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Xiao Y, Tan M, Song J, Huang Y, Lv M, Liao M, Yu Z, Gao Z, Qu S, Liang W. Developmental validation of an mRNA kit: A 5-dye multiplex assay designed for body-fluid identification. Forensic Sci Int Genet 2024; 71:103045. [PMID: 38615496 DOI: 10.1016/j.fsigen.2024.103045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024]
Abstract
Identifying the sources of biosamples found at crime scenes is crucial for forensic investigations. Among the markers used for body fluid identification (BFI), mRNA has emerged as a well-studied marker because of its high specificity and remarkable stability. Despite this potential, commercially available mRNA kits specifically designed for BFI are lacking. Therefore, we developed an mRNA kit that includes 21 specific mRNA markers of body fluids, along with three housekeeping genes for BFI, to identify four forensic-relevant fluids (blood, semen, saliva, and vaginal fluids). In this study, we tested 451 single-body-fluid samples, validated the universality of the mRNA kit, and obtained a gene expression profile. We performed the validation studies in triplicates and determined the sensitivity, specificity, stability, precision, and repeatability of the mRNA kit. The sensitivity of the kit was found to be 0.1 ng. Our validation process involved the examination of 59 RNA mixtures, 60 body fluids mixtures, and 20 casework samples, which further established the reliability of the kit. Furthermore, we constructed five classifiers that can handle single-body fluids and mixtures using this kit. The classifiers output possibility values and identify the specific body fluids of interest. Our results showed the reliability and suitability of the BFI kit, and the Random Forest classifier performed the best, with 94% precision. In conclusion, we developed an mRNA kit for BFI which can be a promising tool for forensic practice.
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Affiliation(s)
- Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jinlong Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yihang Huang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Zailiang Yu
- Suzhou Microread Genetics Co.,Ltd, Suzhou, Jiangsu, PR China
| | - Zhixiao Gao
- Suzhou Microread Genetics Co.,Ltd, Suzhou, Jiangsu, PR China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China.
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2
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Liu Z, Yang J, Wang N, Liu J, Geng J, Zhu J, Cong B, Sun H, Wu R. Integrative lncRNA, circRNA, and mRNA analysis reveals expression profiles of six forensic body fluids/tissue. Int J Legal Med 2024; 138:731-742. [PMID: 37994925 DOI: 10.1007/s00414-023-03131-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
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.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, 050017, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou, 510080, China.
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Li S, Liu J, Zhao M, Su Y, Cong B, Wang Z. RNA quality score evaluation: A preliminary study of RNA integrity number (RIN) and RNA integrity and quality number (RNA IQ). Forensic Sci Int 2024; 357:111976. [PMID: 38447345 DOI: 10.1016/j.forsciint.2024.111976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/17/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
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.
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Affiliation(s)
- Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Song B, Qian J, Fu J. Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine. Int J Legal Med 2024; 138:329-350. [PMID: 37770641 DOI: 10.1007/s00414-023-03091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
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.
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Affiliation(s)
- Binghui Song
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Precision Medicine and DNA Forensic Medicine, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Laboratory of Forensic DNA, the Judicial Authentication Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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Liu Z, Liu J, Geng J, Wu E, Zhu J, Cong B, Wu R, Sun H. Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study. Forensic Sci Int Genet 2024; 68:102978. [PMID: 37995518 DOI: 10.1016/j.fsigen.2023.102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/21/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Enlin Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510080, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
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Chen X, Xu H, Zhu B. 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. Electrophoresis 2023; 44:1714-1724. [PMID: 37847880 DOI: 10.1002/elps.202300059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/12/2023] [Accepted: 09/07/2023] [Indexed: 10/19/2023]
Abstract
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.
