Profiling of RNA degradation for estimation of post mortem [corrected] interval

Age estimation of Phormia regina pupae based on ATR-FTIR and chemometrics

Accurate postmortem interval estimation is vital in the investigation of homicides, suicides, and accidental deaths. It is key in narrowing suspect lists, improving crime-solving efficiency, and offering solace to bereaved families. The intra-puparial period, comprising about half of a fly's developmental cycle, presents challenges for morphological age estimation. External changes are limited to color shifts and the appearance of respiratory horns on the puparium only within several hours after pupariation, while detailed internal development analysis often requires invasive methods like removing the puparium, which can be damaging. Additionally, these techniques usually depend on a forensic entomologist's expertise, which lead to subjective biases. This study employed attenuated total reflection-fourier transform infrared spectroscopy, a rapid, non-destructive method for analyzing proteins, chitosan, and chitin in puparia. Data showed a consistent reduction in the concentration of the amide I band within the puparium during the intra-puparial development at five constant temperatures (19 °C, 22 °C, 25 °C, 28 °C and 31 °C). This trend in the spectral data effectively distinguishes pupae at various stages of intra-puparial development, facilitating precise age estimation, which is critical for the estimation of the minimum postmortem interval (PMImin). Finally, this work combined the total reflection-fourier transform infrared spectroscopy with chemometric analysis and successfully developed a partial least squares discriminant analysis model and a random forest model, with accuracies of 88 % and 81 %, respectively. These models enable the non-invasive age estimation of P. regina in its intra-puparial period, a stage traditionally difficult to assess morphologically, thus laying the groundwork for PMImin estimation using fly pupae.

The role of miRNA-21 and hypoxia inducible factor-1 in predicting post mortem interval in cardiac muscles of aluminum phosphide deaths

BACKGROUND

The assessment of the postmortem interval (PMI) represents one of the major challenges in forensic pathology. Because of their stability, microRNAs, or miRNAs, are anticipated to be helpful in forensic research.

OBJECTIVE

To see if estimation of PMI is possible using miRNA-21 and Hypoxia-inducible factor-1α (HIF-1α) expression levels in the heart samples from aluminum phosphide toxicity (Alpt).

METHODS

This was a cross sectional study on 60 post-mortem samples (heart tissues) collected at different intervals during forensic autopsies. The two groups were allocated equally according to the cause of death into Group I (non-toxicated deaths, n = 30): Deaths caused by other than toxicity, and Group II (toxicated deaths, n = 30): Deaths due to Alpt. MDA (Malondialdehyde) and GSH (Glutathione), were measured in heart tissues using ELIZA. MiRNA- 21and HIF-1α expression levels were measured in heart tissues at different PMI using RT-Q PCR. ROC curve for detection of toxicated deaths using miRNA-21 and HIF was carried out.

RESULTS

miRNA-21 and HIF-1α expression levels in Alp deaths were up regulated while GSH was downregulated with statistically significant difference. There was positive correlation between miRNA-21, HIF-1α and MDA with PMI while there was negative correlation between GSH and PMI in Alp deaths. In prediction of post mortem interval in Alp deaths miRNA-21 sensitivity and specificity were (75.9 %, 51.7 %, respectively) while HIF-1α sensitivity and specificity were 100 %.

CONCLUSION

PMI can be calculated using the degree to which particular miRNA-21 and HIF-1α are expressed in the heart tissue. The combination of miRNA-21 with HIF-1α in post mortem estimation is precious indicators.

Life in Suspension with Death: Biocultural Ontologies, Perceptual Cues, and Biomarkers for the Tibetan Tukdam Postmortem Meditative State

This article presents two cases from a collaborative study among Tibetan monastic populations in India on the postdeath meditative state called tukdam (thugs dam). Entered by advanced Tibetan Buddhist practitioners through a variety of different practices, this state provides an ontological frame that is investigated by two distinct intellectual traditions-the Tibetan Buddhist and medical tradition on one hand and the Euroamerican biomedical and scientific tradition on the other-using their respective means of inquiry. Through the investigation, the traditions enact two paradigms of the body at the time of death alongside attendant conceptualizations of what constitutes life itself. This work examines when epistemologies of these two traditions might converge, under what ontological contexts, and through which correlated indicators of evidence. In doing so, this work explores how these two intellectual traditions might answer how the time course and characteristics of physiological changes during the postmortem period might exhibit variation across individuals. Centrally, this piece presents an epistemological inquiry delineating the types of valid evidence that constitute exceptional processes post-clinical death and their potential ontological implications.

Complexity of human death: its physiological, transcriptomic, and microbiological implications

Human death is a complex, time-governed phenomenon that leads to the irreversible cessation of all bodily functions. Recent molecular and genetic studies have revealed remarkable experimental evidence of genetically programmed cellular death characterized by several physiological processes; however, the basic physiological function that occurs during the immediate postmortem period remains inadequately described. There is a paucity of knowledge connecting necrotic pathologies occurring in human organ tissues to complete functional loss of the human organism. Cells, tissues, organs, and organ systems show a range of differential resilience and endurance responses that occur during organismal death. Intriguingly, a persistent ambiguity in the study of postmortem physiological systems is the determination of the trajectory of a complex multicellular human body, far from life-sustaining homeostasis, following the gradual or sudden expiry of its regulatory systems. Recent groundbreaking investigations have resulted in a paradigm shift in understanding the cell biology and physiology of death. Two significant findings are that (i) most cells in the human body are microbial, and (ii) microbial cell abundance significantly increases after death. By addressing the physiological as well as the microbiological aspects of death, future investigations are poised to reveal innovative insights into the enigmatic biological activities associated with death and human decomposition. Understanding the elaborate crosstalk of abiotic and biotic factors in the context of death has implications for scientific discoveries important to informing translational knowledge regarding the transition from living to the non-living. There are important and practical needs for a transformative reestablishment of accepted models of biological death (i.e., artificial intelligence, AI) for more precise determinations of when the regulatory mechanisms for homeostasis of a living individual have ceased. In this review, we summarize mechanisms of physiological, genetic, and microbiological processes that define the biological changes and pathways associated with human organismal death and decomposition.

