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Makowska A, Weiskirchen R. Nasopharyngeal Carcinoma Cell Lines: Reliable Alternatives to Primary Nasopharyngeal Cells? Cells 2024; 13:559. [PMID: 38606998 PMCID: PMC11011377 DOI: 10.3390/cells13070559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a type of cancer that originates from the mucosal lining of the nasopharynx and can invade and spread. Although contemporary chemoradiotherapy effectively manages the disease locally, there are still challenges with locoregional recurrence and distant failure. Therefore, it is crucial to have a deeper understanding of the molecular basis of NPC cell movement in order to develop a more effective treatment and to improve patient survival rates. Cancer cell line models are invaluable in studying health and disease and it is not surprising that they play a critical role in NPC research. Consequently, scientists have established around 80 immortalized human NPC lines that are commonly used as in vitro models. However, over the years, it has been observed that many cell lines are misidentified or contaminated by other cells. This cross-contamination leads to the creation of false cell lines that no longer match the original donor. In this commentary, we discuss the impact of misidentified NPC cell lines on the scientific literature. We found 1159 articles from 2000 to 2023 that used NPC cell lines contaminated with HeLa cells. Alarmingly, the number of publications and citations using these contaminated cell lines continued to increase, even after information about the contamination was officially published. These articles were most commonly published in the fields of oncology, pharmacology, and experimental medicine research. These findings highlight the importance of science policy and support the need for journals to require authentication testing before publication.
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Affiliation(s)
- Anna Makowska
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, RWTH University Hospital Aachen, D-52074 Aachen, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
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2
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Abboosh TS, Kassab AC, Al-Dogmi AM, Safhi FA, Alshehri E, Alotaibi AM, Al-Qahtani WS. Identification, forensic evidences and effect of the most used lip cosmetics on the human STR profiling at Kingdom of Saudi Arabia. Forensic Sci Int 2023; 350:111684. [PMID: 37536076 DOI: 10.1016/j.forsciint.2023.111684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/09/2023] [Indexed: 08/05/2023]
Abstract
This study aimed to identify the DNA STR profiles that were obtained from the lips with various lip cosmetics involved in lip pencil, lipsticks and lip gloss for a brand - Makeup Forever and lip balms (Labello brand) - have been popularly used by Saudi women at KSA. The study was involved 35 unrelated participants (healthy female donors) aged between 26 and 32. The swabbing of lip cosmetics was done prior to using them as negative control samples, other sterilized swabs were collected from the used lip cosmetics which contained the lip cells for each participant as a study sample. Moreover, the buccal swabs were firmly collected from the cleaned oral cavities for the same donors as reference samples. The air-drying of the collected swabs was done for ten minutes at room temperature and then stored them at - 20 °C before the DNA analysis. The 7500 Real-Time PCR (qRT-PCR) was quantified the extracted DNA. The amplification of 16 STR loci was done using the AmpFlSTR® Identifiler® PCR amplification kit using the Thermocycler ABI 9700 to amplify the extracted DNA. The Applied Bio-systems 3130™ Genetic Analyzer with Gene Mapper® ID-X Software v3.5 was used to analyze the PCR products. The data for quantifying DNA recorded significant decrease in the concentrations of DNA samples ranged from 0.15 to 0.55 ng/µL in comparison to the reference samples, while DNA was not detected in all the negative control samples. Some STR loci showed considerably high inhibition and low heterozygosity loss in the study samples compared to the reference and negative samples. The possibility of extracting DNA samples from lip cosmetics were used in the present study could be useful and successful in some cases due to the effect of the chemical compositions such as heavy pigments, organic components, and aromatic wax on the STR profiles in the lip cosmetics, especially in the lipsticks, lip glosses and lip pencils.
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Affiliation(s)
- Tahani Saeed Abboosh
- Ministry of Interior, Public Security, Forensic Evidence Laboratories, Criminal Examinations, Riyadh, Saudi Arabia
| | - Ahmed Ch Kassab
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, P.O. Box 6830, Riyadh 11452, Saudi Arabia.
| | - Amal M Al-Dogmi
- Department of Biology, College of Science, Jouf University, Sakakah, Saudi Arabia
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Eman Alshehri
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, P.O. Box 6830, Riyadh 11452, Saudi Arabia.
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3
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Ahmed AM, Alotaibi AM, Al-Qahtani WS, Tripet F, Amer SA. Forensic DNA Analysis of Mixed Mosquito Blood Meals: STR Profiling for Human Identification. Insects 2023; 14:insects14050467. [PMID: 37233095 DOI: 10.3390/insects14050467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Mosquito vectors captured at a crime scene are forensically valuable since they feed on human blood, and hence, human DNA can be recovered to help identify the victim and/or the suspect. This study investigated the validity of obtaining the human short tandem repeats (STRs) profile from mixed blood meals of the mosquito, Culex pipiens L. (Diptera, Culicidae). Thus, mosquitoes were membrane-feed on blood from six different sources: a human male, a human female, mixed human male-female blood, mixed human male-mouse blood, mixed human female-mouse blood, and mixed human male-female-mouse blood. DNA was extracted from mosquito blood meals at 2 h intervals up to 72 h post-feeding to amplify 24 human STRs. Data showed that full DNA profiles could be obtained for up to 12 h post-feeding, regardless of the type of blood meal. Complete and partial DNA profiles were obtained up to 24 h and 36 h post-feeding, respectively. The frequencies of STR loci decreased over time after feeding on mixed blood until they became weakly detectable at 48 h post-feeding. This may indicate that a blood meal of human blood mixed with animal blood would contribute to maximizing DNA degradation and thus affects STR identification beyond 36 h post-feeding. These results confirm the feasibility of human DNA identification from mosquito blood meals, even if it is mixed with other types of non-human blood, for up to 36 h post-feeding. Therefore, blood-fed mosquitoes found at the crime scene are forensically valuable, as it is possible to obtain intact genetic profiles from their blood meals to identify a victim, a potential offender, and/or exclude a suspect.
