# Commensal microbiome impact on CD4 T cell lymphopenia in HIV-1 infection

> **NIH NIH R01** · EMORY UNIVERSITY · 2023 · $767,675

## Abstract

Project Summary/Abstract
HIV-infected Immune non-responders (INR) persons are at greater risk of comorbidity and mortality than are
immune responders (IR) who restore their CD4 T cells count (IR) after anti- retroviral therapy (ART). INR
have low CD4 T cell counts (<350 c/ul), heightened systemic inflammation, and increased CD4 T cell cycling
(KI67+). We previously reported dysfunctional mitochondria in INR CD4 T cells by transcriptomic and flow
cytometric assays. In here we report the metabolic profiles of sorted memory CD3+CD4+CD45RO+T cells
from healthy controls (HC), IR, and INR and found dysregulation of the tricarboxylic acid cycle (TCA)
intermediates suggestive of mitochondrial dysfunction confirmed by Electron Microscopy Imaging (EMI).
Disrupted Golgi structure, reduced mitochondrial numbers, inactive mitochondrial cristae, and evidence of
mitophagy were detected in INR EMI sections. We report the novel observation that memory CD4 T cells and
plasma samples of INR from several cohorts are enriched for levels of the gut-derived bacterial toxins p-
cresol-sulfate (PCS) and indoxyl sulfate (IS) that both negatively correlate with CD4 T cell counts. Incubation of
peripheral blood mononuclear cells (PBMCs) from HC with PCS or IS blocks CD4 T cell proliferation in vitro,
induces apoptosis, and diminishes the expression of the mitochondrial proteins (COX-IV and mTFA). EMI
reveals perturbations of mitochondria network similar to those found in INR following incubation of sorted
memory CD4 T cells from HC with PCS or IS suggesting that PCS and IS may contribute to the diminished
mitochondrial fitness of INR CD4 T cells. Using bacterial 16S rDNA assay INR stool were found enriched
with proteolytic bacterial genera (Bifidobacterium, Ruminococcus, Lactobacillus) that metabolize tyrosine
and phenylalanine amino acids to produce PCS. We propose that gut bacterial flora toxins may impair CD4
T cell recovery during ART and may contribute to CD4 T cell lymphopenia characteristic of INR. We
propose, mechanistically, that PCS/IS induce toxicity to the mitochondrial network, mitochondrial DNA is then
released in the cytosol and activates STING that triggers caspases of the mitochondrial death pathway, IRF3,
and Interferon-Sensitive- Response Element (ISRE) genes implicated in apoptosis and pyroptosis induction
(AIM1). We will address whether enrichment of plasma PCS/IS in a large cohort of INR is correlated to low
CD4 T cell count, apoptosis/STING levels, and mitochondrial dysfunction in a set of ex-vivo experiments
(AIM2). We will then explore, by performing metagenomics, metaproteomics, and metabolic analyses,
whether commensal bacteria in the gut of INR subjects are in dysbiosis and enriched in bacterial strains
overproducing PCS and IS (AIM3).

## Key facts

- **NIH application ID:** 10698152
- **Project number:** 5R01AG076373-02
- **Recipient organization:** EMORY UNIVERSITY
- **Principal Investigator:** Souheil Antoine Younes
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $767,675
- **Award type:** 5
- **Project period:** 2022-09-15 → 2027-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10698152

## Citation

> US National Institutes of Health, RePORTER application 10698152, Commensal microbiome impact on CD4 T cell lymphopenia in HIV-1 infection (5R01AG076373-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10698152. Licensed CC0.

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