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Affiliation(s)
- Xuebing Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R. China
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Wang HX, Liu XZ, He XM, Xiao C, Huang DX, Yi SH. Identification of Mixtures of Two Types of Body Fluids Using the Multiplex Methylation System and Random Forest Models. Curr Med Sci 2023; 43:908-918. [PMID: 37700190 DOI: 10.1007/s11596-023-2770-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/08/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVE Body fluid mixtures are complex biological samples that frequently occur in crime scenes, and can provide important clues for criminal case analysis. DNA methylation assay has been applied in the identification of human body fluids, and has exhibited excellent performance in predicting single-source body fluids. The present study aims to develop a methylation SNaPshot multiplex system for body fluid identification, and accurately predict the mixture samples. In addition, the value of DNA methylation in the prediction of body fluid mixtures was further explored. METHODS In the present study, 420 samples of body fluid mixtures and 250 samples of single body fluids were tested using an optimized multiplex methylation system. Each kind of body fluid sample presented the specific methylation profiles of the 10 markers. RESULTS Significant differences in methylation levels were observed between the mixtures and single body fluids. For all kinds of mixtures, the Spearman's correlation analysis revealed a significantly strong correlation between the methylation levels and component proportions (1:20, 1:10, 1:5, 1:1, 5:1, 10:1 and 20:1). Two random forest classification models were trained for the prediction of mixture types and the prediction of the mixture proportion of 2 components, based on the methylation levels of 10 markers. For the mixture prediction, Model-1 presented outstanding prediction accuracy, which reached up to 99.3% in 427 training samples, and had a remarkable accuracy of 100% in 243 independent test samples. For the mixture proportion prediction, Model-2 demonstrated an excellent accuracy of 98.8% in 252 training samples, and 98.2% in 168 independent test samples. The total prediction accuracy reached 99.3% for body fluid mixtures and 98.6% for the mixture proportions. CONCLUSION These results indicate the excellent capability and powerful value of the multiplex methylation system in the identification of forensic body fluid mixtures.
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Affiliation(s)
- Han-Xiao Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiao-Zhao Liu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xi-Miao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dai-Xin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shao-Hua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Fang C, Zhou P, Li R, Guo J, Qiu H, Zhang J, Li M, Yu C, Meng D, Xu X, Liu X, Guan D, Yan J. Development of a novel forensic age estimation strategy for aged blood samples by combining piRNA and miRNA markers. Int J Legal Med 2023; 137:1327-1335. [PMID: 37264192 DOI: 10.1007/s00414-023-03028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/22/2023] [Indexed: 06/03/2023]
Abstract
In forensic investigations, age estimation is vital for determining whether a suspect is under or over the legally defined adult age. With breakthroughs in RNA sequencing technology, small noncoding RNAs have provided new ways to solve problems related to the age estimation of trace or aged samples, owing to their small molecular weight and better stability. In our previous study, we had applied miRNAs for the age estimation of bloodstains; however, further improvement of the existing model is needed. PIWI-interacting RNAs (PiRNAs), which are 24-32 nt noncoding small RNA molecules involved in the PIWI-piRNA pathway, play an important role in the aging process. In this study, we explored the possibility of simultaneously analyzing piRNAs and miRNAs for better age estimation purpose. Through massively parallel sequencing, five age-related piRNAs were identified in blood samples that had been stored for eight years. Further real-time PCR analysis revealed that two piRNAs (piR-000753 and piR-020548) showed relatively higher efficiency in age estimation. Additionally, two age-related miRNAs (miR-324-3p and miR-330-5p) were used to build the estimation model. Among all algorithms tested, gradient boosting showed the lowest mean absolute error (MAE) and root mean square error (RMSE) values (3.171 and 4.403 years, respectively) for the validation dataset (n = 110). The errors of the model were less than 5 years and 10 years for 81.82% and 96.36% of the samples, respectively. The results suggest that the combined use of piRNA and miRNA markers may increase the accuracy of age estimation, and our new model has great potential for application in forensic casework.
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Affiliation(s)
- Chen Fang
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China.
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China.
| | - Peng Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Ran Li
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Jinghan Guo
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Huixian Qiu
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Jingjuan Zhang
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Min Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Chunjiang Yu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Deping Meng
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Xiaoqun Xu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People's Republic of China
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China
| | - Xu Liu
- Institute of Analysis and Testing, Beijing Academy of Science and Technology (Beijing Center for Physical and Chemical Analysis), Beijing, 100094, People's Republic of China
| | - Di Guan
- Institute of Analysis and Testing, Beijing Academy of Science and Technology (Beijing Center for Physical and Chemical Analysis), Beijing, 100094, People's Republic of China
| | - Jiangwei Yan
- Shanxi Medical University, 030001, Taiyuan, People's Republic of China.
- Department of Pathology and Forensic Medicine, School of Clinical and Basic Medical Sciences, Shandong First Medical University& Shandong Academy of Medical Sciences, Jinan, 250117, People's Republic of China.
