Potential applications of microRNA profiling to forensic investigations

Forensic stability evaluation of selected miRNA and circRNA markers in human bloodstained samples exposed to different environmental conditions

Recently, RNA markers have been used to identify tissue origins of different kinds of body fluids. Herein, circRNA and miRNA markers were carried out to examine the presence or absence of peripheral blood (PB) in bloodstained samples exposed to different external environmental conditions, which mimicked PB samples left at the crime scenes. PB samples were placed on sterile swabs and then exposed to different high temperatures (37°C, 55°C and 95°C) and ultraviolet light irradiation for 0 d, 0.5 d, 1 d, 3 d, and 7 d, ultra-low and low temperatures (-80°C, -20°C, and 4°C) for 30 d, 180 d and 365 d and different kinds of disinfectants. Total RNA was extracted from bloodstained samples under the above different conditions, and the expressions of target RNAs (including miR16-5p, miR451a, circ0000095, and two reference genes RNU6b and 18 S rRNA) were detected by the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method. Results showed that these selected RNA markers could be successfully measured at all observation points with their unique degradation rates, which exhibited relative stability in degraded bloodstained samples exposed to different environmental conditions. This study provides insights into the applications of these studied miRNA and circRNA markers in forensic science.

Differentiation of five forensically relevant body fluids using a small set of microRNA markers

In forensic investigations, identifying the type of body fluid allows for the interpretation of biological evidence at the activity level. Over the past two decades, significant research efforts have focused on developing molecular methods for this purpose. MicroRNAs (miRNAs) hold great promise due to their tissue-specific expression, abundance, lack of splice variants, and relative stability. Although initial findings are promising, achieving consistent results across studies is still challenging, underscoring the necessity for both original and replication studies. To address this, we selected 18 miRNA candidates and tested them on 6 body fluids commonly encountered in forensic cases: peripheral blood, menstrual blood, saliva, semen, vaginal secretion, and skin. Using reverse transcription quantitative PCR analysis, we confirmed eight miRNA candidates (miR-144-3p, miR-451a, miR-205-5p, miR-214-3p, miR-888-5p, miR-891a-5p, miR-193b-3p, miR-1260b) with high tissue specificity and four (miR-203a-3p, miR-141-3p, miR-200b-3p, miR-4286) with lesser discrimination ability but still contributing to body fluid differentiation. Through principal component analysis and hierarchical clustering, the set of 12 miRNAs successfully distinguished all body fluids, including the challenging discrimination of blood from menstrual blood and saliva from vaginal secretion. In conclusion, our results provide additional data supporting the use of a small set of miRNAs for predicting common body fluids in forensic contexts. Large population data need to be gathered to develop a body fluid prediction model and assess its accuracy.

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.

Mass spectrometry-based proteomic analysis of biological stains identifies body fluids specific markers

The identification of biological stains and their tissue resource is an important part of forensic research. Current methods suffer from several limitations including poor sensitivity and specificity, trace samples, and sample destruction. In this study, we profiled the proteomes of menstrual blood, peripheral blood, saliva, semen, and vaginal fluid with mass spectrometry technology. Tissue-enhanced and tissue-specific proteins of each group have been proposed as potential biomarkers. These candidate proteins were further annotated and screened through the combination with the Human Protein Atlas database. Our data not only validates the protein biomarkers reported in previous studies but also identifies novel candidate biomarkers for human body fluids. These candidates lay the foundation for the development of rapid and specific forensic examination methods.

RNA quality score evaluation: A preliminary study of RNA integrity number (RIN) and RNA integrity and quality number (RNA IQ)

