A 17-month time course study of human RNA and DNA degradation in body fluids under dry and humid environmental conditions

Identification of individuals from low template blood samples using whole transcriptome shotgun sequencing

Biological trace samples consisting of very few cells pose a challenge to conventional forensic genetic DNA analysis. RNA may be an alternative to DNA when handling low template samples. Whereas each cell only contains two copies of an autosomal DNA segment, the transcriptome retains much of the genomic variation replicated in abundant RNA fragments. In this study, we describe the development of a prototype RNA-based SNP selection set for forensic human identification from low template samples (50 pg gDNA). Whole blood from a subset of the Danish population (41 individuals) and blood stains subjected to degradation at room temperature for up to two weeks were analysed by whole transcriptome shotgun sequencing. Concordance was determined by DNA genotyping with the Infinium Omni5-4 SNP chip. In the 100 protein-coding genes with the most reads, 5214 bi-allelic SNPs with gnomAD minor allele frequencies > 0.1 in the African/African American, East Asian, and (non-Finnish) European populations were identified. Of these, 24 SNPs in 21 genes passed screening in whole blood and degraded blood stains, with a resulting mean match probability of 4.5 ∙ 10-9. Additionally, ancestry informative SNPs and SNPs in genes useful for body fluid identification were identified in the transcriptome. Consequently, shotgun sequencing of RNA from low template samples may be used for a vast host of forensic genetics purposes, including simultaneous human and body fluid identification, leading to direct donor identification in the identified body fluid.

DNA degradation of bloodstains on cotton fabric caused by different washing procedures

DNA degradation in biological material needs to be better understood. Bloodstains on washed clothing are disturbed by washing procedures, sometimes transferred to other fabrics, often with latent bloodstains and usually with significantly degraded DNA. The samples (cotton fabric with bloodstains) are divided into six main groups, depending on the washing method regarding water temperature (95, 60, and 30 °C) and the detergent use. After completing the washing process, samples were stored for a certain period (1 day to 6 months) and subsequently analyzed. Analyses were performed using standard protocols and commercial kits to measure the remaining DNA quantity (concentration) and DNA degradation index in the processed samples. Our results revealed that the high washing temperature (60 and 95 °C) and the application of detergent have a synergic action on DNA degradation, while at 30 °C this effect is absent. Furthermore, the effect of detergent on accelerated DNA degradation is observed about a month after the washing. This delayed effect of detergent has no explanation in current literature data. To obtain optimal results from the bloodstains, we recommended that the period from the crime event and attempted cleaning by a perpetrator to the laboratory analysis should be less than 1 month.

One-tube, two-step isothermal amplification of histatin 3 mRNA for saliva screening

Saliva samples are frequently collected at crime scenes. Salivary mRNA profiling, such as that of histatin 3 (HTN3), is a highly specific approach that overcomes the limitation of traditional amylase tests. However, typical mRNA detection methods based on reverse transcription PCR (RT-PCR) are time-consuming and labor-intensive. Here, we report a one-tube, two-step isothermal amplification assay for HTN3 mRNA, which enables rapid, simple, and sensitive screening of saliva. The first step is an RT-recombinase polymerase amplification (RT-RPA) assay at 42 °C for 20 min; the second step is a loop-mediated isothermal amplification (LAMP) assay at 65 °C for 30 min. The reactions can be performed in a closed tube, and the products are detected using real-time fluorescence analysis. The assay sensitivity was 0.5 µL of saliva samples. It also detected HTN3 mRNA in mixed and mock samples, demonstrating its applicability to actual forensic samples. These findings suggest that our strategy is promising for screening of saliva from forensic samples.

TrACES of time: Transcriptomic analyses for the contextualization of evidential stains - Identification of RNA markers for estimating time-of-day of bloodstain deposition

Obtaining forensically relevant information beyond who deposited a biological stain on how and under which circumstances it was deposited is a question of increasing importance in forensic molecular biology. In the past few years, several studies have been produced on the potential of gene expression analysis to deliver relevant contextualizing information, e.g. on nature and condition of a stain as well as aspects of stain deposition timing. However, previous attempts to predict the time-of-day of sample deposition were all based on and thus limited by previously described diurnal oscillators. Herein, we newly approached this goal by applying current sequencing technologies and statistical methods to identify novel candidate markers for forensic time-of-day predictions from whole transcriptome analyses. To this purpose, we collected whole blood samples from ten individuals at eight different time points throughout the day, performed whole transcriptome sequencing and applied biostatistical algorithms to identify 81 mRNA markers with significantly differential expression as candidates to predict the time of day. In addition, we performed qPCR analysis to assess the characteristics of a subset of 13 candidate predictors in dried and aged blood stains. While we demonstrated the general possibility of using the selected candidate markers to predict time-of-day of sample deposition, we also observed notable variation between different donors and storage conditions, highlighting the relevance of employing accurate quantification methods in combination with robust normalization procedures.This study's results are foundational and may be built upon when developing a targeted assay for time-of-day predictions from forensic blood samples in the future.

Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics

The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.

An mRNA Profiling Study of Vaginal Swabs from Pre- and Postmenopausal Women

Body fluid identification by means of mRNA profiling provides valuable supplementary information in forensic investigations. In particular, the detection of vaginal mucosa mRNA markers is highly relevant in sexual assault cases. Although the vagina undergoes characteristic age-related physiological changes over a lifetime, few studies have evaluated the efficacy of vaginal mRNA markers in women of different ages. In this multicentric study, a 19-plex mRNA profiling assay including vaginal-specific markers (CYP2B7P1, MUC4, MYOZ1) was tested in a collection of 6-20-month-old vaginal swabs obtained from pre- (n = 84) and postmenopausal (n = 55) female volunteer donors. Overall, participating laboratories were able to correctly identify ~85% of samples as vaginal mucosa by mRNA profiling. The assay's success rate did not differ between the two age groups and was not affected by the time interval between swab collection and RNA analysis. MYOZ1 resulted a less sensitive vaginal marker compared to MUC4 and CYP2B7P1. A significant relative increase in the contribution to the total amplification signal was observed for MUC4, compared to CYP2B7P1 and MYOZ1, in postmenopausal women. Observation of other body fluids and tissues different from vaginal mucosa was also evaluated in connection to information on previous sexual activity and menstrual cycle phase at the time of sampling.

Validation of a novel fluorescent probe-based real-time PCR assay to detect saliva-specific unmethylated CpG sites for saliva identification

The identification of saliva from forensic samples is often important to establish what happened at a crime scene, especially in sexual assault cases. Recently, CpG sites that are specifically methylated or unmethylated in saliva have been reported as markers for saliva identification. In this study, we designed a fluorescent probe-based real-time polymerase chain reaction (PCR) assay for analyzing the methylation status of two neighboring CpG sites, which we previously found were saliva-specifically unmethylated. Specificity analysis using various types of body fluid/tissue samples demonstrated a probe detecting the unmethylation of the two CpG sites reacted only to saliva DNA, indicating this probe as an all-or-nothing marker for the presence of saliva DNA. Sensitivity analysis demonstrated that the detection limit was 0.5 ng saliva DNA as input for bisulfite conversion, while we confirmed a negative effect of larger amounts of non-saliva DNA on sensitivity in the analysis of saliva-vaginal DNA mixtures. We finally validated the applicability of this test to swabs from licked skin and bottles after drinking as mock forensic samples in comparison with other saliva-specific markers. We confirmed the potential usefulness of this test for skin samples, from which a saliva-specific mRNA was not detected reliably, while the ingredients in several beverages might affect methylation analysis. Given the simplicity of real-time PCR as well as the high specificity and sensitivity of the test, we believe the developed method is suitable for routine forensic analysis and can play an important role in saliva identification.

Sperm mRNA screening by reverse transcription-recombinase polymerase amplification (RT-RPA) assay: Decision-making for differential extraction

The presence of sperm cells is an indicator for differential extraction on sexual assault samples. In general, sperm cells are identified by microscopic analysis; however, this conventional method takes time and effort, even for trained personnel. Here, we present a reverse transcription-recombinase polymerase amplification (RT-RPA) assay targeting sperm mRNA marker (PRM1). The RT-RPA assay requires only 40 min for PRM1 detection and demonstrates a sensitivity of 0.1 μL of semen. Our results indicate that the RT-RPA assay may be a rapid, simple, and specific strategy for screening sperm cells in sexual assault samples.

Substantial decrease in SARS-CoV-2 RNA after fixation of cadavers intended for anatomical dissection

With the onset of the COVID-19 pandemic, a problem arose with classic body donation programmes for obtaining cadavers for anatomical dissections, science and research. The question has emerged whether bodies of individuals who died of COVID-19 or were infected by SARS-CoV-2 could be admitted to Departments of Anatomy. To determine the risk of SARS-CoV-2 transmission to employees or students, the presence and stability of SARS-CoV-2 RNA in cadavers after fixation agents' application and subsequent post-fixation baths over time were examined. The presence of viral RNA in swabs from selected tissues was assessed by the standardized routine RNA isolation protocol and subsequent real-time PCR analysis. To support the results obtained from the tissue swabs, samples of RNA were exposed in vitro to short and long-term exposure to the components of the injection and fixation solutions used for the bodies' conservation. Substantial removal of SARS-CoV-2 RNA was observed in post-mortem tissue following perfusion with 3.5% phenol, 2.2% formaldehyde, 11.8% glycerol and 55% ethanol, and subsequent post-fixation in an ethanol bath. In vitro experiments showed significant effects of formaldehyde on SARS-CoV-2 RNA, while phenol and ethanol showed only negligible effects. We conclude that cadavers subjected to fixation protocols as described here should not pose a considerable risk of SARS-CoV-2 infection while being handled by students and staff and are, therefore, suitable for routine anatomical dissections and teaching.

