SIV-specific neutralizing antibody induction following selection of a PI3K drive-attenuated nef variant
- AIDS Research Center, National Institute of Infectious Diseases, Japan
- Department of Biomedicine, University Hospital Basel, Switzerland
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Japan
- The Institute of Medical Science, The University of Tokyo, Japan
Figures
Figure 1 with 4 supplements
Neutralizing antibody (NAb) induction against NAb-resistant SIVmac239.
(A) Study design. (B) Plasma viral loads (simian immunodeficiency virus [SIV] gag RNA copies/ml plasma) in NAb non-inducers (left) and inducers (right). (C) Plasma SIVmac239 100% neutralizing end …
Figure 1—figure supplement 1
Profile of SIVmac239-NAb non-inducer subgroup cohort.
Summary of a SIVmac239-NAb non-inducer subgroup cohort (n = 19), composed from previously partially characterized, major histocompatibility complex class I (MHC-I) haplotype-balanced naïve animals. …
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Figure 1—figure supplement 1—source data 1
Source table for Figure 1—figure supplement 1.
- https://cdn.elifesciences.org/articles/88849/elife-88849-fig1-figsupp1-data1-v1.xlsx
Figure 1—figure supplement 2
IgG class-switched neutralizing antibodies (NAbs) in the inducers.
Titration of SIVmac239-neutralizing IgGs in the NAb inducers. SIVmac239-specific IgGs, purified from pools of plasma with SIVmac239-specific NAb titers, were obtained from each animal as described (Y…
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Figure 1—figure supplement 2—source data 1
Source table for Figure 1—figure supplement 2.
- https://cdn.elifesciences.org/articles/88849/elife-88849-fig1-figsupp2-data1-v1.xlsx
Figure 1—figure supplement 3
Anti-SIV binding IgG profiles in neutralizing antibody (NAb) inducers and non-inducers.
(A) Temporal changes in SIVmac251 Env gp120-specific antibody titers in the NAb non-inducers without rapid progression [NAb-negative non-rapid progressors, NAb(-) non-RPs] (left, n = 11) and NAb …
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Figure 1—figure supplement 3—source data 1
PDF file containing original western blots for Figure 1—figure supplement 3, labeling the corresponding viral protein bands and IDs.
- https://cdn.elifesciences.org/articles/88849/elife-88849-fig1-figsupp3-data1-v1.zip
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Figure 1—figure supplement 3—source data 2
Original file for western blot analysis displayed in Figure 1—figure supplement 3.
- https://cdn.elifesciences.org/articles/88849/elife-88849-fig1-figsupp3-data2-v1.zip
Figure 1—figure supplement 4
Env sequence variation pattern is not a major characteristic of neutralizing antibody (NAb) induction.
SIVmac239 Env sequence variations before and after NAb induction. For each animal, the upper time point shows pre-induction and the lower time point (in purple) shows post-induction (first or second …
Figure 2
Selection of a viral nef mutation (Nef-G63E) before neutralizing antibody (NAb) induction.
(A) Viral nef mutations in NAb inducers. A linear schema indicating Nef functional domains is aligned above. Mutations at time points with NAb- (indicated by white wedge; mostly before 6 months …
Figure 3 with 1 supplement
Nef-G63E is a CD8+ T-cell escape mutation.
(A) Nef62–70 QW9-specific CD8+ T-cell frequencies and related major histocompatibility complex class I (MHC-I) alleles in seven neutralizing antibody (NAb) inducers selecting Nef-G63E. Mamu-B*039:01 …
Figure 3—figure supplement 1
Selection of Nef-G63E mutant simian immunodeficiency virus (SIV) is linked with Nef62-70-specific CD8+ T-cell response positivity.
(A) Nef62-70-specific CD8+ T cell responses around week 20 post-SIV challenge in seven viremic NAb non-inducers possessing either of the major histocompatibility complex class I (MHC-I) alleles …
Figure 4 with 2 supplements
Nef-G63E mutation reduces PI3K/mTORC2 binding and pAkt drive.
(A) Representative surface expression level histograms of CD3, CD4, major histocompatibility complex class I (MHC-I), CXCR4, and BST-2 in CD4loNef+ subpopulations after wild-type (WT) or Nef-G63E …
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Figure 4—source data 1
Original western blots for Figure 4E indicating the relevant bands and treatments.
- https://cdn.elifesciences.org/articles/88849/elife-88849-fig4-data1-v1.zip
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Figure 4—source data 2
Original file for the western blot analysis displayed in Figure 4E.
- https://cdn.elifesciences.org/articles/88849/elife-88849-fig4-data2-v1.zip
Figure 4—figure supplement 1
Decreased Akt hyperactivation properties of Nef-G63E mutant simian immunodeficiency virus (SIV).
(A) Plasma ferritin levels (ng/ml) in examined neutralizing antibody (NAb) non-inducers versus Nef-G63E mutant SIV-selecting NAb inducers around year 1 post-infection (p.i.). Bars represent mean in …
Figure 4—figure supplement 2
Nef-G63R mutant simian immunodeficiency virus (SIV) properties.
(A) Comparison of frequencies of macaques selecting for Nef-G63R mutant in plasma between neutralizing antibody (NAb) non-inducers and inducers. Compared by Fisher’s exact test. (B) Temporal …
Figure 5 with 1 supplement
Preferential targeting of lymph node Env-specific B cells by Nef in vivo.
(A) Representative gating of triple noise cancellation in vivo Nef staining in B cells analyzed using ImageStreamX MKII. Pre-experimental damaged cells are first excluded with Live/Dead from …
Figure 5—figure supplement 1
Machine learning-verified morphological gating of Nef-invaded B cells in vivo.
(A) Representative gating strategy plus schematic of inguinal lymph node Nef+CD19+ B cells of an SIVmac239-infected rhesus macaque analyzed using ImageStreamX MK II imaging flow cytometry (R10-012, …
Figure 6
Contact-dependent enhancement of B-cell Nef acquisition in reconstitution.
(A) Imaging flow cytometric analyses of stimuli-dependent enhancement of infected HSC-F cell adhesion to non-permissive CD19+ Ramos B cells with the indicated gating (left). Cocultured doublet cells …
Figure 7 with 1 supplement
Enhanced simian immunodeficiency virus (SIV) Env-specific B-cell output up to neutralizing antibody (NAb) induction following Nef-G63E selection.
(A) Representative gating (R02-004, week 32 post-infection [p.i.]) of SIV Env gp140-specific memory B cells (Bmem) and plasmablasts (PBs). Two panels for PB gating are shown in lower resolution for …
Figure 7—figure supplement 1
Full gating strategy of SIVmac239 Env gp140-specific B-cell responses.
Full gating (R02-004, week 32 p.i.) of SIV Env gp140-specific memory B cells (Bmem) and plasmablasts (PBs) shown in Figure 7. For lineage-specific exclusion, CD10 was stained independently for Bmem.