In the past several years, with the in-depth development of RNA-related research, exploring the application of transcriptome and corresponding RNA biomarkers has become one of the research hotspots in the field of forensic science. High-quality RNA is essential for successful downstream workflows, especially in the steps of screening biomarkers by microarray or RNA sequencing (RNA-seq). Thus, accurately evaluating the quality of RNA samples is a critical step in obtaining meaningful expression data. The RNA integrity number (RIN) generated from the Agilent Bioanalyzer system has been widely used for RNA quality control in the past two decades. Recently, Thermo Fisher Scientific launched a ratiometric fluorescence-based method to quickly check whether an RNA sample has degraded, and the results are presented as RNA integrity and quality number (RNA IQ). Both quality score systems determine RNA quality using a numerical system based on a scale of 1-10, with 1 denoting significantly degraded specimens and 10 representing high-quality, intact RNA samples. In this preliminary study, we evaluated the consistency, reproducibility and linearity of two quality scores in RNA quality determination by analyzing heat- and RNase- artificially degraded samples. Meanwhile, the expression levels of three microRNAs (hsa-let-7 g-5p, hsa-miR-93-5p and hsa-miR-191-5p) in intact and severely degraded RNA samples were estimated by TaqMan-qPCR and droplet digital PCR. Overall, both quality scores showed good repeatability and reproducibility in their respective tests. In the samples subjected to thermal degradation, RIN showed a trend corresponding to heating time, while RNA IQ value showed almost no change on the time gradient. However, in RNase A mediated degradation, RNA IQ value observed better linearity. Furthermore, the expression levels of three microRNAs in the severely degraded samples did not show significant changes compared to the intact RNA samples. RNA degradation is a very complex and highly variable process, which is difficult to comprehensively evaluate through any one index and cannot directly compare these two parameters. Nevertheless, combined with previous research results and the expression levels of three microRNAs in this study, analyzing RNA biomarkers with stable regions or small sizes in challenged samples may be a conservative and reliable approach.

Special Issue "Molecular Biology in Forensic Science: Past, Present and Future"

Molecular biology has always represented an enviable tool in the fields of biosciences, diagnostics, and forensic sciences [...].

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.

Forensic validation of a combined analysis of mRNA and miRNA markers for precise tissue origin inferences of five kinds of body fluids by RT-qPCR

Correctly inferring the tissue origin types of forensic-relevant body fluids left at a crime scene is beneficial for reconstructing a crime scene. However, it is still a challenge to accurately identify different kinds of body fluids at a crime scene. Shorter sequence length and anti-degradation microRNA (miRNA) can be used to infer the tissue sources of biological fluid traces, but a limited number of miRNAs are tissue specific. The application of messenger RNA (mRNA) has been confirmed by different studies based on its high tissue specificity. According to the differential expression features of mRNA or miRNA in forensically relevant body fluids, this study developed a simultaneously reversed mRNA and miRNA system and then used these two types of RNAs for the determinations of five common kinds of body fluids. Compared with previously reported single kind of mRNA or miRNA assay, the combined mRNA and miRNA system showed good advantages for human body fluid identifications, especially it could be applied in mixed samples. In conclusion, the obtained results indicated that this combined mRNA and miRNA system might provide a scientific and accurate reference for body fluid identifications.

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.

An Overview on the Use of miRNAs as Possible Forensic Biomarkers for the Diagnosis of Traumatic Brain Injury

Determining the cause of death is one of the main goals of forensic pathology. However, conditions can occur in which common approaches—external inspection, autopsy, histology, etc.—might not be conclusive. With the advancement of molecular biology, several investigative techniques have been developed over the years, and the application as approaches complementary to routine procedures has proved useful in these cases. In this context, microRNA (miRNA) profiling has attracted increasing interest due to these molecules’ ability to regulate physiological and pathological processes. The evidence of differential miRNA expression in both animal models and human samples of traumatic brain injury (TBI) has laid the basis for comprehension of the underlying pathophysiological mechanisms, thus allowing us to identify some of them as possible TBI diagnostic biomarkers. The present narrative review aims to explore the primary miRNAs involved in the mechanisms underlying TBI, which could be considered for future evaluation as possible markers in a post mortem setting.

Screening and evaluation of endogenous reference genes for miRNA expression analysis in forensic body fluid samples

