NARP Laboratory Research Reveals the Impact of SIV Infection on Spinal Cord Gene Expression

Background

Despite the implementation of antiretroviral therapy (ART), HIV-associated peripheral neuropathy (HIV-DSP) remains one of the most common neurological manifestations of HIV infection. Clinical symptoms of HIV-DSP include weakness, numbness, burning sensation, and hypersensitivity. Although ART controls viral replication, up to one-third of HIV patients continue to exhibit symptoms of HIV-DSP. The exact mechanism of this phenomenon is not fully understood, but it is currently believed that HIV-DSP is caused by a combination of direct and indirect effects of the virus and the potential toxicity of certain ART drugs (such as reverse transcriptase inhibitors and protease inhibitors). Additionally, certain conditions such as diabetes and aging may also play a promoting role.

The spinal cord is a core component of pain and sensory pathways, with sensory receptors transmitting nociceptive sensations through sensory neurons in the dorsal root ganglia (DRG) to the spinal cord, while neurons in the dorsal horn of the spinal cord transmit sensory information to the thalamus through multiple pathways, ultimately projecting to the sensory cortex of the brain. However, detailed molecular and morphological data on the spinal cord of HIV-infected patients have been limited since the widespread application of ART.

Research Source

This article was co-authored by scientists including Kathleen R. Mulka, Suzanne E. Queen, Lisa M. Mangus, Sarah E. Beck, Audrey C. Knight, Megan E. McCarron, Clarisse V. Solis, Arlon J. Wizzard, Jyotsna Jayaram, Carlo Colantuoni, and Joseph L. Mankowski from Johns Hopkins University School of Medicine, published in the Journal of Neuroimmune Pharmacology in 2024 (DOI: 10.1007/s11481-024-10130-0).

Research Process

Experimental Model

The study used a rhesus macaque SIV infection model, which allows for the assessment of spinal cord changes at key time points of experimental infection and ART-induced viral suppression. The research team performed RNA sequencing (RNA-Seq) on the spinal cords of uninfected (control), infected only (SIV+), and infected and ART-treated (SIV + ART) macaques, and mapped gene expression changes to specific cell types through the SeqSeek platform.

Sample Processing

Male monkeys aged 2 to 9 years were selected for the experiment, all of which tested negative for SIV and did not express the neuroprotective gene Mane-A1*084:01:01. The study was divided into three groups: control group (uninfected and untreated), SIV+ group (infected with SIV virus and untreated), and SIV + ART group (infected with SIV virus and treated with ART). A standard SIV infection protocol was used in the experiment, involving intravenous injection combining Neurovirulent molecular clone SIV/17E-FR and immunosuppressive SIV/DeltaB670.

Sample Collection and RNA Extraction

Experimental monkeys were euthanized at different time points, and spinal cord samples were rapidly frozen and stored at -80°C. RNA was extracted from 100 mg of frozen lumbar spinal cord samples, and the samples underwent global RNA-Seq sequencing analysis.

Data Analysis

The Bioinformatics Analysis Center was used for read alignment, gene and transcript expression levels were calculated using DESeq2 software, and differential gene expression analysis was performed. Enrichr and SeqSeek platforms were used for gene pathway analysis.

Main Research Findings

Impact of SIV Infection on Gene Expression

RNA-Seq sequencing revealed that in SIV-infected spinal cord samples, upregulated genes were mainly concentrated in pathways related to interferon signaling and viral response, including ISG15, OAS1, IFI27, etc. The upregulation of these genes demonstrates a strong antiviral response after SIV infection. Statistical analysis identified 563 upregulated genes and 437 downregulated genes, with the latter mainly involving cholesterol biosynthesis and extracellular matrix organization.

Comparison of SIV+ART Group with Control Group

In the SIV + ART group, SIV viral RNA was not detected in spinal cord tissue, but DNA was still present. Compared to the control group, 501 genes were upregulated and 279 genes were downregulated in the SIV + ART group. Upregulated genes mainly involved neurotransmitter receptor and postsynaptic signaling pathways, indicating active neural signaling pathways in the spinal cord of the SIV+ART group.

Gene Expression Heterogeneity

In the SIV+ART group, there was heterogeneity in gene expression, with some monkeys showing upregulation of genes related to neuronal synaptic signaling, while others showed upregulation of inflammatory markers. This suggests that although ART suppressed the virus, gene expression responses still varied between individuals.

Conclusion

This study demonstrates the different effects of SIV infection and ART on gene expression in the rhesus macaque spinal cord: the SIV-infected group without ART treatment showed strong antiviral and inflammatory responses, while the SIV-infected group receiving ART treatment showed significant activation of neurotransmitter and postsynaptic signaling pathways. These findings lay the foundation for further research on the effects of SIV and HIV infection and ART treatment on the spinal cord, and may provide new directions for future therapeutic interventions targeting HIV-associated neuropathies.