1
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Arbee S, Himeno T, Miura-Yura E, Kato M, Islam S, Jahan N, Kamiya H, Watanabe H. Versican maintains the homeostasis of adipose tissues and regulates energy metabolism. Biochem Biophys Res Commun 2024; 727:150309. [PMID: 38936224 DOI: 10.1016/j.bbrc.2024.150309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/14/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
Versican is a large chondroitin sulfate proteoglycan in the extracellular matrix. It plays a pivotal role in the formation of the provisional matrix. S100a4, previously known as fibroblast-specific protein, functions as a calcium channel-binding protein. To investigate the role of versican expressed in fibroblasts, we generated conditional knockout mice in which versican expression is deleted in cells expressing S100a4. We found that S100a4 is expressed in adipose tissues, and these mice exhibit obesity under a normal diet, which becomes apparent as early as five months. The white adipose tissues of these mice exhibited decreased expression levels of S100a4 and versican and hypertrophy of adipocytes. qRT-PCR showed a reduced level of UCP1 in their white adipose tissues, indicating that the basic energy metabolism is diminished. These results suggest that versican in adipose tissues maintains the homeostasis of adipose tissues and regulates energy metabolism.
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Affiliation(s)
- Shahida Arbee
- Insitute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Tatsuhito Himeno
- Division of Diabetes, Department of Internal Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Emiri Miura-Yura
- Division of Diabetes, Department of Internal Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Makoto Kato
- Division of Diabetes, Department of Internal Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Shamima Islam
- Insitute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Nushrat Jahan
- Insitute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Hideki Kamiya
- Division of Diabetes, Department of Internal Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan
| | - Hideto Watanabe
- Insitute for Molecular Science of Medicine, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, Aichi, 480-1195, Japan.
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2
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Li X, Du M, Liu Y, Wang M, Shen Y, Xing J, Zhang L, Zhao Y, Bou G, Bai D, Dugarjaviin M, Xia W. Proteome and metabolomic profile of Mongolian horse follicular fluid during follicle development. Sci Rep 2024; 14:19788. [PMID: 39187528 PMCID: PMC11347562 DOI: 10.1038/s41598-024-66686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 07/03/2024] [Indexed: 08/28/2024] Open
Abstract
During follicular development, changes in the composition of the follicular fluid are synchronized with the development of oocytes. Our aim was to screen the key factors affecting oocyte maturation and optimize the in vitro culture protocol by understanding the changes of proteins and metabolites in follicular fluid. Follicles are divided into three groups according to their diameter (small follicle fluid (SFF): 10 mm < d < 20 mm; medium follicle fluid (MFF): 20 mm < d < 30 mm; large follicle fluid (LFF): 30 mm < d). Proteins and metabolites from the follicular fluid were analyzed by mass spectrometry. The results showed that: in LFF vs MFF, 20 differential abundant protein (DAP) and 88 differential abundant metabolites (DAM) were screened out; In SFF vs MFF, 3 DAPs and 65 DAMs were screened out; In MFF vs SFF, 24 DAPs and 35 DAMs were screened out. The analysis of differential proteins and metabolites showed that glycerophosphate hydrolysis decreased during follicular development, and proteins played a major role in metabolism and binding. In addition, DAMs and DAPs are co-enriched in the "linoleic acid metabolism" pathway. Combinatorial analysis reveals the dynamic profile of follicular fluid during follicular development and provides fundation for further exploring the function of follicular fluid in Mongolian horse.
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Affiliation(s)
- Xinyu Li
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Ming Du
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yuanyi Liu
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Min Wang
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yingchao Shen
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jingya Xing
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266000, China
| | - Lei Zhang
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yiping Zhao
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Gerelchimeg Bou
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dongyi Bai
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Wei Xia
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China.
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3
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Hanuman S, B HK, Pai KSR, Nune M. Surface-Conjugated Galactose on Electrospun Polycaprolactone Nanofibers: An Innovative Scaffold for Uterine Tissue Engineering. ACS OMEGA 2024; 9:34314-34328. [PMID: 39157094 PMCID: PMC11325431 DOI: 10.1021/acsomega.3c10445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/20/2024]
Abstract
The uterus, a vital organ in the female reproductive system, nurtures and supports developing embryos until maturity. This study focuses on addressing uterine related problems by creating a nanofibrous scaffold to regenerate uterine myometrial tissue, closely resembling the native extracellular matrix (ECM) for enhanced efficacy. To achieve this, we utilized polycaprolactone (PCL) as a biomaterial and employed an electrospinning technique to generate PCL nanofibers in both random and aligned orientations. Due to the inherent hydrophobic nature of PCL nanofibers, a two-step wet chemistry surface modification technique is used, involving the conjugation of galactose onto them. Galactose, a lectin-binding sugar, was chosen to enhance the scaffold's hydrophilicity, thereby improving cell adhesion and fostering l-selectin-based interactions between the scaffold and uterine cells. These interactions, in turn, activated uterine fibroblasts, leading to ECM remodeling. The optimized electrospinning process successfully generated random and aligned nanofibers. Subsequent surface modification was carried out, and the modified scaffold was subjected to various physicochemical characterization, such as the ninhydrin assay, enzyme-linked lectin assay techniques that revealed successful galactose conjugation, and mechanical characterization to assess any changes in material bulk properties resulting from the modification. The tensile strength of random galactose-modified PCL fibers reached 0.041 ± 0.01 MPa, outperforming random unmodified PCL fibers (0.026 ± 0.01 MPa), aligned unmodified PCL fibers (0.011 ± 0.001 MPa), and aligned modified PCL fibers (0.016 ± 0.002 MPa). Cytocompatibility studies with human uterine fibroblast cells showed enhanced viability and proliferation on the modified scaffolds. Initial pilot studies were attempted in the current study involving subcutaneous implantation in the dorsal area of Wistar rats to assess biocompatibility and tissue response before proceeding to intrauterine implantation indicated that the modification did not induce adverse inflammation in vivo. In conclusion, our study introduces a surface-modified PCL nanofibrous material for myometrial tissue engineering, offering promise in addressing myometrial damage and advancing uterine health and reproductive well-being.
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Affiliation(s)
- Srividya Hanuman
- Manipal
Institute of Regenerative Medicine, Manipal
Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Harish Kumar B
- Department
of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - K. Sreedhara Ranganath Pai
- Department
of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Manasa Nune
- Manipal
Institute of Regenerative Medicine, Manipal
Academy of Higher Education, Manipal, Karnataka 576104, India
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4
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Elhashani S, Glenn M, Raymant M, Schmid MC, Mielgo A. Expression of versican isoforms V0/V1 by pancreatic cancer associated fibroblasts increases fibroblast proliferation. Pancreatology 2024; 24:719-731. [PMID: 38719756 DOI: 10.1016/j.pan.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Versican is a large extracellular matrix (ECM) proteoglycan with four isoforms V0-3. Elevated V0/V1 levels in breast cancer and glioma regulate cell migration and proliferation, but the role of versican in pancreatic ductal adenocarcinoma (PDAC) remains unclear. METHODS In this study, we evaluated the expression levels of versican isoforms, as well as their cellular source and interacting partners, in vivo, in human and mouse primary and metastatic PDAC tumours and in vitro, in pancreatic tumour cells and fibroblasts using immunostaining, confocal microscopy and qPCR techniques. We also investigated the effect of versican expression on fibroblast proliferation and migration using genetic and pharmacological approaches. RESULTS We found that versican V0/V1 is highly expressed by cancer-associated fibroblasts (CAFs) in mouse and human primary and metastatic PDAC tumours. Our data also show that exposing fibroblasts to tumour-conditioned media upregulates V0 and V1 expressions, while Verbascoside (a CD44 inhibitor) downregulates V0/V1 expression. Importantly, V0/V1 knockdown significantly inhibits fibroblast proliferation. Mechanistically, we found that inhibiting hyaluronan synthesis does not affect versican co-localisation with CD44 in fibroblasts. CONCLUSION CAFs express high levels of versican V0/V1 in primary and liver metastatic PDAC tumours and versican V0/V1 supports fibroblast proliferation.
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Affiliation(s)
- Sufyan Elhashani
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - Mark Glenn
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - Meirion Raymant
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - Michael C Schmid
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - Ainhoa Mielgo
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK.
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5
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Kobayashi T, Yamashita A, Tsumaki N, Watanabe H. Subpopulations of fibroblasts derived from human iPS cells. Commun Biol 2024; 7:736. [PMID: 38890483 PMCID: PMC11189496 DOI: 10.1038/s42003-024-06419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Organ fibrosis causes collagen fiber overgrowth and impairs organ function. Cardiac fibrosis after myocardial infarction impairs cardiac function significantly, pulmonary fibrosis reduces gas exchange efficiency, and liver fibrosis disturbs the natural function of the liver. Its development is associated with the differentiation of fibroblasts into myofibroblasts and increased collagen synthesis. Fibrosis has organ specificity, defined by the heterogeneity of fibroblasts. Although this heterogeneity is established during embryonic development, it has not been defined yet. Fibroblastic differentiation of induced pluripotent stem cells (iPSCs) recapitulates the process by which fibroblasts acquire diversity. Here, we differentiated iPSCs into cardiac, hepatic, and dermal fibroblasts and analyzed their properties using single-cell RNA sequencing. We observed characteristic subpopulations with different ratios in each organ-type fibroblast group, which contained both resting and distinct ACTA2+ myofibroblasts. These findings provide crucial information on the ontogeny-based heterogeneity of fibroblasts, leading to the development of therapeutic strategies to control fibrosis.
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Affiliation(s)
- Takashi Kobayashi
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi, Japan
| | - Akihiro Yamashita
- Department of Tissue Biochemistry, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Noriyuki Tsumaki
- Department of Tissue Biochemistry, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi, Japan.
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6
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Kwok T, Huerta-White T, Briegel K, Singh A, Yeguvapalli S, Chitrala KN. Bioinformatics analysis of the potential biomarkers of Multiple Sclerosis and Guillain-Barré syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.595759. [PMID: 38853933 PMCID: PMC11160789 DOI: 10.1101/2024.05.29.595759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Recent research emphasizes the intricate interplay of genetics and epigenetics in neurological disorders, notably Multiple Sclerosis (MS) and Guillain-Barre Syndrome (GBS), both of which exhibit cardiovascular dysregulation, with GBS often featuring serious bradyarrhythmias requiring prompt recognition and treatment. While cardiovascular autonomic dysfunction in MS is typically less severe, orthostatic intolerance affects around half of MS patients. Their distinction lies in their autoimmune responses, MS is an autoimmune disease affecting the central nervous system, causes demyelination and axon damage, leading to cognitive, ocular, and musculoskeletal dysfunction. In contrast, GBS primarily affects the peripheral nervous system, resulting in paralysis and respiratory complications. Despite their differences, both diseases share environmental risk factors such as viral infections and Vitamin D deficiency. This study aims to explore shared gene expression pathways, functional annotations, and molecular pathways between MS and GBS to enhance diagnostics, pathogenesis understanding, and treatment strategies through molecular analysis techniques. Through the gene expression analysis, five significant genes were found UTS2, TNFSF10, GBP1, VCAN, FOS. Results shows that Common DEGs are linked to apoptosis, bacterial infections, and atherosclerosis. Molecular docking analysis suggests Aflatoxin B1 as a potential therapeutic compound due to its high binding affinity with common differentially expressed proteins.
