A capillary electrophoresis method for identifying forensically relevant body fluids using miRNAs

Body fluid identification (BFID) can provide crucial information during the course of an investigation. In recent years, microRNAs (miRNAs) have shown considerable body fluid specificity, are able to be co-extracted with DNA, and their small size (18–25 nucleotides) make them ideal for analyzing highly degraded forensic samples. In this study, we designed a preliminary 8-marker system for BFID including an endogenous reference gene (let-7g) to differentiate between venous blood (miR-451a and miR-142-3p), menstrual blood (miR-141-3p and miR-412-3p), semen (miR-891a and miR-10b), and saliva (miR-205) using a capillary electrophoresis approach. This panel uses a linear primer system in order to incorporate additional miRNA markers by forming a multiplex system. The miRNA system was able to distinguish between venous blood, menstrual blood, semen, and saliva using a rudimentary data interpretation strategy. All STR amplifications from co-extracted DNA yielded complete profiles from human identification purposes.     

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.     

Massively parallel sequencing of microRNA in bloodstains and evaluation of environmental influences on miRNA candidates using realtime polymerase chain reaction

MicroRNAs (miRNA) are small (22–24 nucleotides) non-coding RNAs with potential application in forensic science because of their anti-degradation property and tissue specificity. Recent studies on the use of miRNA in forensic applications have mainly focused on body fluid identification using realtime polymerase chain reaction or microarray analysis. However, the exploration of miRNA in bloodstains, which are the most valuable source of biological evidence during case investigations, is currently lacking, particularly for aged and environmentally compromised forensic samples. Recent developments in massively parallel sequencing (MPS) technology provide the opportunity to establish a whole-genome miRNA profile with high throughput and efficiency. However, MPS analysis of genome-wide miRNA profiles from bloodstains has not been reported to date. In this study, the whole-genome miRNA profiles of bloodstains were examined using MPS, revealing 633 known miRNAs and 266 novel miRNAs. To further explore the stability of miRNAs in bloodstains under various circumstances, the expression levels of six miRNAs (miR-16-5p, miR-20a-5p, miR-486-5p, miR-148a-3p, miR-151a-3p, and miR-451a) that were abundant in blood/bloodstains were examined. The results showed that freezing/thawing and a high concentration of oxidant solution affects the absolute expression of miRNA significantly, while storage for up to 5 months and a temperature of 37 °C did not have any observed effects. This study not only provides a novel method to explore miRNA profiles in bloodstains using MPS, but also points to the circumstantial influences on miRNA expression, which are an important consideration for practical application. Collectively, our work may shed light on MPS-based approaches with miRNA analysis of bloodstains in forensics.     

X射线诱导非小细胞肺癌A549细胞凋亡的适应性反应及相关miRNA筛选的研究

目的 研究X射线辐射诱导非小细胞肺癌（NSCLC）A549细胞凋亡的适应性反应,并筛选适应性反应相关的微RNA（miRNA）。 方法 将NSCLC A549细胞分为6组,包括 50 mGy+20 Gy、200 mGy+20 Gy、20 Gy、50 mGy、200 mGy照射组及对照组（0 Gy）,前2组细胞分别用50、200 mGy初始剂量进行照射,培养6 h后用20 Gy的效应剂量进行照射,20 Gy、50 mGy、200 mGy照射组同时进行照射。培养24 h后使用流式细胞仪检测细胞凋亡情况。利用小RNA测序技术筛选差异表达miRNA,并对其靶基因进行基因本体（GO）及京都基因与基因组百科全书（KEGG）通路的功能富集分析。采用实时荧光定量PCR（qRT-PCR）对部分差异表达miRNA进行验证。2组间数据的比较采用Welch t检验。 结果 50 mGy+20 Gy照射组和200 mGy+20 Gy照射组的A549细胞早期凋亡率分别为（1.81±0.11）%和（2.17±0.19）%,低于20 Gy照射组的（4.54±0.23）%,且差异均有统计学意义（t=10.680、8.006,均P<0.01）。与20 Gy照射组相比,50 mGy+20 Gy照射组和200 mGy+20 Gy照射组共同差异表达趋势miRNA有1个上调（miR-3662）、15个下调（miR-185-3p、miR-1908-5p、miR-1307-5p、miR-182-3p、miR-92a-3p、miR-582-5p、miR-501-3p、miR-138-5P、miR-1260b、miR-484、miR-378d、miR-193b-3P、miR-127-3p、miR-1303及miR-654-5p）。GO富集分析结果显示,差异表达miRNA调控靶基因功能显著富集于细胞通讯调节、代谢过程的正向调节、代谢信号的调节、酶结合及催化活性等过程。KEGG富集分析结果显示,靶基因相关信号通路显著富集于溶酶体、丝裂原活化蛋白激酶、Ras和内吞作用等信号通路。qRT-PCR检测结果显示,miRNA表达情况与基因芯片结果趋势一致（10个miRNA表达水平得到验证）。 结论 X射线50、200 mGy照射剂量均能诱导NSCLC A549细胞凋亡的适应性反应,并筛选到一组共同差异表达的miRNA,可能在X射线辐射诱导细胞凋亡的适应性反应中发挥了重要作用,有可能成为调节电离辐射生物效应的潜在靶点。     