Next-Generation Sequencing Application: A Systematic Approach for High-Quality RNA Isolation from Skeletal Muscles

RNA extraction and analyses from tissues using bulk RNA-Sequencing (RNA-Seq) provide a more accurate picture of the gene expression compared to other molecular biology techniques for RNA quantification. Challenges associated with high-quality RNA extraction from skeletal muscles require a modification of standard protocols. Here, we describe a procedure for high-quality RNA isolation from intrinsic laryngeal muscles transferable to skeletal muscles with comparable technical and biological difficulties. Standard protocols for RNA isolation were optimized by maximizing the pooling strategy, determining the sample weight, applying cryogenic muscle disruption, and incorporating RNase-inhibiting reagents during the tissue preparation steps.

Endothelial Cell APOE3 Regulates Neurovascular, Neuronal, and Behavioral Function

BACKGROUND

Specialized brain endothelial cells and human APOE3 are independently important for neurovascular function, yet whether APOE3 expression by endothelial cells contributes to brain function is currently unknown. In the present study, we determined whether the loss of endothelial cell APOE3 impacts brain vascular and neural function.

METHODS

We developed APOE3fl/fl/Cdh5(PAC)-CreERT2+/- (APOE3Cre+/-) and APOE3fl/fl/Cdh5(PAC)-CreERT2-/- (APOE3Cre-/-, control) mice and induced endothelial cell APOE3 knockdown with tamoxifen at ≈4 to 5 weeks of age. Neurovascular and neuronal function were evaluated by biochemistry, immunohistochemistry, behavioral testing, and electrophysiology at 9 months of age.

RESULTS

We found that the loss of endothelial APOE3 expression was sufficient to cause neurovascular dysfunction including higher permeability and lower vessel coverage in tandem with deficits in spatial memory and fear memory extinction and a disruption of cortical excitatory/inhibitory balance.

CONCLUSIONS

Our data collectively support the novel concept that endothelial APOE3 plays a critical role in the regulation of the neurovasculature, neural circuit function, and behavior.

A miRNome analysis at the early postmortem interval

The postmortem interval (PMI) is the time elapsing since the death of an individual until the body is examined. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI as they can better support degradation. In the present work, we analyzed the miRNome at early PMI in rats' skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 microarrays. We found 156 dysregulated miRNAs in rats' skeletal muscle at 24 h of PMI, out of which 84 were downregulated, and 72 upregulated. The miRNA most significantly downregulated was miR-139-5p (FC = -160, p = 9.97 × 10^-11), while the most upregulated was rno-miR-92b-5p (FC = 241.18, p = 2.39 × 10^-6). Regarding the targets of these dysregulated miRNAs, the rno-miR-125b-5p and rno-miR-138-5p were the miRNAs with more mRNA targets. The mRNA targets that we found in the present study participate in several biological processes such as interleukin secretion regulation, translation regulation, cell growth, or low oxygen response. In addition, we found a downregulation of SIRT1 mRNA and an upregulation of TGFBR2 mRNA at 24 h of PMI. These results suggest there is an active participation of miRNAs at early PMI which could be further explored to identify potential biomarkers for PMI estimation.

Ecological drivers of sustained enzootic yellow fever virus transmission in Brazil, 2017-2021

Beginning December 2016, sylvatic yellow fever (YF) outbreaks spread into southeastern Brazil, and Minas Gerais state experienced two sylvatic YF waves (2017 and 2018). Following these massive YF waves, we screened 187 free-living non-human primate (NHPs) carcasses collected throughout the state between January 2019 and June 2021 for YF virus (YFV) using RTqPCR. One sample belonging to a Callithrix, collected in June 2020, was positive for YFV. The viral strain belonged to the same lineage associated with 2017-2018 outbreaks, showing the continued enzootic circulation of YFV in the state. Next, using data from 781 NHPs carcasses collected in 2017-18, we used generalized additive mixed models (GAMMs) to identify the spatiotemporal and host-level drivers of YFV infection and intensity (an estimation of genomic viral load in the liver of infected NHP). Our GAMMs explained 65% and 68% of variation in virus infection and intensity, respectively, and uncovered strong temporal and spatial patterns for YFV infection and intensity. NHP infection was higher in the eastern part of Minas Gerais state, where 2017-2018 outbreaks affecting humans and NHPs were concentrated. The odds of YFV infection were significantly lower in NHPs from urban areas than from urban-rural or rural areas, while infection intensity was significantly lower in NHPs from urban areas or the urban-rural interface relative to rural areas. Both YFV infection and intensity were higher during the warm/rainy season compared to the cold/dry season. The higher YFV intensity in NHPs in warm/rainy periods could be a result of higher exposure to vectors and/or higher virus titers in vectors during this time resulting in the delivery of a higher virus dose and higher viral replication levels within NHPs. Further studies are needed to better test this hypothesis and further compare the dynamics of YFV enzootic cycles between different seasons.

