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Labelle-Dumais C, Mazur C, Kaya S, Obata Y, Lee B, Acevedo C, Alliston T, Gould DB. Skeletal pathology in mouse models of Gould syndrome is partially alleviated by genetically reducing TGFβ signaling. Matrix Biol 2024; 133:1-13. [PMID: 39097038 DOI: 10.1016/j.matbio.2024.07.005] [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: 05/25/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Skeletal defects are hallmark features of many extracellular matrix (ECM) and collagen-related disorders. However, a biological function in bone has never been defined for the highly evolutionarily conserved type IV collagen. Collagen type IV alpha 1 (COL4A1) and alpha 2 (COL4A2) form α1α1α2 (IV) heterotrimers that represent a fundamental basement membrane constituent present in every organ of the body, including the skeleton. COL4A1 and COL4A2 mutations cause Gould syndrome, a variable and clinically heterogenous multisystem disorder generally characterized by the presence of cerebrovascular disease with ocular, renal, and muscular manifestations. We have previously identified elevated TGFβ signaling as a pathological insult resulting from Col4a1 mutations and demonstrated that reducing TGFβ signaling ameliorate ocular and cerebrovascular phenotypes in Col4a1 mutant mouse models of Gould syndrome. In this study, we describe the first characterization of skeletal defects in Col4a1 mutant mice that include a developmental delay in osteogenesis and structural, biomechanical and vascular alterations of mature bones. Using distinct mouse models, we show that allelic heterogeneity influences the presentation of skeletal pathology resulting from Col4a1 mutations. Importantly, we found that TGFβ target gene expression is elevated in developing bones from Col4a1 mutant mice and show that genetically reducing TGFβ signaling partially ameliorates skeletal manifestations. Collectively, these findings identify a novel and unsuspected role for type IV collagen in bone biology, expand the spectrum of manifestations associated with Gould syndrome to include skeletal abnormalities, and implicate elevated TGFβ signaling in skeletal pathogenesis in Col4a1 mutant mice.
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Affiliation(s)
- Cassandre Labelle-Dumais
- Departments of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Courtney Mazur
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, 94143, USA; UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - Serra Kaya
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Yoshihiro Obata
- Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Bryson Lee
- Departments of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Claire Acevedo
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, 94143, USA; Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, 94143, USA; UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA 94143, USA
| | - Douglas B Gould
- Departments of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, Institute for Human Genetics, Bakar Aging Research Institute, and Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143, USA.
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Joshi A, Nigam A, Narayan Mudgal L, Mondal B, Basak T. ColPTMScape: An open access knowledge base for tissue-specific collagen PTM maps. Matrix Biol Plus 2024; 22:100144. [PMID: 38469247 PMCID: PMC10926295 DOI: 10.1016/j.mbplus.2024.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Collagen is a key component of the extracellular matrix (ECM). In the remodeling of ECM, a remarkable variation in collagen post-translational modifications (PTMs) occurs. This makes collagen a potential target for understanding extracellular matrix remodeling during pathological conditions. Over the years, scientists have gathered a huge amount of data about collagen PTM during extracellular matrix remodeling. To make such information easily accessible in a consolidated space, we have developed ColPTMScape (https://colptmscape.iitmandi.ac.in/), a dedicated knowledge base for collagen PTMs. The identified site-specific PTMs, quantitated PTM sites, and PTM maps of collagen chains are deliverables to the scientific community, especially to matrix biologists. Through this knowledge base, users can easily gain information related to the difference in the collagen PTMs across different tissues in different organisms.