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Affiliation(s)
- Ashraf Mohamed Ahmed
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Amani Mohammed Alotaibi
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 11587, Saudi Arabia
| | - Wedad Saeed Al-Qahtani
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 11587, Saudi Arabia
| | - Frederic Tripet
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
| | - Sayed Amin Amer
- Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh 11587, Saudi Arabia
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Kaesler T, Kirkbride KP, Linacre A. Persistence of touch DNA on commonly encountered substrates in different storage conditions. Forensic Sci Int 2023; 348:111728. [PMID: 37209547 DOI: 10.1016/j.forsciint.2023.111728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 05/08/2023] [Indexed: 05/22/2023]
Abstract
The persistence of touch DNA deposited after realistic handling of items typically encountered in forensic investigations has been the subject of few studies. Understanding the long-term persistence of touch DNA on different substrates in varying conditions can be central to the effective triage of samples for further processing. As the time between an alleged incident and collection of evidence may vary from a few days to years after an alleged event, this study assessed three different common substrates for the persistence of touch DNA over a time span up to 9 months. These substrates included fabric, steel, and rubber, each of which were handled in a way to imitate what may happen during a criminal act. The three substrates were exposed to two different environments for up to 9 months: inside a dark cupboard with no traffic to act as a control and an outside semi-exposed environment. Ten replicates from each of the 3 substrates were tested at 5 time points to create 300 samples. All samples were processed using a standard operating workflow to provide genotype data after exposure to different environments. It was found that the fabric samples produced informative STR profiles (defined here as 12 or more alleles) up to the 9 month timepoint for either environment. The rubber and steel substrates for the inside condition produced informative STR profiles up to the 9 month timepoint, but only generated informative STR profiles for the outside condition up to 3 and 6 months, respectively. These data add to our understanding of the external factors that affect DNA persistence.
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Affiliation(s)
- Todd Kaesler
- College of Science & Engineering, Flinders University, Adelaide 5042, South Australia.
| | - K Paul Kirkbride
- College of Science & Engineering, Flinders University, Adelaide 5042, South Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide 5042, South Australia
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5
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Weiskirchen S, Schröder SK, Buhl EM, Weiskirchen R. A Beginner's Guide to Cell Culture: Practical Advice for Preventing Needless Problems. Cells 2023; 12. [PMID: 36899818 DOI: 10.3390/cells12050682] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/18/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
The cultivation of cells in a favorable artificial environment has become a versatile tool in cellular and molecular biology. Cultured primary cells and continuous cell lines are indispensable in investigations of basic, biomedical, and translation research. However, despite their important role, cell lines are frequently misidentified or contaminated by other cells, bacteria, fungi, yeast, viruses, or chemicals. In addition, handling and manipulating of cells is associated with specific biological and chemical hazards requiring special safeguards such as biosafety cabinets, enclosed containers, and other specialized protective equipment to minimize the risk of exposure to hazardous materials and to guarantee aseptic work conditions. This review provides a brief introduction about the most common problems encountered in cell culture laboratories and some guidelines on preventing or tackling respective problems.
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6
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Winnepenninckx A, Verhoeven E, Vermeulen S, Jeurissen B, Borgers E, Bekaert B. Time since contact influences DNA profiling success of cartridges and fired cartridge casings. Forensic Sci Int 2022; 340:111474. [PMID: 36174383 DOI: 10.1016/j.forsciint.2022.111474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/18/2022] [Indexed: 11/04/2022]
Abstract
Forensic DNA analysis of cartridges and fired cartridge casings remains challenging, possibly due to the heat and pressure generated during firing of the weapon as well as metal ions from the casings that have been suggested to initiate DNA degradation and inhibit PCR during the DNA profiling process. Even though recently developed DNA recovery protocols have shown to significantly improve DNA yields and DNA profile success rates no information is available on whether the time interval between contact and the DNA recovery process has an influence on these outcomes. In the current study 40 cartridges and 40 fired cartridge casings were left untreated for 24 h or 1 week after which the rinse-and-swab technique was used to collect DNA. Higher DNA yields and higher DNA profile success rates were obtained from cartridges compared to fired cartridge casings. The same general observation was made when cartridges and fired cartridge casings were processed after 24 h compared to after 1 week. In addition, DNA profiles suitable for comparison could still be generated from samples when real-time PCR quantification indicated DNA concentrations < 0.001 ng/μl, suggesting that quantification results may not be reliable when assessing the presence of DNA on such items. In conclusion, the results indicate that cartridges and fired cartridge casings should be processed for DNA profiling as soon as possible and that DNA quantification results should be interpreted with caution as DNA profiles suitable for comparison could be missed.
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Affiliation(s)
- Astrid Winnepenninckx
- KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium
| | - Elke Verhoeven
- Technical and Scientific Police, Federal Judicial Police, Leuven, Belgium
| | - Steve Vermeulen
- Technical and Scientific Police, Federal Judicial Police, Leuven, Belgium
| | - Bert Jeurissen
- Technical and Scientific Police, Federal Judicial Police, Leuven, Belgium
| | | | - Bram Bekaert
- KU Leuven, Forensic Biomedical Sciences, Department of Imaging & Pathology, Leuven, Belgium; UZ Leuven, Laboratory of Forensic Genetics, Leuven, Belgium.
