1
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Ding Y, Zhou Q, Ding B, Zhang Y, Shen Y. Transcriptome analysis reveals the clinical significance of CXCL13 in Pan-Gyn tumors. J Cancer Res Clin Oncol 2024; 150:116. [PMID: 38459390 PMCID: PMC10923744 DOI: 10.1007/s00432-024-05619-3] [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: 12/02/2023] [Accepted: 01/09/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Gynecologic and breast tumors (Pan-Gyn) exhibit similar characteristics, and the role of CXCL13 in anti-tumor immunity and it's potential as a biomarker for immune checkpoint blockade (ICB) therapy have been gradually revealed. However, the precise role of CXCL13 in Pan-Gyn remains unclear, lacking a systematic analysis. METHODS We analyzed 2497 Pan-Gyn samples from the TCGA database, categorizing them into high and low CXCL13 expression groups. Validation was conducted using tumor expression datasets sourced from the GEO database. Correlation between CXCL13 and tumor immune microenvironment (TIME) was evaluated using multiple algorithms. Finally, we established nomograms for 3-year and 5-year mortality. RESULTS High expression of CXCL13 in Pan-Gyn correlates with a favorable clinical prognosis, increased immune cell infiltration, and reduced intra-tumor heterogeneity. Model was assessed using the C-index [BRCA: 0.763 (0.732-0.794), UCEC: 0.821 (0.793-0.849), CESC: 0.736 (0.684-0.788), and OV: 0.728 (0.707-0.749)], showing decent prediction of discrimination and calibration. CONCLUSION Overall, this study provides comprehensive insights into the commonalities and differences of CXCL13 in Pan-Gyn, potentially opening new avenues for personalized treatment.
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Affiliation(s)
- Yue Ding
- Zhongda Hospital Southeast University, Nanjing, China
| | - Quan Zhou
- Zhongda Hospital Southeast University, Nanjing, China
| | - Bo Ding
- Zhongda Hospital Southeast University, Nanjing, China
| | - Yang Zhang
- Department of Obstetrics and Gynecology, First People's Hospital of Lianyungang, No. 6 East Zhenhua Road, Haizhou, Lianyungang, China
| | - Yang Shen
- Zhongda Hospital Southeast University, Nanjing, China.
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2
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Blanchet X, Weber C, von Hundelshausen P. Chemokine Heteromers and Their Impact on Cellular Function-A Conceptual Framework. Int J Mol Sci 2023; 24:10925. [PMID: 37446102 DOI: 10.3390/ijms241310925] [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: 05/26/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Chemoattractant cytokines or chemokines are proteins involved in numerous biological activities. Their essential role consists of the formation of gradient and (immune) cell recruitment. Chemokine biology and its related signaling system is more complex than simple ligand-receptor interactions. Beside interactions with their cognate and/or atypical chemokine receptors, and glycosaminoglycans (GAGs), chemokines form complexes with themselves as homo-oligomers, heteromers and also with other soluble effector proteins, including the atypical chemokine MIF, carbohydrate-binding proteins (galectins), damage-associated molecular patterns (DAMPs) or with chemokine-binding proteins such as evasins. Likewise, nucleic acids have been described as binding targets for the tetrameric form of CXCL4. The dynamic balance between monomeric and dimeric structures, as well as interactions with GAGs, modulate the concentrations of free chemokines available along with the nature of the gradient. Dimerization of chemokines changes the canonical monomeric fold into two main dimeric structures, namely CC- and CXC-type dimers. Recent studies highlighted that chemokine dimer formation is a frequent event that could occur under pathophysiological conditions. The structural changes dictated by chemokine dimerization confer additional biological activities, e.g., biased signaling. The present review will provide a short overview of the known functionality of chemokines together with the consequences of the interactions engaged by the chemokines with other proteins. Finally, we will present potential therapeutic tools targeting the chemokine multimeric structures that could modulate their biological functions.
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Affiliation(s)
- Xavier Blanchet
- Institute for Cardiovascular Prevention (IPEK), LMU Munich, 80336 Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), LMU Munich, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80636 Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, 6229 HX Maastricht, The Netherlands
| | - Philipp von Hundelshausen
- Institute for Cardiovascular Prevention (IPEK), LMU Munich, 80336 Munich, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80636 Munich, Germany
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3
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Hogwood J, Mulloy B, Lever R, Gray E, Page CP. Pharmacology of Heparin and Related Drugs: An Update. Pharmacol Rev 2023; 75:328-379. [PMID: 36792365 DOI: 10.1124/pharmrev.122.000684] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/17/2023] Open
Abstract
Heparin has been used extensively as an antithrombotic and anticoagulant for close to 100 years. This anticoagulant activity is attributed mainly to the pentasaccharide sequence, which potentiates the inhibitory action of antithrombin, a major inhibitor of the coagulation cascade. More recently it has been elucidated that heparin exhibits anti-inflammatory effect via interference of the formation of neutrophil extracellular traps and this may also contribute to heparin's antithrombotic activity. This illustrates that heparin interacts with a broad range of biomolecules, exerting both anticoagulant and nonanticoagulant actions. Since our previous review, there has been an increased interest in these nonanticoagulant effects of heparin, with the beneficial role in patients infected with SARS2-coronavirus a highly topical example. This article provides an update on our previous review with more recent developments and observations made for these novel uses of heparin and an overview of the development status of heparin-based drugs. SIGNIFICANCE STATEMENT: This state-of-the-art review covers recent developments in the use of heparin and heparin-like materials as anticoagulant, now including immunothrombosis observations, and as nonanticoagulant including a role in the treatment of SARS-coronavirus and inflammatory conditions.