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Affiliation(s)
- Ashutosh Joshi
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Ayush Nigam
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Lalit Narayan Mudgal
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Bhaskar Mondal
- School of Chemical Sciences, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Mandi, Himachal Pradesh 175075, India
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Mousa M, Albarguthi S, Albreiki M, Farooq Z, Sajid S, El Hajj Chehadeh S, ElBait GD, Tay G, Deeb AA, Alsafar H. Whole-Exome Sequencing in Family Trios Reveals De Novo Mutations Associated with Type 1 Diabetes Mellitus. BIOLOGY 2023; 12:biology12030413. [PMID: 36979105 PMCID: PMC10044903 DOI: 10.3390/biology12030413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease characterized by insulin deficiency and loss of pancreatic islet β-cells. The objective of this study is to identify de novo mutations in 13 trios from singleton families that contribute to the genetic basis of T1DM through the application of whole-exome sequencing (WES). Of the 13 families sampled for this project, 12 had de novo variants, with Family 7 having the highest number (nine) of variants linked to T1DM/autoimmune pathways, whilst Family 4 did not have any variants past the filtering steps. There were 10 variants of 7 genes reportedly associated with T1DM (MST1; TDG; TYRO3; IFIHI; GLIS3; VEGFA; TYK2). There were 20 variants of 13 genes that were linked to endocrine, metabolic, or autoimmune diseases. Our findings demonstrate that trio-based WES is a powerful approach for identifying new candidate genes for the pathogenesis of T1D. Genotyping and functional annotation of the discovered de novo variants in a large cohort is recommended to ascertain their association with disease pathogenesis.
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Affiliation(s)
- Mira Mousa
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Sara Albarguthi
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Mohammed Albreiki
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Zenab Farooq
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Sameeha Sajid
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
| | - Sarah El Hajj Chehadeh
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Gihan Daw ElBait
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Guan Tay
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Asma Al Deeb
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates
- Department of Endocrinology, Mafraq Hospital, Abu Dhabi 127788, United Arab Emirates
| | - Habiba Alsafar
- Center of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
- Correspondence:
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Wang S, He L, Xiao F, Gao M, Wei H, Yang J, Shu Y, Zhang F, Ye X, Li P, Hao X, Zhou X, Wei H. Upregulation of GLT25D1 in Hepatic Stellate Cells Promotes Liver Fibrosis via the TGF-β1/SMAD3 Pathway In Vivo and In vitro. J Clin Transl Hepatol 2023; 11:1-14. [PMID: 36406310 PMCID: PMC9647113 DOI: 10.14218/jcth.2022.00005] [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] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND AND AIMS Collagen β(1-O) galactosyltransferase 25 domain 1 (GLT25D1) is associated with collagen production and glycosylation, and its knockout in mice results in embryonic death. However, its role in liver fibrosis remains elusive, particularly in hepatic stellate cells (HSCs), the primary collagen-producing cells associated with liver fibrogenesis. Herein, we aimed to elucidate the role of GLT25D1 in HSCs. METHODS Bile duct ligation (BDL)-induced mouse liver fibrosis models, primary mouse HSCs (mHSCs), and transforming growth factor beta 1 (TGF-β1)-stimulated LX-2 human hepatic stellate cells were used in in vivo and in vitro studies. Stable LX-2 cell lines with either GLT25D1 overexpression or knockdown were established using lentiviral transfection. RNA-seq was performed to investigate the genomic differences. HPLC-MS/MS were used to identify glycosylation sites. Scanning electronic microscopy (SEM) and second-harmonic generation/two-photon excited fluorescence (SHG/TPEF) were used to image collagen fibril morphology. RESULTS GLT25D1 expression was upregulated in nonparenchymal cells in human cirrhotic liver tissues. Meanwhile, its knockdown attenuated collagen deposition in BDL-induced mouse liver fibrosis and inhibited mHSC activation. GLT25D1 was overexpressed in activated versus quiescence LX-2 cells and regulated in vitro LX-2 cell activation, including proliferation, contraction, and migration. GLT25D1 also significantly increased liver fibrogenic gene and protein expression. GLT25D1 upregulation promoted HSC activation and enhanced collagen expression through the TGF-β1/SMAD signaling pathway. Mass spectrometry showed that GLT25D1 regulated the glycosylation of collagen in HSCs, affecting the diameter of collagen fibers. CONCLUSIONS Collectively, the upregulation of GLT25D1 in HSCs promoted the progression of liver fibrosis by affecting HSCs activation and collagen stability.
