Dataset Information

Bone Diagenesis in Short Timescales: Insights from an Explor-atory Proteomic Analysis

ABSTRACT: The evaluation of bone diagenetic phenomena in archaeological timescales has a long history, however little is known about the origins of the microbes driving bone diagenesis and on the ex-tent of bone diagenesis on short timeframes such as in forensic contexts. Previously, the analysis of non-collagenous proteins (NCPs) through bottom-up proteomics revealed the presence of potential biomarkers useful to estimate the postmortem interval (PMI). However, there is still a great need for enhancing the understanding of the diagenetic processes taking place in forensic timeframes, and to clarify if proteomic analyses can help to develop better models for estimating PMI reliably. To address these knowledge gaps, we designed an experiment based on whole rat carcasses, defleshed rat long bones and excised but still fleshed rat limbs that were either buried in soil or exposed on a clean plastic surface, left to decompose for 28 weeks and retrieved at different time intervals. This aimed to assess differences in bone protein relative abundances for the various deposition modalities and intervals. We further evaluated the effects that extrinsic factors, autol-ysis, and gut and soil bacteria had on bone diagenesis via bottom-up proteomics. Results showed six proteins whose abundance was significantly different between samples subjected to either mi-crobial decomposition (gut or soil bacteria) or to environmental factors. In particular, muscle and calcium-binding proteins were found to be more prone to degradation by bacterial attack where-as plasma and bone marrow proteins by the exposure to extrinsic agents. Results suggest that both gut and soil bacteria play a key role in bone diagenesis and protein decay on relatively short timescales and that bone proteomics is a proficient resource to identify microbially-driven versus extrinsically-driven diagenesis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Rattus Rattus (black Rat)

TISSUE(S): Bone

SUBMITTER: Noemi Procopio

LAB HEAD: Noemi Procopio

PROVIDER: PXD026042 | Pride | 2022-02-17

REPOSITORIES: Pride

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Bone Diagenesis in Short Timescales: Insights from an Exploratory Proteomic Analysis.

Procopio Noemi N Mein Caley A CA Starace Sefora S Bonicelli Andrea A Bonicelli Andrea A Williams Anna A

Biology 20210523 6

The evaluation of bone diagenetic phenomena in archaeological timescales has a long history; however, little is known about the origins of the microbes driving bone diagenesis, nor about the extent of bone diagenesis in short timeframes-such as in forensic contexts. Previously, the analysis of non-collagenous proteins (NCPs) through bottom-up proteomics revealed the presence of potential biomarkers useful in estimating the post-mortem interval (PMI). However, there is still a great need for enha ...[more]

PMID: 34071025

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Project description:The combined use of multiple omics methods to answer complex system biology questions is growing in biological and medical sciences, as the importance of studying interrelated biological processes in their entirety is increasingly recognized. We applied a combination of metabolomics, lipidomics and proteomics to human bone to investigate the potential of this multi-omics approach to estimate the time elapsed since death (i.e., the post-mortem interval, PMI). This “ForensOMICS” approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors in a fresh stage of decomposition before placement of the bodies to decompose outdoors at the human taphonomy facility managed by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219, 790, 834 and 872 days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic and proteomic profiles from the pre- and post-placement bone samples. Multivariate analysis was used to investigate the three omics blocks by means of Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers that could effectively describe post-mortem changes and classify the individuals based on their PMI. The resulting model showed that pre-placement bone metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement profiles. Metabolites associated with the pre-placement samples, suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules from the three groups that show excellent potential for estimation of the PMI, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different post-mortem stability, in future studies we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by including more stable proteins.

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	NEW_MASCOT_RUN_2021.mgf	Mgf
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