silencing NDNF promoted tumor cell growth in culture and in xenograft models. We determined that NDNF is downregulated through DNA hypermethylation near CpG island shores in human lung adenocarcinoma. Furthermore, the lung cancer-related DNA hypermethylation sites corresponded to the methylation sites that occurred in tissues with low NDNF expression. Thus, by analyzing the tissue-specific secretome, we identified a tumor-suppressive factor, NDNF, which is associated with patient outcomes in lung adenocarcinoma.
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Affiliation(s)
- Ya Zhang
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Xuefeng Wu
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Yan Kai
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Physics, George Washington University Columbian College of Arts and Sciences, Washington, DC, USA
| | - Chia-Han Lee
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.,Department of Biochemistry and Molecular Medicine
| | - Fengdong Cheng
- GW Cancer Center and.,Division of Hematology and Oncology, Department of Medicine, and
| | - Yixuan Li
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Yongbao Zhuang
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Javid Ghaemmaghami
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Kun-Han Chuang
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Zhuo Liu
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Yunxiao Meng
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Meghana Keswani
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Nancy R Gough
- Center for Translational Medicine, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Xiaojun Wu
- Department of Pathology, Johns Hopkins Sibley Memorial Hospital, Washington, DC, USA.,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wenge Zhu
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Alexandros Tzatsos
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Weiqun Peng
- GW Cancer Center and.,Department of Physics, George Washington University Columbian College of Arts and Sciences, Washington, DC, USA
| | - Edward Seto
- GW Cancer Center and.,Department of Biochemistry and Molecular Medicine
| | - Eduardo M Sotomayor
- GW Cancer Center and.,Division of Hematology and Oncology, Department of Medicine, and
| | - Xiaoyan Zheng
- GW Cancer Center and.,Department of Anatomy and Cell Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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41
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Chang-Panesso M, Kadyrov FF, Lalli M, Wu H, Ikeda S, Kefaloyianni E, Abdelmageed MM, Herrlich A, Kobayashi A, Humphreys BD. FOXM1 drives proximal tubule proliferation during repair from acute ischemic kidney injury. J Clin Invest 2019; 129:5501-5517. [PMID: 31710314 PMCID: PMC6877314 DOI: 10.1172/jci125519] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
The proximal tubule has a remarkable capacity for repair after acute injury, but the cellular lineage and molecular mechanisms underlying this repair response are incompletely understood. Here, we developed a Kim1-GFPCreERt2 knockin mouse line (Kim1-GCE) in order to perform genetic lineage tracing of dedifferentiated cells while measuring the cellular transcriptome of proximal tubule during repair. Acutely injured genetically labeled clones coexpressed KIM1, VIMENTIN, SOX9, and KI67, indicating a dedifferentiated and proliferative state. Clonal analysis revealed clonal expansion of Kim1+ cells, indicating that acutely injured, dedifferentiated proximal tubule cells, rather than fixed tubular progenitor cells, account for repair. Translational profiling during injury and repair revealed signatures of both successful and unsuccessful maladaptive repair. The transcription factor Foxm1 was induced early in injury, was required for epithelial proliferation in vitro, and was dependent on epidermal growth factor receptor (EGFR) stimulation. In conclusion, dedifferentiated proximal tubule cells effect proximal tubule repair, and we reveal an EGFR/FOXM1-dependent signaling pathway that drives proliferative repair after injury.
