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Takigawa H, Yuge R, Miyamoto R, Otani R, Kadota H, Hiyama Y, Hayashi R, Urabe Y, Sentani K, Oue N, Kitadai Y, Oka S, Tanaka S. Comprehensive Analysis of Gene Expression Profiling to Explore Predictive Markers for Eradication Therapy Efficacy against Helicobacter pylori-Negative Gastric MALT Lymphoma. Cancers (Basel) 2023; 15:1206. [PMID: 36831547 PMCID: PMC9954119 DOI: 10.3390/cancers15041206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Although radiotherapy is the standard treatment for Helicobacter pylori (Hp)-negative gastric mucosa-associated lymphoid tissue (MALT) lymphoma, eradication therapy using antibiotics and an acid secretion suppressor can sometimes induce complete remission. We explored predictive markers for the response to eradication therapy for gastric MALT lymphoma that were negative for both API2-MALT1 and Hp infection using comprehensive RNA sequence analysis. Among 164 gastric MALT lymphoma patients who underwent eradication therapy as primary treatment, 36 were negative for both the API2-MALT1 fusion gene and Hp infection. Based on eradication therapy efficacy, two groups were established: complete response (CR) and no change (NC). The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that cancer-related genes and infection-related genes were highly expressed in the NC and CR groups, respectively. Based on this finding and transcription factor, gene ontology enrichment, and protein-protein interaction analyses, we selected 16 candidate genes for predicting eradication therapy efficacy. Real-time PCR validation in 36 Hp-negative patients showed significantly higher expression of olfactomedin-4 (OLFM4) and the Nanog homeobox (NANOG) in the CR and NC groups, respectively. OLFM4 and NANOG could be positive and negative predictive markers, respectively, for eradication therapy efficacy against gastric MALT lymphoma that is negative for both API2-MALT1 and Hp infection.
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Affiliation(s)
- Hidehiko Takigawa
- Department of Endoscopy, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Ryo Yuge
- Department of Gastroenterology, Hiroshima University, Hiroshima 734-8551, Japan
| | - Ryo Miyamoto
- Department of Gastroenterology, Hiroshima University, Hiroshima 734-8551, Japan
| | - Rina Otani
- Department of Gastroenterology, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hiroki Kadota
- Department of Gastroenterology, Hiroshima University, Hiroshima 734-8551, Japan
| | - Yuichi Hiyama
- Department of Clinical Research Center, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Ryohei Hayashi
- Department of Endoscopy, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Yuji Urabe
- Gastrointestinal Endoscopy and Medicine, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Hiroshima University Hospital, Hiroshima 734-8551, Japan
| | - Yasuhiko Kitadai
- Department of Health and Science, Prefectural University of Hiroshima, Hiroshima 734-8558, Japan
| | - Shiro Oka
- Department of Gastroenterology, Hiroshima University, Hiroshima 734-8551, Japan
| | - Shinji Tanaka
- Department of Endoscopy, Hiroshima University Hospital, Hiroshima 734-8551, Japan
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Bapat PR, Epari S, Joshi PV, Dhanavade DS, Rumde RH, Gurav MY, Shetty OA, Desai SB. Comparative Assessment of DNA Extraction Techniques From Formalin-Fixed, Paraffin-Embedded Tumor Specimens and Their Impact on Downstream Analysis. Am J Clin Pathol 2022; 158:739-749. [PMID: 36197908 DOI: 10.1093/ajcp/aqac122] [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: 06/09/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Good-quality nucleic acid extraction from formalin-fixed, paraffin-embedded (FFPE) specimens remains a challenge in molecular-oncopathology practice. This study evaluates the efficacy of an in-house developed FFPE extraction buffer compared with other commercially available kits. METHODS Eighty FFPE specimens processed in different surgical pathology laboratories formed the study sample. DNA extraction was performed using three commercial kits and the in-house developed FFPE extraction buffer. DNA yield was quantified by a NanoDrop spectrophotometer and Qubit Fluorometer, and its purity was measured by the 260/280-nm ratio. A fragment analyzer system was used for accurate sizing of DNA fragments of FFPE DNA. The downstream effects of all extraction methods were evaluated by polymerase chain reaction (PCR) and Sanger sequencing. RESULTS In comparison with the commercial kits, the in-house buffer yielded higher DNA quantity and quality number (P < .0001). In addition, DNA integrity and fragment size were preserved in a significantly greater number of samples isolated with the in-house buffer (P < .05). The target PCR amplification rate with the in-house buffer extracted samples was also significantly higher, with 98% of the samples showing interpretable sequencing results. CONCLUSIONS The in-house developed FFPE extraction buffer performed superior to other methods in terms of suitability for downstream applications, time, cost-efficiency, and ease of performance.
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Affiliation(s)
- Prachi R Bapat
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Pradnya V Joshi
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Dipika S Dhanavade
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Rachna H Rumde
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Mamta Y Gurav
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree A Shetty
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sangeeta B Desai
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
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van Deventer BS, du Toit-Prinsloo L, van Niekerk C. Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting. Afr J Lab Med 2022; 11:1587. [PMID: 35811747 PMCID: PMC9257738 DOI: 10.4102/ajlm.v11i1.1587] [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: 03/16/2021] [Accepted: 03/21/2022] [Indexed: 11/05/2022] Open
Abstract
Background Formalin-fixed paraffin-embedded (FFPE) tissue archives in hospitals, biobanks, and others offer a vast collection of extensive, readily available specimens for molecular testing. Unfortunately, the use of tissue samples for molecular diagnostic applications is challenging; thus, the forensic pathology FFPE tissue archives in Africa have been a largely unexploited genetic resource, with the usability of DNA obtainable from these samples being unknown. Intervention The study, conducted from January 2015 to August 2016, determined the usefulness of FFPE tissue as a reliable source of genetic material for successful post-mortem molecular applications and diagnostics. Formalin-fixed paraffin-embedded tissue samples were collected and archived from autopsies conducted over 13 years in the forensic medicine department of the University of Pretoria (Pretoria, South Africa). Deoxyribonucleic acid from FFPE tissue samples and control blood samples was amplified by high-resolution melt real-time polymerase chain reaction before sequencing. The procurement parameters and fixation times were compared with the quantity and quality of the extracted DNA and the efficiency of its subsequent molecular applications. Lessons learnt This study has shown that FFPE samples are still usable in molecular forensics, despite inadequate sample preparation, and offer immense value to forensic molecular diagnostics. Recommendations FFPE samples fixed in formalin for more than 24 h should still be used in molecular diagnostics or research, as long as the primer design targets amplicons not exceeding 300 base pairs.
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Affiliation(s)
- Barbara S van Deventer
- Department of Forensic Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Lorraine du Toit-Prinsloo
- Department of Forensic Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Chantal van Niekerk
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma. Diagnostics (Basel) 2022; 12:diagnostics12051219. [PMID: 35626372 PMCID: PMC9139996 DOI: 10.3390/diagnostics12051219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Recovery and amplification of nucleic acids from archived formalin-fixed tissue samples is the most developing field in retrospective genetic studies. We compared different deparaffinization methods and DNA isolation techniques, and intergroup comparisons were performed to evaluate the effectiveness of different storing methods for archival OSCC samples based on obtained mean DNA quantity, quality, and PCR amplification of the P53 gene. The study comprised 75 archival histologically diagnosed OSCC samples which were divided into Group I: Formalin-fixed paraffin-embedded tissue blocks and Group II: Long-term formalin-fixed tissue. A comparison of different deparaffinization methods showed that xylene deparaffinization is an efficient method to obtain suitable DNA. Comparing different DNA isolation techniques illustrated that the conventional phenol–chloroform method gives better integrity to DNA in contrast with the kit method. Comparison between FFPET and long-term FFT samples demonstrated that samples fixed in formalin overnight and embedded in wax yield better quality and quantity DNA in comparison with long-term samples fixed in formalin. To obtain suitable integrity of DNA, tissue samples should be stored by fixing in formalin overnight followed by preparation of paraffin tissue blocks, deparaffinization by xylene, and subjecting them to the conventional phenol–chloroform DNA isolation protocol.
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Viljoen R, Reid KM, Mole CG, Rangwaga M, Heathfield LJ. Towards molecular autopsies: Development of a FFPE tissue DNA extraction workflow. Sci Justice 2022; 62:137-144. [DOI: 10.1016/j.scijus.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/02/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022]
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The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues. Int J Mol Sci 2022; 23:ijms23031103. [PMID: 35163027 PMCID: PMC8834906 DOI: 10.3390/ijms23031103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer cells accumulate epigenomic aberrations that contribute to cancer initiation and progression by altering both the genomic stability and the expression of genes. The awareness of such alterations could improve our understanding of cancer dynamics and the identification of new therapeutic strategies and biomarkers to refine tumor classification and treatment. Formalin fixation and paraffin embedding (FFPE) is the gold standard to preserve both tissue integrity and organization, and, in the last decades, a huge number of biological samples have been archived all over the world following this procedure. Recently, new chromatin immunoprecipitation (ChIP) techniques have been developed to allow the analysis of histone post-translational modifications (PTMs) and transcription factor (TF) distribution in FFPE tissues. The application of ChIP to genome-wide chromatin studies using real archival samples represents an unprecedented opportunity to conduct retrospective clinical studies thanks to the possibility of accessing large cohorts of samples and their associated diagnostic records. However, although recent attempts to standardize have been made, fixation and storage conditions of clinical specimens are still extremely variable and can affect the success of chromatin studies. The procedures introduced in the last few years dealt with this problem proponing successful strategies to obtain high-resolution ChIP profiles from FFPE archival samples. In this review, we compare the different FFPE-ChIP techniques, highlighting their strengths, limitations, common features, and peculiarities, as well as pitfalls and caveats related to ChIP studies in FFPE samples, in order to facilitate their application.