Improved reverse transcription-recombinase polymerase amplification assay for blood mRNA screening: comparison with one-step RT-qPCR assay

mRNA profiling is effective for body fluid identification because of its sensitivity, specificity, and multiplexing capability. Body fluid mRNA markers can typically be detected using RT-qPCR, RT-PCR followed by capillary electrophoresis, or targeted RNA sequencing. However, due to the multiple handling steps involved, the analysis of many forensic samples using these methods requires time and effort. Here, we describe a rapid and simple method for detecting the blood mRNA marker hemoglobin β (HBB), intended for use in screening before definitive blood identification. We employed a reverse transcription-recombinase polymerase amplification (RT-RPA) assay that can detect target mRNA within 20 min in a single tube. For comparison, we used a one-step RT-qPCR assay. We optimized the RT-RPA assay and found that it could detect HBB from 10^-3-10^-4 ng of leukocyte RNA and approximately 10^-3 µL of blood. The sensitivity was 10-fold lower than that of the one-step RT-qPCR assay but higher than that of the comprehensive analysis methods for definitive blood identification. Thus, the rapidity and sensitivity of the RT-RPA assay support its use as a screening tool. We also found that the RT-RPA assay was highly tolerant to common inhibitors such as humic acid, hematin, tannic acid, and melanin. Considering the inhibitor tolerability, we integrated a simple lysis method (addition of TCEP/EDTA and heating at 95 °C for 5 min) without the RNA purification process into the RT-RPA assay. This direct assay successfully detected HBB in crude blood samples. Our findings suggest that the RT-RPA assay for HBB is a promising strategy for mRNA-based blood screening.

Detecting STR profiles from degrading menstrual blood samples and their use as possible evidence in forensic investigations

This research explores DNA consistency and attempts to detect STR profiles from the degrading menstrual blood samples (MBS) as reliable forensic evidence. Peripheral (PBS) and MBS of 30 healthy fertile females were taken on the menstrual cycle's second day. They were obtained at different time periods (0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 24, and 48 h) at 25 °C. DNA evaluation was fulfilled to analyze DNA profiles. A considerable elevation in the median concentrations of DNA between 0 and 14-h intervals were documented, whereas decreased extents were registered between 16 and 48 h. Moreover, complete STR profiles (24/24) for DNA were discovered in all the intervals (0, 2, and 48 h). Periods of 0-8 h demonstrated the maximum extents of DNA materials. Full STR were discovered in all the intervals (0, 2, and 48 h). Eventually, MBS can be utilized as forensic evidence.

Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures

The evidentiary value of DNA profiles varies depending upon the context in which the DNA was found. Linking a DNA profile to a particular cellular phenotype in mixtures may aid in assessing its evidentiary relevance and value. We report the development of two dual-function high-resolution messenger RNA (mRNA) sequencing assays that can each identify the presence of 6 body fluids/tissues (blood, semen, saliva, vaginal secretions, menstrual blood, skin) and, via coding region SNPs (cSNPs) present in the body fluid-specific mRNA transcripts, directly associate particular body fluids with their specific DNA donors in mixtures. The original blood, semen, and saliva (BSS) assay contains 23 cSNPs for blood, semen, and saliva, while the expanded 6F (all 6 fluids/tissues) assay encompasses the BSS assay and also contains 23 additional cSNPs for vaginal secretions, menstrual blood, and skin. Software tools were developed to infer the identity of the body fluids present as well as providing the corresponding cSNP genotypes. Concomitant genomic DNA assays (BSS-d and 6F-d), required to genotype the same cSNPs from persons of interest/inferred contributors to the body fluid mixture, were also developed. Body fluid specificity was demonstrated by the ability to identify the body fluid origin of single-source and two-fluid admixtures. The discriminatory power (European Caucasians) for all body fluids is 0.957-0.997, with linkage disequilibrium considered. Reciprocal body fluid admixtures (mixture pairs with the same two donors but reversed body fluid types) were used to demonstrate the ability to identify the body fluid source of origin as well as associate the donor of each of the two fluids.

