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Quantitative and qualitative characterization of expanded CD4+ T cell clones in rheumatoid arthritis patients.

Ishigaki K, Shoda H, Kochi Y, Yasui T, Kadono Y, Tanaka S, Fujio K, Yamamoto K - Sci Rep (2015)

Bottom Line: Our in-depth characterization of ECs in RA successfully demonstrated the presence of the specific immunological selection pressure, which determines the phenotype of ECs.Moreover, transcriptome tracking added novel aspects to the underlying sequential immune processes.Our approach may provide new insights into the pathophysiology of RA.

View Article: PubMed Central - PubMed

Affiliation: Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.

ABSTRACT
Rheumatoid arthritis (RA) is an autoimmune destructive arthritis associated with CD4(+) T cell-mediated immunity. Although expanded CD4(+) T cell clones (ECs) has already been confirmed, the detailed characteristics of ECs have not been elucidated in RA. Using combination of a single-cell analysis and next-generation sequencing (NGS) in TCR repertoire analysis, we here revealed the detailed nature of ECs by examining peripheral blood (PB) from 5 RA patients and synovium from 1 RA patient. When we intensively investigated the single-cell transcriptome of the most expanded clones in memory CD4(+) T cells (memory-mECs) in RA-PB, senescence-related transcripts were up-regulated, indicating circulating ECs were constantly stimulated. Tracking of the transcriptome shift within the same memory-mECs between PB and the synovium revealed the augmentations in senescence-related gene expression and the up-regulation of synovium-homing chemokine receptors in the synovium. Our in-depth characterization of ECs in RA successfully demonstrated the presence of the specific immunological selection pressure, which determines the phenotype of ECs. Moreover, transcriptome tracking added novel aspects to the underlying sequential immune processes. Our approach may provide new insights into the pathophysiology of RA.

No MeSH data available.


Related in: MedlinePlus

Gene expression profiles of synovium memory-mECs.Three single-cell cDNA samples were randomly selected from both memory-mECs and memory-NECs in the synovium, and analyzed by single-cell RNA-Seq. (A) A heatmap of TNF target genes and immune senescent markers. The TNF targets genes were shown to be significantly up-regulated in memory-mECs by the gene set enrichment analysis (see details in the text and supplementary methods). (B) cDNAs of synovium memory-mECs and memory-NECs obtained by the single-cell analysis were mixed (2 pooled samples in total), and qPCR was performed. ACTB was used as an internal control gene. *p < 0.05, **p < 0.005.
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f5: Gene expression profiles of synovium memory-mECs.Three single-cell cDNA samples were randomly selected from both memory-mECs and memory-NECs in the synovium, and analyzed by single-cell RNA-Seq. (A) A heatmap of TNF target genes and immune senescent markers. The TNF targets genes were shown to be significantly up-regulated in memory-mECs by the gene set enrichment analysis (see details in the text and supplementary methods). (B) cDNAs of synovium memory-mECs and memory-NECs obtained by the single-cell analysis were mixed (2 pooled samples in total), and qPCR was performed. ACTB was used as an internal control gene. *p < 0.05, **p < 0.005.

Mentions: We next performed single-cell transcriptome analysis of synovium of RA1 (Fig. 5). Three single-cell cDNA samples were randomly selected from both synovium memory-mECs and memory-NECs, and analyzed using single-cell RNA-Seq. An average of 1.46 million reads was mapped per sample. In order to assess differentially expressed gene sets, we performed a gene set enrichment analysis36 and found that the expression of the gene sets of TNF targets were significantly higher in synovium memory-mECs than in synovium memory-NECs (FDR = 0.029. Heatmap was shown in Fig. 5A).


Quantitative and qualitative characterization of expanded CD4+ T cell clones in rheumatoid arthritis patients.

Ishigaki K, Shoda H, Kochi Y, Yasui T, Kadono Y, Tanaka S, Fujio K, Yamamoto K - Sci Rep (2015)

Gene expression profiles of synovium memory-mECs.Three single-cell cDNA samples were randomly selected from both memory-mECs and memory-NECs in the synovium, and analyzed by single-cell RNA-Seq. (A) A heatmap of TNF target genes and immune senescent markers. The TNF targets genes were shown to be significantly up-regulated in memory-mECs by the gene set enrichment analysis (see details in the text and supplementary methods). (B) cDNAs of synovium memory-mECs and memory-NECs obtained by the single-cell analysis were mixed (2 pooled samples in total), and qPCR was performed. ACTB was used as an internal control gene. *p < 0.05, **p < 0.005.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542667&req=5

f5: Gene expression profiles of synovium memory-mECs.Three single-cell cDNA samples were randomly selected from both memory-mECs and memory-NECs in the synovium, and analyzed by single-cell RNA-Seq. (A) A heatmap of TNF target genes and immune senescent markers. The TNF targets genes were shown to be significantly up-regulated in memory-mECs by the gene set enrichment analysis (see details in the text and supplementary methods). (B) cDNAs of synovium memory-mECs and memory-NECs obtained by the single-cell analysis were mixed (2 pooled samples in total), and qPCR was performed. ACTB was used as an internal control gene. *p < 0.05, **p < 0.005.
Mentions: We next performed single-cell transcriptome analysis of synovium of RA1 (Fig. 5). Three single-cell cDNA samples were randomly selected from both synovium memory-mECs and memory-NECs, and analyzed using single-cell RNA-Seq. An average of 1.46 million reads was mapped per sample. In order to assess differentially expressed gene sets, we performed a gene set enrichment analysis36 and found that the expression of the gene sets of TNF targets were significantly higher in synovium memory-mECs than in synovium memory-NECs (FDR = 0.029. Heatmap was shown in Fig. 5A).

Bottom Line: Our in-depth characterization of ECs in RA successfully demonstrated the presence of the specific immunological selection pressure, which determines the phenotype of ECs.Moreover, transcriptome tracking added novel aspects to the underlying sequential immune processes.Our approach may provide new insights into the pathophysiology of RA.

View Article: PubMed Central - PubMed

Affiliation: Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.

ABSTRACT
Rheumatoid arthritis (RA) is an autoimmune destructive arthritis associated with CD4(+) T cell-mediated immunity. Although expanded CD4(+) T cell clones (ECs) has already been confirmed, the detailed characteristics of ECs have not been elucidated in RA. Using combination of a single-cell analysis and next-generation sequencing (NGS) in TCR repertoire analysis, we here revealed the detailed nature of ECs by examining peripheral blood (PB) from 5 RA patients and synovium from 1 RA patient. When we intensively investigated the single-cell transcriptome of the most expanded clones in memory CD4(+) T cells (memory-mECs) in RA-PB, senescence-related transcripts were up-regulated, indicating circulating ECs were constantly stimulated. Tracking of the transcriptome shift within the same memory-mECs between PB and the synovium revealed the augmentations in senescence-related gene expression and the up-regulation of synovium-homing chemokine receptors in the synovium. Our in-depth characterization of ECs in RA successfully demonstrated the presence of the specific immunological selection pressure, which determines the phenotype of ECs. Moreover, transcriptome tracking added novel aspects to the underlying sequential immune processes. Our approach may provide new insights into the pathophysiology of RA.

No MeSH data available.


Related in: MedlinePlus