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Identification of Pneumocystis jirovecii with Fluorescence In-Situ Hybridization (FISH) in Patient Samples-A Proof-of-Principle. J Fungi (Basel) 2021; 8:jof8010013. [PMID: 35049953 PMCID: PMC8778293 DOI: 10.3390/jof8010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
In resource-limited settings, where pneumocystosis in immunocompromised patients is infrequently observed, cost-efficient, reliable, and sensitive approaches for the diagnostic identification of Pneumocystis jirovecii in human tissue samples are desirable. Here, an in-house fluorescence in situ hybridization assay was comparatively evaluated against Grocott’s staining as a reference standard with 30 paraffin-embedded tissue samples as well as against in-house real-time PCR with 30 respiratory secretions from immunocompromised patients with clinical suspicion of pneumocystosis. All pneumocystosis patients included in the study suffered from HIV/AIDS. Compared with Grocott’s staining as the reference standard, sensitivity of the FISH assay was 100% (13/13), specificity was 41% (7/17), and the overall concordance was 66.7% with tissue samples. With respiratory specimens, sensitivity was 83.3% (10/12), specificity was 100% (18/18), and the overall concordance was 93.3% as compared with real-time PCR. It remained unresolved to which proportions sensitivity limitations of Grocott’s staining or autofluorescence phenomena affecting the FISH assay accounted for the recorded reduced specificity with the tissue samples. The assessment confirmed Pneumocystis FISH in lung tissue as a highly sensitive screening approach; however, dissatisfying specificity in paraffin-embedded biopsies calls for confirmatory testing with other techniques in case of positive FISH screening results. In respiratory secretions, acceptable sensitivity and excellent specificity were demonstrated for the diagnostic application of the P. jirovecii-specific FISH assay.
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Khodaverdi N, Zeighami H, Jalilvand A, Haghi F, Hesami N. High frequency of enterotoxigenic Bacteroides fragilis and Enterococcus faecalis in the paraffin-embedded tissues of Iranian colorectal cancer patients. BMC Cancer 2021; 21:1353. [PMID: 34937552 PMCID: PMC8693489 DOI: 10.1186/s12885-021-09110-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
Background The association between specific bacteria and colorectal cancer (CRC) has been proposed. Only a few studies have, however, investigated this relationship directly in colorectal tissue with conflicting results. So, we aimed to quantitate Streptococcus gallolyticus, Fusobacterium spp, Enterococcus faecalis and enterotoxigenic Bacteroides fragilis (ETBF) in formalin-fixed and paraffin-embedded (FFPE) colorectal tissue samples of Iranian CRC patients and healthy controls. Methods A total of 80 FFPE colorectal tissue samples of CRC patients (n = 40) and healthy controls (n = 40) were investigated for the presence and copy number of above bacterial species using quantitative PCR. Relative quantification was determined using ΔΔCT method and expressed as relative fold difference compared to reference gene. Results Relative abundance and copy number of E. faecalis and ETBF were significantly higher in CRC samples compared to control group. E. faecalis was more prevalent than ETBF in tumor samples. Frequency of ETBF and E. faecalis in late stages (III/IV) of cancer was significantly higher than early stages (I/II). We did not detect a significant difference in abundance of S. gallolyticus and Fusobacterium spp between two groups. Conclusion Our study revealed the higher concentration of E. faecalis and ETBF in FFPE samples of CRC patients than controls. However, additional investigations on fecal and fresh colorectal cancer tissue samples are required to substantiate this correlation.
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Oranratanaphan S, Khongthip Y, Areeruk W, Triratanachat S, Tantbirojn P, Phupong V, Vongpaisarnsin K, Lertkhachonsuk R. Determination of morphologic and immunohistochemical stain (p57 kip2) discrepancy of complete and partial hydatidiform mole by using microsatellite genotyping. Taiwan J Obstet Gynecol 2021; 59:570-574. [PMID: 32653131 DOI: 10.1016/j.tjog.2020.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE to evaluate the role of microsatellite genotyping in discordant results between morphologic examination and p57Kip2 staining in hydatidiform mole. MATERIALS AND METHODS 127 cases of hydatidiform mole who had morphologic examination and p57Kip2immunohistochemical staining were evaluated. Six discrepant cases between morphologic examination and p57Kip2 staining were recruited. DNA was extracted from chorionic villi and paired maternal decidual tissue in Formalin fixed paraffin embedded tissue sections. The STR DNA genotyping was performed by Applied Biosystems 3500 Genetic Analyzer. Genetic data analysis was performed by Gene mapper ID-X software. Three concordant cases were used as control. Results were compared to histopathology, p57Kip2 stain and development of post-molar GTN. RESULTS All controlled cases were confirmed PHM. Two cases of histologic CHM with positive p57Kip2and 2 cases of PHM with negative p57Kip2 were reported as PHM from microsatellite. Other 2 cases of histologic diagnosis PHM with negative p57Kip2 reported as CHM from microsatellite test and both of them developed post-molar GTN. CONCLUSION Microsatellite genotyping is a high accuracy method for differential diagnosis from complete and partial hydatidiform moles. However, cost of microsatellite genotyping is still too high to use routinely. Therefore, selected use in discrepancy cases may be suitable.
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Affiliation(s)
- Shina Oranratanaphan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Yuthana Khongthip
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wilasinee Areeruk
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Surang Triratanachat
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patou Tantbirojn
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Placental Related Diseases Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorapong Phupong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Placental Related Diseases Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ruangsak Lertkhachonsuk
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Placental Related Diseases Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Siemanowski J, Heydt C, Merkelbach-Bruse S. Predictive molecular pathology of lung cancer in Germany with focus on gene fusion testing: Methods and quality assurance. Cancer Cytopathol 2021; 128:611-621. [PMID: 32885916 DOI: 10.1002/cncy.22293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022]
Abstract
Predictive molecular testing has become an important part of the diagnosis of any patient with lung cancer. Using reliable methods to ensure timely and accurate results is inevitable for guiding treatment decisions. In the past few years, parallel sequencing has been established for mutation testing, and its use is currently broadened for the detection of other genetic alterations, such as gene fusion and copy number variations. In addition, conventional methods such as immunohistochemistry and in situ hybridization are still being used, either for formalin-fixed, paraffin-embedded tissue or for cytological specimens. For the development and broad implementation of such complex technologies, interdisciplinary and regional networks are needed. The Network Genomic Medicine (NGM) has served as a model of centralized testing and decentralized treatment of patients and incorporates all German comprehensive cancer centers. Internal quality control, laboratory accreditation, and participation in external quality assessment is mandatory for the delivery of reliable results. Here, we provide a summary of current technologies used to identify patients who have lung cancer with gene fusions, briefly describe the structures of NGM and the national NGM (nNGM), and provide recommendations for quality assurance.
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Affiliation(s)
- Janna Siemanowski
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Ramesh PS, Madegowda V, Kumar S, Narasimha S, S R P, Manoli NN, Devegowda D. DNA extraction from archived hematoxylin and eosin-stained tissue slides for downstream molecular analysis. World J Methodol 2019; 9:32-43. [PMID: 31799154 PMCID: PMC6885493 DOI: 10.5662/wjm.v9.i3.32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Histopathologically stained archived tissue slides are stored in hospital archives for years to decades. They are the largest available source of biological materials and are a potentially useful resource that can be used for retrospective epidemiological studies. DNA recovered from the slides can be used for several downstream molecular processes including polymerase chain reaction, single nucleotide polymorphism analysis, and whole genome sequencing. The DNA from these slides can be utilized to compare gene signatures of normal and diseased tissues. However, extraction of high-quality DNA from archived stained hematoxylin and eosin (H&E) slides remains challenging.
AIM To standardize a new protocol for extracting DNA from archived H&E-stained tissue slides for further molecular assays.
METHODS A total of 100 archived H&E-stained cancer slides were subjected to a total of five methods of DNA extraction. Methods were varied in the deparaffinization step, tissue rehydration, duration of lysis, and presence or absence of proteinase K. The extracted DNA was quantified using a NanoDrop spectrophometer and the quality was analyzed by agarose gel electrophoresis. Then each sample was subjected to polymerase chain reaction (PCR) to amplify the internal control gene GAPDH, thereby confirming the DNA intactness, which could be further utilized for other downstream applications.
