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The potential of the human immune system to develop broadly neutralizing HIV-1 antibodies: implications for vaccine development.

Zhang Y, Yuan T, Li J, Zhang Y, Xu J, Shao Y, Chen Z, Zhang MY - AIDS (2013)

Bottom Line: Developing an effective HIV-1 vaccine that elicits broadly neutralizing HIV-1 human antibodies (bnAbs) remains a challenging goal.However, we found relatively high frequencies of the heavy and kappa and lambda light chain variable regions that used the same V-genes and had the same CDR3 lengths as known HIV-1 bnmAbs regardless of (D)J-gene usage.B-cells bearing B-cell receptors of such heavy and kappa and lambda light chain variable regions may be stimulated to induce HIV-1 bnAbs.

View Article: PubMed Central - PubMed

Affiliation: aAIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong bInstitutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai cDivision of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China.

ABSTRACT

Objectives and design: Developing an effective HIV-1 vaccine that elicits broadly neutralizing HIV-1 human antibodies (bnAbs) remains a challenging goal. Extensive studies on HIV-1 have revealed various strategies employed by the virus to escape host immune surveillance. Here, we investigated the human antibody gene repertoires of uninfected and HIV-1-infected individuals at genomic DNA (gDNA) and cDNA levels by deep sequencing followed by high-throughput sequence analysis to determine the frequencies of putative germline antibody genes of known HIV-1 monoclonal bnAbs (bnmAbs).

Methods: Combinatorial gDNA and cDNA antibody libraries were constructed using the gDNAs and mRNAs isolated from uninfected and HIV-1-infected human peripheral blood mononuclear cells (PBMCs). All libraries were deep sequenced and sequences analysed using IMGT/HighV-QUEST software (http://imgt.org/HighV-QUEST/index.action). The frequencies of putative germline antibodies of known bnmAbs in the gDNA and cDNA libraries were determined.

Results and conclusion: The human gDNA antibody libraries were more diverse in heavy and light chain V-gene lineage usage than the cDNA libraries, indicating that the human gDNA antibody gene repertoires may have more potential than the cDNA repertoires to develop HIV-1 bnAbs. The frequencies of the heavy and kappa and lambda light chain variable regions with identical V(D)J recombinations to known HIV-1 bnmAbs were extremely low in human antibody gene repertoires. However, we found relatively high frequencies of the heavy and kappa and lambda light chain variable regions that used the same V-genes and had the same CDR3 lengths as known HIV-1 bnmAbs regardless of (D)J-gene usage. B-cells bearing B-cell receptors of such heavy and kappa and lambda light chain variable regions may be stimulated to induce HIV-1 bnAbs.

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Percentage of heavy chain V-gene lineages in the nonimmune and immune genomic DNA and cDNA libraries.
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Figure 2: Percentage of heavy chain V-gene lineages in the nonimmune and immune genomic DNA and cDNA libraries.

Mentions: We amplified the scFvs from the gDNA libraries and the Fds and light chains from the cDNA libraries using primers that annealed to the pComb3X vector or to the constant regions of heavy or light chains (CH1 and CL, respectively) (Table S1 and S2) and sent the PCR products for deep sequencing. We obtained trim sequences (>290 nt) from each library ranging from 23 530 to 88 331 for heavy chain variable regions, and from 17 285 to 28 110 for kappa light chain variable regions and from 21 480 to 30 199 for lambda light chain variable regions. Sequence analysis showed different patterns of using various IGHV and IGKV/IGLV (kappa and lambda light chain V-genes) lineages in different gDNA and cDNA libraries, and the differences between the gDNA and corresponding cDNA libraries were more significant than those between the nonimmune and immune gDNA or cDNA libraries (Figs 1–3). The gDNA libraries were more diverse overall than the cDNA libraries in using various IGHV lineages (Figs 1 and 2). Among the four gDNA heavy chain libraries, NIgH and pt1gH showed a similar pattern of various IGHV lineage usage, whereas pt2gH and pt3gH were significantly different from NIgH and pt1gH in using IGHV1, IGHV2 and IGHV6 lineages (Figs 1 and 2). Compared with the gDNA heavy chain libraries, the corresponding cDNA heavy chain libraries had significantly higher percentages of clones using IGHV1 and IGHV3 lineages (Fig. 1), and were biased to certain VH1 and VH3 subfamilies, including IGHV1–18, 1–2 and 1–69, and IGHV 3–11, 3–21, 3–23, 3–30, 3–33, 3–49, 3–7 and 3–74 (Fig. 2). The patterns of various IGKV/IGLV lineage usages in the nonimmune and immune gDNA libraries were similar except for pt1gK library (Figs 1 and 3). The nonimmune and immune cDNA libraries also showed a similar pattern in using various IGKV/IGLV lineages. Both nonimmune and immune cDNA antibody libraries heavily used IGKV3 and IGLV1 lineages (Figs 1 and 3). These results indicate that HIV-1 infection shapes the patterns of various IGHV lineage usages, but the caused changes at the cDNA level are much less significant compared with the changes at the gDNA level. The differences between the gDNA and cDNA antibody gene repertoires in HIV-1 uninfected (nonimmune) humans reflect host immune regulations, and such regulations may largely determine the host-dependent immune response to HIV-1 infection.


The potential of the human immune system to develop broadly neutralizing HIV-1 antibodies: implications for vaccine development.

