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Rhesus Macaque B-Cell Responses to an HIV-1 Trimer Vaccine Revealed by Unbiased Longitudinal Repertoire Analysis.

Dai K, He L, Khan SN, O'Dell S, McKee K, Tran K, Li Y, Sundling C, Morris CD, Mascola JR, Karlsson Hedestam GB, Wyatt RT, Zhu J - MBio (2015)

Bottom Line: Next-generation sequencing of B-cell repertoires provides a quantitative tool to analyze B-cell responses to a vaccine.In this study, the longitudinal B-cell repertoire analysis of a rhesus macaque immunized with an HIV-1 trimer vaccine revealed complex B-cell lineage patterns and showed the potential to facilitate the evaluation of future HIV-1 vaccines.The repertoire sequencing technologies and antibodyomics methods reported here can be extended to vaccine development for other human pathogens utilizing the nonhuman primate model.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

No MeSH data available.


Longitudinal analysis of the GE140 lineage development. (A) Identity-divergence analysis of the unbiased heavy (H) and light (λ) chain repertoires. The sequences are plotted as a function of sequence identity to GE140 and of sequence divergence from putative germline V genes. Color coding denotes sequence density. The VH4.11 heavy chain family at each time point is visualized by black contour lines (middle row). The GE140-like heavy chains with an HCDR3 identity of over 95% are shown as red dots on the plots; the numbers are numbers of sequences. (B) ML tree of selected GE140 heavy chain variants rooted by the putative germline VH4.11 gene (see Fig. 4 for sequence selection and labeling). The bar represents a 0.001 change per nucleotide site. (C) ELISA analysis of antigen binding is shown for six antibodies reconstituted from GE140 heavy chain variants with SD bars. (D) Analysis of GE140-like light chains. (Left) The VL2.7 light chain family at the last time point is visualized with black contours. Light chains with an LCDR3 identity of 95% or greater are shown as red dots on the 2D plot. (Right) ELISA analysis of HIV-1 trimer vaccine antigen binding (right) is shown for three antibodies reconstituted from GE140 light chain variants, with SD bars.
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fig5: Longitudinal analysis of the GE140 lineage development. (A) Identity-divergence analysis of the unbiased heavy (H) and light (λ) chain repertoires. The sequences are plotted as a function of sequence identity to GE140 and of sequence divergence from putative germline V genes. Color coding denotes sequence density. The VH4.11 heavy chain family at each time point is visualized by black contour lines (middle row). The GE140-like heavy chains with an HCDR3 identity of over 95% are shown as red dots on the plots; the numbers are numbers of sequences. (B) ML tree of selected GE140 heavy chain variants rooted by the putative germline VH4.11 gene (see Fig. 4 for sequence selection and labeling). The bar represents a 0.001 change per nucleotide site. (C) ELISA analysis of antigen binding is shown for six antibodies reconstituted from GE140 heavy chain variants with SD bars. (D) Analysis of GE140-like light chains. (Left) The VL2.7 light chain family at the last time point is visualized with black contours. Light chains with an LCDR3 identity of 95% or greater are shown as red dots on the 2D plot. (Right) ELISA analysis of HIV-1 trimer vaccine antigen binding (right) is shown for three antibodies reconstituted from GE140 light chain variants, with SD bars.

Mentions: A group of diverse somatic variants (n = 75) was identified for the GE140 heavy chain from the 454 sequencing of a sample after 5 immunizations (Fig. 1B). Given the transient presence of the GE136 lineage, we asked whether we could detect a similar pattern of lineage development for GE140. We first visualized the unbiased heavy and light chain repertoires with respect to GE140 using the 2D plots (Fig. 5A). Interestingly, GE140-like heavy chains were found from all time points except for the one after 2 immunizations. This finding suggests that the GE140 lineage formed within a time frame similar to that of GE136 but undertook a different developmental pathway, such that it remained detectable over the remaining course of the vaccination regimen (Fig. 5A, row 1). It should also be noted that two GE140-like MAbs were isolated from a different post-2 sample by single B-cell sorting (our unpublished data), suggesting an earlier birth time of the GE140 lineage. GE140-like heavy chains possessed a lower divergence after the third immunization yet continued to mature and form a separate lineage over the following 2 months, as indicated by the more divergent sequences along the 100% identity line and a wedge-shaped density departing from the main population (Fig. 5A, row 1). To quantify the GE140 lineage development, we identified all heavy chains of the VH4.11 origin and determined the fraction of heavy chains with an HCDR3 identity of 95% or more to GE140 within the VH4.11 family (Fig. 5A, row 2). The GE140 lineage evolved rapidly between post-3 and -4, with the fraction increasing from 0.83 to 6.07‰ before reaching a plateau of 5.59‰ between post-4 and -5. The GE140 lineage continued to diversify during maturation, as indicated by more sequences with higher divergence but lower GE140 identity (Fig. 5A, row 2). In contrast, the light chain repertoires contained sequences that were nearly 100% identical to the GE140 light chain, displaying little change over time (Fig. 5A, row 3).