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Affiliation(s)
- John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Rebeca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
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4
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Pyle CJ, Patel DF, Peiró T, Joulia R, Grabiec AM, Hussell T, Tavernier G, Simpson A, Pease J, Harker JA, Lloyd CM, Snelgrove RJ. Matrix Metalloproteinase-12 Supports Pulmonary B Cell Follicle Formation and Local Antibody Responses During Asthma. Am J Respir Crit Care Med 2022; 206:1424-1428. [PMID: 35944138 PMCID: PMC9746859 DOI: 10.1164/rccm.202109-2082le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | | | - Teresa Peiró
- Imperial College LondonLondon, United Kingdom,Universidad de ValenciaValencia, Spain
| | | | - Aleksander M. Grabiec
- University of ManchesterManchester, United Kingdom,Jagiellonian UniversityKraków, Poland
| | | | - Gael Tavernier
- University of ManchesterManchester, United Kingdom,Manchester University National Health Service (NHS) Foundation TrustManchester, United Kingdom
| | - Angela Simpson
- University of ManchesterManchester, United Kingdom,Manchester University National Health Service (NHS) Foundation TrustManchester, United Kingdom
| | - James Pease
- Imperial College LondonLondon, United Kingdom
| | | | | | - Robert J. Snelgrove
- Imperial College LondonLondon, United Kingdom,Corresponding author (e-mail: )
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5
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Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states. Curr Opin Struct Biol 2022; 74:102356. [DOI: 10.1016/j.sbi.2022.102356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/08/2022] [Accepted: 02/13/2022] [Indexed: 11/18/2022]
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6
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Pan Z, Zhu T, Liu Y, Zhang N. Role of the CXCL13/CXCR5 Axis in Autoimmune Diseases. Front Immunol 2022; 13:850998. [PMID: 35309354 PMCID: PMC8931035 DOI: 10.3389/fimmu.2022.850998] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
CXCL13 is a B-cell chemokine produced mainly by mesenchymal lymphoid tissue organizer cells, follicular dendritic cells, and human T follicular helper cells. By binding to its receptor, CXCR5, CXCL13 plays an important role in lymphoid neogenesis, lymphoid organization, and immune responses. Recent studies have found that CXCL13 and its receptor CXCR5 are implicated in the pathogenesis of several autoimmune diseases, such as rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, primary Sjögren’s syndrome, myasthenia gravis, and inflammatory bowel disease. In this review, we discuss the biological features of CXCL13 and CXCR5 and the recent findings on the pathogenic roles of the CXCL13/CXCR5 axis in autoimmune diseases. Furthermore, we discuss the potential role of CXCL13 as a disease biomarker and therapeutic target in autoimmune diseases.
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Affiliation(s)
- Zijian Pan
- National Center for Birth Defect Monitoring, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, and State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tong Zhu
- National Center for Birth Defect Monitoring, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, and State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yanjun Liu
- National Center for Birth Defect Monitoring, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, and State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
| | - Nannan Zhang
- National Center for Birth Defect Monitoring, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, and State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
- *Correspondence: Nannan Zhang,
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7
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Mayfosh AJ, Nguyen TK, Hulett MD. The Heparanase Regulatory Network in Health and Disease. Int J Mol Sci 2021; 22:ijms222011096. [PMID: 34681753 PMCID: PMC8541136 DOI: 10.3390/ijms222011096] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
The extracellular matrix (ECM) is a structural framework that has many important physiological functions which include maintaining tissue structure and integrity, serving as a barrier to invading pathogens, and acting as a reservoir for bioactive molecules. This cellular scaffold is made up of various types of macromolecules including heparan sulfate proteoglycans (HSPGs). HSPGs comprise a protein core linked to the complex glycosaminoglycan heparan sulfate (HS), the remodeling of which is important for many physiological processes such as wound healing as well as pathological processes including cancer metastasis. Turnover of HS is tightly regulated by a single enzyme capable of cleaving HS side chains: heparanase. Heparanase upregulation has been identified in many inflammatory diseases including atherosclerosis, fibrosis, and cancer, where it has been shown to play multiple roles in processes such as epithelial-mesenchymal transition, angiogenesis, and cancer metastasis. Heparanase expression and activity are tightly regulated. Understanding the regulation of heparanase and its downstream targets is attractive for the development of treatments for these diseases. This review provides a comprehensive overview of the regulators of heparanase as well as the enzyme’s downstream gene and protein targets, and implications for the development of new therapeutic strategies.
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Affiliation(s)
- Alyce J. Mayfosh
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3083, Australia; (A.J.M.); (T.K.N.)
| | - Tien K. Nguyen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3083, Australia; (A.J.M.); (T.K.N.)
| | - Mark D. Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3083, Australia; (A.J.M.); (T.K.N.)