RESULTS Of the five different methods tested, the third method wherein xylene was used for tissue deparaffinization followed by 72 h of digestion and without proteinase K inactivation yielded the highest amount of DNA with good purity. The yield was significantly higher when compared to other methods. In addition, 90% of the extracted DNA showed amplifiable GAPDH gene.
CONCLUSION Here we present a step-by-step, cost-effective, and reproducible protocol for the extraction of PCR-friendly DNA from archived H&E-stained cancer tissue slides that can be used for further downstream molecular applications.
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Affiliation(s)
- Pushkal Sinduvadi Ramesh
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Venkatesh Madegowda
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Suprith Kumar
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Shailashree Narasimha
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Parichay S R
- CIPHER Healthcare Pvt Ltd., Hyderabad 500034, India
| | - Nandini Nandish Manoli
- Department of Pathology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Devananda Devegowda
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
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Norgan AP, Sloan LM, Pritt BS. Detection of Naegleria fowleri, Acanthamoeba spp, and Balamuthia mandrillaris in Formalin-Fixed, Paraffin-Embedded Tissues by Real-Time Multiplex Polymerase Chain Reaction. Am J Clin Pathol 2019; 152:799-807. [PMID: 31415080 DOI: 10.1093/ajcp/aqz103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES Pathogenic free-living amebae (FLAs) cause skin, ocular, and central nervous system (CNS) infections with significant morbidity and mortality. Diagnosis of FLA infections by pathologic examination of tissue sections can be aided using molecular assays. This study investigated the performance characteristics of a multiplex real-time polymerase chain reaction (PCR) assay (FLA-PCR) for detection and differentiation of FLAs in clinical specimens. METHODS FLA-PCR was performed on 39 human specimens comprising one cutaneous, 14 corneal, and 24 CNS formalin-fixed, paraffin-embedded (FFPE) tissues with a histopathologic diagnosis of FLA infection and four CNS FFPE tissues with inflammation but no evidence of FLAs. In addition, clinical specificity and assay limit of detection were determined. RESULTS FLA detection sensitivities ranged from 79% to 84% in FFPE tissues. No cross-reactivity was observed. CONCLUSIONS While sensitivity is limited, FLA-PCR assay may serve as a useful adjunct for detection or confirmation of FLA infections in FFPE tissues.
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Affiliation(s)
- Andrew P Norgan
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN
| | - Lynne M Sloan
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Mayo Clinic, Rochester, MN
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Boos GS, Nobach D, Failing K, Eickmann M, Herden C. Optimization of RNA extraction protocol for long-term archived formalin-fixed paraffin-embedded tissues of horses. Exp Mol Pathol 2019; 110:104289. [PMID: 31348903 DOI: 10.1016/j.yexmp.2019.104289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/24/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022]
Abstract
A suitable RNA extraction protocol was established to gain high quality RNA from formalin-fixed paraffin-embedded tissues to perform reliable molecular assays either applicable for using FFPE tissue archives or tissues with harsh formalin-fixation. Eighteen FFPE samples from the central nervous system of horses, stored up to 11 years, were used as archive cases. To test the influence of the fixation period, brain, liver, kidney, and skeletal muscle tissue fragments from another horse, were treated either with water or tris-acetate-EDTA buffer after fixation under different timepoints with 10% unbuffered formalin. Two deparaffinization methods and three proteinase K-based lysis step were tested and translated into three protocols. After detailed statistical analysis it was determined that a longer period and increase in volume of proteinase K incubation provide higher yields and purity of RNA (P < 0.01) of archived samples. Alongside, amplification of equid-housekeeping gene up to 298 bp was successful with the protocol adaptations. For different formalin-fixation timepoints, it was demonstrated that the right choice for treatment and formalin-fixation period is organ-related (P ≤ 0.05). Essentially, little alterations to pre-existing extraction protocols unwound the RNA of up to 11-year-old samples, enabling the use of FFPE tissue archives or e.g. harshly fixed material needed in infection research under high biosafety levels for a variety of molecular analysis.
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Affiliation(s)
- Gisele Silva Boos
- Institute of Veterinary Pathology, Justus-Liebig-University, Gießen 35392, Germany.
| | - Daniel Nobach
- Institute of Veterinary Pathology, Justus-Liebig-University, Gießen 35392, Germany
| | - Klaus Failing
- Unit for Biomathematics and Data Processing, Justus-Liebig-Universität, Gießen 35392, Germany
| | - Markus Eickmann
- Institute of Virology, Philipps-University, Marburg 35043, Germany
| | - Christiane Herden
- Institute of Veterinary Pathology, Justus-Liebig-University, Gießen 35392, Germany; Center of Mind, Brain and Behavior, Justus-Liebig-University Gießen, Gießen, Germany
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15
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Mathieson W, Thomas G. Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Frickmann H, Künne C, Hagen RM, Podbielski A, Normann J, Poppert S, Looso M, Kreikemeyer B. Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples - a proof-of-principle assessment. BMC Microbiol 2019; 19:75. [PMID: 30961537 PMCID: PMC6454699 DOI: 10.1186/s12866-019-1448-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/28/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question. RESULTS For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis. CONCLUSIONS The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization.
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Affiliation(s)
- Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Bernhard-Nocht Str. 74, 20359, Hamburg, Germany. .,Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany.
| | - Carsten Künne
- Department of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad Nauheim, Parkstraße 1, 61231, Bad Nauheim, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy, Neuherbergstraße 11, 80937, Munich, Germany
| | - Andreas Podbielski
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Jana Normann
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,Faculty of Medicine, University Basel, Socinstrasse 57, 4051, Basel, Switzerland
| | - Mario Looso
- Department of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad Nauheim, Parkstraße 1, 61231, Bad Nauheim, Germany
| | - Bernd Kreikemeyer
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
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17
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Carlsson J, Davidsson S, Fridfeldt J, Giunchi F, Fiano V, Grasso C, Zelic R, Richiardi L, Andrén O, Pettersson A, Fiorentino M, Akre O. Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies. BMC Med Res Methodol 2018; 18:161. [PMID: 30518332 PMCID: PMC6280346 DOI: 10.1186/s12874-018-0628-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/26/2018] [Indexed: 01/10/2023] Open
Abstract
Background In Sweden, human tissue samples obtained from diagnostic and surgical procedures have for decades been routinely stored in a formalin-fixed, paraffin-embedded, form. Through linkage with nationwide registers, these samples are available for molecular studies to identify biomarkers predicting mortality even in slow-progressing prostate cancer. However, tissue fixation causes modifications of nucleic acids, making it challenging to extract high-quality nucleic acids from formalin fixated tissues. Methods In this study, the efficiency of five commercial nucleic acid extraction kits was compared on 30 prostate biopsies with normal histology, and the quantity and quality of the products were compared using spectrophotometry and Agilent’s BioAnalyzer. Student’s t-test’s and Bland-Altman analyses were performed in order to investigate differences in nucleic acid quantity and quality between the five kits. The best performing extraction kits were subsequently tested on an additional 84 prostate tumor tissues. A Spearman’s correlation test and linear regression analyses were performed in order to investigate the impact of tissue age and amount of tissue on nucleic acid quantity and quality. Results Nucleic acids extracted with RNeasy® FFPE and QIAamp® DNA FFPE Tissue kit had the highest quantity and quality, and was used for extraction from 84 tumor tissues. Nucleic acids were successfully extracted from all biopsies, and the amount of tumor (in millimeter) was found to have the strongest association with quantity and quality of nucleic acids. Conclusions To conclude, this study shows that the choice of nucleic acid extraction kit affects the quantity and quality of extracted products. Furthermore, we show that extraction of nucleic acids from archival formalin-fixed prostate biopsies is possible, allowing molecular studies to be performed on this valuable sample collection.
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Affiliation(s)
- Jessica Carlsson
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden.
| | - Sabina Davidsson
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Jonna Fridfeldt
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Francesca Giunchi
- Department of Pathology, F. Addari Institute of Oncology S. Orsola Hospital, Bologna, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Chiara Grasso
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Renata Zelic
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Ove Andrén
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Andreas Pettersson
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | | | - Olof Akre
- Department of Medicine Solna, Karolinska Institute, and Department of Urology, Karolinska University Hospital, Stockholm, Sweden
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18
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Kresse SH, Namløs HM, Lorenz S, Berner JM, Myklebost O, Bjerkehagen B, Meza-Zepeda LA. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples. PLoS One 2018; 13:e0197456. [PMID: 29771965 PMCID: PMC5957415 DOI: 10.1371/journal.pone.0197456] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated. DNA and RNA were isolated from five sarcoma archival FFPE blocks, using eight extraction protocols from seven kits from three different commercial vendors. For DNA extraction, the truXTRAC FFPE DNA kit from Covaris gave higher yields and better amplifiable DNA, but all protocols gave comparable HTS library yields using Agilent SureSelect XT and performed well in downstream variant calling. For RNA extraction, all protocols gave comparable yields and amplifiable RNA. However, for fusion gene detection using the Archer FusionPlex Sarcoma Assay, the truXTRAC FFPE RNA kit from Covaris and Agencourt FormaPure kit from Beckman Coulter showed the highest percentage of unique read-pairs, providing higher complexity of HTS data and more frequent detection of recurrent fusion genes. truXTRAC simultaneous DNA and RNA extraction gave similar outputs as individual protocols. These findings show that although successful HTS libraries could be generated in most cases, the different protocols gave variable quantity and quality for FFPE nucleic acid extraction. Selecting the optimal procedure is highly valuable and may generate results in borderline quality specimens.
