In the brain, death doesn’t occur all at once, certainly not at the transcriptional level. And it doesn’t happen uniformly. Although the transcription of most genes gradually winds down, the transcription of some genes fades especially quickly, and that of some other genes actually surges, at least for a while.

These differences should be considered whenever gene expression information is derived from postmortem brain tissue. Otherwise, gene expression information might be poorly calibrated, leading to erroneous findings in studies that use postmortem brain tissues to find treatments and potential cures for disorders such as autism, schizophrenia, and Alzheimer’s disease.

The varying rates at which genes in the postmortem brain give up the ghost were recently determined by scientists at the University of Illinois, Chicago (UIC). The scientists, led by Jeffrey A. Loeb, MD, PhD, began by comparing the transcription patterns and histological features of postmortem brain to fresh human neocortex. (The fresh tissue was isolated immediately following surgical removal.) Then the scientists noticed that the transcription patterns were different.

“Compared to a number of neuropsychiatric disease-associated postmortem transcriptomes, the fresh human brain transcriptome had an entirely unique transcriptional pattern,” the scientists observed. “To understand this difference, we measured genome-wide transcription as a function of time after fresh tissue removal to mimic the postmortem interval.”

The results of this work appeared March 23 in Science Reports, in an article titled, “Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain.”

“Within a few hours, a selective reduction in the number of neuronal activity-dependent transcripts occurred with relative preservation of housekeeping genes commonly used as a reference for RNA normalization,” the article’s authors wrote. “Gene clustering indicated a rapid reduction in neuronal gene expression with a reciprocal time-dependent increase in astroglial and microglial gene expression that continued to increase for at least 24 h after tissue resection.”

In other words, the scientists distinguished between three groups of genes. In one group, which included 80% of the genes analyzed, gene expression remained relatively stable for 24 hours. These included genes often referred to as housekeeping genes that provide basic cellular functions and are commonly used in research studies to show the quality of the tissue. Another group of genes, known to be present in neurons and shown to be intricately involved in human brain activity such as memory, thinking, and seizure activity, rapidly degraded in the hours after death. These genes are important to researchers studying disorders like schizophrenia and Alzheimer’s disease.

A third group of genes increased their activity at the same time the neuronal genes were ramping down. In glial cells, these genes presumably contributed to notable postmortem changes, which included an increase in process outgrowth, which peaked at about 12 hours.

The genes in this last group might be called zombie genes even though their presence shouldn’t occasion shock. “That glial cells enlarge after death isn’t too surprising given that they are inflammatory,” said Loeb, the John S. Garvin professor and head of neurology and rehabilitation at the UIC College of Medicine. “Their job is to clean things up after brain injuries like oxygen deprivation or stroke.”

This image shows glial cells in which so-called zombie genes came to be expressed at higher levels after the death of the human brain. Notice the outgrowth of the glial cells’ processes. [Jeffrey Loeb/UIC]
What should matter most, Loeb continued, are the implications of this discovery—most studies that use postmortem human brain tissues to shed light on neuropsychiatric disorders do not account for the postmortem gene expression or cell activity.

“Most studies assume that everything in the brain stops when the heart stops beating, but this is not so,” Loeb emphasized. “Our findings will be needed to interpret research on human brain tissues. We just haven’t quantified these changes until now.”

Loeb and his team noticed that the global pattern of gene expression in fresh human brain tissue didn’t match any of the published reports of postmortem brain gene expression from people without neurological disorders or from people with a wide variety of neurological disorders, ranging from autism to Alzheimer’s.

“We decided to run a simulated death experiment by looking at the expression of all human genes, at time points from 0 to 24 hours, from a large block of recently collected brain tissues, which were allowed to sit at room temperature to replicate the postmortem interval,” Loeb said.

Loeb and colleagues are at a particular advantage when it comes to studying brain tissue. Loeb is director of the UI NeuroRepository, a bank of human brain tissues from patients with neurological disorders who have consented to having tissue collected and stored for research either after they die, or during standard of care surgery to treat disorders such as epilepsy. For example, during certain surgeries to treat epilepsy, epileptic brain tissue is removed to help eliminate seizures. Not all of the tissue is needed for pathological diagnosis, so some can be used for research. This is the tissue that Loeb and colleagues analyzed in their research.

“Our findings don’t mean that we should throw away human tissue research programs,” Loeb remarked. “It just means that researchers need to take into account these genetic and cellular changes, and to reduce the postmortem interval as much as possible to reduce the magnitude of these changes.

“The good news from our findings is that we now know which genes and cell types are stable, which degrade, and which increase over time, so that results from postmortem brain studies can be better understood.”