B-cell lineage-based approach to vaccine design.

<p>Mature bnAbs can be isolated from HIV-1–infected donors using modern methods such as memory B-cell culture or sorting of antigen-specific B-cells. Based on the known bnAb sequence, next generation sequencing can be used to find numerous clonal relatives of the mature bnAb. If appropriate longitudinal samples are available, it is possible to infer the full antibody lineage, including the UA and IAs. The expressed UA and IA sequences can then be used as templates for the design of HIV-1 immunogens with high-affinity binding. As the antibody lineage is known to evolve in response to viral evolution, it may be possible to design sequential immunogens with high-affinity binding for the UA and IA, thus guiding the antibody response toward the mature antibody with broad neutralizing activity (with permission from <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004073#ppat.1004073-Mascola1" target="_blank">[4]</a>).</p

Additional file 6 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 6. Table S9: Genes differentially expressed between HIV-1-infected compared to seronegative CD4+ T cells

Additional file 10 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 10. Table S13: Genes correlated or anti-correlated with HIV-1 gag transcript expression

Additional file 9 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 9. Table S12: Genes differentially expressed between HIV-1-treated compared to seronegative CD8+ T cells

Additional file 3 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 3. Table S4: Genes differentially expressed between HIV-1-infected compared to seronegative

Additional file 4 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 4. Table S5: Genes differentially expressed between HIV-1-treated compared to seronegative

Additional file 7 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 7. Table S10: Genes differentially expressed between HIV-1-infected compared to seronegative CD8+ T cells

Additional file 8 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 8. Table S11: Genes differentially expressed between HIV-1-treated compared to seronegative CD4+ T cells

Additional file 5 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 5. Table S8: Genes upregulated in each cluster in scRNA-seq T and NK cells

Additional file 1 of Single-cell analysis of immune cell transcriptome during HIV-1 infection and therapy

Additional file 1. Table S1: Individual sample scRNA-seq results. Table S2 Cell cluster computational inference of cell type. Table S6 GSEA enrichment of untreated HIV-1 compared to control. Table S7 GSEA enrichment of ART-treated HIV-1 compared to control. Fig. S1. scRNA-seq individual cell QC data. Fig. S2. Determining cell types and genes in each cluster. Fig. S3. NK and T cell reclustering