RNA degradation as described by a mathematical model for postmortem interval determination

The mechanism of serum cell-free DNA release in postmortem subjects and novel markers to estimate the postmortem intervals

Cell-free DNA (cfDNA) is DNA released from dying cells into the serum. The aim of the present study is to elucidate the mechanism of cell-free DNA (cfDNA) release in postmortem subjects by assaying Cytokeratin 18 (M30 and M65), cyclophilin A (CyPA), and myeloperoxidase (MPO) levels and to evaluate whether these levels are useful as markers for estimating postmortem intervals. Serum (n = 54) was sampled from postmortem autopsied Japanese subjects. cfDNA was extracted and M30, M65, CyPA, and MPO in serum were assayed by enzyme-linked immunosorbent assay. Significantly higher serum levels of M30, M65, and MPO were observed in postmortem subjects than in living subjects. Although the difference was smaller, CyPA was also significantly higher in postmortem subjects than in living subjects. In addition, serum M30 and MPO levels were significantly correlated with cfDNA concentrations in postmortem subjects. Furthermore, M30 levels slightly increased according to the postmortem interval, and MPO levels at 2.5 days were significantly higher than those at <2 days. The result of regression analysis revealed a significant difference between M30/MPO levels and postmortem intervals. These findings suggested that elevated levels of cfDNA in postmortem subjects are released by apoptosis and neutrophils via NETosis and that M30 and MPO levels can be used as markers to estimate postmortem intervals.

Untargeted and targeted metabolomics analysis of CO poisoning and mechanical asphyxia postmortem interval biomarkers in rat and human plasma by GCMS

Accurate and objective estimation of the postmortem interval (PMI) is crucial in forensic practice. This study aimed to infer PMI through equations based on the relationship between PMI and metabolomics biomarkers.Rats were subjected to models representing various temperatures and causes of death, with blood collected at different intervals. Untargeted gas chromatographymass spectrometry metabolomics detection methods were developed, and candidate biomarkers were chosen as co-differentially expressed metabolites in four models. A targeted method was then developed for quantitatively determining candidate biomarkers. Animal tests and human cadaver samples with clearly documented causes of death and time were used to verify the reliability of the regression equation.Results: Unique differential metabolites for CO poisoning deaths included 2,3-butanediol, hypoxanthine, and dehydrated hexanol, while those for mechanical asphyxia deaths comprised propylamine, 1,3-propylene glycol, phosphoric acid, and sorbitol. Pyruvate, glycerol and isoleucine were identified as candidate biomarkers. Human case results demonstrated the method's potential (error rate < 20 %). The findings of this study may offer reference points for estimating PMI and causes of death in forensic practice.

Lycium barbarum polysaccharides (LBP) suppresses hypoxia/reoxygenation (H/R)-induced rat H9C2 cardiomyocytes pyroptosis via Nrf2/HO-1 signaling pathway

This study aimed to explore the mechanism that Lycium barbarum polysaccharides (LBP) suppress hypoxia/reoxygenation (H/R)-caused pyroptosis in cardiomyocytes (H9C2) via the Nrf2/HO-1 pathway. Initially, we established the cell model of H/R (6 h hypoxia plus with 24 h reoxygenation), and found that 90 μg/mL LBP was the optimal concentration. Subsequently, we confirmed that LBP reduced the apoptosis rate of cells after H/R, the activity of LDH, the inflammatory factors IL-1β and IL-18, and the levels of pyroptosis-specific markers ASC, NLRP3, and Caspase-1 (mRNAs and proteins). It increased the cell survival rate and the mRNA levels of the Nrf2/HO-1 pathway markers Nrf2 and HO-1, and allowed cytoplasmic Nrf2 protein to enter the nucleus to activate HO-1 protein. The Nrf2 siRNA2 caused the following events in H/R model: (1) the increases of the apoptosis rate, LDH activity, the levels of inflammatory factors (IL-1β and IL-18), the levels of ACS, NLRP3, and Caspase-1 (mRNAs and proteins); and (2) the decreases of the cell survival rate, the mRNA levels of Nrf2 and HO-1, and the protein levels of cytoplasm-Nrf2, nucleus-Nrf2, and HO-1. Therefore we concluded that 90 μg/mL LBP suppressed H/R-induced H9C2 cardiomyocyte pyroptosis via the Nrf2/HO-1 pathway.

