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Liang R, Zhi Y, Zheng G, Zhang B, Zhu H, Wang M. Analysis of long non-coding RNAs in glioblastoma for prognosis prediction using weighted gene co-expression network analysis, Cox regression, and L1-LASSO penalization. Onco Targets Ther 2018; 12:157-168. [PMID: 30613154 PMCID: PMC6306053 DOI: 10.2147/ott.s171957] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Purpose This study focused on identification of long non-coding RNAs (lncRNAs) for prognosis prediction of glioblastoma (GBM) through weighted gene co-expression network analysis (WGCNA) and L1-penalized least absolute shrinkage and selection operator (LASSO) Cox proportional hazards (PH) model. Materials and methods WGCNA was performed based on RNA expression profiles of GBM from Chinese Glioma Genome Atlas (CGGA), National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), and the European Bioinformatics Institute ArrayExpress for the identification of GBM-related modules. Subsequently, prognostic lncRNAs were determined using LASSO Cox PH model, followed by constructing a risk scoring model based on these lncRNAs. The risk score was used to divide patients into high- and low-risk groups. Difference in survival between groups was analyzed using Kaplan-Meier survival analysis. IncRNA-mRNA networks were built for the prognostic lncRNAs, followed by pathway enrichment analysis for these networks. Results This study identified eight preserved GBM-related modules, including 188 lncRNAs. Consequently, C20orf166-AS1, LINC00645, LBX2-AS1, LINC00565, LINC00641, and PRRT3-AS1 were identified by LASSO Cox PH model. A risk scoring model based on the lncRNAs was constructed that could divide patients into different risk groups with significantly different survival rates. Prognostic value of this six-lncRNA signature was validated in two independent sets. C20orf166-AS1 was associated with antigen processing and presentation and cell adhesion molecule pathways, involving nine common genes. LBX2-AS1, LINC00641, PRRT3-AS1, and LINC00565 were related to focal adhesion, extracellular matrix receptor interaction, and mitogen-activated protein kinase signaling pathways, which shared 12 common genes. Conclusion This prognostic six-lncRNA signature may improve prognosis prediction of GBM. This study reveals many pathways and genes involved in the mechanisms behind these lncRNAs.
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Affiliation(s)
- Ruqing Liang
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong Province 272000, China
| | - Yaqin Zhi
- Department of Oncology, Jining No 1 People's Hospital, Jining, Shandong Province 272000, China,
| | - Guizhi Zheng
- College of Integrated Chinese and Western Medicine, Jining Medical College, Jining, Shangdong 272067, China
| | - Bin Zhang
- Department of Oncology, Jining No 1 People's Hospital, Jining, Shandong Province 272000, China,
| | - Hua Zhu
- Department of Oncology, Jining No 1 People's Hospital, Jining, Shandong Province 272000, China,
| | - Meng Wang
- Department of Oncology, Jining No 1 People's Hospital, Jining, Shandong Province 272000, China,
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Leherte L, Petit A, Jacquemin D, Vercauteren DP, Laurent AD. Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods. J Comput Aided Mol Des 2018; 32:1295-1313. [PMID: 30368623 DOI: 10.1007/s10822-018-0172-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
The CD2-CD58 protein-protein interaction is known to favor the recognition of antigen presenting cells by T cells. The structural, energetics, and dynamical properties of three known cyclic CD58 ligands, named P6, P7, and RTD-c, are studied through molecular dynamics (MD) simulations and molecular docking calculations. The ligands are built so as to mimic the C and F β-strands of protein CD2, connected via turn inducers. The MD analyses focus on the location of the ligands with respect to the experimental binding site and on the direct and water-mediated hydrogen bonds (H bonds) they form with CD58. Ligand P6, with a sequence close to the experimental β-strands of CD2, presents characteristics that explain its higher experimental affinity, e.g., the lower mobility and flexibility at the CD58 surface, and the larger number and occurrence frequency of ligand-CD58 H bonds. For the two other ligands, the structural modifications lead to changes in the binding pattern with CD58 and its dynamics. In parallel, a large set of molecular docking calculations, carried out with various search spaces and docking algorithms, are compared to provide a consensus view of the preferred ligand binding modes. The analysis of the ligand side chain locations yields results that are consistent with the CD2-CD58 crystal structure and suggests various binding modes of the experimentally identified hot spot of the ligands, i.e., Tyr86. P6 is shown to form a number of contacts that are also present in the experimental CD2-CD58 structure.