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Affiliation(s)
| | | | - Karl Briegel
- Department of Engineering Technology, Division of Technology, University of Houston, 13850, University Blvd, Room SAB1 214, Sugar Land, TX 77479
| | - Aaisha Singh
- Department of Engineering Technology, Division of Technology, University of Houston, 13850, University Blvd, Room SAB1 214, Sugar Land, TX 77479
| | - Suneetha Yeguvapalli
- Department of Engineering Technology, Division of Technology, University of Houston, 13850, University Blvd, Room SAB1 214, Sugar Land, TX 77479
| | - Kumaraswamy Naidu Chitrala
- Department of Engineering Technology, Division of Technology, University of Houston, 13850, University Blvd, Room SAB1 214, Sugar Land, TX 77479
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7
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Xu Y, Benedikt J, Ye L. Hyaluronic Acid Interacting Molecules Mediated Crosstalk between Cancer Cells and Microenvironment from Primary Tumour to Distant Metastasis. Cancers (Basel) 2024; 16:1907. [PMID: 38791985 PMCID: PMC11119954 DOI: 10.3390/cancers16101907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Hyaluronic acid (HA) is a prominent component of the extracellular matrix, and its interactions with HA-interacting molecules (HAIMs) play a critical role in cancer development and disease progression. This review explores the multifaceted role of HAIMs in the context of cancer, focusing on their influence on disease progression by dissecting relevant cellular and molecular mechanisms in tumour cells and the tumour microenvironment. Cancer progression can be profoundly affected by the interactions between HA and HAIMs. They modulate critical processes such as cell adhesion, migration, invasion, and proliferation. The TME serves as a dynamic platform in which HAIMs contribute to the formation of a unique niche. The resulting changes in HA composition profoundly influence the biophysical properties of the TME. These modifications in the TME, in conjunction with HAIMs, impact angiogenesis, immune cell recruitment, and immune evasion. Therefore, understanding the intricate interplay between HAIMs and HA within the cancer context is essential for developing novel therapeutic strategies. Targeting these interactions offers promising avenues for cancer treatment, as they hold the potential to disrupt critical aspects of disease progression and the TME. Further research in this field is imperative for advancing our knowledge and the treatment of cancer.
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Affiliation(s)
- Yali Xu
- Cardiff China Medical Research Collaborative, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK;
- School of Engineering, Cardiff University, Cardiff CF24 3AA, UK;
| | | | - Lin Ye
- Cardiff China Medical Research Collaborative, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK;
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8
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Mori Y, Smith S, Wang J, Munjal A. Versican controlled by Lmx1b regulates hyaluronate density and hydration for semicircular canal morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592968. [PMID: 38766227 PMCID: PMC11100707 DOI: 10.1101/2024.05.07.592968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
During inner ear semicircular canal morphogenesis in zebrafish, patterned canal-genesis zones express genes for extracellular matrix component synthesis. These include hyaluronan and the hyaluronan-binding chondroitin sulfate proteoglycan Versican, which are abundant in the matrices of many developing organs. Charged hyaluronate polymers play a key role in canal morphogenesis through osmotic swelling. However, the developmental factor(s) that control the synthesis of the matrix components and regulation of hyaluronate density and swelling are unknown. Here, we identify the transcription factor, Lmx1b, as a positive transcriptional regulator of hyaluronan, Versican, and chondroitin synthesis genes crucial for canal morphogenesis. We show that Versican regulates hyaluronan density through its protein core, whereas the charged chondroitin side chains contribute to the osmotic swelling of hyaluronate. Versican-tuned properties of hyaluronate matrices may be a broadly used mechanism in morphogenesis with important implications for understanding diseases where these matrices are impaired, and for hydrogel engineering for tissue regeneration.
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Affiliation(s)
- Yusuke Mori
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
| | - Sierra Smith
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
| | - Jiacheng Wang
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
| | - Akankshi Munjal
- Department of Cell Biology, Duke University School of Medicine, Durham NC 27710
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9
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Li MD, Lu JW, Zhang F, Lei WJ, Pan F, Lin YK, Ling LJ, Myatt L, Wang WS, Sun K. ADAMTS4 is a crucial proteolytic enzyme for versican cleavage in the amnion at parturition. Commun Biol 2024; 7:301. [PMID: 38461223 PMCID: PMC10924920 DOI: 10.1038/s42003-024-06007-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 03/03/2024] [Indexed: 03/11/2024] Open
Abstract
Hyalectan cleavage may play an important role in extracellular matrix remodeling. However, the proteolytic enzyme responsible for hyalectan degradation for fetal membrane rupture at parturition remains unknown. Here, we reveal that versican (VCAN) is the major hyalectan in the amnion, where its cleavage increases at parturition with spontaneous rupture of membrane. We further reveal that ADAMTS4 is a crucial proteolytic enzyme for VCAN cleavage in the amnion. Inflammatory factors may enhance VCAN cleavage by inducing ADAMTS4 expression and inhibiting ADAMTS4 endocytosis in amnion fibroblasts. In turn, versikine, the VCAN cleavage product, induces inflammatory factors in amnion fibroblasts, thereby forming a feedforward loop between inflammation and VCAN degradation. Mouse studies show that intra-amniotic injection of ADAMTS4 induces preterm birth along with increased VCAN degradation and proinflammatory factors abundance in the fetal membranes. Conclusively, there is enhanced VCAN cleavage by ADAMTS4 in the amnion at parturition, which can be reenforced by inflammation.
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Affiliation(s)
- Meng-Die Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Jiang-Wen Lu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Fan Zhang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Wen-Jia Lei
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Fan Pan
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Yi-Kai Lin
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China
| | - Li-Jun Ling
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, PR China
| | - Leslie Myatt
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Wang-Sheng Wang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China.
| | - Kang Sun
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, PR China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, PR China.
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10
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Mahmoudi A, Butler AE, De Vincentis A, Jamialahmadi T, Sahebkar A. Microarray-based Detection of Critical Overexpressed Genes in the Progression of Hepatic Fibrosis in Non-alcoholic Fatty Liver Disease: A Protein-protein Interaction Network Analysis. Curr Med Chem 2024; 31:3631-3652. [PMID: 37194229 DOI: 10.2174/0929867330666230516123028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/26/2023] [Accepted: 04/11/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD) is a prevalent cause of chronic liver disease and encompasses a broad spectrum of disorders, including simple steatosis, steatohepatitis, fibrosis, cirrhosis, and liver cancer. However, due to the global epidemic of NAFLD, where invasive liver biopsy is the gold standard for diagnosis, it is necessary to identify a more practical method for early NAFLD diagnosis with useful therapeutic targets; as such, molecular biomarkers could most readily serve these aims. To this end, we explored the hub genes and biological pathways in fibrosis progression in NAFLD patients. METHODS Raw data from microarray chips with GEO accession GSE49541 were downloaded from the Gene Expression Omnibus database, and the R package (Affy and Limma) was applied to investigate differentially expressed genes (DEGs) involved in the progress of low- (mild 0-1 fibrosis score) to high- (severe 3-4 fibrosis score) fibrosis stage NAFLD patients. Subsequently, significant DEGs with pathway enrichment were analyzed, including gene ontology (GO), KEGG and Wikipathway. In order to then explore critical genes, the protein-protein interaction network (PPI) was established and visualized using the STRING database, with further analysis undertaken using Cytoscape and Gephi software. Survival analysis was undertaken to determine the overall survival of the hub genes in the progression of NAFLD to hepatocellular carcinoma. RESULTS A total of 311 significant genes were identified, with an expression of 278 being upregulated and 33 downregulated in the high vs. low group. Gene functional enrichment analysis of these significant genes demonstrated major involvement in extracellular matrix (ECM)-receptor interaction, protein digestion and absorption, and the AGE-RAGE signaling pathway. The PPI network was constructed with 196 nodes and 572 edges with PPI enrichment using a p-value < 1.0 e-16. Based on this cut-off, we identified 12 genes with the highest score in four centralities: Degree, Betweenness, Closeness, and Eigenvector. Those twelve hub genes were CD34, THY1, CFTR, COL3A1, COL1A1, COL1A2, SPP1, THBS1, THBS2, LUM, VCAN, and VWF. Four of these hub genes, namely CD34, VWF, SPP1, and VCAN, showed significant association with the development of hepatocellular carcinoma. CONCLUSION This PPI network analysis of DEGs identified critical hub genes involved in the progression of fibrosis and the biological pathways through which they exert their effects in NAFLD patients. Those 12 genes offer an excellent opportunity for further focused research to determine potential targets for therapeutic applications.
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Affiliation(s)
- Ali Mahmoudi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Antonio De Vincentis
- Unit of Internal Medicine and Geriatrics, Università Campus Bio-Medico di Roma, Fondazione Policlinico Universitario Campus Bio-Medico di Roma, Via Alvaro del Portillo 200, Rome 00128, Italy
| | - Tannaz Jamialahmadi
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Medicine, The University of Western Australia, Perth, Australia
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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11
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Papadas A, Huang Y, Cicala A, Dou Y, Fields M, Gibbons A, Hong D, Lagal DJ, Quintana V, Rizo A, Zomalan B, Asimakopoulos F. Emerging roles for tumor stroma in antigen presentation and anti-cancer immunity. Biochem Soc Trans 2023; 51:2017-2028. [PMID: 38031753 PMCID: PMC10754280 DOI: 10.1042/bst20221083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Advances in immunotherapy in the last decade have revolutionized treatment paradigms across multiple cancer diagnoses. However, only a minority of patients derive durable benefit and progress with traditional approaches, such as cancer vaccines, remains unsatisfactory. A key to overcoming these barriers resides with a deeper understanding of tumor antigen presentation and the complex and dynamic heterogeneity of tumor-infiltrating antigen-presenting cells (APCs). Reminiscent of the 'second touch' hypothesis proposed by Klaus Ley for CD4+ T cell differentiation, the acquisition of full effector potential by lymph node- primed CD8+ T cells requires a second round of co-stimulation at the site where the antigen originated, i.e. the tumor bed. The tumor stroma holds a prime role in this process by hosting specialized APC niches, apparently distinct from tertiary lymphoid structures, that support second antigenic touch encounters and CD8+ T cell effector proliferation and differentiation. We propose that APC within second-touch niches become licensed for co-stimulation through stromal-derived instructive signals emulating embryonic or wound-healing provisional matrix remodeling. These immunostimulatory roles of stroma contrast with its widely accepted view as a physical and functional 'immune barrier'. Stromal control of antigen presentation makes evolutionary sense as the host stroma-tumor interface constitutes the prime line of homeostatic 'defense' against the emerging tumor. In this review, we outline how stroma-derived signals and cells regulate tumor antigen presentation and T-cell effector differentiation in the tumor bed. The re-definition of tumor stroma as immune rheostat rather than as inflexible immune barrier harbors significant untapped therapeutic opportunity.
