Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis.

Liana Basova,Ronald J Ellis,Anne Marie Mcgovern,Alexander Lindsey,Maria Cecilia Garibaldi Marcondes

doi:10.3390/v13040544

Liana Basova, Ronald J Ellis + Show 3 more

Open Access

https://doi.org/10.3390/v13040544

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Abstract

Human postmortem specimens are extremely valuable resources for investigating translational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic signatures would be more stable than RNA for assessing global changes associated with outcomes of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was abundant and stable up to the 72 h postmortem. We tested our ability to use H3K4me3 in human prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not (Meth +/−) which exhibited poor RNA quality and were not suitable for transcriptional profiling. Systems strategies that are typically used in transcriptional metadata were applied to H3K4me3 peaks revealing consistent genomic activity differences in regions where addiction and neuronal synapses pathway genes are represented, including genes of the dopaminergic system, as well as inflammatory pathways. The resulting comparisons mirrored previously observed effects of Meth on suppressing gene expression and provided insights on neurological processes affected by Meth. The results suggested that H3K4me3 detection in chromatin may reflect transcriptional patterns, thus providing opportunities for analysis of larger numbers of specimens from cases with substance use and neurological deficits. In conclusion, the detection of H3K4me3 in isolated chromatin can be an alternative to transcriptome strategies to increase the power of association using specimens with long postmortem intervals and low RNA quality.

Highlights

Postmortem human specimens represent an extremely valuable resource with direct translational implications
We investigated whether changes in epigenetic marks such as enhancer histone modifications may be stable surrogates to indicate consequential information about gene transcription patterns, which would otherwise be lost due to poor RNA quality in postmortem specimens
The stability of H3K27Ac, H3K4me3 and RNA Pol was tested in mouse brains, at different postmortem intervals, from 0 to 96 h time points

Summary

Introduction

Postmortem human specimens represent an extremely valuable resource with direct translational implications. Postmortem time interval prior to tissue harvest is one of the main causes of poor RNA quality and presents a challenge to retrieve transcriptional information from a large number of human specimens, the ones from drug users [1,2,3]. To address this challenge, we investigated whether changes in epigenetic marks such as enhancer histone modifications may be stable surrogates to indicate consequential information about gene transcription patterns, which would otherwise be lost due to poor RNA quality in postmortem specimens. This could enhance the investigation of global changes associated with HIV infection and neurological outcomes, as well as pathways involved in addiction, in a larger number of specimens

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