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Martin B, Kaesler T, Kirkbride KP, Linacre A. The influences of dusty environments on the STR typing success of post-detonation touch DNA samples. Forensic Sci Int Genet 2021; 57:102651. [PMID: 34896974 DOI: 10.1016/j.fsigen.2021.102651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 11/04/2022]
Abstract
As the use of improvised explosive devices (IEDs) in a broad spectrum of offences continues, it is vital that research is performed to assess the capabilities of the forensic DNA profiling technology currently available to provide information as to potential perpetrators. This work investigates some of the most important gaps in our understanding surrounding the poor success rates in DNA profiling obtained through the sampling of touch DNA on post-detonation IED samples. It has been previously suggested that the use of Diamond™ Nucleic Acid Dye may fix cells to a surface, therefore reducing the effect of an experimental process to remove or damage those cells. This was found not to be the case for samples undergoing a detonation as there was no difference in the resultant post-detonation profiles between the stained samples, stained prior to detonation, and unstained samples. The comparison of data from previously performed research, within an enclosed explosives chamber, to real-world outdoor detonation events in a rural and dusty environment was investigated. It was found that there was a significant difference between the environments for the aluminium but not for the battery or electrical tape substrates indicating that environment has the potential to influence STR success through the introduction of PCR inhibitors; humic acid within rural natural dust was introduced here. No difference was observed in cell loss due to the detonation between environments and the dirt within the PCR was higher in the 'outdoor' samples. The effect on cellular retention and damage due to the sample's distance from the charge has been thoroughly investigated through incremental 100 mm exposure. Distance from the charge was found to affect every metric analysed; these being the cell loss from samples, the number of alleles amplified in resultant direct PCR profiles, and the total RFU of the subsequent profiles. These data outline the importance of this work allowing results to be assessed and triage decisions be made accordingly. The analysis of wood, PVC pipe, a mobile phone with rubber buttons, a SIM card, and a circuit board showed that none of these samples at 400 mm from the charge caused substrate specific PCR inhibition. On-site collection teams do not need to triage collection based on these sample types as there was no significant difference observed in their ability to return DNA profiling data. Surface area and inhibitor presence are key variables to consider when determining STR processing workflow for post-detonation samples as for samples with larger surface areas within the outdoor environment PCR post-extraction is preferential to direct PCR.
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Affiliation(s)
- Belinda Martin
- College of Science and Engineering, FlindersUniversity; Biological Sciences Building, 5042 Bedford Park, South Australia, Australia.
| | - Todd Kaesler
- College of Science and Engineering, FlindersUniversity; Biological Sciences Building, 5042 Bedford Park, South Australia, Australia
| | - K Paul Kirkbride
- College of Science and Engineering, FlindersUniversity; Biological Sciences Building, 5042 Bedford Park, South Australia, Australia
| | - Adrian Linacre
- College of Science and Engineering, FlindersUniversity; Biological Sciences Building, 5042 Bedford Park, South Australia, Australia
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8
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Hill E, Linacre A, Toop S, Murphy N, Strugnell JM. Development of an STR panel for a non-native population of an endangered species. Mol Biol Rep 2021; 49:839-845. [PMID: 34739689 DOI: 10.1007/s11033-021-06905-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The establishment of non-native populations of threatened and legally protected species can have many implications for the areas where these species have been introduced. Non-native populations of threatened species have the potential to be exploited and therefore the subject of legal protection, while conversely, if they have become invasive in their introduced range, there is the likelihood that population control will be carried out to reduce abundance and negative impacts associated with introduced species. From both a legal and invasive species monitoring standpoint, it is important to know how many individuals are present. METHODS AND RESULTS Short tandem repeats (STRs) were developed for the hog deer, an endangered species that was introduced following European settlement to Victoria, Australia using Illumina MiSeq sequencing technology. These markers were combined with previous STRs characterised for hog deer to create a 29-plex identification system. A total of 224 samples were genotyped across the population in Victoria, and further analyses of null allele frequencies, deviation from Hardy-Weinberg equilibrium, and the removal of monomorphic or low amplifying markers resulted in a final marker panel of 15 loci. Despite low values for number of alleles at each locus (2-4), probability of identity showed sufficient discrimination power, with an average probability of identity at 2.94 × 10-6, and a probability of sibling identity of 8.9 × 10-4 across all sites. CONCLUSIONS It is feasible to create an informative DNA profiling system that can distinguish between individuals for applications in both wildlife forensic and population control research.
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Affiliation(s)
- Erin Hill
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042, Australia
| | - Simon Toop
- Game Management Authority, Melbourne, VIC, 3000, Australia
| | - Nicholas Murphy
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,Research Centre for Future Landscapes, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
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Sahoo S, Samal R, Biswas S. Efficacy of a novel bone preprocessing method for better DNA yield. Forensic Sci Int 2021; 325:110887. [PMID: 34198074 DOI: 10.1016/j.forsciint.2021.110887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/06/2021] [Accepted: 06/18/2021] [Indexed: 11/28/2022]
Abstract
In cases involving identification of missing persons, mass disasters and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA profiling. Standard methods for extraction of DNA from such samples involve grinding of the bone and teeth samples. Here, we present an extremely efficient protocol for recovery of DNA from bone samples by a method of scrapping. The study was carried out on 25 samples and it was found that the quantity of DNA isolated by the scrapping method was up to 1.131 ng/µl with a success rate of 93% as compared to a much lower yield of 0.359 ng/µl DNA isolated with a success rate of 28% through the grinding method. The scrapping method of DNA extraction has been proven to be extremely useful in forensic examination of challenging samples that had multiple failures using the traditional grinding method.
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Affiliation(s)
- Subhasish Sahoo
- DNA Profiling Unit, State Forensic Science Laboratory, Rasulgarh, Bhubaneswar 751010, Odisha, India; ViStA Lab, Department of Biological Sciences, BITS, Pilani - K K Birla Goa Campus, Goa 403726, India
| | - Rashmita Samal
- DNA Profiling Unit, State Forensic Science Laboratory, Rasulgarh, Bhubaneswar 751010, Odisha, India
| | - Sumit Biswas
- ViStA Lab, Department of Biological Sciences, BITS, Pilani - K K Birla Goa Campus, Goa 403726, India.