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Affiliation(s)
- Athanasios Papadas
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Yun Huang
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Alexander Cicala
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Yaling Dou
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Matteo Fields
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Alicia Gibbons
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Duncan Hong
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Daniel J. Lagal
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Victoria Quintana
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Alejandro Rizo
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Brolyn Zomalan
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
| | - Fotis Asimakopoulos
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, U.S.A
- Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, U.S.A
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12
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Liu H, Caliz AD, Learnard H, Koupenova M, Keaney JF, Kant S, Zhu LJ, Vertii A. Inflammatory stress-mediated chromatin changes underlie dysfunction in endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561959. [PMID: 37905100 PMCID: PMC10614786 DOI: 10.1101/2023.10.11.561959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Inflammatory stresses underlie endothelial dysfunction and contribute to the development of chronic cardiovascular disorders such as atherosclerosis and vascular fibrosis. The initial transcriptional response of endothelial cells to pro-inflammatory cytokines such as TNF-alpha is well established. However, very few studies uncover the effects of inflammatory stresses on chromatin architecture. We used integrative analysis of ATAC-seq and RNA-seq data to investigate chromatin alterations in human endothelial cells in response to TNF-alpha and febrile-range heat stress exposure. Multi-omics data analysis suggests a correlation between the transcription of stress-related genes and endothelial dysfunction drivers with chromatin regions exhibiting differential accessibility. Moreover, microscopy identified the dynamics in the nuclear organization, specifically, the changes in a subset of heterochromatic nucleoli-associated chromatin domains, the centromeres. Upon inflammatory stress exposure, the centromeres decreased association with nucleoli in a p38-dependent manner and increased the number of transcripts from pericentromeric regions. Overall, we provide two lines of evidence that suggest chromatin alterations in vascular endothelial cells during inflammatory stresses.
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Affiliation(s)
- Haibo Liu
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Amada D. Caliz
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather Learnard
- Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Milka Koupenova
- Cardiovascular Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - John F. Keaney
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Shashi Kant
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lihua Julie Zhu
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anastassiia Vertii
- Molecular, Cell and Cancer Biology Department, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
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13
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Li H, Ghorbani S, Ling CC, Yong VW, Xue M. The extracellular matrix as modifier of neuroinflammation and recovery in ischemic stroke and intracerebral hemorrhage. Neurobiol Dis 2023; 186:106282. [PMID: 37683956 DOI: 10.1016/j.nbd.2023.106282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023] Open
Abstract
Stroke is the second leading cause of death worldwide and has two major subtypes: ischemic stroke and hemorrhagic stroke. Neuroinflammation is a pathological hallmark of ischemic stroke and intracerebral hemorrhage (ICH), contributing to the extent of brain injury but also in its repair. Neuroinflammation is intricately linked to the extracellular matrix (ECM), which is profoundly altered after brain injury and in aging. In the early stages after ischemic stroke and ICH, immune cells are involved in the deposition and remodeling of the ECM thereby affecting processes such as blood-brain barrier and cellular integrity. ECM components regulate leukocyte infiltration into the central nervous system, activate a variety of immune cells, and induce the elevation of matrix metalloproteinases (MMPs) after stroke. In turn, excessive MMPs may degrade ECM into components that are pro-inflammatory and injurious. Conversely, in the later stages after stroke, several ECM molecules may contribute to tissue recovery. For example, thrombospondin-1 and biglycan may promote activity of regulatory T cells, inhibit the synthesis of proinflammatory cytokines, and aid regenerative processes. We highlight these roles of the ECM in ischemic stroke and ICH and discuss their potential cellular and molecular mechanisms. Finally, we discuss therapeutics that could be considered to normalize the ECM in stroke. Our goal is to spur research on the ECM in order to improve the prognosis of ischemic stroke and ICH.
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Affiliation(s)
- Hongmin Li
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, China; Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
| | - Samira Ghorbani
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Alberta, Canada
| | - Chang-Chun Ling
- Department of Chemistry, University of Calgary, Alberta, Canada
| | - V Wee Yong
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Alberta, Canada.
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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14
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Wight TN, Day AJ, Kang I, Harten IA, Kaber G, Briggs DC, Braun KR, Lemire JM, Kinsella MG, Hinek A, Merrilees MJ. V3: an enigmatic isoform of the proteoglycan versican. Am J Physiol Cell Physiol 2023; 325:C519-C537. [PMID: 37399500 PMCID: PMC10511178 DOI: 10.1152/ajpcell.00059.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 07/05/2023]
Abstract
V3 is an isoform of the extracellular matrix (ECM) proteoglycan (PG) versican generated through alternative splicing of the versican gene such that the two major exons coding for sequences in the protein core that support chondroitin sulfate (CS) glycosaminoglycan (GAG) chain attachment are excluded. Thus, versican V3 isoform carries no GAGs. A survey of PubMed reveals only 50 publications specifically on V3 versican, so it is a very understudied member of the versican family, partly because to date there are no antibodies that can distinguish V3 from the CS-carrying isoforms of versican, that is, to facilitate functional and mechanistic studies. However, a number of in vitro and in vivo studies have identified the expression of the V3 transcript during different phases of development and in disease, and selective overexpression of V3 has shown dramatic phenotypic effects in "gain and loss of function" studies in experimental models. Thus, we thought it would be useful and instructive to discuss the discovery, characterization, and the putative biological importance of the enigmatic V3 isoform of versican.
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Affiliation(s)
- Thomas N Wight
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States
| | - Anthony J Day
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Inkyung Kang
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States
| | - Ingrid A Harten
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States
| | - Gernot Kaber
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Kathleen R Braun
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States
| | - Joan M Lemire
- Department of Biology, Tufts University, Medford, Massachusetts, United States
| | - Michael G Kinsella
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States
| | - Aleksander Hinek
- Translational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mervyn J Merrilees
- Department of Anatomy and Medical Imaging, University of Auckland, Auckland, New Zealand
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15
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Alcaide-Ruggiero L, Cugat R, Domínguez JM. Proteoglycans in Articular Cartilage and Their Contribution to Chondral Injury and Repair Mechanisms. Int J Mol Sci 2023; 24:10824. [PMID: 37446002 DOI: 10.3390/ijms241310824] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Proteoglycans are vital components of the extracellular matrix in articular cartilage, providing biomechanical properties crucial for its proper functioning. They are key players in chondral diseases, specifically in the degradation of the extracellular matrix. Evaluating proteoglycan molecules can serve as a biomarker for joint degradation in osteoarthritis patients, as well as assessing the quality of repaired tissue following different treatment strategies for chondral injuries. Despite ongoing research, understanding osteoarthritis and cartilage repair remains unclear, making the identification of key molecules essential for early diagnosis and effective treatment. This review offers an overview of proteoglycans as primary molecules in articular cartilage. It describes the various types of proteoglycans present in both healthy and damaged cartilage, highlighting their roles. Additionally, the review emphasizes the importance of assessing proteoglycans to evaluate the quality of repaired articular tissue. It concludes by providing a visual and narrative description of aggrecan distribution and presence in healthy cartilage. Proteoglycans, such as aggrecan, biglycan, decorin, perlecan, and versican, significantly contribute to maintaining the health of articular cartilage and the cartilage repair process. Therefore, studying these proteoglycans is vital for early diagnosis, evaluating the quality of repaired cartilage, and assessing treatment effectiveness.
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Affiliation(s)
- Lourdes Alcaide-Ruggiero
- Departamento de Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad de Córdoba, Hospital Clínico Veterinario, Campus de Rabanales, Ctra. Madrid-Cádiz Km 396, 14014 Córdoba, Spain
- Fundación García-Cugat, Plaza Alfonso Comín 5-7, 08023 Barcelona, Spain
| | - Ramón Cugat
- Fundación García-Cugat, Plaza Alfonso Comín 5-7, 08023 Barcelona, Spain
- Instituto Cugat y Mutualidad de Futbolistas Españoles, Delegación Catalana, 08023 Barcelona, Spain
| | - Juan Manuel Domínguez
- Departamento de Medicina y Cirugía Animal, Facultad de Veterinaria, Universidad de Córdoba, Hospital Clínico Veterinario, Campus de Rabanales, Ctra. Madrid-Cádiz Km 396, 14014 Córdoba, Spain
- Fundación García-Cugat, Plaza Alfonso Comín 5-7, 08023 Barcelona, Spain
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16
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Díez-Del-Molino D, Dehasque M, Chacón-Duque JC, Pečnerová P, Tikhonov A, Protopopov A, Plotnikov V, Kanellidou F, Nikolskiy P, Mortensen P, Danilov GK, Vartanyan S, Gilbert MTP, Lister AM, Heintzman PD, van der Valk T, Dalén L. Genomics of adaptive evolution in the woolly mammoth. Curr Biol 2023; 33:1753-1764.e4. [PMID: 37030294 DOI: 10.1016/j.cub.2023.03.084] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/24/2023] [Accepted: 03/29/2023] [Indexed: 04/10/2023]
Abstract
Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
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Affiliation(s)
- David Díez-Del-Molino
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
| | - Marianne Dehasque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - J Camilo Chacón-Duque
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alexei Tikhonov
- Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | | | - Foteini Kanellidou
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, 119017 Moscow, Russia
| | - Peter Mortensen
- Department of Zoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | - Gleb K Danilov
- Peter the Great Museum of Anthropology and Ethnography, Kunstkamera, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), 685000 Magadan, Russia
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway
| | | | - Peter D Heintzman
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Geological Sciences, Stockholm University, 11418 Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
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17
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Luo HL, Chang YL, Liu HY, Wu YT, Sung MT, Su YL, Huang CC, Wang PC, Peng JM. VCAN Hypomethylation and Expression as Predictive Biomarkers of Drug Sensitivity in Upper Urinary Tract Urothelial Carcinoma. Int J Mol Sci 2023; 24:ijms24087486. [PMID: 37108649 PMCID: PMC10139123 DOI: 10.3390/ijms24087486] [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: 02/24/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Versican (VCAN), also known as extracellular matrix proteoglycan 2, has been suggested as a potential biomarker in cancers. Previous research has found that VCAN is highly expressed in bladder cancer. However, its role in predicting outcomes for patients with upper urinary tract urothelial cancer (UTUC) is not well understood. In this study, we collected tissues from 10 patients with UTUC, including 6 with and 4 without lymphovascular invasion (LVI), a pathological feature that plays a significant role in determining metastasis. Results from RNA sequencing revealed that the most differentially expressed genes were involved in extracellular matrix organization. Using the TCGA database for clinical correlation, VCAN was identified as a target for study. A chromosome methylation assay showed that VCAN was hypomethylated in tumors with LVI. In our patient samples, VCAN expression was also found to be high in UTUC tumors with LVI. In vitro analysis showed that knocking down VCAN inhibited cell migration but not proliferation. A heatmap analysis also confirmed a significant correlation between VCAN and migration genes. Additionally, silencing VCAN increased the effectiveness of cisplatin, gemcitabine and epirubicin, thus providing potential opportunities for clinical application.