microRNAs as New Biomolecular Markers to Estimate Time since Death: A Systematic Review

Estimating the post-mortem interval is still one of the most complex challenges in forensics. In fact, the main tools currently used are burdened by numerous limitations, which sometimes allow the time of death to be placed only within too large time intervals. In recent years, researchers have tried to identify new tools to try to narrow down the interval within which to place the time of death; among these, the analysis of microRNAs seems to be promising. An evidence-based systematic review of the literature has been conducted to evaluate the state of the art of knowledge, focusing on the potential correlation between miRNA degradation and PMI estimation. The research has been performed using the electronic databases PubMed, Scopus, and WOS. The results allowed us to highlight the usefulness of miRNAs both as markers for PMI estimation and for normalization, especially due to their stability. In fact, some miRNAs remain particularly stable for long periods and in different tissues, while others degrade faster. Furthermore, there are numerous factors capable of influencing the behavior of these molecules, among which the type of tissue, the cause of death, and the circadian rhythm appear to be the most relevant. Despite the promising results of the few articles present in the literature, because of the numerous limitations they are burdened by, further research is still necessary to achieve more solid and shareable results.

Potential Role of mRNA in Estimating Postmortem Interval: A Systematic Review

Although the postmortem interval estimation still represents one of the main goals of forensic medicine, there are still several limitations that weigh on the methods most used for its determination: for this reason, even today, precisely estimating the postmortem interval remains one of the most important challenges in the forensic pathology field. To try to overcome these limitations, in recent years, numerous studies have been conducted on the potential use of the mRNA degradation time for reaching a more precise post mortem interval (PMI) estimation. An evidence-based systematic review of the literature has been conducted to evaluate the state of the art of the knowledge focusing on the potential correlation between mRNA degradation and PMI estimation. The research has been performed using the electronic databases PubMed and Scopus. The analysis conducted made it possible to confirm the potential applicability of mRNA for reaching a more precise PMI estimation. The analysis of the results highlighted the usefulness of some mRNAs, such as β-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA, especially in short time frames, within a few hours or days of death. The matrices on which these analyses were conducted were also analyzed, resulting in less exposure to the external environment, including the heart, brain, and dental pulp. The major limitations were also reported, including the short time intervals analyzed in most of the articles, the lack of mathematical models, and the failure to report the error rate between the mRNA degradation time and PMI. Given the still small number of published articles, the lack of globally recognized standardized methods, and the numerous techniques used to evaluate the mRNA degradation times, numerous and larger studies are still necessary to reach more solid and shared evidence.

A pilot study investigating early postmortem interval of rats based on ambient temperature and postmortem interval-related metabolites in blood

Estimation of the postmortem interval (PMI), especially the early PMI, plays a key role in forensic practice. Although several studies based on metabolomics approaches have presented significant findings for PMI estimation, most did not examine the effects of ambient temperature. In this study, gas chromatography-mass spectrometry (GC‒MS)‒based metabolomics was adopted to explore the changes in metabolites in the cardiac blood of suffocated rats at various ambient temperatures (5 °C, 15 °C, 25 °C, and 35 °C) from 0 to 24 h after death. Isoleucine, alanine, proline, valine, glycerol, glycerol phosphate, xanthine, and hypoxanthine were found to contribute to PMI in all temperature groups. Hypoxanthine and isoleucine were chosen to establish estimation models (equations) with an interpolation function using PMI as the dependent variable (f(x, y)), relative intensity as the independent variable x, and temperature as the independent variable y. Thereafter, these two models were validated with predictive samples and shown to have potential predictive ability. The findings indicate that isoleucine, alanine, proline, valine, glycerol, glycerol phosphate, xanthine, and hypoxanthine may be significant for PMI estimation at various ambient temperatures. Furthermore, a method to determine PMI based on ambient temperature and PMI-related metabolites was explored, which may provide a basis for future studies and practical applications.

FOXM1 promotes the progression of non-small cell lung cancer by inhibiting miR-509-5p expression via binding to the miR-509-5p promoter region

Background

Forkhead box M1 (FOXM1) functions as a transcription factor and is consistently overexpressed in various cancers, including non-small-cell lung-, breast-, cervical-, and colorectal cancer. Its overexpression is associated with poor prognosis in patients with non-small-cell lung cancer, although the detailed mechanisms by which FOXM1 promotes the development of non-small-cell lung cancer remain unclear.

