Fig 1.
SIV-specific CD8+ T cell repertoire fluctuates throughout infection and during ARV treatment.
PBMCs, LN biopsies and BAL were sampled from 7 different SIVmac239X or SIVmac239-infected rhesus macaques during acute infection, chronic infection and after 2–7 months of ARV treatment. (A-G). Clonotypes consisting of more than 1% of the TCR repertoire were represented as percentage of the TCR repertoire during acute and chronic infection and with ARV treatment. “Public” clonotypes are the same clonotype (same V and J segments and same CDR3 amino acid sequence) found in multiple animals in this study, and matching clonotypes previously identified in the VDJdb database. “Shared” clonotypes were those found only in one animal but observed in multiple tissues. “Private” clonotypes were identified in a single anatomical site in a single animal. n = 7 animals. Total cell and TCR sequences numbers are listed above each column.
Fig 2.
SIV-specific CD8+ T cells exhibit similar TCR diversity and similarity throughout SIV infection.
PBMCs, LN biopsies and BAL were sampled from SIVmac239X or SIVmac239-infected rhesus macaques during acute infection, chronic infection and after 2–6 months of ARV treatment. (A) The number of unique clonotypes in multiple anatomical sites at all timepoints. (B) The normalized Shannon-Weiner diversity index for the TCR repertoires of all tissues throughout SIV infection. (C) The d50 diversity index for the TCR repertoires of all tissues throughout SIV infection. (D) The Jaccard similarity index for comparisons between each tissue’s TCR repertoire. In (A-D), data is represented by mean and SD, with each individual animal represented by a unique symbol. (E) MDS plot of the TCR repertoires of each animal, tissue and timepoint throughout infection. Two-way ANOVA was used to determine statistical significance for panels A to D. n = 7 animals.
Fig 3.
SIV-gag DNA vaccine induced a diverse TCR repertoire and tissue-specific clonotypes.
PBMCs, BAL, LN, and jejunum (jej) biopsies were sampled from rhesus macaques who had been administered with SIV-gag DNA vaccine. (A) CM9-specific CD8+ T cells in all tissues pre- and post- vaccine administration as a percentage of total CD8+ cells. (B) Clonotypes consisting of more than 1% of the TCR repertoire are represented as percentage of the TCR repertoire. “Public” clonotypes are the same clonotype (same V and J segments and same CDR3 amino acid sequence) found in multiple animals in this study, and matching clonotypes previously identified in the VDJdb database. “Shared” clonotypes were those found only in one animal but observed in multiple tissues. “Private” clonotypes were identified in a single anatomical site in a single animal. Total cell and TCR sequences numbers are listed above each column. (C) The normalized Shannon-Weiner diversity index for the TCR repertoires of all tissues. (D) The d50 diversity index for the TCR repertoires of all tissues. (E) The Jaccard similarity index for comparisons between each tissue’s TCR repertoire. In (C) to (E), data are presented as mean, with individual data points shown. Two-way ANOVA (A) and one-way ANOVA (C-E) were used to determine statistical significance. n = 5 animals.
Fig 4.
CMV-specific CD8+ T cells exhibit public, shared and tissue-specific clonotypes upon natural infection.
PBMCs, LN, liver biopsies, and BAL were sampled from rhesus macaques who had been naturally infected with CMV. (A) The number of AN10-specific CD8+ T cells in multiple anatomical sites as a percentage of total CD8+ cells. (B) The number of VY9-specific CD8+ T cells in multiple anatomical sites as a percentage of total CD8+ cells. (C) Clonotypes consisting of more than 1% of the TCR repertoire of AN10-specific CD8+ T cells are represented as a percentage of the total TCR repertoire. “Public” clonotypes are the same clonotype (same V and J segments and same CDR3 amino acid sequence) found in multiple animals in this study, and matching clonotypes previously identified in the VDJdb database. “Shared” clonotypes were those found only in one animal but observed in multiple tissues. “Private” clonotypes were identified in a single anatomical site in a single animal. Total cell and TCR sequences numbers are listed above each column. (D) Clonotypes consisting of more than 1% of the TCR repertoire of VY9-specific CD8+ T cells are represented as a percentage of the total TCR repertoire. (E) The normalized Shannon-Weiner diversity index for the TCR repertoires of VY9-specific CD8+ T cells. (F) The d50 diversity index for the TCR repertoires of VY9-specific CD8+ T cells. (G) The Jaccard similarity index for comparisons between each tissue’s VY9-specific CD8+ T cell repertoire. In (A), (B) and (E)-(G), data are presented as mean, with individual data points. One-way ANOVA or mixed effects analysis was used to determine statistical significance. n = 2 to 5 animals.
Fig 5.
The TCR repertoires of SIV- and CMV- specific CD8+ T cells exhibit similar diversity and tissue similarity.
PBMCs, LN and BAL were sampled from rhesus macaques who were chronically infected with SIVmac239X (without ARV treatment) or naturally infected with CMV. (A) The normalized Shannon-Weiner diversity index of the TCR repertoires. (B) The d50 diversity index of the TCR repertoires. (C) The Jaccard similarity index for comparisons between each tissue’s TCR repertoire. Data are presented as mean, with individual data points. One way ANOVA was used to determine statistical significance. n = 3 to 6 animals.
Fig 6.
Expression patterns of CD69 and CD103 among virus-specific CD8+ T cells.
The expression of CD69 and CD103 on antigen specific CD8+ T cells were assessed by flow cytometry across all experimental groups. (A-E) Average percentage of CD69-CD103-, CD69+CD103-, CD69-CD103+ and CD69+CD103+ antigen-specific (CM9) CD8+ T cells after exposure to SIV-gag DNA vaccine (A); during acute (B), chronic (C), and chronic SIVmac239X or SIVmac239 infection with ARV treatment (D); or during CMV infection (E). (F) The number of CD69+CD103+ antigen-specific CD8+ T cells during all experimental conditions. In (F) data are presented as mean with SD. Two-way ANOVA was used to determine statistical significance in (F). n = 3 to 6 animals.