Monitoring Post-Mortem Gene Transcription in Mice and Zebrafish

Genes linked to embryonic development, stress, and cancer are increasingly transcribed into RNA after these animals die.

By | January 26, 2017

NICHDNinety-six hours after 43 zebrafish were frozen to death and 48 hours after 20 mice had their necks snapped, specific cells within their bodies were still hard at work. Gene transcription continued apace, and occasionally increased, according to a study published today (January 25) in Royal Society Open Biology. Genes linked to embryonic development, stress, and cancer were among those increasingly transcribed into RNA, researchers at the University of Washington and their colleagues reported. The results suggest that organismal death is an orderly, predictable process, and could help forensic scientists pinpoint time of death, plus help explain why organs from recently deceased donors seem to be more prone to cancer. 

“Death is a time-dependent process,” said coauthor Peter Noble, whose group studies the postmortem transcriptome and microbiome. “We define the window between the time of organismal death and the time when not all cells are dead as ‘the twilight of death,’” he explained. “We found that there was a successional pattern to this time—more or less waves of transcription abundances. The shutdown is not random, it’s step-wise.”

Forensic scientists have long been interested in how bodies decay, especially as a way of determining time of death in criminal investigations. When Noble first began studying the phenomenon five years ago at Alabama State University, others had already tried to determine time of death by measuring microbial populations on the body surfaces of dead animals. Noble wondered whether he could obtain more robust results by studying how microbes invade internal organs after death, and he published his results in the Journal of Microbiological Methods in 2014. “My general feeling is that looking at different microbes invading the organs cannot be used as an indicator of postmortem interval, or lapsed time since death,” Noble said.

So Noble shifted his focus, studying gene expression in recently deceased animals. An opportunity arose when a colleague at the Max Planck Institute for Evolutionary Biology in Germany shared that the organization planned to close a zebrafish lab to make more room for mouse studies. “They had all these fish they didn’t know what to do with,” Noble said. “We said, ‘Let’s kill the fish and see what gene expression occurs.’”

Noble and colleagues ultimately analyzed rates of gene transcription in 43 zebrafish (up until 96 hours postmortem) and 20 mice (through 48 hours postmortem). The researchers found that messenger RNA (mRNA) transcript profiles greatly increased for 1,063 genes, suggesting that some genes may upregulate their transcription after organismal death. “Although most genes decreased in expression, a certain percent actually increased,” Noble said. “We were astounded that some gene appear to be upregulated in postmortem time.”

The team then ran a functional characterization of the most abundant transcripts, using so-called gene meter technology, which Nobel developed. The researchers found that the transcripts most active after death were associated with stress, immunity, inflammation, apoptosis, transport, embryonic development, and cancer.  

“I find the methodology to be technically sound and the calculations of abundance profiles likely to be accurate,” Andrew Harrison, an expert in bioinformantics at the University of Essex in the UK who was not involved in the study, wrote in an email to The Scientist. “The article elucidates that there is a broad range of pathways still progressing, and in some cases increasing, beyond death.”

Most surprising to the team was that developmental genes necessary for embryogenesis, which are normally silenced in adulthood, appeared to increase in abundance throughout the “twilight of death” in both fish and mice. “It could be that the genome unwinds as DNA degrades through postmortem time, allowing access to sites that have been previously silenced,” Noble said. “But we don’t know.”

Still surprising was that many of the genes upregulated in death have been linked to various cancers. Pending further study, Noble suggested that this could help explain increased rates of cancer observed in organs transplanted from deceased donors.  “This may provide a different idea as to why cancer rates are much higher in liver transplant patients,” Noble said. “It’s only preliminary data, but it could be because, in death, the donor’s genes that are associated with cancer are still active when transplanted into the recipient.”

Arne Traulsen from the Max Planck Institute for Evolutionary Biology, who was not involved in the study, noted that the findings could shed light on the molecular biology of death. “This could be the start of a much more detailed analysis how processes are being shut down after organismal death,” he wrote in an email to The Scientist. “In spirit, death is probably more like turning a computer off and much less like turning a light bulb off. I would not be surprised if this provides entirely new insights on the function of complex biological systems.” 

Going forward, the study’s results might also help researchers determine time of death—adding a new level of precision to one of the trickiest parts of forensic science. “Once you know what genes to look at, you can just measure the genes and take a genetic ‘selfie’ and put that into an algorithm to calculate how long this person has been dead,” Noble said. “We made it work for zebrafish and mice. Now we have to try it on humans.”

A. Pozhitkov et al., "Tracing the dynamics of gene transcripts after organismal death," Royal Society Open Biology, doi:10.1098/rsob.160267, 2017.

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Comments

Avatar of: Baxter Zappa

Baxter Zappa

Posts: 11

January 26, 2017

These genes may prove to be important in Zombie formation.

Avatar of: Neurona

Neurona

Posts: 70

January 26, 2017

Incredible that so many changes occurred within 0.5 hour of death. When collecting tissue for a transcriptomics project, it sounds to me like a long drawn-out dissection versus a rapid one could quite alter the outcomes. (e.g. an experienced dissecter versus a newbie, or a simple access tissue versus a complex one).

I bet we don't record/report how long it took from euthanasia to freezing. 

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