Objective

The mechanism of FOXM1 in migration, invasion, apoptosis, and viability of lung cancer cells was investigated.

Methods

Transwell assay, scratch test, and flow cytometry were employed to study the effects of FOXM1 on migration, invasion, and apoptosis in A549 cells. A quantitative polymerase chain reaction was used to determine the impact of FOXM1 on miR-509-5p expression in A549 cells. Dual-luciferase reporter gene assay and chromatin immunoprecipitation were adopted to investigate the molecular mechanisms of FOXM1 on miR-509-5p expression.

Results

FDI-6 (a FOXM1 inhibitor) reduced the protein abundance of FOXM1, thereby increasing the expression of miR-509-5p in A549 cells. Moreover, FDI-6 treatment significantly reduced migration, invasion, and viability of A549 cells while promoting cell apoptosis. Furthermore, miR-509-5p inhibitor obviously alleviated the biological effects of FDI-6 on A549 cells, suggesting that FOXM1 primarily exerted its cancer promoting effect by regulating miR-509-5p. Mechanistically, FOXM1 directly bound to the miR-509-5p promoter to inhibit miR-509-5p expression.

Conclusion

FOXM1 directly binds to the promoter region of miR-509-5p to form a negative feedback loop, thereby inhibiting miR-509-5p expression and promoting the development of non-small-cell lung cancer. This study is expected to complement research on the pathogenesis of non-small-cell lung cancer and promote the development of novel therapeutic targets for this disease.

Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine

At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.

The suitability of using domestic pigs (Sus spp.) as human proxies in the geophysical detection of clandestine graves

Research in many forensic science fields commonly uses domestic pigs (Sus spp.) as proxies for human remains, due to their physiological and anatomical similarities, as well as being more readily available. Unfortunately, previous research, especially that which compares the decompositional process, has shown that pigs are not appropriate proxies for humans. To date, there has not been any published research that specifically addresses whether domestic pigs are adequate human proxies for the geophysical detection of clandestine graves. As such, the aim of this paper was to compare the geophysical responses of pig cadavers and human donor graves, in order to determine if pigs can indeed be used as adequate human proxies. To accomplish this, ground penetrating radar (GPR) and electrical resistivity tomography (ERT) responses on single and multiple pig cadaver graves were compared to single and multiple human donor graves, all of which are in known locations within the same geological environment. The results showed that under field conditions, both GPR and ERT were successful at observing human and pig burials, with no obvious differences between the detected geophysical responses. The results also showed that there were no differences in the geophysical responses of those who were clothed and unclothed. The similarity of the responses may reflect that the geophysical techniques can detect graves despite what their contents are. The study implications suggest that experimental studies in other soil and climate conditions can be easily replicated, benefiting law enforcement with missing persons cases.

miR-26a/30d/152 are reliable reference genes for miRNA quantification in skin wound age estimation

MicroRNAs (miRNAs) are a class of small non-coding RNAs that exert their biological functions as negative regulators of gene expression. They are involved in the skin wound healing process with a dynamic expression pattern and can therefore potentially serve as biomarkers for skin wound age estimation. However, no reports have described any miRNAs as suitable reference genes (RGs) for miRNA quantification in wounded skin or samples with post-mortem changes. Here, we aimed to identify specific miRNAs as RGs for miRNA quantification to support further studies of skin wound age estimation. Overall, nine miRNAs stably expressed in mouse skin at certain posttraumatic intervals (PTIs) were preselected by next-generation sequencing as candidate RGs. These nine miRNAs and the commonly used reference genes (comRGs: U6, GAPDH, ACTB, 18S, 5S, LC-Ogdh) were quantitatively examined using quantitative real-time reverse-transcription polymerase chain reaction at different PTIs during skin wound healing in mice. The stabilities of these genes were evaluated using four independent algorithms: GeNorm, NormFinder, BestKeeper, and comparative Delta Ct. Stability was further evaluated in mice with different post-mortem intervals (PMIs). Overall, mmu-miR-26a-5p, mmu-miR-30d-5p, and mmu-miR-152-3p were identified as the most stable genes at both different PTIs and PMIs. These three miRNA RGs were additionally validated and compared with the comRGs in human samples. After assessing using one, two, or three miRNAs in combination for stability at different PTIs, PMIs, or in human samples, the set of miR-26a/30d/152 was approved as the best normalizer. In conclusion, our data suggest that the combination of miR-26a/30d/152 is recommended as the normalization strategy for miRNA qRT-PCR quantification in skin wound age estimation.