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Affiliation(s)
- Stine H. Kresse
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Heidi M. Namløs
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Jeanne-Marie Berner
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Norwegian Cancer Genomics Consortium (cancergenomics.no), Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Leonardo A. Meza-Zepeda
- Department of Tumor Biology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Genomics Core Facility, Department of Core Facilities, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Norwegian Cancer Genomics Consortium (cancergenomics.no), Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- * E-mail:
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19
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Urbanovska I, Megova MH, Dwight Z, Kalita O, Uvirova M, Simova J, Tuckova L, Buzrla P, Palecek T, Hajduch M, Dvorackova J, Drabek J. IDH Mutation Analysis in Glioma Patients by CADMA Compared with SNaPshot Assay and two Immunohistochemical Methods. Pathol Oncol Res 2018; 25:971-978. [PMID: 29556922 PMCID: PMC6614140 DOI: 10.1007/s12253-018-0413-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/08/2018] [Indexed: 02/02/2023]
Abstract
Mutations in IDH1/2 genes are a marker of good prognosis for glioma patients, associated with low grade gliomas and secondary glioblastomas. Immunohistochemistry and Sanger sequencing are current standards for IDH1/2 genotyping while many other methods exist. The aim of this study was to validate Competitive amplification of differentially melting amplicons (CADMA) PCR for IDH genotyping by comparison with SNaPshot assay and two immunohistochemical methods. In our study, 87 glioma patients (46 from Olomouc and 41 from Ostrava) were analyzed. IDH1/2 mutations in native bioptical samples were analyzed at DNA level by CADMA and SNaPshot while IDH1 mutations in FFPE samples were analyzed at protein level by two IHC methods. CADMA PCR sensitivity for IDH1 was 96.4% and specificity 100% for 86 concluded samples. SNaPshot assay sensitivity was 92.9% and specificity of 100% for 85 concluded samples. IHC in the laboratory no. 2 reached sensitivity 85.7% and specificity 100% for 86 concluded samples. IHC in the laboratory no. 4 reached sensitivity of 96.4% and specificity of 79.7% in 74 concluded samples. Only one IDH2 mutation was found by SNaPshot while CADMA yielded false negative result. In conclusion, CADMA is a valid method for IDH1 p.(R132H) testing with higher sensitivity than SNaPshot assay. Also, molecular genetic methods of IDH1 testing from native samples were more robust than IHC from FFPE.
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Affiliation(s)
- Irena Urbanovska
- CGB Laboratory Inc., Ostrava, Czech Republic.,Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Magdalena Houdova Megova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic
| | - Zachary Dwight
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Ondrej Kalita
- Department of Neurosurgery, University Hospital Olomouc, Olomouc, Czech Republic
| | | | | | - Lucie Tuckova
- Department of Clinical and Molecular Pathology, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czech Republic
| | - Petr Buzrla
- Institute of Pathology, Faculty of Medicine and University Hospital, University of Ostrava, Syllabova 19, 703 00, Ostrava - Zábřeh, Czech Republic
| | - Tomas Palecek
- Neurosurgery Clinic, University Hospital Ostrava, Ostrava, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic
| | - Jana Dvorackova
- Department of Biomedical Sciences, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic. .,Institute of Pathology, Faculty of Medicine and University Hospital, University of Ostrava, Syllabova 19, 703 00, Ostrava - Zábřeh, Czech Republic.
| | - Jiri Drabek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 779 00, Olomouc, Czech Republic.
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20
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Gielda L, Rigg S. Extraction of amplifiable DNA from embalmed human cadaver tissue. BMC Res Notes 2017; 10:737. [PMID: 29237482 PMCID: PMC5729266 DOI: 10.1186/s13104-017-3066-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/05/2017] [Indexed: 01/18/2023] Open
Abstract
Objective The expansion of molecular techniques in medical diagnosis, forensics, and education requires the development of improved techniques of DNA extraction from fixed tissues. Cadaver tissues are not commonly used for genetic analysis due to DNA degradation resulting from the embalming fixation. Modification of existing techniques of tissue disruption combined with phenol–chloroform treatment was done to produce an efficient method of extracting amplifiable DNA of high quality and quantity from non-paraffin embedded embalmed cadaver tissue. Results Tissues (cerebellum, cerebral cortex, heart, and bone) from four cadavers were used to develop a procedure for DNA isolation, which includes a high heat treatment. The location and age of the tissue had a significant effect on the quantity of DNA recovered. Targeted PCR amplification of the Apolipoprotein gene was used to assess the efficacy of genotypic analysis from the recovered DNA. We report the development of a simple, reliable, and low-cost method of DNA isolation utilizing brain tissue from embalmed tissues that could be used for PCR amplification and genetic analysis. Electronic supplementary material The online version of this article (10.1186/s13104-017-3066-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lindsay Gielda
- Department of Biological Sciences, Purdue University-Northwest, 1401 S. US 421, Westville, IN, 46391, USA.
| | - Stefanie Rigg
- Department of Biological Sciences, Purdue University-Northwest, 1401 S. US 421, Westville, IN, 46391, USA
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21
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Ullah S, Garg RK, Noor F. DNA perspectives of fixed and paraffin embedded human tissues as resource materials for the identification. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0027-5] [Citation(s) in RCA: 4] [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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22
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Obersteller S, Neubauer H, Hagen RM, Frickmann H. Comparison of Five Commercial Nucleic Acid Extraction Kits for the PCR-based Detection of Burkholderia Pseudomallei DNA in Formalin-Fixed, Paraffin-Embedded Tissues. Eur J Microbiol Immunol (Bp) 2016; 6:244-252. [PMID: 27766174 PMCID: PMC5063018 DOI: 10.1556/1886.2016.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/20/2023] Open
Abstract
The extraction and further processing of nucleic acids (NA) from formalin-fixed paraffin-embedded (FFPE) tissues for microbiological diagnostic polymerase chain reaction (PCR) approaches is challenging. Here, we assessed the effects of five different commercially available nucleic acid extraction kits on the results of real-time PCR. FFPE samples from organs of Burkholderia pseudomallei-infected Swiss mice were subjected to processing with five different extraction kits from QIAGEN (FFPE DNA Tissue Kit, EZ1 DNA Tissue Kit, DNA Mini Kit, DNA Blood Mini Kit, and FlexiGene DNA Kit) in combination with three different real-time PCRs targeting B. pseudomallei-specific sequences of varying length after 16 years of storage. The EZ1 DNA Tissue Kit and the DNA Mini Kit scored best regarding the numbers of successful PCR reactions. In case of positive PCR, differences regarding the cycle-threshold (Ct) values were marginal. The impact of the applied extraction kits on the reliability of PCR from FFPE material seems to be low. Interfering factors like the quality of the dewaxing procedure or the sample age appear more important than the selection of specialized FFPE kits.
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Affiliation(s)
| | - Heinrich Neubauer
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health , Jena, Germany
| | - Ralf Matthias Hagen
- NATO Center of Excellence for Military Medicine (MilMedCOE), Deployment Health Surveillance Capability (DHSC) , Munich, Germany
| | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany; Institut for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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23
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Suleman E, Mtshali MS, Lane E. Investigation of false positives associated with loop-mediated isothermal amplification assays for detection of Toxoplasma gondii in archived tissue samples of captive felids. J Vet Diagn Invest 2016; 28:536-42. [DOI: 10.1177/1040638716659864] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Toxoplasma gondii is a ubiquitous protozoan parasite that infects humans and many different animals, including felids. Many molecular and serologic tests have been developed for detection of T. gondii in a wide range of hosts. Loop-mediated isothermal amplification (LAMP) is a field-friendly technique that lacks the practical drawbacks of other molecular and serologic tests, and LAMP assays have been successfully developed for detection of T. gondii in fresh tissue samples. In the current study, both a previously published and a de-novo designed LAMP assay were compared to a quantitative real-time (q)PCR assay, for the detection of T. gondii in archived formalin-fixed, paraffin-embedded (FFPE) tissue samples from captive wildlife. The LAMP assays produced conflicting results, generating both false positives and false negatives. Furthermore, the LAMP assays were unable to positively identify samples with low levels of parasites as determined by qPCR and histopathology. Therefore, these LAMP assays may not be the most suitable assays for detection of T. gondii in archived FFPE and frozen tissue samples.