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9
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Kyrgiafini MA, Mamuris Z. Circular RNAs and Their Role in Male Infertility: A Systematic Review. Biomolecules 2023; 13:1046. [PMID: 37509082 PMCID: PMC10377305 DOI: 10.3390/biom13071046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Male infertility is a global health problem that is on the rise. Today, many noncoding RNAs (ncRNAs) are associated with male infertility. Circular RNAs (circRNAs) have recently drawn attention, but a comprehensive understanding of the role of circRNAs in male infertility is limited. This systematic review investigates the differential expression of circRNAs in male infertility or circRNAs that could serve as candidate biomarkers. The PRISMA guidelines were used to search PubMed and Web of Science on 11 January 2023. Inclusion criteria were human participants, experimental studies aiming to associate circRNAs with male infertility reporting differentially expressed circRNAs, and the English language. A total of 156 articles were found, and after the screening and eligibility stages, 13 studies were included in the final sample. Many circRNAs are deregulated in male infertility, and their interactions with miRNAs play an important role in affecting cellular processes and pathways. CircRNAs could also be used as biomarkers to screen patients before sperm retrieval. However, most studies focus on the role of circRNAs in azoospermia, and there is a knowledge gap regarding other subtypes of male infertility. Future research is needed to explore the exact mechanism of action of circRNAs and investigate their use as biomarkers.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis Mezourlo, 41500 Larissa, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis Mezourlo, 41500 Larissa, Greece
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10
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Li Y, Wang Z, Ishmael D, Lvy Y. The potential of using non-coding RNAs in forensic science applications. Forensic Sci Res 2023; 8:98-106. [PMID: 37621455 PMCID: PMC10445561 DOI: 10.1093/fsr/owad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/21/2022] [Accepted: 01/29/2023] [Indexed: 08/26/2023] Open
Abstract
With the continuous development and integration of molecular biology and forensic science, non-coding RNAs (ncRNAs), especially ncRNAs with regulatory functions such as microRNA, long non-coding RNA, and circular RNA, have recently been actively explored by forensic scholars. In this study, we review the literature on these ncRNAs in various fields of forensic science, including postmortem interval determination, wound age estimation, forensic age assessment, cause of death analysis, and body fluid identification, aiming to evaluate the current research and provide a perspective for future applications.
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Affiliation(s)
- Yawen Li
- School of Basic Medical Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Zhuoqun Wang
- School of Basic Medical Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Dikeledi Ishmael
- School of Basic Medical Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Yehui Lvy
- School of Basic Medical Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Institute of Wound Prevention and Treatment, Shanghai University of Medicine and Health Sciences, Shanghai, China
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11
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Wei S, Hu S, Han N, Wang G, Chen H, Yao Q, Zhao Y, Ye J, Ji A, Sun Q. Screening and evaluation of endogenous reference genes for miRNA expression analysis in forensic body fluid samples. Forensic Sci Int Genet 2023; 63:102827. [PMID: 36642061 DOI: 10.1016/j.fsigen.2023.102827] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
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.
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Affiliation(s)
- Sunxiang Wei
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China; Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan 030001, Shanxi, People's Republic of China
| | - Sheng Hu
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China
| | - Na Han
- Chinese Center For Disease Control And Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing 102206, China
| | - Guoli Wang
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China; Marine College, Shandong University, Weihai 264209, Shandong, China
| | - Huixiang Chen
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China; Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan 030001, Shanxi, People's Republic of China
| | - Qianwei Yao
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China; Faculty of Forensic Sciences, Shanxi Medical University, Taiyuan 030001, Shanxi, People's Republic of China
| | - Yixia Zhao
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China
| | - Jian Ye
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China
| | - Anquan Ji
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China.
| | - Qifan Sun
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science, Ministry of Public Security (MPS), Beijing 100038, China.
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12
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A Comprehensive Characterization of Small RNA Profiles by Massively Parallel Sequencing in Six Forensic Body Fluids/Tissue. Genes (Basel) 2022; 13:genes13091530. [PMID: 36140698 PMCID: PMC9498867 DOI: 10.3390/genes13091530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
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.