Key points

The small size of miRNAs makes them less susceptible to post-mortem autolysis or putrefaction, leading to their potential use in wound age estimation.Studying miRNAs as biological indicators of skin wound age estimation requires the selection and validation of stable reference genes because commonly used reference genes, such as U6, ACTB, GAPDH, 5S, 18S, and LC-Ogdh, are not stable.miR-26a/30d/152 are stable and reliable as reference genes and their use in combination is a recommended normalization strategy for miRNA quantitative analysis in wounded skin.

A small RNA, microRNA as a potential biomolecular marker to estimate post mortem interval in forensic science: a systematic review

BACKGROUND

Post-mortem interval (PMI) is the cornerstone of the forensic field to investigate. The examination technique by seeing the changes in the body such as algor mortis, rigor mortis, and livor mortis is a traditional technique in which accuracy is influenced by many factors. A biomolecular technique that uses microRNA (miRNA) biomarkers is developing because miRNA has good stability than other RNA, so it meets the requirements to be used for PMI estimation.

METHOD

Following the PRISMA guidelines, journals were taken from 5 databases: Scopus, Science Direct, PubMed, Embase, and Springer. The review was carried out by two people. Inclusion criteria in this review are original research, published in the last 10 years, discussing miRNA as a biomarker for PMI estimation, and free full access. While exclusion criteria are not original research and not using English.

RESULT

Eighteen journals were reviewed in this study. The study was conducted using test animals (rats) and human samples with tissue sources taken from the liver, skeletal muscle, blood, bone, heart, skin, saliva, semen, brain, lung, vitreous humor, spleen, and kidney. miRNA expression levels after death showed different results based on miRNA target, tissue source, and others.

DISCUSSION

The results of each study are different due to the use of different types of miRNA targets and tissue sources. miRNA has great potential to estimate PMI in forensic science, but it is necessary to control the influencing factors to obtain an accurate conclusion.

Post-mortem interval estimation using miRNAs of road traffic accident cases: A forensic molecular approach

In forensic examination accurate estimation of post-mortem interval (PMI) is a challenging task, particularly in the advanced stages of decomposition. The existing methods (algor mortis, livor mortis, rigor mortis, putrefaction etc) used for estimating PMI rely on analyzing the physical, biochemical, and metabolic changes that occur in the corpse after death. While these methods have shown some level of effectiveness in estimating PMI during the early stages of decomposition, accurate estimation becomes increasingly challenging during the later stages of putrefaction when the body undergoes significant changes. Recently, microRNA (miRNA) profiling due to its relatively small size and stability has emerged as a promising tool in several areas of forensics. This study demonstrates the potential of miRNA for PMI estimation in advanced stages of death. In this study, miRNA-195, miRNA-206, and miRNA-378 were selected as target miRNAs and miRNA-1 as reference miRNA. Left ventricle tissue (5 g) of the heart from 20 forensic autopsies of traffic accident victims (18-32 years) were collected and processed. The samples were held at room temperature for eight different time intervals (12, 24, 48, 72, 96, 120, 168 and 196 h), and RNA was extracted from all the samples using Trizol-based RNA isolation protocol, followed by cDNA synthesis and amplification with commercially available specific miRNA probes in Real-Time PCR (RT-PCR), Ct was calculated. The result showed that miRNAs were associated with PMI. Over time, there were substantial changes in the Ct values of all three miRNAs, with significant reductions observed at 196 h compared to 12 h. miRNA-206 demonstrated significant changes at multiple time intervals, while miRNA-1 remained stable for up to 196 h and thus holds caas an endogenous marker. In conclusion, miRNA has the potential to serve as a valuable tool for estimating PMI, especially during the advanced stages of decomposition, when used in conjunction with established techniques. However, further validation of the study is required to obtain more accurate estimates of PMI.