Estimating the time since deposition (TsD) in saliva stains using temporal changes in microbial markers

Determining the time since deposition (TsD) of traces could be helpful in the investigation of criminal offenses. However, there are no reliable markers and models available for the inference of short-term TsD. The goal of this study was to investigate the potential of the succession pattern of human salivary microbial communities to serve as an efficiency TsD prediction tool in the resolution of the forensic cases. Saliva stains exposed to indoor conditions up to 20 days were collected and analyzed by 16S rRNA profiling using high-throughput sequencing technique. Noticeable differences in microbial composition were observed between different time points, and the indoor exposure time of saliva stains were inversely correlated with alpha diversity estimates across the measured time period. The sequencing results were used to identify TsD-dependent bacterial indicators to regress a generalized random forest model, resulting in a mean absolute deviation (MAD) of 1.41 days. Furthermore, a simplified TsD predictive model was also developed utilizing Enhydrobacter, Paenisporosarcina, and Janthinobacterium by quantitative PCR (qPCR) with a MAD of 1.32 days, and then forensic practice assessment were also performed by using mock samples with a MAD of 3.53 days. In conclusion, this study revealed significant changes in salivary microbial abundance as the prolongation of TsD. It demonstrated that the microbial biomarkers could be invoked as a "clock" for TsD estimation in human dried saliva stains.

Using total RNA quality metrics for time since deposition estimates in degrading bloodstains

The physicochemical changes occurring in biomolecules in degrading bloodstains can be used to approximate the time since deposition (TSD) of bloodstains. This would provide forensic scientists with critical information regarding the timeline of the events involving bloodshed. Our study aims to quantify the timewise degradation trends and temperature dependence found in total RNA from bloodstains without the use of amplification, expanding the scope of the RNA TSD research which has traditionally targeted mRNA and miRNA. Bovine blood with ACD-A anticoagulant was deposited and stored in plastic microcentrifuge tubes at 21 or 4°C and tested over different timepoints spanning 1 week. Total RNA was extracted from each sample and analyzed using automated high sensitivity gel electrophoresis. Nine RNA metrics were visually assessed and quantified using linear and mixed models. The RNA Integrity Number equivalent (RINe) and DV200 were not influenced by the addition of anticoagulant and demonstrated strong negative trends over time. The RINe model fit was high (R²  = 0.60), and while including the biological replicate as a random effect increased the fit for all RNA metrics, no significant differences were found between biological replicates stored at the same temperature for the RINe and DV200. This suggests that these standardized metrics can be directly compared between scenarios and individuals, with DV200 having an inflection point at approximately 28 h. This study provides a novel approach for blood TSD research, revealing metrics that are not affected by inter-individual variation, and improving our understanding of the rapid RNA degradation occurring in bloodstains.

Evaluation of the Effects of Different Sample Collection Strategies on DNA/RNA Co-Analysis of Forensic Stains

The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater^®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). Analyses were conducted on whole blood, luminol-treated diluted blood, saliva, semen, and mock skin stains. The effects of swab storage temperature and the time interval between sample collection and DNA/RNA extraction were also investigated. Water provided significantly higher DNA yields than ethanol in whole blood and semen samples, while ethanol and RNAlater^® significantly outperformed water in skin samples, with full STR profiles obtained from over 98% of the skin samples collected with either ethanol or RNAlater^®, compared to 71% of those collected with water. A significant difference in mRNA profiling success rates was observed in whole blood samples between swabs treated with either ethanol or RNAlater^® (100%) and water (37.5%). Longer swab storage times before processing significantly affected mRNA profiling in saliva stains, with the success rate decreasing from 91.7% after 1 day of storage to 25% after 7 days. These results may contribute to the future development of optimal procedures for the collection of different types of biological traces.

Schwere sexualisierte Gewalt – Aufklärung eines Falls durch Kombination aus DNA- und mRNA-Analyse

Mithilfe der Analyse von mRNA-Expressionsmustern durch Einsatz der PCR-Amplifikation von zellspezifischen cDNA-Transkripten und Nachweis der Amplifikate mittels Kapillarelektrophorese (CE) lässt sich die Frage klären, aus welchen Zelltypen (Blut, Speichel, Sperma, Vaginalschleimhaut, Menstrual- und Nasensekret) sich eine biologische Spur zusammensetzt. Durch Verwendung der DNA-RNA-Koextraktion kann dieses Verfahren unabhängig von der STR-Typisierung durchgeführt werden. Am Beispiel des hier dargestellten Falles, bei dem Vaginalsekret der verletzten Frau am Mittelfinger des Beschuldigten nachgewiesen wurde, wird gezeigt, dass der Einsatz dieser Methode besonders bei Fällen von sexualisierter Gewalt sinnvoll ist.

Identification of body fluids—menstrual blood, saliva, and nasal secretions—over different periods of time, using mRNA

Background

Forensic examination of biological samples started at the beginning of the twentieth century by applying the ABO blood group system in evidence related to crimes or human identification. In the present study, real-time PCR multiplex was used to identify dried and stored swabs (saliva, nasal secretions, and menstrual blood) through the target genes of saliva (histatin 3 and statherin), nasal secretions (statherin and BPIFA1), and menstrual blood (metalloproteinases 10 and 7).

