A sandwich enzyme immunoassay for brain S-100 protein and its forensic application

Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue

RNAs have attracted much attention in forensic body fluid/tissue identification (BFID) due to their tissue-specific expression characteristics. Among RNAs, long RNAs (e.g., mRNA) have a higher probability of containing more polymorphic sites that can be used to assign the specific donor of the body fluid/tissue. However, few studies have characterized their overall profiles in forensic science. In this study, we sequenced the transcriptomes of 30 samples from venous blood, menstrual blood, semen, saliva, vaginal secretion, and skin tissue, obtaining a comprehensive picture of mRNA, lncRNA, and circRNA profiles. A total of 90,305 mRNAs, 102,906 lncRNAs (including 19,549 novel lncRNAs), and 40,204 circRNAs were detected. RNA type distribution, length distribution, and expression distribution were presented according to their annotation and expression level, and many novel body fluid/tissue-specific RNA markers were identified. Furthermore, the cognate relations among the three RNAs were analyzed according to gene annotations. Finally, SNPs and InDels from RNA transcripts were genotyped, and 21,611 multi-SNP and 4,471 multi-InDel transcriptomic microhaplotypes (tMHs) were identified. These results provide a comprehensive understanding of transcriptome profiles, which could provide new avenues for tracing the origin of the body fluid/tissue and identifying an individual.

A Comprehensive Characterization of Small RNA Profiles by Massively Parallel Sequencing in Six Forensic Body Fluids/Tissue

Body fluids/tissue identification (BFID) is an essential procedure in forensic practice, and RNA profiling has become one of the most important methods. Small non-coding RNAs, being expressed in high copy numbers and resistant to degradation, have great potential in BFID but have not been comprehensively characterized in common forensic stains. In this study, the miRNA, piRNA, snoRNA, and snRNA were sequenced in 30 forensic relevant samples (menstrual blood, saliva, semen, skin, venous blood, and vaginal secretion) using the BGI platform. Based on small RNA profiles, relative specific markers (RSM) and absolute specific markers (ASM) were defined, which can be used to identify a specific body fluid/tissue out of two or six, respectively. A total of 5204 small RNAs were discovered including 1394 miRNAs (including 236 novel miRNA), 3157 piRNAs, 636 snoRNAs, and 17 snRNAs. RSMs for 15 pairwise body fluid/tissue groups were discovered by differential RNA analysis. In addition, 90 ASMs that were specifically expressed in a certain type of body fluid/tissue were screened, among them, snoRNAs were reported first in forensic genetics. In brief, our study deepened the understanding of small RNA profiles in forensic stains and offered potential BFID markers that can be applied in different forensic scenarios.

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.

Potential applications of microRNA profiling to forensic investigations

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

An evidence based strategy for normalization of quantitative PCR data from miRNA expression analysis in forensic organ tissue identification

Messenger-RNA (mRNA)-based analysis of organ tissues and their differentiation in complex crime stains has recently been introduced as a potential and powerful tool to forensic genetics. Given the notoriously low quality of many forensic samples it seems advisable, though, to substitute mRNA with micro-RNA (miRNA) which is much less susceptible to degradation. However, reliable miRNA detection and quantification using quantitative PCR requires a solid and forensically relevant normalization strategy. In our study we evaluated a panel of 15 carefully selected reference genes for their suitability as endogenous controls in miRNA qPCR normalization in forensically relevant settings. We analyzed assay performances and expression variances in 35 individual samples and mixtures thereof integrating highly standardized protocols with contemporary methodologies and included several well-established computational algorithms. Based on these empirical results, we recommend SNORD48, SNORD24, and RNU6-2 as endogenous references since these exhibit the most stable expression levels and the least expected variation among the evaluated candidate reference genes in the given set of forensically relevant organ tissues including skin. To account for the lack of consensus on how best to perform and interpret quantitative PCR experiments, our study's documentation is according to MIQE guidelines, defining the "minimum information for publication of quantitative real-time PCR experiments".

Development of a mRNA profiling multiplex for the inference of organ tissues

Forensic characterisation of organ tissue generally occurs through histological and immunological assays of limited sensitivity. Here, we explore an alternative approach and examine a total of 41 candidate mRNA markers for their ability to differentiate between brain, lung, liver, skeletal muscle, heart, kidney and skin. Various selection rounds are applied involving 85 organ tissues (36 excised autopsy specimens and 49 frozen tissue sections, with at least ten specimens for each organ type), 20 commercially available RNAs from different human tissues and at least two specimens of blood, saliva, semen, vaginal mucosa, menstrual secretion or touch samples. Finally, 14 markers are regarded tissue-specific and included in an endpoint RT-PCR multiplex together with one general muscle, one blood and one housekeeping marker. This 17-plex is successfully used to analyse a blind test set of 20 specimens including mixtures, and samples derived from stabbing of organ tissues. With the blind test set samples, it is shown that an earlier described interpretation strategy for RNA cell typing results [1] is also effective for tissue inference. As organ-typing is embedded in a procedure of combined DNA/RNA extraction and analysis, both donor and organ type information is derived from the same sample. Some autopsy specimens presented DNA profiles characteristic for degraded DNA. Nevertheless, the organ-typing multiplex could generate full RNA profiles, which is probably due to small sizes of the amplicons. This assay provides a novel tool for analysis of samples from violent crimes.

