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Wang Y, Wang X, Niu X, Han K, Ru N, Xiang J, Linghu E. Identification of COL3A1 as a candidate protein involved in the crosstalk between obesity and diarrhea using quantitative proteomics and machine learning. Eur J Pharmacol 2024; 981:176881. [PMID: 39127300 DOI: 10.1016/j.ejphar.2024.176881] [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: 01/22/2024] [Revised: 06/05/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Increasing epidemiologic studies have shown a positive correlation between obesity and chronic diarrhea. Nevertheless, the precise etiology remains uncertain. METHODS We performed a comprehensive proteomics analysis utilizing the data-independent acquisition (DIA) technique on jejunal tissues from patients with obesity and chronic diarrhea (OD, n = 33), obese patients (OB, n = 10), and healthy controls (n = 8). Differentially expressed proteins (DEPs) in OD vs. control and OD vs. OB comparisons were subjected to pathway enrichment and protein-protein interaction (PPI) network analysis. Machine learning algorithms were adopted on overlapping DEPs in both comparisons. The candidate protein was further validated using Western blot, immunohistochemistry (IHC), and in vitro experiments. RESULTS We identified 189 and 228 DEPs in OD vs. control and OD vs. OB comparisons, respectively. DEPs in both comparisons were co-enriched in extracellular matrix (ECM) organization. Downregulated DEPs were associated with tight junction and ECM-receptor interaction in OD vs. control and OD vs. OB comparisons, respectively. Machine learning algorithms selected 3 proteins from 14 overlapping DEPs in both comparisons, among which collagen alpha-1(III) chain (COL3A1) was identified as a core protein in PPI networks. Western blot and IHC verified the expression of COL3A1. Moreover, the tight junction-related proteins decreased after the knockdown of COL3A1 in Caco2 intestinal cells upon PA challenge, consistent with the proteomics results. CONCLUSIONS We generated in-depth profiling of a proteomic dataset from samples of OD patients and provided unique insights into disease pathogenesis. COL3A1 was involved in the crosstalk between obesity and intestinal homeostasis via the ECM-receptor interaction pathway.
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Affiliation(s)
- Yan Wang
- Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiangyao Wang
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaotong Niu
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China; Medical School of Chinese PLA, Beijing, 100853, China
| | - Ke Han
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China; Medical School of Chinese PLA, Beijing, 100853, China
| | - Nan Ru
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jingyuan Xiang
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China; Medical School of Chinese PLA, Beijing, 100853, China
| | - Enqiang Linghu
- Nankai University School of Medicine, Nankai University, Tianjin, 300071, China; Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China.
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2
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Zane F, MacMurray C, Guillermain C, Cansell C, Todd N, Rera M. Ageing as a two-phase process: theoretical framework. FRONTIERS IN AGING 2024; 5:1378351. [PMID: 38651031 PMCID: PMC11034523 DOI: 10.3389/fragi.2024.1378351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 04/25/2024]
Abstract
Human ageing, along with the ageing of conventional model organisms, is depicted as a continuous and progressive decline of biological capabilities accompanied by an exponentially increasing mortality risk. However, not all organisms experience ageing identically and our understanding of the phenomenon is coloured by human-centric views. Ageing is multifaceted and influences a diverse range of species in varying ways. Some undergo swift declines post-reproduction, while others exhibit insubstantial changes throughout their existence. This vast array renders defining universally applicable "ageing attributes" a daunting task. It is nonetheless essential to recognize that not all ageing features are organism-specific. These common attributes have paved the way for identifying "hallmarks of ageing," processes that are intertwined with age, amplified during accelerated ageing, and manipulations of which can potentially modulate or even reverse the ageing process. Yet, a glaring observation is that individuals within a single population age at varying rates. To address this, demographers have coined the term 'frailty'. Concurrently, scientific advancements have ushered in the era of molecular clocks. These innovations enable a distinction between an individual's chronological age (time since birth) and biological age (physiological status and mortality risk). In 2011, the "Smurf" phenotype was unveiled in Drosophila, delineating an age-linked escalation in intestinal permeability that presages imminent mortality. It not only acts as a predictor of natural death but identifies individuals exhibiting traits normally described as age-related. Subsequent studies have revealed the phenotype in organisms like nematodes, zebrafish, and mice, invariably acting as a death predictor. Collectively, these findings have steered our conception of ageing towards a framework where ageing is not linear and continuous but marked by two distinct, necessary phases, discernible in vivo, courtesy of the Smurf phenotype. This framework includes a mathematical enunciation of longevity trends based on three experimentally measurable parameters. It facilitates a fresh perspective on the evolution of ageing as a function. In this article, we aim to delineate and explore the foundational principles of this innovative framework, emphasising its potential to reshape our understanding of ageing, challenge its conventional definitions, and recalibrate our comprehension of its evolutionary trajectory.