Rhesus Macaque B-Cell Responses to an HIV-1 Trimer Vaccine Revealed by Unbiased Longitudinal Repertoire Analysis.

Dai K, He L, Khan SN, O'Dell S, McKee K, Tran K, Li Y, Sundling C, Morris CD, Mascola JR, Karlsson Hedestam GB, Wyatt RT, Zhu J - MBio (2015)

Longitudinal analysis of the GE140 lineage development. (A) Identity-divergence analysis of the unbiased heavy (H) and light (λ) chain repertoires. The sequences are plotted as a function of sequence identity to GE140 and of sequence divergence from putative germline V genes. Color coding denotes sequence density. The VH4.11 heavy chain family at each time point is visualized by black contour lines (middle row). The GE140-like heavy chains with an HCDR3 identity of over 95% are shown as red dots on the plots; the numbers are numbers of sequences. (B) ML tree of selected GE140 heavy chain variants rooted by the putative germline VH4.11 gene (see Fig. 4 for sequence selection and labeling). The bar represents a 0.001 change per nucleotide site. (C) ELISA analysis of antigen binding is shown for six antibodies reconstituted from GE140 heavy chain variants with SD bars. (D) Analysis of GE140-like light chains. (Left) The VL2.7 light chain family at the last time point is visualized with black contours. Light chains with an LCDR3 identity of 95% or greater are shown as red dots on the 2D plot. (Right) ELISA analysis of HIV-1 trimer vaccine antigen binding (right) is shown for three antibodies reconstituted from GE140 light chain variants, with SD bars.
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fig5: Longitudinal analysis of the GE140 lineage development. (A) Identity-divergence analysis of the unbiased heavy (H) and light (λ) chain repertoires. The sequences are plotted as a function of sequence identity to GE140 and of sequence divergence from putative germline V genes. Color coding denotes sequence density. The VH4.11 heavy chain family at each time point is visualized by black contour lines (middle row). The GE140-like heavy chains with an HCDR3 identity of over 95% are shown as red dots on the plots; the numbers are numbers of sequences. (B) ML tree of selected GE140 heavy chain variants rooted by the putative germline VH4.11 gene (see Fig. 4 for sequence selection and labeling). The bar represents a 0.001 change per nucleotide site. (C) ELISA analysis of antigen binding is shown for six antibodies reconstituted from GE140 heavy chain variants with SD bars. (D) Analysis of GE140-like light chains. (Left) The VL2.7 light chain family at the last time point is visualized with black contours. Light chains with an LCDR3 identity of 95% or greater are shown as red dots on the 2D plot. (Right) ELISA analysis of HIV-1 trimer vaccine antigen binding (right) is shown for three antibodies reconstituted from GE140 light chain variants, with SD bars.
Mentions: A group of diverse somatic variants (n = 75) was identified for the GE140 heavy chain from the 454 sequencing of a sample after 5 immunizations (Fig. 1B). Given the transient presence of the GE136 lineage, we asked whether we could detect a similar pattern of lineage development for GE140. We first visualized the unbiased heavy and light chain repertoires with respect to GE140 using the 2D plots (Fig. 5A). Interestingly, GE140-like heavy chains were found from all time points except for the one after 2 immunizations. This finding suggests that the GE140 lineage formed within a time frame similar to that of GE136 but undertook a different developmental pathway, such that it remained detectable over the remaining course of the vaccination regimen (Fig. 5A, row 1). It should also be noted that two GE140-like MAbs were isolated from a different post-2 sample by single B-cell sorting (our unpublished data), suggesting an earlier birth time of the GE140 lineage. GE140-like heavy chains possessed a lower divergence after the third immunization yet continued to mature and form a separate lineage over the following 2 months, as indicated by the more divergent sequences along the 100% identity line and a wedge-shaped density departing from the main population (Fig. 5A, row 1). To quantify the GE140 lineage development, we identified all heavy chains of the VH4.11 origin and determined the fraction of heavy chains with an HCDR3 identity of 95% or more to GE140 within the VH4.11 family (Fig. 5A, row 2). The GE140 lineage evolved rapidly between post-3 and -4, with the fraction increasing from 0.83 to 6.07‰ before reaching a plateau of 5.59‰ between post-4 and -5. The GE140 lineage continued to diversify during maturation, as indicated by more sequences with higher divergence but lower GE140 identity (Fig. 5A, row 2). In contrast, the light chain repertoires contained sequences that were nearly 100% identical to the GE140 light chain, displaying little change over time (Fig. 5A, row 3).

Bottom Line: Next-generation sequencing of B-cell repertoires provides a quantitative tool to analyze B-cell responses to a vaccine.In this study, the longitudinal B-cell repertoire analysis of a rhesus macaque immunized with an HIV-1 trimer vaccine revealed complex B-cell lineage patterns and showed the potential to facilitate the evaluation of future HIV-1 vaccines.The repertoire sequencing technologies and antibodyomics methods reported here can be extended to vaccine development for other human pathogens utilizing the nonhuman primate model.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA.

No MeSH data available.