Additional file 2 of IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis
Creators: name: Zhang, Zhenhua
name: Trypsteen, Wim
name: Blaauw, Marc
name: Chu, Xiaojing
name: Rutsaert, Sofie
name: Vandekerckhove, Linos
name: van der Heijden, Wouter
name: dos Santos, Jéssica Cristina
name: Xu, Cheng-Jian
name: Swertz, Morris A.
name: van der Ven, Andre
name: Li, Yang
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Three panels of the figure are respective differences of CA HIV-1 RNA, CA HIV-1 DNA, and RNA:DNA ratio between male and female. However, by a student test, sex does not affect any of the three traits at the threshold of P &lt; 0.05. Figure S2. A, B, and C are Manhattan plots for CA HIV-1 DNA, CA HIV-1 RNA, and CA HIV-1 RNA (adjusted by CA HIV-1 DNA). However, no association was found at the threshold of P &lt; 5 × 10-7. Moreover, all the associative analyses have an inflation factor close to 1. Figure S3. (A) Gene Ontology (biological process) annotation and enrichment of genes at locus identified as genome-wide significantly associated with CA HIV-1 DNA. (B) Gene Ontology (biological process) annotation and enrichment of genes at locus identified as genome-wide suggestively associated with RNA:DNA ratio. Figure S4. (A) Correlation between two types of PS and RNA:DNA ratio. The horizontal axis represents the Log2 transformed RNA:DA ratio. The vertical axis represents the PS intensity transformed by Log10. (B) PS intensity transformed by Log10 per genotype of rs7113204. No significant difference among three genotypes was found for each PS. (C) PS intensity transformed by Log10 per genotype of rs2613996. No significant difference among three genotypes was found for each PS. Figure S5. (A) Box plot for each genotype of rs7817589 from QTL mapping analysis for RNA:DNA ratio. This locus is identified as suggestively associated with the trait at the threshold of P = 2.17 × 10-7. (B) LocusZoom plot of the top SNP of QTL mapping analysis for RNA:DNA ratio on chromosome 8. Figure S6. (A) Box plot of relative expression of PTDSS2 compared in a subset of subjects with variant rs2613996-A (n = 10) compared to subjects with variant rs2613996-G (n = 19). (B) Box plot of relative expression of PTDSS2 in subjects with SNP rs7113204-A (n = 11) compared to SNP rs7113204-G (n = 14). Data in these box plots are visualized in log transformation. Groups are compared by using the two-sample Wilcoxon test because of the non-normal distribution. Figure S7. Relative expression of four prioritized genes (DEAF1, IRF7, PTDSS2, and RNH1). We downloaded gene expression data of in vitro primary human CD4+ T cells from GEO GSE127468 and estimated the differential expression of four genes identified by us. The horizontal axis are time-points at which the mRNA were measured and the vertical axis are relative expression quantified by RNA-seq. The red boxes (dots) and blue boxes (dots) represent relative expression level of each gene in HIV-1 infected CD4+ T cells and control CD4+ T cells in vitro, respectively. The double stars (**) mark p-value &lt; 0.01 and the single star (*) mark p-value &lt; 0.05. Figure S8. Box plot of interferon-alpha (IFN-α) production 24 hours after poly I:C stimulation in PBMCs in subjects with SNP rs7113204-A (n = 16) and with rs7113204-G (n = 121). Groups are compared with two samples Wilcoxon test because of the non-normal distribution.