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Affiliation(s)
- Flaminia Zane
- Université Paris Cité, INSERM UMR U1284, Paris, France
| | | | | | - Céline Cansell
- Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, Palaiseau, France
| | - Nicolas Todd
- Eco-Anthropologie (EA), Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Musée de l’Homme, Paris, France
| | - Michael Rera
- Université Paris Cité, Institut Jacques Monod, CNRS UMR 7592, Paris, France
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3
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Serna-Morales E, Sánchez-Sánchez BJ, Marcotti S, Nichols A, Bhargava A, Dragu A, Hirvonen LM, Díaz-de-la-Loza MDC, Mink M, Cox S, Rayfield E, Lee RM, Hobson CM, Chew TL, Stramer BM. Extracellular matrix assembly stress initiates Drosophila central nervous system morphogenesis. Dev Cell 2023; 58:825-835.e6. [PMID: 37086718 PMCID: PMC10390342 DOI: 10.1016/j.devcel.2023.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 12/12/2022] [Accepted: 03/05/2023] [Indexed: 04/24/2023]
Abstract
Forces controlling tissue morphogenesis are attributed to cellular-driven activities, and any role for extracellular matrix (ECM) is assumed to be passive. However, all polymer networks, including ECM, can develop autonomous stresses during their assembly. Here, we examine the morphogenetic function of an ECM before reaching homeostatic equilibrium by analyzing de novo ECM assembly during Drosophila ventral nerve cord (VNC) condensation. Asymmetric VNC shortening and a rapid decrease in surface area correlate with the exponential assembly of collagen IV (Col4) surrounding the tissue. Concomitantly, a transient developmentally induced Col4 gradient leads to coherent long-range flow of ECM, which equilibrates the Col4 network. Finite element analysis and perturbation of Col4 network formation through the generation of dominant Col4 mutations that affect assembly reveal that VNC morphodynamics is partially driven by a sudden increase in ECM-driven surface tension. These data suggest that ECM assembly stress and associated network instabilities can actively participate in tissue morphogenesis.
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Affiliation(s)
- Eduardo Serna-Morales
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | | | - Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Angus Nichols
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Anushka Bhargava
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Anca Dragu
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Liisa M Hirvonen
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | | | - Matyas Mink
- Institute of Medical Biology, University of Szeged, 6720 Szeged, Hungary
| | - Susan Cox
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK
| | - Emily Rayfield
- School of Earth Sciences, University of Bristol, BS8 1QU Bristol, UK
| | - Rachel M Lee
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Chad M Hobson
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Brian M Stramer
- Randall Centre for Cell and Molecular Biophysics, King's College London, SE1 1UL London, UK.
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4
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Chen X, Liu T, Wu J, Zhu C, Guan G, Zou C, Guo Q, Ren X, Li C, Cheng P, Cheng W, Wu A. Molecular profiling identifies distinct subtypes across TP53 mutant tumors. JCI Insight 2022; 7:156485. [PMID: 36256461 PMCID: PMC9746906 DOI: 10.1172/jci.insight.156485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 10/14/2022] [Indexed: 01/12/2023] Open
Abstract
Tumor protein 53 mutation (TP53mut) is one of the most important driver events facilitating tumorigenesis, which could induce a series of chain reactions to promote tumor malignant transformation. However, the malignancy progression patterns under TP53 mutation remain less known. Clarifying the molecular landscapes of TP53mut tumors will help us understand the process of tumor development and aid precise treatment. Here, we distilled genetic and epigenetic features altered in TP53mut cancers for cluster-of-clusters analysis. Using integrated classification, we derived 5 different subtypes of TP53mut patients. These subtypes have distinct features in genomic alteration, clinical relevance, microenvironment dysregulation, and potential therapeutics. Among the 5 subtypes, COCA3 was identified as the subtype with worst prognosis, causing an immunosuppressive microenvironment and immunotherapeutic resistance. Further drug efficacy research highlighted olaparib as the most promising therapeutic agents for COCA3 tumors. Importantly, the therapeutic efficacy of olaparib in COCA3 and immunotherapy in non-COCA3 tumors was validated via in vivo experimentation. Our study explored the important molecular events and developed a subtype classification system with distinct targeted therapy strategies for different subtypes of TP53mut tumors. These multiomics classification systems provide a valuable resource that significantly expands the knowledge of TP53mut tumors and may eventually benefit in clinical practice.
