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Chierto E, Aneli S, Nocco N, Riem A, Onofri M, Carnevali E, Robino C. Assessing DNA Degradation through Differential Amplification Efficiency of Total Human and Human Male DNA in a Forensic qPCR Assay. Genes (Basel) 2024; 15:622. [PMID: 38790251 PMCID: PMC11120943 DOI: 10.3390/genes15050622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The assessment of degradation is crucial for the analysis of human DNA samples isolated from forensic specimens. Forensic quantitative PCR (qPCR) assays can include multiple targets of varying amplicon size that display differential amplification efficiency, and thus different concentrations, in the presence of degradation. The possibility of deriving information on DNA degradation was evaluated in a forensic qPCR assay not specifically designed to detect DNA fragmentation, the Plexor HY (Promega), by calculating the ratio between the estimated concentrations of autosomal (99 bp) and Y-chromosomal (133 bp) targets ("[Auto]/[Y]"). The [Auto]/[Y] ratio measured in 57 formalin-fixed, paraffin-embedded samples was compared to a quality score (QS) calculated for corresponding STR profiles using quantitative data (allele peak height). A statistically significant inverse correlation was observed between [Auto]/[Y] and QS (R = -0.65, p < 0.001). The [Auto]/[Y] values were highly correlated (R = 0.75, p < 0.001) with the "[Auto]/[D]" values obtained using the PowerQuant (Promega) assay, expressly designed to detect DNA degradation through simultaneous quantification of a short (Auto) and a long (D) autosomal target. These results indicate that it is possible to estimate DNA degradation in male samples through Plexor HY data and suggest an alternative strategy for laboratories lacking the equipment required for the assessment of DNA integrity through dedicated qPCR assays.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Nicola Nocco
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Alessia Riem
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Martina Onofri
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy (E.C.)
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy
| | - Eugenia Carnevali
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy (E.C.)
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
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2
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Saniee P, Ghadersoltani P, Noroozpour M, Sadjadi A. An Efficient and Easy- to- Use Method for Extraction of H. pylori DNA from Archival Formalin-Fixed and Paraffin-Embedded Gastric Tissues. IRANIAN JOURNAL OF PATHOLOGY 2023; 18:410-414. [PMID: 38024551 PMCID: PMC10646749 DOI: 10.30699/ijp.2023.562113.2974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/09/2023] [Indexed: 12/01/2023]
Abstract
Background & Objective Formalin-fixed paraffin-embedded archived tissues are useful for the genetic analyses and assessment of some patients' disease history, including infectious diseases. However, there is no established protocol for extracting bacterial DNA from the archived specimens. In this study DNA was extracted from the archived H. pylori-positive gastric biopsies by some modifications applied to the previously published protocols. The quality of the extracted DNA was assessed by amplifying H. pylori-specific 16S rRNA gene. Methods Fifty H. pylori-positive gastric biopsies obtained, fixed, and embedded in paraffin blocks during 2002-2008 were recruited. After paraffin removal, simultaneous proteinase K treatment and mechanical disruption using glass beads were used for the digestion of gastric tissues. DNA extraction was performed by adding one step of phenol treatment and two steps of incubation to the conventional phenol-chloroform method. The quantity and quality of the extracted DNA samples were assessed. Also, PCR was performed using primers specific for the H. pylori-specific 16S rRNA. Results The electrophoresis showed that intact DNAs were recovered from all biopsy samples. Amplification of the PCR products with the size of 519bp confirmed the presence of H. pylori-specific 16S rRNA gene in all the biopsies. Conclusion A 100% success rate for the amplification of H. pylori-specific 16S rRNA gene was achieved from all the samples. In this regard, the designed modified method resulted in the effective removal of interfering contaminations and enhanced the quality of the extracted bacterial DNA from the archived tissues. These modifications may contribute to better extraction of the intact DNA from different bacteria present in human tissues.