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Affiliation(s)
| | | | - Matthew Lalli
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, and
| | - Shiyo Ikeda
- Division of Nephrology, Department of Medicine, and
| | | | - Mai M. Abdelmageed
- Division of Nephrology, Department of Medicine, and
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, British University in Egypt, Cairo, Egypt
| | | | - Akio Kobayashi
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, and
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
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42
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Day EA, Ford RJ, Smith BK, Mohammadi-Shemirani P, Morrow MR, Gutgesell RM, Lu R, Raphenya AR, Kabiri M, McArthur AG, McInnes N, Hess S, Paré G, Gerstein HC, Steinberg GR. Metformin-induced increases in GDF15 are important for suppressing appetite and promoting weight loss. Nat Metab 2019; 1:1202-1208. [PMID: 32694673 DOI: 10.1038/s42255-019-0146-4] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/06/2019] [Indexed: 01/22/2023]
Abstract
Metformin is the most commonly prescribed medication for type 2 diabetes, owing to its glucose-lowering effects, which are mediated through the suppression of hepatic glucose production (reviewed in refs. 1-3). However, in addition to its effects on the liver, metformin reduces appetite and in preclinical models exerts beneficial effects on ageing and a number of diverse diseases (for example, cognitive disorders, cancer, cardiovascular disease) through mechanisms that are not fully understood1-3. Given the high concentration of metformin in the liver and its many beneficial effects beyond glycemic control, we reasoned that metformin may increase the secretion of a hepatocyte-derived endocrine factor that communicates with the central nervous system4. Here we show, using unbiased transcriptomics of mouse hepatocytes and analysis of proteins in human serum, that metformin induces expression and secretion of growth differentiating factor 15 (GDF15). In primary mouse hepatocytes, metformin stimulates the secretion of GDF15 by increasing the expression of activating transcription factor 4 (ATF4) and C/EBP homologous protein (CHOP; also known as DDIT3). In wild-type mice fed a high-fat diet, oral administration of metformin increases serum GDF15 and reduces food intake, body mass, fasting insulin and glucose intolerance; these effects are eliminated in GDF15 null mice. An increase in serum GDF15 is also associated with weight loss in patients with type 2 diabetes who take metformin. Although further studies will be required to determine the tissue source(s) of GDF15 produced in response to metformin in vivo, our data indicate that the therapeutic benefits of metformin on appetite, body mass and serum insulin depend on GDF15.
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Affiliation(s)
- Emily A Day
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Rebecca J Ford
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Brennan K Smith
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Pedrum Mohammadi-Shemirani
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
- Department of Pathology, McMaster University, Hamilton, Ontario, Canada
| | - Marisa R Morrow
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Robert M Gutgesell
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Rachel Lu
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mostafa Kabiri
- Sanofi Aventis Deutschland, Translational in vivo Models, Sanofi Research and Development, Frankfurt, Germany
| | - Andrew G McArthur
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Natalia McInnes
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
| | - Sibylle Hess
- Sanofi Aventis Deutschland GmbH, Research and Development Division, Translational Medicine and Early Development, Biomarkers and Clinical Bioanalyses, Frankfurt, Germany
| | - Guillaume Paré
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
- Department of Pathology, McMaster University, Hamilton, Ontario, Canada
- Thrombosis and Atherosclerosis Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
| | - Hertzel C Gerstein
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, Ontario, Canada
| | - Gregory R Steinberg
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, Ontario, Canada.
- Division of Endocrinology and Metabolism, Department of Medicine, McMaster University, Hamilton, Ontario, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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43
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Chen G, Chen J, Liu H, Chen S, Zhang Y, Li P, Thierry-Mieg D, Thierry-Mieg J, Mattes W, Ning B, Shi T. Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. Front Cell Dev Biol 2019; 7:299. [PMID: 31824949 PMCID: PMC6881247 DOI: 10.3389/fcell.2019.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
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Affiliation(s)
- Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwei Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huanlong Liu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangguan Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peng Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - William Mattes
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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44
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Ankney JA, Xie L, Wrobel JA, Wang L, Chen X. Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients. BMC Med Genomics 2019; 12:78. [PMID: 31146747 PMCID: PMC6543675 DOI: 10.1186/s12920-019-0530-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/13/2019] [Indexed: 02/08/2023] Open
Abstract
Background Presently, a 50-gene expression model (PAM50) serves as a breast cancer (BC) subtype classifier that is insufficient to distinguish, within each single PAM50-classified subtype, patient subpopulations having different prognosis. There is a pressing need for inexpensive and minimally invasive biomarker tests to easily and accurately predict individuals’ clinical outcomes and response to treatments. Although quantitative proteomic approaches have been developed to identify/profile proteins secreted (secretome) from various cancer cell lines in vitro, missing are the clinicopathological relevance and the associated prognostic value of these secretomic identifications. Methods To discover biomarkers to predict individualized prognosis we introduce a new multi-omics (secreto-transcriptomics) method that identifies, in their oncogenically secreted states, candidate markers of BC subtypes whose genes bear patient-specific mRNA expression alterations of prognostic significance. First, we used label-free quantitative (LFQ) proteomics to identify the proteins showing BC-subtypic secretion from a series of BC cell lines representing major BC-subtypes. To determine and externally validate the prognostic value of these secreted proteins, we developed a secreto-transcriptomic approach that discovered a PAM50-subtypic