Elucidating the RNA-Protein Interactomes of Target RNAs in Tissue

RNA-protein interactions are key to many aspects of cellular homeostasis and their identification is important to understanding cellular function. Multiple strategies have been developed for the RNA-centric characterization of RNA-protein complexes. However, these studies have all been done in immortalized cell lines that do not capture the complexity of heterogeneous tissue samples. Here, we develop hybridization purification of RNA-protein complexes followed by mass spectrometry (HyPR-MS) for use in tissue samples. We isolated both polyadenylated RNA and the specific long noncoding RNA MALAT1 and characterized their protein interactomes. These results demonstrate the feasibility of HyPR-MS in tissue for the multiplexed characterization of specific RNA-protein complexes.

Systematic dissection, preservation, and multiomics in whole human and bovine hearts

OBJECTIVES

We sought to develop a rigorous, systematic protocol for the dissection and preservation of human hearts for biobanking that expands previous success in postmortem transcriptomics to multiomics from paired tissue.

BACKGROUND

Existing cardiac biobanks consist largely of biopsy tissue or explanted hearts in select diseases and are insufficient for correlating whole organ phenotype with clinical data.

METHODS

We demonstrate optimal conditions for multiomics interrogation (ribonucleic acid (RNA) sequencing, untargeted metabolomics) in hearts by evaluating the effect of technical variables (storage solution, temperature) and simulated postmortem interval (PMI) on RNA and metabolite stability. We used bovine (n=3) and human (n=2) hearts fixed in PAXgene or snap-frozen with liquid nitrogen.

RESULTS

Using a paired Wald test, only two of the genes assessed were differentially expressed between left ventricular samples from bovine hearts stored in PAXgene at 0 and 12 hours PMI (FDR q<0.05). We obtained similar findings in human left ventricular samples, suggesting stability of RNA transcripts at PMIs up to 12 hours. Different library preparation methods (mRNA poly-A capture vs. rRNA depletion) resulted in similar quality metrics with both library preparations achieving >95% of reads properly aligning to the reference genomes across all PMIs for bovine and human hearts. PMI had no effect on RNA Integrity Number or quantity of RNA recovered at the time points evaluated. Of the metabolites identified (855 total) using untargeted metabolomics of human left ventricular tissue, 503 metabolites remained stable across PMIs (0, 4, 8, 12 hours). Most metabolic pathways retained several stable metabolites.

CONCLUSIONS

Our data demonstrate a technically rigorous, reproducible protocol that will enhance cardiac biobanking practices and facilitate novel insights into human CVD.

CONDENSED ABSTRACT

Cardiovascular disease (CVD) is the leading cause of mortality worldwide. Current biobanking practices insufficiently capture both the diverse array of phenotypes present in CVDs and the spatial heterogeneity across cardiac tissue sites. We have developed a rigorous and systematic protocol for the dissection and preservation of human cardiac biospecimens to enhance the availability of whole organ tissue for multiple applications. When combined with longitudinal clinical phenotyping, our protocol will enable multiomics in hearts to deepen our understanding of CVDs.

An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model

Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.

Analysis of human brain tissue derived from DBS surgery

Background

Transcriptomic and proteomic profiling of human brain tissue is hindered by the availability of fresh samples from living patients. Postmortem samples usually represent the advanced disease stage of the patient. Furthermore, the postmortem interval can affect the transcriptomic and proteomic profiles. Therefore, fresh brain tissue samples from living patients represent a valuable resource of metabolically intact tissue. Implantation of deep brain stimulation (DBS) electrodes into the human brain is a neurosurgical treatment for, e.g., movement disorders. Here, we describe an improved approach to collecting brain tissues from surgical instruments used in implantation of DBS device for transcriptomics and proteomics analyses.

Methods

Samples were extracted from guide tubes and recording electrodes used in routine DBS implantation procedure to treat patients with Parkinson’s disease, genetic dystonia and tremor. RNA sequencing was performed in tissues extracted from the recording microelectrodes and liquid chromatography-mass spectrometry (LC-MS) performed in tissues from guide tubes. To assess the performance of the current approach, the obtained datasets were compared with previously published datasets representing brain tissues.

Results

Altogether, 32,034 RNA transcripts representing the unique Ensembl gene identifiers were detected from eight samples representing both hemispheres of four patients. By using  LC-MS, we identified 734 unique proteins from 31 samples collected from 14 patients. The datasets are available in the BioStudies database (accession number S-BSST667). Our results indicate that surgical instruments used in DBS installation retain brain material sufficient for protein and gene expression studies. Comparison with previously published datasets obtained with similar approach proved the robustness and reproducibility of the protocol.

Conclusions

The instruments used during routine DBS surgery are a useful source for obtaining fresh brain tissues from living patients. This approach overcomes the issues that arise from using postmortem tissues, such as the effect of postmortem interval on transcriptomic and proteomic landscape of the brain, and can be used for studying molecular aspects of DBS-treatable diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40035-022-00297-y.