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Affiliation(s)
- Essa Suleman
- National Zoological Gardens of South Africa, Research and Scientific Services Department, Pretoria, South Africa (Suleman, Mtshali, Lane)
- University of Witwatersrand, Strategic Planning Division, Wits, South Africa (Mtshali)
- University of the Free State, Department of Zoology and Entomology, Phuthaditjhaba, South Africa (Mtshali)
| | - Moses Sibusiso Mtshali
- National Zoological Gardens of South Africa, Research and Scientific Services Department, Pretoria, South Africa (Suleman, Mtshali, Lane)
- University of Witwatersrand, Strategic Planning Division, Wits, South Africa (Mtshali)
- University of the Free State, Department of Zoology and Entomology, Phuthaditjhaba, South Africa (Mtshali)
| | - Emily Lane
- National Zoological Gardens of South Africa, Research and Scientific Services Department, Pretoria, South Africa (Suleman, Mtshali, Lane)
- University of Witwatersrand, Strategic Planning Division, Wits, South Africa (Mtshali)
- University of the Free State, Department of Zoology and Entomology, Phuthaditjhaba, South Africa (Mtshali)
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24
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Salloum T, Khalifeh I, Tokajian S. Detection, molecular typing and phylogenetic analysis of Leishmania isolated from cases of leishmaniasis among Syrian refugees in Lebanon. Parasite Epidemiol Control 2016; 1:159-168. [PMID: 29988171 PMCID: PMC5991828 DOI: 10.1016/j.parepi.2016.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 01/06/2023] Open
Abstract
Leishmania is a parasitic protozoan with more than two-dozen species causing the disease leishmaniasis. It is transmitted to humans through the bite of an infected female phlebotomine sand-fly vector. In the past two years the incidence of leishmaniasis has been drastically increasing in Lebanon. This was in parallel with the deterioration of the security in Syria forcing thousands to flee and seek shelter in poorly maintained refugee camps and collective shelters. Cutaneous leishmaniasis (CL) is now considered a public health problem, but its epidemiology has not been fully elucidated. To our knowledge, this is the first study comparing two different molecular methods for the detection and identification of Leishmania tropica in Lebanon. Two molecular typing methods of 39 FFPE Leishmania isolates were used: the ITS1-PCR RFLP and the nested ITS1-5.8S rDNA gene amplification followed by sequencing and phylogenetic analysis. The efficiency of these two techniques in Leishmania identification was compared and the phylogenetic relationships among these isolates were illustrated based on the neighbor-joining (NJ) method. The results were statistically correlated with the parasitic index (PI). The DNA storage in formalin-fixed paraffin embedded (FFPE) tissues was assessed as well. The parasites identified were all L. tropica as determined by both techniques. ITS1-5.8S rDNA gene based typing proved to be more sensitive in the detection of parasites (positive in 69.2% of the isolates) as opposed to the ITS1-PCR RFLP method that was successful in identifying L. tropica in only 43.6% of the isolates. Sequencing and phylogenetic analysis revealed high levels of heterogeneity. A statistically significant correlation was observed between PI and the results of the nested ITS1-5.8S rDNA gene PCR. Genotyping at the species level is essential for monitoring the relative frequency of CL in the Mediterranean area that is correlated to three different Leishmania species (Leishmania infantum, Leishmania major and L. tropica), each characterized by distinct epidemiological features. The obtained results highlight the need to find a universally accepted diagnostic tool for Leishmania typing.
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Key Words
- 5.8S rDNA gene
- Bp, base pair
- CL, cutaneous leishmaniasis
- FFPE, formalin-fixed paraffin embedded
- ITS, internal transcribed spacer
- ITS1
- L. tropica, Leishmania tropica
- Leishmania
- MLST, multilocus sequence typing
- NJ, neighbor-joining
- PCR, polymerase chain reaction
- PI, parasitic index
- RFLP
- RFLP, restriction fragment length polymorphism
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Affiliation(s)
- Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Ibrahim Khalifeh
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
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25
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Gaignaux A, Ashton G, Coppola D, De Souza Y, De Wilde A, Eliason J, Grizzle W, Guadagni F, Gunter E, Koppandi I, Shea K, Shi T, Stein JA, Sobel ME, Tybring G, Van den Eynden G, Betsou F. A Biospecimen Proficiency Testing Program for Biobank Accreditation: Four Years of Experience. Biopreserv Biobank 2016; 14:429-439. [PMID: 27195612 DOI: 10.1089/bio.2015.0108] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Biobanks produce and distribute biospecimens, ensuring their fitness for purpose and accurately qualifying them before distribution. In their efforts toward professionalization, biobanks can nowadays seek certification or accreditation. One of the requirements of these standards is regular participation in Proficiency Testing (PT) programs. An international PT program has been developed and provided to biobanks and other laboratories that perform specific tests to qualify different types of biospecimens. This PT program includes biospecimen testing schemes, as well as biospecimen processing interlaboratory exercises. This PT program supports the development of biobank quality assurance by providing the possibility to assess biobank laboratory performance and useful insights into biobank laboratory method performance characteristics and thus fulfill the demands from accreditation authorities.
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Affiliation(s)
| | - Garry Ashton
- 2 Cancer Research UK Manchester Institute , Manchester, United Kingdom
| | | | - Yvonne De Souza
- 4 AIDS Specimen Bank, University of California , San Francisco, San Francisco, California
| | | | - James Eliason
- 6 Great Lakes Stem Cell Innovation Center , Detroit, Michigan
| | - William Grizzle
- 7 Tissue Collection and Banking Facility, University of Alabama , Birmingham, Birmingham, Alabama
| | - Fiorella Guadagni
- 8 BioBIM (Multidisciplinary Interinstitutional Biobank) IRCCS San Raffaele , Rome, Italy
| | | | - Iren Koppandi
- 10 Cellular Technology Limited , Shaker Heights, Ohio
| | | | - Tim Shi
- 12 GlobalMD Network Corporation , Catonsville, Maryland
| | - Julie A Stein
- 13 PPD Vaccines and Biologics Lab , Wayne, Pennsylvania
| | - Mark E Sobel
- 14 American Society for Investigative Pathology , Bethesda, Maryland
| | | | - Gert Van den Eynden
- 16 Molecular Immunology Unit, Institut Jules Bordet , Brussels, Belgium .,17 Pathobiology Group , EORTC, Brussels, Belgium
| | - Fay Betsou
- 1 Integrated Biobank of Luxembourg , Luxembourg, Luxembourg
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Formalin fixed paraffin embedded (FFPE) material is amenable to HPV detection by the Xpert® HPV assay. J Clin Virol 2016; 77:55-9. [DOI: 10.1016/j.jcv.2016.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/21/2015] [Accepted: 02/10/2016] [Indexed: 01/05/2023]
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Smolina M, Goormaghtigh E. FTIR imaging of the 3D extracellular matrix used to grow colonies of breast cancer cell lines. Analyst 2016; 141:620-9. [DOI: 10.1039/c5an01997d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Infrared imaging was applied to investigate a reconstituted basement membrane, known as Matrigel, in three-dimensional cell cultures.
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Affiliation(s)
- Margarita Smolina
- Laboratory for the Structure and Function of Biological Membranes
- Center for Structural Biology and Bioinformatics
- Université Libre de Bruxelles (ULB)
- B-1050 Brussels
- Belgium
| | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes
- Center for Structural Biology and Bioinformatics
- Université Libre de Bruxelles (ULB)
- B-1050 Brussels
- Belgium
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Tang Y, Chen J, Wang J, Zheng K, Liao D, Liao X, Liu W, Wang L. Fixed nuclei as alternative template of BIOMED-2 multiplex polymerase chain reaction for immunoglobulin gene clonality testing in B-cell malignancies. AMERICAN JOURNAL OF BLOOD RESEARCH 2015; 5:62-78. [PMID: 27069754 PMCID: PMC4769348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
Evaluation of immunoglobulin (Ig) gene rearrangements with BIOMED-2 multiplex PCR has become a standard detection of clonality in mature B cell malignancies. Conventionally, this method is relatively labor-intensive and time-consuming, as it requires DNA isolation from bone marrow aspirates (BM) or peripheral blood (PB) in patients with BM or PB involvement. On the other hand, fluorescence in situ hybridization (FISH) is routinely used as genetic screening in B cell malignancies, but the surplus fixed nuclei initially prepared for FISH usually turn useless afterwards. We sought to use these surplus nuclei after FISH as a template to perform PCR-based Ig gene clonality testing. Templates of 12 patients with mature B cell malignancies, which consisted of both DNA isolated with commercial DNA isolation kit from fresh BM or PB (DNA group) and the fixed nuclei initially prepared for FISH (nuclei group) from the same individuals, were subjected to PCR with BIOMED-2 primer sets for immunoglobulin heavy chain and kappa light chain under recommended conditions. Our result, for the first time, showed a high consistency between the two groups in detecting B cell clonality, which indicates that nuclei for FISH can function as a reliable template comparable to fresh tissue-isolated DNA in PCR based Ig clonality testing. This offers a simple, rapid and more economical alternative to standard Ig testing based on regular DNA.
