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A proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritis.

Hayashi J, Kihara M, Kato H, Nishimura T - Clin Proteomics (2015)

Bottom Line: Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear.With the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (R SC ) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues.Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1.

View Article: PubMed Central - PubMed

Affiliation: Niizashiki Central General Hospital, Saitama, Japan.

ABSTRACT

Background: Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial joints. Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear. Regardless of numerous investigations of RA by means of genomic and proteomic approaches, proteins interplaying in RA synovial tissues that contain various types of synoviocytes, are not yet sufficiently understood. Hence we have conducted an HPLC/mass spectrometry-based exploratory proteomic analysis focusing on synoviocyte lesions laser-microdissected (LMD) from formalin-fixed paraffin-embedded (FFPE) synovial tissues (RA, n = 15; OA, n = 5), where those of Osteoarthritis (OA) were used as the control.

Results: A total of 508 proteins were identified from the RA and OA groups. With the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (R SC ) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues. These include stromelysin-1 (MMP3), proteins S100-A8 and S100-A9, plastin-2, galectin-3, calreticulin, cathepsin Z, HLA-A, HLA-DRB1, ferritin, neutrophil defensin 1, CD14, MMP9 etc.

Conclusions: Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1. Network analyses of protein-protein interaction for those proteins significant to RA revealed a dominant participation of ribosome pathway (p = 5.91 × 10(-45)), and, interestingly, the associations of the p53 signaling (p = 2.34 × 10(-5)). An involvement of proteins including CD14, S100-A8/S100-A9 seems to suggest an activation of the NF-kB/MAPK signaling pathway. Our strategy of laser-microdissected FFPE-tissue proteomic analysis in Rheumatoid Arthritis thus demonstrated its technical feasibility in profiling proteins expressed in synovial tissues, which may play important roles in the RA pathogenesis.

No MeSH data available.


Related in: MedlinePlus

STRING protein–protein interaction networks of 98 differentially expressed proteins in RA synoviocyte lesions. This interaction map shown in evidence view was generated using default setting in network depth of 50 interactions under medium confidence (0.4) and the criteria for linkage only including experiments, databases, and textmining. Node proteins of potentially importance in RA were indicated by red circles.
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Fig2: STRING protein–protein interaction networks of 98 differentially expressed proteins in RA synoviocyte lesions. This interaction map shown in evidence view was generated using default setting in network depth of 50 interactions under medium confidence (0.4) and the criteria for linkage only including experiments, databases, and textmining. Node proteins of potentially importance in RA were indicated by red circles.

Mentions: Network analysis of significant proteins is helpful in understanding how these proteins interplay with other key proteins and pathways. This study utilized significant proteins (n = 98) relevant in RA to develop a predictive network model, which has the potential to be used for further biological investigation. This was done using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, [43, 44] in which data were obtained from biological functions of local networks surrounding the protein candidates. The STRING network of proteins differentially expressed in RA is shown in Fig. 2, where node proteins of potentially importance in RA are indicated by red circles. STRING network enrichment analyses suggested a preferable association of RA with hematopoietic system disease (DOID 74: p = 3.53 × 10−10) and immune system disease (DOID 2914: p = 5.28 × 10−9). Enrichment analyses on the KEGG pathways indicated that RA was dominantly associated with ribosome (has03010: p = 5.91 × 10−45). Interestingly, such would indicate that RA may involve protein networks that interplay with both p53 signaling (has04115: p = 2.34 × 10−5) and leukocyte transendothelial migration (has04670: p = 5.75 × 10−4).Fig. 2


A proteomic profile of synoviocyte lesions microdissected from formalin-fixed paraffin-embedded synovial tissues of rheumatoid arthritis.