- Correspondence:
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8
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De Zutter A, Van Damme J, Struyf S. The Role of Post-Translational Modifications of Chemokines by CD26 in Cancer. Cancers (Basel) 2021; 13:cancers13174247. [PMID: 34503058 PMCID: PMC8428238 DOI: 10.3390/cancers13174247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 02/06/2023] Open
Abstract
Chemokines are a large family of small chemotactic cytokines that fulfill a central function in cancer. Both tumor-promoting and -impeding roles have been ascribed to chemokines, which they exert in a direct or indirect manner. An important post-translational modification that regulates chemokine activity is the NH2-terminal truncation by peptidases. CD26 is a dipeptidyl peptidase (DPPIV), which typically clips a NH2-terminal dipeptide from the chemokine. With a certain degree of selectivity in terms of chemokine substrate, CD26 only recognizes chemokines with a penultimate proline or alanine. Chemokines can be protected against CD26 recognition by specific amino acid residues within the chemokine structure, by oligomerization or by binding to cellular glycosaminoglycans (GAGs). Upon truncation, the binding affinity for receptors and GAGs is altered, which influences chemokine function. The consequences of CD26-mediated clipping vary, as unchanged, enhanced, and reduced activities are reported. In tumors, CD26 most likely has the most profound effect on CXCL12 and the interferon (IFN)-inducible CXCR3 ligands, which are converted into receptor antagonists upon truncation. Depending on the tumor type, expression of CD26 is upregulated or downregulated and often results in the preferential generation of the chemokine isoform most favorable for tumor progression. Considering the tight relationship between chemokine sequence and chemokine binding specificity, molecules with the appropriate characteristics can be chemically engineered to provide innovative therapeutic strategies in a cancer setting.
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9
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Sankaranarayanan NV, Nagarajan B, Desai UR. Combinatorial Virtual Library Screening Study of Transforming Growth Factor-β2-Chondroitin Sulfate System. Int J Mol Sci 2021; 22:7542. [PMID: 34299163 PMCID: PMC8305211 DOI: 10.3390/ijms22147542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
Transforming growth factor-beta (TGF-β), a member of the TGF-β cytokine superfamily, is known to bind to sulfated glycosaminoglycans (GAGs), but the nature of this interaction remains unclear. In a recent study, we found that preterm human milk TGF-β2 is sequestered by chondroitin sulfate (CS) in its proteoglycan form. To understand the molecular basis of the TGF-β2-CS interaction, we utilized the computational combinatorial virtual library screening (CVLS) approach in tandem with molecular dynamics (MD) simulations. All possible CS oligosaccharides were generated in a combinatorial manner to give 24 di- (CS02), 192 tetra- (CS04), and 1536 hexa- (CS06) saccharides. This library of 1752 CS oligosaccharides was first screened against TGF-β2 using the dual filter CVLS algorithm in which the GOLDScore and root-mean-square-difference (RMSD) between the best bound poses were used as surrogate markers for in silico affinity and in silico specificity. CVLS predicted that both the chain length and level of sulfation are critical for the high affinity and high specificity recognition of TGF-β2. Interestingly, CVLS led to identification of two distinct sites of GAG binding on TGF-β2. CVLS also deduced the preferred composition of the high specificity hexasaccharides, which were further assessed in all-atom explicit solvent MD simulations. The MD results confirmed that both sites of binding form stable GAG-protein complexes. More specifically, the highly selective CS chains were found to engage the TGF-β2 monomer with high affinity. Overall, this work present key principles of recognition with regard to the TGF-β2-CS system. In the process, it led to the generation of the in silico library of all possible CS oligosaccharides, which can be used for advanced studies on other protein-CS systems. Finally, the study led to the identification of unique CS sequences that are predicted to selectively recognize TGF-β2 and may out-compete common natural CS biopolymers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Balaji Nagarajan
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Umesh R. Desai
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, USA; (N.V.S.); (B.N.)
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
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10
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Unexpected enhancement of FVIII immunogenicity by endothelial expression in lentivirus-transduced and transgenic mice. Blood Adv 2021; 4:2272-2285. [PMID: 32453842 DOI: 10.1182/bloodadvances.2020001468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/24/2020] [Indexed: 12/16/2022] Open
Abstract
Factor VIII (FVIII) replacement therapy for hemophilia A is complicated by development of inhibitory antibodies (inhibitors) in ∼30% of patients. Because endothelial cells (ECs) are the primary physiologic expression site, we probed the therapeutic potential of genetically restoring FVIII expression selectively in ECs in hemophilia A mice (FVIIInull). Expression of FVIII was driven by the Tie2 promoter in the context of lentivirus (LV)-mediated in situ transduction (T2F8LV) or embryonic stem cell-mediated transgenesis (T2F8Tg). Both endothelial expression approaches were associated with a strikingly robust immune response. Following in situ T2F8LV-mediated EC transduction, all FVIIInull mice developed inhibitors but had no detectable plasma FVIII. In the transgenic approach, the T2F8Tg mice had normalized plasma FVIII levels, but showed strong sensitivity to developing an FVIII immune response upon FVIII immunization. A single injection of FVIII with incomplete Freund adjuvant led to high titers of inhibitors and reduction of plasma FVIII to undetectable levels. Because ECs are putative major histocompatibility complex class II (MHCII)-expressing nonhematopoietic, "semiprofessional" antigen-presenting cells (APCs), we asked whether they might directly influence the FVIII immune responses. Imaging and flow cytometric studies confirmed that both murine and human ECs express MHCII and efficiently bind and take up FVIII protein in vitro. Moreover, microvascular ECs preconditioned ex vivo with inflammatory cytokines could functionally present exogenously taken-up FVIII to previously primed CD4+/CXCR5+ T follicular helper (Tfh) cells to drive FVIII-specific proliferation. Our results show an unanticipated immunogenicity of EC-expressed FVIII and suggest a context-dependent role for ECs in the regulation of inhibitors as auxiliary APCs for Tfh cells.