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Affiliation(s)
- Shiwei Wang
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Lingling He
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fan Xiao
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Meixin Gao
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Herui Wei
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Junru Yang
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Yang Shu
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fuyang Zhang
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Ye
- Department of Gastroenterology, Beijing Huaxin Hospital, the First Affiliated Hospital of Tsinghua University, Beijing, China
| | - Ping Li
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaohua Hao
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xingang Zhou
- Department of Pathology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Hongshan Wei
- Department of Gastroenterology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Department of Gastroenterology, Peking University Ditan Teaching Hospital, Beijing, China
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Liu B, Kong Y, Alimi OA, Kuss MA, Tu H, Hu W, Rafay A, Vikas K, Shi W, Lerner M, Berry WL, Li Y, Carlson MA, Duan B. Multifunctional Microgel-Based Cream Hydrogels for Postoperative Abdominal Adhesion Prevention. ACS NANO 2023; 17:3847-3864. [PMID: 36779870 PMCID: PMC10820954 DOI: 10.1021/acsnano.2c12104] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Postoperative abdominal adhesions are a common problem after surgery and can produce serious complications. Current antiadhesive strategies focus mostly on physical barriers and are unsatisfactory and inefficient. In this study, we designed and synthesized advanced injectable cream-like hydrogels with multiple functionalities, including rapid gelation, self-healing, antioxidation, anti-inflammation, and anti-cell adhesion. The multifunctional hydrogels were facilely formed by the conjugation reaction of epigallocatechin-3-gallate (EGCG) and hyaluronic acid (HA)-based microgels and poly(vinyl alcohol) (PVA) based on the dynamic boronic ester bond. The physicochemical properties of the hydrogels including antioxidative and anti-inflammatory activities were systematically characterized. A mouse cecum-abdominal wall adhesion model was implemented to investigate the efficacy of our microgel-based hydrogels in preventing postoperative abdominal adhesions. The hydrogels, with a high molecular weight HA, significantly decreased the inflammation, oxidative stress, and fibrosis and reduced the abdominal adhesion formation, compared to the commercial Seprafilm group or Injury-only group. Label-free quantitative proteomics analysis demonstrated that S100A8 and S100A9 expressions were associated with adhesion formation; the microgel-containing hydrogels inhibited these expressions. The microgel-containing hydrogels with multifunctionality decreased the formation of postoperative intra-abdominal adhesions in a murine model, demonstrating promise for clinical applications.
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Affiliation(s)
- Bo Liu
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Yunfan Kong
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Olawale A. Alimi
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Mitchell A. Kuss
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Huiyin Tu
- Department of Emergency Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wenfeng Hu
- Department of Emergency Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Abu Rafay
- Mass Spectrometry & Proteomics Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kumar Vikas
- Mass Spectrometry & Proteomics Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wen Shi
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Megan Lerner
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - William L. Berry
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Yulong Li
- Department of Emergency Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Mark A. Carlson
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Surgery-General Surgery, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Bin Duan
- Mary & Dick Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Division of Cardiology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Surgery-General Surgery, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Mechanical and Materials Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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Zhang J, Wen H, Qi X, Zhang Y, Dong X, Zhang K, Zhang M, Li J, Li Y. Morphological and Molecular Responses of Lateolabrax maculatus Skeletal Muscle Cells to Different Temperatures. Int J Mol Sci 2022; 23:ijms23179812. [PMID: 36077203 PMCID: PMC9456278 DOI: 10.3390/ijms23179812] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