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Affiliation(s)
- Hao-Lun Luo
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Yin-Lun Chang
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Hui-Ying Liu
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Yen-Ting Wu
- Department of Urology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Ming-Tse Sung
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Yu-Li Su
- Department of Hematology and Oncology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Chun-Chieh Huang
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Pei-Chia Wang
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Jei-Ming Peng
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
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18
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Sagae Y, Horie A, Yanai A, Ohara T, Nakakita B, Kitawaki Y, Okunomiya A, Tani H, Yamaguchi K, Hamanishi J, Lydon JP, Daikoku T, Watanabe H, Mandai M. Versican provides the provisional matrix for uterine spiral artery dilation and fetal growth. Matrix Biol 2023; 115:16-31. [PMID: 36423736 DOI: 10.1016/j.matbio.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Abstract
The extracellular matrix (ECM) in the endometrium plays a crucial role in mammalian pregnancy. We have shown that versican secreted from the endometrial epithelium promotes embryo implantation. Versican is a proteoglycan, a major player in the provisional matrix, and versikine, its N-terminal fragment cleaved by ADAMTS proteinases, serves as a bioactive molecule. Here, since versican expression in the placenta was dynamically altered in humans and mice, we investigated the role of versican in pregnancy using uterine-specific Vcan deletion mice (uKO mice) and ADAMTS-resistant versican expressing mice (V1R mice). uKO mice exhibited insufficient spiral artery dilation, followed by fetal growth restriction and maternal hypertension. Further analysis revealed impaired proliferation of tissue-resident natural killer cells required for spiral artery dilation. V1R mice showed the same results as the control, eliminating the involvement of versikine. Our results provide a new concept that versican, one factor of ECM, contributes to placentation and following fetal growth.
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Affiliation(s)
- Yusuke Sagae
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akihito Horie
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Akihiro Yanai
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tsutomu Ohara
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Baku Nakakita
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshimi Kitawaki
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Asuka Okunomiya
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hirohiko Tani
- Department of Gynecology and Obstetrics, Shizuoka General Hospital, Shizuoka, Japan
| | - Ken Yamaguchi
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Junzo Hamanishi
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - John P Lydon
- Department of Pathology and Immunology, Center for Drug Discovery, Center for Reproductive Medicine, Baylor College of Medicine, Houston, TX, United States of America
| | - Takiko Daikoku
- Division of Animal Disease Model, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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19
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Zhong J, Shi J, Zhang X, Xu K, Zhang X, Xie Y, Li Y. A novel splicing variant of VCAN identified in a Chinese family initially diagnosed with familial exudative vitreoretinopathy. Mol Genet Genomic Med 2022; 11:e2083. [PMID: 36333947 PMCID: PMC9938748 DOI: 10.1002/mgg3.2083] [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: 04/24/2022] [Revised: 08/30/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Wagner vitreoretinopathy (WVR) is a rare autosomal dominant vitreoretinopathy caused by pathogenic variants in the VCAN gene. The aim of this study was to report a novel splicing variant in VCAN identified in a three-generation Chinese family initially diagnosed with familial exudative vitreoretinopathy and to describe the patients' clinical features. METHODS Four affected individuals from a three-generation family underwent detailed ophthalmic examinations, including best-corrected visual acuity by Snellen E chart, slit-lamp biomicroscopy, indirect ophthalmoscopy under pupil dilatation, ocular B-ultrasonography, optical coherence tomography scans, and fundus autofluorescence. Targeted next-generation sequencing was performed to identify variants of the disease-causing gene for the proband, followed by co-segregation analysis using Sanger-DNA sequencing. Reverse transcriptase-polymerase chain reaction (RT-PCR) was carried out to verify the effects of a variant on VCAN pre-mRNA splicing in the lymphocytes from the patients. RESULTS We detected a novel heterozygous variant c.4004-4_c.4004-3delinsCA of VCAN in all four affected individuals. RT-PCR revealed that the novel variant caused an abnormal splicing in exon 8 of the VCAN and imbalanced versican transcripts. All four patients presented vitreous syneresis and bilateral retinal detachment occurring at different ages. The patients also showed different extents of visual defects and diverse clinical manifestations, including cataract, iris-lens synechiae, inverted papillae, and ectopic foveas. CONCLUSIONS Our results expand the mutation spectrum of VCAN and further confirm that the splicing sites for exon 8 are mutation hot spots. Patients with WVR may present high phenotype variation; therefore, molecular analysis is very important for precise diagnosis of patients with inherited vitreoretinopathy.
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Affiliation(s)
- Junwei Zhong
- Beijing Institute of Ophthalmology, Beijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical UniversityBeijingChina
| | - Jie Shi
- Beijing Institute of Ophthalmology, Beijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical UniversityBeijingChina
| | - Xiaotian Zhang
- Clinical College of OphthalmologyTianjin Medical UniversityTianjinChina,Nankai University Eye HospitalTianjinChina,Tianjin Key Laboratory of Ophthalmology and Visual ScienceTianjin Eye HospitalTianjinChina
| | - Ke Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical UniversityBeijingChina
| | - Xiaohui Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical UniversityBeijingChina
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical UniversityBeijingChina
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Hospital, Capital Medical UniversityBeijingChina
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20
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McDaniels JM, Shetty AC, Rousselle TV, Bardhi E, Maluf DG, Mas VR. The cellular landscape of the normal kidney allograft: Main players balancing the alloimmune response. FRONTIERS IN TRANSPLANTATION 2022; 1:988238. [PMID: 38994377 PMCID: PMC11235379 DOI: 10.3389/frtra.2022.988238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/22/2022] [Indexed: 07/13/2024]
Abstract
Despite recent advances made in short-term outcomes; minimal improvements have been observed in long-term kidney transplantation outcomes. Due to an imbalance between organ transplant availability and patient waiting list, expanding kidney allograft longevity is a critical need in the field. Prior studies have either focused on early ischemic and immunological conditions affecting kidney allografts (e.g., delayed graft function, acute rejection) or late stage chronic injury when interventions are no longer feasible. However, studies characterizing kidney allografts with normal function by its cellular distribution, cell-cell interactions, and associated molecular pathways are lacking. Herein, we used single nuclei RNA-sequencing to uncover the cellular landscape and transcriptome of the normal kidney allograft. We profiled 40,950 nuclei from seven human kidney biopsies (normal native, N = 3; normal allograft, N = 4); normal allograft protocol biopsies were collected ≥15-months post-transplant. A total of 17 distinct cell clusters were identified with proximal tubules (25.70 and 21.01%), distal tubules (15.22 and 18.20%), and endothelial cells (EC) (4.26 and 9.94%) constituting the major cell populations of normal native and normal allograft kidneys, respectively. A large proportion of cycling cells from normal native kidneys were in G1-phase (43.96%) whereas cells from normal allograft were predominantly in S-phase (32.69%). This result suggests that transcriptional differences between normal native and normal allograft biopsies are dependent on the new host environment, immunosuppression, and injury-affliction. In the normal allograft, EC-specific genes upregulated metabolism, the immune response, and cellular growth, emphasizing their role in maintaining homeostasis during the ongoing alloreactive stress response. Immune cells, including B (2.81%), macrophages (24.96%), monocytes (15.29%), natural killer (NK) (12.83%), neutrophils (8.44%), and T cells (14.41%, were increased in normal allografts despite lack of histological or clinical evidence of acute rejection. Phenotypic characterization of immune cell markers supported lymphocyte activation and proinflammatory cytokines signaling pathways (i.e., IL-15, IL-32). The activation of B, NK, and T cells reveals potential immune cells underlying subclinical inflammation and repair. These single nuclei analyses provide novel insights into kidney and immune cell associated signaling pathways that portray kidney grafts with normal allograft function beyond 2-years post-transplant, revealing a novel perspective in understanding long-term allograft graft survival.
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Affiliation(s)
- Jennifer M McDaniels
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Amol C Shetty
- Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Thomas V Rousselle
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Elissa Bardhi
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
| | - Daniel G Maluf
- Program in Transplantation, School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Valeria R Mas
- Surgical Sciences Division, Department of Surgery, University of Maryland, Baltimore, MD, United States
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21
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Yuan M, Hu X, Yao L, Liu P, Jiang Y, Li L. Comprehensive bioinformatics and machine learning analysis identify VCAN as a novel biomarker of hepatitis B virus-related liver fibrosis. Front Mol Biosci 2022; 9:1010160. [PMID: 36275632 PMCID: PMC9585216 DOI: 10.3389/fmolb.2022.1010160] [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: 08/10/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatitis B virus (HBV) infection remains the leading cause of liver fibrosis (LF) worldwide, especially in China. Identification of decisive diagnostic biomarkers for HBV-associated liver fibrosis (HBV-LF) is required to prevent chronic hepatitis B (CHB) from progressing to liver cancer and to more effectively select the best treatment strategy. We obtained 43 samples from CHB patients without LF and 81 samples from CHB patients with LF (GSE84044 dataset). Among these, 173 differentially expressed genes (DEGs) were identified. Functional analysis revealed that these DEGs predominantly participated in immune-, extracellular matrix-, and metabolism-related processes. Subsequently, we integrated four algorithms (LASSO regression, SVM-RFE, RF, and WGCNA) to determine diagnostic biomarkers for HBV-LF. These analyses and receive operating characteristic curves identified the genes for phosphatidic acid phosphatase type 2C (PPAP2C) and versican (VCAN) as potentially valuable diagnostic biomarkers for HBV-LF. Single-sample gene set enrichment analysis (ssGSEA) further confirmed the immune landscape of HBV-LF. The two diagnostic biomarkers also significantly correlated with infiltrating immune cells. The potential regulatory mechanisms of VCAN underlying the occurrence and development of HBV-LF were also analyzed. These collective findings implicate VCAN as a novel diagnostic biomarker for HBV-LF, and infiltration of immune cells may critically contribute to the occurrence and development of HBV-LF.