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Affiliation(s)
- Laurence Leherte
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur MEdicine and Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium.
| | - Axel Petit
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur MEdicine and Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Denis Jacquemin
- University of Nantes, CEISAM UMR CNRS 6230, UFR Sciences et Techniques, 2 Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 03, France.,Institut Universitaire de France, 103 Bd St Michel, 75005, Paris Cedex 5, France
| | - Daniel P Vercauteren
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur MEdicine and Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Adèle D Laurent
- University of Nantes, CEISAM UMR CNRS 6230, UFR Sciences et Techniques, 2 Rue de la Houssinière, BP 92208, 44322, Nantes Cedex 03, France
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Gokhale A, Kanthala S, Latendresse J, Taneja V, Satyanarayanajois S. Immunosuppression by co-stimulatory molecules: inhibition of CD2-CD48/CD58 interaction by peptides from CD2 to suppress progression of collagen-induced arthritis in mice. Chem Biol Drug Des 2014; 82:106-18. [PMID: 23530775 DOI: 10.1111/cbdd.12138] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/06/2013] [Accepted: 03/16/2013] [Indexed: 12/21/2022]
Abstract
Targeting co-stimulatory molecules to modulate the immune response has been shown to have useful therapeutic effects for autoimmune diseases. Among the co-stimulatory molecules, CD2 and CD58 are very important in the early stages of generation of an immune response. Our goal was to utilize CD2-derived peptides to modulate protein-protein interactions between CD2 and CD58, thereby modulating the immune response. Several peptides were designed based on the structure of the CD58-binding domain of CD2 protein. Among the CD2-derived peptides, peptide 6 from the F and C β-strand region of CD2 protein exhibited inhibition of cell-cell adhesion in the nanomolar concentration range. Peptide 6 was evaluated for its ability to bind to CD58 in Caco-2 cells and to CD48 in T cells from rodents. A molecular model was proposed for binding a peptide to CD58 and CD48 using docking studies. Furthermore, in vivo studies were carried out to evaluate the therapeutic ability of the peptide to modulate the immune response in the collagen-induced arthritis (CIA) mouse model. In vivo studies indicated that peptide 6 was able to suppress the progression of CIA. Evaluation of the antigenicity of peptides in CIA and transgenic animal models indicated that this peptide is not immunogenic.
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Affiliation(s)
- Ameya Gokhale
- Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA 71201, USA
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Paul BK, Guchhait N. A spectral deciphering of the binding interaction of an intramolecular charge transfer fluorescence probe with a cationic protein: thermodynamic analysis of the binding phenomenon combined with blind docking study. Photochem Photobiol Sci 2011; 10:980-91. [DOI: 10.1039/c0pp00309c] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bhunia A, Vivekanandan S, Eckert T, Burg-Roderfeld M, Wechselberger R, Romanuka J, Bächle D, Kornilov AV, von der Lieth CW, Jiménez-Barbero J, Nifantiev NE, Schachner M, Sewald N, Lütteke T, Hans-Joachim G, Siebert HC. Why structurally different cyclic peptides can be glycomimetics of the HNK-1 carbohydrate antigen. J Am Chem Soc 2010; 132:96-105. [PMID: 19958024 DOI: 10.1021/ja904334s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The cyclic peptides c-(LSETTl) and c-(RTLPFS) are of potential clinical interest--they stimulate neurite outgrowth in a way that is similar to the effects of the HNK-1 (human natural killer cell-1) antigenic carbohydrate chains, which are terminated by 3'-sulfated glucuronic acid attached to an N-acetyllactosamine unit. To investigate the structure-activity relationships of the ability of the cyclic peptides to mimic HNK-1 carbohydrates, conformational analysis and examination of hydrophobic and hydrophilic patterns were performed and compared with the characteristics of a synthetic HNK-1 trisaccharide derivative. Data obtained demonstrate that both the trisaccharide and the glycomimetic peptide c-(LSETTl) exhibit a similar relationship between their hydrophobic moieties and their negatively charged sites. However, the second cyclic glycomimetic peptide investigated here, c-(RTLPFS), has a positively charged group as a potential contact point due to its Arg residue. Therefore, we studied the amino acid composition of all known receptor structures in the Protein Data Bank that are in contact with uronic acid and/or sulfated glycans. Interactions of the HNK-1 trisaccharide, c-(LSETTl), and c-(RTLPFS) with a laminin fragment involved in HNK-1 carbohydrate binding (i.e., the 21mer peptide: KGVSSRSYVGCIKNLEISRST) were also analyzed. Because the structure of the HNK-1-binding laminin domain is not available in the Protein Data Bank, we used the HNK-1-binding 21mer peptide fragment of laminin for the construction of a model receptor that enabled us to compare the molecular interplay of the HNK-1 trisaccharide and the two cyclopeptides c-(LSETTl) and c-(RTLPFS) with a reliable receptor structure in considerable detail.
