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Prešern U, Goličnik M. Enzyme Databases in the Era of Omics and Artificial Intelligence. Int J Mol Sci 2023; 24:16918. [PMID: 38069254 PMCID: PMC10707154 DOI: 10.3390/ijms242316918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Enzyme research is important for the development of various scientific fields such as medicine and biotechnology. Enzyme databases facilitate this research by providing a wide range of information relevant to research planning and data analysis. Over the years, various databases that cover different aspects of enzyme biology (e.g., kinetic parameters, enzyme occurrence, and reaction mechanisms) have been developed. Most of the databases are curated manually, which improves reliability of the information; however, such curation cannot keep pace with the exponential growth in published data. Lack of data standardization is another obstacle for data extraction and analysis. Improving machine readability of databases is especially important in the light of recent advances in deep learning algorithms that require big training datasets. This review provides information regarding the current state of enzyme databases, especially in relation to the ever-increasing amount of generated research data and recent advancements in artificial intelligence algorithms. Furthermore, it describes several enzyme databases, providing the reader with necessary information for their use.
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Affiliation(s)
| | - Marko Goličnik
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia;
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2
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Lee J, Guo HF, Wang S, Maghsoud Y, Vázquez-Montelongo EA, Jing Z, Sammons RM, Cho EJ, Ren P, Cisneros GA, Kurie JM, Dalby KN. Unleashing the Potential of 1,3-Diketone Analogues as Selective LH2 Inhibitors. ACS Med Chem Lett 2023; 14:1396-1403. [PMID: 37849534 PMCID: PMC10577891 DOI: 10.1021/acsmedchemlett.3c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
Lysyl hydroxylase 2 (LH2) catalyzes the formation of highly stable hydroxylysine aldehyde-derived collagen cross-links (HLCCs), thus promoting lung cancer metastasis through its capacity to modulate specific types of collagen cross-links within the tumor stroma. Using 1 and 2 from our previous high-throughput screening (HTS) as lead probes, we prepared a series of 1,3-diketone analogues, 1-18, and identified 12 and 13 that inhibit LH2 with IC50's of approximately 300 and 500 nM, respectively. Compounds 12 and 13 demonstrate selectivity for LH2 over LH1 and LH3. Quantum mechanics/molecular mechanics (QM/MM) modeling indicates that the selectivity of 12 and 13 may stem from noncovalent interactions like hydrogen bonding between the morpholine/piperazine rings with the LH2-specific Arg661. Treatment of 344SQ WT cells with 13 resulted in a dose-dependent reduction in their migration potential, whereas the compound did not impede the migration of the same cell line with an LH2 knockout (LH2KO).
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Affiliation(s)
- Juhoon Lee
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Hou-fu Guo
- Department
of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536, United States
| | - Shike Wang
- Department
of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Yazdan Maghsoud
- Department
of Chemistry and Biochemistry, The University
of Texas at Dallas, Richardson, Texas 75080, United States
| | - Erik Antonio Vázquez-Montelongo
- Department
of Physical Medicine and Rehabilitation, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Zhifeng Jing
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Rae M. Sammons
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Eun Jeong Cho
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department
of Biomedical Engineering, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - G. Andrés Cisneros
- Department
of Chemistry and Biochemistry, The University
of Texas at Dallas, Richardson, Texas 75080, United States
- Department
of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jonathan M. Kurie
- Department
of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Kevin N. Dalby
- Division
of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College
of Pharmacy, University of Texas, Austin, Texas 78712, United States
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3
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Mattoteia D, Chiapparino A, Fumagalli M, De Marco M, De Giorgi F, Negro L, Pinnola A, Faravelli S, Roscioli T, Scietti L, Forneris F. Identification of Regulatory Molecular "Hot Spots" for LH/PLOD Collagen Glycosyltransferase Activity. Int J Mol Sci 2023; 24:11213. [PMID: 37446392 DOI: 10.3390/ijms241311213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Hydroxylysine glycosylations are post-translational modifications (PTMs) essential for the maturation and homeostasis of fibrillar and non-fibrillar collagen molecules. The multifunctional collagen lysyl hydroxylase 3 (LH3/PLOD3) and the collagen galactosyltransferase GLT25D1 are the human enzymes that have been identified as being responsible for the glycosylation of collagen lysines, although a precise description of the contribution of each enzyme to these essential PTMs has not yet been provided in the literature. LH3/PLOD3 is thought to be capable of performing two chemically distinct collagen glycosyltransferase reactions using the same catalytic site: an inverting beta-1,O-galactosylation of hydroxylysines (Gal-T) and a retaining alpha-1,2-glucosylation of galactosyl hydroxylysines (Glc-T). In this work, we have combined indirect luminescence-based assays with direct mass spectrometry-based assays and molecular structure studies to demonstrate that LH3/PLOD3 only has Glc-T activity and