Review of the current and potential use of biological and molecular methods for the estimation of the postmortem interval in animals and humans

We provide here an overview of the state of applied techniques in the estimation of the early period of the postmortem interval (PMI). The biological methods included consist of body cooling, CSF potassium, body cooling combined with CSF potassium, and tissue autolysis. For each method, we present its application in human and veterinary medicine and provide current methodology, strengths, and weaknesses, as well as target areas for improvement. We examine current and future molecular methods as they pertain to DNA and primarily to messenger RNA degradation for the estimation of the PMI, as well as the use of RNA in aging wounds, aging blood stains, and the identification of body fluids. Various types of RNA have different lengths, structures, and functions in cells. These differences in RNAs determine various intrinsic properties, such as their half-lives in cells, and, hence, their decay rate as well as their unique use for specific forensic tests. Future applications and refinements of RNA-based techniques provide opportunities for the use of molecular methods in the estimation of PMI and other general forensic applications.

MicroRNAs in Various Body Fluids and its importance in Forensic Medicine

MicroRNAs (miRNAs) are a class of noncoding RNAs which regulate gene expression. miRNAs have tissue-specific expression and are also present in various extracellular body fluids, including blood, tears, semen, vaginal fluid and urine. Additionally, expression of miRNAs in body fluids is linked to various pathological diseases, including cancer and neurodegenerative diseases. Examination of body fluids is important in forensic medicine as they serve as a valuable form of evidence. Due to its stability, miRNA offers an advantage for body fluid identification, which can be detected even after several months or from compromised samples. Identification of unique miRNA profiles for different body fluids enable the identification of these body fluid. Furthermore, miRNAs profiling can be used to estimate post-mortem interval. Various biochemical and molecular methods have been used for identification of miRNAs have shown promising results. We discuss different miRNAs as specific biomarkers and their clinical importance regarding different pathological conditions, as well as their medico-legal importance.

Dynamics of insects, microorganisms and muscle mRNA on pig carcasses and their significances in estimating PMI

The accurate estimate of the postmortem interval (PMI) is of vital significance in the investigation of homicide cases. In this study, three pig carcasses were placed in the field to study the pattern of insect succession, the change of microorganisms and the degradation of muscle tissue RNA during the decomposition process. The results showed that insects could quickly colonize the carcasses and still exist on them until the end of the experiment (41 days). Their development and succession patterns are useful indicators for PMI estimation. The diversity of rectal microorganisms decreased with the decomposition time. In different decomposition periods, significant differences in the rectal and soil microbial composition and relative abundance were found, which could be used to estimate the PMI with an accuracy of 3-4 days. The RNA of muscle tissue was found to have a time-dependent relationship with the PMI. Ppia and Gapdh showed a linear upward trend within 10 h after the death, followed by a gradual downward trend from 10 to 240 h. The expression of β-actin gene showed a gradual downward trend during 0-240 h. This is the first study in China to analyze the changes of insects, muscle RNA and microorganisms on pig carcasses in the same natural environment, which provide basic data for the PMI estimation.

Individualised and non-contact post-mortem interval determination of human bodies using visible and thermal 3D imaging

Determining the time since death, i.e., post-mortem interval (PMI), often plays a key role in forensic investigations. The current standard PMI-estimation method empirically correlates rectal temperatures and PMIs, frequently necessitating subjective correction factors. To overcome this, we previously developed a thermodynamic finite-difference (TFD) algorithm, providing a rigorous method to simulate post-mortem temperatures of bodies assuming a straight posture. However, in forensic practice, bodies are often found in non-straight postures, potentially limiting applicability of this algorithm in these cases. Here, we develop an individualised approach, enabling PMI reconstruction for bodies in arbitrary postures, by combining photogrammetry and TFD modelling. Utilising thermal photogrammetry, this approach also represents the first non-contact method for PMI reconstruction. The performed lab and crime scene validations reveal PMI reconstruction accuracies of 0.26 h ± 1.38 h for true PMIs between 2 h and 35 h and total procedural durations of ~15 min. Together, these findings broaden the potential applicability of TFD-based PMI reconstruction.

Establishing the time since death (TSD) is vital in many forensic investigations. By combining thermometry, photogrammetry and numerical thermodynamic modelling, the TSD can be determined non-invasively for bodies of arbitrary shape and posture with an unprecedented accuracy of 0.26 h ± 1.38 h.

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.