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Affiliation(s)
- Anirban Bhunia
- Institut für Biochemie und Endokrinologie, Veterinrmedizinische Fakultät, Justus-Liebig-Universität Giessen, Frankfurter Str. 100, 35392 Giessen, Germany
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Barzegar A, Moosavi-Movahedi AA, Mahnam K, Ashtiani SH. Chaperone-like activity of α-cyclodextrin via hydrophobic nanocavity to protect native structure of ADH. Carbohydr Res 2010; 345:243-9. [DOI: 10.1016/j.carres.2009.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 11/05/2009] [Indexed: 11/25/2022]
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Giddu S, Subramanian V, Yoon HS, Satyanarayanajois SD. Design of beta-hairpin peptides for modulation of cell adhesion by beta-turn constraint. J Med Chem 2009; 52:726-36. [PMID: 19123855 DOI: 10.1021/jm8008212] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The CD2-CD58 interaction in immune regulation and disease pathology has provided new targets for developing potential immunosuppressive agents. In the present study, we report the introduction of constraints to generate beta-hairpin structures from the strand sequences of CD2 protein. The beta-hairpin structures were induced in the designed peptides by introducing Pro-Gly sequences in the peptides. Results from NMR and MD simulation indicated that the peptides exhibited beta-turn structure at the X-Pro-Gly-Y sequence and formed the beta-hairpin structure in solution. The ability of these peptides to inhibit cell adhesion was evaluated by two cell adhesion assays. Among the peptides studied (1-4) (P1-P4), peptides 2-4 were able to inhibit cell adhesion between Jurkat cells and SRBC nearly 50% at 180 microM, and 80% inhibition between Jurkat cells and Caco-2 cells was seen at 90 microM. Peptide 1 did not show significant inhibition activity compared to control.
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Affiliation(s)
- Sumana Giddu
- Department of Basic Pharmaceutical Sciences, University of Louisiana at Monroe, 700 University Avenue, Monroe, Louisiana 71209, USA
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Limaye N, Belobrajdic KA, Wandstrat AE, Bonhomme F, Edwards SV, Wakeland EK. Prevalence and evolutionary origins of autoimmune susceptibility alleles in natural mouse populations. Genes Immun 2007; 9:61-8. [DOI: 10.1038/sj.gene.6364446] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Li C, Satyanarayanajois SD. Structure-function studies of peptides for cell adhesion inhibition: identification of key residues by alanine mutation and peptide-truncation approach. Peptides 2007; 28:1498-508. [PMID: 17689835 DOI: 10.1016/j.peptides.2007.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Revised: 07/03/2007] [Accepted: 07/03/2007] [Indexed: 11/24/2022]
Abstract
Blockage of the interaction of CD2 with its ligand CD58 is expected to bring out potential therapeutic value for autoimmune diseases and organ transplantation. Three series of peptides (cVL, cIL and cAQ series) were designed from ratCD2 and humanCD2 to modulate CD2-CD58 interaction. To determine the specific segments in parent peptides responsible for inhibitory activity as lead sequence, we generated shorter fragments of the parent peptides and evaluated their biological activity with cell adhesion assay. The structure-activity relationship studies indicated that small cyclic peptides derived from CD2 ligand binding epitopes could mimic native beta-turn structure, and thus modulate CD2-CD58 interaction.
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Affiliation(s)
- Cheng Li
- Department of Pharmacy, 18 Science Drive 4, National University of Singapore, Singapore 117543, Singapore
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Liu J, Li C, Ke S, Satyanarayanajois SD. Structure-based rational design of beta-hairpin peptides from discontinuous epitopes of cluster of differentiation 2 (CD2) protein to modulate cell adhesion interaction. J Med Chem 2007; 50:4038-47. [PMID: 17658775 DOI: 10.1021/jm0700868] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modulation or inhibition of interaction of cluster of differentiation (CD) adhesion molecules CD2-CD58 has been shown to be therapeutically useful. The analysis of the crystal structure of CD2 complexed with CD58 was carried out to define the epitopes that are important for the interaction of the two proteins. The crystal structure of CD2 indicated that the interaction surface of CD2 with CD58 has two beta-strand structures (F and C strands) with charged residues. On the basis of the crystal structure of the complex CD2-CD58, we have designed beta-hairpin peptides from the beta-strand region of CD2 by conjugating the discontinuous sequences in the protein. The peptides were modeled by molecular dynamics simulation, and their inhibitory activities were evaluated in vitro using two heterotypic cell adhesion assays, E-rosetting and lymphocyte-epithelial cell adhesion assays. Results indicated that 12- and 14-residue conjugate cyclic peptides cKS12 and cDD14 exhibited 60% and 50% inhibition activity, respectively, at 90 microM.