MicroRNA (miRNA)-based methods for body fluid identification are promising tools in the practice of forensic science. The selection of appropriate endogenous reference genes as normalizers for the relative quantification of miRNA expression levels using quantitative reverse transcription-polymerase chain reaction (RTqPCR) is essential to avoid errors and improve the comparability of miRNA expression level data among different body fluids. In this study, small RNAs were isolated from individual donations of five forensically relevant body fluids (peripheral blood, menstrual blood, saliva, semen and vaginal secretions). Thirty-seven samples were subjected to high-throughput miRNA sequencing. By combining our results with those obtained through a literature investigation, 28 candidate RNAs were identified. Following RTqPCR validation, the candidate RNAs were preliminarily evaluated in 15 samples to exclude miRNAs with low expression and high variation. Then, the expression levels of 10 relatively stable candidate reference RNAs in 100 samples were determined and further analysed using four commonly employed programs (geNorm, NormFinder, BestKeeper and ΔCq). According to the comprehensive stability rankings of the four algorithms, miR-320a-3p was validated as the most stable endogenous reference gene among the five forensically relevant body fluids, followed by miR-484, SNORD43, miR-320c and RNU6b. Moreover, the combined application of miR-320a-3p with RNU6b could increase the normalization effect. In addition, a total of 56 mock samples placed outdoors and indoors for different times were prepared to further evaluate the stability of candidate reference RNAs, and miR-320a-3p remained the preferred reference gene. Furthermore, the relative expression levels of publicly accepted body fluid-specific miRNAs were determined in 30 samples to verify the practicality and effectiveness of the reference genes. Our results revealed a set of alternative reference genes and could promote the development and application of miRNA-based body fluid identification by determining optional reference genes for strict normalization.

Postmortem Genetic Testing in Sudden Unexpected Death: A Narrative Review

Sudden unexpected death (SUD) is one of the challenging situations encountered in forensic medicine. As a rule, a comprehensive forensic assessment is performed to identify the cause of death in such cases; however, the absence of findings suggestive of a cause, i.e., a negative autopsy, warrants further investigation such as a molecular autopsy. In this review, we aim to highlight the genetic causes of SUD, tools used in a molecular autopsy, and the role of screening in surviving relatives. As per several guidelines, the most preferred samples for DNA extraction are whole blood and fresh frozen tissues. Furthermore, Sanger sequencing and next-generation sequencing are the technologies that are used for genetic analysis; the latter overcomes the former's drawbacks in terms of cost-effectiveness, time consumption, and the ability to sequence the whole exome. SUD have diverse etiologies; we can generally classify them into cardiac and non-cardiac causes. Regarding cardiac causes, many conditions having an underlying genetic basis are included, such as channelopathies and cardiomyopathies. Regarding non-cardiac causes of SUD, the main etiologies are epilepsy and metabolic disorders. Nevertheless, it has been proposed that there is a genetic overlap between channelopathies, especially long QT syndromes and epilepsy. Additionally, fatty acid oxidation disorders are major metabolic conditions that are caused by certain genetic mutations that can lead to SUD in infancy. Since many SUD causes have an underlying genetic mutation, it is important to understand the genetic variations not only to recognize the cause of death but also to undertake further preventive measures for surviving relatives. In conclusion, a molecular autopsy has a major role in the forensic examination of cases of SUD.

Forensic age estimation from human blood using age-related microRNAs and circular RNAs markers

Aging is a complicated process characterized by progressive and extensive changes in physiological homeostasis at the organismal, tissue, and cellular levels. In modern society, age estimation is essential in a large variety of legal rights and duties. Accumulating evidence suggests roles for microRNAs (miRNAs) and circular RNAs (circRNAs) in regulating numerous processes during aging. Here, we performed circRNA sequencing in two age groups and analyzed microarray data of 171 healthy subjects (17-104 years old) downloaded from Gene Expression Omnibus (GEO) and ArrayExpress databases with integrated bioinformatics methods. A total of 1,403 circular RNAs were differentially expressed between young and old groups, and 141 circular RNAs were expressed exclusively in elderly samples while 10 circular RNAs were expressed only in young subjects. Based on their expression pattern in these two groups, the circular RNAs were categorized into three classes: age-related expression between young and old, age-limited expression-young only, and age-limited expression-old only. Top five expressed circular RNAs among three classes and a total of 18 differentially expressed microRNAs screened from online databases were selected to validate using RT-qPCR tests. An independent set of 200 blood samples (20-80 years old) was used to develop age prediction models based on 15 age-related noncoding RNAs (11 microRNAs and 4 circular RNAs). Different machine learning algorithms for age prediction were applied, including regression tree, bagging, support vector regression (SVR), random forest regression (RFR), and XGBoost. Among them, random forest regression model performed best in both training set (mean absolute error = 3.68 years, r = 0.96) and testing set (MAE = 6.840 years, r = 0.77). Models using one single type of predictors, circular RNAs-only or microRNAs-only, result in bigger errors. Smaller prediction errors were shown in males than females when constructing models according to different-sex separately. Putative microRNA targets (430 genes) were enriched in the cellular senescence pathway and cell homeostasis and cell differentiation regulation, indirectly indicating that the microRNAs screened in our study were correlated with development and aging. This study demonstrates that the noncoding RNA aging clock has potential in predicting chronological age and will be an available biological marker in routine forensic investigation to predict the age of biological samples.

Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases

Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.

Tanshinone IIA improves diabetes‐induced renal fibrosis by regulating the miR ‐34‐5p/Notch1 axis

The purpose of this study was to evaluate the improvement of tanshinone in renal fibrosis in vitro and in vivo study. It used streptozotocin to model diabetic nephropathy (DN) mice, and treated with different Tanshinone IIA concentrations. The pathology of kidney tissues was evaluated by hematoxylin and eosin (H&E) and Masson's staining; the ultrastructure and apoptosis cell number of kidney tissues were evaluated by transmission electron microscopy (TEM) and TUNEL assay. Relative gene and protein expression was evaluated by reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR), immunohistochemical (IHC) analysis, or western blot (WB) assay. In vitro study, using high‐glucose stimulated HK‐2 cell to model DN cell model, measuring cell proliferation, apoptosis rate, relative gene and protein expression, and LC 3B and P62 proteins expression by Cell Counting Kit‐8 (CCK‐8), flow cytometry, RT‐qPCR, WB, and cell immunofluorescence. Analysis correlation between Notch1 and miRNA‐34a‐5p was carried out by dual‐luciferase reporter. Fibrosis area and apoptosis cell rate were significantly up‐regulated (p < .001), with Tanshinone IIA supplement. The fibrosis area and apoptosis cell rate were also significantly improved in a dose‐dependent manner (p < .05). With si‐miRNA‐34a‐5p transfection, the Tanshinone IIA's treatment effects were significantly depressed. By dual‐luciferase reporter, miRNA‐34a‐5p could target Notch1 in the HK‐2 cell line. Tanshinone IIA improved DN‐induced renal fibrosis by regulating miRNA‐34a‐5p in vitro and in vivo study.

A new strategy for distinguishing menstrual blood from peripheral blood by the miR-451a/miR-21-5p ratio

Distinction between menstrual blood and peripheral blood is vital for forensic casework, as it could provide strong evidence to figure out the nature of some criminal cases. However, to date no single blood-specific gene, including the most variable microRNAs (miRNAs) could work well in identification of blood source. In this study, we developed a new strategy for identification of human blood samples by using the copy number ratios of miR-451a to miR-21-5p based on 133 samples, including 56 menstrual blood and 47 peripheral blood, as well as 30 non-blood samples of saliva (10), semen (10) and vaginal secretion (10). The cut-off value and efficacy of the identification strategy were determined through receiver operating characteristic (ROC) analysis. Our results showed that when the miR-451a/miR-21-5p ratio below 0.929, the sample should be non-blood. In contrast, when the miR-451a/miR-21-5p ratio above 0.929 and below 10.201, the sample should be menstrual blood; and when this ratio above 10.201, the sample should be peripheral blood. External validation using 86 samples (62 menstrual blood and 24 peripheral blood samples) fully supported this strategy with the 100% sensitivity and 100% specificity. We confirmed that this result accuracy was not affected by various potential confounding factors of samples and different experimental platforms. We showed that 0.2 ng of total RNA from menstrual blood and peripheral blood was sufficient for qPCR quantification. In conclusion, our results provide an accurate reference to distinguish menstrual blood from peripheral blood for forensic authentication.

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.

Developments in forensic DNA analysis

The analysis of DNA from biological evidence recovered in the course of criminal investigations can provide very powerful evidence when a recovered profile matches one found on a DNA database or generated from a suspect. However, when no profile match is found, when the amount of DNA in a sample is too low, or the DNA too degraded to be analysed, traditional STR profiling may be of limited value. The rapidly expanding field of forensic genetics has introduced various novel methodologies that enable the analysis of challenging forensic samples, and that can generate intelligence about the donor of a biological sample. This article reviews some of the most important recent advances in the field, including the application of massively parallel sequencing to the analysis of STRs and other marker types, advancements in DNA mixture interpretation, particularly the use of probabilistic genotyping methods, the profiling of different RNA types for the identification of body fluids, the interrogation of SNP markers for predicting forensically relevant phenotypes, epigenetics and the analysis of DNA methylation to determine tissue type and estimate age, and the emerging field of forensic genetic genealogy. A key challenge will be for researchers to consider carefully how these innovations can be implemented into forensic practice to ensure their potential benefits are maximised.