Secretion-Correlated mRNA Expression Pattern (SeCEP) wherein the PAM50-subtypic secretion of select proteins statistically correlated with cis-mRNA expression of their encoding genes in patients of the corresponding PAM50-subtypes. Kaplan-Meier analysis of SeCEP genes was used to identify new liquid biopsy biomarkers for predicting individualized prognosis. Results The mRNA expression-to-secretion correlation (SeCEP) pinpointed multiple genes that are fully translated into the oncogenically active secretome in a PAM50-subtypic manner. Further, multiple SeCEP genes in distinct combinations or panels of multiple SeCEP genes were identified as ‘systems prognostic markers’ that showed mRNA co-overexpression patterns in the distinct subpopulations of PAM50-subtypic patients with poor prognosis or high-risk of relapse. Thus, our secreto-transcriptomic approach statistically linked BC subtypic secretome genes with patient-specific information about their mRNA expression alterations and significantly improved the sensitivity and specificity in patient stratification in the context of clinical outcomes or prognosis. Conclusions By combining LFQ secretome screening with proteo-transcriptomic retrospective analysis of patient data our integrated multi-omics approach bypasses costly, tedious, genome-wide fishing and predictive modeling that are commonly required to distinguish a few prognostically altered genes from thousands of other non-BC related genes in a genome. Electronic supplementary material The online version of this article (10.1186/s12920-019-0530-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Astor Ankney
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ling Xie
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - John A Wrobel
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Li Wang
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xian Chen
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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45
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Sun Y, Wen J, Chen R, Deng Y. Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress. Sci Rep 2019; 9:7819. [PMID: 31127180 PMCID: PMC6534621 DOI: 10.1038/s41598-019-44305-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/13/2019] [Indexed: 12/01/2022] Open
Abstract
Transcript levels are the primary factor determining protein levels, but for the majority of genes, fold changes in transcript levels are larger than the corresponding changes in protein levels, a phenomenon that is termed “protein homeostasis”. However, this phenomenon is not well characterized in the context of environmental changes. In this study, we sequenced the entire transcriptome and proteome of chicken primary hepatocytes administered three mycotoxin treatments Aflatoxin B1 (AFB1), Ochoratoxin A (OTA) and Zearalenone (ZEN). Each mycotoxin induced unique set of differential expressed transcripts and proteins, suggesting variable cytotoxicity and biochemical action in cell. We found a weak positive correlation between transcript and protein changes, and the transcript changes were higher than the protein changes. Furthermore, we observed pathway-specific protein homeostasis pattern under mycotoxin stress. Specifically, the “Metabolism”, “Transcription” and “Translation” pathways (housekeeping pathways) showed lower fold changes in protein/mRNA levels than non-housekeeping pathways such as “Cell growth and death” and “Immune system”. Protein molecular weight had a weak negative effect on protein production, and this effect was stronger for non-housekeeping pathways. Overall, we hypothesize housekeeping pathways maintain stable protein production for baseline cellular function, whereas non-housekeeping pathways is associated with the fitness response to environmental stress.
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Affiliation(s)
- Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China.,Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China.,Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China
| | - Ruohong Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China.,Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China. .,Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510642, P.R. China.
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46
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Montgomery MK, De Nardo W, Watt MJ. Impact of Lipotoxicity on Tissue "Cross Talk" and Metabolic Regulation. Physiology (Bethesda) 2019; 34:134-149. [PMID: 30724128 DOI: 10.1152/physiol.00037.2018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Obesity-associated comorbidities include non-alcoholic fatty liver disease, Type 2 diabetes, and cardiovascular disease. These diseases are associated with accumulation of lipids in non-adipose tissues, which can impact many intracellular cellular signaling pathways and functions that have been broadly defined as "lipotoxic." This review moves beyond understanding intracellular lipotoxic outcomes and outlines the consequences of lipotoxicity on protein secretion and inter-tissue "cross talk," and the impact this exerts on systemic metabolism.
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Affiliation(s)
| | - William De Nardo
- Department of Physiology, The University of Melbourne , Melbourne, Victoria , Australia
| | - Matthew J Watt
- Department of Physiology, The University of Melbourne , Melbourne, Victoria , Australia
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Feyertag F, Berninsone PM, Alvarez-Ponce D. N-glycoproteins exhibit a positive expression level-evolutionary rate correlation. J Evol Biol 2019; 32:390-394. [PMID: 30697857 DOI: 10.1111/jeb.13420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 12/22/2022]
Abstract
The different proteins of any proteome evolve at enormously different rates. One of the primary factors influencing rates of protein evolution is expression level, with highly expressed proteins tending to evolve at slow rates. This phenomenon, known as the expression level-evolutionary rate (E-R) anticorrelation, has been attributed to the abundance-dependent deleterious effects of misfolding or misinteraction. We have recently shown that secreted proteins either lack an E-R anticorrelation or exhibit a significantly reduced E-R anticorrelation. This effect may be due to the strict quality control to which secreted proteins are subject in the endoplasmic reticulum (which is expected to reduce the rate of misfolding and its deleterious effects) or to their extracellular location (expected to reduce the rate of misinteraction and its deleterious effects). Among secreted proteins, N-glycosylated ones are under particularly strong quality control. Here, we investigate how N-linked glycosylation affects the E-R anticorrelation. Strikingly, we observe a positive E-R correlation among N-glycosylated proteins. That is, N-glycoproteins that are highly expressed evolve at faster rates than lowly expressed N-glycoproteins, in contrast to what is observed among intracellular proteins.