Temperature strongly modulates muscle development and growth in ectothermic teleosts; however, the underlying mechanisms remain largely unknown. In this study, primary cultures of skeletal muscle cells of Lateolabrax maculatus were conducted and reared at different temperatures (21, 25, and 28 °C) in both the proliferation and differentiation stages. CCK-8, EdU, wound scratch and nuclear fusion index assays revealed that the proliferation, myogenic differentiation, and migration processes of skeletal muscle cells were significantly accelerated as the temperature raises. Based on the GO, GSEA, and WGCNA, higher temperature (28 °C) induced genes involved in HSF1 activation, DNA replication, and ECM organization processes at the proliferation stage, as well as HSF1 activation, calcium activity regulation, myogenic differentiation, and myoblast fusion, and sarcomere assembly processes at the differentiation stage. In contrast, lower temperature (21 °C) increased the expression levels of genes associated with DNA damage, DNA repair and apoptosis processes at the proliferation stage, and cytokine signaling and neutrophil degranulation processes at the differentiation stage. Additionally, we screened several hub genes regulating myogenesis processes. Our results could facilitate the understanding of the regulatory mechanism of temperature on fish skeletal muscle growth and further contribute to utilizing rational management strategies and promoting organism growth and development.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yun Li
- Correspondence: ; Tel.: +86-0532-82-031-792
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7
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Sarohi V, Srivastava S, Basak T. Comprehensive Mapping and Dynamics of Site-Specific Prolyl-Hydroxylation, Lysyl-Hydroxylation and Lysyl O-Glycosylation of Collagens Deposited in ECM During Zebrafish Heart Regeneration. Front Mol Biosci 2022; 9:892763. [PMID: 35782869 PMCID: PMC9245515 DOI: 10.3389/fmolb.2022.892763] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 12/30/2022] Open
Abstract
Cardiac fibrosis-mediated heart failure (HF) is one of the major forms of end-stage cardiovascular diseases (CVDs). Cardiac fibrosis is an adaptive response of the myocardium upon any insult/injury. Excessive deposition of collagen molecules in the extracellular matrix (ECM) is the hallmark of fibrosis. This fibrotic response initially protects the myocardium from ventricular rupture. Although in mammals this fibrotic response progresses towards scar-tissue formation leading to HF, some fishes and urodeles have mastered the art of cardiac regeneration following injury-mediated fibrotic response. Zebrafish have a unique capability to regenerate the myocardium after post-amputation injury. Following post-amputation, the ECM of the zebrafish heart undergoes extensive remodeling and deposition of collagen. Being the most abundant protein of ECM, collagen plays important role in the assembly and cell-matrix interactions. However, the mechanism of ECM remodeling is not well understood. Collagen molecules undergo heavy post-translational modifications (PTMs) mainly hydroxylation of proline, lysine, and glycosylation of lysine during biosynthesis. The critical roles of these PTMs are emerging in several diseases, embryonic development, cell behavior regulation, and cell-matrix interactions. The site-specific identification of these collagen PTMs in zebrafish heart ECM is not known. As these highly modified peptides are not amenable to mass spectrometry (MS), the site-specific identification of these collagen PTMs is challenging. Here, we have implemented our in-house proteomics analytical pipeline to analyze two ECM proteomics datasets (PXD011627, PXD010092) of the zebrafish heart during regeneration (post-amputation). We report the first comprehensive site-specific collagen PTM map of zebrafish heart ECM. We have identified a total of 36 collagen chains (19 are reported for the first time here) harboring a total of 95 prolyl-3-hydroxylation, 108 hydroxylysine, 29 galactosyl-hydroxylysine, and 128 glucosylgalactosyl-hydroxylysine sites. Furthermore, we comprehensively map the three chains (COL1A1a, COL1A1b, and COL1A2) of collagen I, the most abundant protein in zebrafish heart ECM. We achieved more than 95% sequence coverage for all the three chains of collagen I. Our analysis also revealed the dynamics of prolyl-3-hydroxylation occupancy oscillations during heart regeneration at these sites. Moreover, quantitative site-specific analysis of lysine-O-glycosylation microheterogeneity during heart regeneration revealed a significant (p < 0.05) elevation of site-specific (K1017) glucosylgalactosyl-hydroxylysine on the col1a1a chain. Taken together, these site-specific PTM maps and the dynamic changes of site-specific collagen PTMs in ECM during heart regeneration will open up new avenues to decode ECM remodeling and may lay the foundation to tinker the cardiac regeneration process with new approaches.