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Affiliation(s)
- Yuan Tang
- Department of Pathology, West China Hospital, Sichuan UniversityChina
| | - Jie Chen
- Department of Pathology, West China Hospital, Sichuan UniversityChina
| | - Jianchao Wang
- Department of Pathology, West China Hospital, Sichuan UniversityChina
| | - Ke Zheng
- Department of Pathology, West China Hospital, Sichuan UniversityChina
| | - Dianying Liao
- Department of Pathology, West China Hospital, Sichuan UniversityChina
| | - Xiaomei Liao
- Department of Hematology, West China Hospital, Sichuan UniversityChina
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan UniversityChina
| | - Lin Wang
- Department of Pathology, West China Hospital, Sichuan UniversityChina
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Ruiz-Fuentes JL, Díaz A, Entenza AE, Frión Y, Suárez O, Torres P, de Armas Y, Acosta L. Comparison of four DNA extraction methods for the detection of Mycobacterium leprae from Ziehl–Neelsen-stained microscopic slides. Int J Mycobacteriol 2015; 4:284-9. [DOI: 10.1016/j.ijmyco.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/01/2015] [Accepted: 06/06/2015] [Indexed: 10/23/2022] Open
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Loonen AJM, Wolffs PFG, de Bresser M, Habraken M, Bruggeman CA, Hermans MHA, van den Brule AJC. Tuf mRNA rather than 16S rRNA is associated with culturable Staphylococcus aureus. World J Clin Infect Dis 2015; 5:86-93. [DOI: 10.5495/wjcid.v5.i4.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/20/2015] [Accepted: 06/11/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To study the presence of various nucleic acids targets of Staphylococcus aureus (S. aureus) during bacterial growth and antibiotic induced killing in relation to viability.
METHODS: S. aureus was cultured to log phase and spiked in Todd Hewitt (TH) broth and whole blood of healthy human volunteers. Viability of S. aureus after flucloxacillin treatment (0, 1, 3 and 6 d) was assessed by culture on bloodagar plates. DNA and RNA were isolated from 200 μL. cDNA synthesis was performed by using random primers. The presence of S. aureus DNA, rRNA, and mRNA were determined by real-time polymerase chain reaction of the 16S rDNA and tuf gene (elongation factor Tu).
RESULTS: S. aureus spiked in TH broth without antibiotics grew from day 0-6 and DNA (tuf and 16S), and 16S rRNA remained detectable during this whole period. During flucloxacillin treatment S. aureus lost viability from day 3 onwards, while the 16S rRNA-gene and its RNA transcripts remained detectable. DNA and rRNA can be detected in flucloxacillin treated S. aureus cultures that do not further contain culturable bacteria. However, tuf mRNA became undetectable from day 3 onwards. Tuf mRNA can only be detected from samples with culturable bacteria. When spiking S. aureus in whole blood instead of broth no bacterial growth was seen, neither in the absence nor in the presence of flucloxacillin. Accordingly, no increase in DNA and RNA levels of both 16S rDNA and the tuf gene were detected.
CONCLUSION: Tuf mRNA expression is associated with culturable S. aureus and might be used to monitor antibiotic effects.
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Roemen GM, zur Hausen A, Speel EJM. Adequate tissue for adequate diagnosis: what do we really need? Lung Cancer 2015. [DOI: 10.1183/2312508x.10010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Rodriguez-Palacios A, Kodani T, Kaydo L, Pietropaoli D, Corridoni D, Howell S, Katz J, Xin W, Pizarro TT, Cominelli F. Stereomicroscopic 3D-pattern profiling of murine and human intestinal inflammation reveals unique structural phenotypes. Nat Commun 2015; 6:7577. [PMID: 26154811 PMCID: PMC4510646 DOI: 10.1038/ncomms8577] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 05/15/2015] [Indexed: 02/06/2023] Open
Abstract
Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes ('cobblestones' versus 'villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In humans, stereomicroscopy reveals 'liquefaction' lesions and hierarchical fistulous complexes, enriched with clostridia/segmented filamentous bacteria, running under healthy mucosa in Crohn's disease. We suggest that stereomicroscopic (3D-SMAPgut) profiling can be easily implemented and enable the comprehensive study of inflammatory 3D structures, genetics and flora in IBD.
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Affiliation(s)
- Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Tomohiro Kodani
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Lindsey Kaydo
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Davide Pietropaoli
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Daniele Corridoni
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Scott Howell
- Department of Visual Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Jeffry Katz
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Department of Digestive Health Institute, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
| | - Wei Xin
- Department of Digestive Health Institute, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Theresa T. Pizarro
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Fabio Cominelli
- Division of Gastroenterology and Liver Disease, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
- Department of Digestive Health Institute, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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de Leeuw BH, Voskuil WS, Maraha B, van der Zee A, Westenend PJ, Kusters JG. Evaluation of different real time PCRs for the detection of Pneumocystis jirovecii DNA in formalin-fixed paraffin-embedded bronchoalveolar lavage samples. Exp Mol Pathol 2015; 98:390-2. [DOI: 10.1016/j.yexmp.2015.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
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34
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Huijsmans CJJ, van den Brule AJC, Rigter H, Poodt J, van der Linden JC, Savelkoul PHM, Hilbink M, Hermans MHA. Allelic imbalance at the HER2/TOP2A locus in breast cancer. Diagn Pathol 2015; 10:56. [PMID: 26022247 PMCID: PMC4448206 DOI: 10.1186/s13000-015-0289-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/05/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Breast cancer is a heterogeneous disease with various histological features and molecular markers. These are utilized for the prediction of clinical outcome and therapeutic decision making. In addition to well established markers such as HER2 overexpression and estrogen and progesterone receptor (ER and PR) status, chromosomal instability is evolving as an important hallmark of cancers. The HER2/TOP2A locus is of great importance in breast cancer. The copy number variability at this locus has been proposed to be a marker for the degree of chromosomal instability. We therefore developed a Single Nucleotide Polymorphism (SNP) assay to evaluate allelic imbalance at the HER2/TOP2A locus in three different entities of primary breast tumors. METHODS Eleven SNPs were carefully selected and detected by real time PCR using DNA extracted from paired (histologically normal and tumor) paraffin-embedded tissues. Primary breast tumors of 44 patients were included, 15 tumors with HER2 overexpression, 16 triple negative tumors, defined by the absence of HER2 overexpression and a negative ER and PR status and 13 ER and PR positive tumors without HER2 overexpression. As controls, histologically normal breast tissues from 10 patients with no breast tumor were included. RESULTS Allelic imbalance was observed in 13/15 (87 %) HER2 positive tumors, the remaining 2 being inconclusive. Of the 16 triple negative tumors, 12 (75 %) displayed instability, 3 (19 %) displayed no instability, and 1 was inconclusive. Of the 13 hormone receptor positive tumors, 5 (38 %) displayed allelic imbalance, while 8 did not. CONCLUSIONS We conclude that the SNP assay is suitable for rapid testing of allelic (im)balance at the HER2/TOP2A locus using paraffin-embedded tissues. Based on allelic imbalance at this locus, both triple negative and ER and PR positive breast tumors can be subcategorized. The clinical relevance of the allelic (im)balance status at the HER2/TOP2A locus in breast cancer is subject of future study. VIRTUAL SLIDES The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2086062232155220.
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Affiliation(s)
- Cornelis J J Huijsmans
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, PO Box 90153, 5200 ME, 's-Hertogenbosch, The Netherlands.
| | - Adriaan J C van den Brule
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, PO Box 90153, 5200 ME, 's-Hertogenbosch, The Netherlands.
| | - Henny Rigter
- Laboratory of Pathology, Jeroen Bosch Hospital, PO Box 90153, 5223 GZ, 's-Hertogenbosch, The Netherlands.
| | - Jeroen Poodt
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, PO Box 90153, 5200 ME, 's-Hertogenbosch, The Netherlands.
| | - Johannes C van der Linden
- Laboratory of Pathology, Jeroen Bosch Hospital, PO Box 90153, 5223 GZ, 's-Hertogenbosch, The Netherlands.
| | - Paul H M Savelkoul
- Medical Microbiology and Infection Control, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands. .,Department Medical Microbiology, Maastricht University Medical Center, PO box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Mirrian Hilbink
- Jeroen Bosch Academy, Jeroen Bosch Hospital, PO Box 90153, 5223 GZ, 's-Hertogenbosch, The Netherlands.
| | - Mirjam H A Hermans
- Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, PO Box 90153, 5200 ME, 's-Hertogenbosch, The Netherlands.
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Walton LA, Bradley RS, Withers PJ, Newton VL, Watson REB, Austin C, Sherratt MJ. Morphological Characterisation of Unstained and Intact Tissue Micro-architecture by X-ray Computed Micro- and Nano-Tomography. Sci Rep 2015; 5:10074. [PMID: 25975937 PMCID: PMC4650804 DOI: 10.1038/srep10074] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/27/2015] [Indexed: 02/08/2023] Open
Abstract
Characterisation and quantification of tissue structures is limited by sectioning-induced artefacts and by the difficulties of visualising and segmenting 3D volumes. Here we demonstrate that, even in the absence of X-ray contrast agents, X-ray computed microtomography (microCT) and nanotomography (nanoCT) can circumvent these problems by rapidly resolving compositionally discrete 3D tissue regions (such as the collagen-rich adventitia and elastin-rich lamellae in intact rat arteries) which in turn can be segmented due to their different X-ray opacities and morphologies. We then establish, using X-ray tomograms of both unpressurised and pressurised arteries that intra-luminal pressure not only increases lumen cross-sectional area and straightens medial elastic lamellae but also induces profound remodelling of the adventitial layer. Finally we apply microCT to another human organ (skin) to visualise the cell-rich epidermis and extracellular matrix-rich dermis and to show that conventional histological and immunohistochemical staining protocols are compatible with prior X-ray exposure. As a consequence we suggest that microCT could be combined with optical microscopy to characterise the 3D structure and composition of archival paraffin embedded biological materials and of mechanically stressed dynamic tissues such as the heart, lungs and tendons.