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Affiliation(s)
- Xin Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tianqi Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianqi Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Cunyi Zou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qing Guo
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiaolin Ren
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.,Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, Liaoning, China
| | - Chen Li
- Department of Orthodontics, Stomatological Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wen Cheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.,Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Anhua Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.,Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
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5
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Miotelo L, Ferro M, Maloni G, Otero IVR, Nocelli RCF, Bacci M, Malaspina O. Transcriptomic analysis of Malpighian tubules from the stingless bee Melipona scutellaris reveals thiamethoxam-induced damages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158086. [PMID: 35985603 DOI: 10.1016/j.scitotenv.2022.158086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/21/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
The concern about pesticide exposure to neotropical bees has been increasing in the last few years, and knowledge gaps have been identified. Although stingless bees, (e.g.: Melipona scutellaris), are more diverse than honeybees and they stand out in the pollination of several valuable economical crops, toxicity assessments with stingless bees are still scarce. Nowadays new approaches in ecotoxicological studies, such as omic analysis, were pointed out as a strategy to reveal mechanisms of how bees deal with these stressors. To date, no molecular techniques have been applied for the evaluation of target and/or non-target organs in stingless bees, such as the Malpighian tubules (Mt). Therefore, in the present study, we evaluated the differentially expressed genes (DEGs) in the Mt of M. scutellaris after one and eight days of exposure to LC50/100 (0.000543 ng a.i./μL) of thiamethoxam (TMX). Through functional annotation analysis of four transcriptome libraries, the time course line approach revealed 237 DEGs (nine clusters) associated with carbon/energy metabolism and cellular processes (lysosomes, autophagy, and glycan degradation). The expression profiles of Mt were altered by TMX in processes, such as detoxification, excretion, tissue regeneration, oxidative stress, apoptosis, and DNA repair. Transcriptome analysis showed that cell metabolism in Mt was mainly affected after 8 days of exposure. Nine genes were selected from different clusters and validated by RT-qPCR. According to our findings, TMX promotes several types of damage in Mt cells at the molecular level. Therefore, interference of different cellular processes directly affects the health of M. scutellaris by compromising the function of Mt.
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Affiliation(s)
- Lucas Miotelo
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil.
| | - Milene Ferro
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Geovana Maloni
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Igor Vinicius Ramos Otero
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | | | - Mauricio Bacci
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
| | - Osmar Malaspina
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, SP, Brazil
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6
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Scholl A, Ndoja I, Jiang L. Drosophila Trachea as a Novel Model of COPD. Int J Mol Sci 2021; 22:ijms222312730. [PMID: 34884534 PMCID: PMC8658011 DOI: 10.3390/ijms222312730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/23/2022] Open
Abstract
COPD, a chronic obstructive pulmonary disease, is one of the leading causes of death worldwide. Clinical studies and research in rodent models demonstrated that failure of repair mechanisms to cope with increased ROS and inflammation in the lung leads to COPD. Despite this progress, the molecular mechanisms underlying the development of COPD remain poorly understood, resulting in a lack of effective treatments. Thus, an informative, simple model is highly valued and desired. Recently, the cigarette smoke-induced Drosophila COPD model showed a complex set of pathological phenotypes that resemble those seen in human COPD patients. The Drosophila trachea has been used as a premier model to reveal the mechanisms of tube morphogenesis. The association of these mechanisms to structural changes in COPD can be analyzed by using Drosophila trachea. Additionally, the timeline of structural damage, ROS, and inflammation can be studied in live organisms using fluorescently-tagged proteins. The related function of human COPD genes identified by GWAS can be screened using respective fly homologs. Finally, the Drosophila trachea can be used as a high-throughput drug screening platform to identify novel treatments for COPD. Therefore, Drosophila trachea is an excellent model that is complementary to rodent COPD models.
