Science Immunology

Supplementary Materials

Supplementary Material for:

Immune perturbations in HIV-1–infected individuals who make broadly reactive neutralizing antibodies

M. Anthony Moody,* Isabela Pedroza-Pacheco, Nathan A. Vandergrift, Cecilia Chui, Krissey E. Lloyd, Robert Parks, Kelly A. Soderberg, Ane T. Ogbe, Myron S. Cohen, Hua-Xin Liao, Feng Gao, Andrew J. McMichael, David C. Montefiori, Laurent Verkoczy, Garnett Kelsoe, Jinghe Huang, Patrick R. Shea, Mark Connors, Persephone Borrow,* Barton F. Haynes*

*Corresponding author. Email: hayne002{at}mc.duke.edu (B.F.H.); moody007{at}mc.duke.edu (M.A.M.); persephone.borrow{at}ndm.ox.ac.uk (P.B.)

Published 29 July 2016, Sci. Immunol. 1, aag0851 (2016)
DOI: 10.1126/sciimmunol.aag0851

This PDF file includes:

  • Methods
  • Fig. S1. Eigenvalues and amount of variance explained up to PC6.
  • Fig. S2. Cohort A PC1 scores in descending order.
  • Fig. S3. Plots of individual autoantibody assay results.
  • Fig. S4. Gating strategy for flow cytometric analysis of T cell subsets.
  • Fig. S5. Comparison of Helios expression in CD4+ Treg cells in cohort A individuals with and without bnAbs and matched HIV-1–seronegative controls.
  • Fig. S6. Comparison of Tfr subsets (as defined using alternative phenotyping strategies) in cohort A individuals with and without bnAbs and matched HIV-1–seronegative controls.
  • Table S1. Country of origin for cohort A individuals.
  • Table S2. Cohort A individuals included and excluded from principal components analysis and control group.
  • Table S3. Cohort A bnAb group reciprocal dilution ID50 neutralization results.
  • Table S4. Cohort A control group reciprocal dilution ID50 neutralization results.
  • Table S5. Cohort A differences between bnAb and control groups for biological sex.
  • Table S6. Cohort A differences between bnAb and control groups for country of origin.
  • Table S7. Cohort A differences between bnAb and control groups.
  • Table S8. Cohort A mean duration individuals were followed.
  • Table S9. Cohort A clade of HIV-1 infection.
  • Table S10. General linear model results for the effect of clade of HIV-1 infection in cohort A on PC1 score.
  • Table S11. Logistic model results for the effect of clade of HIV-1 infection in cohort A in the presence of autoantibodies.
  • Table S12. Poisson model results for the effect of clade of HIV-1 infection in cohort A in the presence of autoantibodies.
  • Table S13. Cohort B bnAb individuals reciprocal dilution ID50 neutralization results.
  • Table S14. Cohort B control individuals reciprocal dilution ID50 neutralization results.
  • Table S15. Cohort B differences between bnAb and control groups for biological sex.
  • Table S16. Cohort B differences between bnAb and control groups.
  • Table S17. General linear model results for the difference between bnAb and control groups of cohorts A and B for binding to additional antigens.
  • Table S18. General linear model results for the difference in T cell subsets between cohort A bnAb and control groups and African seronegative individuals.
  • Table S19. Logistic model results for the effect of viral load in cohort A in the presence of autoantibodies.
  • Table S20. Poisson model results for the effect of viral load in cohort A in the presence of autoantibodies.
  • Table S21. General linear model results for cohort A bnAb and control groups with covariates for group, for viral load, and as an interaction term.
  • Table S22. General linear model results for cohort A bnAb and control groups with viral load as a main effect.
  • Table S23. General linear model results for the difference in alternatively defined Tfr subsets between cohort A bnAb and control groups and African seronegative individuals.
  • Table S24. General linear model results for Treg activation/exhaustion marker expression between cohort A bnAb and control groups and African seronegative individuals.
  • Table S25. General linear model results for Treg marker expression levels on Treg subsets defined by PD-1 expression levels for the cohort A bnAb group.
  • Table S26. General linear model results for Treg marker expression levels on Treg subsets defined by PD-1 expression levels for the African seronegative individuals.
  • Table S27. Sign test results for suppression of T cell proliferation by subsets of Treg cells with differing levels of PD-1 expression, normalized to Tconv plus Tconv.
  • Table S28. General linear model results for the difference in T cell subsets within cohort A HIV-1–seronegative individuals who were autoantibody-positive and autoantibody-negative.
  • Table S29. Cohort A bnAb group two-digit HLA class I types.
  • Table S30. Cohort A control group two-digit HLA class I types.
  • Table S31. Cohort A bnAb group two-digit HLA class II types.
  • Table S32. Cohort A control group two-digit HLA class II types.
  • Table S33. Top 20 most highly associated functional variants in exome sequencing of bnAbs versus non-bnAbs (dominant genetic model).
  • Table S34. Top 20 most highly associated functional variants in exome sequencing of autoimmune bnAbs versus non-bnAbs (dominant genetic model).
  • References (99111)

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Correction (17 October 2016): Full patient IDs were removed from tables S3, S9, and S29 to S3.

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