Results

The expressions of histatin 3 and statherin in the dried saliva decreased over days of storage with a significant p value of <0.001. BPIFA1 was highly expressed in nasal secretions, and the expression level significantly decreased throughout the study with a significant p value of <0.001. The MMP7 and MMP10 genes were highly expressed in the menstrual blood, and the expression level decreased over days of storage with a significant p value of p<0.001.

Conclusions

Dried swabs of the saliva, Nasal secretions, Menstrual blood can be identified over the storage duration of the study using mRNA profiling of specific markers.

The effect of infertile semen on the mRNA-based body fluid identification

In the past decade, mRNA markers have been well demonstrated as promising molecular markers in forensic body fluid identification (BFI), and successfully used in wide applications. Several studies have assessed the performance of semen-specific mRNA markers in distinguishing semen from other common body fluids at the crime scene. Infertility has been reported as a global health problem that is affecting approximately 15% of couples worldwide. Therefore, it is important for forensic researchers to consider the impact of infertility on semen identification. This study aimed to explore the effect of semen from infertile men (hereinafter "infertile semen") on BFI and to identify semen-specific mRNAs that can efficiently and accurately distinguish normal and infertile semen samples from other body fluids. Results showed that the selected five mRNAs (KLK3, TGM4, SEMG1, PRM1, and PRM2) performed a significantly high semen specificity in normal semen. Moreover, KLK3 was slightly influenced by infertile semen samples with over 98% positive results in all semen samples. The accuracy to predict normal semen reached up to 96.6% using the discrimination function Y1 with KLK3 and PRM1. However, when the infertile semen samples were included in discrimination function (function Y2 with KLK3), the accuracy rate of semen identification (including the normal and infertile semen) was down to 89.5%. Besides, the sensitivity of multiplex assay could reach down to 50pg. Our results suggest that it is important to consider the presence of infertile semen when using mRNAs to identify semen samples, which would have a far-reaching impact in forensic identification.

Development and validation of an mRNA-based multiplex body fluid identification workflow and a rectal mucosa marker pilot study

Molecular identification of body fluids and tissues is crucial in order to understand the circumstances of crimes. For that reason, molecular investigations used to identify body fluids/tissues have increasingly been examined recently. Various studies have proved that messenger RNA (mRNA) profiling is a sensitive and robust method for body fluid/tissue identification. The forensically relevant body fluids/tissues blood, semen, saliva, vaginal secretion, menstrual blood and skin have all been detected successfully by applying suitable mRNA assay. However, rectal mucosa, which can be found as evidence in sexual assault cases, has been neglected in forensic investigations. So far there is no mRNA marker to detect rectal mucosa, although anal penetration occurs in a large number of sexual assaults (23.2% of female victims and 50% of male victims). In this study, specific and sensitive mRNA markers for forensically relevant body fluids were adapted and validated in an mRNA multiplex assay for routine casework. This included the implementation of a DNA/RNA re-extraction method for automated extraction that can be integrated into casework without loss of DNA. This re-extraction method and the mRNA multiplex assay were tested using casework samples. PCR-primers were designed for the identification of rectal mucosa and the more effective marker MUC12 was integrated into an extended multiplex assay. The result of our study is a highly specific and sensitive mRNA multiplex assay plus an automated DNA/RNA re-extraction method, that can be integrated into casework and identify rectal mucosa for the first time.

Degradation of human mRNA transcripts over time as an indicator of the time since deposition (TsD) in biological crime scene traces

Knowledge about the age of a stain, also termed as time since deposition (TsD), would provide law-enforcing authorities with valuable information for the prosecution of criminal offenses. Yet, there is no reliable method for the inference / assessment of TsD available. The aim of this study was to gain further insight into the RNA degradation pattern of forensically relevant body fluids and to find candidate markers for TsD estimation. Blood, menstrual blood, saliva, semen and vaginal secretion samples were exposed to indoor (dark, room temperature) and outdoor (exposed to sun, wind, etc. but protected from rain) conditions for up to 1.5 years. Based on expression and degradation analyses, we were able to identify body fluid specific signatures and RNA degradation patterns. The indoor samples showed a marked drop in RNA integrity after 6 months, while the outdoor samples were difficult to interpret and therefore excluded for some of the analyses. Up to 4 weeks, indoor samples showed more stable and less degrading transcripts than outdoor samples. Stable transcripts tended to be significantly shorter than degrading ones or transcripts, which are neither degrading nor stable. We reinforced the body fluid specific and the housekeeping gene nature of previously reported markers. With an unbiased approach, we selected stable and degrading genes for each body fluid in the short term and assessed their integrity during extended storage. We identified several stable and degrading gene transcripts, which could be tested in a targeted assay to assess the TsD interval e.g. by analyzing the ratio of degrading vs stable transcripts. In conclusion, we were able to detect RNA degradation patterns in samples being aged up to 1.5 years and identified several candidate markers, which could be evaluated for TsD estimation.