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Affiliation(s)
- Mengqin Yuan
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xue Hu
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lichao Yao
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Pingji Liu
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yingan Jiang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
- *Correspondence: Lanjuan Li, ; Yingan Jiang,
| | - Lanjuan Li
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Lanjuan Li, ; Yingan Jiang,
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22
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Sin YJA, MacLeod R, Tanguay AP, Wang A, Braender-Carr O, Vitelli TM, Jay GD, Schmidt TA, Cowman MK. Noncovalent hyaluronan crosslinking by TSG-6: Modulation by heparin, heparan sulfate, and PRG4. Front Mol Biosci 2022; 9:990861. [PMID: 36275631 PMCID: PMC9579337 DOI: 10.3389/fmolb.2022.990861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The size, conformation, and organization of the glycosaminoglycan hyaluronan (HA) affect its interactions with soluble and cell surface-bound proteins. HA that is induced to form stable networks has unique biological properties relative to unmodified soluble HA. AlphaLISA assay technology offers a facile and general experimental approach to assay protein-mediated networking of HA in solution. Connections formed between two end-biotinylated 50 kDa HA (bHA) chains can be detected by signal arising from streptavidin-coated donor and acceptor beads being brought into close proximity when the bHA chains are bridged by proteins. We observed that incubation of bHA with the protein TSG-6 (tumor necrosis factor alpha stimulated gene/protein 6, TNFAIP/TSG-6) leads to dimerization or higher order multimerization of HA chains in solution. We compared two different heparin (HP) samples and two heparan sulfate (HS) samples for the ability to disrupt HA crosslinking by TSG-6. Both HP samples had approximately three sulfates per disaccharide, and both were effective in inhibiting HA crosslinking by TSG-6. HS with a relatively high degree of sulfation (1.75 per disaccharide) also inhibited TSG-6 mediated HA networking, while HS with a lower degree of sulfation (0.75 per disaccharide) was less effective. We further identified Proteoglycan 4 (PRG4, lubricin) as a TSG-6 ligand, and found it to inhibit TSG-6-mediated HA crosslinking. The effects of HP, HS, and PRG4 on HA crosslinking by TSG-6 were shown to be due to HP/HS/PRG4 inhibition of HA binding to the Link domain of TSG-6. Using the AlphaLISA platform, we also tested other HA-binding proteins for ability to create HA networks. The G1 domain of versican (VG1) effectively networked bHA in solution but required a higher concentration than TSG-6. Cartilage link protein (HAPLN1) and the HA binding protein segment of aggrecan (HABP, G1-IGD-G2) showed only low and variable magnitude HA networking effects. This study unambiguously demonstrates HA crosslinking in solution by TSG-6 and VG1 proteins, and establishes PRG4, HP and highly sulfated HS as modulators of TSG-6 mediated HA crosslinking.
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Affiliation(s)
- Yun Jin Ashley Sin
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, NY, United States
| | - Rebecca MacLeod
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, NY, United States
| | - Adam P. Tanguay
- Department of Biomedical Engineering, School of Dental Medicine, UConn Health, Farmington, CT, United States
| | - Andrew Wang
- New York Medical College, Valhalla, NY, United States
| | - Olivia Braender-Carr
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, NY, United States
| | - Teraesa M. Vitelli
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, NY, United States
| | - Gregory D. Jay
- Department of Emergency Medicine, Warren Alpert Medical School and School of Engineering, Brown University, Providence, RI, United States
| | - Tannin A. Schmidt
- Department of Biomedical Engineering, School of Dental Medicine, UConn Health, Farmington, CT, United States
- *Correspondence: Mary K. Cowman, ; Tannin A. Schmidt,
| | - Mary K. Cowman
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, NY, United States
- Department of Orthopedic Surgery, Grossman School of Medicine, New York University, New York, NY, United States
- *Correspondence: Mary K. Cowman, ; Tannin A. Schmidt,
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23
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Mead TJ, Bhutada S, Martin DR, Apte SS. Proteolysis: a key post-translational modification regulating proteoglycans. Am J Physiol Cell Physiol 2022; 323:C651-C665. [PMID: 35785985 PMCID: PMC9448339 DOI: 10.1152/ajpcell.00215.2022] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/22/2022]
Abstract
Proteoglycans are composite molecules comprising a protein backbone, i.e., the core protein, with covalently attached glycosaminoglycan chains of distinct chemical types. Most proteoglycans are secreted or attached to the cell membrane. Their specialized structures, binding properties, and biophysical attributes underlie diverse biological roles, which include modulation of tissue mechanics, cell adhesion, and the sequestration and regulated release of morphogens, growth factors, and cytokines. As an irreversible post-translational modification, proteolysis has a profound impact on proteoglycan function, abundance, and localization. Proteolysis is required for molecular maturation of some proteoglycans, clearance of extracellular matrix proteoglycans during tissue remodeling, generation of bioactive fragments from proteoglycans, and ectodomain shedding of cell-surface proteoglycans. Genetic evidence shows that proteoglycan core protein proteolysis is essential for diverse morphogenetic events during embryonic development. In contrast, dysregulated proteoglycan proteolysis contributes to osteoarthritis, cardiovascular disorders, cancer, and inflammation. Proteolytic fragments of perlecan, versican, aggrecan, brevican, collagen XVIII, and other proteoglycans are associated with independent biological activities as so-called matrikines. Yet, proteoglycan proteolysis has been investigated to only a limited extent to date. Here, we review the actions of proteases on proteoglycans and illustrate their functional impact with several examples. We discuss the applications and limitations of strategies used to define cleavage sites in proteoglycans and explain how proteoglycanome-wide proteolytic mapping, which is desirable to fully understand the impact of proteolysis on proteoglycans, can be facilitated by integrating classical proteoglycan isolation methods with mass spectrometry-based proteomics.
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Affiliation(s)
- Timothy J Mead
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Sumit Bhutada
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Daniel R Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio
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24
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Papadas A, Deb G, Cicala A, Officer A, Hope C, Pagenkopf A, Flietner E, Morrow ZT, Emmerich P, Wiesner J, Arauz G, Bansal V, Esbona K, Capitini CM, Matkowskyj KA, Deming DA, Politi K, Abrams SI, Harismendy O, Asimakopoulos F. Stromal remodeling regulates dendritic cell abundance and activity in the tumor microenvironment. Cell Rep 2022; 40:111201. [PMID: 35977482 PMCID: PMC9402878 DOI: 10.1016/j.celrep.2022.111201] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 06/10/2022] [Accepted: 07/20/2022] [Indexed: 11/24/2022] Open
Abstract
Stimulatory type 1 conventional dendritic cells (cDC1s) engage in productive interactions with CD8+ effectors along tumor-stroma boundaries. The paradoxical accumulation of “poised” cDC1s within stromal sheets is unlikely to simply reflect passive exclusion from tumor cores. Drawing parallels with embryonic morphogenesis, we hypothesized that invasive margin stromal remodeling generates developmentally conserved cell fate cues that regulate cDC1 behavior. We find that, in human T cell-inflamed tumors, CD8+ T cells penetrate tumor nests, whereas cDC1s are confined within adjacent stroma that recurrently displays site-specific proteolysis of the matrix proteoglycan versican (VCAN), an essential organ-sculpting modification in development. VCAN is necessary, and its proteolytic fragment (matrikine) versikine is sufficient for cDC1 accumulation. Versikine does not influence tumor-seeding pre-DC differentiation; rather, it orchestrates a distinctive cDC1 activation program conferring exquisite sensitivity to DNA sensing, supported by atypical innate lymphoid cells. Thus, peritumoral stroma mimicking embryonic provisional matrix remodeling regulates cDC1 abundance and activity to elicit T cell-inflamed tumor microenvironments. T cell-inflamed tumor microenvironments are a prerequisite for immunotherapy efficacy; however, why some tumors are inflamed and others not remains poorly understood. Papadas et al. link stromal reaction dynamics with T cell-induced inflammation. Peritumoral stroma emulating embryonic provisional matrix remodeling regulates cDC1-NK-CD8+ crosstalk to promote T cell repriming and penetration into tumor nests.
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Affiliation(s)
- Athanasios Papadas
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA; Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Gauri Deb
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Alexander Cicala
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Adam Officer
- Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA; Division of Biomedical Informatics, Department of Medicine, University of California, San Diego (UCSD), Moores Cancer Center, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Chelsea Hope
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA; Division of Hematology and Oncology, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Pagenkopf
- Division of Hematology and Oncology, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Evan Flietner
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA; Division of Hematology and Oncology, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary T Morrow
- Division of Hematology and Oncology, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Philip Emmerich
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua Wiesner
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Garrett Arauz
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Varun Bansal
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Karla Esbona
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Christian M Capitini
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA; Division of Hematology and Oncology, Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristina A Matkowskyj
- UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Dustin A Deming
- Division of Hematology and Oncology, Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA; McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA; Department of Medicine, Yale School of Medicine, New Haven, CT, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Scott I Abrams
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Olivier Harismendy
- Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA; Division of Biomedical Informatics, Department of Medicine, University of California, San Diego (UCSD), Moores Cancer Center, La Jolla, CA, USA
| | - Fotis Asimakopoulos
- Division of Blood and Marrow Transplantation, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego (UCSD), La Jolla, CA, USA.
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25
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Mechanical Properties of the Extracellular Environment of Human Brain Cells Drive the Effectiveness of Drugs in Fighting Central Nervous System Cancers. Brain Sci 2022; 12:brainsci12070927. [PMID: 35884733 PMCID: PMC9313046 DOI: 10.3390/brainsci12070927] [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: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of nanomechanical properties of tissues in health and disease is of increasing interest to scientists. It has been confirmed that these properties, determined in part by the composition of the extracellular matrix, significantly affect tissue physiology and the biological behavior of cells, mainly in terms of their adhesion, mobility, or ability to mutate. Importantly, pathophysiological changes that determine disease development within the tissue usually result in significant changes in tissue mechanics that might potentially affect the drug efficacy, which is important from the perspective of development of new therapeutics, since most of the currently used in vitro experimental models for drug testing do not account for these properties. Here, we provide a summary of the current understanding of how the mechanical properties of brain tissue change in pathological conditions, and how the activity of the therapeutic agents is linked to this mechanical state.
