Cell-type independent differentially methylated loci associated with acute HIV infection.

• Main Authors: Michael J. Corley (7447133), Carlo Sacdalan (11273544), Alina P. S. Pang (7447139), Nitiya Chomchey (327683), Nisakorn Ratnaratorn (11273550), Victor Valcour (22964), Eugene Kroon (673318), Kyu S. Cho (11273553), Andrew C. Belden (10296401), Donn Colby (447929), Merlin Robb (373375), Denise Hsu (11273556), Serena Spudich (202054), Robert Paul (22962), Sandhya Vasan (102251), Lishomwa C. Ndhlovu (7122293)
• Format: Still Image
• Language: unknown
• Published: 2021
• Subjects: Medicine; Genetics; Molecular Biology; Cancer; Science Policy; Infectious Diseases; Virology; Biological Sciences not elsewhere classified; RV; CD 4 count; AHI; DNA methylation profiles; monocyte; precision HIV medicine; CD 4; HIV-associated; initiation; Monocyte DNA methylation patterns; T lymphocytes; genome-wide DNA methylation; HIV infection; NCT; Venn; DML
• Online Access: https://doi.org/10.1371/journal.ppat.1009785.g003

(a) Diagram of experimental design displaying comparison utilized to identify DML in CD4+ T cells associated with AHI. Created with BioRender.com (b) Volcano plot displaying gene symbol and CpG ID (cg#) for top hypomethylated and hypermethylated sites associated with AHI in CD4 + T lymphocytes. Difference in DNA methylation displayed as delta beta values plotted against P values transformed using -log10(P). (c) Venn diagram displaying the number of overlapping DML and cell-type specific DML identified in CD4+ T cells and monocyte cells (d-s) Plots demonstrating changes in DNA methylation in AHI Fiebig I (red dots), Fiebig II (blue dots) Fiebig III-V (purple dots) participants compared to HIV- (green dots) at single CpGs sites related to annotated protein-coding genes displayed in bold italic above CpG ID (cg#) for CD4 + T lymphocytes and monocytes. Significance determined comparing HIV- vs. AHI and using FDR adjusted P-values <0.05.