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Ekka MM, Arya L, Patel BC. A systematic evaluation of 'Bidi - a hand-rolled cigarette' as a forensic DNA evidence. Forensic Sci Int 2021; 324:110821. [PMID: 34000618 DOI: 10.1016/j.forsciint.2021.110821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/10/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
Bidis are small handmade cigarettes consisting of ~0.2 g of tobacco flakes rolled in a dried leaf of 'Tendu' (Diospyros melanoxylon) or Piliostigma racemosum and tied with a thin thread. They have gained worldwide popularity among smokers and are often collected as forensic DNA evidence from crime scenes and processed similarly to cigarette butts. However, bidi's composition and manufacturing process differs distinctly from the cigarette, and hence the optimal processing for DNA analysis should not be assumed to be similar to cigarette butts. In the present study, the methodical evaluation of the bidi for DNA analysis is reported and an additional process of cell elution from bidi stubs prior to DNA extraction is systematically compared with the direct lysis of bidi stubs which is identical to the standard practice in forensic labs for cigarette butts. In terms of cell recovery from bidi stubs, the SDS based Cell Elution Buffer (CEB) proved to be better than Tween20 based CEB. The three components (cell-elute, supernatant, and processed stub) obtained after the cell elution process of smoked bidi stubs showed varying amounts of DNA. The cell-elute and processed stub exhibited high quality DNA, resulting in 90-100% of the samples giving a full STR profile. On the contrary, the directly lysed stubs yielded high quantity but low quality of DNA, resulting in only 40% of the samples with full STR profiles. The cell elution process enables three components namely cell-elute, supernatant and processed stub from the same bidi to be used for forensic DNA analysis, although the cell-elute proved to be the best source of DNA for STR profiling. The current study demonstrates that the additional cell elution process proved to be an essential step prior to DNA extraction procedure for bidi stubs.
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Affiliation(s)
- Molina Madhulika Ekka
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar 382007, Gujarat, India
| | - Lakshita Arya
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar 382007, Gujarat, India
| | - Bhargav C Patel
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar 382007, Gujarat, India.
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11
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Fernandez MV, Delviks-Frankenberry KA, Scheiblin DA, Happel C, Pathak VK, Freed EO. Authentication Analysis of MT-4 Cells Distributed by the National Institutes of Health AIDS Reagent Program. J Virol 2019; 93:e01390-19. [PMID: 31554688 DOI: 10.1128/JVI.01390-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The MT-4 human T-cell line expresses HTLV-1 Tax and is permissive for replication of an HIV-1 gp41 mutant lacking the cytoplasmic tail. MT-4 cells (lot 150048), distributed by the NIH AIDS Reagent Program (NIH-ARP), were found to be Tax deficient and unable to host replication of the gp41-truncated HIV-1 mutant. These findings, together with short tandem repeat profiling, established that lot 150048 are not bona fide MT-4 cells.
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12
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Robin T, Capes-Davis A, Bairoch A. CLASTR: The Cellosaurus STR similarity search tool - A precious help for cell line authentication. Int J Cancer 2019; 146:1299-1306. [PMID: 31444973 DOI: 10.1002/ijc.32639] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/02/2019] [Accepted: 08/14/2019] [Indexed: 11/06/2022]
Abstract
Despite an increased awareness of the problematic of cell line cross-contamination and misidentification, it remains nowadays a major source of erroneous experimental results in biomedical research. To prevent it, researchers are expected to frequently test the authenticity of the cell lines they are working on. STR profiling was selected as the international reference method to perform cell line authentication. While the experimental protocols and manipulations for generating a STR profile are well described, the available tools and workflows to analyze such data are lacking. The Cellosaurus knowledge resource aimed to improve the situation by compiling all the publicly available STR profiles from the literature and other databases. As a result, it grew to become the largest database in terms of human STR profiles, with 6,474 distinct cell lines having an associated STR profile (release July 31, 2019). Here we present CLASTR, the Cellosaurus STR similarity search tool enabling users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication by providing numerous functionalities. The tool is publicly accessible on the SIB ExPASy server (https://web.expasy.org/cellosaurus-str-search) and its source code is available on GitHub under the GPL-3.0 license.
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Affiliation(s)
- Thibault Robin
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland.,Microbiology and Molecular Medicine Department, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland.,Computer Science Department, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Amos Bairoch
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland.,Microbiology and Molecular Medicine Department, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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13
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Ruf-Zamojski F, Ge Y, Pincas H, Shan J, Song Y, Hines N, Kelley K, Montagna C, Nair P, Toufaily C, Bernard DJ, Mellon PL, Nair V, Turgeon JL, Sealfon SC. Cytogenetic, Genomic, and Functional Characterization of Pituitary Gonadotrope Cell Lines. J Endocr Soc 2019; 3:902-920. [PMID: 31020055 PMCID: PMC6469952 DOI: 10.1210/js.2019-00064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/08/2019] [Indexed: 01/01/2023] Open
Abstract
LβT2 and αT3-1 are important, widely studied cell line models for the pituitary gonadotropes that were generated by targeted tumorigenesis in transgenic mice. LβT2 cells are more mature gonadotrope precursors than αT3-1 cells. Microsatellite authentication patterns, chromosomal characteristics, and their intercellular variation have not been reported. We performed microsatellite and cytogenetic analysis of both cell types at early passage numbers. Short tandem repeat (STR) profiling was consistent with a mixed C57BL/6J × BALB/cJ genetic background, with distinct patterns for each cell type. Spectral karyotyping in αT3-1 cells revealed cell-to-cell variation in chromosome composition and pseudodiploidy. In LβT2 cells, chromosome counting and karyotyping demonstrated pseudotriploidy and high chromosomal variation among cells. Chromosome copy number variation was confirmed by single-cell DNA sequencing. Chromosomal compositions were consistent with a male sex for αT3-1 and a female sex for LβT2 cells. Among LβT2 stocks used in multiple laboratories, we detected two genetically similar but distinguishable lines via STR authentication, LβT2a and LβT2b. The two lines differed in morphological appearance, with LβT2a having significantly smaller cell and nucleus areas. Analysis of immediate early gene and gonadotropin subunit gene expression revealed variations in basal expression and responses to continuous and pulsatile GnRH stimulation. LβT2a showed higher basal levels of Egr1, Fos, and Lhb but lower Fos induction. Fshb induction reached significance only in LβT2b cells. Our study highlights the heterogeneity in gonadotrope cell line genomes and provides reference STR authentication patterns that can be monitored to improve experimental reproducibility and facilitate comparisons of results within and across laboratories.