Estimating the Postmortem Interval of Carcasses in the Water Using the Carrion Insect, Brain Tissue RNA, Bacterial Biofilm, and Algae

The accurate estimation of postmortem interval (PMI) is crucial in the investigation of homicide cases. Unlike carcasses on land, various biological and abiotic factors affect the decomposition of carcasses in water. In addition, the insect evidence (e.g., blow flies) that is commonly used to estimate the PMI are unavailable before the carcasses float on water. Therefore, it is difficult to estimate the PMI of a carcass in water. This study aimed to explore an effective way of estimating the PMI of a carcass in water. Carrion insects, brain tissue RNA, bacterial biofilm on the skin surface, and algae in water with PMI were studied using 45 rat carcasses in a small river. The results showed that carrion insects might not be suitable for the estimation of PMI of a carcass in water since they do not have a regular succession pattern as a carcass on land, and the flies only colonized six of the carcasses. The target genes (β-actin, GAPDH, and 18S) in the brain tissue were associated with the PMI in a time-dependent manner within 1 week after death. A polynomial regression analysis was used to assess the relationship between the gene expression profiles and PMI. The correlation coefficient R² of each regression equation was ≥ 0.924. A third-generation sequencing analysis showed that the bacteria on the skin surface of the carcass and the algae in the water samples around the carcass had a regular succession pattern, where Cryptomonas and Placoneis incased and decreased, respectively, within first 9 days. The results of this study provide a promising way to use the brain tissue RNA, bacterial biofilm, and algae to estimate the PMI of a carcass in water.

Clinico-histopathologic and single nuclei RNA sequencing insights into cardiac injury and microthrombi in critical COVID-19

Acute cardiac injury is prevalent in critical COVID-19 and associated with increased mortality. Its etiology remains debated, as initially presumed causes--- myocarditis and cardiac necrosis--- have proven uncommon. To elucidate the pathophysiology of COVID-19-associated cardiac injury, we conducted a prospective study of the first 69 consecutive COVID-19 decedents at Columbia University Irving Medical Center in New York City. Of six acute cardiac histopathologic features, microthrombi was the most commonly detected amongst our cohort (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak erythrocyte sedimentation rate and c-reactive protein were independently associated with increased odds of microthrombi, supporting an immunothrombotic etiology. Using single nuclei RNA-sequencing analysis on 3 patients with and 4 patients without cardiac microthrombi, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive, relative to microthrombi-negative, COVID-19 hearts. Non-COVID-19 non-failing hearts were used as reference controls. Our study identifies a specific transcriptomic signature in cardiac fibroblasts as a salient feature of microthrombi-positive COVID-19 hearts. Our findings warrant further mechanistic study as cardiac fibroblasts may represent a potential therapeutic target for COVID-19-associated cardiac microthrombi.

Role of molecular techniques in PMI estimation: An update

The time frames between death and reporting of the cadaver, known as post Mortem interval (PMI), is essential in investigation of homicide deaths, suspicious deaths, or other untimely deaths as well as natural deaths. Such information helps to connect the missing links in homicide or other relevant cases. Over the time several methods are developed which depends upon factors as several methods physiological, biochemical, entomological, and archaeological for the estimation of degradation of body with time. These methods lack precision, require expertise to achieve worthy results or authentic estimate. Although these methods are currently in use but, these evaluations are still unreliable and imprecise. Hence, we still need new methods for better estimation of PMI. Initially, the predictable morphological and chemical changes in cadaver are used as PMI indicators but, as the time since death increases, the above methods become less useful for as they can't pin point the time of death rather give a ballpark idea. With the advent of the field of molecular biology, the estimation of PMI is proposed to be executed by evaluating the degradation pattern of the biological markers (DNA, RNA, and Proteins). It is now proved that the DNA is fairly unwavering over long post-mortem phases, RNA is much more labile in nature, and sensitive to degradation in a tissue-specific manner. Thus, the main purpose (aim, agenda) of this document is to provide review that mainly focuses on potential use of RNA markers in estimation of PMI. For this Critical Review, the systematic evaluation of 47 studies is executed according to the chosen inclusion and exclusion criteria.

Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses

Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.

Insights into how environment shapes post-mortem RNA transcription in mouse brain

Most biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

MicroRNAs as Useful Tools to Estimate Time Since Death. A Systematic Review of Current Literature

Estimating the time of death remains the most challenging question in forensic medicine, because post-mortem interval (PMI) estimation can be a remarkably difficult goal to achieve. The aim of this review is to analyze the potential of microRNAs (miRNAs) to evaluate PMI. MiRNAs have been studied as hallmarks and biomarkers in several pathologies and have also showed interesting applications in forensic science, such as high sensible biomarkers in body fluid and tissue, for wound age determination and PMI evaluation due to their low molecular weight and tissue-specific expression. The present systematic review was carried out according to the Preferred Reporting Items for Systematic Review (PRISMA) standards. We performed an electronic search of PubMed, Science Direct Scopus, and Excerpta Medica Database (EMBASE) from the inception of these databases to 12 August 2020. The search terms were (“PMI miRNA” or “PMI micro RNA”) and (“miRNA” and “time of death”) in the title, abstract and keywords. Through analysis of scientific literature regarding forensic uses of miRNAs, has emerged that the intrinsic characteristics of such molecules, and their subsequent resistance to degradation, make them suitable as endogenous markers in order to determine PMI. However, further and larger studies with human samples and standardized protocols are still needed.