基于microRNA差异表达的精神分裂症与抑郁症共病研究

目的 观察精神分裂症(SZ)患者中差异表达的microRNA(miRNA),从miRNA表达水平上分析SZ与抑郁症的关系.方法 通过基因芯片筛选在SZ患者中差异表达的miRNA.采用实时定量PCR(qRT-PCR)在40例SZ患者外周血单核细胞中验证芯片筛查结果,并进行精神分裂症阳性和阴性症状量表(队NSS)评定,同时检测抑郁症中差异表达的5种miRNA(miR-1972、miR-26b、miR-4485、miR-4498、miR-4743)的表达改变及其与SZ中差异表达的miRNA及PANSS评分的相关性.结果 与正常人相比,SZ患者中33种miRNA存在差异表达(32种表达上调,1种表达下调),且其中8种上调的miRNA(miR-1273d、miR-1303、miR-3064-5p、miR-3131、miR-3687、miR-4428、miR-4725-3p、miR-5096)表达差异有统计学意义(P＜0.05).在抑郁症中差异表达的5种miRNA在SZ患者中差异表达也有统计学意义(P＜0.05),且与SZ中差异表达的8种miRNA呈中、高度相关(r=0.607～0.909,P＜0.01),其中miR-1972与PANSS量表阳性症状得分呈显著正相关(r=0.339,P＜0.05),miR-26b与复合量表因子分呈显著正相关(r=0.342,p＜0.05).结论 SZ与抑郁症不仅具有某些共同的临床表现,二者在分子遗传学方面也可能有共同的病理基础.     

放疗对血清miR-150-5p和miR-23a-3p表达水平的影响

目的 通过采集肿瘤患者放疗前后外周血,探讨照射对人外周血血清miR-150-5p、miR-23a-3p表达的影响,以期为寻找辐射生物标志物提供科学依据。方法 以2021年10月至2022年3月63例行放疗的肿瘤患者为研究对象,采用实时荧光定量PCR(qPCR)方法,检测患者放疗前后外周血血清miR-150-5p与miR-23a-3p的相对表达水平。比较两种miRNAs放疗前后在患者外周血血清中的差异表达变化,分析其与肿瘤类型等因素的关系。结果 放疗后,患者外周血血清miR-150-5p与miR-23a-3p的相对表达量明显低于放疗前(t=4.97,Z=-2.77,P<0.05)。不同的肿瘤类型中,乳腺癌、食管癌和其他消化道肿瘤患者放疗后miR-150-5p的相对表达量降低(t=3.47、2.47、2.87,P<0.05),消化道肿瘤患者放疗后miR-23a-3p相对表达量下降(Z=-1.99,P<0.05)。在放疗前、后miR-150-5p的表达改变均不受性别、年龄、化疗和肿瘤类型等因素影响(P>0.05),而miR-23a-3p的表达改变在放疗后受性别、年龄和化疗等因素影响(t=2.04、 -3.34、-2.29,P<0.05)。结论 放疗可影响肿瘤患者血清中miR-150-5p的表达,其有作为辐射生物学标志物的潜力。     

Thermal Ablation and Transarterial Chemoembolization are Characterized by Changing Dynamics of Circulating MicroRNAs