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Affiliation(s)
- Frederique Ruf-Zamojski
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jidong Shan
- Molecular Cytogenetic Core, Albert Einstein College of Medicine, New York, New York
| | - Yinghui Song
- Molecular Cytogenetic Core, Albert Einstein College of Medicine, New York, New York
| | - Nika Hines
- Mouse Genetics and Gene Targeting CoRE, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kevin Kelley
- Mouse Genetics and Gene Targeting CoRE, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Cristina Montagna
- Molecular Cytogenetic Core, Albert Einstein College of Medicine, New York, New York
| | - Pranav Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chirine Toufaily
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Daniel J Bernard
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Pamela L Mellon
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California
| | - Venugopalan Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judith L Turgeon
- Department of Internal Medicine, University of California Davis, Davis, California
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
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14
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Mcleish K, Ferguson S, Gannicliffe C, Campbell S, Thomson PIT, Webster LMI. Profiling in wildlife crime: Recovery of human DNA deposited outside. Forensic Sci Int Genet 2018; 35:65-69. [PMID: 29673693 DOI: 10.1016/j.fsigen.2018.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
Incidents of bird of prey persecution receive a lot of media coverage in the UK, with investigations rarely recovering sufficient evidence to proceed to prosecution. One of the main challenges is to identify a suspect, as these offences are carried out in remote locations without witnesses, and crime scenes may not be found for days. However, traps, poisoned baits and bird of prey carcasses can be recovered from these crime scenes. This study aimed to determine whether reportable human DNA profiles could be recovered from any of these substrates after periods of time outside. Experiments depositing human touch DNA on duplicate substrates (traps, rabbit baits and corvid carcasses) set for 0, 1, 2, 4, 7 and 10 days outside were carried out, with DNA recovery and profiling following standard operating procedures for Scottish Police Authority Forensic Services. Weather conditions varied among experiments, including some heavy rainfall. Results demonstrated that it was possible to obtain reportable DNA profiles from all substrates after at least 1 day outside. Most promisingly, the traps showed no drop-off in DNA persistence over the experiments as complete DNA profiles were obtained after the full 10 days outside. A further experiment using 4 bird of prey carcasses confirmed that it is possible to obtain reportable human DNA profiles from them after 1 day outside (n = 2 reportable profiles). These results show that touch DNA can persist in an outdoor environment, and provide a tantalising avenue for inquiry in bird of prey persecution investigations.
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Affiliation(s)
- K Mcleish
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom
| | - S Ferguson
- Forensic Services, Scottish Police Authority, United Kingdom.
| | - C Gannicliffe
- Forensic Services, Scottish Police Authority, United Kingdom
| | - S Campbell
- Wildlife DNA Forensics Unit, Science and Advice for Scottish Agriculture, Edinburgh, United Kingdom
| | - P I T Thomson
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom
| | - L M I Webster
- Wildlife DNA Forensics Unit, Science and Advice for Scottish Agriculture, Edinburgh, United Kingdom
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15
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Chen Z, Ai L, Mboge MY, McKenna R, Frost CJ, Heldermon CD, Frost SC. UFH-001 cells: A novel triple negative, CAIX-positive, human breast cancer model system. Cancer Biol Ther 2018; 19:598-608. [PMID: 29561695 DOI: 10.1080/15384047.2018.1449612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Human cell lines are an important resource for research, and are often used as in vitro models of human diseases. In response to the mandate that all cells should be authenticated, we discovered that the MDA-MB-231 cells that were in use in our lab, did not validate based on the alleles of 9 different markers (STR Profile). We had been using this line as a model of triple negative breast cancer (TNBC) that has the ability to form tumors in immuno-compromised mice. Based on marker analysis, these cells most closely resembled the MCF10A line, which are a near diploid and normal mammary epithelial line. Yet, the original cells express carbonic anhydrase IX (CAIX) both constitutively and in response to hypoxia and are features that likely drive the aggressive nature of these cells. Thus, we sought to sub-purify CAIX-expressing cells using Fluorescence Activated Cell Sorting (FACS). These studies have revealed a new line of cells that we have name UFH-001, which have the TNBC phenotype, are positive for CAIX expression, both constitutively and in response to hypoxia, and behave aggressively in vivo. These cells may be useful for exploring mechanisms that underlie progression, migration, and metastasis of this phenotype. In addition, constitutive expression of CAIX allows its evaluation as a therapeutic target, both in vivo and in vitro.