The applicability of forensic time since death estimation methods for buried bodies in advanced decomposition stages

Estimation of the postmortem interval in advanced postmortem stages is a challenging task. Although there are several approaches available for addressing postmortem changes of a (human) body or its environment (ecologically and/or biochemically), most are restricted to specific timeframes and/or individual and environmental conditions. It is well known, for instance, that buried bodies decompose in a remarkably different manner than on the ground surface. However, data on how established methods for PMI estimation perform under these conditions are scarce. It is important to understand whether and how postmortem changes are affected under burial conditions, if corrective factors could be conceived, or if methods have to be excluded for respective cases. We present the first multi-methodological assessment of human postmortem decomposition carried out on buried body donors in Europe, at the Amsterdam Research Initiative for Sub-surface Taphonomy and Anthropology (ARISTA) in the Netherlands. We used a multidisciplinary approach to investigate postmortem changes of morphology, skeletal muscle protein decomposition, presence of insects and other necrophilous animals as well as microbial communities (i.e., microbiomes) from August to November 2018 associated with two complete body exhumations and eight partial exhumations. Our results clearly display the current possibilities and limitations of methods for PMI estimation in buried remains and provide a baseline for future research and application.

Postmortomics: The Potential of Untargeted Metabolomics to Highlight Markers for Time Since Death

The success of forensic investigations involving fatalities very often depends on the establishment of the correct timeline of events. Currently used methods for estimating the postmortem interval (PMI) are mostly dependent on the professional and tacit experience of the investigator, and often with poor reliability in the absence of robust biological markers. The aim of this study was to investigate the potential of metabolomic approaches to highlight molecular markers for PMI. Rat and human muscle tissues, collected at various times postmortem, were analyzed using an untargeted metabolomics approach. Levels of certain metabolites (skatole, xanthine, n-acetylneuraminate, 1-methylnicotinamide, choline phosphate, and uracil) as well as most proteinogenic amino acids increased steadily postmortem. Threonine, tyrosine, and lysine show the most predictable evolution over the postmortem period, and may thus have potential for possible PMI markers in the future. This study demonstrates how a biomarker discovery approach can be extended to forensic investigations using untargeted metabolomics.

Evaluating the use of hypoxia sensitive markers for body fluid stain age prediction

To augment DNA profiling and body fluid identification techniques efforts are being made to increase the amount of information available from a crime scene stain, which includes efforts to identify externally visible characteristics through phenotypic analysis. A key question surrounding crime scene stains is the length of time between deposition of the stain and its subsequent recovery, in that is the stain recovered related to the incident in question or from a previously deposited stain number of weeks earlier? The inability to answer this fundamental question has a detrimental effect upon the successful completion of a criminal investigation. Once a body fluid leaves the body, the oxygen concentration in the environment changes; therefore, it may be that this change could cause a change in the expression of hypoxia-sensitive biomarkers. Here, a range of bloodstains, liquid saliva and liquid semen samples were collected at 0 days, 7 days, 14 days, 21 days and 28 days of degrading at room temperature (19-22 °C), before undergoing total RNA extraction and cDNA synthesis. Blood was recovered from filter paper with 3 mm², with saliva and semen being left in their tubes and swabbed at the appropriate times. All samples then underwent quantitative PCR targeting Vascular Endothelial Growth Factor A (VEGFA) and Hypoxia-Inducible Factor 1 Alpha (HIF1A), with B-Actin (ACTB) as a reference gene. A range of linear and quadratic correlation values was obtained from the qPCR data and used to develop a predictive model with a mean absolute deviation (MAD) of 4.2, 2.1, and 5 days for blood, saliva, and semen respectively. Blind testing indicated that a stain age prediction model based upon VEGFA with ACTB as a reference gene could be used on samples up to four weeks old with a margin of error ranging from 2 days through to 5 days. While a sizeable potential time frame exists using this model; this represents a significant step towards the target of having an accurate stain age prediction model.

Postmortem expression of apoptosis-related genes in the liver of mice and their use for estimation of the time of death

PURPOSE

A major challenge in forensic medicine is to estimate the postmortem interval (PMI). Several approaches had been tried to determine the time of death, including physical and chemical changes. This study aims to explore the postmortem changes in the expression of apoptosis-related genes in the liver of mice and to use these changes for estimation of the PMI.

METHODS

Hepatic tissue was collected from sacrificed mice immediately after death (the control group) and at 3, 6, 9, 12, 18, and 24 hours after death. Four apoptosisrelated genes were selected as target genes, which are Caspase 3 (Casp3), B cell leukemia/ lymphoma 2 (Bcl2), BCL2-associated X protein (Bax), and Transformation related protein 53 (Trp53), and their relative expression was measured using quantitative PCR. miR-122 was used as a reference gene for normalization of the Ct (threshold cycle) values of the target genes.

RESULTS

The results revealed that the postmortem expression of Casp3 increased in a time-dependent manner; the expression of Bax increased from 3 to 18 hours followed by a decrease at 24 hours after death; the expression of Bcl2 decreased in a time-dependent manner after death; the expression of Trp53 increased from 3 to 6 hours and then started to decrease from 9 to 24 hours after death.

CONCLUSION

Based on the observed changes in the expression level of these genes, mathematical models were established to estimate the PMI. Further research is needed to investigate these markers and mathematical models in human tissues.