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Affiliation(s)
- Jining Liu
- Department of Pharmacy, National University of Singapore, 117543, Singapore
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11
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Hetényi C, van der Spoel D. Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett 2006; 580:1447-50. [PMID: 16460734 DOI: 10.1016/j.febslet.2006.01.074] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 12/20/2005] [Accepted: 01/24/2006] [Indexed: 10/25/2022]
Abstract
Blind docking was introduced for the detection of possible binding sites and modes of peptide ligands by scanning the entire surface of protein targets. In the present study, the method is tested on a group of drug-sized compounds and proteins with up to a thousand amino acid residues. Both proteins from complex structures and ligand-free proteins were used as targets. Robustness, limitations and future perspectives of the method are discussed. It is concluded that blind docking can be used for unbiased mapping of the binding patterns of drug candidates.
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Affiliation(s)
- Csaba Hetényi
- Department of Biochemistry, Eötvös Loránd University, 1/C Pázmány P. sétány, 1117 Budapest, Hungary.
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Liu J, Ying J, Chow VTK, Hruby VJ, Satyanarayanajois SD. Structure-activity studies of peptides from the "hot-spot" region of human CD2 protein: development of peptides for immunomodulation. J Med Chem 2005; 48:6236-49. [PMID: 16190751 PMCID: PMC1351114 DOI: 10.1021/jm0503547] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CD2 is a cell surface protein belonging to the immunoglobulin superfamily (IgSF) that plays a key role in mediating adhesion between human T-lymphocytes and target cells. The interaction between cell-adhesion molecules CD2 and CD58 is critical for immune response. Modulation or inhibition of these interactions has been shown to be therapeutically useful. Synthetic 12-mer linear and cyclic peptides and cyclic hexapeptides from the beta-turn and beta-strand region (hot spot) of human CD2 protein were designed to modulate CD2-CD58 interaction. The 12-amino acid synthetic cyclic peptides effectively blocked the interaction between CD2 and CD58 proteins as demonstrated by E-rosetting and heterotypic adhesion assays. NMR and molecular modeling studies indicated that these cyclic peptides exhibit beta-turn structure in solution and closely mimic the beta-turn structure of the surface epitopes of CD2 protein. The designed cyclic peptides with beta-turn structure have the ability to modulate CD2-CD58 interaction.
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Affiliation(s)
| | | | | | | | - Seetharama D. Satyanarayanajois
- * To whom correspondence should be addressed: Department of Pharmacy, 18 Science Drive 4, National University of Singapore, Singapore 117543. Telephone: (65)-6-874-2653. Fax: (65)-6-779-1554. E-mail:
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Wandstrat AE, Nguyen C, Limaye N, Chan AY, Subramanian S, Tian XH, Yim YS, Pertsemlidis A, Garner HR, Morel L, Wakeland EK. Association of extensive polymorphisms in the SLAM/CD2 gene cluster with murine lupus. Immunity 2005; 21:769-80. [PMID: 15589166 DOI: 10.1016/j.immuni.2004.10.009] [Citation(s) in RCA: 223] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Revised: 10/21/2004] [Accepted: 10/27/2004] [Indexed: 01/12/2023]
Abstract
Susceptibility to autoimmunity in B6.Sle1b mice is associated with extensive polymorphisms between two divergent haplotypes of the SLAM/CD2 family of genes. The B6.Sle1b-derived SLAM/CD2 family haplotype is found in many other laboratory mouse strains but only causes autoimmunity in the context of the C57Bl/6 (B6) genome. Phenotypic analyses have revealed variations in the structure and expression of several members of the SLAM/CD2 family in T and B lymphocytes from B6.Sle1b mice. T lymphocytes from B6.Sle1b mice have modified signaling responses to stimulation at 4-6 weeks of age. While autoimmunity may be mediated by a combination of genes in the SLAM/CD2 family cluster, the strongest candidate is Ly108, a specific isoform of which is constitutively upregulated in B6.Sle1b lymphocytes.
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Affiliation(s)
- Amy E Wandstrat
- Center for Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
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