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Affiliation(s)
- Parastoo Saniee
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, Iran
| | - Paria Ghadersoltani
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, Iran
| | - Masoumeh Noroozpour
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C, Tehran, Iran
| | - Alireza Sadjadi
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Steiert TA, Parra G, Gut M, Arnold N, Trotta JR, Tonda R, Moussy A, Gerber Z, Abuja P, Zatloukal K, Röcken C, Folseraas T, Grimsrud M, Vogel A, Goeppert B, Roessler S, Hinz S, Schafmayer C, Rosenstiel P, Deleuze JF, Gut I, Franke A, Forster M. A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 2023; 51:7143-7162. [PMID: 37351572 PMCID: PMC10415133 DOI: 10.1093/nar/gkad519] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
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Affiliation(s)
- Tim A Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Genís Parra
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Marta Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Jean-Rémi Trotta
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Raúl Tonda
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Alice Moussy
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
| | - Zuzana Gerber
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Peter M Abuja
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
| | - Marit M Grimsrud
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover 30625, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, Ludwigsburg 71640, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Sebastian Hinz
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Clemens Schafmayer
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Jean-François Deleuze
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Ivo G Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
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Abuja PM, Pabst D, Bourgeois B, Loibner M, Ulz C, Kufferath I, Fackelmann U, Stumptner C, Kraemer R, Madl T, Zatloukal K. Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability. Int J Mol Sci 2023; 24:8010. [PMID: 37175716 PMCID: PMC10178321 DOI: 10.3390/ijms24098010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Molecular diagnostics in healthcare relies increasingly on genomic and transcriptomic methodologies and requires appropriate tissue specimens from which nucleic acids (NA) of sufficiently high quality can be obtained. Besides the duration of ischemia and fixation type, NA quality depends on a variety of other pre-analytical parameters, such as storage conditions and duration. It has been discussed that the improper dehydration of tissue during processing influences the quality of NAs and the shelf life of fixed tissue. Here, we report on establishing a method for determining the amount of residual water in fixed, paraffin-embedded tissue (fixed by neutral buffered formalin or a non-crosslinking fixative) and its correlation to the performance of NAs in quantitative real-time polymerase chain reaction (qRT-PCR) analyses. The amount of residual water depended primarily on the fixative type and the dehydration protocol and, to a lesser extent, on storage conditions and time. Moreover, we found that these parameters were associated with the qRT-PCR performance of extracted NAs. Besides the cross-linking of NAs and the modification of nucleobases by formalin, the hydrolysis of NAs by residual water was found to contribute to reduced qRT-PCR performance. The negative effects of residual water on NA stability are not only important for the design and interpretation of research but must also be taken into account in clinical diagnostics where the reanalysis of archived tissue from a primary tumor may be required (e.g., after disease recurrence). We conclude that improving the shelf life of fixed tissue requires meticulous dehydration and dry storage to minimize the degradative influence of residual water on NAs.
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Affiliation(s)
- Peter M. Abuja
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Pabst
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Martina Loibner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Christine Ulz
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Iris Kufferath
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Ulrike Fackelmann
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Cornelia Stumptner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Rainer Kraemer
- Berghof Products & Instruments GmbH, 72800 Eningen, Germany
| | - Tobias Madl
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
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Kottarathil M, Thayanidhi P, P S, Jyoti Kindo A. Rise of mucormycosis during the COVID-19 pandemic and the challenges faced. Curr Med Mycol 2023; 9:44-55. [PMID: 37867589 PMCID: PMC10590187 DOI: 10.18502/cmm.2023.345032.1400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 10/24/2023] Open
Abstract
Mucormycosis (previously called zygomycosis) is a diverse group of increasingly recognized and frequently fatal mycotic diseases caused by members of the class zygomycetes. Mucormycosis is around 80 times more common in India, compared to other developed countries, with a frequency of 0.14 cases per 1,000 population. The most frequent causative agent of mucormycosis is the following genera from the Order Mucorales Rhizopus, Mucor, Rhizomucor, Absidia, Apophysomyces, Cunninghamella, and Saksenaea. The major risk factors for the development of mucormycosis are diabetic ketoacidosis, deferoxamine treatment, cancer, solid organ or bone marrow transplantations, prolonged steroid use, extreme malnutrition, and neutropenia. The common clinical forms of mucormycosis are rhino-orbital-cerebral, pulmonary, cutaneous, and gastrointestinal. During the second wave of COVID-19, there was a rapid increase in mucormycosis with more severity than before. Amphotericin B is currently found to be an effective drug as it is found to have a broad-spectrum activity and posaconazole is used as a salvage therapy. Newer triazole isavuconazole is also found effective against mucormycosis. This study aimed to review various studies on the laboratory diagnosis and treatment of mucormycosis.
