MALDI-TOF MS as a Novel Tool for the Estimation of Postmortem Interval in Liver Tissue Samples

Morphometric Indicators of Liver Acini of Deceased Newborns Depending on the Time of Death

We studied morphometric changes in the liver acini of dead newborns depending on the duration of the postmortem period. Autopsy samples of the liver tissue from 49 dead newborns were divided into 7 groups depending on the time of death. Liver tissue samples were taken from the upper and lower areas of the liver in the supine position of newborns; paraffin sections were prepared and stained with hematoxylin and eosin. The morphometric analysis of histological preparations revealed a progressive decrease in the mean size of the liver plates (trabeculae) and, conversely, an increase in the area of sinusoids with increasing the duration of the postmortem period; these changes were due to the postmortem redistribution of the blood and autolysis processes. More significant changes were noted in acinar zone 3 of the lower part of the liver. The revealed intra-acinar features of postmortem changes should be taken into account for their differential diagnosis with pathological processes that developed during life, in particular, the signs of congestion and peliosis of the liver.

Molecular characterization of human peripheral nerves using desorption electrospray ionization mass spectrometry imaging

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) is a molecular imaging method that can be used to elucidate the small-molecule composition of tissues and map their spatial information using two-dimensional ion images. This technique has been used to investigate the molecular profiles of variety of tissues, including within the central nervous system, specifically the brain and spinal cord. To our knowledge, this technique has yet to be applied to tissues of the peripheral nervous system (PNS). Data generated from such analyses are expected to advance the characterization of these structures. The study aimed to: (i) establish whether DESI-MSI can discriminate the molecular characteristics of peripheral nerves and distinguish them from surrounding tissues and (ii) assess whether different peripheral nerve subtypes are characterized by unique molecular profiles. Four different nerves for which are known to carry various nerve fiber types were harvested from a fresh cadaveric donor: mixed, motor and sensory (sciatic and femoral); cutaneous, sensory (sural); and autonomic (vagus). Tissue samples were harvested to include the nerve bundles in addition to surrounding connective tissue. Samples were flash-frozen, embedded in optimal cutting temperature compound in cross-section, and sectioned at 14 μm. Following DESI-MSI analysis, identical tissue sections were stained with hematoxylin and eosin. In this proof-of-concept study, a combination of multivariate and univariate statistical methods was used to evaluate molecular differences between the nerve and adjacent tissue and between nerve subtypes. The acquired mass spectral profiles of the peripheral nerve samples presented trends in ion abundances that seemed to be characteristic of nerve tissue and spatially corresponded to the associated histology of the tissue sections. Principal component analysis (PCA) supported the separation of the samples into distinct nerve and adjacent tissue classes. This classification was further supported by the K-means clustering analysis, which showed separation of the nerve and background ions. Differences in ion expression were confirmed using ANOVA which identified statistically significant differences in ion expression between the nerve subtypes. The PCA plot suggested some separation of the nerve subtypes into four classes which corresponded with the nerve types. This was supported by the K-means clustering. Some overlap in classes was noted in these two clustering analyses. This study provides emerging evidence that DESI-MSI is an effective tool for metabolomic profiling of peripheral nerves. Our results suggest that peripheral nerves have molecular profiles that are distinct from the surrounding connective tissues and that DESI-MSI may be able to discriminate between nerve subtypes. DESI-MSI of peripheral nerves may be a valuable technique that could be used to improve our understanding of peripheral nerve anatomy and physiology. The ability to utilize ambient mass spectrometry techniques in real time could also provide an unprecedented advantage for surgical decision making, including in nerve-sparing procedures in the future.

Proteomic analysis by mass spectrometry of postmortem muscle protein degradation for PMI estimation: A pilot study

The determination of the postmortem interval is a topic of great forensic interest. The possibility of using new technologies has allowed the study of postmortem decay of biomolecules in the determination of PMI. Skeletal muscle proteins are promising candidates because skeletal muscle exhibits slower postmortem decay compared to other internal organs and nervous tissues, while its degradation is faster than cartilage and bone. In this pilot study, skeletal muscle tissue from pigs was degraded at two different controlled temperatures, 21 °C and 6 °C, and analysed at predefined times points: 0, 24, 48, 72, 96, and 120 h. The obtained samples were analysed by mass spectrometry proteomics approach for qualitative and quantitative evaluation of proteins and peptides. Immunoblotting validation was performed for the candidate proteins. The results obtained appeared significant and identified several proteins useful for possible postmortem interval estimation. Of these proteins, PDLIM7, TPM1, and ATP2A2 were validated by immunoblotting at a larger number of experimental points and at different temperatures. The results obtained are in agreement with those observed in similar works. In addition, the use of a mass spectrometry approach increased the number of protein species identified, providing a larger panel of proteins for PMI assessment.