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11
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Vlodavsky I, Barash U, Nguyen HM, Yang SM, Ilan N. Biology of the Heparanase-Heparan Sulfate Axis and Its Role in Disease Pathogenesis. Semin Thromb Hemost 2021; 47:240-253. [PMID: 33794549 DOI: 10.1055/s-0041-1725066] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell surface proteoglycans are important constituents of the glycocalyx and participate in cell-cell and cell-extracellular matrix (ECM) interactions, enzyme activation and inhibition, and multiple signaling routes, thereby regulating cell proliferation, survival, adhesion, migration, and differentiation. Heparanase, the sole mammalian heparan sulfate degrading endoglycosidase, acts as an "activator" of HS proteoglycans, thus regulating tissue hemostasis. Heparanase is a multifaceted enzyme that together with heparan sulfate, primarily syndecan-1, drives signal transduction, immune cell activation, exosome formation, autophagy, and gene transcription via enzymatic and nonenzymatic activities. An important feature is the ability of heparanase to stimulate syndecan-1 shedding, thereby impacting cell behavior both locally and distally from its cell of origin. Heparanase releases a myriad of HS-bound growth factors, cytokines, and chemokines that are sequestered by heparan sulfate in the glycocalyx and ECM. Collectively, the heparan sulfate-heparanase axis plays pivotal roles in creating a permissive environment for cell proliferation, differentiation, and function, often resulting in the pathogenesis of diseases such as cancer, inflammation, endotheliitis, kidney dysfunction, tissue fibrosis, and viral infection.
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Affiliation(s)
- Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Uri Barash
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hien M Nguyen
- Department of Chemistry, Wayne State University, Detroit, Michigan
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, People's Republic of China
| | - Neta Ilan
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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12
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Bu C, Jin L. NMR Characterization of the Interactions Between Glycosaminoglycans and Proteins. Front Mol Biosci 2021; 8:646808. [PMID: 33796549 PMCID: PMC8007983 DOI: 10.3389/fmolb.2021.646808] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs) constitute a considerable fraction of the glycoconjugates found on cellular membranes and in the extracellular matrix of virtually all mammalian tissues. The essential role of GAG-protein interactions in the regulation of physiological processes has been recognized for decades. However, the underlying molecular basis of these interactions has only emerged since 1990s. The binding specificity of GAGs is encoded in their primary structures, but ultimately depends on how their functional groups are presented to a protein in the three-dimensional space. This review focuses on the application of NMR spectroscopy on the characterization of the GAG-protein interactions. Examples of interpretation of the complex mechanism and characterization of structural motifs involved in the GAG-protein interactions are given. Selected families of GAG-binding proteins investigated using NMR are also described.
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Affiliation(s)
- Changkai Bu
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
| | - Lan Jin
- National Glycoengineering Research Center, Shandong Key Laboratory of Carbohydrate Chemistry and Glycobiology, Shandong University, Qingdao, China
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13
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Rosenberg EM, Herrington J, Rajasekaran D, Murphy JW, Pantouris G, Lolis EJ. The N-terminal length and side-chain composition of CXCL13 affect crystallization, structure and functional activity. Acta Crystallogr D Struct Biol 2020; 76:1033-1049. [PMID: 33021505 PMCID: PMC7543660 DOI: 10.1107/s2059798320011687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/25/2020] [Indexed: 01/18/2023] Open
Abstract
CXCL13 is the cognate chemokine agonist of CXCR5, a class A G-protein-coupled receptor (GPCR) that is essential for proper humoral immune responses. Using a `methionine scanning' mutagenesis method on the N-terminus of CXCL13, which is the chemokine signaling region, it was shown that minor length alterations and side-chain substitutions still result in CXCR5 activation. This observation indicates that the orthosteric pocket of CXCR5 can tolerate these changes without severely affecting the activity. The introduction of bulk on the ligand was well tolerated by the receptor, whereas a loss of contacts was less tolerated. Furthermore, two crystal structures of CXCL13 mutants were solved, both of which represent the first uncomplexed structures of the human protein. These structures were stabilized by unique interactions formed by the N-termini of the ligands, indicating that CXCL13 exhibits substantial N-terminal flexibility while the chemokine core domain remains largely unchanged. Additionally, it was observed that CXCL13 harbors a large degree of flexibility in the C-terminal extension of the ligand. Comparisons with other published structures of human and murine CXCL13 validate the relative rigidity of the core domain as well as the N- and C-terminal mobilities. Collectively, these mutants and their structures provide the field with additional insights into how CXCL13 interacts with CXCR5.
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Affiliation(s)
- Eric M. Rosenberg
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - James Herrington
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Deepa Rajasekaran
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - James W. Murphy
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Georgios Pantouris
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Elias J. Lolis
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
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14
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Cosgrove J, Novkovic M, Albrecht S, Pikor NB, Zhou Z, Onder L, Mörbe U, Cupovic J, Miller H, Alden K, Thuery A, O'Toole P, Pinter R, Jarrett S, Taylor E, Venetz D, Heller M, Uguccioni M, Legler DF, Lacey CJ, Coatesworth A, Polak WG, Cupedo T, Manoury B, Thelen M, Stein JV, Wolf M, Leake MC, Timmis J, Ludewig B, Coles MC. B cell zone reticular cell microenvironments shape CXCL13 gradient formation. Nat Commun 2020; 11:3677. [PMID: 32699279 PMCID: PMC7376062 DOI: 10.1038/s41467-020-17135-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 03/12/2020] [Indexed: 02/07/2023] Open
Abstract
Through the formation of concentration gradients, morphogens drive graded responses to extracellular signals, thereby fine-tuning cell behaviors in complex tissues. Here we show that the chemokine CXCL13 forms both soluble and immobilized gradients. Specifically, CXCL13+ follicular reticular cells form a small-world network of guidance structures, with computer simulations and optimization analysis predicting that immobilized gradients created by this network promote B cell trafficking. Consistent with this prediction, imaging analysis show that CXCL13 binds to extracellular matrix components in situ, constraining its diffusion. CXCL13 solubilization requires the protease cathepsin B that cleaves CXCL13 into a stable product. Mice lacking cathepsin B display aberrant follicular architecture, a phenotype associated with effective B cell homing to but not within lymph nodes. Our data thus suggest that reticular cells of the B cell zone generate microenvironments that shape both immobilized and soluble CXCL13 gradients.