Identification of coding region SNPs from specific and sensitive mRNA biomarkers for the deconvolution of the semen donor in a body fluid mixture

mRNA markers provide a very promising method for the identification of human body fluids or tissues in the context of forensic investigations. Previous studies have shown that different body fluids can be distinguished from each other according to their specific mRNA biomarkers. In this study, we evaluated eight semen-specific mRNA markers (KLK3, NKX3-1, CKB, KLK2, PRAC1, SEMG1, TGM4, and SORD) that encompass 12 coding single nucleotide polymorphisms (cSNPs) to identify the semen contributor in a mixed stain. Five highly specific and sensitive mRNA markers for blood, menstrual blood, saliva, vaginal secretions, and skin were also incorporated into the PCR system as body fluid-positive controls. Reverse transcription polymerase chain reaction (RT-PCR), multiplex PCR and SNaPshot mini-sequencing assays were established for the identification of semen-specific mRNA. The amplicon size ranged from 133 to 337 bp. The semen-specific system was examined against blood, menstrual blood, saliva, vaginal secretions, and skin swabs. The eight mRNA biomarkers were semen-specific and could be successfully typed in laboratory-generated mixtures composed of different body fluids supplemented with 1 ng of semen cDNA. This system possessed a high sensitivity that ranged from 1:10-1:100 for detecting trace amounts of semen in semen-containing body fluid mixtures. Additionally, our results demonstrated that the cSNPs polymorphisms included in the mRNA markers were concordant with genomic DNA (gDNA). Despite the presence of other body fluids, the system exhibited high sensitivity and specificity to the semen in the mixture. In future studies, we will add other cSNPs from the semen-specific genes using massively parallel sequencing to further improve our system.

The persistence and stability of miRNA in bloodstained samples under different environmental conditions

miRNA markers have been an area of forensic interest to identify body fluid sources in recent years. In this study, reverse transcription and quantitative real time polymerase chain reaction (RT-qPCR) were performed to detect the existence of blood-specific miRNA markers in bloodstained samples under different environmental conditions, Blood samples from 6 individuals were deposited onto glass plates and exposed to different temperature, humidity, ultraviolet light intensity, and natural condition. When samples were stored to a series of estimated test times, total RNA was extracted and the Ct values of the target RNAs were detected, targets included two miRNA markers (hsa-miR-16-5p, hsa-miR-451a) and one reference gene (U6 snRNA). Analysis results showed that miR-451a represented strong stability and could be detected at all detection points. Meanwhile, each RNAs exhibited unique degradation characteristics, compared to U6, miRNAs showed stronger stability. Additionally, rain had an adverse effect on RNAs stability and accelerates its degradation rate.

mRNA profiling of mock casework samples: Results of a FoRNAP collaborative exercise

In recent years, forensic mRNA profiling has increasingly been used to identify the origin of human body fluids. By now, several laboratories have implemented mRNA profiling and also use it in criminal casework. In 2018 the FoRNAP (Forensic RNA Profiling) group was established among a number of these laboratories with the aim of sharing experiences, discussing optimization potential, identifying challenges and suggesting solutions with regards to mRNA profiling and casework. To compare mRNA profiling methods and results a collaborative exercise was organized within the FoRNAP group. Seven laboratories from four countries received 16 stains, comprising six pure body fluid / tissue stains and ten mock casework samples. The laboratories were asked to analyze the provided stains with their in-house method (PCR/CE or MPS) and markers of choice. Five laboratories used a DNA/RNA co-extraction strategy. Overall, up to 11 mRNA markers per body fluid were analyzed. We found that mRNA profiling using different extraction and analysis methods as well as different multiplexes can be applied to casework-like samples. In general, high input samples were typed with high accuracy by all laboratories, regardless of the method used. Irrespective of the analysis strategy, samples of low input or mixed stains were more challenging to analyze and interpret since, alike to DNA profiling, a higher number of markers dropped out and/or additional unexpected markers not consistent with the cell type in question were detected. It could be shown that a plethora of different but valid analysis and interpretation strategies exist and are successfully applied in the Forensic Genetics community. Nevertheless, efforts aiming at optimizing and harmonizing interpretation approaches in order to achieve a higher consistency between laboratories might be desirable in the future. The simultaneous extraction of DNA alongside RNA showed to be an effective approach to identify not only the body fluid present but also to identify the donor(s) of the stain. This allows investigators to gain valuable information about the origin of crime scene samples and the course of events in a crime case.