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7
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Zhang W, Shen J, Zhang S, Liu X, Pan S, Li Y, Zhang L, He L, Niu Y. Silencing integrin α6 enhances the pluripotency-differentiation transition in human dental pulp stem cells. Oral Dis 2021; 28:711-722. [PMID: 33404136 DOI: 10.1111/odi.13771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVES Although integrins have been shown to be associated with proliferation and differentiation in some stem cells, the regulatory effect of integrin α6 (ITGα6) on the human dental pulp stem cells (hDPSCs) has not been reported. Here, we detected the roles of ITGα6 in hDPSCs. MATERIALS AND METHODS Attached to Cytodex 3 microcarriers, hDPSCs grown under stimulated microgravity (SMG) or conventional culture conditions were measured the proliferation and different gene expression. Further, ITGα6 was silenced in hDPSCs, and its effect on proliferation, differentiation, and cytoskeletal organization was analyzed. RESULTS SMG conditions increased the number of Ki67-positive hDPSCs and progression into S phase of cell cycle. WB analysis showed the expression of ITGα6 was upregulated in hDPSCs under SMG conditions. Knockdown of ITGα6 decreased the expression of stemness markers, CD105 and STRO-1 in hDPSCs, but promoted the osteogenic and odontogenic differentiation by increased ALP expression and Alizarin Red nodules. Moreover, RNA-seq demonstrated that RHO/ROCK signaling pathway upregulated silencing ITGα6-hDPSCs. Treatment with Y-27632 inhibited the effect of ITGα6 depletion on hDPSCs stemness, rearranged the cytoskeleton, promoted the pluripotency, proliferation ability, and inhibited the differentiation. CONCLUSION ITGα6 promotes hDPSCs stemness via inhibiting RHO/ROCK and restoring cytoskeleton.
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Affiliation(s)
- Weiwei Zhang
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
| | - Jingling Shen
- Institute of Life Science, Wenzhou University, Wenzhou, China
| | - Shuang Zhang
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
| | - Xu Liu
- Department of Stomatology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuang Pan
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
| | - Yanping Li
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
| | - Lin Zhang
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
| | - Lina He
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
| | - Yumei Niu
- Department of Endodontics, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Endodontics, School of Stomatology, Harbin Medical University, Harbin, China
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8
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Houdelet C, Sinpoo C, Chantaphanwattana T, Voisin SN, Bocquet M, Chantawannakul P, Bulet P. Proteomics of Anatomical Sections of the Gut of Nosema-Infected Western Honeybee ( Apis mellifera) Reveals Different Early Responses to Nosema spp. Isolates. J Proteome Res 2020; 20:804-817. [PMID: 33305956 DOI: 10.1021/acs.jproteome.0c00658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Honeybees play an important role in pollinating native plants and agricultural crops and produce valuable hive products. Within the last decade, honeybee colonies have been reported to be in decline, due to both biotic and abiotic stress factors including pathogens and pesticides. This study evaluated the impact of different isolates of Nosema spp. [Nosema apis spores (NA), Nosema ceranae from Apis mellifera from France (NF), N. ceranae from Apis cerana from Thailand (NC1), and N. ceranae from A. mellifera from Thailand (NC2)] on the different gut sections of newly emerged adult A. mellifera bees. With an attempt to decipher the early impact of Nosema spp. on the first barrier against Nosema infection, we used off-gel bottom-up proteomics on the different anatomical sections of the gut four days post inoculation. A total of 2185 identified proteins in the esophagus, 2095 in the crop, 1571 in the midgut, 2552 in the ileum, and 3173 in the rectum were obtained. Using label-free quantification, we observed that the response of the host varies according to the Nosema spp. (N. apis versus N. ceranae) and the geographical origin of Nosema. The proteins in the midgut of A. mellifera, orally inoculated with spores of N. ceranae isolated from France, were the most altered, when compared with controls, exhibiting 50 proteins down-regulated and 16 up-regulated. We thereby established the first mass-spectrometry-based proteomics of different anatomical sections of the gut tissue of Nosema-infected A. mellifera four days post inoculation, following infection by different isolates of Nosema spp. that provoked differential host responses. We reported an alteration of proteins involved in the metabolic pathways and specifically eight proteins of the oxidative phosphorylation pathway. More importantly, we propose that the collagen IV NC1 domain-containing protein may represent an early prognostic marker of the impact of Nosema spores on the A. mellifera health status. Data are available via ProteomeXchange with the identifier PXD021848.