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Affiliation(s)
- Jason Cosgrove
- York Computational Immunology Lab, University of York, York, UK
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, UK
- Department of Electronic Engineering, University of York, York, UK
| | - Mario Novkovic
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Stefan Albrecht
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Natalia B Pikor
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Zhaoukun Zhou
- Department of Biology, University of York, York, UK
- Biological Physical Sciences Institute (BPSI), University of York, York, UK
- Department of Physics, University of York, York, UK
| | - Lucas Onder
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Urs Mörbe
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Jovana Cupovic
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Helen Miller
- Department of Biology, University of York, York, UK
- Biological Physical Sciences Institute (BPSI), University of York, York, UK
- Department of Physics, University of York, York, UK
| | - Kieran Alden
- York Computational Immunology Lab, University of York, York, UK
- Department of Electronic Engineering, University of York, York, UK
| | - Anne Thuery
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, UK
| | | | - Rita Pinter
- Kennedy Institute of Rheumatology at the University of Oxford, Oxford, UK
| | - Simon Jarrett
- Kennedy Institute of Rheumatology at the University of Oxford, Oxford, UK
| | - Emily Taylor
- Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, UK
| | - Daniel Venetz
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Manfred Heller
- Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Daniel F Legler
- Biotechnology Institute Thurgau (BITg) at the University of Konstanz, Kreuzlingen, Switzerland
| | - Charles J Lacey
- York Computational Immunology Lab, University of York, York, UK
| | | | - Wojciech G Polak
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Tom Cupedo
- Department of Hematology, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Bénedicte Manoury
- Institut Necker Enfants Malades, INSERM U1151- CNRS UMR 8253, 149 rue de Sèvres 75015 Paris, France Université René Descartes, 75005, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Jens V Stein
- Department of Oncology, Microbiology and Immunology, University of Fribourg, Fribourg, Switzerland
| | - Marlene Wolf
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Mark C Leake
- Department of Biology, University of York, York, UK.
- Biological Physical Sciences Institute (BPSI), University of York, York, UK.
- Department of Physics, University of York, York, UK.
| | - Jon Timmis
- York Computational Immunology Lab, University of York, York, UK.
- Department of Electronic Engineering, University of York, York, UK.
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.
| | - Mark C Coles
- York Computational Immunology Lab, University of York, York, UK.
- Kennedy Institute of Rheumatology at the University of Oxford, Oxford, UK.
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15
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Pilz G, Sakic I, Wipfler P, Kraus J, Haschke-Becher E, Hitzl W, Trinka E, Harrer A. Chemokine CXCL13 in serum, CSF and blood-CSF barrier function: evidence of compartment restriction. Fluids Barriers CNS 2020; 17:7. [PMID: 32089130 PMCID: PMC7038591 DOI: 10.1186/s12987-020-0170-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/16/2020] [Indexed: 01/02/2023] Open
Abstract
Background and purpose Elevation of the chemokine CXCL13 in CSF frequently occurs during active and acute CNS inflammatory processes and presumably is associated with B cell-related immune activation. Elevation levels, however, vary a lot and “leaking” of CXCL13 from blood across dysfunctional brain barriers is a possible source. The aim was to clarify the relation between CXCL13 concentrations in CSF, CXCL13 concentrations in serum and blood–CSF barrier (BCSFB) function for a correct interpretation of the intrathecal origin of CXCL13. Methods We retrospectively analyzed CXCL13 of banked CSF/serum samples (n = 69) selected from patient records and categorized the CSF CXCL13 elevations as CXCL13 negative (< 30 pg/ml), low (30–100 pg/ml), medium (101–250 pg/ml), or high (> 250 pg/ml). CXCL13 concentrations in CSF and serum and the corresponding CSF/serum CXCL13 quotients (Qcxcl13) were compared to CSF/serum albumin quotients (QAlb) as a measure for BCSFB function. The CXCL13 negative category included two subgroups with normal and dysfunctional BCSFB. Results Serum CXCL13 concentrations were similar across categories with median levels around 100 pg/ml but differed between individuals (29 to > 505 pg/ml). Despite clear evidence in serum, CXCL13 was detectable only at trace amounts (medians 3.5 and 7.5 pg/ml) in CSF of the two CXCL13 negative subgroups irrespective of a normal or pathological QAlb. Moreover, we found no association between CSF and serum CXCL13 levels or between QAlb and CSF CXCL13 levels in any of the CSF CXCL13-delineated categories. CXCL13 apparently does not “leak” from blood into CSF. This implies an intrathecal origin also for low CSF CXCL13 levels and a caveat for analyzing the Qcxcl13, because higher serum than CSF concentrations arithmetically depress the Qcxcl13 resulting in misleadingly low CSF/serum quotients. Conclusion We demonstrated that CXCL13 does not cross from blood into CSF, not even during severe BCSFB dysfunction. CSF CXCL13 elevations therefore most likely always are CNS-derived, which highlights their relevance as indicator of inflammatory CNS processes. We recommend data should not be corrected for BCSFB permeability (QAlb) and not to calculate CSF/serum quotients for CXCL13 as these may introduce error.