Hayashi J, Kihara M, Kato H, Nishimura T - Clin Proteomics (2015)

STRING protein–protein interaction networks of 98 differentially expressed proteins in RA synoviocyte lesions. This interaction map shown in evidence view was generated using default setting in network depth of 50 interactions under medium confidence (0.4) and the criteria for linkage only including experiments, databases, and textmining. Node proteins of potentially importance in RA were indicated by red circles.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4527102&req=5

Fig2: STRING protein–protein interaction networks of 98 differentially expressed proteins in RA synoviocyte lesions. This interaction map shown in evidence view was generated using default setting in network depth of 50 interactions under medium confidence (0.4) and the criteria for linkage only including experiments, databases, and textmining. Node proteins of potentially importance in RA were indicated by red circles.
Mentions: Network analysis of significant proteins is helpful in understanding how these proteins interplay with other key proteins and pathways. This study utilized significant proteins (n = 98) relevant in RA to develop a predictive network model, which has the potential to be used for further biological investigation. This was done using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, [43, 44] in which data were obtained from biological functions of local networks surrounding the protein candidates. The STRING network of proteins differentially expressed in RA is shown in Fig. 2, where node proteins of potentially importance in RA are indicated by red circles. STRING network enrichment analyses suggested a preferable association of RA with hematopoietic system disease (DOID 74: p = 3.53 × 10−10) and immune system disease (DOID 2914: p = 5.28 × 10−9). Enrichment analyses on the KEGG pathways indicated that RA was dominantly associated with ribosome (has03010: p = 5.91 × 10−45). Interestingly, such would indicate that RA may involve protein networks that interplay with both p53 signaling (has04115: p = 2.34 × 10−5) and leukocyte transendothelial migration (has04670: p = 5.75 × 10−4).Fig. 2

Bottom Line: Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear.With the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (R SC ) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues.Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1.

View Article: PubMed Central - PubMed

Affiliation: Niizashiki Central General Hospital, Saitama, Japan.

ABSTRACT

Background: Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation of the synovial joints. Early intervention followed by early diagnosis can result in disease remission; however, both early stage diagnosis and provision of effective treatment have been impeded by the heterogeneity of RA, which details of pathological mechanism are unclear. Regardless of numerous investigations of RA by means of genomic and proteomic approaches, proteins interplaying in RA synovial tissues that contain various types of synoviocytes, are not yet sufficiently understood. Hence we have conducted an HPLC/mass spectrometry-based exploratory proteomic analysis focusing on synoviocyte lesions laser-microdissected (LMD) from formalin-fixed paraffin-embedded (FFPE) synovial tissues (RA, n = 15; OA, n = 5), where those of Osteoarthritis (OA) were used as the control.

Results: A total of 508 proteins were identified from the RA and OA groups. With the semi-quantitative comparisons, the spectral index (SpI), log2 protein ratio (R SC ) based on spectral counting, and statistical G-test, 98 proteins were found to be significant (pair-wise p < 0.05) to the RA synovial tissues. These include stromelysin-1 (MMP3), proteins S100-A8 and S100-A9, plastin-2, galectin-3, calreticulin, cathepsin Z, HLA-A, HLA-DRB1, ferritin, neutrophil defensin 1, CD14, MMP9 etc.

Conclusions: Our results confirmed the involvement of known RA biomarkers such as stromelysin-1 (MMP3) and proteins S100-A8 and S100-A9, and also that of leukocyte antigens such as HLA-DRB1. Network analyses of protein-protein interaction for those proteins significant to RA revealed a dominant participation of ribosome pathway (p = 5.91 × 10(-45)), and, interestingly, the associations of the p53 signaling (p = 2.34 × 10(-5)). An involvement of proteins including CD14, S100-A8/S100-A9 seems to suggest an activation of the NF-kB/MAPK signaling pathway. Our strategy of laser-microdissected FFPE-tissue proteomic analysis in Rheumatoid Arthritis thus demonstrated its technical feasibility in profiling proteins expressed in synovial tissues, which may play important roles in the RA pathogenesis.

No MeSH data available.


Related in: MedlinePlus