Antiretroviral therapy restores the homeostatic state of microglia in SIV-infected rhesus macaques

Abstract

Microglia and macrophages are essential for homeostatic maintenance and innate immune response in the brain. They are the first line of defense against infections such as HIV/SIV in the brain. However, they are susceptible to infection and function as viral reservoirs even under effective viral suppression. While current antiretroviral regimens successfully suppress viremia and improve quality of life and lifespan, neurologic complications persist and are in part attributed to activated microglia. We sought to test the hypothesis that brain microglia return to a more homeostatic‐like state when viremia is suppressed by combination antiretroviral therapy. Using the SIV‐rhesus macaque model, we combined single‐cell RNA sequencing, bioinformatics, and pathway analysis to compare gene expression profiles of brain myeloid cells under 4 conditions: uninfected, SIV infected, SIV infected with cART suppression, and SIV encephalitis (SIVE). Our study reveals greater myeloid diversity and an elevated proinflammatory state are associated with untreated SIV infection compared with uninfected animals. The development of encephalitis and suppression of viremia both reduced myeloid diversity. However, they had converse effects on the activation state of microglia and inflammation. Notably, suggestive of a restoration of a homeostatic state in microglia, gene expression and activation of pathways related to inflammation and immune response in cART‐suppressed monkeys were most similar to that in uninfected monkeys. Untreated SIV infection shared characteristics, especially in brain macrophages to SIVE, with SIVE showing dramatic inflammation. In support of our hypothesis, our study demonstrates that cART indeed restores this key component of the brain's homeostatic state. Summary: ScRNA‐seq of rhesus monkey microglia reveals clusters of cells in activated states in the setting of SIV infection, which is primarily reversed by suppressing viremia with combination antiretroviral therapy.

Morphine suppresses peripheral responses and transforms brain myeloid gene expression to favor neuropathogenesis in SIV infection

“…For scRNA-seq of microglia, the saline group consisted of samples from animals 74T (referred to as CI47 in ( 57 )), 77T (CK40), 82T (CI04), and 83T (CK03), and the morphine group samples from animals 73T (CK22), 75T (CK48), 78T (CI90), and 80T (CH89). The scRNA-seq data for the three of the members of the saline group, 74T, 82T, and 83T, were reported previously ( 63 ). For the snRNA-seq several animal samples were substituted within the groups due to the availability or suitability of samples for processing and analysis.…”

“…Using scRNA-seq of microglia from SIV-infected animals, we recently found that in untreated animals, microglia exhibited a proinflammatory state, and that viral suppression with cART restored the microglia to a homeostatic-like state ( 63 ). Here we find that in the setting of viral suppression with cART, morphine had numerous other effects on the microglia as well as brain macrophages.…”

Microglia and macrophages alterations in the CNS during acute SIV infection: a single-cell analysis in rhesus macaques

“…While not as extensively characterized as neurons, they are indeed heterogeneous, and with the advent of scRNA-seq our studies and those of others have identified a number of classes of microglia. (47)(48)(49)(50) To maintain a steady state while gaining some immunogenic properties, microglia express several homeostatic genes. Downregulation and/or mutations of these homeostatic genes can lead to uncontrolled neuroinflammation, neurotoxicity and multiple neurocognitive diseases.…”

Morphine Suppresses Peripheral Responses and Transforms Brain Myeloid Gene Expression to Favor Neuropathogenesis in SIV Infection

“…Using scRNA-seq of microglia from SIV-infected animals, we recently found that in untreated animals, microglia exhibited a proinflammatory state, and that viral suppression with cART restored the microglia to a homeostatic-like state (130). Here we find that in the setting of viral suppression with cART, morphine had numerous other effects on the microglia as well as brain macrophages.…”

“…For scRNA-seq of microglia, the saline group consisted of samples from animals 74T (referred to as CI47 in (57)), 77T (CK40), 82T (CI04), and 83T (CK03), and the morphine group samples from animals 73T (CK22), 75T (CK48), 78T (CI90), and 80T (CH89). The scRNA-seq data for the three of the members of the saline group, 74T, 82T, and 83T, were reported previously (130). For the snRNA-seq several animal samples were substituted within the groups due to the availability or suitability of samples for processing and analysis.…”