PP2A-C may be a promising candidate for postmortem interval estimation

Determining the postmortem interval (PMI) is an important task in forensic pathology. However, a reliable means of determining the PMI between 24 h and approximately 7 days after death has not yet been established. A previous study demonstrated that subunit A of protein phosphatase 2A (PP2A-A) is a promising candidate to estimate the PMI during the first 96 h. However, more detailed work is still needed to investigate PP2A's function in PMI estimation. PP2A is a serine/threonine phosphatase consisting of three subunits (PP2A-A, PP2A-B, and PP2A-C), and its activation is reflected by Tyr-307 phosphorylation of the catalytic subunit (P-PP2A-C). In this study, we speculated that the other two subunits of PP2A and the activation of PP2A may play different roles in estimating the PMI. For this purpose, mice were euthanized and stored at different temperatures (4, 15, and 25 °C). At each temperature, the musculus vastus lateralis was collected at different time points (0, 24, 48, and 96 h) to investigate the degradation of PP2A-B, PP2A-C, and P-PP2A-C (Tyr-307). Homocysteine (Hcy) was used to establish a hyperhomocysteinemia animal model to explore the effects of plasma Hcy on PMI estimation. The data showed not only that PP2A-C was more stable than PP2A-B, but also that it was not affected by homocysteine (Hcy). These characteristics make PP2A-C a promising candidate for short-term (24 h to 48 h) PMI estimation.

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.

MicroRNAs: An Update of Applications in Forensic Science

MicroRNAs (miRNAs) are a class of non-coding RNAs containing 18–24 nucleotides that are involved in the regulation of many biochemical mechanisms in the human body. The level of miRNAs in body fluids and tissues increases because of altered pathophysiological mechanisms, thus they are employed as biomarkers for various diseases and conditions. In recent years, miRNAs obtained a great interest in many fields of forensic medicine given their stability and specificity. Several specific miRNAs have been studied in body fluid identification, in wound vitality in time of death determination, in drowning, in the anti-doping field, and other forensic fields. However, the major problems are (1) lack of universal protocols for diagnostic expression testing and (2) low reproducibility of independent studies. This review is an update on the application of these molecular markers in forensic biology.

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.

Estimation of the post-mortem interval using microRNA in the bones

MicroRNAs (miRNAs) can be useful in forensic science because of their numerous characteristics, especially stability. Post-mortem interval (PMI) is crucial for death scene investigations. However, estimating PMI is challenging in cases involving significantly decomposed or destroyed bodies, such as those involving skeletonized remains. In this study, 71 bones (patella) were collected from the bodies during autopsies (PMI ranging from 1 day to 2 years). As the let-7e and miR-16 miRNAs were used as internal controls for the bone tissue in previous studies, these miRNAs were selected as targets to estimate PMI. The miRNA Ce_miR-39_1 was used as a spike-in internal control to normalize the target miRNA levels. Real-time quantitative reverse transcription polymerase chain reaction was performed to correlate the expression levels of let-7e and miR-16 with increasing PMI. A negative correlation was observed between miRNA expression and increasing PMI. The expression of both let-7e and miR-16 was observed to be significantly different between group A and the other PMI groups (group A < 1 month; 1 month < group B < 3 months; 3 months < group C < 6 months; group D > 6 months). In conclusion, these data suggest that the expression level of specific miRNAs (let-7e and miR-16) in the bone tissue could be used to estimate PMI. However, more studies using long-term PMI samples are required to further corroborate these findings.

Reconstructing the time since death using noninvasive thermometry and numerical analysis

The early postmortem interval (PMI), i.e., the time shortly after death, can aid in the temporal reconstruction of a suspected crime and therefore provides crucial information in forensic investigations. Currently, this information is often derived from an empirical model (Henssge's nomogram) describing posthumous body cooling under standard conditions. However, nonstandard conditions necessitate the use of subjective correction factors or preclude the use of Henssge's nomogram altogether. To address this, we developed a powerful method for early PMI reconstruction using skin thermometry in conjunction with a comprehensive thermodynamic finite-difference model, which we validated using deceased human bodies. PMIs reconstructed using this approach, on average, deviated no more than ±38 minutes from their corresponding true PMIs (which ranged from 5 to 50 hours), significantly improving on the ±3 to ±7 hours uncertainty of the gold standard. Together, these aspects render this approach a widely applicable, i.e., forensically relevant, method for thermometric early PMI reconstruction.