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Affiliation(s)
- Georg Pilz
- Department of Neurology, Paracelsus Medical University, Ignaz-Harrer-Str 79, Salzburg, 5020, Austria
| | - Irma Sakic
- Department of Neurology, Paracelsus Medical University, Ignaz-Harrer-Str 79, Salzburg, 5020, Austria
| | - Peter Wipfler
- Department of Neurology, Paracelsus Medical University, Ignaz-Harrer-Str 79, Salzburg, 5020, Austria
| | - Jörg Kraus
- Department of Laboratory Medicine, Paracelsus Medical University, Salzburg, Austria.,Departent of Neurology, Medical Faculty, Heinrich-Heine University of Düsseldorf, Düsseldorf, Germany
| | | | - Wolfgang Hitzl
- Research Office, Biostatistics, Paracelsus Medical University, Salzburg, Austria.,Department of Ophthalmology and Optometry, Paracelsus Medical University, Salzburg, Austria.,Research Program Experimental Ophthalmology and Glaucoma Research, Paracelsus Medical University, Salzburg, Austria
| | - Eugen Trinka
- Department of Neurology, Paracelsus Medical University, Ignaz-Harrer-Str 79, Salzburg, 5020, Austria
| | - Andrea Harrer
- Department of Neurology, Paracelsus Medical University, Ignaz-Harrer-Str 79, Salzburg, 5020, Austria.
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16
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Lu E, Cyster JG. G-protein coupled receptors and ligands that organize humoral immune responses. Immunol Rev 2020; 289:158-172. [PMID: 30977196 DOI: 10.1111/imr.12743] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 01/22/2019] [Indexed: 12/26/2022]
Abstract
B-cell responses are dynamic processes that depend on multiple types of interactions. Rare antigen-specific B cells must encounter antigen and specialized systems are needed-unique to each lymphoid tissue type-to ensure this happens efficiently. Lymphoid tissue barrier cells act to ensure that pathogens, while being permitted entry for B-cell recognition, are blocked from replication or dissemination. T follicular helper (Tfh) cells often need to be primed by dendritic cells before supporting B-cell responses. For most responses, antigen-specific helper T cells and B cells need to interact, first to initiate clonal expansion and the plasmablast response, and later to support the germinal center (GC) response. Newly formed plasma cells need to travel to supportive niches. GC B cells must become confined to the follicle center, organize into dark and light zones, and interact with Tfh cells. Memory B cells need to be positioned for rapid responses following reinfection. Each of these events requires the actions of multiple G-protein coupled receptors (GPCRs) and their ligands, including chemokines and lipid mediators. This review will focus on the guidance cue code underlying B-cell immunity, with an emphasis on findings from our laboratory and on newer advances in related areas. We will discuss our recent identification of geranylgeranyl-glutathione as a ligand for P2RY8. Our goal is to provide the reader with a focused knowledge about the GPCRs guiding B-cell responses and how they might be therapeutic targets, while also providing examples of how multiple types of GPCRs can cooperate or act iteratively to control cell behavior.
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Affiliation(s)
- Erick Lu
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California
| | - Jason G Cyster
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California
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17
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Sepuru KM, Rajarathnam K. Structural basis of chemokine interactions with heparan sulfate, chondroitin sulfate, and dermatan sulfate. J Biol Chem 2019; 294:15650-15661. [PMID: 31455633 DOI: 10.1074/jbc.ra119.009879] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Indexed: 11/06/2022] Open
Abstract
Chemokines play diverse roles in human pathophysiology, ranging from trafficking leukocytes and immunosurveillance to the regulation of metabolism and neural function. Chemokine function is intimately coupled to binding tissue glycosaminoglycans (GAGs), heparan sulfate (HS), chondroitin sulfate (CS), and dermatan sulfate (DS). Currently, very little is known about how the structural features and sequences of a given chemokine, the structure and sulfation pattern of a given GAG, and structural differences among GAGs and among chemokines impact binding interactions. In this study, we used solution NMR spectroscopy to characterize the binding interactions of two related neutrophil-activating chemokines, CXCL1 and CXCL5, with HS, CS, and DS. For both chemokines, the dimer bound all three GAGs with higher affinity than did the monomer, and affinities of the chemokines for CS and DS were lower than for HS. NMR-based structural models reveal diverse binding geometries and show that the binding surfaces for each of the three GAGs were different between the two chemokines. However, a given chemokine had similar binding interactions with CS and DS that were different from HS. Considering the fact that CXCL1 and CXCL5 activate the same CXCR2 receptor, we conclude that GAG interactions play a role in determining the nature of chemokine gradients, levels of free chemokine available for receptor activation, how chemokines bind their receptors, and that differences in these interactions determine chemokine-specific function.
