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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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Hanson E, Dørum G, Zamborlin M, Wang S, Gysi M, Ingold S, Lagace R, Roth C, Haas C, Ballantyne J. Targeted S5 RNA sequencing assay for the identification and direct association of common body fluids with DNA donors in mixtures. Int J Legal Med 2023; 137:13-32. [PMID: 36333511 DOI: 10.1007/s00414-022-02908-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
The evidentiary value of DNA profiles varies depending upon the context in which the DNA was found. Linking a DNA profile to a particular cellular phenotype in mixtures may aid in assessing its evidentiary relevance and value. We report the development of two dual-function high-resolution messenger RNA (mRNA) sequencing assays that can each identify the presence of 6 body fluids/tissues (blood, semen, saliva, vaginal secretions, menstrual blood, skin) and, via coding region SNPs (cSNPs) present in the body fluid-specific mRNA transcripts, directly associate particular body fluids with their specific DNA donors in mixtures. The original blood, semen, and saliva (BSS) assay contains 23 cSNPs for blood, semen, and saliva, while the expanded 6F (all 6 fluids/tissues) assay encompasses the BSS assay and also contains 23 additional cSNPs for vaginal secretions, menstrual blood, and skin. Software tools were developed to infer the identity of the body fluids present as well as providing the corresponding cSNP genotypes. Concomitant genomic DNA assays (BSS-d and 6F-d), required to genotype the same cSNPs from persons of interest/inferred contributors to the body fluid mixture, were also developed. Body fluid specificity was demonstrated by the ability to identify the body fluid origin of single-source and two-fluid admixtures. The discriminatory power (European Caucasians) for all body fluids is 0.957-0.997, with linkage disequilibrium considered. Reciprocal body fluid admixtures (mixture pairs with the same two donors but reversed body fluid types) were used to demonstrate the ability to identify the body fluid source of origin as well as associate the donor of each of the two fluids.
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Affiliation(s)
- Erin Hanson
- Department of Chemistry, University of Central Florida, P.O. Box 162367, Orlando, FL, 32816-2367, USA.,National Center for Forensic Science, Orlando, FL, USA
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Manuel Zamborlin
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Shouyu Wang
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Sabrina Ingold
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Robert Lagace
- Life Sciences/HID, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Chantal Roth
- Life Sciences/HID, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Jack Ballantyne
- Department of Chemistry, University of Central Florida, P.O. Box 162367, Orlando, FL, 32816-2367, USA. .,National Center for Forensic Science, Orlando, FL, USA.
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A recombinase polymerase amplification (RPA) combined with strip visualization method for RNA-based presumptive tests of saliva and vaginal secretion. Forensic Sci Int Genet 2023; 62:102788. [PMID: 36265335 DOI: 10.1016/j.fsigen.2022.102788] [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: 06/23/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Identifying the origin of body fluids is a critical step in a forensic investigation. One widely used method to identify human body fluids is based on the color visualization of immune antigen detection strips for detecting hemoglobin in blood and prostate-specific antigen in semen. It is highly imperative to construct an easy-to-perform, mRNA-based method for the point-of-care identification of other human body fluids, such as saliva and vaginal secretion. Here, we established specific strips with the mRNA markers STATH (for saliva) and SPINK5 (for vaginal secretion) via reverse transcription recombinase polymerase amplification (RT-RPA) and lateral flow dipstick (LFD) assays (RT-RPA-LFD). RT-RPA could be accomplished in a single tube at a wide temperature range of 30-42 ℃ within 10-25 min if we do not count time for RNA extraction. The diluted RPA products were added onto the LFD strip pad to visually observe the color change of the Control/Test line. The tissue specificity and detection limit of the assays were evaluated using the optimized reaction conditions of RPA at 37 ℃ for 15 min. The positive signals of STATH were observed both in saliva and nasal secretions. SPINK5 was positive in a template-dependent manner in 4 out of 30 female urine samples in addition to vaginal secretion and menstrual blood samples. Cross-reactions were not detected in semen, skin swabs, sweat, or male urine. Both assays were capable of detecting aged samples, which were stored for 180 days (saliva) or 300 days (vaginal secretion) at room temperature. Moreover, saliva or vaginal secretion was successfully detected in all kinds of mixtures made from various body fluids. Overall, the rapid strip test method by the RT-RPA-LFD assay is simple, time-saving and highly sensitive for estimating the tissue origin of saliva and vaginal secretion. This method for the rapid RNA-based presumptive tests of the tissue type of body fluids is easy to perform prior to a multiplex mRNA analysis, which can demonstrate more reliable saliva or vaginal secretion identification.
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Layne TR, Nouwairi RL, Fleming R, Blair H, Landers JP. Rapid Microchip Electrophoretic Separation of Novel Transcriptomic Body Fluid Markers for Forensic Fluid Profiling. MICROMACHINES 2022; 13:1657. [PMID: 36296010 PMCID: PMC9609788 DOI: 10.3390/mi13101657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Initial screening of criminal evidence often involves serological testing of stains of unknown composition and/or origin discovered at a crime scene to determine the tissue of origin. This testing is presumptive but critical for contextualizing the scene. Here, we describe a microfluidic approach for body fluid profiling via fluorescent electrophoretic separation of a published mRNA panel that provides unparalleled specificity and sensitivity. This centrifugal microfluidic approach expedites and automates the electrophoresis process by allowing for simple, rotationally driven flow and polymer loading through a 5 cm separation channel; with each disc containing three identical domains, multi-sample analysis is possible with a single disc and multi-sample detection per disc. The centrifugal platform enables a series of sequential unit operations (metering, mixing, aliquoting, heating, storage) to execute automated electrophoretic separation. Results show on-disc fluorescent detection and sizing of amplicons to perform comparably with a commercial 'gold standard' benchtop instrument and permitted sensitive, empirical discrimination between five distinct body fluids in less than 10 min. Notably, our microfluidic platform represents a faster, simpler method for separation of a transcriptomic panel to be used for forensically relevant body fluid identification.