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Affiliation(s)
| | | | | | - Victoria L. Newton
- Institute of Inflammation and Repair, University of Manchester, Manchester, United Kingdom
| | - Rachel E. B. Watson
- Institute of Inflammation and Repair, University of Manchester, Manchester, United Kingdom
| | - Clare Austin
- Institute of Cardiovascular Sciences
- Faculty of Health and Social Care, Edge Hill University, Ormskirk, United Kingdom
| | - Michael J. Sherratt
- Institute of Inflammation and Repair, University of Manchester, Manchester, United Kingdom
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Hu YC, Zhang Q, Huang YH, Liu YF, Chen HL. Comparison of two methods to extract DNA from formalin-fixed, paraffin-embedded tissues and their impact on EGFR mutation detection in non-small cell lung carcinoma. Asian Pac J Cancer Prev 2015; 15:2733-7. [PMID: 24761893 DOI: 10.7314/apjcp.2014.15.6.2733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Molecular pathology tests are often carried for clinicopathological diagnosis and pathologists have established large collections of formalin-fixed, paraffin-embedded tissue (FFPE) banks. However, extraction of DNA from FFPE is a laborious and challenging for researchers in clinical laboratories. The aim of this study was to compare two widely used DNA extraction methods: using a QIAamp DNA FFPE kit from Qiagen and a Cobas Sample Preparation Kit from Roche, and evaluated the effect of the DNA quality on molecular diagnostics. METHODS DNA from FFPE non-small cell lung carcinoma tissues including biopsy and surgical specimens was extracted with both QIAamp DNA FFPE and Cobas Sample Preparation Kits and EGFR mutations of non-small cell lung carcinomas were detected by real-time quantitative PCR using the extracted DNA. RESULTS AND CONCLUSION Our results showed that DNA extracted by QIAamp and Cobas methods were both suitable to detect downstream EGFR mutation in surgical specimens. Howover, Cobas method could yield more DNA from biopsy specimens, and gain much better EGFR mutation results.
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Affiliation(s)
- Yu-Chang Hu
- Department of Pathology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China E-mail :
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Abstract
BACKGROUND Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay. CONTENT Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made. SUMMARY Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample.
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Alvarez-Aldana A, Martínez JW, Sepúlveda-Arias JC. Comparison of five protocols to extract DNA from paraffin-embedded tissues for the detection of human papillomavirus. Pathol Res Pract 2014; 211:150-5. [PMID: 25444238 DOI: 10.1016/j.prp.2014.10.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 10/14/2014] [Accepted: 10/23/2014] [Indexed: 12/22/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable source of DNA with which to perform large retrospective studies on the epidemiology of HPV infection. Five different DNA extraction protocols were carried out to evaluate the DNA obtained from FFPE samples with polymerase chain reaction (PCR) using two primer sets to amplify a constitutive human gene, β-globin, and two primer sets to detect the L1 and E6 HPV genes. From the five DNA extraction protocols evaluated, the best results were obtained with protocol A, corresponding to a crude extract from the sample. With the procedures described herein, we were able to amplify DNA extracted from archival paraffin blocks stored for six years. However, the amplification products were more efficiently obtained with primers that amplified shorter fragments. This result indicates that a major factor limiting the extraction process in these samples is DNA fragmentation, a factor that will naturally vary between the different specimens evaluated. Also, depending upon the extraction method, PCR amplification of a human gene does not necessarily guarantee the successful extraction of viral DNA. In conclusion, different DNA and HPV detection methods can significantly influence the results. Therefore, the DNA extraction methods and primers used for DNA amplification in fixed tissues need to be chosen carefully, depending on the specific requirements of the study being carried out.
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Affiliation(s)
- Adalucy Alvarez-Aldana
- Facultad de Ciencias de la Salud, Departamento de Ciencias Básicas, Grupo Infección e Inmunidad, Universidad Tecnológica de Pereira, Pereira, Colombia.
| | - José William Martínez
- Facultad de Ciencias de la Salud, Departamento de Medicina Comunitaria, Grupo Epidemiología, Salud y Violencia, Universidad Tecnológica de Pereira, Pereira, Colombia.
| | - Juan C Sepúlveda-Arias
- Facultad de Ciencias de la Salud, Departamento de Ciencias Básicas, Grupo Infección e Inmunidad, Universidad Tecnológica de Pereira, Pereira, Colombia.
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Use of transrenal DNA for the diagnosis of extrapulmonary tuberculosis in children: a case of tubercular otitis media. J Clin Microbiol 2014; 53:336-8. [PMID: 25339389 DOI: 10.1128/jcm.02548-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diagnosis of tuberculosis (TB) is difficult in children, especially for smear-negative pulmonary and extrapulmonary TB, which are common at this age. We report an 11-year-old girl with TB otitis media with negative smear microscopy and Xpert MTB/RIF but positive Mycobacterium tuberculosis-specific transrenal DNA (Tr-MTB-DNA) test results and culture for M. tuberculosis.
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40
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Luka PD, Jambol AR, Yakubu B. Detection of African swine fever virus from formalin fixed and non-fixed tissues by polymerase chain reaction. Vet World 2014. [DOI: 10.14202/vetworld.2014.811-815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Surat G, Wallace WA, Laurenson IF, Seagar AL. Rapid real-time PCR for detection of Mycobacterium tuberculosis complex DNA in formalin-fixed paraffin embedded tissues: 16% of histological 'sarcoid' may contain such DNA. J Clin Pathol 2014; 67:1084-7. [PMID: 25170093 DOI: 10.1136/jclinpath-2014-202307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIMS To investigate the diagnostic accuracy of IS6110 real-time PCR for detection of Mycobacterium tuberculosis complex (MTBC) in DNA extracted from formalin-fixed paraffin embedded (FFPE) tissues using two different methods. In the absence of material submitted for tuberculosis (TB) culture, MTBC detection in FFPE tissue can be an important aid to diagnosis. METHODS We collected 144 FFPE tissue blocks (lung and lymph node) for IS6110 real-time PCR. Two DNA extraction methods (QIAamp FFPE tissue kit and NucliSENS easyMAG) were assessed within a general laboratory setting. PCR results were compared with histology and culture. RESULTS In the histological MTBC and culture MTBC (TB-positive) groups, 72.4% were IS6110-positive and 27.6% negative. IS6110-negative results were obtained from 98%, 61.5% and 84% of the histologically MTBC-negative (TB-negative) group, histologically TB/no culture group and sarcoidosis group, respectively. Review of 19 IS6110-positive patients in the latter three groups showed that 15 had clinical TB. Thirteen of 15 (86.7%) IS6110-positive patients in the histological TB/no culture group and 2 of 4 (50%) IS6110-positive patients in the sarcoidosis group were clinically diagnosed with TB which highlights the difficulty of a pathological diagnosis. CONCLUSIONS IS6110 real-time PCR using easyMAG extracted DNA is a moderately sensitive, specific and rapid method for MTBC detection in FFPE material, but must be interpreted in the overall clinical context. PCR results can be available in around 5 h from FFPE specimen receipt, with minimal hands-on time.
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Affiliation(s)
- Güzin Surat
- Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
| | - William A Wallace
- Department of Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Ian F Laurenson
- Scottish Mycobacteria Reference Laboratory (SMRL), Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Amie-Louise Seagar
- Scottish Mycobacteria Reference Laboratory (SMRL), Royal Infirmary of Edinburgh, Edinburgh, UK
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Heydt C, Fassunke J, Künstlinger H, Ihle MA, König K, Heukamp LC, Schildhaus HU, Odenthal M, Büttner R, Merkelbach-Bruse S. Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics. PLoS One 2014; 9:e104566. [PMID: 25105902 PMCID: PMC4126727 DOI: 10.1371/journal.pone.0104566] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022] Open
Abstract
Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for downstream applications like massively parallel sequencing.