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Affiliation(s)
- Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1055
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1055 .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1055.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1055
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18
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Sepuru KM, Nagarajan B, Desai UR, Rajarathnam K. Structural basis, stoichiometry, and thermodynamics of binding of the chemokines KC and MIP2 to the glycosaminoglycan heparin. J Biol Chem 2018; 293:17817-17828. [PMID: 30257866 DOI: 10.1074/jbc.ra118.004866] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Indexed: 01/21/2023] Open
Abstract
Keratinocyte-derived chemokine (KC or mCXCL1) and macrophage inflammatory protein 2 (MIP2 or mCXCL2) play nonredundant roles in trafficking blood neutrophils to sites of infection and injury. The functional responses of KC and MIP2 are intimately coupled to their interactions with glycosaminoglycans (GAGs). GAG interactions orchestrate chemokine concentration gradients and modulate receptor activity, which together regulate neutrophil trafficking. Here, using NMR, molecular dynamics (MD) simulations, and isothermal titration calorimetry (ITC), we characterized the molecular basis of KC and MIP2 binding to the GAG heparin. Both chemokines reversibly exist as monomers and dimers, and the NMR analysis indicates that the dimer binds heparin with higher affinity. The ITC experiments indicate a stoichiometry of two GAGs per KC or MIP2 dimer and that the enthalpic and entropic contributions vary significantly between the two chemokine-heparin complexes. NMR-based structural models of heparin-KC and heparin-MIP2 complexes reveal that different combinations of residues from the N-loop, 40s turn, β3-strand, and C-terminal helix form a binding surface within a monomer and that both conserved residues and residues unique to a particular chemokine mediate the binding interactions. MD simulations indicate significant residue-specific differences in their contribution to binding and affinity for a given chemokine and between chemokines. On the basis of our observations that KC and MIP2 bind to GAG via distinct molecular interactions, we propose that the differences in these GAG interactions lead to differences in neutrophil recruitment and play nonoverlapping roles in resolution of inflammation.
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Affiliation(s)
- Krishna Mohan Sepuru
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555
| | - Balaji Nagarajan
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Umesh R Desai
- Department of Medicinal Chemistry and Institute for Structural Biology, and Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Krishna Rajarathnam
- From the Departments of Biochemistry and Molecular Biology; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555; Microbiology and Immunology.
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19
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Du H, Shi J, Wang M, An S, Guo X, Wang Z. Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats. J Neuroinflammation 2018; 15:280. [PMID: 30253787 PMCID: PMC6156955 DOI: 10.1186/s12974-018-1316-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/18/2018] [Indexed: 12/29/2022] Open
Abstract
Background Neuropathic pain is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. Methods Wistar rats were employed for the establishment of the chronic constriction injury (CCI) models. Using the Illumina HiSeq 4000 platform, we examined differentially expressed genes (DEGs) in the rat dorsal horn by RNA sequencing (RNA-seq) between CCI and control groups. Then, enrichment analyses were performed for these DEGs using Gene Ontology (GO) function, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Hierarchical Cluster, and protein-protein interaction (PPI) network. Results A total of 63 DEGs were found significantly changed with 56 upregulated (e.g., Cxcl13, C1qc, Fcgr3a) and 7 downregulated (e.g., Dusp1) at 14 days after CCI. Quantitative reverse-transcribed PCR (qRT-PCR) verified changes in 13 randomly selected DEGs. GO and KEGG biological pathway analyses showed that the upregulated DEGs were mostly enriched in immune response-related biological processes, as well as 14 immune- and inflammation-related pathways. The downregulated DEGs were enriched in inactivation of mitogen-activated protein kinase (MAPK) activity. PPI network analysis showed that Cd68, C1qc, C1qa, Laptm5, and Fcgr3a were crucial nodes with high connectivity degrees. Most of these genes which have previously been linked to immune and inflammation-related pathways have not been reported in neuropathic pain (e.g., Laptm5, Fcgr3a). Conclusions Our results revealed that immune and defense pathways may contribute to the generation of neuropathic pain after CCI. These mRNAs may represent new therapeutic targets for the treatment of neuropathic pain. Electronic supplementary material The online version of this article (10.1186/s12974-018-1316-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Du
- Department of Histology and Embryology, Taishan Medical University, Taian, 271000, China
| | - Juan Shi
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China
| | - Ming Wang
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China
| | - Shuhong An
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China
| | - Xingjing Guo
- Department of Physiology, Taishan Medical University, Taian, 271000, China
| | - Zhaojin Wang
- Department of Human Anatomy, Taishan Medical University, Taian, 271000, China.