Current Methods for Body Fluid Identification Related to Sexual Crime: Focusing on Saliva, Semen, and Vaginal Fluid

Although, DNA typing plays a decisive role in the identification of persons from blood and body fluid stains in criminal investigations, clarifying the origin of extracted DNA has also been considered an essential task in proving a criminal act. This review introduces the importance of developing precise methods for body fluid identification. Body fluid identification has long relied on enzymatic methods as a presumptive assay and histological or serological methods as a confirmatory assay. However, because the latest DNA typing methods can rapidly obtain results from very small and even old, poorly preserved samples, the development of a novel corresponding body fluid identification method is required. In particular, an immunochromatographic method has been introduced to identify saliva and semen from sexual crimes. In addition, for vaginal fluid identification, attempts have been made in the past decade to introduce a method relying on body fluid-specific mRNA expression levels. At present, the development of molecular biological methods involving microRNA, DNA methylation, and resident bacterial DNA is ongoing. Therefore, in criminal investigations, body fluid identification is an essential task for correctly applying the results of DNA typing, although further research and development are required.

Highly degraded RNA can still provide molecular information: An in vitro approach

The long-term survival of RNA in postmortem tissues is a tricky topic. Many aged/forensic specimens show, in fact, high rates of null/inconclusive PCR-based results, while reliable outcomes were sometimes achieved from archaeological samples. On the other hand, several data show that the RNA is a molecule that survives even to several physical-chemical stresses. In the present study, a simple protocol, which was already developed for the prolonged hydrolysis of DNA, was applied to a RNA sample extracted from blood. This protocol is based on the heat-mediated (70°C) hydrolysis for up to 36 h using ultrapure water and di-ethyl-pyro-carbonate-water as hydrolysis medium. Measurable levels of depurination were not found even if microfluidic devices showed a progressive pattern of degradation. The reverse transcription/quantitative PCR analysis of two (60 bp long) housekeeping targets (glyceraldehyde-3-phosphate dehydrogenase and porphobilinogen deaminase) showed that the percentage of amplifiable target (%AT) decreased in relation to the duration of the damaging treatment (r² > 0.973). The comparison of the %AT in the degraded RNA and in the DNA samples that underwent the same damaging treatment showed that the %AT is always higher in RNA, reaching up to three orders of magnitude. Lastly, even the end-point PCR of blood-specific markers gave reliable results, which is in agreement with the body fluid origin of the sample. In conclusion, all the PCR-based results show that RNA maintains the ability to be retro-transcribed in short cDNA fragments even after 36 h of incubation at 70°C in mildly acidic buffers. It is therefore likely that the long-term survival of RNA samples depends mainly on the protection against RNAase attacks rather than on environmental factors (such as humidity and acidity) that are instead of great importance for the stability of DNA. As a final remark, our results suggest that the RNA analysis can be successfully performed even when DNA profiling failed.

Evaluation of a co-extraction kit for mRNA, miRNA and DNA methylation-based body fluid identification

Recently, messenger RNA (mRNA), micro RNA (miRNA), and DNA methylation (DNAm) have been reported as novel markers for body fluid identification (BFID). Comprehensive analysis of these markers should be a flexible and reliable BFID method for various types of forensic samples. However, independent extraction of all targets can be difficult depending on the usable amounts of samples. In this study, the applicability of a co-extraction kit for these molecules, the AllPrep DNA/RNA/miRNA Universal Kit (APU), was evaluated by comparing RNA and DNA extracted from blood and saliva stains by the APU with those extracted by standard kits for each molecule and by previously reported methods for mRNA/DNA or miRNA/DNA co-extraction. Electrophoresis using the Bioanalyzer platform and real-time PCR analysis revealed that the APU performed almost equivalently to each standard kit in the quality of RNA or DNA extracted and extraction efficiency of mRNAs, miRNAs, and DNA. Moreover, the APU outperformed the co-extraction methods, especially in RNA integrity and miRNA extraction efficiency. In addition, pyrosequencing revealed that the methylation ratios of DNA extracted by the APU were not different from those extracted by standard DNA extraction kits. Overall, the APU is applicable to comprehensive analysis of mRNA/miRNA/DNAm markers for BFID analysis. Because the DNA eluate can also be used for DNA typing, the APU may be among the best choices for forensic examination of body fluid samples in terms of its flexibility and reliability in BFID and efficiency in sample consumption.