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Affiliation(s)
- Vivek Sarohi
- School of Biosciences and Bioengineering (BSBE), Indian Institute of Technology (IIT)- Mandi, Mandi, India
- BioX Center, IIT-Mandi, Mandi, India
| | - Shriya Srivastava
- School of Biosciences and Bioengineering (BSBE), Indian Institute of Technology (IIT)- Mandi, Mandi, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering (BSBE), Indian Institute of Technology (IIT)- Mandi, Mandi, India
- BioX Center, IIT-Mandi, Mandi, India
- *Correspondence: Trayambak Basak,
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8
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Detection of Target Genes for Drug Repurposing to Treat Skeletal Muscle Atrophy in Mice Flown in Spaceflight. Genes (Basel) 2022; 13:genes13030473. [PMID: 35328027 PMCID: PMC8953707 DOI: 10.3390/genes13030473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle atrophy is a common condition in aging, diabetes, and in long duration spaceflights due to microgravity. This article investigates multi-modal gene disease and disease drug networks via link prediction algorithms to select drugs for repurposing to treat skeletal muscle atrophy. Key target genes that cause muscle atrophy in the left and right extensor digitorum longus muscle tissue, gastrocnemius, quadriceps, and the left and right soleus muscles are detected using graph theoretic network analysis, by mining the transcriptomic datasets collected from mice flown in spaceflight made available by GeneLab. We identified the top muscle atrophy gene regulators by the Pearson correlation and Bayesian Markov blanket method. The gene disease knowledge graph was constructed using the scalable precision medicine knowledge engine. We computed node embeddings, random walk measures from the networks. Graph convolutional networks, graph neural networks, random forest, and gradient boosting methods were trained using the embeddings, network features for predicting links and ranking top gene-disease associations for skeletal muscle atrophy. Drugs were selected and a disease drug knowledge graph was constructed. Link prediction methods were applied to the disease drug networks to identify top ranked drugs for therapeutic treatment of skeletal muscle atrophy. The graph convolution network performs best in link prediction based on receiver operating characteristic curves and prediction accuracies. The key genes involved in skeletal muscle atrophy are associated with metabolic and neurodegenerative diseases. The drugs selected for repurposing using the graph convolution network method were nutrients, corticosteroids, anti-inflammatory medications, and others related to insulin.
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Boyd A, Montandon M, Wood AJ, Currie PD. FKRP directed fibronectin glycosylation: A novel mechanism giving insights into muscular dystrophies? Bioessays 2022; 44:e2100270. [PMID: 35229908 DOI: 10.1002/bies.202100270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 12/15/2022]
Abstract
The recently uncovered role of Fukutin-related protein (FKRP) in fibronectin glycosylation has challenged our understanding of the basis of disease pathogenesis in the muscular dystrophies. FKRP is a Golgi-resident glycosyltransferase implicated in a broad spectrum of muscular dystrophy (MD) pathologies that are not fully attributable to the well-described α-Dystroglycan hypoglycosylation. By revealing a new role for FKRP in the glycosylation of fibronectin, a modification critical for the development of the muscle basement membrane (MBM) and its associated muscle linkages, new possibilities for understanding clinical phenotype arise. This modification involves an interaction between FKRP and myosin-10, a protein involved in the Golgi organization and function. These observations suggest a FKRP nexus exists that controls two critical aspects to muscle fibre integrity, both fibre stability at the MBM and its elastic properties. This review explores the new potential disease axis in the context of our current knowledge of muscular dystrophies.
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Affiliation(s)
- Andrew Boyd
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Margo Montandon
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Alasdair J Wood
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,EMBL Australia, Monash University, Clayton, Victoria, Australia
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10
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Collagen hydroxylysine glycosylation: non-conventional substrates for atypical glycosyltransferase enzymes. Biochem Soc Trans 2021; 49:855-866. [PMID: 33704379 DOI: 10.1042/bst20200767] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/22/2022]
Abstract
Collagen is a major constituent of the extracellular matrix (ECM) that confers fundamental mechanical properties to tissues. To allow proper folding in triple-helices and organization in quaternary super-structures, collagen molecules require essential post-translational modifications (PTMs), including hydroxylation of proline and lysine residues, and subsequent attachment of glycan moieties (galactose and glucose) to specific hydroxylysine residues on procollagen alpha chains. The resulting galactosyl-hydroxylysine (Gal-Hyl) and less abundant glucosyl-galactosyl-hydroxylysine (Glc-Gal-Hyl) are amongst the simplest glycosylation patterns found in nature and are essential for collagen and ECM homeostasis. These collagen PTMs depend on the activity of specialized glycosyltransferase enzymes. Although their biochemical reactions have been widely studied, several key biological questions about the possible functions of these essential PTMs are still missing. In addition, the lack of three-dimensional structures of collagen glycosyltransferase enzymes hinders our understanding of the catalytic mechanisms producing this modification, as well as the impact of genetic mutations causing severe connective tissue pathologies. In this mini-review, we summarize the current knowledge on the biochemical features of the enzymes involved in the production of collagen glycosylations and the current state-of-the-art methods for the identification and characterization of this important PTM.