PurposeTo determine whether the levels of circulating microRNAs (miRNAs) are altered in patients undergoing thermal ablation and chemoembolization and whether these changes are predictive of a clinical outcome.Material and MethodsThis prospective study consisted of 43 patients diagnosed with hepatocellular carcinoma (n = 15) and intrahepatic colorectal cancer metastases (n = 28) treated with thermal ablation (n = 23; radiofrequency [n = 6] or microwave [n = 19]), chemoembolization using drug-eluting embolics (n = 18), or both (n = 2). Four blood samples (immediately before the intervention and 60–90 minutes, 24 hours, and 7 days after the intervention) were taken to measure the plasma concentrations of miRNAs related to hypoxia (miR-21 and miR-210), liver injury (miR-122), epithelial–mesenchymal transition (miR-200a), and apoptosis (miR-34a) using miRNA-specific TaqMan assays and quantitative real-time polymerase chain reaction. Tumor burden and treatment response at 3 months were evaluated using the modified response evaluation criteria in solid tumors. The miRNA results were compared with clinical outcomes (Mann-Whitney U test, Wilcoxon matched-pair test).ResultsDynamic changes in the circulating miRNA levels were observed following both the interventions. For thermal ablation, significant increases in miR-21, miR-210, miR-122, miR-200a, and miR-34a concentrations peaked 60–90 minutes after the intervention (P < .01). However, for transarterial chemoembolization, maximum increases in the miRNA concentrations were observed at 24 hours after the intervention for miR-21, miR-210, miR-122, miR-200a, and miR-34a (P < .05). The increased concentrations of the circulating miRNAs were followed by a subsequent decline to baseline by 7 days. For the thermal ablation (but not chemoembolization) patients, elevations in the miR-210 and miR-200a levels were associated with early progressive disease at 3 months (P = .040 and P = .012, respectively).ConclusionsIncreased but dynamic levels of circulating miRNAs are present following interventional oncologic procedures and may prove useful as biomarkers for the monitoring of clinical outcomes.     

MicroRNA-17-5p post-transcriptionally regulates p21 expression in irradiated betel quid chewing-related oral squamous cell carcinoma cells

Background and purpose

Betel nut chewing is associated with oral cavity cancer in Taiwan. OC3 is an oral carcinoma cell line that was established from cells collected from a long-term betel nut chewer who does not smoke. After we found that microRNA-17-5p (miR-17-5p) is induced in OC3 cells, we used this cell line to examine the biological role(s) of this microRNA in response to exposure to ionizing radiation.

Materials and methods

A combined SYBR green-based real-time PCR and oligonucleotide ligation assay was used to examine the expression of the miR-17 polycistron in irradiated OC3 cells. The roles of miR-17-5p and p21 were evaluated with specific antisense oligonucleotides (ODN) that were designed and used to inhibit their expression. Expression of the p21 protein was evaluated by Western blotting. The clonogenic assay and annexin V staining were used to evaluate cell survival and apoptosis, respectively. Cells in which miR-17-5p was stably knocked down were used to create ectopic xenografts to evaluate in vivo the role of miR-17-5p.

Results

A radiation dose of 5 Gy significantly increased miR-17-5p expression in irradiated OC3 cells. Inhibition of miR-17-5p expression enhanced the radiosensitivity of the OC3 cells. We found that miR-17-5p downregulates radiation-induced p21 expression in OC3 cells and, by using a tumor xenograft model, it was found that p21 plays a critical role in increasing the radiosensitivity of OC3 cells in vitro and in vivo.

Conclusion

miR-17-5p is induced in irradiated OC3 cells and it downregulates p21 protein expression, contributing to the radioresistance of OC3 cells.     

心房颤动患者循环microRNAs表达谱的初步研究

目的 利用microRNA(miRNA)芯片研究持续性和阵发性心房颤动(房颤)患者循环miRNAs表达谱的改变,为进一步探讨miRNA对房颤的调控机制提供依据.方法 解放军总医院心内科2010年11月-2011年2月持续性房颤患者、阵发性房颤患者和健康对照者各5例,取其全血标本,提取血清总RNA,采用microRNA芯片进行杂交,得到miRNA表达谱,通过Volcano Plot方法寻找差异表达的miRNAs,并采用MEV软件进行聚类分析.结果 和健康对照者相比,阵发性和持续性房颤患者血清中表达都有明显差异的miRNA共有13个,其中表达上调的有8个:miR-3169,miR-3612,miR-634,miR-376a,miR-517b,miR-377*,miR-590-3p,miR-664;表达下调的有5个:miR-1,kshv-miR-K12-5,miR-378c,miR-204,miR-27a.阵发性房颤和持续性房颤患者间miRNA的表达谱也有显著差异.结论 持续性和阵发性房颤患者循环miRNAs表达谱有显著改变,提示循环miRNAs可用于房颤发生和发展过程中调控机制的研究.     