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Affiliation(s)
- Zhijuan Chen
- a Department of Biochemistry and Molecular Biology , Gainesville , FL
| | - Lingbao Ai
- b Department of Medicine , University of Florida , Gainesville , FL
| | - Mam Y Mboge
- a Department of Biochemistry and Molecular Biology , Gainesville , FL
| | - Robert McKenna
- a Department of Biochemistry and Molecular Biology , Gainesville , FL
| | | | - Coy D Heldermon
- b Department of Medicine , University of Florida , Gainesville , FL
| | - Susan C Frost
- a Department of Biochemistry and Molecular Biology , Gainesville , FL
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16
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Korch C, Hall EM, Dirks WG, Ewing M, Faries M, Varella-Garcia M, Robinson S, Storts D, Turner JA, Wang Y, Burnett EC, Healy L, Kniss D, Neve RM, Nims RW, Reid YA, Robinson WA, Capes-Davis A. Authentication of M14 melanoma cell line proves misidentification of MDA-MB-435 breast cancer cell line. Int J Cancer 2017; 142:561-572. [PMID: 28940260 PMCID: PMC5762610 DOI: 10.1002/ijc.31067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/23/2017] [Accepted: 09/13/2017] [Indexed: 12/16/2022]
Abstract
A variety of analytical approaches have indicated that melanoma cell line UCLA‐SO‐M14 (M14) and breast carcinoma cell line MDA‐MB‐435 originate from a common donor. This indicates that at some point in the past, one of these cell lines became misidentified, meaning that it ceased to correspond to the reported donor and instead became falsely identified (through cross‐contamination or other means) as a cell line from a different donor. Initial studies concluded that MDA‐MB‐435 was the misidentified cell line and M14 was the authentic cell line, although contradictory evidence has been published, resulting in further confusion. To address this question, we obtained early samples of the melanoma cell line (M14), a lymphoblastoid cell line from the same donor (ML14), and donor serum preserved at the originator's institution. M14 samples were cryopreserved in December 1975, before MDA‐MB‐435 cells were established in culture. Through a series of molecular characterizations, including short tandem repeat (STR) profiling and cytogenetic analysis, we demonstrated that later samples of M14 and MDA‐MB‐435 correspond to samples of M14 frozen in 1975, to the lymphoblastoid cell line ML14, and to the melanoma donor's STR profile, sex and blood type. This work demonstrates conclusively that M14 is the authentic cell line and MDA‐MB‐435 is misidentified. With clear provenance information and authentication testing of early samples, it is possible to resolve debates regarding the origins of problematic cell lines that are widely used in cancer research. What's new? A variety of analytical approaches have indicated that melanoma cell line M14 and breast carcinoma cell line MDA‐MB‐435 originate from a common donor, but there is ongoing debate regarding which is the misidentified cell line. Here, authentication testing of M14 from 1975 (prior to the establishment of MDA‐MB‐435), with comparison to donor serum and lymphoblastoid cell line ML14, shows that M14 is the authentic cell line and MDA‐MB‐435 is a misidentified derivative. With clear provenance information and authentication testing of early samples, debates regarding the origins of problematic cell lines that are widely used in cancer research can be resolved.
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Affiliation(s)
- Christopher Korch
- International Cell Line Authentication Committee (ICLAC).,Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora CO
| | - Erin M Hall
- International Cell Line Authentication Committee (ICLAC).,Genetica Cell Line Testing - a LabCorp brand, Burlington, NC
| | - Wilhelm G Dirks
- International Cell Line Authentication Committee (ICLAC).,Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | | | - Mark Faries
- John Wayne Cancer Institute, Santa Monica, CA
| | | | - Steven Robinson
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora CO
| | - Douglas Storts
- International Cell Line Authentication Committee (ICLAC).,Promega Corporation, Madison, WI
| | - Jacqueline A Turner
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora CO
| | - Ying Wang
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora CO
| | - Edward C Burnett
- International Cell Line Authentication Committee (ICLAC).,Culture Collections Public Health England, Porton Down, United Kingdom
| | - Lyn Healy
- International Cell Line Authentication Committee (ICLAC).,Biological Research Facility, The Francis Crick Institute, London, United Kingdom
| | - Douglas Kniss
- International Cell Line Authentication Committee (ICLAC).,Departments of Obstetrics and Gynecology and Biomedical Engineering, The Ohio State University, Columbus, OH
| | - Richard M Neve
- International Cell Line Authentication Committee (ICLAC).,Gilead Sciences Inc, Foster City, CA
| | - Raymond W Nims
- International Cell Line Authentication Committee (ICLAC).,RMC Pharmaceutical Solutions, Inc., Longmont, CO
| | - Yvonne A Reid
- International Cell Line Authentication Committee (ICLAC).,American Type Culture Collection (ATCC), Manassas, VA
| | - William A Robinson
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora CO
| | - Amanda Capes-Davis
- International Cell Line Authentication Committee (ICLAC).,CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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17
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Katherine Philpott M, Stanciu CE, Kwon YJ, Bustamante EE, Greenspoon SA, Ehrhardt CJ. Analysis of cellular autofluorescence in touch samples by flow cytometry: implications for front end separation of trace mixture evidence. Anal Bioanal Chem 2017; 409:4167-79. [PMID: 28516277 DOI: 10.1007/s00216-017-0364-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/20/2022]
Abstract
The goal of this study was to survey optical and biochemical variation in cell populations deposited onto a surface through touch or contact and identify specific features that may be used to distinguish and then sort cell populations from separate contributors in a trace biological mixture. Although we were not able to detect meaningful biochemical variation in touch samples deposited by different contributors through preliminary antibody surveys, we did observe distinct differences in red autofluorescence emissions (650-670 nm), with as much as a tenfold difference in mean fluorescence intensities observed between certain pairs of donors. Results indicate that the level of red autofluorescence in touch samples can be influenced by a donor's contact with specific material prior to handling the substrate from which cells were collected. In particular, we observed increased red autofluorescence in cells deposited subsequent to handling laboratory gloves, plant material, and certain types of marker ink, which could be easily visualized microscopically or using flow cytometry, and persisted after hand washing. To test whether these observed optical differences could potentially be used as the basis for a cell separation workflow, a controlled two-person touch mixture was separated into two fractions via fluorescence-activated cell sorting (FACS) using gating criteria based on intensity of 650-670 nm emissions and then subjected to DNA analysis. Genetic analysis of the sorted fractions provided partial DNA profiles that were consistent with separation of individual contributors from the mixture suggesting that variation in autofluorescence signatures, even if driven by extrinsic factors, may nonetheless be a useful means of isolating contributors to some touch mixtures. Graphical Abstract Conceptual workflow diagram. Trace biological mixtures containing cells from multiple individuals are analyzed by flow cytometry. Cells are then physically separated into two populations based on intensity of red autofluorescence using Fluorescence Activated Cell Sorting. Each isolated cell fraction is subjected to DNA analysis resulting in a DNA profile for each contributor.