mRNA and microRNA stability validation of blood samples under different environmental conditions

RNA molecules, including mRNAs and microRNAs (miRNAs), have been used for forensic body fluid identification. Specific body fluids present unique mRNA expression patterns, while miRNAs identifying body fluids are mainly differentially expressed. miRNAs are thought to be more stable than mRNAs, although this lacks adequate supporting data. In this study, we addressed perceived concerns regarding the stability of miRNAs and mRNAs in blood samples. The samples used in this study involved three groups. First, environmentally-degraded blood stain samples were exposed to a range of environmental conditions over 1-360 days to degrade naturally. Second, simulated-degraded samples were prepared using RNase A or high temperature (80 °C). Furthermore, two authentic casework samples that were proven to be degraded from short tandem repeat (STR) profiles were analyzed. mRNAs and miRNAs present in the same blood samples were simultaneously detected through reverse transcriptase qPCR (RT-qPCR). Furthermore, mRNAs expression was determined by an mRNA multiplex PCR system. Our results showed that both mRNAs and miRNAs were stable in dry environments. The stability of miRNAs was relatively higher than that of mRNAs in humid environments or at high temperature. RNase A had the most serious impact on RNA stability, both mRNA profiles and miRNAs expression patterns were altered. The results of this study provide data and support to demonstrate that miRNAs represent more stable RNA molecules in body fluid identification compared to mRNAs.

Forensic transcriptome analysis using massively parallel sequencing

The application of transcriptome analyses in forensic genetics has experienced tremendous growth and development in the past decade. The earliest studies and main applications were body fluid and tissue identification, using targeted RNA transcripts and a reverse transcription endpoint PCR method. A number of markers have been identified for the forensically most relevant body fluids and tissues and the method has been successfully used in casework. The introduction of Massively Parallel Sequencing (MPS) opened up new perspectives and opportunities to advance the field. Contrary to genomic DNA where two copies of an autosomal DNA segment are present in a cell, abundant RNA species are expressed in high copy numbers. Even whole transcriptome sequencing (RNA-Seq) of forensically relevant body fluids and of postmortem material was shown to be possible. This review gives an overview on forensic transcriptome analyses and applications. The methods cover whole transcriptome as well as targeted MPS approaches. High resolution forensic transcriptome analyses using MPS are being applied to body fluid/ tissue identification, determination of the age of stains and the age of the donor, the estimation of the post-mortem interval and to post mortem death investigations.

Difference in microRNA levels in the post-mortem blood from different sampling sites: A proof of concept

MicroRNAs have various characteristics, including stability, and tissue and disease specificity. One of the important issues in forensics is that biomarkers can differ quantitatively depending on the sampling site. We aimed at evaluating the differences in microRNA levels in the post-mortem (PM) blood from different sampling sites. The study subjects comprised seventeen males and eleven females. The number of cardiac deaths (CD) and non-cardiac deaths (NCD) was eleven and seventeen, respectively. A cardiopulmonary resuscitation (CPR) was performed in fifteen cases. Venous blood was obtained from the external iliac vein for peripheral blood (PB), inferior vena cava for pre-cardiac blood (CB), and coronary sinus for post-cardiac blood (coronary sinus blood, CSB). The selected target microRNAs were cardiac-specific (miR208 and miR-1) and non-cardiac microRNAs (miR-16 and let-7e). The levels of miR-208b and miR-1 in the PM blood differed according to its sampling site and showed an increasing order of tendency in the PB, CB, and CSB. However, these variations according to sampling sites did not correlate with the post-mortem interval and the levels did not differ between the CD and NCD groups, and between the CPR and non-CPR groups. MiR-16 and let-7e levels did not vary according to the sampling site. The present study confirms that the cardiac-specific microRNA levels in the PM blood from different sampling sites are different. In addition, this study showed that the characteristics of target microRNAs, such as tissue-specificity, should be considered and the sampling site for microRNAs should be presented in forensic applications.

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.

Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene

DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue-specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 years, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by a) the presence of canid / Caniformia-specific sequences that never evolved outside of this clade, b) tissue-specific expression patterns (cartilage, liver and muscle) that resemble those of modern dogs and c) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing. .