that GLT25D1 only has Gal-T activity. Structure-guided mutagenesis confirmed that the Glc-T activity is defined by key residues in the first-shell environment of the glycosyltransferase catalytic site as well as by long-range contributions from residues within the same glycosyltransferase (GT) domain. By solving the molecular structures and characterizing the interactions and solving the molecular structures of human LH3/PLOD3 in complex with different UDP-sugar analogs, we show how these studies could provide insights for LH3/PLOD3 glycosyltransferase inhibitor development. Collectively, our data provide new tools for the direct investigation of collagen hydroxylysine PTMs and a comprehensive overview of the complex network of shapes, charges, and interactions that enable LH3/PLOD3 glycosyltransferase activities, expanding the molecular framework and facilitating an improved understanding and manipulation of glycosyltransferase functions in biomedical applications.
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Affiliation(s)
- Daiana Mattoteia
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Antonella Chiapparino
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Marco Fumagalli
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Matteo De Marco
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Francesca De Giorgi
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Lisa Negro
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Alberta Pinnola
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Silvia Faravelli
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Tony Roscioli
- NSW Health Pathology Randwick Genomics Laboratory, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Neuroscience Research Australia (NeuRA), Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Luigi Scietti
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
| | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9A, 27100 Pavia, Italy
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, 27100 Pavia, Italy
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4
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Scietti L, Forneris F. Modeling of Protein Complexes. Methods Mol Biol 2023; 2627:349-371. [PMID: 36959458 DOI: 10.1007/978-1-0716-2974-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The recent advances in structural biology, combined with continuously increasing computational capabilities and development of advanced softwares, have drastically simplified the workflow for protein homology modeling. Modeling of individual proteins is nowadays quick and straightforward for a large variety of protein targets, thanks to guided pipelines relying on advanced computational tools and user-friendly interfaces, which have extended and promoted the use of modeling also to scientists not focusing on molecular structures of proteins. Nevertheless, construction of models of multi-protein complexes remains quite challenging for the non-experts, often due to the usage of specific procedures depending on the system under investigation and the need for experimental validation approaches to strengthen the generated output.In this chapter, we provide a brief overview of the approaches enabling generation of multi-protein complex models starting from homology models of individual protein components. Using real-life examples, we include two examples to guide the reader in the generation of homomeric and heteromeric protein models.
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Affiliation(s)
- Luigi Scietti
- Department of Biology and Biotechnology, The Armenise-Harvard Laboratory of Structural Biology, University of Pavia, Pavia, Italy.
| | - Federico Forneris
- Department of Biology and Biotechnology, The Armenise-Harvard Laboratory of Structural Biology, University of Pavia, Pavia, Italy.
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5
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Wu W, Kim JS, Bailey AO, Russell WK, Richards SJ, Chen T, Chen T, Chen Z, Liang B, Yamauchi M, Guo H. Comparative genomic and biochemical analyses identify a collagen galactosylhydroxylysyl glucosyltransferase from Acanthamoeba polyphaga mimivirus. Sci Rep 2022; 12:16806. [PMID: 36207453 PMCID: PMC9546862 DOI: 10.1038/s41598-022-21197-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
Humans and Acanthamoeba polyphaga mimivirus share numerous homologous genes, including collagens and collagen-modifying enzymes. To explore this homology, we performed a genome-wide comparison between human and mimivirus using DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) and identified 52 new putative mimiviral proteins that are homologous with human proteins. To gain functional insights into mimiviral proteins, their human protein homologs were organized into Gene Ontology (GO) and REACTOME pathways to build a functional network. Collagen and collagen-modifying enzymes form the largest subnetwork with most nodes. Further analysis of this subnetwork identified a putative collagen glycosyltransferase R699. Protein expression test suggested that R699 is highly expressed in Escherichia coli, unlike the human collagen-modifying enzymes. Enzymatic activity assay and mass spectrometric analyses showed that R699 catalyzes the glucosylation of galactosylhydroxylysine to glucosylgalactosylhydroxylysine on collagen using uridine diphosphate glucose (UDP-glucose) but no other UDP-sugars as a sugar donor, suggesting R699 is a mimiviral collagen galactosylhydroxylysyl glucosyltransferase (GGT). To facilitate further analysis of human and mimiviral homologous proteins, we presented an interactive and searchable genome-wide comparison website for quickly browsing human and Acanthamoeba polyphaga mimivirus homologs, which is available at RRID Resource ID: SCR_022140 or https://guolab.shinyapps.io/app-mimivirus-publication/ .