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Affiliation(s)
- Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
- * E-mail:
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Katharina König
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | | | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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Marisi G, Passardi A, Calistri D, Zoli W, Amadori D, Ulivi P. Discrepancies between VEGF -1154 G>A polymorphism analysis performed in peripheral blood samples and FFPE tissue. Int J Mol Sci 2014; 15:13333-43. [PMID: 25079441 PMCID: PMC4159797 DOI: 10.3390/ijms150813333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/02/2014] [Accepted: 07/23/2014] [Indexed: 01/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) may be associated with the response or toxicity to different types of treatment. Although SNP analysis is usually performed on DNA from peripheral blood, formalin fixed paraffin-embedded (FFPE) tissue is often used for retrospective studies. We analyzed VEGF (-2578C>A, -1498C>T, -1154G>A, -634C>G, +936C>T) and eNOS (+894G>T, -786T>C, VNTR (variable number of tandem repeats) 27bp intron 4) polymorphisms by direct sequencing or Real Time PCR in 237 patients with advanced colorectal cancer. Peripheral blood was used for 153 patients, whereas only FFPE tumor tissue was available for 84 patients. All SNP frequencies were in Hardy-Weinberg Equilibrium (HWE), with the exception of VEGF -1154, which was only in HWE in peripheral blood specimens. We therefore analyzed this SNP in DNA extracted from FFPE tumor tissue compared to FFPE healthy tissue and peripheral blood from 20 patients. Numerous heterozygous patients in peripheral blood DNA were homozygous for the A-allele in both tumor and healthy FFPE tissues. Our findings indicate that, although FFPE tissue might be a suitable specimen for genotyping, VEGF -1154 does not give reliable results on this type of material. As other SNPs may also have this limitation, genotype concordance should first be confirmed by comparing results obtained from FFPE and fresh sample analyses.
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Affiliation(s)
- Giorgia Marisi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
| | - Alessandro Passardi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
| | - Wainer Zoli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
| | - Dino Amadori
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola (FC), Italy.
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Hagenaars JCJP, Koning OHJ, van den Haak RFF, Verhoeven BAN, Renders NHM, Hermans MHA, Wever PC, van Suylen RJ. Histological characteristics of the abdominal aortic wall in patients with vascular chronic Q fever. Int J Exp Pathol 2014; 95:282-9. [PMID: 24953727 DOI: 10.1111/iep.12086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/26/2014] [Indexed: 12/28/2022] Open
Abstract
The aim of this study was to describe specific histological findings of the Coxiella burnetii-infected aneurysmal abdominal aortic wall. Tissue samples of the aneurysmal abdominal aortic wall from seven patients with chronic Q fever and 15 patients without evidence of Q fever infection were analysed and compared. Chronic Q fever was diagnosed using serology and tissue PCR analysis. Histological sections were stained using haematoxylin and eosin staining, Elastica van Gieson staining and immunohistochemical staining for macrophages (CD68), T lymphocytes (CD3), T lymphocyte subsets (CD4 and CD8) and B lymphocytes (CD20). Samples were scored by one pathologist, blinded for Q fever status, using a standard score form. Seven tissue samples from patients with chronic Q fever and 15 tissue samples from patients without Q fever were collected. Four of seven chronic Q fever samples showed a necrotizing granulomatous response of the vascular wall, which was characterized by necrotic core of the arteriosclerotic plaque (P = 0.005) and a presence of high numbers of macrophages in the adventitia (P = 0.007) distributed in typical palisading formation (P = 0.005) and surrounded by the presence of high numbers of T lymphocytes located diffusely in media and adventitia. Necrotizing granulomas are a histological finding in the C. burnetii-infected aneurysmal abdominal aortic wall. Chronic Q fever should be included in the list of infectious diseases with necrotizing granulomatous response, such as tuberculosis, cat scratch disease and syphilis.
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45
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DNA and RNA analysis of blood and muscle from bodies with variable postmortem intervals. Forensic Sci Med Pathol 2014; 10:322-8. [DOI: 10.1007/s12024-014-9567-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2014] [Indexed: 10/25/2022]
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46
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Rafiee M, Jahangiri-rad M, Hajjaran H, Mesdaghinia A, Hajaghazadeh M. Detection and identification of Legionella species in hospital water supplies through Polymerase Chain Reaction (16S rRNA). JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2014; 12:83. [PMID: 24860661 PMCID: PMC4032159 DOI: 10.1186/2052-336x-12-83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/20/2014] [Indexed: 06/03/2023]
Abstract
Legionella spp. are important waterborne pathogens that are normally transmitted through aerosols. The present work was conducted to investigate the presence of Legionella spp. and its common species in hospital water supplies. Considering the limitations of culture method, polymerase chain reaction (PCR) assays were developed to detect the gene 16S rRNA irrespective of the bacterial serotype. Four well-established DNA extraction protocols (freeze & thaw and phenol-chloroform as two manual protocols and two commercial kits) were tested and evaluated to release DNA from bacterial cells. A total of 45 samples were collected from seven distinct hospitals' sites during a period of 10 months. The PCR assay was used to amplify a 654-bp fragment of the 16S rRNA gene. Legionella were detected in 13 samples (28.9%) by all of the methods applied for DNA extraction. Significant differences were noted in the yield of extracted nucleic acids. Legionella were not detected in any of the samples when DNA extraction by freeze & thaw was used. Excluding this method and comparing manual protocol with commercial kits, Kappa coefficient was calculated as 0.619 with p < 0.05. Although no meaningful differences were found between the kits, DNA extraction with Bioneer kit exhibited a higher sensitivity than classical Qiagen. Showerheads and cold-water taps were the most and least contaminated sources with 55.5 and 9 percent positive samples, respectively. Moreover two positive samples were identified for species by DNA sequencing and submitted to the Gene Bank database with accession Nos. FJ480932 and FJ480933. The results obtained showed that despite the advantages of molecular assays in Legionella tracing in environmental sources, the use of optimised DNA extraction methods is critical.
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Affiliation(s)
- Mohammad Rafiee
- Department of Environmental Health Engineering, School of Public Health, Alborz University of Medical Sciences, Alborz, Iran
| | - Mahsa Jahangiri-rad
- Department of Environmental Health Engineering, Islamic Azad University, Tehran Medical Sciences Branch, Tehran, Iran
| | - Homa Hajjaran
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mesdaghinia
- Department of Environmental Health Engineering, School of Public Health, Center for Water Quality Research, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hajaghazadeh
- Department of Occupational Health, Health Faculty, Urmia University of Medical Sciences, Urmia, Iran
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Cai HY, Caswell JL, Prescott JF. Nonculture Molecular Techniques for Diagnosis of Bacterial Disease in Animals. Vet Pathol 2014; 51:341-50. [DOI: 10.1177/0300985813511132] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The past decade has seen remarkable technical advances in infectious disease diagnosis, and the pace of innovation is likely to continue. Many of these techniques are well suited to pathogen identification directly from pathologic or clinical samples, which is the focus of this review. Polymerase chain reaction (PCR) and gene sequencing are now routinely performed on frozen or fixed tissues for diagnosis of bacterial infections of animals. These assays are most useful for pathogens that are difficult to culture or identify phenotypically, when propagation poses a biosafety hazard, or when suitable fresh tissue is not available. Multiplex PCR assays, DNA microarrays, in situ hybridization, massive parallel DNA sequencing, microbiome profiling, molecular typing of pathogens, identification of antimicrobial resistance genes, and mass spectrometry are additional emerging technologies for the diagnosis of bacterial infections from pathologic and clinical samples in animals. These technical advances come, however, with 2 caveats. First, in the age of molecular diagnosis, quality control has become more important than ever to identify and control for the presence of inhibitors, cross-contamination, inadequate templates from diagnostic specimens, and other causes of erroneous microbial identifications. Second, the attraction of these technologic advances can obscure the reality that medical diagnoses cannot be made on the basis of molecular testing alone but instead through integrated consideration of clinical, pathologic, and laboratory findings. Proper validation of the method is required. It is critical that veterinary diagnosticians understand not only the value but also the limitations of these technical advances for routine diagnosis of infectious disease.
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Affiliation(s)
- H. Y. Cai
- Animal Health Laboratory, University of Guelph, Guelph, Ontario, Canada
| | - J. L. Caswell
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - J. F. Prescott
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
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48
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Bonin S, Stanta G. Nucleic acid extraction methods from fixed and paraffin-embedded tissues in cancer diagnostics. Expert Rev Mol Diagn 2014; 13:271-82. [DOI: 10.1586/erm.13.14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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49
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Sengüven B, Baris E, Oygur T, Berktas M. Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues. Int J Med Sci 2014; 11:494-9. [PMID: 24688314 PMCID: PMC3970103 DOI: 10.7150/ijms.8842] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/13/2014] [Indexed: 01/25/2023] Open
Abstract
AIM Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. METHODS DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. RESULTS The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. CONCLUSION Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.
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Affiliation(s)
- Burcu Sengüven
- 1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey
| | - Emre Baris
- 1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey
| | - Tulin Oygur
- 1. Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey
| | - Mehmet Berktas
- 2. Pharmacoeconomy and Pharmacoepidemiology Research Center (PEPIRC), Yeditepe University, Istanbul, Turkey
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Fatal subacute myocarditis associated with human bocavirus 2 in a 13-month-old child. J Clin Microbiol 2013; 52:1006-8. [PMID: 24371238 DOI: 10.1128/jcm.03013-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human bocavirus has rarely been incriminated in fatal or life-threatening respiratory infections. We report a case of fatal disseminated infection with subacute lymphocytic myocarditis in a 13-month-old child. The human bocavirus 2 genome was detected by PCR analysis in nasal swab, plasma, urine, ascitic fluid, and mesenteric node, skeletal muscle, and lung tissue specimens.
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