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Affiliation(s)
- Camille Houdelet
- CR University Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, 38000 Grenoble, France.,Plateform BioPark Archamps, 260 Avenue Marie Curie, Archparc, 74166 Saint Julien-en Genevois, France
| | - Chainarong Sinpoo
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Sébastien N Voisin
- Plateform BioPark Archamps, 260 Avenue Marie Curie, Archparc, 74166 Saint Julien-en Genevois, France
| | | | - Panuwan Chantawannakul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Philippe Bulet
- CR University Grenoble Alpes, Institute for Advanced Biosciences, Inserm U1209, CNRS UMR 5309, 38000 Grenoble, France.,Plateform BioPark Archamps, 260 Avenue Marie Curie, Archparc, 74166 Saint Julien-en Genevois, France
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9
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Funk MC, Zhou J, Boutros M. Ageing, metabolism and the intestine. EMBO Rep 2020; 21:e50047. [PMID: 32567155 PMCID: PMC7332987 DOI: 10.15252/embr.202050047] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/18/2020] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
The intestinal epithelium serves as a dynamic barrier to the environment and integrates a variety of signals, including those from metabolites, commensal microbiota, immune responses and stressors upon ageing. The intestine is constantly challenged and requires a high renewal rate to replace damaged cells in order to maintain its barrier function. Essential for its renewal capacity are intestinal stem cells, which constantly give rise to progenitor cells that differentiate into the multiple cell types present in the epithelium. Here, we review the current state of research of how metabolism and ageing control intestinal stem cell function and epithelial homeostasis. We focus on recent insights gained from model organisms that indicate how changes in metabolic signalling during ageing are a major driver for the loss of stem cell plasticity and epithelial homeostasis, ultimately affecting the resilience of an organism and limiting its lifespan. We compare findings made in mouse and Drosophila and discuss differences and commonalities in the underlying signalling pathways and mechanisms in the context of ageing.
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Affiliation(s)
- Maja C Funk
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
| | - Jun Zhou
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg University, Heidelberg, Germany
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10
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Gao N, Wang J, Zhang Q, Zhou T, Mu W, Hou P, Wang D, Lv X, Li A. Aberrant Distributions of Collagen I, III, and IV in Hirschsprung Disease. J Pediatr Gastroenterol Nutr 2020; 70:450-456. [PMID: 31939867 DOI: 10.1097/mpg.0000000000002627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is the most common congenital gut motility disorder, involving a severe anomaly of the enteric nervous system, and is characterized by functional intestinal obstruction due to lack of intrinsic innervation (aganglionosis) in the distal bowel. OBJECTIVE The aim of this study was to examine the distribution patterns of collagens I (Col I), III (Col III), and IV (Col IV) in the enteric nervous system of HSCR patients, to determine whether or not collagen levels are altered in the aganglionic bowel. METHODS We measured the expression levels of Col I, Col III, and Col IV in colonic muscle from 129 children with HSCR. The localizations of the 3 collagens and myenteric ganglia were assessed morphologically by immunofluorescence staining. western blots and real-time fluorescence quantitative polymerase chain reaction were performed to examine the relative levels of these collagens in aganglionic, transitional, and ganglionic colon segments. RESULTS Immunoreactivities of Col I and Col III were high around and within myenteric ganglia in the ganglionic segment, moderate in the transitional segment, and weak in the aganglionic segment. Col IV immunoreactivity showed the opposite pattern, being lowest in the ganglionic segment and highest in the aganglionic segment. CONCLUSION Col I and Col III are decreased and Col IV is increased in the distal colon of patients with HSCR.
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Affiliation(s)
- Ni Gao
- Department of Pediatric Surgery, Qilu Hospital, Shandong University, Jinan, Shandong Province, China
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11
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Hughes CJR, Turner S, Andrews RM, Vitkin A, Jacobs JR. Matrix metalloproteinases regulate ECM accumulation but not larval heart growth in Drosophila melanogaster. J Mol Cell Cardiol 2020; 140:42-55. [PMID: 32105665 DOI: 10.1016/j.yjmcc.2020.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/12/2020] [Accepted: 02/19/2020] [Indexed: 02/06/2023]
Abstract
The Drosophila heart provides a simple model to examine the remodelling of muscle insertions with growth, extracellular matrix (ECM) turnover, and fibrosis. Between hatching and pupation, the Drosophila heart increases in length five-fold. If major cardiac ECM components are secreted remotely, how is ECM "self assembly" regulated? We explored whether ECM proteases were required to maintain the morphology of a growing heart while the cardiac ECM expanded. An increase in expression of Drosophila's single tissue inhibitor of metalloproteinase (TIMP), or reduced function of metalloproteinase MMP2, resulted in fibrosis and ectopic deposition of two ECM Collagens; type-IV and fibrillar Pericardin. Significant accumulations of Collagen-IV (Viking) developed on the pericardium and in the lumen of the heart. Congenital defects in Pericardin deposition misdirected further assembly in the larva. Reduced metalloproteinase activity during growth also increased Pericardin fibre accumulation in ECM suspending the heart. Although MMP2 expression was required to remodel and position cardiomyocyte cell junctions, reduced MMP function did not impair expansion of the heart. A previous study revealed that MMP2 negatively regulates the size of the luminal cell surface in the embryonic heart. Cardiomyocytes align at the midline, but do not adhere to enclose a heart lumen in MMP2 mutant embryos. Nevertheless, these embryos hatch and produce viable larvae with bifurcated hearts, indicating a secondary pathway to lumen formation between ipsilateral cardiomyocytes. MMP-mediated remodelling of the ECM is required for organogenesis, and to prevent assembly of excess or ectopic ECM protein during growth. MMPs are not essential for normal growth of the Drosophila heart.