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Affiliation(s)
- Wenhui Wu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Arvinas, LLC, 5 Science Park, New Haven, CT, USA
| | - Jeong Seon Kim
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Stephen J Richards
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Tiantian Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Tingfei Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zhenhang Chen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Mitsuo Yamauchi
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Houfu Guo
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA. .,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
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6
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Zhang J, Tian Y, Mo S, Fu X. Overexpressing PLOD Family Genes Predict Poor Prognosis in Pancreatic Cancer. Int J Gen Med 2022; 15:3077-3096. [PMID: 35330878 PMCID: PMC8938171 DOI: 10.2147/ijgm.s341332] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
Background Pancreatic cancer is a common malignant tumor. Multiple studies have shown that procollagen lysyl-hydroxylase (PLOD) family genes were closely related to tumor progression and metastasis in a variety of human cancers. This study aimed to explore the prognosis and biological role of PLOD family genes in pancreatic adenocarcinoma (PAAD). Methods GEPIA, GEO, HPA, CCLE, Kaplan-Meier plotter, cBioPortal, LinkedOmics, DAVID6.8, STRING, and TIMER were employed to determine the prognostic values and biological function of PLOD family members in PAAD. Results The mRNA and protein expression patterns of PLOD family members were noticeably up-regulated in PAAD compared with normal tissues. PLOD family gene expression was also up-regulated in pancreatic cancer cell lines. PLOD1 was correlated with histological and pathological grades of pancreatic cancer. PLOD2 was related to histological grade. The high expression of PLOD1-2 was correlated with the poor overall survival rate and relapse-free survival rate in patients with PAAD. Additionally, PLODs showed high sensitivity and specificity in distinguishing pancreatic cancer from normal tissues. Through the functional enrichment analysis of PLOD-related genes in PAAD, we found that PLODs were enriched in collagen fiber tissue structure, lysine degradation, and collagen biosynthesis. Pathway analysis confirmed that PLODs regulated the proliferation, migration, and metastasis of pancreatic cancer through the RalGEF-Ral signaling pathway. Furthermore, the level of expression of PLOD1-2 was positively correlated with the activity of tumor-infiltrating immune cells, including CD8+T cells, neutrophils, macrophages, and dendritic cells. The level of expression of PLOD3 was inversely correlated with the level of infiltration of CD8+T cells. PLOD1 and PLOD2 were highly expressed in pancreatic cancer tissues with TP53 and KRAS mutations, respectively. However, the level of expression of PLOD3 in SMAD4 wild-type pancreatic cancer was increased. Conclusion The findings showed that individual PLOD genes or PLOD family genes could be potential prognostic biomarkers for PAAD.