Evaluating the forensic application of 19 target microRNAs as biomarkers in body fluid and tissue identification

RNA‐based body fluid and tissue identification has evolved as a promising and reliable new technique to classify type and source of biological evidence in crime cases. In particular, mRNA‐based approaches are currently on the rise to replace conventional protein‐based methods and are increasingly implemented into forensic casework. However, degradation of these nucleic acid molecules can cause issues on laboratory scale and need to be considered for a credible investigation. For this reason, the analysis of miRNAs using qPCR has been proposed to be a sensitive and specific approach to identify the origin of a biological trace taking advantage of their small size and resistance to degradation. Despite the straightforward workflow of this method, suitable endogenous controls are inevitable when performing real-time PCR to ensure accurate normalization of gene expression data in order to allow a meaningful interpretation. In this regard, we have validated reference genes for a set of forensically relevant body fluids and tissues (blood, saliva, semen, vaginal secretions, menstrual blood and skin) and tested 15 target genes aiming to identify abovementioned sample types. Our data showed that preselected endogenous controls (miR26b, miR92 and miR484) and miR144, initially selected as potential marker for the detection of menstrual blood, were the most stable expressed genes among our set of samples. Normalizing qPCR data with these four validated references revealed that only five miRNA markers are necessary to differentiate between the six different cell types selected in this study. Nevertheless, our observations in the present study indicate that miRNA analysis methods may not provide straightforward data interpretation strategies required for an implementation in forensic casework.     

miRNA analysis in vitreous humor to determine the time of death: a proof-of-concept pilot study

We hypothesized that miRNAs present in vitreous humor could be a sort of “biological black box,” storing information about physiological and environmental circumstances at death. As a proof of concept, we analyzed the vitreous humor miRNA signature to explore its forensic potential applications, such as determining the time of the day at death. The miRNAs present in vitreous humor from individuals who died at daytime or at nighttime were analyzed by quantitative real-time polymerase chain reaction (qPCR) array. Target miRNAs showing significant differences between groups were studied in a larger sample by individual qPCR assays. After array analysis of miRNAs in seven samples, significant expression differences were detected between individuals who died at daytime and at nighttime regarding mir-34c, mir-541, mir-888, mir-484, and mir-142-5p. miR-222 appeared as the best reference gene. The results were replicated in 34 vitreous humor samples, and the day–night differences were confirmed for miR-142-5p and miR-541, suggesting that miRNA levels may be related to either the ambient light or the circadian clock at the time of death. There was no correlation between miRNA levels and the time elapsed after death, suggesting that they were stable at least for 24 h. In conclusion, this report supports the potential forensic utility of the analysis of miRNAs in the vitreous humor in applications such as determining the time of death.     

Microbiome-based body fluid identification of samples exposed to indoor conditions

In the forensic reconstruction of crime scene activities, the identification of biological traces and their bodily origin are valuable evidence that can be presented in court. While several presumptive and confirmatory tests are currently available, the limitations in specificity and sensitivity have instigated a search for alternative methods. Bacterial markers have been proposed as a novel approach for forensic body fluid/tissue identification. Bacteria are not only ubiquitous throughout the human body, but also, as shown by recent microbiome sequencing studies of the 16S rRNA gene, bacterial community structures are distinct across body sites. Traces and stains at crime scenes are, however, often exposed to the environment outside the human body for variable periods of time before laboratory processing. Thus, it is not clear whether exposed samples continue to harbor microbial signatures characteristic of their body site of origin. In this proof-of-concept study we collected samples from six different body sites: saliva, skin, peripheral blood, vaginal fluid, menstrual blood and semen. We exposed a subset of these samples to indoor conditions for 30 days while the remaining samples were processed directly after extraction. Our analyses of 16S rRNA gene sequence data for a total of 46 control and exposed samples show that both types of samples group by body site, although a few outliers are observed. Based on our results, vaginal and menstrual samples share their microbial signatures, and cannot be distinguished using bacterial markers. Overall, our findings indicate that bacterial markers are a promising avenue for forensic body fluid/tissue identification.     

