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  Division Category Core matrisome Collagens Gene Symbol Col1a2 Gene Name Ref Core matrisome ECM Glycoproteins Igfbp4 collagen, type I, alpha 2 Teague insulin-like growth factor binding protein 4 matrix Gla protein Teague Core matrisome ECM Glycoproteins Mgp Matrisome-associated ECM Regulators P4ha1 Teague CCL5 procollagen-proline, 2oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha 1 polypeptide lectin, galactoside-binding, soluble, 3 sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B chemokine (C-C motif) ligand 5 Matrisome-associated ECM-affiliated Proteins LGALS3 Matrisome-associated ECM-affiliated Proteins Sema4b Matrisome-associated Secreted Factors Matrisome-associated Secreted Factors S100A9 S100 calcium binding protein A9 Matrisome-associated Secreted Factors Howden Wnt1 wingless-related MMTV integration site 1 Teague 159 Teague Howden Teague Howden Table 6.
  
  Up
  
  -regulated matrisome upon T cell activation. Division
  
  Category Gene Name Ref Collagens Gene Symbol Col12a1 Core matrisome Core matrisome collagen, type XII, alpha 1 Teague Collagens Col1a1 collagen, type I, alpha 1 Teague Core matrisome Proteoglycans SRGN serglycin Howden Matrisome-associated ECM Regulators Cela2a Teague Matrisome-associated ECM Regulators Prss2 chymotrypsin-like elastase family, member 2A protease, serine, 2 Matrisome-associated ECM-affiliated Proteins Anxa2 annexin A2 Teague Matrisome-associated ECM-affiliated Proteins Lgals3 Teague Matrisome-associated Secreted Factors CSF2 lectin, galactose binding, soluble 3 colony stimulating factor 2 (granulocyte-macrophage) Matrisome-associated Secreted Factors IFNG interferon, gamma Howden Matrisome-associated Secreted Factors Ntf3 neurotrophin 3 Teague Matrisome-associated Secreted Factors S100a4 S100 calcium binding protein A4 Teague Matrisome-associated Secreted Factors S100a6 S100 calcium binding protein A6 (calcyclin) Teague
  
  Teague Howden Teague et al. activated T cells in C57BL/10 mice by intraveinous injection of staphylococcal enterotoxin B (SEB). T cells were sorted out and gene expression was assessed 8 and 48 h after activation using Affymetrix gene arrays. Genes were considered down(resp. up-.) regulated when they displayed decreased (resp. increased) fold change at 8 and/or at 48h post-injection (Teague et al., 1999). Howden et al. activated freshly isolated primary human CD4+ T cells with Phorbol 12-myristate 13acetate (PMA) and ionomycin and identified modulated proteome at 2 and 4 h post-activation by nanoLC-MS/MS QuaNCAT, a conjunction of Bio-Orthogonal Non Canonical Amino acid Tagging (BONCAT) and Stable Isotope Labeling of Amino acids in Cell culture (SILAC). Genes were considered down(resp. up-) regulated when they ed decreased (resp. increased) fold change at 2 and/or at 4 h post-activation (Howden et al., 2013).
  
  2. Modulated matrisome upon HIV-1 infection
  
  HIV-1 infection deeply affects cellular gene expression profiles, both through direct gene modulation by viral factors and through the peculiar activation state it induces in T cells. Retrieving data collected from different systems exposed in Table 7, we undertook a comprehensive analysis of T cell matrisome modulated upon HIV-1 infection. We expose down-regulated and up-regulated matrisomes upon HIV-1 infection in Table 8 and Table 9 resp. Strikingly, while no genes are common between down-regulated matrisomes upon Tcell activation and HIV-1 infection, only interferon γ IFNg, serglycin SRGN and collagen type 1 alpha 1 are common between both up-regulated matrisomes. These data support the concept that HIV-1 infection and T cell activation pathways exhibit a complex interplay.
  