Identification of human brain from a tissue fragment by detection of neurofilament proteins

We developed a method for identifying human brain from a tissue-like fragment by detection of neurofilament protein (NF) using enzyme-linked immunosorbent assay (ELISA). NF was extracted from 0.1 g of organ/tissue homogenized with Tris-HCl buffer (pH 7.2) containing urea, phenylmethylsulfonyl fluoride (PMSF), EDTA and, EGTA. It was necessary to dilute the extract at more than 2(3)-fold to avoid immunosuppression by urea. Positive reaction was always obtained for NF-H in 2(3)-fold diluted extract of brain tissue, however, NF-L and NF-M were not always detected when a brain fragment contained gray matter. Human cerebral white matter could be easily distinguished from other organs/tissues by detecting any of the NF-subunits. Brains of human and some animals could be discriminated by detecting NF-L or NF-M, although the species specificity of NF-H was not good. Our findings suggested that detection of NF-H was more useful than NF-L and NF-M for identifying a brain from a tissue-like fragment. The present ELISA method for NF-H could identify human brain specimens under the following conditions: putrefied at 4 degrees C for up to 3 weeks, dried at 37 degrees C for at least 4 months, heated at 50 degrees C for at least 4 weeks. Our results showed that our method is useful for identification of brain tissue in forensic stain analysis. Two practical cases are described.

Determination of pancreas injury from bloodstains using human pancreatic elastase III as a marker

A sensitive sandwich enzyme immunoassay for human pancreatic elastase III as a method to identify pancreas injuries from blood or bloodstains was evaluated. The serum levels of human elastase III from healthy adults (n=24) were estimated to be 1.15 +/- 0.6 (+/- SD) ng/ml. The recovery rates of elastase III added to normal human serum were estimated to be 96.3%. Elastase III levels in contents of various digestive organs were assayed and found to be high in the contents of the large intestine. For detection of human elastase III on weapons, samples were prepared from disposable scalpels that had been used to cut skin and skeletal muscle, and then to cut various organs. The mean ratio of elastase III to total protein (ng elastase III/mg protein) on scalpels that had been cut the pancreas (n=11) was 4956+/-3067 (+/- SD), whereas the ratios from other organs were much lower except, in case of several digestive organs. The higher elastase III levels detected in these digestive organs seemed to stem from the amount of intestinal contents adhering to the scalpels. These results suggest that determination of pancreatic elastase III in blood or bloodstains using a sandwich enzyme immunoassay is a very useful and effective tool for identification of pancreas injury in forensic practice.

A sandwich enzyme immunoassay for human pancreatic elastase III

To develop a method for the determination of pancreas injuries using a pancreas-specific antigen as a marker, human elastase III was purified from the pancreas by chromatographic methods. A rabbit anti-human elastase III antibody was prepared, and this antibody was confirmed using immunoblotting to react only with elastase III among proteins from the pancreas. A sensitive sandwich enzyme immunoassay for human elastase III was developed. The detection limit for human elastase III was 0.3 pg (10 amol) per assay. Proteins extracted from the pancreas showed the strongest response, whereas reactions of the other organs were less than the detection limit. These results suggest that a sandwich enzyme immunoassay for human elastase III is useful for the determination of pancreas injury.

A sandwich enzyme immunoassay for human muscle-specific beta-enolase and its application for the determination of skeletal muscle injury

A sensitive sandwich enzyme immunoassay for human beta-enolase was developed and used to examine beta-enolase in blood or bloodstains as a marker for the determination of skeletal muscle injury. Human beta-enolase was purified from human skeletal muscle, and then an antibody against it was prepared. Polystyrene balls coated with rabbit anti-human beta-enolase IgG were incubated with human beta-enolase and then with anti-human beta-enolase Fab'-peroxidase conjugate. Peroxidase activity bound to the polystyrene balls was assayed by fluorometry using 3-(4-hydroxyphenyl)propionic acid as a hydrogen donor. The detection limit for human beta-enolase was 2.6 pg (30 amol) per assay. The degree of cross-reaction of the sandwich enzyme immunoassay for other organs except for heart (1/10) was about 1/150 or less. Moreover, the localization of beta-enolase in various human tissues was examined by Northern blot analysis, and this confirmed that beta-enolase was expressed only in skeletal and cardiac muscle. Antigenic activity in bloodstains containing beta-enolase was recovered well after storage for 60 days at room temperature. The ratio of beta-enolase to total protein in bloodstains made from non-traumatic blood, nasal hemorrhage and menstrual blood, was within the normal range. In contrast, the ratio of beta-enolase in bloodstains from traumatic blood was obviously elevated (10-30 fold) in comparison with non-traumatic blood. Furthermore, the ratio of beta-enolase was proved to be higher in stains adhering to weapons that had passed through skeletal muscle, indicating that detection of beta-enolase in bloodstains could be used to distinguish crime weapons. These results suggest that beta-enolase is a useful marker for identification of skeletal muscle injury as well as for detecting the origin of bleeding.