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26
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Garantziotis S, Savani RC. Proteoglycans in Toll-like receptor responses and innate immunity. Am J Physiol Cell Physiol 2022; 323:C202-C214. [PMID: 35675639 DOI: 10.1152/ajpcell.00088.2022] [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: 11/22/2022]
Abstract
The extracellular matrix (ECM) is an active and dynamic feature of tissues that not only provides gross structure but also plays key roles in cellular responses. The ever-changing microenvironment responds dynamically to cellular and external signals, and in turn influences cell fate, tissue development, and response to environmental injury or microbial invasion. It is therefore paramount to understand how the ECM components interact with each other, the environment and cells, and how they mediate their effects. Among the ECM components that have recently garnered increased attention, proteoglycans (PGs) deserve special note. Recent evidence strongly suggests that they play a crucial role both in health maintenance and disease development. In particular, proteoglycans dictate whether homeostasis or cell death will result from a given injury, by triggering and modulating activation of the innate immune system, via a conserved array of receptors that recognize exogenous (infectious) or endogenous (tissue damage) molecular patterns. Innate immune activation by proteoglycans has important implications for the understanding of cell-matrix interactions in health and disease. In this review, we will summarize the current state of knowledge of innate immune signaling by proteoglycans, discuss the implications, and explore future directions to define progress in this area of extracellular matrix biology.
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Affiliation(s)
- Stavros Garantziotis
- Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Rashmin C Savani
- Division of Neonatal-Perinatal Medicine, Center for Pulmonary & Vascular Biology, University of Texas Southwestern Medical Center, Dallas, Texas
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27
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Ding C, Zhang Q, Jiang X, Wei D, Xu S, Li Q, Wu M, Wang H. The Analysis of Potential Diagnostic and Therapeutic Targets for the Occurrence and Development of Gastric Cancer Based on Bioinformatics. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:4321466. [PMID: 35756405 PMCID: PMC9232307 DOI: 10.1155/2022/4321466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/09/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
Objective Gastric cancer is among the most common malignant tumors of the digestive system. This study explored the molecular mechanisms and potential therapeutic targets for gastric cancer occurrence and progression using bioinformatics. Methods The gastric cancer microarray dataset was downloaded from the Gene Expression Omnibus (GEO) database. The R package was used for data mining and screening differentially expressed genes (DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Based on the protein-protein interaction (PPI) network analysis, core targets and core subsets were screened. Then, the relationship between the expression level of the core genes and the prognosis of gastric cancer patients was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA) database. Results Using the GSE19826 and GSE54129 datasets, a total of 550 DEGs were identified, including 248 upregulated and 302 downregulated genes. GO and KEGG analyses showed that the upregulated DEGs were mainly enriched in the extracellular matrix (ECM) organization of the biological process (BP), the collagen-containing ECM of cellular component (CC), and the ECM structural constituent of molecular function (MF). DEGs were also enriched in human papillomavirus infections, the focal adhesion pathway, PI3K-Akt signaling pathway, and among others. The downregulated DEGs were mainly enriched in digestion, basal part of the cell, and aldo-keto reductase (NADP) activity. And the above pathways were enriched primarily in the metabolism of xenobiotics by cytochrome P450, drug metabolism-cytochrome P450, and retinol metabolism. Five core genes, including COL1A2, COL3A1, BGN, FN1, and VCAN, were significantly highly expressed in gastric cancer patients and were associated with poor prognosis. Conclusion This study identified new potential molecular targets closely related to gastric cancer occurrence and development via mining public data using bioinformatics analysis methods.
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Affiliation(s)
- Chuan Ding
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Qiqi Zhang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Xinying Jiang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Diandian Wei
- Department of Laboratory, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Shu Xu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Qingdai Li
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
| | - Meng Wu
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Hongbin Wang
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221000, China
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Tang F, Brune JE, Chang MY, Reeves SR, Altemeier WA, Frevert CW. Defining the Versican Interactome in Lung Health and Disease. Am J Physiol Cell Physiol 2022; 323:C249-C276. [PMID: 35649251 PMCID: PMC9291419 DOI: 10.1152/ajpcell.00162.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The extracellular matrix (ECM) imparts critical mechanical and biochemical information to cells in the lungs. Proteoglycans are essential constituents of the ECM and play a crucial role in controlling numerous biological processes, including regulating cellular phenotype and function. Versican, a chondroitin sulfate proteoglycan required for embryonic development, is almost absent from mature, healthy lungs and is re-expressed and accumulates in acute and chronic lung disease. Studies using genetically engineered mice show that the versican-enriched matrix can be pro- or anti-inflammatory depending on the cellular source or disease process studied. The mechanisms whereby versican develops a contextual ECM remain largely unknown. The primary goal of this review is to provide an overview of the interaction of versican with its many binding partners, the "versican interactome," and how through these interactions, versican is an integrator of complex extracellular information. Hopefully, the information provided in this review will be used to develop future studies to determine how versican and its binding partners can develop contextual ECMs that control select biological processes. While this review focuses on versican and the lungs, what is described can be extended to other proteoglycans, tissues, and organs.
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Affiliation(s)
- Fengying Tang
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Jourdan E Brune
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Mary Y Chang
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States
| | - Stephen R Reeves
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, United States.,Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - William A Altemeier
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,ivision of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Charles W Frevert
- Center for Lung Biology, the University of Washington at South Lake Union, Seattle, WA, United States.,Department of Comparative Medicine, University of Washington, Seattle, WA, United States.,ivision of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
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Wang C, Martins-Bach AB, Alfaro-Almagro F, Douaud G, Klein JC, Llera A, Fiscone C, Bowtell R, Elliott LT, Smith SM, Tendler BC, Miller KL. Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging. Nat Neurosci 2022; 25:818-831. [PMID: 35606419 PMCID: PMC9174052 DOI: 10.1038/s41593-022-01074-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 04/11/2022] [Indexed: 12/17/2022]
Abstract
A key aim in epidemiological neuroscience is identification of markers to assess brain health and monitor therapeutic interventions. Quantitative susceptibility mapping (QSM) is an emerging magnetic resonance imaging technique that measures tissue magnetic susceptibility and has been shown to detect pathological changes in tissue iron, myelin and calcification. We present an open resource of QSM-based imaging measures of multiple brain structures in 35,273 individuals from the UK Biobank prospective epidemiological study. We identify statistically significant associations of 251 phenotypes with magnetic susceptibility that include body iron, disease, diet and alcohol consumption. Genome-wide associations relate magnetic susceptibility to 76 replicating clusters of genetic variants with biological functions involving iron, calcium, myelin and extracellular matrix. These patterns of associations include relationships that are unique to QSM, in particular being complementary to T2* signal decay time measures. These new imaging phenotypes are being integrated into the core UK Biobank measures provided to researchers worldwide, creating the potential to discover new, non-invasive markers of brain health.
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Affiliation(s)
- Chaoyue Wang
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Aurea B Martins-Bach
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Fidel Alfaro-Almagro
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Gwenaëlle Douaud
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Johannes C Klein
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Alberto Llera
- Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Nijmegen, the Netherlands
| | - Cristiana Fiscone
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Richard Bowtell
- Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham, Nottingham, UK
| | - Lloyd T Elliott
- Department of Statistics and Actuarial Science, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Stephen M Smith
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Benjamin C Tendler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
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Rekad Z, Izzi V, Lamba R, Ciais D, Van Obberghen-Schilling E. The Alternative Matrisome: alternative splicing of ECM proteins in development, homeostasis and tumor progression. Matrix Biol 2022; 111:26-52. [DOI: 10.1016/j.matbio.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
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Abstract
Aggrecan (Acan) and versican (Vcan) are large chondroitin sulfate proteoglycans of the extracellular matrix. They share the same structural domains at both N and C-termini. The N-terminal G1 domain binds hyaluronan (HA), forms an HA-rich matrix, and regulates HA-mediated signaling. The C-terminal G3 domain binds other extracellular matrix molecules and forms a supramolecular structure that stores TGFb and BMPs and regulates their signaling. EGF-like motifs in the G3 domain may directly act like an EGF ligand. Both Acan and Vcan are present in cartilage, intervertebral disc, brain, heart, and aorta. Their localizations are essentially reciprocal. This review describes their structural domains, expression patterns and functions, and regulation of their expression.
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Affiliation(s)
- Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
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Vojtusek IK, Laganovic M, Burek Kamenaric M, Bulimbasic S, Hrkac S, Salai G, Ivkovic V, Coric M, Novak R, Grgurevic L. First Characterization of ADAMTS-4 in Kidney Tissue and Plasma of Patients with Chronic Kidney Disease-A Potential Novel Diagnostic Indicator. Diagnostics (Basel) 2022; 12:diagnostics12030648. [PMID: 35328201 PMCID: PMC8947148 DOI: 10.3390/diagnostics12030648] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 01/04/2023] Open
Abstract
Background: We have previously shown that metzincin protease ADAMTS-4 accompanies renal fibrogenesis, as it appears in the blood of hemodialysis patients. Methods: Native kidney (NKB) and kidney transplant (TXCI) biopsy samples as well as plasma from patients with various stages of CKD were compared to controls. In paired analysis, 15 TXCI samples were compared with their zero-time biopsies (TX0). Tissues were evaluated and scored (interstitial fibrosis and tubular atrophy (IFTA) for NKB and Banff ci for TXCI). Immunohistochemical (IHC) staining for ADAMTS-4 and BMP-1 was performed. Plasma ADAMTS-4 was detected using ELISA. Results: ADAMTS-4 IHC expression was significantly higher in interstitial compartment (INT) of NKB and TXCI group in peritubular capillaries (PTC) and interstitial stroma (INT). Patients with higher stages of interstitial fibrosis (ci > 1 and IFTA > 1) expressed ADAMTS-4 in INT more frequently in both groups (p = 0.005; p = 0.013; respectively). In paired comparison, TXCI samples expressed ADAMTS-4 in INT and PTC more often than TX0. ADAMTS-4 plasma concentration varied significantly across CKD stages, being highest in CKD 2 and 3 compared to other groups (p = 0.0064). Hemodialysis patients had higher concentrations of ADAMTS-4 compared to peritoneal dialysis (p < 0.00001). Conclusion: ADAMTS-4 might have a significant role in CKD as a potential novel diagnostic indicator.