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Affiliation(s)
- Jing Zhang
- Department of Biliary and Pancreatic Surgery, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi, 030032, People’s Republic of China
- The Fifth People’s Hospital of Datong, Datong, Shanxi Province, 037006, People’s Republic of China
| | - YanZhang Tian
- Department of Biliary and Pancreatic Surgery, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi, 030032, People’s Republic of China
| | - ShaoJian Mo
- Department of Biliary and Pancreatic Surgery, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi, 030032, People’s Republic of China
| | - XiFeng Fu
- Department of Biliary and Pancreatic Surgery, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi, 030032, People’s Republic of China
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7
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Yuan B, Xu Y, Zheng S. PLOD1 acts as a tumor promoter in glioma via activation of the HSF1 signaling pathway. Mol Cell Biochem 2022; 477:549-557. [PMID: 34845571 DOI: 10.1007/s11010-021-04289-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/04/2021] [Indexed: 02/05/2023]
Abstract
Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) is a collagen-related lysyl hydroxylase and its prognostic value in glioma patients was verified. However, its biological function in glioma has yet to be fully investigated. The PLOD1 mRNA status and clinical significance in gliomas were assessed via the GEPIA database. Overexpression or targeted depletion of PLOD1 was carried out in the human glioma cell line U87 and verified by western blotting. CCK8 and colony formation assays were implemented to examine the impact of PLOD1 on the proliferative and colony-forming phenotypes of U87 cells. Luciferase reporter assays and HSF1-specific pharmacologic inhibitors (KRIBB11) were employed to determine the regulatory relationship between PLOD1 and heat shock factor 1 (HSF1). High expression of PLOD1 was observed in tissue samples of glioblastoma multiforme (GBM) and brain lower-grade glioma (LGG). GEPIA overall survival further demonstrated that both GBM and LGG patients with high PLOD1 displayed worse clinical outcomes compared with those with low PLOD1. Overexpression and targeted depletion of PLOD1 enhanced and suppressed U87 cell proliferation and colony formation, respectively. Luciferase reporter assays showed that PLOD1 significantly enhanced the transcriptional activity of HSF1 in HEK293T cells. PLOD1 deficiency in U87 cells inhibited HSF1-induced survivin accumulation, whereas KRIBB11 also blocked the PLOD1-overexpressing induced survivin expression. An inhibitor of HSF1 signaling events abolished the increased clonogenic potential caused by PLOD1 overexpression in U87 cells. High expression of PLOD1 can increase the proliferation and colony formation of U87 cells by activating the HSF1 signaling pathway. This study suggested PLOD1/HSF1 as an effective therapeutic target for gliomas.
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Affiliation(s)
- Bo Yuan
- Department of Neurosurgery, The First Affiliated Hospital, Shantou University Medical College, No. 57, Changping Road, Shantou, 515041, Guangdong, People's Republic of China.
| | - Yimin Xu
- Department of Neurosurgery, The First Affiliated Hospital, Shantou University Medical College, No. 57, Changping Road, Shantou, 515041, Guangdong, People's Republic of China
| | - Shaoqin Zheng
- Department of Neurosurgery, The First Affiliated Hospital, Shantou University Medical College, No. 57, Changping Road, Shantou, 515041, Guangdong, People's Republic of China
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8
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Koenig SN, Cavus O, Williams J, Bernier M, Tonniges J, Sucharski H, Dew T, Akel M, Baker P, Madiai F, De Giorgi F, Scietti L, Faravelli S, Forneris F, Mohler PJ, Bradley EA. New mechanistic insights to PLOD1-mediated human vascular disease. Transl Res 2022; 239:1-17. [PMID: 34400365 PMCID: PMC8671190 DOI: 10.1016/j.trsl.2021.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 01/03/2023]
Abstract
Heritable thoracic aortic disease and familial thoracic aortic aneurysm/dissection are important causes of human morbidity/mortality, most without identifiable genetic cause. In a family with familial thoracic aortic aneurysm/dissection, we identified a missense p. (Ser178Arg) variant in PLOD1 segregating with disease, and evaluated PLOD1 enzymatic activity, collagen characteristics and in human aortic vascular smooth muscle cells, studied the effect on function. Comparison with homologous PLOD3 enzyme indicated that the pathogenic variant may affect the N-terminal glycosyltransferase domain, suggesting unprecedented PLOD1 activity. In vitro assays demonstrated that wild-type PLOD1 is capable of processing UDP-glycan donor substrates, and that the variant affects the folding stability of the glycosyltransferase domain and associated enzymatic functions. The PLOD1 substrate lysine was elevated in the proband, however the enzymatic product hydroxylysine and total collagen content was not different, albeit despite collagen fibril narrowing and preservation of collagen turnover. In VSMCs overexpressing wild-type PLOD1, there was upregulation in procollagen gene expression (secretory function) which was attenuated in the variant, consistent with loss-of-function. In comparison, si-PLOD1 cells demonstrated hypercontractility and upregulation of contractile markers, providing evidence for phenotypic switching. Together, the findings suggest that the PLOD1 product is preserved, however newly identified glucosyltransferase activity of PLOD1 appears to be affected by folding stability of the variant, and is associated with compensatory vascular smooth muscle cells phenotypic switching to support collagen production, albeit with less robust fibril girth. Future studies should focus on the impact of PLOD1 folding/variant stability on the tertiary structure of collagen and ECM interactions.