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Affiliation(s)
- Felix Feyertag
- Department of Biology, University of Nevada, Reno, Reno, Nevada
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Najgebauer H, Jarnuczak AF, Varro A, Sanderson CM. Integrative Omic Profiling Reveals Unique Hypoxia Induced Signatures in Gastric Cancer Associated Myofibroblasts. Cancers (Basel) 2019; 11:cancers11020263. [PMID: 30813438 PMCID: PMC6406696 DOI: 10.3390/cancers11020263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/15/2022] Open
Abstract
Although hypoxia is known to contribute to several aspects of tumour progression, relatively little is known about the effects of hypoxia on cancer-associated myofibroblasts (CAMs), or the consequences that conditional changes in CAM function may have on tumour development and metastasis. To investigate this issue in the context of gastric cancer, a comparative multiomic analysis was performed on populations of patient-derived myofibroblasts, cultured under normoxic or hypoxic conditions. Data from this study reveal a novel set of CAM-specific hypoxia-induced changes in gene expression and secreted proteins. Significantly, these signatures are not observed in either patient matched adjacent tissue myofibroblasts (ATMs) or non-cancer associated normal tissue myofibroblasts (NTMs). Functional characterisation of different myofibroblast populations shows that hypoxia-induced changes in gene expression not only enhance the ability of CAMs to induce cancer cell migration, but also confer pro-tumorigenic (CAM-like) properties in NTMs. This study provides the first global mechanistic insight into the molecular changes that contribute to hypoxia-induced pro-tumorigenic changes in gastric stromal myofibroblasts.
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Affiliation(s)
- Hanna Najgebauer
- Department of Cellular and Molecular Physiology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Andrew F Jarnuczak
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Andrea Varro
- Department of Cellular and Molecular Physiology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK.
| | - Christopher M Sanderson
- Department of Cellular and Molecular Physiology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK.
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Giambra V, Gusscott S, Gracias D, Song R, Lam SH, Panelli P, Tyshchenko K, Jenkins CE, Hoofd C, Lorzadeh A, Carles A, Hirst M, Eaves CJ, Weng AP. Epigenetic Restoration of Fetal-like IGF1 Signaling Inhibits Leukemia Stem Cell Activity. Cell Stem Cell 2018; 23:714-726.e7. [PMID: 30269902 DOI: 10.1016/j.stem.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 06/15/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022]
Abstract
Acute leukemias are aggressive malignancies of developmentally arrested hematopoietic progenitors. We sought here to explore the possibility that changes in hematopoietic stem/progenitor cells during development might alter the biology of leukemias arising from this tissue compartment. Using a mouse model of acute T cell leukemia, we found that leukemias generated from fetal liver (FL) and adult bone marrow (BM) differed dramatically in their leukemia stem cell activity with FL leukemias showing markedly reduced serial transplantability as compared to BM leukemias. We present evidence that this difference is due to NOTCH1-driven autocrine IGF1 signaling, which is active in FL cells but restrained in BM cells by EZH2-dependent H3K27 trimethylation. Further, we confirmed this mechanism is operative in human disease and show that enforced IGF1 signaling effectively limits leukemia stem cell activity. These findings demonstrate that resurrecting dormant fetal programs in adult cells may represent an alternate therapeutic approach in human cancer.
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Affiliation(s)
- Vincenzo Giambra
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy.
| | - Samuel Gusscott
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Deanne Gracias
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Raymond Song
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Sonya H Lam
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Patrizio Panelli
- Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | | | | | - Catherine Hoofd
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Alireza Lorzadeh
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Annaick Carles
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Martin Hirst
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
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Pei J, Kinch LN, Grishin NV. FlyXCDB—A Resource for Drosophila Cell Surface and Secreted Proteins and Their Extracellular Domains. J Mol Biol 2018; 430:3353-3411. [DOI: 10.1016/j.jmb.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 02/06/2023]
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