Scientists at Spain’s Center for Genomic Regulation weren’t so interested in forensics—not at first. Instead, they were focused on subtracting postmortem artefacts from tissue-specific analyses of gene expression, so that results from postmortem tissues could be correlated with results from live tissues. These results tend to differ because even after death our genes continue to be expressed, with some genes producing transcripts more falteringly than others, until at last every gene falls silent.
While investigating the gene expression changes triggered by death, and how these changes unfold over time, the scientists chanced upon tissue-specific patterns. These patterns, which the scientists attribute to active and ongoing regulation of the transcriptome after death, point to the time of death, provided they are interpreted correctly.
“We found that many genes change expression over relatively short postmortem intervals, in a largely tissue specific manner,” noted Pedro G. Ferreira, Ph.D., a researcher formerly affiliated with the Center for Genomic Regulation, and currently at Portugal’s University of Porto. “This information helps us to better understand variation and also it allows us to identify the transcriptional events triggered by death in an organism.”
Ferreira is the co-corresponding author of a paper (“The Effects of Death and Post-Mortem Cold Ischemia on Human Tissue Transcriptomes”) that appeared February 13 in the journal Nature Communications. This paper describes how analysis of a few readily available tissues, such as lung or skin, can be used to determine the postmortem interval (PMI) with considerable accuracy. Such an analysis has clear implications for forensic analysis.
“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,” the article’s authors wrote. “By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism.”
To understand the tissue-specific changes to gene expression following the death of a person, the scientists studied RNA sequencing data of over 7000 samples from 36 different tissues obtained from 540 donors within the Genotype – Tissue Expression (GTEx) Project, a kind of reference database and tissue bank. Then the scientists developed models for the prediction of the PMI based on these tissue-specific gene expression changes detected using high-throughput sequencing.
“GTEx data allow us to ask questions about genetic variation and its effects on gene expression both in one tissue and across many tissues,” explained Roderic Guigó, Ph.D., the other corresponding author of the current study and the coordinator of the Bioinformatics and Genomics Program at the Center for Genomic Regulation. “Since the samples we are using all come from deceased donors, we need to find out if there were changes in gene expression related to the death or the time of death, so we could better model our predictions of variation between tissues or in disease.”
As Guigó suggests, the study’s results could enhance the value of postmortem human tissue samples for biological research. They also point to new protocols for forensic pathology, and other applications as well.
“Our analyses show that the investigation of the impact of post-mortem ischemia in tissue transcriptomes is essential to properly interpret gene expression estimates obtained from post-mortem tissue samples,” the authors of the Nature Communications article concluded. “Furthermore, understanding the transcriptional changes occurring with time after death could have multiple applications. Here, we illustrated an application specific to forensic pathology, but other applications could include improving biospecimen procurement and organ preservation protocols. These could, in turn, have an impact on the procedures employed for organ transplantation.”