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Affiliation(s)
- Ivana Kovacevic Vojtusek
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (I.K.V.); (V.I.)
| | - Mario Laganovic
- Department of Nephrology, University Hospital Merkur, 10000 Zagreb, Croatia;
| | - Marija Burek Kamenaric
- Tissue Typing Center, Clinical Department for Transfusion Medicine and Transplantation Biology, University Hospital Center Zagreb, 10000 Zagreb, Croatia;
| | - Stela Bulimbasic
- Clinical Department of Pathology and Cytology, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (S.B.); (M.C.)
| | - Stela Hrkac
- Department of Emergency Medicine, University Hospital Center Zagreb, 10000 Zagreb, Croatia;
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (G.S.); (R.N.)
| | - Grgur Salai
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (G.S.); (R.N.)
- Teaching Institute of Emergency Medicine of the City of Zagreb, 10000 Zagreb, Croatia
| | - Vanja Ivkovic
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (I.K.V.); (V.I.)
- Department of Public Health, Faculty of Health Studies, University of Rijeka, 51000 Rijeka, Croatia
| | - Marijana Coric
- Clinical Department of Pathology and Cytology, University Hospital Center Zagreb, 10000 Zagreb, Croatia; (S.B.); (M.C.)
| | - Rudjer Novak
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (G.S.); (R.N.)
| | - Lovorka Grgurevic
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (G.S.); (R.N.)
- Department of Anatomy, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-91-589-52-40
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Zhang Z, Peng Y, Dang J, Liu X, Zhu D, Zhang Y, Shi Y, Fan H. Identification of key biomarkers related to epithelial-mesenchymal transition and immune infiltration in ameloblastoma using integrated bioinformatics analysis. Oral Dis 2022; 29:1657-1667. [PMID: 35226761 DOI: 10.1111/odi.14173] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/04/2022] [Accepted: 02/19/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE This study aimed to elucidate the underlying mechanisms of ameloblastoma (AM) through integrated bioinformatics analysis. METHODS We downloaded two microarrays of AMs from the GEO database and identified differentially expressed genes (DEGs) by integrated bioinformatics analysis. The enrichment analysis of DEGs was conducted to characterize GO and KEGG pathways. Protein-protein interaction (PPI) network and hub genes were screened via STRING and Cytoscape. CIBERSORT algorithm was utilized to analyze immune infiltration in AMs. We also verified the diagnostic and therapeutic value of hub genes. RESULTS Overall, 776 DEGs were identified in AMs through bioinformatics analysis. The function enrichment analysis shed light on pathways involved in AMs. Subsequently, we screened six hub genes via PPI network. Furthermore, we evaluated immune infiltration in AMs and found that macrophages may be participating in the progression of AMs. The upregulated expression of FN1 was related to the macrophages M2 polarization. Finally, ROC analysis indicated that six hub genes had high diagnostic value for AMs and 11 drugs interacted with upregulated hub genes were identified by screening the DGIdb database. CONCLUSION This study revealed the underlying mechanisms of pathogenesis and biological behavior of AMs and provided candidate targets for the diagnosis and treatment of AMs.
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Affiliation(s)
- Zhao Zhang
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Ye Peng
- Department of Orthopaedics, Air Force Medical Center, PLA, Beijing, China
| | - Jingyi Dang
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Xincheng Liu
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Dongze Zhu
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Yushen Zhang
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Yubo Shi
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
| | - Hongbin Fan
- Division of Musculoskeletal Cancer Service, Department of Orthopaedic Surgery, Xi-jing Hospital, The Fourth Military Medical University, Shaanxi, China
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Brune JE, Chang MY, Altemeier WA, Frevert CW. Type I Interferon Signaling Increases Versican Expression and Synthesis in Lung Stromal Cells During Influenza Infection. J Histochem Cytochem 2021; 69:691-709. [PMID: 34666527 PMCID: PMC8554580 DOI: 10.1369/00221554211054447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/09/2021] [Indexed: 12/20/2022] Open
Abstract
Versican, a chondroitin sulfate proteoglycan, is an essential component of the extracellular matrix (ECM) in inflammatory lung disease. Versican's potential as an immunomodulatory molecule makes it a promising therapeutic target for controlling host immune responses in the lungs. To establish changes to versican expression and accumulation during influenza A viral pneumonia, we document the temporal and spatial changes to versican mRNA and protein in concert with pulmonary inflammatory cell infiltration. These studies were performed in the lungs of wild-type C57BL6/J mice on days 3, 6, 9, and 12 post-infection with influenza A virus using immunohistochemistry, in situ hybridization, and quantitative digital pathology. Using duplex in situ hybridization, we demonstrate that type I interferon signaling contributes significantly to versican expression in lung stromal cells. Our findings show that versican is a type I interferon-stimulated gene in pulmonary fibroblasts and pericytes in the context of viral pneumonia. These data also provide a guide for future studies to determine the role of versican in the pulmonary immune response to influenza infection.
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Affiliation(s)
- Jourdan E. Brune
- Center for Lung Biology, University of Washington, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - Mary Y. Chang
- Center for Lung Biology, University of Washington, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - William A. Altemeier
- Center for Lung Biology, University of Washington, Seattle, Washington
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Charles W. Frevert
- Center for Lung Biology, University of Washington, Seattle, Washington
- Department of Comparative Medicine, University of Washington, Seattle, Washington
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
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35
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Hirani P, Gauthier V, Allen CE, Wight TN, Pearce OMT. Targeting Versican as a Potential Immunotherapeutic Strategy in the Treatment of Cancer. Front Oncol 2021; 11:712807. [PMID: 34527586 PMCID: PMC8435723 DOI: 10.3389/fonc.2021.712807] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/11/2021] [Indexed: 12/25/2022] Open
Abstract
A growing body of literature links events associated with the progression and severity of immunity and inflammatory disease with the composition of the tissue extracellular matrix as defined by the matrisome. One protein in the matrisome that is common to many inflammatory diseases is the large proteoglycan versican, whose varied function is achieved through multiple isoforms and post-translational modifications of glycosaminoglycan structures. In cancer, increased levels of versican are associated with immune cell phenotype, disease prognosis and failure to respond to treatment. Whether these associations between versican expression and tumour immunity are the result of a direct role in the pathogenesis of tumours is not clear. In this review, we have focused on the role of versican in the immune response as it relates to tumour progression, with the aim of determining whether our current understanding of the immunobiology of versican warrants further study as a cancer immunotherapy target.
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Affiliation(s)
- Priyanka Hirani
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Valentine Gauthier
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Carys E Allen
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Thomas N Wight
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - Oliver M T Pearce
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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Hayes AJ, Melrose J. Neural Tissue Homeostasis and Repair Is Regulated via CS and DS Proteoglycan Motifs. Front Cell Dev Biol 2021; 9:696640. [PMID: 34409033 PMCID: PMC8365427 DOI: 10.3389/fcell.2021.696640] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
Chondroitin sulfate (CS) is the most abundant and widely distributed glycosaminoglycan (GAG) in the human body. As a component of proteoglycans (PGs) it has numerous roles in matrix stabilization and cellular regulation. This chapter highlights the roles of CS and CS-PGs in the central and peripheral nervous systems (CNS/PNS). CS has specific cell regulatory roles that control tissue function and homeostasis. The CNS/PNS contains a diverse range of CS-PGs which direct the development of embryonic neural axonal networks, and the responses of neural cell populations in mature tissues to traumatic injury. Following brain trauma and spinal cord injury, a stabilizing CS-PG-rich scar tissue is laid down at the defect site to protect neural tissues, which are amongst the softest tissues of the human body. Unfortunately, the CS concentrated in gliotic scars also inhibits neural outgrowth and functional recovery. CS has well known inhibitory properties over neural behavior, and animal models of CNS/PNS injury have demonstrated that selective degradation of CS using chondroitinase improves neuronal functional recovery. CS-PGs are present diffusely in the CNS but also form denser regions of extracellular matrix termed perineuronal nets which surround neurons. Hyaluronan is immobilized in hyalectan CS-PG aggregates in these perineural structures, which provide neural protection, synapse, and neural plasticity, and have roles in memory and cognitive learning. Despite the generally inhibitory cues delivered by CS-A and CS-C, some CS-PGs containing highly charged CS disaccharides (CS-D, CS-E) or dermatan sulfate (DS) disaccharides that promote neural outgrowth and functional recovery. CS/DS thus has varied cell regulatory properties and structural ECM supportive roles in the CNS/PNS depending on the glycoform present and its location in tissue niches and specific cellular contexts. Studies on the fruit fly, Drosophila melanogaster and the nematode Caenorhabditis elegans have provided insightful information on neural interconnectivity and the role of the ECM and its PGs in neural development and in tissue morphogenesis in a whole organism environment.
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Affiliation(s)
- Anthony J. Hayes
- Bioimaging Research Hub, Cardiff School of Biosciences, Cardiff University, Wales, United Kingdom
| | - James Melrose
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, Australia
- Raymond Purves Bone and Joint Research Laboratories, Kolling Institute of Medical Research, Royal North Shore Hospital and The Faculty of Medicine and Health, The University of Sydney, St. Leonard’s, NSW, Australia
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Zhong A, Ding N, Zhou Y, Yang G, Peng Z, Zhang H, Chai X. Identification of Hub Genes Associated with the Pathogenesis of Intracranial Aneurysm via Integrated Bioinformatics Analysis. Int J Gen Med 2021; 14:4039-4050. [PMID: 34354366 PMCID: PMC8331219 DOI: 10.2147/ijgm.s320396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/09/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND At present, the pathogenesis of intracranial aneurysms (IA) remains unclear, which significantly hinders the development of novel strategies for the clinical treatment. In this study, bioinformatics methods were used to identify the potential hub genes and pathways associated with the pathogenesis of IA. METHODS The gene expression datasets of patients with intracranial aneurysm were downloaded from the Gene Expression Database (GEO), and the different data sets were integrated by the robust rank aggregation (RRA) method to identify the differentially expressed genes between patients with intracranial aneurysm and the controls. The functional enrichment analyses of the significant differentially expressed genes (DEGs) were performed and the protein-protein interaction (PPI) network was constructed; thereafter, the hub genes were screened by cytoHubba plug-in of Cytoscape, and finally sequencing dataset GSE122897 was used to verify the hub genes. RESULTS The GSE15629, GSE75436, GSE26969, and GSE6551 expression profiles have been included in this study, including 34 intracranial aneurysm samples and 26 control samples. The four datasets obtained 136 significant DEGs (45 up-regulated, 91 down-regulated). Enrichment analysis showed that the extracellular matrix structural constituent and the ECM-receptor interaction were closely related to the occurrence of IA. It was finally determined that eight hub genes associated with the development of IA, including VCAN, COL1A1, COL11A1, COL5A1, COL5A2, POSTN, THBS2, and CDH2. CONCLUSION The discovery of potential hub genes and pathways could enhance the understanding of the molecular mechanisms associated with the development of IA. These hub genes may be potential therapeutic targets for the management and new biomarker for the diagnosis of IA.