Zhang Y, Yuan T, Li J, Zhang Y, Xu J, Shao Y, Chen Z, Zhang MY - AIDS (2013)

Percentage of heavy chain V-gene lineages in the nonimmune and immune genomic DNA and cDNA libraries.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815086&req=5

Figure 2: Percentage of heavy chain V-gene lineages in the nonimmune and immune genomic DNA and cDNA libraries.
Mentions: We amplified the scFvs from the gDNA libraries and the Fds and light chains from the cDNA libraries using primers that annealed to the pComb3X vector or to the constant regions of heavy or light chains (CH1 and CL, respectively) (Table S1 and S2) and sent the PCR products for deep sequencing. We obtained trim sequences (>290 nt) from each library ranging from 23 530 to 88 331 for heavy chain variable regions, and from 17 285 to 28 110 for kappa light chain variable regions and from 21 480 to 30 199 for lambda light chain variable regions. Sequence analysis showed different patterns of using various IGHV and IGKV/IGLV (kappa and lambda light chain V-genes) lineages in different gDNA and cDNA libraries, and the differences between the gDNA and corresponding cDNA libraries were more significant than those between the nonimmune and immune gDNA or cDNA libraries (Figs 1–3). The gDNA libraries were more diverse overall than the cDNA libraries in using various IGHV lineages (Figs 1 and 2). Among the four gDNA heavy chain libraries, NIgH and pt1gH showed a similar pattern of various IGHV lineage usage, whereas pt2gH and pt3gH were significantly different from NIgH and pt1gH in using IGHV1, IGHV2 and IGHV6 lineages (Figs 1 and 2). Compared with the gDNA heavy chain libraries, the corresponding cDNA heavy chain libraries had significantly higher percentages of clones using IGHV1 and IGHV3 lineages (Fig. 1), and were biased to certain VH1 and VH3 subfamilies, including IGHV1–18, 1–2 and 1–69, and IGHV 3–11, 3–21, 3–23, 3–30, 3–33, 3–49, 3–7 and 3–74 (Fig. 2). The patterns of various IGKV/IGLV lineage usages in the nonimmune and immune gDNA libraries were similar except for pt1gK library (Figs 1 and 3). The nonimmune and immune cDNA libraries also showed a similar pattern in using various IGKV/IGLV lineages. Both nonimmune and immune cDNA antibody libraries heavily used IGKV3 and IGLV1 lineages (Figs 1 and 3). These results indicate that HIV-1 infection shapes the patterns of various IGHV lineage usages, but the caused changes at the cDNA level are much less significant compared with the changes at the gDNA level. The differences between the gDNA and cDNA antibody gene repertoires in HIV-1 uninfected (nonimmune) humans reflect host immune regulations, and such regulations may largely determine the host-dependent immune response to HIV-1 infection.

Bottom Line: Developing an effective HIV-1 vaccine that elicits broadly neutralizing HIV-1 human antibodies (bnAbs) remains a challenging goal.However, we found relatively high frequencies of the heavy and kappa and lambda light chain variable regions that used the same V-genes and had the same CDR3 lengths as known HIV-1 bnmAbs regardless of (D)J-gene usage.B-cells bearing B-cell receptors of such heavy and kappa and lambda light chain variable regions may be stimulated to induce HIV-1 bnAbs.

View Article: PubMed Central - PubMed

Affiliation: aAIDS Institute, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong bInstitutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai cDivision of Research on Virology and Immunology, National Center for AIDS/STD Control and Prevention, China CDC, Beijing, China.

ABSTRACT

Objectives and design: Developing an effective HIV-1 vaccine that elicits broadly neutralizing HIV-1 human antibodies (bnAbs) remains a challenging goal. Extensive studies on HIV-1 have revealed various strategies employed by the virus to escape host immune surveillance. Here, we investigated the human antibody gene repertoires of uninfected and HIV-1-infected individuals at genomic DNA (gDNA) and cDNA levels by deep sequencing followed by high-throughput sequence analysis to determine the frequencies of putative germline antibody genes of known HIV-1 monoclonal bnAbs (bnmAbs).

Methods: Combinatorial gDNA and cDNA antibody libraries were constructed using the gDNAs and mRNAs isolated from uninfected and HIV-1-infected human peripheral blood mononuclear cells (PBMCs). All libraries were deep sequenced and sequences analysed using IMGT/HighV-QUEST software (http://imgt.org/HighV-QUEST/index.action). The frequencies of putative germline antibodies of known bnmAbs in the gDNA and cDNA libraries were determined.

Results and conclusion: The human gDNA antibody libraries were more diverse in heavy and light chain V-gene lineage usage than the cDNA libraries, indicating that the human gDNA antibody gene repertoires may have more potential than the cDNA repertoires to develop HIV-1 bnAbs. The frequencies of the heavy and kappa and lambda light chain variable regions with identical V(D)J recombinations to known HIV-1 bnmAbs were extremely low in human antibody gene repertoires. However, we found relatively high frequencies of the heavy and kappa and lambda light chain variable regions that used the same V-genes and had the same CDR3 lengths as known HIV-1 bnmAbs regardless of (D)J-gene usage. B-cells bearing B-cell receptors of such heavy and kappa and lambda light chain variable regions may be stimulated to induce HIV-1 bnAbs.

Show MeSH
Related in: MedlinePlus