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13
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Ouyang B, Han D, Guo Z, Deng J, Li W, Huang L, Liu J, Cai Z, Bian J, Huang S. Altered small non‑coding RNA expression profiles of extracellular vesicles in the prostatic fluid of patients with chronic pelvic pain syndrome. Exp Ther Med 2022; 23:382. [PMID: 35495611 PMCID: PMC9019767 DOI: 10.3892/etm.2022.11310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/21/2022] [Indexed: 11/06/2022] Open
Abstract
Chronic pelvic pain syndrome (CPPS) and chronic prostatitis (CP) is difficult to distinguish from each other, herein termed CP/CPPS. The present study aimed at gaining further insight into the change in extracellular vesicles (EVs) in the prostatic fluid of males with CPPS. From December 2019 to November 2020, after clinical screening, 24 patients with CPPS without obvious urinary symptoms and 13 healthy male participants were included. EVs were isolated from expressed prostatic secretion (EPS) of all subjects. The small non-coding ribonucleic acid (sncRNA) expression of EVs was sequenced, analyzed, and validated by quantitative real-time polymerase chain reaction (qPCR) assays. The results showed that numerous sncRNAs were differentially expressed between the patients and healthy participants. Further qPCR assays validated that several chronic pain-related miRNAs, including miR-204-5p, let-7d-3p, let-7b-3p, let-7c-3p, miR-146a-5p, and miR-320a-5p, were differentially expressed. Series sncRNAs including several chronic pain-related miRNAs were altered in EVs in prostatic fluid of patients with CPPS, which may serve as diagnostic markers for CPPS.
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Affiliation(s)
- Bin Ouyang
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Dayu Han
- Department of Andrology, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zexin Guo
- Reproductive Centre, The First Affiliated Hospital of Sun Yat‑sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Junhong Deng
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Weilong Li
- Department of Urology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 51018, P.R. China
| | - Liangliang Huang
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Jianming Liu
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Zhouda Cai
- Department of Andrology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Jun Bian
- Department of Urology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510700, P.R. China
| | - Shaoming Huang
- Department of Andrology, Ganzhou Municipal Hospital, Ganzhou, Jiangxi 341000, P.R. China
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14
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Bamberg M, Bruder M, Dierig L, Kunz SN, Schmidt M, Wiegand P. Best of both: a simultaneous analysis of mRNA and miRNA markers for body fluid identification. Forensic Sci Int Genet 2022; 59:102707. [DOI: 10.1016/j.fsigen.2022.102707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/19/2022]
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15
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Mokarram P, Niknam M, Sadeghdoust M, Aligolighasemabadi F, Siri M, Dastghaib S, Brim H, Ashktorab H. PIWI interacting RNAs perspectives: a new avenues in future cancer investigations. Bioengineered 2021; 12:10401-10419. [PMID: 34723746 PMCID: PMC8809986 DOI: 10.1080/21655979.2021.1997078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As a currently identified small non-coding RNAs (ncRNAs) category, the PIWI-interacting RNAs (piRNAs) are crucial mediators of cell biology. The human genome comprises over 30.000 piRNA genes. Although considered a new field in cancer research, the piRNA pathway is shown by the existing evidence as an active pathway in a variety of different types of cancers with critical impacts on main aspects of cancer progression. Among the regulatory molecules that contribute to maintaining the dynamics of cancer cells, the P-element Induced WImpy testis (PIWI) proteins and piRNAs, as new players, have not been broadly studied so far. Therefore, the identification of cancer-related piRNAs and the assessment of target genes of piRNAs may lead to better cancer prevention and therapy strategies. This review articleaimed to highlight the role and function of piRNAs based on existing data. Understanding the role of piRNA in cancer may provide perspectives on their applications as particular biomarker signature in diagnosis in early stage, prognosis and therapeutic strategies.
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Affiliation(s)
- Pooneh Mokarram
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran,Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran,CONTACT Pooneh Mokarram Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Niknam
- Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammadamin Sadeghdoust
- Department of Internal Medicine, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Farnaz Aligolighasemabadi
- Department of Internal Medicine, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sanaz Dastghaib
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Brim
- Pathology and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, Dc, USA
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16
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Sijen T, Harbison S. On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime. Genes (Basel) 2021; 12:1728. [PMID: 34828334 PMCID: PMC8617621 DOI: 10.3390/genes12111728] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.