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Affiliation(s)
- Aifang Zhong
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Ning Ding
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Yang Zhou
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Guifang Yang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Zhenyu Peng
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Hongliang Zhang
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Emergency Medicine and Difficult Disease Institute, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
| | - Xiangping Chai
- Department of Emergency Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Trauma center, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People’s Republic of China
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Poole JJA, Mostaço-Guidolin LB. Optical Microscopy and the Extracellular Matrix Structure: A Review. Cells 2021; 10:1760. [PMID: 34359929 PMCID: PMC8308089 DOI: 10.3390/cells10071760] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Biological tissues are not uniquely composed of cells. A substantial part of their volume is extracellular space, which is primarily filled by an intricate network of macromolecules constituting the extracellular matrix (ECM). The ECM serves as the scaffolding for tissues and organs throughout the body, playing an essential role in their structural and functional integrity. Understanding the intimate interaction between the cells and their structural microenvironment is central to our understanding of the factors driving the formation of normal versus remodelled tissue, including the processes involved in chronic fibrotic diseases. The visualization of the ECM is a key factor to track such changes successfully. This review is focused on presenting several optical imaging microscopy modalities used to characterize different ECM components. In this review, we describe and provide examples of applications of a vast gamut of microscopy techniques, such as widefield fluorescence, total internal reflection fluorescence, laser scanning confocal microscopy, multipoint/slit confocal microscopy, two-photon excited fluorescence (TPEF), second and third harmonic generation (SHG, THG), coherent anti-Stokes Raman scattering (CARS), fluorescence lifetime imaging microscopy (FLIM), structured illumination microscopy (SIM), stimulated emission depletion microscopy (STED), ground-state depletion microscopy (GSD), and photoactivated localization microscopy (PALM/fPALM), as well as their main advantages, limitations.
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Affiliation(s)
- Joshua J A Poole
- Department of Systems and Computer Engineering, Faculty of Engineering and Design, Carleton University 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Leila B Mostaço-Guidolin
- Department of Systems and Computer Engineering, Faculty of Engineering and Design, Carleton University 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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Wang Y, Xiao Y, Zheng Y, Yang L, Wang D. An anti-ADAMTS1 treatment relieved muscle dysfunction and fibrosis in dystrophic mice. Life Sci 2021; 281:119756. [PMID: 34175316 DOI: 10.1016/j.lfs.2021.119756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 11/27/2022]
Abstract
Duchenne Muscular Dystrophy (DMD) is caused by mutations in the dystrophin gene, accompanied by aberrant extracellular matrix synthesis and muscle damage. ADAMTS1 metalloproteinase was reported increased in dystrophin-deficient mdx mouse. The aim of this study was to explore the role of ADAMTS1 in muscle function, fibrosis and damage, and respiratory function of mdx mice. 102 DMD patients and their mothers were included in this study. Multiplex ligation dependent probe amplification (MLPA) assay and Next-generation sequencing (NGS) were adopted to do genetic diagnosis. Dystrophin-deficient mdx mice were treated with anti-ADAMTS1 antibody (anti-ADAMTS1) for three weeks. The results showed that ADAMTS1 was increased in gastrocnemius muscle of mdx mice and serum of DMD patients. Anti-ADAMTS1 treatment increased Versican transcription but suppressed versican protein expression. Besides, we found anti-ADAMTS1 improved muscle strength, diaphragm and extensor digitorum longus muscles functions in mdx mice. Meanwhile, muscle fibrosis and damage were attenuated in anti-ADAMTS1 treated dystrophic mice. In summary, anti-ADAMTS1 antibody relieved muscle dysfunction and fibrosis in dystrophic mice. It is suggested that ADAMTS1 is a potential target for developing new biological therapies for DMD.
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Affiliation(s)
- Yan Wang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi 'an 710004, Shaanxi Province, China; Department of Neurology, Xi'an Children's Hospital, Xi'an 710000, Shaanxi Province, China
| | - Yanfeng Xiao
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi 'an 710004, Shaanxi Province, China.
| | - Yanyan Zheng
- Department of Neurology, Xi'an Children's Hospital, Xi'an 710000, Shaanxi Province, China
| | - Le Yang
- Department of Neurology, Xi'an Children's Hospital, Xi'an 710000, Shaanxi Province, China
| | - Dong Wang
- Department of Neurology, Xi'an Children's Hospital, Xi'an 710000, Shaanxi Province, China
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40
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Higuchi T, Suzuki D, Watanabe T, Fanhchaksai K, Ota K, Yokoo K, Furukawa H, Watanabe H. Versican contributes to ligament formation of knee joints. PLoS One 2021; 16:e0250366. [PMID: 33886644 PMCID: PMC8061984 DOI: 10.1371/journal.pone.0250366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Versican is a large proteoglycan in the extracellular matrix. During embryonic stages, it plays a crucial role in the development of cartilage, heart, and dermis. Previously, we reported that Prx1-Vcan conditional knockout mice, lacking Vcan expression in mesenchymal condensation areas of the limb bud, show the impaired joint formation and delayed cartilage development. Here, we investigated their phenotype in adults and found that they develop swelling of the knee joint. Histologically, their newborn joint exhibited impaired formation of both anterior and posterior cruciate ligaments. Immunostaining revealed a decrease in scleraxis-positive cells in both articular cartilage and ligament of Prx1-Vcan knee joint, spotty patterns of type I collagen, and the presence of type II collagen concomitant with the absence of versican expression. These results suggest that versican expression during the perinatal period is required for cruciate ligaments’ formation and that its depletion affects joint function in later ages.
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Affiliation(s)
- Tomoko Higuchi
- Department of Plastic Surgery, Aichi Medical University, Nagakute, Japan
| | - Daisuke Suzuki
- Department of Health Sciences, Hokkaido Chitose College of Rehabilitation, Chitose, Japan
| | - Takafumi Watanabe
- Laboratory of Veterinary Anatomy, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Kanda Fanhchaksai
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
| | - Keiko Ota
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
| | - Kazuhisa Yokoo
- Department of Plastic Surgery, Aichi Medical University, Nagakute, Japan
| | - Hiroshi Furukawa
- Department of Plastic Surgery, Aichi Medical University, Nagakute, Japan
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Nagakute, Japan
- * E-mail:
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Fontanil T, Mohamedi Y, Espina-Casado J, Obaya ÁJ, Cobo T, Cal S. Hyalectanase Activities by the ADAMTS Metalloproteases. Int J Mol Sci 2021; 22:ijms22062988. [PMID: 33804223 PMCID: PMC8000579 DOI: 10.3390/ijms22062988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
The hyalectan family is composed of the proteoglycans aggrecan, versican, brevican and neurocan. Hyalectans, also known as lecticans, are components of the extracellular matrix of different tissues and play essential roles in key biological processes including skeletal development, and they are related to the correct maintenance of the vascular and central nervous system. For instance, hyalectans participate in the organization of structures such as perineural nets and in the regulation of neurite outgrowth or brain recovery following a traumatic injury. The ADAMTS (A Disintegrin and Metalloprotease domains, with thrombospondin motifs) family consists of 19 secreted metalloproteases. These enzymes also perform important roles in the structural organization and function of the extracellular matrix through interactions with other matrix components or as a consequence of their catalytic activity. In this regard, some of their preferred substrates are the hyalectans. In fact, ADAMTSs cleave hyalectans not only as a mechanism for clearance or turnover of proteoglycans but also to generate bioactive fragments which display specific functions. In this article we review some of the physiological and pathological effects derived from cleavages of hyalectans mediated by ADAMTSs.
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Affiliation(s)
- Tania Fontanil
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain; (T.F.); (Y.M.)
- Departamento de Investigación, Instituto Ordóñez, 33012 Oviedo, Spain
| | - Yamina Mohamedi
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain; (T.F.); (Y.M.)
| | - Jorge Espina-Casado
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo, Spain;
| | - Álvaro J. Obaya
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología, IUOPA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Teresa Cobo
- Departamento de Cirugía y Especialidades Médico-Quirúrgicas, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto Asturiano de Odontología, 33006 Oviedo, Spain
- Correspondence: (T.C.); (S.C.); Tel.: +34-985966014 (T.C.); +34-985106282 (S.C.)
| | - Santiago Cal
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, 33006 Oviedo, Spain; (T.F.); (Y.M.)
- Instituto Universitario de Oncología, IUOPA, Universidad de Oviedo, 33006 Oviedo, Spain
- Correspondence: (T.C.); (S.C.); Tel.: +34-985966014 (T.C.); +34-985106282 (S.C.)
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Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines. Biomolecules 2021; 11:biom11020177. [PMID: 33525507 PMCID: PMC7912277 DOI: 10.3390/biom11020177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/13/2022] Open
Abstract
Neuroblastoma (NBL) is a pediatric cancer responsible for more than 15% of cancer deaths in children, with 800 new cases each year in the United States alone. Genomic amplification of the MYC oncogene family member MYCN characterizes a subset of high-risk pediatric neuroblastomas. Several cellular models have been implemented to study this disease over the years. Two of these, SK-N-BE-2-C (BE2C) and Kelly, are amongst the most used worldwide as models of MYCN-Amplified human NBL. Here, we provide a transcriptome-wide quantitative measurement of gene expression and transcriptional network activity in BE2C and Kelly cell lines at an unprecedented single-cell resolution. We obtained 1105 Kelly and 962 BE2C unsynchronized cells, with an average number of mapped reads/cell of roughly 38,000. The single-cell data recapitulate gene expression signatures previously generated from bulk RNA-Seq. We highlight low variance for commonly used housekeeping genes between different cells (ACTB, B2M and GAPDH), while showing higher than expected variance for metallothionein transcripts in Kelly cells. The high number of samples, despite the relatively low read coverage of single cells, allowed for robust pathway enrichment analysis and master regulator analysis (MRA), both of which highlight the more mesenchymal nature of BE2C cells as compared to Kelly cells, and the upregulation of TWIST1 and DNAJC1 transcriptional networks. We further defined master regulators at the single cell level and showed that MYCN is not constantly active or expressed within Kelly and BE2C cells, independently of cell cycle phase. The dataset, alongside a detailed and commented programming protocol to analyze it, is fully shared and reusable.
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