Ndungu, T. | Search bioRxiv

bioRxiv2025

Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection

Understanding the selective forces acting upon HIV early in infection is crucial to design prevention strategies. By leveraging deep sequencing and the short diagnostic intervals of the FRESH and RV217 cohorts (median 4 days) between the last-negative and first-positive RNA tests, we captured a precise and early snapshot of acute HIV infection. The frequency of multiple transmitted viruses of 38% in these as well as placebo recipients from the AMP trials was higher than previously published, with the true frequency likely to be higher. The relative abundance of lineages fluctuated substantially over time in two-thirds of the multilineage infections, generating uncertainty in identifying the specific viruses that were transmitted and founding the infection. Viral populations exhibited diversity and selection on the Gag and Env proteins at the earliest times examined, with sites inferred to be undergoing negative selection most evident. These data may help explain vaccination failures and provide new targets for prevention.

microbiology↗

bioRxiv2020

CXCR5 gene expression in human lymph node CD8+ T cells is regulated by DNA methylation and nucleosomal occupancy

CD8+ T cells play an important role in viral and tumour control. However, in human lymph nodes (LNs), only a small subset of CD8+ T cells called follicular CD8+ T cells (fCD8s) expresses CXCR5, the chemokine receptor required for cell migration into B cell follicles, thought to promote immune evasion. Here we obtained LNs from HIV infected persons to investigate regulation of CXCR5 expression in lymphoid CD8+ T cells, and compared this to the more abundant CXCR5 expressing T follicular CD4+ helper cells (GCTfh). Our results show that DNA hypermethylation and closed chromatin at the transcriptional start site (TSS) prevent CXCR5 expression in non-fCD8s. We also found that greater nucleosomal density at the CXCR5 TSS could be responsible for reduced CXCR5 expression in fCD8s relative to GCTfh. Together, these data provide critical insights into both the underlying molecular mechanisms that repress CXCR5 expression in non-fCD8s and the plausible mechanism responsible for the low CXCR5 expression in fCD8s, with implications for HIV cure strategies. Author SummaryA paucity of CD8+ T cells that express CXCR5, the chemokine receptor critical for entering the B cell follicles of secondary lymphoid tissues have recently been described. Animal studies have revealed transcriptional networks that govern the expression of CXCR5 in CD8+ T cells. However, it is not known if similar or additional networks regulate the expression of CXCR5 in human CD8+ T cells. In this study, we demonstrated that DNA methylation coupled with chromatin compaction at the transcriptional start site (TSS) of CXCR5 gene prevent the expression CXCR5 in human CD8+ T cells. In addition, we observed greater nucleosomal occupancy at the TSS of CXCR5 gene which could impact expression levels of CXCR5 in human CXCR5+CD8+ T cells. This study revealed multitiered epigenetic mechanisms that repress CXCR5 expression in human CD8+ T cells, with implications for HIV cure strategy or eradication of B cell-derived tumours.

genetics↗