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11
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Salo AM, Myllyharju J. Prolyl and lysyl hydroxylases in collagen synthesis. Exp Dermatol 2020; 30:38-49. [PMID: 32969070 DOI: 10.1111/exd.14197] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Collagens are the most abundant proteins in the extracellular matrix. They provide a framework to build organs and tissues and give structural support to make them resistant to mechanical load and forces. Several intra- and extracellular modifications are needed to make functional collagen molecules, intracellular post-translational modifications of proline and lysine residues having key roles in this. In this article, we provide a review on the enzymes responsible for the proline and lysine modifications, that is collagen prolyl 4-hydroxylases, 3-hydroxylases and lysyl hydroxylases, and discuss their biological functions and involvement in diseases.
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Affiliation(s)
- Antti M Salo
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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Bieniasz-Krzywiec P, Martín-Pérez R, Ehling M, García-Caballero M, Pinioti S, Pretto S, Kroes R, Aldeni C, Di Matteo M, Prenen H, Tribulatti MV, Campetella O, Smeets A, Noel A, Floris G, Van Ginderachter JA, Mazzone M. Podoplanin-Expressing Macrophages Promote Lymphangiogenesis and Lymphoinvasion in Breast Cancer. Cell Metab 2019; 30:917-936.e10. [PMID: 31447322 PMCID: PMC7616630 DOI: 10.1016/j.cmet.2019.07.015] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 01/11/2023]
Abstract
Among mammary tumor-infiltrating immune cells, the highest expression of podoplanin (PDPN) is found in a subset of tumor-associated macrophages (TAMs). We hereby demonstrate that PDPN is involved in the attachment of this TAM subset to lymphatic endothelial cells (LECs). Mechanistically, the binding of PDPN to LEC-derived galectin 8 (GAL8) in a glycosylation-dependent manner promotes the activation of pro-migratory integrin β1. When proximal to lymphatics, PDPN-expressing macrophages (PoEMs) stimulate local matrix remodeling and promote vessel growth and lymphoinvasion. Anti-integrin β1 blockade, macrophage-specific Pdpn knockout, or GAL8 inhibition impairs TAM adhesion to LECs, restraining lymphangiogenesis and reducing lymphatic cancer spread. In breast cancer patients, association of PoEMs with tumor lymphatic vessels correlates with incidences of lymph node and distant organ metastasis.
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Affiliation(s)
- Paweł Bieniasz-Krzywiec
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium; Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels B1050, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels B1050, Belgium
| | - Rosa Martín-Pérez
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Manuel Ehling
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Melissa García-Caballero
- Laboratory of Tumor and Developmental Biology, GIGA-Cancer, University of Liège, Sart-Tilman, B4000 Liège, Belgium
| | - Sotiria Pinioti
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Samantha Pretto
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Roel Kroes
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Chiara Aldeni
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Mario Di Matteo
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Hans Prenen
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium; Oncology Department, University Hospital Antwerp, 2650 Edegem, Belgium
| | - María Virginia Tribulatti
- Institute for Research in Biotechnology, National University of San Martín, CONICET, Buenos Aires 1650, Argentina
| | - Oscar Campetella
- Institute for Research in Biotechnology, National University of San Martín, CONICET, Buenos Aires 1650, Argentina
| | - Ann Smeets
- Surgical Oncology Unit, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Agnes Noel
- Laboratory of Tumor and Developmental Biology, GIGA-Cancer, University of Liège, Sart-Tilman, B4000 Liège, Belgium
| | - Giuseppe Floris
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Leuven B3000, Belgium
| | - Jo A Van Ginderachter
- Myeloid Cell Immunology Laboratory, VIB Center for Inflammation Research, Brussels B1050, Belgium; Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels B1050, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium.
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