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Affiliation(s)
- Sara N Koenig
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Omer Cavus
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Jordan Williams
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Matthew Bernier
- The Ohio State University Mass Spectrometry and Proteomics Facility, Office of Research, Columbus, Ohio
| | - Jeff Tonniges
- The Ohio State University Microscopy and Imaging Facility (CMIF), Office of Research, Columbus, Ohio
| | - Holly Sucharski
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Trevor Dew
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Muhannad Akel
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Peter Baker
- Nationwide Children's Hospital, Department of Pathology, Columbus, Ohio
| | - Francesca Madiai
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Francesca De Giorgi
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Luigi Scietti
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Silvia Faravelli
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Peter J Mohler
- The Ohio State University College of Medicine, Department of Physiology and Cell Biology, Columbus, Ohio; The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio
| | - Elisa A Bradley
- The Dorothy Davis Heart and Lung Research Institute and the Frick Center for Heart Failure and Arrhythmia, The Ohio State University, Columbus, Ohio; The Ohio State University College of Medicine and Wexner Medical Center, Division of Cardiovascular Medicine, Department of Internal Medicine, Columbus, Ohio.
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9
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Gong S, Duan Y, Wu C, Osterhoff G, Schopow N, Kallendrusch S. A Human Pan-Cancer System Analysis of Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 (PLOD3). Int J Mol Sci 2021; 22:ijms22189903. [PMID: 34576068 PMCID: PMC8467482 DOI: 10.3390/ijms22189903] [Citation(s) in RCA: 4] [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: 07/29/2021] [Revised: 09/07/2021] [Accepted: 09/11/2021] [Indexed: 01/11/2023] Open
Abstract
The overexpression of the enzymes involved in the degradation of procollagen lysine is correlated with various tumor entities. Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (PLOD3) expression was found to be correlated to the progression and migration of cancer cells in gastric, lung and prostate cancer. Here, we analyzed the gene expression, protein expression, and the clinical parameters of survival across 33 cancers based on the Clinical Proteomic Tumor Analysis Consortium (CPTAC), function annotation of the mammalian genome 5 (FANTOM5), Gene Expression Omnibus (GEO), Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA) and The Cancer Genome Atlas (TCGA) databases. Genetic alteration, immune infiltration and relevant cellular pathways were analyzed in detail. PLOD3 expression negatively correlated with survival periods and the infiltration level of CD8+ T cells, but positively correlated to the infiltration of cancer associated fibroblasts in diverse cancers. Immunohistochemistry in colon carcinomas, glioblastomas, and soft tissue sarcomas further confirm PLOD 3 expression in human cancer tissue. Moreover, amplification and mutation accounted for the largest proportion in esophageal adenocarcinoma and uterine corpus endometrial carcinoma, respectively; the copy number alteration of PLOD3 appeared in all cancers from TCGA; and molecular mechanisms further proved the effect of PLOD3 on tumorigenesis. In particular, PLOD3 expression appears to have a tumor immunological effect, and is related to multiple immune cells. Furthermore, it is also associated with tumor mutation burden and microsatellite instability in various tumors. PLOD3 acts as an inducer of various cancers, and it could be a potential biomarker for prognosis and targeted treatment.
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Affiliation(s)
- Siming Gong
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
| | - Yingjuan Duan
- Faculty of Chemistry and Mineralogy, University of Leipzig, 04103 Leipzig, Germany;
| | - Changwu Wu
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
- Correspondence:
| | - Georg Osterhoff
- Sarcoma Center, Department of Orthopedics, Trauma and Plastic Surgery, University Hospital Leipzig, 04103 Leipzig, Germany;
| | - Nikolas Schopow
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
- Sarcoma Center, Department of Orthopedics, Trauma and Plastic Surgery, University Hospital Leipzig, 04103 Leipzig, Germany;
| | - Sonja Kallendrusch
- Institute of Anatomy, University of Leipzig, Liebigstraße 13, 04103 Leipzig, Germany; (S.G.); (N.S.); (S.K.)