Medical Assistance in Death as a Unique Opportunity to Advance Human Immunodeficiency Virus Cure Research

The inability to sample deep-tissue reservoirs in individuals living with human immunodeficiency virus (HIV) has greatly hindered accurate estimates of viral reservoir size and distribution. Animal models and collection of tissues during autopsies of HIV-positive individuals are 2 proposed solutions to this problem. Each, however, has its limitations. In this Viewpoint, we argue that tissue donation following medical assistance in death (MAiD) will form an invaluable resource for the characterization of the viral reservoir in the context of current HIV cure research. In support, we discuss a recent instance in which an individual living with HIV chose to donate their body/tissues to HIV research prior to undergoing MAiD at our institution. Going forward, we hope this will help provide support to individuals in their decisions around tissue donation following MAiD, while highlighting how healthcare providers, by complying with such wishes, can affect patient satisfaction in the last days of life.

Comparative Evaluation of RNAlater Solution and Snap Frozen Methods for Gene Expression Studies in Different Tissues

Introduction: Freezing of tissues with liquid nitrogen is the most common method in studies performed at the RNA level. However, the use of RNA stabilization solutions has become a popular alternative method. The aim of this study is to investigate the effectiveness of RNAlater on RNA stabilization in different tissues.

Material and Methods: In this study, RNA were isolated from the lung, heart, liver and skeletal muscle tissues of rats that were frozen with liquid nitrogen (snap frozen, SF group) or stored in RNAlater solution (RL group), and the changes in concentration, purity, reference genes expression, and fold-change levels between groups were analyzed.

Results: In the RL group, the concentration of RNA isolated from the liver tissues was higher (P<0.05), whereas the A260/280 ratio was lower in the heart and liver tissues (P<0.05). PPIA and SRP72 genes were found to have lower Ct values in the heart tissues of rats in the RL group (P<0.05 and P<0.001, respectively) than the SF group. Expression levels of PPIA, ACTB, and SRP72 genes across the tissues were found to be different between the groups (P<0.05). The gene expression level examined in terms of fold-change was significantly different in the RL group (upregulated up to 4 folds and downregulated about 0.5 fold) (P< 0.05).

Conclusions: The results showed that RNAlater can maintain the RNA integrity and can also change the results of gene expression because it does not inhibit biological activity. The snap freezing method is more reliable because gene expression is more stable in tissues frozen with liquid nitrogen.

Post-mortem changes in metabolomic profiles of human serum, aqueous humor and vitreous humor

INTRODUCTION

Application of metabolomic methods to forensic studies may expand the limits of the post-mortem interval (PMI) estimation, and improve the accuracy of the estimation. To this end, it is important to determine which tissue is the most suitable for analysis, and which compounds are the most promising candidates for PMI estimation.

OBJECTIVES

This work is aimed at the comparison of human serum, aqueous humor (AH), and vitreous humor (VH) as perspective tissues for metabolomic-based PMI estimation, at the determination of most promising PMI biomarkers, and at the development of method of PMI estimation based on the measurement of concentrations of PMI biomarkers.

METHODS

Quantitative metabolomic profiling of samples of the human serum, AH, and VH taken at different PMIs has been performed with the use of NMR spectroscopy.

RESULTS

It is found that the metabolomic changes in anatomically isolated ocular fluids are slower and smoother than that in blood. A good positive time correlation (Pearson coefficient r > 0.5) was observed for several metabolites, including hypoxanthine, choline, creatine, betaine, glutamate, and glycine. A model for PMI estimation based on concentrations of several metabolites in AH and VH is proposed.

CONCLUSIONS

The obtained results demonstrate that the metabolomic analysis of AH and VH is more suitable for the PMI estimation than that of serum. The compounds with good positive time correlation can be considered as potential PMI biomarkers.

Influence of species and processing parameters on recovery and content of brain tissue-derived extracellular vesicles

Extracellular vesicles (EVs) are involved in a wide range of physiological and pathological processes by shuttling material out of and between cells. Tissue EVs may thus lend insights into disease mechanisms and also betray disease when released into easily accessed biological fluids. Since brain-derived EVs (bdEVs) and their cargo may serve as biomarkers of neurodegenerative diseases, we evaluated modifications to a published, rigorous protocol for separation of EVs from brain tissue and studied effects of processing variables on quantitative and qualitative outcomes. To this end, size exclusion chromatography (SEC) and sucrose density gradient ultracentrifugation were compared as final separation steps in protocols involving stepped ultracentrifugation. bdEVs were separated from brain tissues of human, macaque, and mouse. Effects of tissue perfusion and a model of post-mortem interval (PMI) before final bdEV separation were probed. MISEV2018-compliant EV characterization was performed, and both small RNA and protein profiling were done. We conclude that the modified, SEC-employing protocol achieves EV separation efficiency roughly similar to a protocol using gradient density ultracentrifugation, while decreasing operator time and, potentially, variability. The protocol appears to yield bdEVs of higher purity for human tissues compared with those of macaque and, especially, mouse, suggesting opportunities for optimization. Where possible, perfusion should be performed in animal models. The interval between death/tissue storage/processing and final bdEV separation can also affect bdEV populations and composition and should thus be recorded for rigorous reporting. Finally, different populations of EVs obtained through the modified method reported herein display characteristic RNA and protein content that hint at biomarker potential. To conclude, this study finds that the automatable and increasingly employed technique of SEC can be applied to tissue EV separation, and also reveals more about the importance of species-specific and technical considerations when working with tissue EVs. These results are expected to enhance the use of bdEVs in revealing and understanding brain disease.