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Affiliation(s)
- Titia Sijen
- Division Human Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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17
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Sharma S, Chophi R, Jossan JK, Singh R. Detection of bloodstains using attenuated total reflectance-Fourier transform infrared spectroscopy supported with PCA and PCA-LDA. MEDICINE, SCIENCE, AND THE LAW 2021; 61:292-301. [PMID: 33926284 DOI: 10.1177/00258024211010926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The most important task in a criminal investigation is to detect and identify the recovered biological stains beyond reasonable scientific doubt and preserve the sample for further DNA analysis. In the light of this fact, many presumptive and confirmatory tests are routinely employed in the forensic laboratories to determine the type of body fluid. However, the currently used techniques are specific to one type of body fluid and hence it cannot be utilized to differentiate multiple body fluids. Moreover, these tests consume the samples in due process, and thus it becomes a great limitation especially considering the fact that samples are recovered in minute quantity in forensic cases. Therefore, such limitations necessitate the use of non-destructive techniques that can be applied simultaneously to all types of bodily fluids and allow sample preservation for further analysis. In the current work, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy has been used to circumvent the aforementioned limitations. The important factors which could influence the detection of blood such as the effect of substrates, washing/chemical treatment, ageing, and dilution limits on the analysis of blood have been analysed. In addition, blood discrimination from non-blood substance (biological and non-biological in nature) has also been studied. Chemometric technique that is PCA-LDA has been used to discriminate blood from other body fluids and it resulted in 100% accurate classification. Furthermore, blood and non-blood substances including fake blood have also been classified into separate clusters with a 100% accuracy, sensitivity, and specificity. All-inclusive, this preliminary study substantiates the potential application of ATR-FTIR spectroscopy for the non-destructive identification of blood traces in simulated forensic casework conditions with 0% rate of false classification.
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Affiliation(s)
- Sweety Sharma
- Department of Forensic Science, 29766Punjabi University, Patiala, Punjab, India
| | - Rito Chophi
- Department of Forensic Science, 29766Punjabi University, Patiala, Punjab, India
| | | | - Rajinder Singh
- Department of Forensic Science, 29766Punjabi University, Patiala, Punjab, India
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18
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Kunnummal M, Angelin M, Das AV. PIWI proteins and piRNAs in cervical cancer: a propitious dart in cancer stem cell-targeted therapy. Hum Cell 2021; 34:1629-1641. [PMID: 34374035 DOI: 10.1007/s13577-021-00590-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
Any form of cancer is a result of uncontrolled cell growth caused by mutations and/or epigenetic alterations, implying that a balance of chromatin remodeling activities and epigenetic regulators is crucial to prevent the transformation of a normal cell to a cancer cell. Many of the chromatin remodelers do not recognize any specific sites on their targets and require guiding molecules to reach the respective targets. PIWI proteins and their interacting small non-coding RNAs (piRNAs) have proved to act as a guiding signal for such molecules. While epigenetic alterations lead to tumorigenesis, the stemness of cancer cells contributes to recurrence and metastasis of cancer. Various studies have propounded that the PIWI-piRNA complex also promotes stemness of cancer cells, providing new doors for target-mediated anti-cancer therapies. Despite the progress in diagnosis and development of vaccines, cervical cancer remains to be the second most prevalent cancer among women, due to the lack of cost-effective and accessible diagnostic and prevention methods. With the emergence of liquid biopsy, there is a significant demand for the ideal biomarker in the diagnosis of cancer. PIWI and piRNAs have been recommended to serve as prognostic and diagnostic markers, to differentiate early and later stages of cancer, including cervical cancer. This review discusses how PIWIs and piRNAs are involved in disease progression as well as their potential role in diagnostics and therapeutics in cervical cancer.
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Affiliation(s)
- Midhunaraj Kunnummal
- Cancer Research Program-12, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala, P.O. 695 014, India
- Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Mary Angelin
- Cancer Research Program-12, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala, P.O. 695 014, India
| | - Ani V Das
- Cancer Research Program-12, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala, P.O. 695 014, India.