  160 Table 7. Cellular systems and identification methods to analyse HIV-1 modulated transcriptome/proteome. System Inguinal lymph node biopsies from untreated HIV-1-infected subjects at different clinical stages (n = 22) uninfected subjects (n = 5) Gene identification method Whole-genome transcriptional analysis (Human Genome U133 Plus 2.0, Affymetrix) Ref (Li et al., 2009) Whole-genome transcriptional (Rotger et al., 2010) profiling (Human-6 v3 Expression BeadChips, Illumina) kept are genes correlating with a high viral load Whole-genome transcriptional (Salgado et al., CD3(+) T cells from analysis (Agilent microarrays) 2011) progressors (n = 15) kept are genes differentially LTNP (n = 15) modulated between progressors and LTNP Whole-genome transcriptional (Vigneault et al., HLA-DR(-) CD4(+) T cells profiling (WG-DASL 2011) HIV-1-infected persons treated microarrays, Illumina) with ArT (n = 14) kept are genes differentially Elite Controllers (n = 12) modulated in infected persons HIV-1-negative persons (n = 9) and Elite Controllers with regard to non-infected subjects CEMx174 cells non-infected or Differential proteome analysis (Chan et al., 2007) infected with HIV-1 LAI through 16O/18O labeling and quantitative LC-FTICR analyses FTICR = T Fourier transform ion cyclotron resonance mass spectrometer CD4(+) T cells from HIV-1 infected individuals with a known date of seroconversion (n = 182) Elite Controllers (n = 16) 161
  
  Table 8. Down-regulated matrisome upon HIV-1 infection. Division Category Core matrisome
  
  ECM Glycoproteins Gene symbol COCH Gene name Ref Li Core matrisome ECM Glycoproteins CTGF coagulation factor C homolog, cochlin (Limulus polyphemus) connective tissue growth factor Core matrisome ECM Glycoproteins DPT dermatopontin Li Core matrisome ECM Glycoproteins FBLN1 fibulin 1 Li Core matrisome ECM Glycoproteins HMCN1 hemicentin 1 Li Core matrisome ECM Glycoproteins IGFBP3 Li Core matrisome ECM Glycoproteins IGFBP5 Core matrisome ECM Glycoproteins MATN4 insulin-like growth factor binding protein 3 insulin-like growth factor binding protein 5 matrilin 4 Core matrisome ECM Glycoproteins MGP matrix Gla protein Li Li Li Chan Core matrisome ECM Glycoproteins RELN reelin Li Core matrisome ECM Glycoproteins SNED1 sushi, nidogen and EGF-like domains 1 Li Li Core matrisome ECM Glycoproteins THBS1 thrombospondin 1 Core matrisome Proteoglycans DCN decorin Li Core matrisome Proteoglycans NCAN neurocan Chan, Rotger Core matrisome Proteoglycans SPOCK2 Li Core matrisome Proteoglycans SPOCK3 Li Core matrisome Proteoglycans SRGN sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3 serglycin Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated ECM Regulators ADAM12 ADAM metallopeptidase domain 12 Li ECM Regulators CTSB cathepsin B Chan ECM Regulators CTSV cathepsin L2 Chan ECM Regulators F13A1 coagulation factor XIII, A1 polypeptide Li ECM Regulators MMP25 matrix metallopeptidase 25 Chan ECM Regulators SERPIND1 Chan ECM Regulators TIMP3 serpin ase inhibitor, clade D (heparin cofactor), member 1 TIMP metallopeptidase inhibitor 3 Li ECM-affiliated Proteins ANXA7 annexin A7 Chan ECM-affiliated Proteins CLEC4G Li ECM-affiliated Proteins OVGP1 C-type lectin domain family 4, member G oviductal glycoprotein 1, 120kDa Rotger ECM-affiliated Proteins SDC1 syndecan 1 Li Secreted Factors CXCL11 chemokine (C-X-C motif) ligand 11 Chan Secreted Factors CXCL2 chemokine (C-X-C motif) ligand 2 Li Secreted Factors IGF2 Li Secreted Factors MEGF6 insulin-like growth factor 2 (somatomedin A) multiple EGF-like-domains 6 Secreted Factors S100A12 S100 calcium binding protein A12 Chan Matrisomeassociated Matrisomeassociated Matrisomeassociated Matrisomeassociated Secreted Factors S100A5 S100 calcium binding protein A5 Chan Secreted Factors THPO thrombopoietin Chan Secreted Factors TNFSF11 Li Secreted Factors WNT7A tumor necrosis factor (ligand) superfamily, member 11 wingless-type MMTV integration site family, member 7A 162 Li Li Rotger
  