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Affiliation(s)
- Tiffany R. Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - Renna L. Nouwairi
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - Rachel Fleming
- Institute of Environmental Science and Research Limited, Auckland 1025, New Zealand
| | - Haley Blair
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
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Development and validation of molecular methodologies for identification of biological traces from crime scenes. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Evaluation of the Effects of Different Sample Collection Strategies on DNA/RNA Co-Analysis of Forensic Stains. Genes (Basel) 2022; 13:genes13060983. [PMID: 35741745 PMCID: PMC9222428 DOI: 10.3390/genes13060983] [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: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
The aim of this study was to evaluate the impact of different moistening agents (RNase-free water, absolute anhydrous ethanol, RNAlater®) applied to collection swabs on DNA/RNA retrieval and integrity for capillary electrophoresis applications (STR typing, cell type identification by mRNA profiling). Analyses were conducted on whole blood, luminol-treated diluted blood, saliva, semen, and mock skin stains. The effects of swab storage temperature and the time interval between sample collection and DNA/RNA extraction were also investigated. Water provided significantly higher DNA yields than ethanol in whole blood and semen samples, while ethanol and RNAlater® significantly outperformed water in skin samples, with full STR profiles obtained from over 98% of the skin samples collected with either ethanol or RNAlater®, compared to 71% of those collected with water. A significant difference in mRNA profiling success rates was observed in whole blood samples between swabs treated with either ethanol or RNAlater® (100%) and water (37.5%). Longer swab storage times before processing significantly affected mRNA profiling in saliva stains, with the success rate decreasing from 91.7% after 1 day of storage to 25% after 7 days. These results may contribute to the future development of optimal procedures for the collection of different types of biological traces.
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Precise and comprehensive determination of multiple body fluids by applying statistical cutoff values to a multiplex reverse transcription-PCR and capillary electrophoresis procedure for forensic purposes. Leg Med (Tokyo) 2022; 58:102087. [DOI: 10.1016/j.legalmed.2022.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022]
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Evaluation and simultaneous determination of rectal mucosa markers by multiplex reverse transcription-PCR for biological evidence of sexual assault with anal penetration. Forensic Sci Int Genet 2022; 59:102712. [DOI: 10.1016/j.fsigen.2022.102712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/28/2022] [Accepted: 04/13/2022] [Indexed: 11/23/2022]
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Bamberg M, Dierig L, Kulstein G, Kunz SN, Schmidt M, Hadrys T, Wiegand P. Development and validation of an mRNA-based multiplex body fluid identification workflow and a rectal mucosa marker pilot study. Forensic Sci Int Genet 2021; 54:102542. [PMID: 34098418 DOI: 10.1016/j.fsigen.2021.102542] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 01/26/2023]
Abstract
Molecular identification of body fluids and tissues is crucial in order to understand the circumstances of crimes. For that reason, molecular investigations used to identify body fluids/tissues have increasingly been examined recently. Various studies have proved that messenger RNA (mRNA) profiling is a sensitive and robust method for body fluid/tissue identification. The forensically relevant body fluids/tissues blood, semen, saliva, vaginal secretion, menstrual blood and skin have all been detected successfully by applying suitable mRNA assay. However, rectal mucosa, which can be found as evidence in sexual assault cases, has been neglected in forensic investigations. So far there is no mRNA marker to detect rectal mucosa, although anal penetration occurs in a large number of sexual assaults (23.2% of female victims and 50% of male victims). In this study, specific and sensitive mRNA markers for forensically relevant body fluids were adapted and validated in an mRNA multiplex assay for routine casework. This included the implementation of a DNA/RNA re-extraction method for automated extraction that can be integrated into casework without loss of DNA. This re-extraction method and the mRNA multiplex assay were tested using casework samples. PCR-primers were designed for the identification of rectal mucosa and the more effective marker MUC12 was integrated into an extended multiplex assay. The result of our study is a highly specific and sensitive mRNA multiplex assay plus an automated DNA/RNA re-extraction method, that can be integrated into casework and identify rectal mucosa for the first time.
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Affiliation(s)
- Malte Bamberg
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Lisa Dierig
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | | | - Sebastian N Kunz
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Max Schmidt
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, DNA Department, Maillingerstr. 15, 80636 Munich, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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Hassan FM, Razik HAA, Wadie MS, Abdelfattah DS. XIST and RPS4Y1 long non-coding RNA transcriptome as sex biomarkers in different body fluids. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2019. [DOI: 10.1186/s41935-019-0122-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Fabbri M, Venturi M, Talarico A, Inglese R, Gaudio R, Neri M. mRNA profiling: Application to an old casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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