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10
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Guo HF, Bota-Rabassedas N, Terajima M, Leticia Rodriguez B, Gibbons DL, Chen Y, Banerjee P, Tsai CL, Tan X, Liu X, Yu J, Tokmina-Roszyk M, Stawikowska R, Fields GB, Miller MD, Wang X, Lee J, Dalby KN, Creighton CJ, Phillips GN, Tainer JA, Yamauchi M, Kurie JM. A collagen glucosyltransferase drives lung adenocarcinoma progression in mice. Commun Biol 2021; 4:482. [PMID: 33875777 PMCID: PMC8055892 DOI: 10.1038/s42003-021-01982-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer cells are a major source of enzymes that modify collagen to create a stiff, fibrotic tumor stroma. High collagen lysyl hydroxylase 2 (LH2) expression promotes metastasis and is correlated with shorter survival in lung adenocarcinoma (LUAD) and other tumor types. LH2 hydroxylates lysine (Lys) residues on fibrillar collagen's amino- and carboxy-terminal telopeptides to create stable collagen cross-links. Here, we show that electrostatic interactions between the LH domain active site and collagen determine the unique telopeptidyl lysyl hydroxylase (tLH) activity of LH2. However, CRISPR/Cas-9-mediated inactivation of tLH activity does not fully recapitulate the inhibitory effect of LH2 knock out on LUAD growth and metastasis in mice, suggesting that LH2 drives LUAD progression, in part, through a tLH-independent mechanism. Protein homology modeling and biochemical studies identify an LH2 isoform (LH2b) that has previously undetected collagen galactosylhydroxylysyl glucosyltransferase (GGT) activity determined by a loop that enhances UDP-glucose-binding in the GLT active site and is encoded by alternatively spliced exon 13 A. CRISPR/Cas-9-mediated deletion of exon 13 A sharply reduces the growth and metastasis of LH2b-expressing LUADs in mice. These findings identify a previously unrecognized collagen GGT activity that drives LUAD progression.
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Affiliation(s)
- Hou-Fu Guo
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neus Bota-Rabassedas
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Masahiko Terajima
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - B Leticia Rodriguez
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yulong Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyam Banerjee
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaochao Tan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Liu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiang Yu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michal Tokmina-Roszyk
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Roma Stawikowska
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | - Gregg B Fields
- Institute for Human Health & Disease Intervention (I-HEALTH) and Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL, USA
| | | | - Xiaoyan Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Juhoon Lee
- Division of Medicinal Chemistry, Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Kevin N Dalby
- Division of Medicinal Chemistry, Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Chad J Creighton
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mitsuo Yamauchi
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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11
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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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12
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Zhao Y, Zhang X, Yao J. Comprehensive analysis of PLOD family members in low-grade gliomas using bioinformatics methods. PLoS One 2021; 16:e0246097. [PMID: 33503035 PMCID: PMC7840023 DOI: 10.1371/journal.pone.0246097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/13/2021] [Indexed: 12/20/2022] Open
Abstract
Low-grade gliomas (LGGs) is a primary invasive brain tumor that grows slowly but is incurable and eventually develops into high malignant glioma. Novel biomarkers for the tumorigenesis and lifetime of LGG are critically demanded to be investigated. In this study, the expression levels of procollagen-lysine, 2-oxoglutarate 5-dioxygenases (PLODs) were analyzed by ONCOMINE, HPA and GEPIA. The GEPIA online platform was applied to evaluate the interrelation between PLODs and survival index in LGG. Furthermore, functions of PLODs and co-expression genes were inspected by the DAVID. Moreover, we used TIMER, cBioportal, GeneMINIA and NetworkAnalyst analysis to reveal the mechanism of PLODs in LGG. We found that expression levels of each PLOD family members were up-regulated in patients with LGG. Higher expression of PLODs was closely related to shorter disease-free survival (DFS) and overall survival (OS). The findings showed that LGG cases with or without alterations were significantly correlated with the OS and DFS. The mechanism of PLODs in LGG may be involved in response to hypoxia, oxidoreductase activity, Lysine degradation and immune cell infiltration. In general, this research has investigated the values of PLODs in LGG, which could serve as biomarkers for diagnosis, prognosis and potential therapeutic targets of LGG patients.
