Gene activity in the dead

Now you've got another paper you can file with that dead salmon fMRI paper: one that analyzes the transcriptome, or excuse me, the thanatotranscriptome, of dead zebrafish and mice.

You should not be surprised to learn that when a multicellular organism dies, it's not as if every single cell is abruptly extinguished: the integrated, functional activity of the individual as a whole ceases, but individual cells struggle on for a while -- they're not getting oxygen or nutrients, in a mouse they're experiencing thermal stress as the body rapidly cools, but it takes a while for all of the cells to starve or suffocate or undergo necrosis. It seems to take a couple of days, actually. You can measure the declining amounts of RNA present in the dead animals, and yep, it looks like everything is done after a few days. This kind of study has also been done in human corpses, which show that RNA transcription continues for a couple of days.

Total mRNA abundance (arbitrary units, a.u.) by postmortem time determined using all calibrated microarray probes. A, extracted from whole zebrafish; B, extracted from brain and liver tissues of whole mice. Each datum point represents the mRNA from two organisms in the zebrafish and a single organism in the mouse. Total mRNA abundance (arbitrary units, a.u.) by postmortem time determined using all calibrated microarray probes. A, extracted from whole zebrafish; B, extracted from brain and liver tissues of whole mice. Each datum point represents the mRNA from two organisms in the zebrafish and a single organism in the mouse.

This paper went a bit deeper, though, and asked what genes are being transcribed in the dying cells of the dead mouse and fish. Some genes are actually actively upregulated, so it's not as if they all just stop and decay on the instant. And, well, it's a bit unsurprising which ones are switched on: genes involved in stress responses, metabolic activity in reaction to hypoxia, genes involved in inflammation, and immune system genes. Starved cells are stressed, and clearly decaying bodies are being invaded and exploited by bacteria, so the immune system is triggered. Inflammation is a response to injury, and I guess we'd have to say that death is a rather serious injury.

Another activity we take for granted is cell-level transport: your cells are very busy trying to maintain a constant osmotic environment. In death, cells are suddenly leaking, and the extracellular salt concentrations are changing, so yes, again unsurprisingly, dying cells are making a futile struggle to maintain their salt balance, and are desperately switching on all kinds of pumps.

The authors did not expect various developmental genes to be activated by death, but I'm not at all surprised. The inactivation of specific genes is also an active process -- many of these switches are not at all passive, but require ongoing regulatory activity in cells to maintain their state. So at death a whole bizarre, seemingly random collection of developmental genes are increasingly transcribed. What I suspect we're seeing is a gradual release of active deregulation -- that some aspects of the normally active epistatic circuitry are being spuriously switched on as other control elements are falling apart. It's like when the various controls on the bridge of the Enterprise start sparking and catching fire when the Klingons hit them with a phaser burst -- there's probably a pattern to it that reflects the underlying wiring.

The authors argue that there's some utility to this study. It might be a useful assay for forensic research -- which genes are upregulated could tell you something about the time of death, for instance. They also make a case that this is useful information for resuscitation and transplant research.

We initially thought that sudden death of a vertebrate would be analogous to a car driving down a highway and running out of gas. For a short time, engine pistons will move up and down and spark plugs will spark -- but eventually the car will grind to a halt and “die”. Yet, in our study we find hundreds of genes are upregulated many hours postmortem, with some (e.g., Kcnv2, Pafr, Degs2, Ogfod1, Ppp2rla, Ror1, and Iftm1) upregulated days after organismal death. This finding is surprising because in our car analogy, one would not expect window wipers to suddenly turn on and the horn to honk several days after running out of gas.

Since the postmortem upregulation of genes occurred in both the zebrafish and the mouse in our study, it is reasonable to suggest that other multicellular eukaryotes will display a similar phenomenon. What does this phenomenon mean in the context of organismal life? We conjecture that the highly ordered structure of an organism – evolved and refined through natural selection and self-organizing processes – undergoes a thermodynamically driven process of spontaneous disintegration through complex pathways, which apparently involve the upregulation of genes and feedback loops. While evolution played a role in pre-patterning of these pathways, it does not play any role in its disintegration fate. One could argue that some of these pathways have evolved to favor healing or “resuscitation” after severe injury. For example, the upregulation of inflammation response genes indicate that a signal of infection or injury is sensed by the still alive cells after death of the body. Alternatively, the upregulation may be due to fast decay of some repressors of genes or whole pathways (see below). Hence, it will be of interest to study this in more detail, since this could, for example, provide insights into how to better preserve organs retrieved for transplantation.

Eh, I don't find their surprising result at all surprising, but OK, this could be useful information. I don't think this is a very good way to study evolution or development, though -- as they note, the activity of these genes is not a consequence of their selection, but of their functional role in life, and their activities in such a literally pathological state as death are not going to reflect how they were shaped in their formation.

By the way, if you're concerned about the grisly details of how these animals were killed (and you should be!), the mice were executed by snapping their necks, which is very, very quick, and the fish were killed by cooling them (which is the recommended method for humane termination among aquarists) and then dropping them in liquid nitrogen.

Alexander E Pozhitkov, Rafik Neme, Tomislav Domazet-Loso, Brian Leroux, Shivani Soni, Diethard Tautz, Peter Anthony Noble (2016) Thanatotranscriptome: genes actively expressed after organismal death. bioRxiv doi:

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...." and their activities in such a literally pathological state as death are not going to reflect how they were shaped in their formation."

This is from a reductionist perspective. From a systemic perspective, they were shaped just in a non-living environment and they are merely performing its systemic function. The information and function for creating biological systems (aka life) from non-living matter are not in the genes, but in a lateral base-pair of nucleotides. And it cames from the first aminoacids at life's origins, when life was developed inside a "dead" planet.

The universal formula Matrix/DNA for all natural systems makes that the mass coming from an environment without biological organization ( a non living body) receipts an input of systemic energy produced by the object performing Function 4 ( at cells systemic level, this is mitochondria and the input is ATP), so, information in that mass and energy begins a process (Function 1) that creates biological systems. It happened at life's origins, at an individual human body origins, till the Universe origins.

The forces acting at this "resuscitation" came from thermodynamics and for understanding this entire phenomena we need knowing Physics and not be reductionist to the point that mistakenly separates cosmological from biological evolution. See the formula, the F7, representing the cadaver, follow its fragments, see how F5 (ATP) arrives and what are the hidden signals for these genes waking up at the wrong time. You can say what you want but you can not denying the fact that I predicted this process 30 years ago, as proved by my copyrights.

By Louis Morelli (not verified) on 13 Jul 2016 #permalink