Proteome alterations in human autopsy tissues in relation to time after death

Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.

Combining with lab-on-chip technology and multi-organ fusion strategy to estimate post-mortem interval of rat

Background

The estimation of post-mortem interval (PMI) is one of the most important problems in forensic pathology all the time. Although many classical methods can be used to estimate time since death, accurate and rapid estimation of PMI is still a difficult task in forensic practice, so the estimation of PMI requires a faster, more accurate, and more convenient method.

Materials and methods

In this study, an experimental method, lab-on-chip, is used to analyze the characterizations of polypeptide fragments of the lung, liver, kidney, and skeletal muscle of rats at defined time points after death (0, 1, 2, 3, 5, 7, 9, 12, 15, 18, 21, 24, 27, and 30 days). Then, machine learning algorithms (base model: LR, SVM, RF, GBDT, and MLPC; ensemble model: stacking, soft voting, and soft-weighted voting) are applied to predict PMI with single organ. Multi-organ fusion strategy is designed to predict PMI based on multiple organs. Then, the ensemble pruning algorithm determines the best combination of multi-organ.

Results

The kidney is the best single organ for predicting the time of death, and its internal and external accuracy is 0.808 and 0.714, respectively. Multi-organ fusion strategy dramatically improves the performance of PMI estimation, and its internal and external accuracy is 0.962 and 0.893, respectively. Finally, the best organ combination determined by the ensemble pruning algorithm is all organs, such as lung, liver, kidney, and skeletal muscle.

Conclusion

Lab-on-chip is feasible to detect polypeptide fragments and multi-organ fusion is more accurate than single organ for PMI estimation.

[Characteristics of histochemical, molecular genetic and radiation-induced liver changes depending on the postmortem interval]

The aim of this study is to analyze literature data on postmortem changes in the liver and their use in determination of postmortem interval. Biological death expectedly causes the development of postmortem disorders not only in the liver structure, but also changes in its biochemical and histochemical parameters. Literature data about changes of histochemical, immunohistochemical and biomolecular characteristics of liver tissue, as well as bacterial migration to the liver depending on the duration of postmortem period, are presented. The effectiveness of radiology for visualization of postmortem changes and, accordingly, for determining the postmortem interval is noted.

The 'ForensOMICS' approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics

The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem 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 before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in 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 with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins.

Surface Analysis Techniques in Forensic Science: Successes, Challenges, and Opportunities for Operational Deployment

Surface analysis techniques have rapidly evolved in the last decade. Some of these are already routinely used in forensics, such as for the detection of gunshot residue or for glass analysis. Some surface analysis approaches are attractive for their portability to the crime scene. Others can be very helpful in forensic laboratories owing to their high spatial resolution, analyte coverage, speed, and specificity. Despite this, many proposed applications of the techniques have not yet led to operational deployment. Here, we explore the application of these techniques to the most important traces commonly found in forensic casework. We highlight where there is potential to add value and outline the progress that is needed to achieve operational deployment. We consider within the scope of this review surface mass spectrometry, surface spectroscopy, and surface X-ray spectrometry. We show how these tools show great promise for the analysis of fingerprints, hair, drugs, explosives, and microtraces.

Detection of Frozen-Thawed Duck Fatty Liver by MALDI-TOF Mass Spectrometry: A Chemometrics Study

The marketing of poultry livers is only authorized as fresh, frozen, or deep-frozen. The higher consumer demand for these products for a short period of time may lead to the marketing of frozen–thawed poultry livers: this constitutes fraud. The aim of this study was to design a method for distinguishing frozen–thawed livers from fresh livers. For this, the spectral fingerprint of liver proteins was acquired using Matrix-Assisted Laser Dissociation Ionization-Time-Of-Flight mass spectrometry. The spectra were analyzed using the chemometrics approach. First, principal component analysis studied the expected variability of commercial conditions before and after freezing–thawing. Then, the discriminant power of spectral fingerprint of liver proteins was assessed using supervised model generation. The combined approach of mass spectrometry and chemometrics successfully described the evolution of protein profile during storage time, before and after freezing-thawing, and successfully discriminated the fresh and frozen–thawed livers. These results are promising in terms of fraud detection, providing an opportunity for implementation of a reference method for agencies to fight fraud.