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Affiliation(s)
- Yonghui Zhao
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei, People’s Republic of China
- * E-mail:
| | - Xiang Zhang
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei, People’s Republic of China
| | - Junchao Yao
- Department of Neurosurgery, Cangzhou Central Hospital, Cangzhou, Hebei, People’s Republic of China
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13
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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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14
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Wilhelm D, Kempf H, Bianchi A, Vincourt JB. ATDC5 cells as a model of cartilage extracellular matrix neosynthesis, maturation and assembly. J Proteomics 2020; 219:103718. [PMID: 32097723 DOI: 10.1016/j.jprot.2020.103718] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/05/2020] [Accepted: 02/19/2020] [Indexed: 01/03/2023]
Abstract
Fibrillar collagens and proteoglycans (PGs) are quantitatively the major constituents of extracellular matrices (ECM). They carry numerous crucial post-translational modifications (PTMs) that tune the resulting biomechanical properties of the corresponding tissues. The mechanisms determining these PTMs remain largely unknown, notably because available established cell lines do not recapitulate much of the complexity of the machineries involved. ATDC5 cells are a model of chondrogenesis widely used for decades, but it remains described mostly at histological and transcriptional levels. Here, we asked to what extent this model recapitulates the events of ECM synthesis and processing occurring in cartilage. Insulin-stimulated ATDC5 cells exhibit up- or down-regulation of more than one-hundred proteins, including a number of known participants in chondrogenesis and major markers thereof. However, they also lack several ECM components considered of significant, yet more subtle, function in cartilage. Still, they assemble the large PG aggrecan and type II collagen, both carrying most of their in vivo PTMs, into an ECM. Remarkably, collagen crosslinking is fully lysyl oxidase (LOX)-dependent. The ATDC5 model recapitulates critical aspects of the cartilage ECM-processing machinery and should be useful to decipher the mechanisms involved. Proteomics data are available via ProteomeXchange with identifier PXD014121. SIGNIFICANCE: The present work provides the first proteome characterization of the ATDC5 chondrogenesis model, which has been used for decades in the field of cartilage biology. The results demonstrate the up- and down-regulation of more than one hundred proteins. Overall, specific drawbacks of the model are pointed out, that will be important to take into consideration for future studies. However, major cartilage components are massively assembled into an extracellular matrix and carry most of their post-translational modifications occurring in cartilage tissue. Unlike other available established cell lines, the ATDC5 model recapitulates major aspects of cartilage biosynthesis and should be useful in investigating the mechanisms that regulate collagen maturation events.
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Affiliation(s)
- Dafné Wilhelm
- UMR 7365 CNRS-UL IMoPA, Vandoeuvre-lès-Nancy, France
| | - Hervé Kempf
- UMR 7365 CNRS-UL IMoPA, Vandoeuvre-lès-Nancy, France
| | | | - Jean-Baptiste Vincourt
- UMR 7365 CNRS-UL IMoPA, Vandoeuvre-lès-Nancy, France; Proteomics core facility of UMS 2008 UL-CNRS-INSERM IBSLor, Vandoeuvre-lès-Nancy, France.
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15
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Piersma B, Hayward MK, Weaver VM. Fibrosis and cancer: A strained relationship. Biochim Biophys Acta Rev Cancer 2020; 1873:188356. [PMID: 32147542 DOI: 10.1016/j.bbcan.2020.188356] [Citation(s) in RCA: 309] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Tumors are characterized by extracellular matrix (ECM) deposition, remodeling, and cross-linking that drive fibrosis to stiffen the stroma and promote malignancy. The stiffened stroma enhances tumor cell growth, survival and migration and drives a mesenchymal transition. A stiff ECM also induces angiogenesis, hypoxia and compromises anti-tumor immunity. Not surprisingly, tumor aggression and poor patient prognosis correlate with degree of tissue fibrosis and level of stromal stiffness. In this review, we discuss the reciprocal interplay between tumor cells, cancer associated fibroblasts (CAF), immune cells and ECM stiffness in malignant transformation and cancer aggression. We discuss CAF heterogeneity and describe its impact on tumor development and aggression focusing on the role of CAFs in engineering the fibrotic tumor stroma and tuning tumor cell tension and modulating the immune response. To illustrate the role of mechanoreciprocity in tumor evolution we summarize data from breast cancer and pancreatic ductal carcinoma (PDAC) studies, and finish by discussing emerging anti-fibrotic strategies aimed at treating cancer.