Identification of cadaveric liver tissues using thanatotranscriptome biomarkers

Thanatotranscriptome studies involve the examination of mRNA transcript abundance and gene expression patterns in the internal organs of deceased humans. Postmortem gene expression is indicative of the cellular status of a corpse at the time of death, a portion of which may represent a cascade of molecular events occasioned by death. Specific gene biomarkers identify perceptible transcriptional changes induced by stochastic responses to the cessation of biological functions. Transcriptome analyses of postmortem mRNA from a tissue fragment may determine unique molecular identifiers for specific organs and demonstrate unique patterns of gene expression that can provide essential contextual anatomical information. We evaluated the impact of targeted transcriptome analysis using RNA sequencing to reveal global changes in postmortem gene expression in liver tissues from 27 Italian and United States corpses: 3.5-hour-old to 37-day-old. We found that our single blind study using eight liver tissue-specific gene biomarkers (e.g. AMBP and AHSG) is highly specific, with autopsy-derived organ samples correctly identified as tissues originating from postmortem livers. The results demonstrate that 98–100% of sequencing reads were mapped to these liver biomarkers. Our findings indicate that gene expression signatures of mRNA exposed up to 37 days of autolysis, can be used to validate the putative identity of tissue fragments.

Potential applications of microRNA profiling to forensic investigations

Within the forensic science community, there is a continued push to develop novel tools to aid in criminal investigations. microRNA (miRNA) analysis has been the focus of many researcher's attention in the biomedical field since its discovery in 1993; however, the forensic application of miRNA analysis has only been suggested within the last 10 years and has been gaining considerable traction recently. The primary focus of the forensic application of miRNA analysis has been on body fluid identification to provide confirmatory universal analysis of unknown biological stains obtained from crime scenes or evidence items. There are, however, other forensic applications of miRNA profiling that have shown potential, yet are largely understudied, and warrant further investigation such as organ tissue identification, donor age estimation, and more. This review paper aims to evaluate the current literature and future potential of miRNA analysis within the forensic science field.

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium

Accurate analysis of gene expression in human tissues using RNA sequencing is dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lay the foundation for understanding RNA regulation post-mortem and provide novel insights into RNA metabolism in the tissues of the mammalian eye.

Succession of oral microbiota community as a tool to estimate postmortem interval

The establishment of postmortem interval is one of the most important aspects of forensic expertise. Microbes may provide a novel way to estimate the postmortem intervals in order to avoid many of these limitations. The oral cavity harbors one of the most diverse microbiomes that play a key role in the decomposition of corpses. In this study, the oral bacterial community showed obvious changes in relative abundance during the process of mice decomposition. Meanwhile, at different taxonomic levels, specific bacteria were found to be significantly correlated with the postmortem interval. Linear regression models between relative abundance and the postmortem interval were constructed. Among these species, Gamma-proteobacteria and Proteus were the best ones that can be used to infer the postmortem interval, especially late postmortem interval. Therefore, we suggest that succession of oral microbial community can be developed as a forensic tool for estimating the postmortem interval.

A 1H NMR metabolomic approach for the estimation of the time since death using aqueous humour: an animal model

INTRODUCTION

The estimation of the time since death, or post-mortem interval (PMI), still remains a main conundrum in forensic science. Several approaches have been so far proposed from either a qualitative or a quantitative point of view, but they still lack reliability and robustness. Recently, metabolomics has shown to be a potential tool to investigate the time-related post-mortem metabolite modifications in animal models.

OBJECTIVES

Here we propose, for the first time, the use of a ¹H NMR metabolomic approach for the estimation of PMI from aqueous humour (AH) in an ovine model.

METHODS

AH samples were collected at different times after death (from 118 to 1429 min). ¹H NMR experiments were performed and spectral data analysed by multivariate statistical tools.

RESULTS

A multivariate calibration model was built to estimate PMI on the basis of the metabolite content of the samples. The model was validated with an independent test set, obtaining a prediction error of 59 min for PMI < 500 min, 104 min for PMI from 500 to 1000 min, and 118 min for PMI > 1000 min. Moreover, the metabolomic approach suggested a picture of the mechanisms underlying the post-mortem biological modifications, highlighting the role played by taurine, choline, and succinate.

CONCLUSION

The time-related modifications of the ¹H NMR AH metabolomic profile seem to be encouraging in addressing the issue of a reproducible and robust model to be employed for the estimation of the time since death.

Postmortem proteomics to discover biomarkers for forensic PMI estimation

The assessment of postmortem degradation of skeletal muscle proteins has emerged as a novel approach to estimate the time since death in the early to mid-postmortem phase (approximately 24 h postmortem (hpm) to 120 hpm). Current protein-based methods are limited to a small number of skeletal muscle proteins, shown to undergo proteolysis after death. In this study, we investigated the usability of a target-based and unbiased system-wide protein analysis to gain further insights into systemic postmortem protein alterations and to identify additional markers for postmortem interval (PMI) delimitation. We performed proteomic profiling to globally analyze postmortem alterations of the rat and mouse skeletal muscle proteome at defined time points (0, 24, 48, 72, and 96 hpm), harnessing a mass spectrometry-based quantitative proteomics approach. Hierarchical clustering analysis for a total of 579 (rat) and 896 (mouse) quantified proteins revealed differentially expressed proteins during the investigated postmortem period. We further focused on two selected proteins (eEF1A2 and GAPDH), which were shown to consistently degrade postmortem in both rat and mouse, suggesting conserved intra- and interspecies degradation behavior, and thus preserved association with the PMI and possible transferability to humans. In turn, we validated the usefulness of these new markers by classical Western blot experiments in a rat model and in human autopsy cases. Our results demonstrate the feasibility of mass spectrometry-based analysis to discover novel protein markers for PMI estimation and show that the proteins eEF1A2 and GAPDH appear to be valuable markers for PMI estimation in humans.