Suitable biomarkers for post-mortem differentiation of cardiac death causes: Quantitative analysis of miR-1, miR-133a and miR-26a in heart tissue and whole blood

Cardiovascular diseases are the most common causes of death worldwide. Cardiac death can occur as reaction to myocardial infarction (MI). A diagnostic challenge arises for sudden unexpected death (SUD) cases with structural abnormalities (SA) or without any structural abnormalities (without SA). Therefore, the identification of reliable biomarkers to differentiate cardiac cases from each other is necessary. In the current study, the potential of different microRNAs (miRNAs) as biomarkers in tissue and blood samples of cardiac death cases was analyzed. Blood and tissue samples of 24 MI, 21 SUD and 5 control (C) cases were collected during autopsy. Testing for significance and receiver operating characteristic analysis (ROC) were performed. The results show that miR-1, miR-133a and miR-26a possess a high diagnostic power to discriminate between different cardiac death causes in whole blood and in tissue.     

The potential use of Piwi-interacting RNA biomarkers in forensic body fluid identification: A proof-of-principle study

In the forensic community, RNA profiling has been investigated as a potential method to identify body fluids. Several RNA molecules, including messenger RNA (mRNA), microRNA (miRNA) and circular RNA (circRNA), have been explored as biomarkers to distinguish different body fluids and have led to considerable interest in the development of RNA biomarkers for forensic purposes. Piwi-interacting RNA (piRNA), a class of noncoding RNAs, is a potential biomarker for body fluid identification because of its short length (˜24–32 nt) and specific expression pattern in human tissues. In this proof-of-principle study, we examined the expression levels of four carefully selected piRNAs in forensically relevant biological fluids (venous blood, saliva, semen, menstrual blood and vaginal secretions) using TaqMan quantitative real-time polymerase chain reaction (TaqMan qPCR). piR-55521, which was not detectable in saliva, can differentiate semen from other body fluids because it was strongly expressed in semen compared to the remaining three fluids (> 4000-fold change). Furthermore, piR-55521 could be detected in semen samples made from as little as 200 pg of total RNA, and addition of female component had no effect on the detection limit. Furthermore, the expression differences of other piRNAs, piR-61648, piR-43994 and piR-33151, were statistically significant between at least two types of body fluids. Stability tests also indicated that these piRNAs could be effectively detected in dried samples under laboratory and outdoor conditions for at least six months. Although limited to four piRNAs, this study suggests that the expression pattern of piRNAs could be used to identify body fluids, and that piRNA (piR-55521) is specifically expressed in semen. Such findings suggest that additional work could identify other piRNAs that could serve as biomarkers to identify body fluids.     

Body fluid identification by integrated analysis of DNA methylation and body fluid-specific microbial DNA

Identification of body fluids found at crime scenes provides important information that can support a link between sample donors and actual criminal acts. Previous studies have reported that DNA methylation analysis at several tissue-specific differentially methylated regions (tDMRs) enables successful identification of semen, and the detection of certain bacterial DNA can allow for identification of saliva and vaginal fluid. In the present study, a method for detecting bacterial DNA was integrated into a previously reported multiplex methylation-sensitive restriction enzyme-polymerase chain reaction. The developed multiplex PCR was modified by the addition of a new semen-specific marker and by including amplicons for the 16S ribosomal RNA gene of saliva- and vaginal fluid-specific bacteria to improve the efficacy to detect a specific type of body fluid. Using the developed multiplex system, semen was distinguishable by unmethylation at the USP49, DACT1, and PFN3 tDMRs and by hypermethylation at L81528, and saliva could be identified by detection of saliva-specific bacteria, Veillonella atypica and/or Streptococcus salivarius. Additionally, vaginal fluid and menstrual blood were differentiated from other body fluids by hypomethylation at the PFN3 tDMR and the presence of vaginal fluid-specific bacteria, Lactobacillus crispatus and/or Lactobacillus gasseri. Because the developed multiplex system uses the same biological source of DNA for individual identification profiling and simultaneously analyses various types of body fluid in one PCR reaction, this method will facilitate more efficient body fluid identification in forensic casework.