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Kubo S, Amai K, Tanaka J, Niimi H. Female sample screening using colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) targeting non-coding RNA XIST. Forensic Sci Int 2024; 361:112081. [PMID: 38850616 DOI: 10.1016/j.forsciint.2024.112081] [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: 02/22/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/10/2024]
Abstract
Forensic sample screening is important for establishing an effective DNA typing workflow. The detection of sex-specific markers in forensic samples highlights the necessity for further analysis. Y-chromosome DNA can confirm male contributions, but female contributions are difficult to confirm using DNA-based methods. To address this, we developed a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting the long non-coding RNA X-inactive specific transcript (XIST) to screen female samples. Operating at 65 °C for 30 min, the assay yielded results discernible from the color change of the pH indicator dye. The assay showed a detection limit of approximately 0.5 µL of blood. The assay also detected XIST RNA in mixed body fluids and mock samples, indicating its potential applicability to casework samples. Taken together, our assay provides a rapid and simple strategy for screening female samples.
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Affiliation(s)
- Seiji Kubo
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan.
| | - Keito Amai
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Jin Tanaka
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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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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Skinner NE, Vergara C, El-Diwany R, Paul H, Skaist A, Wheelan SJ, Thomas DL, Ray SC, Balagopal A, Bailey JR. Decreased Activated CD4 + T Cell Repertoire Diversity After Antiretroviral Therapy in HIV-1/HCV Coinfection Correlates with CD4 + T Cell Recovery. Viral Immunol 2021; 34:622-631. [PMID: 34672777 PMCID: PMC8917883 DOI: 10.1089/vim.2021.0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Dysfunctional immune activation accumulates during chronic viral infection and contributes to disease pathogenesis. In HIV-1, immune activation is exacerbated by concurrent infection with hepatitis C virus (HCV), accelerating depletion of CD4+ T cells. HIV-1 suppression with antiretroviral therapy (ART) generally reconstitutes CD4+ T cell counts, while also reducing the proportion that is activated. Whether this immune reconstitution also reduces the complexity of the CD4+ T cell population is unknown. We sought to characterize the relationship between activated CD4+ T cell repertoire diversity and immune reconstitution following ART in HIV-1/HCV coinfection. We extracted T cell receptor (TCR) sequences from RNA sequencing data obtained from activated CD4+ T cells of HIV-1/HCV coinfected individuals before and after treatment with ART (clinical trial NCT01285050). There was notable heterogeneity in both the extent of CD4+ T cell reconstitution and in the change in activated CD4+ TCR repertoire diversity following ART. Decreases in activated CD4+ TCR repertoire diversity following ART were predictive of the degree of CD4+ T cell reconstitution. The association of decreased activated CD4+ TCR repertoire diversity and improved CD4+ T cell reconstitution may represent loss of nonspecifically activated TCR clonotypes, and possibly selective expansion of specifically activated CD4+ clones. These results provide insight into the dynamic relationship between activated CD4+ TCR diversity and CD4+ T cell recovery of HIV-1/HCV coinfected individuals after suppression of HIV-1 viremia.
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Affiliation(s)
- Nicole E. Skinner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Candelaria Vergara
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ramy El-Diwany
- Department of Surgery, and Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harry Paul
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alyza Skaist
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah J. Wheelan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David L. Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stuart C. Ray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ashwin Balagopal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Justin R. Bailey
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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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: 34] [Impact Index Per Article: 11.3] [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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Jusic A, Salgado-Somoza A, Paes AB, Stefanizzi FM, Martínez-Alarcón N, Pinet F, Martelli F, Devaux Y, Robinson EL, Novella S. Approaching Sex Differences in Cardiovascular Non-Coding RNA Research. Int J Mol Sci 2020; 21:E4890. [PMID: 32664454 PMCID: PMC7402336 DOI: 10.3390/ijms21144890] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular disease (CVD) is the biggest cause of sickness and mortality worldwide in both males and females. Clinical statistics demonstrate clear sex differences in risk, prevalence, mortality rates, and response to treatment for different entities of CVD. The reason for this remains poorly understood. Non-coding RNAs (ncRNAs) are emerging as key mediators and biomarkers of CVD. Similarly, current knowledge on differential regulation, expression, and pathology-associated function of ncRNAs between sexes is minimal. Here, we provide a state-of-the-art overview of what is known on sex differences in ncRNA research in CVD as well as discussing the contributing biological factors to this sex dimorphism including genetic and epigenetic factors and sex hormone regulation of transcription. We then focus on the experimental models of CVD and their use in translational ncRNA research in the cardiovascular field. In particular, we want to highlight the importance of considering sex of the cellular and pre-clinical models in clinical studies in ncRNA research and to carefully consider the appropriate experimental models most applicable to human patient populations. Moreover, we aim to identify sex-specific targets for treatment and diagnosis for the biggest socioeconomic health problem globally.
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Affiliation(s)
- Amela Jusic
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina;
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Ana B. Paes
- INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain; (A.B.P.); (N.M.-A.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Núria Martínez-Alarcón
- INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain; (A.B.P.); (N.M.-A.)
| | - Florence Pinet
- INSERM, CHU Lille, Institut Pasteur de Lille, University of Lille, U1167 F-59000 Lille, France;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milan, Italy;
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Emma Louise Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Susana Novella
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, and INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain
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