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GNPS_Amazon urbanization skin and environmental samples

ABSTRACT: MS/MS data were collected from skin of Amazon individuals and from their houses (walls and floors of living room, bedroom, kitchen and bathroom).

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Pieter Dorrestein Maria Gloria Dominguez-Bello

PROVIDER: MSV000081694 | GNPS | Wed Nov 08 12:06:00 GMT 2017

REPOSITORIES: GNPS

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Project description:Human death marks the end of organismal life under conditions such that the components of the human body continue to be alive. Such postmortem cellular survival depends on the nature (Hardy scale) of human death. Slow and expected death typically result from terminal illnesses and includes a prolonged terminal phase of life. As such organismal death process unfolds, do cells of the human body adapt for postmortem cellular survival? Organs with low energy cost-of-living, such as the skin, are better suited for postmortem cellular survival. In this work, the effect of different durations of terminal phase of human life on postmortem changes in cellular gene expression was investigated using RNA sequencing data of 701 human skin samples from the Genotype-Tissue Expression database. Longer terminal phase (slow-death) was associated with a more robust induction of survival pathways (PI3K-Akt signaling) in postmortem skin. Such cellular survival response was associated with the upregulation of embryonic developmental transcription factors such as FOXO1, FOXO3, ATF4 and CEBPD. Upregulation of PI3K-Akt signaling was independent of sex or duration of death-related tissue ischemia. Analysis of single nucleus RNA-seq of post-mortem skin tissue specifically identified the dermal fibroblast compartment to be most resilient as marked by adaptive induction of PI3K-Akt signaling. Prospective studies depicted hypomethylation of PI3K-Akt signaling genes in slow compared to fast human death. Compared to fast death, slow death also induced angiogenic pathways in the dermal endothelial cell compartment of postmortem human skin. In contrast, specific pathways supporting functional properties of the skin as an organ were downregulated following slow death. Such pathways included melanogenesis and those representing the skin extracellular matrix. Efforts to understand the significance of death as a biological variable in influencing the transcriptomic composition of surviving component tissues has far-reaching implications including rigorous interpretation of experimental data collected from the dead and mechanisms involved in transplant-tissue obtained from dead donors.

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GNPS_Amazon urbanization skin and environmental samples

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