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Affiliation(s)
- C J R Hughes
- Dept. Biology, McMaster University, Hamilton, Canada.
| | - S Turner
- Dept. Biology, McMaster University, Hamilton, Canada.
| | - R M Andrews
- Dept. Biology, McMaster University, Hamilton, Canada.
| | - A Vitkin
- Dept. Biomedical Physics, University of Toronto, Toronto, Cananda.
| | - J R Jacobs
- Dept. Biology, McMaster University, Hamilton, Canada.
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Davis MN, Horne-Badovinac S, Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biol Plus 2019; 4:100015. [PMID: 33543012 PMCID: PMC7852309 DOI: 10.1016/j.mbplus.2019.100015] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 01/02/2023] Open
Abstract
The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans. Using a similar approach, we report here that our pipeline has identified 641 genes constituting the Drosophila matrisome. We further classify these genes into different structural and functional categories, including an expanded way to classify genes encoding proteins forming apical ECMs. We illustrate how having a comprehensive list of Drosophila matrisome proteins can be used to annotate large proteomic datasets and identify unsuspected roles for the ECM in pathophysiological processes. Last, to aid the dissemination and usage of the proposed definition and categorization of the Drosophila matrisome by the scientific community, our list has been made available through three public portals: The Matrisome Project (http://matrisome.org), The FlyBase (https://flybase.org/), and GLAD (https://www.flyrnai.org/tools/glad/web/).
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Affiliation(s)
- Martin N. Davis
- Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612, USA
| | - Sally Horne-Badovinac
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott Avenue, Chicago, IL 60612, USA
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Type IV Collagen Is Essential for Proper Function of Integrin-Mediated Adhesion in Drosophila Muscle Fibers. Int J Mol Sci 2019; 20:ijms20205124. [PMID: 31623094 PMCID: PMC6829409 DOI: 10.3390/ijms20205124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/09/2019] [Accepted: 10/13/2019] [Indexed: 01/18/2023] Open
Abstract
Congenital muscular dystrophy (CMD), a subgroup of myopathies is a genetically and clinically heterogeneous group of inherited muscle disorders and is characterized by progressive muscle weakness, fiber size variability, fibrosis, clustered necrotic fibers, and central myonuclei present in regenerating muscle. Type IV collagen (COL4A1) mutations have recently been identified in patients with intracerebral, vascular, renal, ophthalmologic pathologies and congenital muscular dystrophy, consistent with diagnoses of Walker–Warburg Syndrome or Muscle–Eye–Brain disease. Morphological characteristics of muscular dystrophy have also been demonstrated Col4a1 mutant mice. Yet, several aspects of the pathomechanism of COL4A1-associated muscle defects remained largely uncharacterized. Based on the results of genetic, histological, molecular, and biochemical analyses in an allelic series of Drosophila col4a1 mutants, we provide evidence that col4a1 mutations arise by transitions in glycine triplets, associate with severely compromised muscle fibers within the single-layer striated muscle of the common oviduct, characterized by loss of sarcomere structure, disintegration and streaming of Z-discs, indicating an essential role for the COL4A1 protein. Features of altered cytoskeletal phenotype include actin bundles traversing over sarcomere units, amorphous actin aggregates, atrophy, and aberrant fiber size. The mutant COL4A1-associated defects appear to recapitulate integrin-mediated adhesion phenotypes observed in RNA-inhibitory Drosophila. Our results provide insight into the mechanistic details of COL4A1-associated muscle disorders and suggest a role for integrin-collagen interaction in the maintenance of sarcomeres.
