The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Abstract

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.

Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation

“…To address the logistical difficulties and rapid transcriptional changes / stress responses observed upon tissue dissociation (20) or storage (21) , a range of cell freezing or fixation methods have been developed. Guillaumet-Adkins et al (2017,22) demonstrate that although viability is reduced, the transcriptional profiles from cultured cells or minced mouse tissue biopsies cryopreserved with DMSO are not significantly altered.…”

“…To provide maximum utility for human research, scRNAseq from multiple human organs with different ischaemic sensitivities is required. Ferreira et al (21) saw organ-related variation in the number of genes that changed expression with post-mortem interval (warm ischaemia) in GTEx bulk RNA seq (31) . For example, spleen showed relatively little change, whereas oesophagus mucosa and lung altered their transcriptional profiles more significantly; oesophagus showing a response that peaked and declined, whereas lung had a more sustained gene expression change.…”

“…In this study, we aimed to identify a method of tissue preservation that would stabilize intact human tissue samples for scRNAseq but that requires minimal processing at the clinic and allows sample transportation time. In order to contribute to the Human Cell Atlas, we tested the method on three human primary tissues expected to have different sensitivities to ischaemia (21) : spleen (most stable), oesophagus mucosa, and lung (least stable) (21) . These tissues contain cell types ranging from immune cells to keratinocytes.…”

Highly degraded RNA can still provide molecular information: An in vitro approach

“…Out of the several fields of application , the tissue‐specific gene expression of RNA makes this molecule the ideal tool for determining the cellular origin of unknown samples . In addition, most recently, tissue‐specific transcriptional changes were described as a response to the death of the human organism, thus opening the frontiers to a molecular evaluation of the postmortem interval .…”

Blood and Brain Gene Expression Trajectories Underlying Neuropathology and Cognitive Impairment in Neurodegeneration

“…In addition, due to its highly invasive nature, brain GE studies in neurodegeneration are based on post-mortem tissue samples. There are major challenges associated with the translation/extrapolation of ex-vivo results to in-vivo conditions (Ferreira et al, 2018). This could imply that disease mechanisms (e.g.…”