Postmortem interval determination using mRNA markers and DNA normalization

Postmortem interval (PMI) determination is an important part of criminal investigations, but it is still subject to uncertainty. Degradation of mRNA in PMI determination has been studied in decays; however, some studies have reported no correlation between PMI and RNA degradation. Thus, we aimed to determine whether RNA quantity was correlated with PMI. Heart and brain tissues were separated from a mouse model of a 0-48 h PMI with 29 time points. We then coextracted the DNA and RNA in one tube with Bioteke coextraction kits and selected some mRNA markers associated with cell oxygen deprivation and apoptosis as target genes, such as hypoxia-associated factor (HAF), apoptosis-inducing factor (AIF), hypoxia-inducible factor 2 alpha (HIF2a), and factor inhibiting HIF (FIH). We measured the quantity of these markers using real-time quantitative PCR (qPCR), and Caspase-3 DNA and 18S were each used for normalization. The results showed that in the heart tissue, the degradation of HIF2a, AIF, and FIH was correlated with PMI, as was the degradation of HIF2a, FIH, and AIF in brain tissue when normalized with Caspase-3 DNA. However, when normalized with 18S, only the degradation of HIF2a in brain tissue was correlated with PMI. Interestingly, the quantity of HAF in brain tissue was found to increase after death with either 18S or Caspase-3 DNA normalization, and it was significantly correlated with 0-48 h PMI. These results indicated that mRNA quantity can be used to determine PMI and that Caspase-3 DNA is feasible for PMI estimation. In summary, we established mathematical models for PMI determination using multiple mRNA markers and multiple tissues and further studies are needed to validate and investigate these markers and mathematical models in human tissues.Duo Peng and Meili Lv contributed equally to this work.

Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues

Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.

microRNA Detection in Blood, Urine, Semen, and Saliva Stains After Compromising Treatments

Evaluation of microRNA (miRNA) expression as a potential method for forensic body fluid identification has been the subject of investigation over the past several years. Because of their size and encapsulation within proteins and lipids, miRNAs are inherently less susceptible to degradation than other RNAs. In this work, blood, urine, semen, and saliva were exposed to environmental and chemical conditions mimicking sample compromise at the crime scene. For many treated samples, including 100% of blood samples, miRNAs remained detectable, comparable to the untreated control. Sample degradation varied by body fluid and treatment, with blood remarkably resistant, while semen and saliva are more susceptible to environmental insult. Body fluid identification using relative miRNA expression of blood and semen of the exposed samples was 100% and 94%, respectively. Given the overall robust results herein, the case is strengthened for the use of miRNAs as a molecular method for body fluid identification.

Early postmortem interval (EPMI) estimation using differentially expressed gene transcripts

Genes differentially expressed after death were selected to construct a mathematical model for early postmortem interval estimation. Sprague Dawley rats were sacrificed and placed at temperatures of 4 °C, 15 °C, 25 °C, and 35 °C. Brain tissues were collected at 0, 6, 12, 18, and 24 h after death and total RNA was extracted. Changes in gene transcript levels after death were detected using microarray expression profiling and differentially expressed genes was screened. Expanded experiments were performed to validate gene transcript levels at different temperatures using the reverse transcription real-time quantitative polymerase chain reaction. Six genes with high coefficients of determination were chosen for construction of mathematical models. Optimal ternary cubic equations were built using R software with temperature, postmortem interval and ΔCq defined as the independent variable x, y and z, respectively. Equations were converted into a three-dimensional visual statistical model using MATLAB. Animal samples were used to validate the mathematical models. Results showed that the 5srRNA showed best stability at four temperatures. The genes Ninj2, Grifin, Arpp19, and Hopx showed high coefficients of determination (>80%) and low error (<3h) in verification experiments which indicate that they are potential markers for early postmortem interval estimation.