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Dissection of Nidogen function in Drosophila reveals tissue-specific mechanisms of basement membrane assembly. PLoS Genet 2018; 14:e1007483. [PMID: 30260959 PMCID: PMC6177204 DOI: 10.1371/journal.pgen.1007483] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/09/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022] Open
Abstract
Basement membranes (BMs) are thin sheet-like specialized extracellular matrices found at the basal surface of epithelia and endothelial tissues. They have been conserved across evolution and are required for proper tissue growth, organization, differentiation and maintenance. The major constituents of BMs are two independent networks of Laminin and Type IV Collagen in addition to the proteoglycan Perlecan and the glycoprotein Nidogen/entactin (Ndg). The ability of Ndg to bind in vitro Collagen IV and Laminin, both with key functions during embryogenesis, anticipated an essential role for Ndg in morphogenesis linking the Laminin and Collagen IV networks. This was supported by results from cultured embryonic tissue experiments. However, the fact that elimination of Ndg in C. elegans and mice did not affect survival strongly questioned this proposed linking role. Here, we have isolated mutations in the only Ndg gene present in Drosophila. We find that while, similar to C.elegans and mice, Ndg is not essential for overall organogenesis or viability, it is required for appropriate fertility. We also find, alike in mice, tissue-specific requirements of Ndg for proper assembly and maintenance of certain BMs, namely those of the adipose tissue and flight muscles. In addition, we have performed a thorough functional analysis of the different Ndg domains in vivo. Our results support an essential requirement of the G3 domain for Ndg function and unravel a new key role for the Rod domain in regulating Ndg incorporation into BMs. Furthermore, uncoupling of the Laminin and Collagen IV networks is clearly observed in the larval adipose tissue in the absence of Ndg, indeed supporting a linking role. In light of our findings, we propose that BM assembly and/or maintenance is tissue-specific, which could explain the diverse requirements of a ubiquitous conserved BM component like Nidogen. Basement membranes (BMs) are thin layers of specialized extracellular matrices present in every tissue of the human body. Its main constituents are two networks of laminin and Type IV Collagen linked by Nidogen (Ndg) and proteoglycans. They form an organized scaffold that regulates organ morphogenesis and function. Mutations affecting BM components are associated with organ dysfunction and several congenital diseases. Thus, a better comprehension of BM assembly and maintenance will not only help to learn more about organogenesis but also to a better understanding and, hopefully, treatment of these diseases. Here, we have used the fruit fly Drosophila to analyse the role of Ndg in BM formation in vivo. Elimination of Ndg in worms and mice does not affect survival, strongly questioning its proposed linking role, derived from in vitro experiments. Here, we show that in the fly, Ndg is dispensable for BM assembly and preservation in many tissues, but absolutely required in others. Furthermore, our functional study of the different Ndg domains challenges the significance of some interactions between BM components derived from in vitro experiments, while confirming others, and reveals a new key requirement for the Rod domain in Ndg function and incorporation into BMs.
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4-Hydroxy-2-nonenal Alkylated and Peroxynitrite Nitrated Proteins Localize to the Fused Mitochondria in Malpighian Epithelial Cells of Type IV Collagen Drosophila Mutants. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3502401. [PMID: 29651426 PMCID: PMC5832051 DOI: 10.1155/2018/3502401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/03/2017] [Accepted: 01/02/2018] [Indexed: 11/18/2022]
Abstract
Background. Human type IV collagenopathy is associated with mutations within the COL4A1 and to a less extent the COL4A2 genes. The proteins encoded by these genes form heterotrimers and are the highest molar ratio components of the ubiquitous basement membrane. The clinical manifestations of the COL4A1/A2 mutations are systemic affecting many tissues and organs among these kidneys. In order to uncover the cellular and biochemical alterations associated with aberrant type IV collagen, we have explored the phenotype of the Malpighian tubules, the secretory organ and insect kidney model, in col4a1 collagen gene mutants of the fruit fly Drosophila melanogaster. In Malpighian epithelial cells of col4a1 mutants, robust mitochondrial fusion indicated mutation-induced stress. Immunohistochemistry detected proteins nitrated by peroxynitrite that localized to the enlarged mitochondria and increased level of membrane peroxidation, assessed by the amount of proteins alkylated by 4-hydroxy-2-nonenal that similarly localized to the fused mitochondria. Nuclei within the Malpighian epithelium showed TUNEL-positivity suggesting cell degradation. The results demonstrated that col4a1 mutations affect the epithelia and, consequently, secretory function of the Malpighian tubules and provide mechanistic insight into col4a1 mutation-associated functional impairments not yet reported in human patients and in mouse models with mutant COL4A1.