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18
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Abstract
Many investigations of the replication and pathogenesis of human T-cell leukemia virus type 1 (HTLV-1) employ chronically infected cell lines, cell lines stabilized from primary adult T-cell leukemia cells, and noninfected T-cell lines. The validity of data obtained from such studies depends on the unambiguous identification of each cell line, which can be performed by short-tandem-repeat (STR) profiling (DNA fingerprinting). While kit-based profiling represents the standard method for cell line authentication, not all labs have ready access to the required capillary electrophoresis equipment, and the costs of such tests can become substantial, especially if the cell lines are to be tested frequently. We analyzed DNA from a panel of HTLV-1-infected cell lines and noninfected T-cell lines using a commercial STR kit and then analyzed the same DNA for individual STR markers followed by nondenaturing polyacrylamide gel electrophoresis. This simplified method should facilitate routine confirmation of cell line identity in diverse laboratory settings.
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Affiliation(s)
- Vittoria Raimondi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Sonia Minuzzo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Vincenzo Ciminale
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Istituto Oncologico Veneto, IRCCS, Padova, Italy
| | - Donna M D'Agostino
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy.
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19
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Huang X, Weimer J, von Wurmb-Schwark N, Fredrik R, Arnold N, Schem C. Alteration of STR profiles in ovarian carcinoma cells during primary culture. Arch Gynecol Obstet 2016; 294:369-76. [PMID: 26825732 DOI: 10.1007/s00404-016-4018-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022]
Abstract
PURPOSE Cell authentication is a necessary procedure to avoid scientific data from cell culture experiments with cross-contamination or false classification. A genetic fingerprint pattern of a specimen by short tandem repeats (STR) is self-evident. Due to high amount of chromosomal rearrangements, known in epithelia ovary cancer cells and the instable STR pattern described in other tumour entities like leukaemia, this study explores the suitability of STR profiling for primary cultured epithelial ovary cancer cells. METHODS STR profiles of epithelial ovary cancers of 16 patients were compared with corresponding blood and corresponding primary cell cultures. The primary cell cultures of epithelial ovary tumours were passaged up to 28 times. In between, cultures were cryo conserved and recultured again, two to five times per patient. RESULTS In two cases, the STR pattern of tumour lost alleles (1/16 and 3/16) in comparison of corresponding STR-pattern from blood. In comparison to blood, cell culture of a third case, lost four alleles (4/16) accompanied with morphologic changes after 14th passage. It is equal after cryo conservation of the seventh passage from the same patient. The only changes in STR profiles we recognized are losses of alleles. Remaining STR markers allow authentication. CONCLUSIONS Very likely, the allelic drop-outs beyond passage 14 assume complex genetic losses of heterozygosis resulting in changed growth behaviour of cells. All other STR-profiles of remaining 15 patients analysed in this study are stable over all passages and freeze-thaw processes. Thus, ovary cancer cell cultures in research should be authenticated by STR-profile in general.
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20
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Ayyoob K, Masoud K, Vahideh K, Jahanbakhsh A. Authentication of newly established human esophageal squamous cell carcinoma cell line (YM-1) using short tandem repeat (STR) profiling method. Tumour Biol 2015; 37:3197-204. [PMID: 26432330 DOI: 10.1007/s13277-015-4133-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/21/2015] [Indexed: 01/13/2023] Open
Abstract
Cross-contamination during or early after establishment of a new cell line could result in the worldwide spread of a misidentified cell line. Therefore, newly established cell lines need to be authenticated by a reference standard method. This study was conducted to investigate the authenticity of a newly established epithelial cell line of human esophageal squamous cell carcinoma (ESCC) called YM-1 using short tandem repeat (STR) DNA profiling method. Primary human ESCC epithelial cells were cultured from the fresh tumor tissue of an adult female patient. Growth characteristics and epithelial originality of YM-1 cells were studied. Genomic DNA was isolated from YM-1 cells harvested at passage 22 and ESCC donor tumor sample on two different days to prevent probable DNA contamination. STR profiling was performed using AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. To address whether YM-1 cells undergo genetic alteration as the passage number increases, STR profiling was performed again on harvested cells at passage 51. YM-1 cells grew as a monolayer with a population doubling time of 40.66 h. Epithelial originality of YM-1 cells was confirmed using ICC/IF staining of cytokeratins AE1/AE3. The STR profile of the ESCC donor tumor sample was the same with YM-1 cells at passage 22. However, STR profile of the donor tumor sample showed an off-ladder (OL) allele in their D7S820 locus. Also, re-profiling of YM-1 cells at passage 51 showed a loss of heterozygosity (LOH) at D18S51 locus. This suggests that long-term culture of cell lines may alter their DNA profile. Comparison of the DNA fingerprinting results in DSMZ, and ATCC STR profiling databases confirmed unique identity of YM-1 cell line. This study provides an easy, fast, and reliable procedure for authentication of newly established cell lines, which helps in preventing the spread of misidentified cells and improving the reproducibility and validity of experiments, consequently.
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Affiliation(s)
- Khosravi Ayyoob
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Khoshnia Masoud
- Golestan Research Center of Gastroenterology and Hepatology-GRCGH, Golestan University of Medical Sciences, Gorgan, Iran
| | - Kazeminejad Vahideh
- Department of Pathology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Asadi Jahanbakhsh
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
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21
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Ogden SJ, Horton JK, Stubbs SL, Tatnell PJ. Performance testing of a semi-automatic card punch system, using direct STR profiling of DNA from blood samples on FTA™ cards. J Forensic Sci 2014; 60 Suppl 1:S207-12. [PMID: 25407399 DOI: 10.1111/1556-4029.12622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/09/2014] [Accepted: 01/20/2014] [Indexed: 11/28/2022]
Abstract
The 1.2 mm Electric Coring Tool (e-Core™) was developed to increase the throughput of FTA(™) sample collection cards used during forensic workflows and is similar to a 1.2 mm Harris manual micro-punch for sampling dried blood spots. Direct short tandem repeat (STR) DNA profiling was used to compare samples taken by the e-Core tool with those taken by the manual micro-punch. The performance of the e-Core device was evaluated using a commercially available PowerPlex™ 18D STR System. In addition, an analysis was performed that investigated the potential carryover of DNA via the e-Core punch from one FTA disc to another. This contamination study was carried out using Applied Biosystems AmpflSTR™ Identifiler™ Direct PCR Amplification kits. The e-Core instrument does not contaminate FTA discs when a cleaning punch is used following excision of discs containing samples and generates STR profiles that are comparable to those generated by the manual micro-punch.