  Table 9. Up-regulated matrisome upon HIV-1 infection. Gene name Ref Collagens Gene symbol COL1A1 collagen, type I, alpha 1 Vigneault ECM Glycoproteins FBN3 fibrillin 3 Vigneault Core matrisome ECM Glycoproteins FGL2 fibrinogen-like 2 Li, Rotger Core matrisome ECM Glycoproteins FNDC7 fibronectin type III domain containing 7 Vigneault Core matrisome ECM Glycoproteins IGFBP3 Vigneault Core matrisome ECM Glycoproteins IGFBP4 Core matrisome ECM Glycoproteins LAMA5 insulin-like growth factor binding protein 3 insulin-like growth factor binding protein 4 laminin, alpha 5 Core matrisome ECM Glycoproteins MATN1 matrilin 1, cartilage matrix protein Vigneault Core matrisome ECM Glycoproteins MFAP4 microfibrillar-associated protein 4 Vigneault Core matrisome ECM Glycoproteins MMRN1 multimerin 1 Vigneault Core matrisome ECM Glycoproteins PXDN peroxidasin homolog (Drosophila) Salgado Core matrisome ECM Glycoproteins SPON2 spondin 2, extracellular matrix protein Vigneault Core matrisome ECM Glycoproteins THBS1 thrombospondin 1 Vigneault Core matrisome ECM Glycoproteins VWA1 Core matrisome ECM Glycoproteins VWCE Core matrisome Proteoglycans HSPG2 von Willebrand factor A domain containing 1 von Willebrand factor C and EGF domains heparan sulfate proteoglycan 2 Chan, Vigneault Chan, Vigneault Vigneault Core matrisome Proteoglycans PODN podocan Vigneault Core matrisome Proteoglycans PRG2 Vigneault Core matrisome Proteoglycans SRGN proteoglycan 2, bone marrow (natural killer cell activator, eosinophil granule major basic protein) serglycin Matrisome-associated ECM Regulators A2M alpha-2-macroglobulin Matrisome-associated ECM Regulators ADAM9 Matrisome-associated ECM Regulators ADAM metallopeptidase domain 9 (meltrin gamma) ADAMDEC1 ADAM-like, decysin 1 Matrisome-associated ECM Regulators CST cystatin F (leukocystatin) Li Matrisome-associated ECM Regulators CSTL1 cystatin-like 1 Chan Matrisome-associated ECM Regulators CTSG cathepsin G Vigneault Matrisome-associated ECM Regulators EGLN3 egl nine homolog 3 (C. elegans) Salgado Matrisome-associated ECM Regulators FAM20C Vigneault Matrisome-associated ECM Regulators LOX family with sequence similarity 20, member C lysyl oxidase Matrisome-associated ECM Regulators MMP28 matrix metallopeptidase 28 Vigneault Matrisome-associated ECM Regulators MMP9 Vigneault Matrisome-associated ECM Regulators SERPINA1 Matrisome-associated ECM Regulators SERPINB2 Matrisome-associated ECM Regulators SERPINF1 Matrisome-associated ECM Regulators SERPING1 Matrisome-associated ECM Regulators SERPINI1 Matrisome-associated ECM-affiliated Proteins ANXA10 matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 serpin peptidase inhibitor, clade B (ovalbumin), member 2 serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1 serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 serpin peptidase inhibitor, clade I (neuroserpin), member 1 annexin A10 Matrisome-associated ECM-affiliated Proteins C1QB Li, Rotger Matrisome-associated ECM-affiliated Proteins CLEC2B Matrisome-associated ECM-affiliated Proteins CLEC7A Matrisome-associated ECM-affiliated Proteins FCN1 complement component 1, q subcomponent, B chain C-type lectin domain family 2, member B C-type lectin domain family 7, member A ficolin (collagen/fibrinogen domain containing) 1 Division Category Core matrisome Core matrisome 163 Vigneault Salgado Vigneault Vigneault Vigneault Li Vigneault Li Vigneault Vigneault Rotger Vigneault Chan Li Li, Vigneault Li, Vigneault Matrisome-associated ECM-affiliated Proteins Matrisome-associated ECM-affiliated Proteins Matrisome-associated ECM-affiliated Proteins Matrisome-associated Matrisome-associated FCN2 Vigneault GPC3 ficolin (collagen/fibrinogen containing lectin) 2 (hucolin) glypican 3 ITLN1 intelectin 1 (galactofuranose binding) Vigneault ECM-affiliated Proteins LMAN1L lectin, mannose-binding, 