Audit of Quality and Quantity of Nucleic Acid Yield from Pediatric Acute Leukemia Cases Following a Bio-banking Initiative

Information which can be harvested from a biological sample has greatly improved with advancements in diagnostic technologies. However, in developing countries, the awareness about usefulness of bio-banking concept is lacking and centres which do offer it, depend mainly on - 20 or - 80 °C for sample storage due to lack of sophisticated infrastructure like vapour phase nitrogen storage preservation. Hence in these resource constraint settings, timely audit of quality of nucleic acids extractable from samples stored is of utmost importance. In this study, we explore the effect of - 20 °C storage over nucleic acids (DNA/RNA) isolated from blood samples of 180 patients with various leukaemia's following a bio-banking initiative. We observed that the integrity and quality of both DNA and RNA were maintained in 70 and 80% samples respectively over time as reflected by their concentration measurements and inherent uniform expression of housekeeping gene GAPDH. Only 3.7% of the RNA samples and 4.2% of the DNA samples yielded very low concentrations despite minimizing processing and technical loss. In nutshell, audit of our biobank sample yield highlights that storage of blood samples at - 20 °C does not compromise the fidelity of nucleic acids for future diagnostic and research work in a resource constraint setting.

HIF1α protein and mRNA expression as a new marker for post mortem interval estimation in human gingival tissue

Estimating the post mortem interval (PMI) is still a crucial step in Forensic Pathology. Although several methods are available for assessing the PMI, a precise estimation is still quite unreliable and can be inaccurate. The present study aimed to investigate the immunohistochemical distribution and mRNA expression of hypoxia inducible factor (HIF-1α) in post mortem gingival tissues to establish a correlation between the presence of HIF-1α and the time since death, with the final goal of achieving a more accurate PMI estimation. Samples of gingival tissues were obtained from 10 cadavers at different PMIs (1-3 days, 4-5 days and 8-9 days), and were processed for immunohistochemistry and quantitative reverse transcription-polymerase chain reaction. The results showed a time-dependent correlation of HIF-1α protein and its mRNA with different times since death, which suggests that HIF-1α is a potential marker for PMI estimation. The results showed a high HIF-1α protein signal that was mainly localized in the stratum basale of the oral mucosa in samples collected at a short PMI (1-3 days). It gradually decreased in samples collected at a medium PMI (4-5 days), but it was not detected in samples collected at a long PMI (8-9 days). These results are in agreement with the mRNA data. These data indicate an interesting potential utility of Forensic Anatomy-based techniques, such as immunohistochemistry, as important complementary tools to be used in forensic investigations.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.

RNA levels in post-mortem tissue can differ greatly from those before death. Studying the effect of post-mortem interval on the transcriptome in 36 human tissues, Ferreira et al. find that the response to death is largely tissue-specific and develop a model to predict time since death based on RNA data.

Using Skin Gene Markers for Estimating Early Postmortem Interval at Different Temperatures

Many researches document long-term RNA persistence in a variety of tissues and its applicability in estimating the postmortem interval (PMI). Skin-specific mRNA marker, late cornified envelope 1C (LCE1C), was used to identified skin samples. Before using the LCE1C in criminal casework, its persistence and applicability for estimating PMI in different temperatures were tested. Twelve skin samples were collected from 6 patients, and 6 samples were kept at 24°C and others were kept at 40°C for 5 days. The expression levels of LCE1C mRNA are serially detected and quantified using real-time polymerase chain reaction. The expression levels of LCE1C were decreased with increasing the time interval in time-dependent manner, whereas changing the surrounding temperatures did not show any statistical significance. These results could suggest using LCE1C in estimation of PMI. Moreover, these encourage investigators and crime laboratories to know environmental conditions before interpreting the results.

Systematic analysis of gene expression patterns associated with postmortem interval in human tissues

Postmortem mRNA degradation is considered to be the major concern in gene expression research utilizing human postmortem tissues. A key factor in this process is the postmortem interval (PMI), which is defined as the interval between death and sample collection. However, global patterns of postmortem mRNA degradation at individual gene levels across diverse human tissues remain largely unknown. In this study, we performed a systematic analysis of alteration of gene expression associated with PMI in human tissues. From the Genotype-Tissue Expression (GTEx) database, we evaluated gene expression levels of 2,016 high-quality postmortem samples from 316 donors of European descent, with PMI ranging from 1 to 27 hours. We found that PMI-related mRNA degradation is tissue-specific, gene-specific, and even genotype-dependent, thus drawing a more comprehensive picture of PMI-associated gene expression across diverse human tissues. Additionally, we also identified 266 differentially variable (DV) genes, such as DEFB4B and IFNG, whose expression is significantly dispersed between short PMI (S-PMI) and long PMI (L-PMI) groups. In summary, our analyses provide a comprehensive profile of PMI-associated gene expression, which will help interpret gene expression patterns in the evaluation of postmortem tissues.