Gene expression patterns in the human prefrontal cortex vary depending on whether the tissue donor was alive or deceased, according to a new preprint.
The magnitude of the change for each gene is small, but the effects are widespread, affecting about 80% of the genes.
The findings suggest that postmortem brains are a poor substitute for living brains in studies of neurological conditions, including autism, the researchers say, though several scientists disagree.
The implications are real, says study researcher Alexander Charney, a neurosurgeon and associate professor of psychiatry, genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai in New York City. People will have to decide how these discoveries will affect their work.
Charney says he and his colleagues were about to launch a clinical trial of an Alzheimer’s disease drug, the target of which was identified in a postmortem brain scan. As a result of these findings, we put a stop to that, he says.
But other researchers say there is nothing surprising about the variation in gene expression between live and postmortem brains, and the divergence bears no relation to the usefulness of postmortem brain studies: what matters is the difference between brains with and without disease.
I think the conclusions they’ve drawn from the differences they see are very premature, and I think their claim that the postmortem brain doesn’t reflect disease at the molecular level is unfounded, says Daniel Weinberger, professor of psychiatry, neurology, neuroscience, and genetic medicine. from Johns Hopkins University School of Medicine and director of the Lieber Institute for Brain Development in Baltimore, Maryland.
The paper contains interesting data, but it doesn’t ask interesting questions and consider carefully what the data shows, says Bernie Devlin, a professor of psychiatry at the University of Pittsburgh School of Medicine in Pennsylvania who was not involved in the work. The conclusions from the data are simply off the mark.
cHarney and his colleagues began their research 10 years ago to test the hypothesis that studies of postmortem brain tissue could reveal the mechanisms of neurological disease, given the fact that RNAs degrade rapidly after death. That’s why brain banks document the postmortem interval—the time between death and the preservation of brain tissue—and strive to get the shortest interval possible.
The team sequenced RNA in pieces of prefrontal cortex tissue from 246 deceased donors and 289 living donors, matching the two groups as closely as possible based on age, gender and neurological diagnosis. Frozen postmortem tissue was sourced from three brain banks in the United States, and postmortem intervals ranged from 20 minutes to 38 hours.
Living donor tissue was harvested during surgery to insert electrodes for deep brain stimulation, a procedure of choice for conditions such as Parkinson’s disease and obsessive-compulsive disorder. The procedure typically involves cauterizing a small amount of tissue to make room for the implant. The researchers modified the procedure to instead biopsy and freeze the tissue immediately, without any risk to the patient.
The two groups show statistically significant differences in gene expression in 17,186 genes, the team found. The magnitude of the differences is on par with that seen in studies comparing gene expression in postmortem tissue of people with and without neurological conditions, Charney says.
The effect isn’t huge, but nearly all genes are affected, he says. The overall co-expression of genes is somewhat rewired.
Most of the tissue in the study came from people with Parkinson’s disease. But the differentially expressed genes from the study overlap with those previously found altered in the postmortem tissue of people with autism, Alzheimer’s disease or other neurological conditions. The team published their findings on the medRxiv preprint server in April.
In the postmortem state, when you compare cases and controls, you see some interaction between the disease process and the death process, Charney says. Our brains are much more similar to each other than they are to any dead brain. The difference between living brain and dead brain dwarfs any difference in disease.
IIn addition to the largely critical reactions to the preprint conclusions, some experts have also disputed the actual data. Weinberger says the researchers did not adequately control RNA degradation in either tissue type, and RNA integrity in living donor tissues was on average lower than in postmortem tissue, a finding he calls surprising. . The living tissue samples also had a smaller percentage of neurons than the postmortem samples.
They’re treating the living samples in this study as if they were the gold standard, but there’s a lot of fuzziness about this gold, Weinberger says.
All model systems have pros and cons: Brain organoids are locked in a fetal state; mice are not people; and postmortem brains are not living brains. Even living tissue has the limitation of reflecting the consequence of the disease rather than the cause, says Stephan Sanders, a professor of neurogenetics at the University of Oxford in the UK who was not involved in the study. This document, I think, falsely creates too much of a problem and offers no solutions.
The paper proposes a solution, however: using living brain biopsies instead of postmortem tissue. But the reactions to this idea have been particularly acute.
The notion that you’ll replace postmortem studies because you can biopsy 1 centimeter of prefrontal cortex in the living brain, I think, is a bit of a stretch, Weinberger says.
Just because you can do it in Parkinson’s disease doesn’t mean it can in autism, schizophrenia, and Alzheimer’s. No one will agree to this, Sanders says. So why say we shouldn’t do postmortem studies anymore? A much more useful statement is: We need to embrace all models, and living brain tissue could help us with our interpretation.
Sanders says researchers should use the new data to control changes in gene expression associated with the dying process. This is possible in theory, Charney says, but more work is needed. Many more groups need to ask the same question of what postmortem tissue can and cannot be used for.
Charney says he and his team performed single-cell RNA sequencing from living and deceased brain donors and found the same pattern of differential gene expression between neurons and non-neuronal cells, such as astrocytes, microglia and oligodendrocytes. The pattern persists even in a comparison of protein expression between the two tissue types, Charney says.
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