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19
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Liu Y, He H, Xiao ZX, Ji A, Ye J, Sun Q, Cao Y. A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification. Brief Bioinform 2020; 22:6032627. [PMID: 33313714 DOI: 10.1093/bib/bbaa324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022] Open
Abstract
Identifying the types of body fluids left at the crime scene can be essential to reconstructing the crime scene and inferring criminal behavior. MicroRNA (miRNA) molecule extracted from the trace of body fluids is one of the most promising biomarkers for the identification due to its high expression, extreme stability and tissue specificity. However, the detection of miRNA markers is not the answer to a yes-no question but the probability of an assumption. Therefore, it is a crucial task to develop complicated methods combining multi-miRNAs as well as computational algorithms to achieve the goal. In this study, we systematically analyzed the expression of 10 most probable body fluid-specific miRNA markers (miR-451a, miR-205-5p, miR-203a-3p, miR-214-3p, miR-144-3p, miR-144-5p, miR-654-5p, miR-888-5p, miR-891a-5p and miR-124-3p) in 605 body fluids-related samples, including peripheral blood, menstrual blood, saliva, semen and vaginal secretion. We introduced the kernel density estimation (KDE) method and six well-established methods to classify the body fluids in order to find the most optimal combinations of miRNA markers as well as the corresponding classifying method. The results show that the combination of miR-451a, miR-891a-5p, miR-144-5p and miR-203a-3p together with KDE can achieve the most accurate and robust performance according to the cross-validation, independent tests and random perturbation tests. This systematic analysis suggests a reference scheme for the identification of body fluids in an accurate and stable manner.
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Affiliation(s)
- Yang Liu
- College of Life Sciences, Sichuan University, China
| | - Hongxia He
- National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science
| | - Zhi-Xiong Xiao
- College of Life Sciences, Sichuan University, Director of the Center of Growth, Metabolism and Aging
| | - Anquan Ji
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination
| | - Jian Ye
- People's Public Security University of China
| | - Qifan Sun
- Institute of Biophysics, Chinese Academy of Sciences
| | - Yang Cao
- Institute of Biophysics, Chinese Academy of Sciences
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20
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Wang S, Tao R, Ming T, Wang M, Liu J, He G, Zou X, Wang Z, Hou Y. Expression profile analysis and stability evaluation of 18 small RNAs in the Chinese Han population. Electrophoresis 2020; 41:2021-2028. [PMID: 32770750 DOI: 10.1002/elps.202000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/03/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022]
Abstract
In recent years, differentially expressed small RNAs have been widely used to identify the compositions of forensically relevant biological samples, and a vast number of such RNA candidates have been proposed. Nevertheless, when assessing the expression levels of target small RNAs using relative quantitative analysis methods, credible internal controls are usually required for reliable data normalization. Therefore, the identification of optimal reference genes is an important task. In this study, the expression profile of 18 small RNA reference genes was characterized in the Chinese Han population using TaqMan real-time quantitative PCR. Systematic evaluations of these candidate genes were performed based on their expression levels and stability in several common types of body fluids (i.e., venous blood, menstrual blood, saliva, semen, and vaginal secretions). Analysis results from the ΔCq method, BestKeeper, NormFinder, and geNorm were integrated by RefFinder for ranking and comparing the candidates in each type of body fluid. Among all the candidates, miR-191 was identified as the most suitable reference gene because it had a favorable ranking value in all tested samples. In addition, miR-423, miR-93, miR-484, and let-7i were also shown to be applicable reference genes. Overall, this study provides detailed assessment results of these candidate genes in different body fluids; thus, it could be used as a guide for the selection of reference genes according to their performance in the sample of choice.
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Affiliation(s)
- Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, P. R. China
| | - Tianyue Ming
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China
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21
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Liu B, Yang Q, Meng H, Shao C, Jiang J, Xu H, Sun K, Zhou Y, Yao Y, Zhou Z, Li H, Shen Y, Zhao Z, Tang Q, Xie J. Development of a multiplex system for the identification of forensically relevant body fluids. Forensic Sci Int Genet 2020; 47:102312. [PMID: 32480323 DOI: 10.1016/j.fsigen.2020.102312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Currently, mRNA profiling is widely investigated for forensic body fluid identification, while it is still required to advance the approach for those casework samples of limited quantity or low quality. The inclusion of circular RNAs (circRNAs) can facilitate the detection of mRNA markers in forensic body fluid identification. In this study, a multiplex assay for forensic body fluid identification (F18plex assay) was developed by incorporating 14 tissue-specific mRNA markers with circRNAs expression, 2 mRNA markers with high abundance and 2 housekeeping markers for the discrimination of the most common forensic body fluids, including blood, menstrual blood, saliva, vaginal secretion, semen and urine. The markers employed in the F18plex assay show similar specificity to previous reports. Additionally, even if all linear transcripts were completely erased, the expected markers in target biofluids could still be identified, which should help the discrimination of those aged biological stains. Results from sensitivity testing and the detection of mixtures demonstrate good sensitivity of the multiplex assay. Generally, full biomarker profiles could be obtained with ≥1 μl of blood, saliva, or semen, and ≥1 ng of total RNAs from menstrual blood, vaginal secretion, or urine samples, respectively, using this multiplex assay under the established conditions. Collectively, the newly established multiplex assay can assist in determining the biological origin of forensic stains.
