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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

Both of naive and memory CD4+ T cells in RA-PB had many ECs.Naïve and memory CD4+ T cells were sorted from the PB of 4 RA patients and 5 healthy controls and the NGS TCR repertoire analysis was performed. (A) Rate of expanded clones (clones with more than 0.2% or 0.1% of total number of reads with functional CDR3 sequences). The cumulative read count of ECs was divided by the total number of reads with functional CDR3 sequences. (B) Rate of clones that were shared by both the naive and memory CD4+ T cell subset. The cumulative read count of shared clones was divided by the total number of reads with functional CDR3 sequences. *p < 0.05, **p < 0.005.
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f2: Both of naive and memory CD4+ T cells in RA-PB had many ECs.Naïve and memory CD4+ T cells were sorted from the PB of 4 RA patients and 5 healthy controls and the NGS TCR repertoire analysis was performed. (A) Rate of expanded clones (clones with more than 0.2% or 0.1% of total number of reads with functional CDR3 sequences). The cumulative read count of ECs was divided by the total number of reads with functional CDR3 sequences. (B) Rate of clones that were shared by both the naive and memory CD4+ T cell subset. The cumulative read count of shared clones was divided by the total number of reads with functional CDR3 sequences. *p < 0.05, **p < 0.005.

Mentions: In order to characterize the TCR repertoire of CD4+ T cells in RA, we sorted naive and memory CD4+ T cells from RA-PB and healthy control (HC) PB and performed the NGS TCR repertoire analysis. We first verified the robustness of our NGS TCR repertoire analysis platform by single-cell analysis and FACS analysis (Fig. S1 and S2). We were able to identify ECs by high-frequency CDR3 sequences in the NGS TCR repertoire analysis. Since there is currently no general definition of ECs in the NGS TCR repertoire analysis, we prepared two thresholds of frequencies for ECs (Fig. 2A, 0.2% and 0.1%). We observed significantly more ECs in not only memory, but also naive CD4+ T cells in RA-PB than in healthy control PB. When the similarities of sequences between memory and naive CD4+ T cells were examined, we found that the majority of clones in each subset were unique and not shared by the other subset both in RA and HC (Fig. 2B). These results revealed marked differences in the TCR repertoire between naive and memory CD4+ T cells.


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)

Both of naive and memory CD4+ T cells in RA-PB had many ECs.Naïve and memory CD4+ T cells were sorted from the PB of 4 RA patients and 5 healthy controls and the NGS TCR repertoire analysis was performed. (A) Rate of expanded clones (clones with more than 0.2% or 0.1% of total number of reads with functional CDR3 sequences). The cumulative read count of ECs was divided by the total number of reads with functional CDR3 sequences. (B) Rate of clones that were shared by both the naive and memory CD4+ T cell subset. The cumulative read count of shared clones was divided by the total number of reads with functional CDR3 sequences. *p < 0.05, **p < 0.005.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Both of naive and memory CD4+ T cells in RA-PB had many ECs.Naïve and memory CD4+ T cells were sorted from the PB of 4 RA patients and 5 healthy controls and the NGS TCR repertoire analysis was performed. (A) Rate of expanded clones (clones with more than 0.2% or 0.1% of total number of reads with functional CDR3 sequences). The cumulative read count of ECs was divided by the total number of reads with functional CDR3 sequences. (B) Rate of clones that were shared by both the naive and memory CD4+ T cell subset. The cumulative read count of shared clones was divided by the total number of reads with functional CDR3 sequences. *p < 0.05, **p < 0.005.
Mentions: In order to characterize the TCR repertoire of CD4+ T cells in RA, we sorted naive and memory CD4+ T cells from RA-PB and healthy control (HC) PB and performed the NGS TCR repertoire analysis. We first verified the robustness of our NGS TCR repertoire analysis platform by single-cell analysis and FACS analysis (Fig. S1 and S2). We were able to identify ECs by high-frequency CDR3 sequences in the NGS TCR repertoire analysis. Since there is currently no general definition of ECs in the NGS TCR repertoire analysis, we prepared two thresholds of frequencies for ECs (Fig. 2A, 0.2% and 0.1%). We observed significantly more ECs in not only memory, but also naive CD4+ T cells in RA-PB than in healthy control PB. When the similarities of sequences between memory and naive CD4+ T cells were examined, we found that the majority of clones in each subset were unique and not shared by the other subset both in RA and HC (Fig. 2B). These results revealed marked differences in the TCR repertoire between naive and memory CD4+ T cells.

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