The stability and persistence of blood and semen mRNA and miRNA targets for body fluid identification in environmentally challenged and laundered samples

The identification of body fluids in evidentiary stains may provide investigators with probative information during an investigation. In this study, quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays were performed to detect the presence of mRNA and miRNA in fresh and environmentally challenged samples. Blood, semen, and reference markers were chosen for both mRNA/miRNA testing. Samples of blood and semen were exposed to heat, humidity, and sunlight, and controlled conditions (room temperature, low humidity, and darkness) for 6 months. All mRNA targets were observed through six months under controlled conditions, but were undetected after 30 days in experimental conditions. However, miRNA targets persisted under all test conditions for the duration of the study. Additionally, cotton stained with blood or semen was laundered using a liquid detergent in various washing and drying conditions. An unstained cutting was evaluated for potential transfer. Both miRNA targets were observed in all stained samples regardless of the wash protocol used. Of the mRNA markers, HBB was detected in all bloodstained samples and PRM1 persisted in all but one semen stained sample. The unstained samples showed transfer of at least one body fluid specific miRNA marker in all samples and at least one body fluid specific mRNA in approximately half of the samples. These results support that RNA markers can be used for body fluid identification in challenging samples, and that miRNA markers may be more persistent than mRNA for blood and semen stains. However, some caution is warranted with laundered items due to possible transfer.

Characterization of tissue-specific biomarkers with the expression of circRNAs in forensically relevant body fluids

Messenger RNA (mRNA) markers have been extensively investigated for the identification of forensically relevant body fluids and tissues based on their expression profiles among cell types. As products of the backsplicing of pre-mRNAs, circular RNAs (circRNAs) share exonic sequences with their linear counterparts. The inclusion of circRNAs in mRNA profiling is shown to facilitate the detection of biomarkers in the identification of body fluids. In this study, we identified the expression of circRNAs of 14 out of 45 biomarkers from five body fluid types using outward-facing primer sets and revealed the ratio of circular to total transcripts of biomarkers by RNase R treatment. Furthermore, our results of qPCR analysis show that the inclusion of circRNAs in the detection of biomarkers, including HBA and ALAS2 for blood; MMP7 and MMP10 for menstrual blood; HTN3 for saliva; SPINK5, SERPINB3, ESR1, and CYP2B7P1 for vaginal secretions; TGM4, KLK3, and PRM2 for semen; and SLC22A6 and MIOX for urine, does not impair the specificity of these biomarkers. Additionally, a high copy number of targets from linear transcripts could be employed to increase the detection sensitivity of TGM4 and KLK3 with a low expression level of circRNAs in urine samples. Altogether, these results will help with the development of robust multiplex assays for body fluid identification.

Evaluation of the inclusion of circular RNAs in mRNA profiling in forensic body fluid identification

The use of messenger RNA (mRNA) profiling is considered a promising method in the identification of forensically relevant body fluids which can provide crucial information for reconstructing a potential crime. However, casework samples are usually of limited quantity or have been subjected to degradation, which requires improvement of body fluid identification. Circular RNAs (circRNAs), a class of products from the backsplicing of pre-mRNAs, are shown to have high abundance, remarkable stability, and cell type-specific expression in human cells. In this study, we investigated whether the inclusion of circRNAs in mRNA profiling improve the detection of biomarkers including δ-aminolevulinate synthase 2 (ALAS2) and matrix metallopeptidase 7 (MMP7) in body fluid identification. The major circRNAs of ALAS2 and MMP7 were first identified and primer sets for the simultaneous detection of linear and circular transcripts were developed. The inclusion of circRNAs in mRNA profiling showed improved detection sensitivity and stability of biomarkers revealed by using serial dilutions, mixed samples, and menstrual bloodstains as well as degraded and aged samples. Therefore, the inclusion of circRNAs in mRNA profiling should facilitate the detection of mRNA markers in forensic body fluid identification.

Practical evaluation of an RNA-based saliva identification method

Identifying saliva in samples found at crime scenes is important to clarify the tissue origin of DNA obtained for identification of individuals. Recently, a novel messenger RNA-based approach using two saliva-specific markers, Statherin (STATH) and Histatin 3 (HTN3), has been reported. This method can identify saliva more specifically than conventional amylase-based methods. Here, we performed several evaluations related to applying this method to real-world forensic work. First, we evaluated the effects of exposure to blue light (450nm) or to the reagent on Phadebas paper, which are direct methods used to locate saliva stains, on the stability of the RNA markers. The results demonstrate that exposure to the two direct tests did not affect the stability of the RNA markers. Second, we performed a comparative analysis of RNA-based and amylase-based conventional methods to examine the sensitivity and stability of the markers under various storage conditions. Although there was no difference in the sensitivity of the two methods for detecting 1-day-old saliva stains, a time-course study demonstrated that the RNA saliva markers were less stable than amylase, especially in wet conditions. During this time-course experiment, the stability of human DNA was also investigated. Although DNA was also unstable in wet conditions, it was more stable than the RNA markers in dry conditions. Taking the above results into consideration, we suggest that the RNA method could be introduced to current saliva identification procedures and should be used as a supplementary method to strongly support identification of saliva by the amylase-based method.