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Affiliation(s)
- Baonian Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jieqing Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Kuan Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxiang Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Yiwen Shen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ziqin Zhao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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22
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Díez López C, Montiel González D, Haas C, Vidaki A, Kayser M. Microbiome-based body site of origin classification of forensically relevant blood traces. Forensic Sci Int Genet 2020; 47:102280. [PMID: 32244163 DOI: 10.1016/j.fsigen.2020.102280] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 12/12/2022]
Abstract
Human blood traces are amongst the most commonly encountered biological stains collected at crime scenes. Identifying the body site of origin of a forensic blood trace can provide crucial information in many cases, such as in sexual and violent assaults. However, means for reliably and accurately identifying from which body site a forensic blood trace originated are missing, but would be highly valuable in crime scene investigations. With this study, we introduce a taxonomy-independent deep neural network approach based on massively parallel microbiome sequencing, which delivers accurate body site of origin classification of forensically-relevant blood samples, such as menstrual, nasal, fingerprick, and venous blood. A total of 50 deep neural networks were trained using a large 16S rRNA gene sequencing dataset from 773 reference samples, including 220 female urogenital tract, 190 nasal cavity, 213 skin, and 150 venous blood samples. Validation was performed with de-novo generated 16S rRNA gene massively parallel sequencing (MPS) data from 94 blood test samples of four different body sites, and achieved high classification accuracy with AUC values at 0.992 for menstrual blood (N = 23), 0.978 for nasal blood (N = 16), 0.978 for fingerprick blood (N = 30), and 0.990 for venous blood (N = 25). The obtained highly accurate classification of menstrual blood was independent of the day of the menses, as established in additional 86 menstrual blood test samples. Accurate body site of origin classification was also revealed for 45 fresh and aged mock casework blood samples from all four body sites. Our novel microbiome approach works based on the assumption that a sample is from blood, as can be obtained in forensic practise from prior presumptive blood testing, and provides accurate information on the specific body source of blood, with high potentials for future forensic applications.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands.
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23
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Fonseca Cabral G, Azevedo dos Santos Pinheiro J, Vidal AF, Santos S, Ribeiro-dos-Santos Â. piRNAs in Gastric Cancer: A New Approach Towards Translational Research. Int J Mol Sci 2020; 21:ijms21062126. [PMID: 32204558 PMCID: PMC7139476 DOI: 10.3390/ijms21062126] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Gastric cancer is currently the third leading cause of cancer-related deaths worldwide, usually diagnosed at late stages. The development of new biomarkers to improve its prevention and patient management is critical for disease control. piRNAs are small regulatory RNAs important for gene silencing mechanisms, mainly associated with the silencing of transposable elements. piRNA pathways may also be involved in gene regulation and the deregulation of piRNAs may be an important factor in carcinogenic processes. Thus, several studies suggest piRNAs as potential cancer biomarkers. Translational studies suggest that piRNAs may regulate key genes and pathways associated with gastric cancer progression, though there is no functional annotation in piRNA databases. The impacts of genetic variants in piRNA genes and their influence in gastric cancer development remains elusive, highlighting the gap in piRNA regulatory mechanisms knowledge. Here, we discuss the current state of understanding of piRNA-mediated regulation and piRNA functions and suggest that genetic alterations in piRNA genes may affect their functionality, thus, it may be associated with gastric carcinogenesis. Conclusions: In the era of precision medicine, investigations about genetic and epigenetic mechanisms are essential to further comprehend gastric carcinogenesis and the role of piRNAs as potential biomarkers for translational research.