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Chioran A, Duncan S, Catalano A, Brown TJ, Ringuette MJ. Collagen IV trafficking: The inside-out and beyond story. Dev Biol 2017; 431:124-133. [PMID: 28982537 DOI: 10.1016/j.ydbio.2017.09.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 09/28/2017] [Accepted: 09/29/2017] [Indexed: 12/20/2022]
Abstract
Collagen IV networks endow basement membranes (BMs) with remarkable tensile strength and function as morphoregulatory substrata for diverse tissue-specific developmental events. A complex repertoire of intracellular and extracellular molecular interactions are required for collagen IV secretion and supramolecular assembly into BMs. These include intracellular chaperones such as Heat shock protein 47 (Hsp47) and the chaperone-binding trafficking protein Transport and Golgi organization protein 1 (Tango1). Mutations in these proteins lead to compromised collagen IV protomer stability and secretion, leading to defective BM assembly and function. In addition to intracellular chaperones, a role for extracellular chaperones orchestrating the transport, supramolecular assembly, and architecture of collagen IV in BM is emerging. We present evidence derived from evolutionarily distant model organisms that supports an extracellular collagen IV chaperone-like activity for the matricellular protein SPARC (Secreted Protein, Acidic, Rich in Cysteine). Loss of SPARC disrupts BM homeostasis and compromises tissue biomechanics and physiological function. Thus, the combined contributions of intracellular and extracellular collagen IV-associated chaperones and chaperone-like proteins are critical to ensure proper secretion and stereotypic assembly of collagen IV networks in BMs.
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Affiliation(s)
- Alexa Chioran
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5
| | - Sebastian Duncan
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5
| | | | - Theodore J Brown
- Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON, Canada
| | - Maurice J Ringuette
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5.
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Cathepsin B Regulates Collagen Expression by Fibroblasts via Prolonging TLR2/NF-κB Activation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:7894247. [PMID: 27648120 PMCID: PMC5018341 DOI: 10.1155/2016/7894247] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/29/2016] [Accepted: 08/08/2016] [Indexed: 12/29/2022]
Abstract
Fibroblasts are essential for tissue repair due to producing collagens, and lysosomal proteinase cathepsin B (CatB) is involved in promoting chronic inflammation. We herein report that CatB regulates the expression of collagens III and IV by fibroblasts in response to a TLR2 agonist, lipopolysaccharide from Porphyromonas gingivalis (P.g. LPS). In cultured human BJ fibroblasts, mRNA expression of CatB was significantly increased, while that of collagens III and IV was significantly decreased at 24 h after challenge with P.g. LPS (1 μg/mL). The P.g. LPS-decreased collagen expression was completely inhibited by CA-074Me, the specific inhibitor of CatB. Surprisingly, expression of collagens III and IV was significantly increased in the primary fibroblasts from CatB-deficient mice after challenge with P.g. LPS. The increase of CatB was accompanied with an increase of 8-hydroxy-2′-deoxyguanosine (8-OHdG) and a decrease of IκBα. Furthermore, the P.g. LPS-increased 8-OHdG and decreased IκBα were restored by CA-074Me. Moreover, 87% of CatB and 86% of 8-OHdG were colocalized with gingival fibroblasts of chronic periodontitis patients. The findings indicate the critical role of CatB in regulating the expression of collagens III and IV by fibroblasts via prolonging TLR2/NF-κB activation and oxidative stress. CatB-specific inhibitors may therefore improve chronic inflammation-delayed tissue repair.
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Kiss AA, Popovics N, Szabó G, Csiszár K, Mink M. Altered stress fibers and integrin expression in the Malpighian epithelium of Drosophila type IV collagen mutants. Data Brief 2016; 7:868-72. [PMID: 27077087 PMCID: PMC4816910 DOI: 10.1016/j.dib.2016.03.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/08/2016] [Accepted: 03/15/2016] [Indexed: 12/30/2022] Open
Abstract
Basement membranes (BMs) are highly specialized extracellular matrices (ECMs) that provide support and polarization cues for epithelial cells. Proper adhesion to the BM is pivotal in epithelial cell function and survival. Type IV collagens are the predominant components of all types of BMs, that form an irregular, polygonal lattice and serve as a scaffold for numerous other BM components and BM-associated cells. Mutations in the ubiquitous human BM components COL4A1 and COL4A2 cause a multisystem disorder involving nephropathy. Affected patients develop renal dysfunction and chronic kidney failure with or without hematuria. Mouse Col4a1 and Col4a2 mutants recapitulate the human symptoms. In vertebrates, excretion is accomplished by the kidneys and by the Malpighian tubules in insects, including the fruit fly Drosophila. Our present results with dominant, temperature-sensitive mutation of the Drosophila col4a1 gene demonstrate altered integrin expression and amplified effects of mechanical stress on the Malpighian epithelial cytoskeleton.
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Affiliation(s)
- András A. Kiss
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
| | - Nikoletta Popovics
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
| | - Gábor Szabó
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
| | - Katalin Csiszár
- John A. Burns School of Medicine, University of Hawaii, 1960 East West Road, Honolulu, HI 96822, USA
| | - Mátyás Mink
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
- Corresponding author. Tel.: +36 62 544269; fax: +36 62 544651.
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