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Affiliation(s)
- Samantha J Ogden
- GE Healthcare Life Sciences R&D, The Maynard Centre, Forest Farm, Whitchurch, Cardiff, CF14 7YT, U.K
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22
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An Q, Fillmore HL, Vouri M, Pilkington GJ. Brain tumor cell line authentication, an efficient alternative to capillary electrophoresis by using a microfluidics-based system. Neuro Oncol 2013; 16:265-73. [PMID: 24335698 DOI: 10.1093/neuonc/not202] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The current method for cell line authentication is genotyping based on short tandem repeat (STR)-PCR involving coamplification of a panel of STR loci by multiplex PCR and downstream fragment length analysis (FLA), usually performed by capillary electrophoresis. FLA by capillary electrophoresis is time-consuming and can be expensive, as the facilities are generally not accessible for many research laboratories. METHODS In the present study, a microfluidic electrophoresis system, the Agilent 2100 Bioanalyzer, was used to analyze the STR-PCR fragments from 10 human genomic loci of a number of human cell lines, including 6 gliomas, 1 astrocyte, 1 primary lung cancer, 1 lung brain metastatic cancer, and 1 rhabdomyosarcoma; and this was compared with the standard method, that is, capillary electrophoresis, using the Applied Biosystems 3130xl Genetic Analyzer. RESULTS The microfluidic electrophoresis method produced highly reproducible results with good sensitivity in sizing of multiple PCR fragments, and each cell line demonstrated a unique DNA profile. Furthermore, DNA fingerprinting of samples from 5 different passage numbers of the same cell line showed excellent reproducibility when FLA was performed with the Bioanalyzer, indicating that no cross-contamination had occurred during the culture period. CONCLUSION This novel application provides a straightforward and cost-effective alternative to STR-based cell line authentication. In addition, this application would be of great value for cell bank repositories to maintain and distribute precious cell lines.
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Affiliation(s)
- Qian An
- Corresponding Author: Dr. Qian An, MD, PhD, School of Pharmacy and Biomedical Sciences, University of Portsmouth, St Michael's Building, White Swan Road, Portsmouth PO1 2DT, UK.
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23
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Shewale JG, Qi L, Calandro LM. Principles, Practice, and Evolution of Capillary Electrophoresis as a Tool for Forensic DNA Analysis. Forensic Sci Rev 2012; 24:79-100. [PMID: 26244266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Capillary electrophoresis (CE) is a versatile and widely used analysis platform with application in diverse areas such as analytical chemistry, chiral separations, clinical, forensics, molecular biology, natural products, organic chemistry, and the pharmaceutical industry. Forensic applications of CE include fragment analysis, DNA sequencing, SNP typing, and analysis of gunshot residues, explosive residues, and drugs. Fragment analysis is a widely used method for short tandem repeat (STR) profiling for human identification (HID) due to the single-base resolution capability of CE. This approach circumvents the tedious and expensive approach of DNA sequencing for STR typing. The high sizing precision, ability to detect fluorescence emitted from multiple dyes, automated electrophoretic runs, and data collection software are key factors in the worldwide adoption of CE as the preferred platform for forensic DNA analysis. The most common CE systems used in forensic DNA analysis include the ABI PRISM® 310, 3100, 3100 Avant, 3130, 3130xl, 3500, and 3500xL Genetic Analyzers (GAs). The 3500 series GAs are developed with features useful for forensic scientists, including a normalization feature for analysis of the data designed to reduce the variation in peak height from instrument to instrument and injection to injection. Other hardware and software features include improved temperature control, radio frequency identification (RFID) tags for monitoring instrument consumables, HID-focused software features, and security and maintenance.
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Affiliation(s)
- J G Shewale
- Life Technologies Corporation, Foster City, CA, USA
| | - L Qi
- Life Technologies Corporation, Foster City, CA, USA
| | - L M Calandro
- Life Technologies Corporation, Foster City, CA, USA.
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24
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Stray JE, Liu JY, Brevnov MG, Shewale JG. Extraction of DNA from Forensic Biological Samples for Genotyping. Forensic Sci Rev 2010; 22:159-175. [PMID: 26242594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms.
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Affiliation(s)
- J E Stray
- Life Technologies Corporation, Foster City, CA, USA
| | - J Y Liu
- Life Technologies Corporation, Foster City, CA, USA
| | - M G Brevnov
- Life Technologies Corporation, Foster City, CA, USA
| | - J G Shewale
- Life Technologies Corporation, Foster City, CA, USA
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Stray JE, Shewale JG. Extraction of DNA from Human Remains. Forensic Sci Rev 2010; 22:177-185. [PMID: 26242595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Improvements to analytical methods have made it possible for highly discriminative genotypic information to be gleaned from smaller and smaller amounts of sample material. This fact makes it practical to genotype samples or remains consisting of bone and tooth-samples that likely would not have yielded interpretable genotypic results a short time ago. In parallel, there have been improvements to protocols specifically designed to recover DNA from very old calcified tissues, i.e., ancient or compromised nature. This review discusses the current best practices for isolating and purifying DNA from bones and teeth with a focus on the processes of lysis and DNA purification linked together to yield DNA from these challenging samples. The mitochondrial and genomic DNA recovered from more recently developed techniques for isolation from skeletal remains and teeth, even very old samples, is surprisingly amenable to genotypic analysis.
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Affiliation(s)
- J E Stray
- Life Technologies Corporation, Foster City, CA, USA
| | - J G Shewale
- Life Technologies Corporation, Foster City, CA, USA
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