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Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Amanda Ferreira Vidal
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
- Correspondence: ; Tel.: +55-091-3201-7843
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24
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Sharma S, Singh R. Detection and discrimination of seminal fluid using attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy combined with chemometrics. Int J Legal Med 2019; 134:411-432. [PMID: 31814056 DOI: 10.1007/s00414-019-02222-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
Semen is most frequently encountered body fluid in forensic cases apart from blood especially in sexual assault cases. The presence and absence of semen can help in conviction or exoneration of a suspect by either confirming or refuting the claims put forward by the suspect and the victim. However, in the wake of limited studies on non-destructive and rapid analysis of semen, it is fairly difficult. Therefore, it is an increasing demand to pioneer the application of available analytical methods in such manner that non-destructive, automated, rapid, and reliable identification and discrimination of body fluids can be established. In the present study, such a methodological application of attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy has been put forward as one of the initial steps towards the identification and discrimination/classification of seminal fluid from vaginal fluid and other human biological as well as non-biological look-alike semen substances using chemometric tools which are principal component analysis (PCA), partial least square regression (PLSR), and linear discriminant analysis (LDA). Effect of other simulated factors such as substrate interference, mixing with other body fluids, dilutions, and washing and chemical treatments to the samples has been studied. PCA resulted in 98.8% of accuracy for the discrimination of seminal fluid from vaginal fluid whilst 100% accuracy was obtained using LDA method. One hundred percent discrimination was achieved to discriminate semen from other biological fluids using PLSR and LDA, and from non-biological substances using PCA-LDA models. Furthermore, results of the effect of substrates, chemical treatment, mixing with vaginal secretions, and dilution have also been described.
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Affiliation(s)
- Sweety Sharma
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India
| | - Rajinder Singh
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India.
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25
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Wang S, Wang Z, Tao R, Song F, Hou Y. Validating the consistency of cSNPs analysis results between DNA and RNA using SNaPshot method. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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26
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Lv Y, Li S, Li Z, Tao R, Shao Y, Chen Y. Quantitative analysis of noncoding RNA from paired fresh and formalin-fixed paraffin-embedded brain tissues. Int J Legal Med 2019; 134:873-884. [PMID: 31788707 DOI: 10.1007/s00414-019-02210-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 11/13/2019] [Indexed: 12/30/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are commonly used both clinically and in forensic pathology. Recently, noncoding RNA (ncRNA) has attracted interest among molecular medical researchers. However, it remains unclear whether newly identified ncRNAs, such as long noncoding RNA (lncRNA) and circular RNA (circRNA), remain stable for downstream molecular analysis in FFPE tissues. Here, we assessed the feasibility of using autoptic FFPE brain tissues from eight individuals to perform quantitative molecular analyses. Selected RNA targets (9 mRNAs and 15 ncRNAs) with different amplicon lengths were studied by RT-qPCR in paired fresh and FFPE specimens. For RNA quality assessment, RNA purity and yield were comparable between the two sample cohorts; however, the RNA integrity number decreased significantly during FFPE sampling. Amplification efficiency also displayed certain variability related with amplicon length and RNA species. We found molecular evidence that short amplicons of mRNA, lncRNA, and circRNA were amplified more efficiently than long amplicons. With the assistance of RefFinder, 5S, SNORD48, miR-103a, and miR-125b were selected as reference genes given their high stability. After normalization, we found that short amplicon markers (e.g., ACTB mRNA and MALAT1 lncRNA) exhibited high consistency of quantification in paired fresh/FFPE samples. In particular, circRNAs (XPO1, HIPK3, and TMEM56) presented relatively consistent and stable expression profiles in FFPE tissues compared with their corresponding linear transcripts. Additionally, we evaluated the influence of prolonged storage time on the amplification of gene transcripts and found that short amplicons still work effectively in archived FFPE biospecimens. In conclusion, our findings demonstrate the possibility of performing accurate quantitative analysis of ncRNAs using short amplicons and standardized RT-qPCR assays in autopsy-derived FFPE samples.
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Affiliation(s)
- Yehui Lv
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China. .,School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China.
| | - Shiying Li
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Zhihong Li
- School of basic medical sciences, Shanghai University of Medicine & Health Science, Shanghai, 201318, China
| | - Ruiyang Tao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China.,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yu Shao
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China
| | - Yijiu Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610065, China. .,Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, 200063, China.
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27
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Wang S, Wang Z, Tao R, Wang M, Liu J, He G, Yang Y, Xie M, Zou X, Hou Y. Expression profile analysis of piwi-interacting RNA in forensically relevant biological fluids. Forensic Sci Int Genet 2019; 42:171-180. [DOI: 10.1016/j.fsigen.2019.07.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/21/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
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