1 like Chan ECM-affiliated Proteins REG1A regenerating islet-derived 1 alpha Vigneault Matrisome-associated ECM-affiliated Proteins SDC4 syndecan 4 Vigneault Matrisome-associated Secreted Factors BMP4 bone morphogenetic protein 4 Vigneault Matrisome-associated Secreted Factors CCL3 chemokine (C-C motif) ligand 3 Vigneault Matrisome-associated Secreted Factors CCL3L3 chemokine (C-C motif) ligand 3-like 3 Vigneault Matrisome-associated Secreted Factors CCL4L1 chemokine (C-C motif) ligand 4-like 1 Vigneault Matrisome-associated Secreted Factors CLCF1 cardiotrophin-like cytokine factor 1 Vigneault Matrisome-associated Secreted Factors CXCL2 chemokine (C-X-C motif) ligand 2 Vigneault Matrisome-associated Secreted Factors EPO erythropoietin Vigneault Matrisome-associated Secreted Factors FASLG Li Matrisome-associated Secreted Factors FGF7 Matrisome-associated Secreted Factors FGFBP1 Matrisome-associated Secreted Factors FGFBP2 Matrisome-associated Secreted Factors FGFBP3 Matrisome-associated Secreted Factors FSTL1 Fas ligand (TNF superfamily, member 6) fibroblast growth factor 7 (keratinocyte growth factor) fibroblast growth factor binding protein 1 fibroblast growth factor binding protein 2 fibroblast growth factor binding protein 3 follistatin-like 1 Matrisome-associated Secreted Factors GDF3 growth differentiation factor 3 Chan Matrisome-associated Secreted Factors IFNG interferon, gamma Li, Vigneault Matrisome-associated Secreted Factors IL13 interleukin 13 Vigneault Matrisome-associated Secreted Factors IL16 Vigneault Matrisome-associated Secreted Factors IL17C interleukin 16 (lymphocyte chemoattractant factor) interleukin 17C Matri associated Secreted Factors IL18 Matrisome-associated Secreted Factors IL1B interleukin 18 (interferon-gammainducing factor) interleukin 1, beta Matrisome-associated Secreted Factors IL1RN interleukin 1 receptor antagonist Li Matrisome-associated Secreted Factors IL2 interleukin 2 Vigneault Matrisome-associated Secreted Factors IL6 interleukin 6 (interferon, beta 2) Vigneault Matrisome-associated Secreted Factors MDK Salgado Matrisome-associated Secreted Factors NODAL midkine (neurite growth-promoting factor 2) nodal homolog (mouse) Matrisome-associated Secreted Factors PDGFB Salgado Matrisome-associated Secreted Factors S100A8 platelet-derived growth factor beta polypeptide (simian sarcoma viral (vsis) oncogene homolog) S100 calcium binding protein A8 Matrisome-associated Secreted Factors S100P S100 calcium binding protein P Vigneault Matrisome-associated Secreted Factors TGFB1 transforming growth factor, beta 1 Vigneault Matrisome-associated Secreted Factors TNFSF10 Rotger Matrisome-associated Secreted Factors TNFSF13B Matrisome-associated Secreted Factors TNFSF9 Matrisome-associated Secreted Factors VEGFA tumor necrosis factor (ligand) superfamily, member 10 tumor necrosis factor (ligand) superfamily, member 13b tumor necrosis factor (ligand) superfamily, member 9 vascular endothelial growth factor A Matrisome-associated Secreted Factors WNT1 wingless-type MMTV integration site family, member 1 164 Vigneault Vigneault Vigneault Vigneault Vigneault Vigneault Vigneault Li
  
  Vigneault Vigneault Li Rotger Vigneault Vigneault Vigneault 3. Table 10. Viral preparations used for identification of associated host proteins. Virus Cell line Proteomics
  
  Ref NL4-3 Hek MS /MS (Bregnard et al.,
  
  2013
  
  ) NLAD8 MDM microcapillary (CD45-depleted) reversed-phase liquid (Chertova et al.,
  
  2006
  
  ) chromatography-MS/MS (μRPLC-MS/MS) SIV PBMCs LC/MS/MS (Stephenson from SM and RM (common proteome to SM and RM) 2010) et al., MDM = Monocyte derived macrophages, PBMCs = Peripheral Blood Mononuclear Cells, SM = Sooty mangabey, RM = Rhesus macaque, MS/MS = tandem Mass Spectrometry
  
  .
  
  165
  
  Table 11. Matrisome associated to HIV-1 and SIV virions.