Using miRNAs and circRNAs to estimate PMI in advanced stage

In our previous study, we evaluated the stability of multi-RNA markers in heart, liver and skeletal muscle tissues of mice within 8 days after death and concluded that microRNAs (miRNAs) and circular (circRNAs) were more stable as reference genes in dead bodies than other kinds of RNAs. Based on their tissue-specific expression, we obtained reference genes for three kinds of tissues: miR-122, miR-133a and 18S in heart tissues; LC-Ogdh, circ-AFF1 and miR-122 in liver tissues; and miR-133a, circ-AFF1 in skeletal muscle tissues. For the estimation of post mortem interval (PMI), we also selected suitable biomarkers, which exhibited the best correlation coefficient with PMI. In our stability analysis of multi-RNA markers, Gapdh, Rps18, U6 and β-actin were unstable and selected as candidate target biomarkers. By analyzing the correlation between the expression levels of candidate target biomarkers and PMI, we obtained suitable target biomarkers for the three kinds of tissues, respectively. Finally, we established mathematical models of PMI estimation using the above selected reference genes and target biomarkers. The low estimated error in the validated samples demonstrated that PMI in advanced stage could be accurately predicted by real-time quantitative polymerase chain reaction (qPCR) through systematically selected effective reference genes and target biomarkers. Besides, combining the estimated results of various tissues and multi-biomarkers could improve the accuracy of PMI estimation.

Bias in recent miRBase annotations potentially associated with RNA quality issues

Although microRNAs are supposed to be stable in-vivo, degradation processes potentially blur our knowledge on the small oligonucleotides. We set to quantify the effect of degradation on microRNAs in mouse to identify causes for distorted microRNAs patterns. In liver, we found 298, 99 and 8 microRNAs whose expression significantly correlated to RNA integrity, storage time at room temperature and storage time at 4 °C, respectively. Expression levels of 226 microRNAs significantly differed between liver samples with high RNA integrity compared to liver samples with low RNA integrity by more than two-fold. Especially the 157 microRNAs with increased expression in tissue samples with low RNA integrity were most recently added to miRBase. Testing potentially confounding sources, e.g. in-vitro degraded RNA depleted of small RNAs, we detected signals for 350 microRNAs, suggesting cross-hybridization of fragmented RNAs. Therefore, we conclude that especially microRNAs added in the latest miRBase versions might be artefacts due to RNA degradation. The results facilitate differentiation between degradation-resilient microRNAs, degradation-sensitive microRNAs, and likely erroneously annotated microRNAs. The latter were largely identified by NGS but not experimentally validated and can severely bias microRNA biomarker research and impact the value of microRNAs as diagnostic, prognostic or therapeutic tools.

Cell Death-Associated Ribosomal RNA Cleavage in Postmortem Tissues and Its Forensic Applications

Estimation of postmortem interval (PMI) is a key issue in the field of forensic pathology. With the availability of quantitative analysis of RNA levels in postmortem tissues, several studies have assessed the postmortem degradation of constitutively expressed RNA species to estimate PMI. However, conventional RNA quantification as well as biochemical and physiological changes employed thus far have limitations related to standardization or normalization. The present study focuses on an interesting feature of the subdomains of certain RNA species, in which they are site-specifically cleaved during apoptotic cell death. We found that the D8 divergent domain of ribosomal RNA (rRNA) bearing cell death-related cleavage sites was rapidly removed during postmortem RNA degradation. In contrast to the fragile domain, the 5' terminal region of 28S rRNA was remarkably stable during the postmortem period. Importantly, the differences in the degradation rates between the two domains in mammalian 28S rRNA were highly proportional to increasing PMI with a significant linear correlation observed in mice as well as human autopsy tissues. In conclusion, we demonstrate that comparison of the degradation rates between domains of a single RNA species provides quantitative information on postmortem degradation states, which can be applied for the estimation of PMI.

Estimation of the human postmortem interval using an established rat mathematical model and multi-RNA markers

In our previous study, a R code-based mathematical model using RNA degradation patterns was developed for PMI determination in rat brain specimens. However, the postmortem changes of RNA are much more complicated in real cases, and there is still a huge challenge in efficiently applying information in animal data to real cases. In the present study, different RNA markers in both rat and human tissues were collected to screen valid biomarkers and the corresponding mathematical models were established and validated. With the same methodology, multi-RNA markers of myocardium and liver tissues were detected by qPCR and the Ct values of ten biomarkers generally increased with prolonged PMIs. 5S, miR-1 and miR-133a were shown to be optimum reference biomarkers that were not affected by a PMI of up to 5 or more days; however, liver-specific miR-122 began to degrade under higher temperatures and only 5S was selected as an endogenous control in the liver. Among the tested target RNAs, similar to our previous study in brain tissue, β-actin (ΔCt) was found to exhibit the best correlation coefficient with PMI and was employed to build mathematical models using R software. Following validation, the relatively low estimated error demonstrated that PMIs can be accurately predicted in human cases through comprehensive consideration of various factors and using effective biomarkers.