Postmortem Protein Degradation as a Tool to Estimate the PMI: A Systematic Review

Objectives: We provide a systematic review of the literature to evaluate the current research status of protein degradation-based postmortem interval (PMI) estimation. Special attention is paid to the applicability of the proposed approaches/methods in forensic routine practice. Method: A systematic review of the literature on protein degradation in tissues and organs of animals and humans was conducted. Therefore, we searched the scientific databases Pubmed and Ovid for publications until December 2019. Additional searches were performed in Google Scholar and the reference lists of eligible articles. Results: A total of 36 studies were included. This enabled us to consider the degradation pattern of over 130 proteins from 11 different tissues, studied with different methods including well-established and modern approaches. Although comparison between studies is complicated by the heterogeneity of study designs, tissue types, methods, proteins and outcome measurement, there is clear evidence for a high explanatory power of protein degradation analysis in forensic PMI analysis. Conclusions: Although only few approaches have yet exceeded a basic research level, the current research status provides strong evidence in favor of the applicability of a protein degradation-based PMI estimation method in routine forensic practice. Further targeted research effort towards specific aims (also addressing influencing factors and exclusion criteria), especially in human tissue will be required to obtain a robust, reliable laboratory protocol, and collect sufficient data to develop accurate multifactorial mathematical decomposition models.

[Problems of establishing the prescription of death]

Based on the analysis of literature data, demonstrated the relevance of further research to establish the prescription of death, including in a hot arid zone. Taking into account the climate of the seasons of Uzbekistan was stressed the importance of a comprehensive assessment of the dynamics of the development of cadaveric changes and supravital reactions, together with the results of biochemical, morphological and morphometric studies of the brain, other organs and tissues at different times of the postmortem period in certain groups. It could be used to develop additional criteria for establishing the onset of death in a hot arid zone.

Mass Spectrometric (MS) Analysis of Proteins and Peptides

The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.

Proteome Imaging: From Classic to Modern Mass Spectrometry-Based Molecular Histology

In order to overcome the limitations of classic imaging in Histology during the actually era of multiomics, the multi-color "molecular microscope" by its emerging "molecular pictures" offers quantitative and spatial information about thousands of molecular profiles without labeling of potential targets. Healthy and diseased human tissues, as well as those of diverse invertebrate and vertebrate animal models, including genetically engineered species and cultured cells, can be easily analyzed by histology-directed MALDI imaging mass spectrometry. The aims of this review are to discuss a range of proteomic information emerging from MALDI mass spectrometry imaging comparative to classic histology, histochemistry and immunohistochemistry, with applications in biology and medicine, concerning the detection and distribution of structural proteins and biological active molecules, such as antimicrobial peptides and proteins, allergens, neurotransmitters and hormones, enzymes, growth factors, toxins and others. The molecular imaging is very well suited for discovery and validation of candidate protein biomarkers in neuroproteomics, oncoproteomics, aging and age-related diseases, parasitoproteomics, forensic, and ecotoxicology. Additionally, in situ proteome imaging may help to elucidate the physiological and pathological mechanisms involved in developmental biology, reproductive research, amyloidogenesis, tumorigenesis, wound healing, neural network regeneration, matrix mineralization, apoptosis and oxidative stress, pain tolerance, cell cycle and transformation under oncogenic stress, tumor heterogeneity, behavior and aggressiveness, drugs bioaccumulation and biotransformation, organism's reaction against environmental penetrating xenobiotics, immune signaling, assessment of integrity and functionality of tissue barriers, behavioral biology, and molecular origins of diseases. MALDI MSI is certainly a valuable tool for personalized medicine and "Eco-Evo-Devo" integrative biology in the current context of global environmental challenges.

Association between protein profile and postmortem interval in human bone remains

Proteomic techniques in bones forensic samples are increasingly, being applied. The main aim of forensic sciences is the estimation of postmortem interval. Most current techniques are useful for the first post-mortem stages. However, in the case of osseous remains, these techniques may be difficult to use due to the high level of decomposition of the sample. Our objective was to attempt to know whether there is a protein profile in human bone remains that would enable a late postmortem. interval ranging from 5 to 20 years postmortem to be estimated. A total of 40 femur bones from 40 different cadavers (data range 5-20 years) were use. Of the 275 total proteins, we excluded the circulating ones (n = 227), leaving a total of 48 proteins (29 structural and 19 functional) were found. A multiple correspondence analysis was applied on the 48 proteins. Finally selecting 32 proteins that allowed us to discriminate between the. two groups of postmortem interval. Analysis of the protein profile present in bone permits an approximation of the date of death within the studied interval, and could be used to complement other tests for estimating the postmortem interval.