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Affiliation(s)
- Bram Piersma
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco (UCSF), USA; Matrix research group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - M K Hayward
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco (UCSF), USA
| | - Valerie M Weaver
- Department of Surgery and Center for Bioengineering and Tissue Regeneration, University of California, San Francisco (UCSF), USA; Departments of Radiation Oncology, Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF, UCSF Helen Diller Comprehensive Cancer Center, 513 Parnassus Avenue, HSE565, San Francisco, CA 94143-0456, USA.
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16
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Naba A, Ricard-Blum S. The Extracellular Matrix Goes -Omics: Resources and Tools. EXTRACELLULAR MATRIX OMICS 2020. [DOI: 10.1007/978-3-030-58330-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Collagen cross-linking mediated by lysyl hydroxylase 2: an enzymatic battlefield to combat fibrosis. Essays Biochem 2019; 63:377-387. [DOI: 10.1042/ebc20180051] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022]
Abstract
AbstractThe hallmark of fibrosis is an excessive accumulation of collagen, ultimately leading to organ failure. It has become evident that the deposited collagen also exhibits qualitative modifications. A marked modification is the increased cross-linking, leading to a stabilization of the collagen network and limiting fibrosis reversibility. Not only the level of cross-linking is increased, but also the composition of cross-linking is altered: an increase is seen in hydroxyallysine-derived cross-links at the expense of allysine cross-links. This results in irreversible fibrosis, as collagen cross-linked by hydroxyallysine is more difficult to degrade. Hydroxyallysine is derived from a hydroxylysine in the telopeptides of collagen. The expression of lysyl hydroxylase (LH) 2 (LH2), the enzyme responsible for the formation of telopeptidyl hydroxylysine, is universally up-regulated in fibrosis. It is expected that inhibition of this enzyme will lead to reversible fibrosis without interfering with the normal repair process. In this review, we discuss the molecular basis of collagen modifications and cross-linking, with an emphasis on LH2-mediated hydroxyallysine cross-links, and their implications for the pathogenesis and treatment of fibrosis.
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18
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Ewans LJ, Colley A, Gaston-Massuet C, Gualtieri A, Cowley MJ, McCabe MJ, Anand D, Lachke SA, Scietti L, Forneris F, Zhu Y, Ying K, Walsh C, Kirk EP, Miller D, Giunta C, Sillence D, Dinger M, Buckley M, Roscioli T. Pathogenic variants in PLOD3 result in a Stickler syndrome-like connective tissue disorder with vascular complications. J Med Genet 2019; 56:629-638. [DOI: 10.1136/jmedgenet-2019-106019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/28/2019] [Accepted: 04/25/2019] [Indexed: 12/24/2022]
Abstract
BackgroundPathogenic PLOD3 variants cause a connective tissue disorder (CTD) that has been described rarely. We further characterise this CTD and propose a clinical diagnostic label to improve recognition and diagnosis of PLOD3-related disease.MethodsReported PLOD3 phenotypes were compared with known CTDs utilising data from three further individuals from a consanguineous family with a homozygous PLOD3 c.809C>T; p.(Pro270Leu) variant. PLOD3 mRNA expression in the developing embryo was analysed for tissue-specific localisation. Mouse microarray expression data were assessed for phylogenetic gene expression similarities across CTDs with overlapping clinical features.ResultsKey clinical features included ocular abnormalities with risk for retinal detachment, sensorineural hearing loss, reduced palmar creases, finger contractures, prominent knees, scoliosis, low bone mineral density, recognisable craniofacial dysmorphisms, developmental delay and risk for vascular dissection. Collated clinical features showed most overlap with Stickler syndrome with variable features of Ehlers-Danlos syndrome (EDS) and epidermolysis bullosa (EB). Human lysyl hydroxylase 3/PLOD3 expression was localised to the developing cochlea, eyes, skin, forelimbs, heart and cartilage, mirroring the clinical phenotype of this disorder.ConclusionThese data are consistent with pathogenic variants in PLOD3 resulting in a clinically distinct Stickler-like syndrome with vascular complications and variable features of EDS and EB. Early identification of PLOD3 variants would improve monitoring for comorbidities and may avoid serious adverse ocular and vascular outcomes.
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