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20
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Karamanos NK, Piperigkou Z, Theocharis AD, Watanabe H, Franchi M, Baud S, Brézillon S, Götte M, Passi A, Vigetti D, Ricard-Blum S, Sanderson RD, Neill T, Iozzo RV. Proteoglycan Chemical Diversity Drives Multifunctional Cell Regulation and Therapeutics. Chem Rev 2018; 118:9152-9232. [DOI: 10.1021/acs.chemrev.8b00354] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nikos K. Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras 26110, Greece
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras 26110, Greece
| | - Hideto Watanabe
- Institute for Molecular Science of Medicine, Aichi Medical University, Aichi 480-1195, Japan
| | - Marco Franchi
- Department for Life Quality Studies, University of Bologna, Rimini 47100, Italy
| | - Stéphanie Baud
- Université de Reims Champagne-Ardenne, Laboratoire SiRMa, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Stéphane Brézillon
- Université de Reims Champagne-Ardenne, Laboratoire de Biochimie Médicale et Biologie Moléculaire, CNRS UMR MEDyC 7369, Faculté de Médecine, 51 rue Cognacq Jay, Reims 51100, France
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Münster 48149, Germany
| | - Alberto Passi
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Davide Vigetti
- Department of Medicine and Surgery, University of Insubria, Varese 21100, Italy
| | - Sylvie Ricard-Blum
- University Claude Bernard Lyon 1, CNRS, UMR 5246, Institute of Molecular and Supramolecular Chemistry and Biochemistry, Villeurbanne 69622, France
| | - Ralph D. Sanderson
- Department of Pathology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Thomas Neill
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
| | - Renato V. Iozzo
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 10107, United States
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21
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How post-translational modifications influence the biological activity of chemokines. Cytokine 2018; 109:29-51. [DOI: 10.1016/j.cyto.2018.02.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/17/2022]
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22
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Sankaranarayanan NV, Nagarajan B, Desai UR. So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again! Curr Opin Struct Biol 2018; 50:91-100. [PMID: 29328962 PMCID: PMC6037615 DOI: 10.1016/j.sbi.2017.12.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) play key roles in virtually all biologic responses through their interaction with proteins. A major challenge in understanding these roles is their massive structural complexity. Computational approaches are extremely useful in navigating this bottleneck and, in some cases, the only avenue to gain comprehensive insight. We discuss the state-of-the-art on computational approaches and present a flowchart to help answer most basic, and some advanced, questions on GAG-protein interactions. For example, firstly, does my protein bind to GAGs?; secondly, where does the GAG bind?; thirdly, does my protein preferentially recognize a particular GAG type?; fourthly, what is the most optimal GAG chain length?; fifthly, what is the structure of the most favored GAG sequence?; and finally, is my GAG-protein system 'specific', 'non-specific', or a combination of both? Recent advances show the field is now poised to enable a non-computational researcher perform advanced experiments through the availability of various tools and online servers.
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Affiliation(s)
- Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Balaji Nagarajan
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA.
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23
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Miller H, Cosgrove J, Wollman AJM, Taylor E, Zhou Z, O'Toole PJ, Coles MC, Leake MC. High-Speed Single-Molecule Tracking of CXCL13 in the B-Follicle. Front Immunol 2018; 9:1073. [PMID: 29872430 PMCID: PMC5972203 DOI: 10.3389/fimmu.2018.01073] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
Soluble factors are an essential means of communication between cells and their environment. However, many molecules readily interact with extracellular matrix components, giving rise to multiple modes of diffusion. The molecular quantification of diffusion in situ is thus a challenging imaging frontier, requiring very high spatial and temporal resolution. Overcoming this methodological barrier is key to understanding the precise spatial patterning of the extracellular factors that regulate immune function. To address this, we have developed a high-speed light microscopy system capable of millisecond sampling in ex vivo tissue samples and submillisecond sampling in controlled in vitro samples to characterize molecular diffusion in a range of complex microenvironments. We demonstrate that this method outperforms competing tools for determining molecular mobility of fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) for evaluation of diffusion. We then apply this approach to study the chemokine CXCL13, a key determinant of lymphoid tissue architecture, and B-cell-mediated immunity. Super-resolution single-molecule tracking of fluorescently labeled CCL19 and CXCL13 in collagen matrix was used to assess the heterogeneity of chemokine mobility behaviors, with results indicating an immobile fraction and a mobile fraction for both molecules, with distinct diffusion rates of 8.4 ± 0.2 and 6.2 ± 0.3 µm2s−1, respectively. To better understand mobility behaviors in situ, we analyzed CXCL13-AF647 diffusion in murine lymph node tissue sections and observed both an immobile fraction and a mobile fraction with an example diffusion coefficient of 6.6 ± 0.4 µm2s−1, suggesting that mobility within the follicle is also multimodal. In quantitatively studying mobility behaviors at the molecular level, we have obtained an increased understanding of CXCL13 bioavailability within the follicle. Our high-speed single-molecule tracking approach affords a novel perspective from which to understand the mobility of soluble factors relevant to the immune system.
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Affiliation(s)
- Helen Miller
- Department of Physics, University of York, York, United Kingdom.,Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Jason Cosgrove
- Centre of Immunology and Infection, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom.,Department of Electronics, University of York, York, United Kingdom
| | - Adam J M Wollman
- Department of Physics, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Emily Taylor
- Centre of Immunology and Infection, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Zhaokun Zhou
- Department of Physics, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
| | - Peter J O'Toole
- Department of Biology, University of York, York, United Kingdom.,Bioscience Technology Facility, University of York, York, United Kingdom
| | - Mark C Coles
- Centre of Immunology and Infection, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom.,Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Mark C Leake
- Department of Physics, University of York, York, United Kingdom.,Department of Biology, University of York, York, United Kingdom
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24
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Abstract
Chemokine signaling is essential for coordinated cell migration in health and disease to specifically govern cell positioning in space and time. Typically, chemokines signal through heptahelical, G protein-coupled receptors to orchestrate cell migration. Notably, chemokine receptors are highly dynamic structures and signaling efficiency largely depends on the discrete contact with the ligand. Promiscuity of both chemokines and chemokine receptors, combined with biased signaling and allosteric modulation of receptor activation, guarantees a tightly controlled recruitment and positioning of individual cells within the local environment at a given time. Here, we discuss recent insights in understanding chemokine gradient formation by atypical chemokine receptors and how typical chemokine receptors can transmit distinct signals to translate guidance cues into coordinated cell locomotion in space and time.
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Affiliation(s)
- Daniel F Legler
- Biotechnology Institute Thurgau (BITg), University of Konstanz, Kreuzlingen, Switzerland
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
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