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Affiliation(s)
- Malavika Kottarathil
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Premamalini Thayanidhi
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Sathyamurthy P
- Department of General Medicine, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
| | - Anupma Jyoti Kindo
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, India
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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:cancers15041206. [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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Jiang X, Jiang Y, Ye F. Detection and identification of Mucorales and Aspergillus in paraffin-embedded samples by real-time quantitative PCR. Front Cell Infect Microbiol 2023; 13:1082347. [PMID: 36936757 PMCID: PMC10017852 DOI: 10.3389/fcimb.2023.1082347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Background In this study, we used real-time quantitative PCR (RQ-PCR) to rapidly detect Mucorales and Aspergillus in formalin-fixed, paraffin-embedded (FFPE) samples, targeting 18SrRNA gene and 28SrRNA gene. Identification of Mucorales and Aspergillus was analysed by combining Mucorales RQ-PCR (Mucorales18SrRNA and Mucorales28SrRNA) with Aspergillus RQ-PCR (Aspergillus18SrRNA and Aspergillus28SrRNA). Objectives The aims of this study were to compare the diagnostic performances of four RQ-PCR assays as single and combined diagnostic and identification tools. Methods We collected 12 control group samples and 81 experimental group samples diagnosed by histopathology, including mucormycosis (19 patients, 21 FFPE samples), aspergillosis (54 patients, 57 FFPE samples) and mucormycosis with aspergillosis (3 patients, 3 FFPE samples). All samples were detected by four RQ-PCR tests to compare and analyze diagnostic performance. Results The sensitivities of Mucorales18SrRNA and Mucorales28SrRNA were both 75%, with the tests having specificities of 97.10% and 94.20%. The sensitivities of Aspergillus18SrRNA and Aspergillus28SrRNA were 73.33% and 65%, with the tests having specificities of 87.88% and 81.82%. The values of the evaluation indexes of the combined detection of Mucorales28SrRNA and Aspergillus18SrRNA (M28A18) were the highest with a kappa coefficient value of 0.353, followed by M18A18. M28A18 had a sensitivity of 67.90% and a specificity of 100%. Conclusions We recommend using the combination of Mucorales RQ-PCR and Aspergillus RQ-PCR as a screening tool to detect samples suspected of mucormycosis and/or aspergillosis.
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Affiliation(s)
- Xiaolin Jiang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
- Department of Pathology, Guangyuan Central Hospital, Guangyuan, China
| | - Yong Jiang
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Yong Jiang,
| | - Feng Ye
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
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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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Le TN, Handt O, Henry J, Linacre A. A novel approach for rapid cell assessment to estimate DNA recovery from human bone tissue. Forensic Sci Med Pathol 2021; 17:649-659. [PMID: 34633584 DOI: 10.1007/s12024-021-00428-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
We report on the use of a DNA staining dye to locate and record nucleated osteocytes and other bone-related cells within sections of archived formalin-fixed and paraffin-embedded human tibia from which informative DNA profiles were obtained. Eleven of these archived tibia samples were sectioned at a thickness of 5 µm. Diamond™ Nucleic Acid Dye was applied to the sections and cells within the matrix of the bone fluoresced so that their location and number of cells could be photographed. DNA was isolated from these 11 samples using a standard extraction process and the yields were quantified by real-time PCR. Complete STR profiles were generated from ten bone extracts where low-level inhibition was recorded with an incomplete STR profile obtained from one sample with higher inhibition. The stained image of this sample showed that few cells were present. There was a significant relationship between the number of DD-stained cells and the number of alleles obtained (p < 0.05). Staining cells to determine the prevalence of bone cell nuclei allows a triage of samples prior to any subsequent DNA profiling.
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Affiliation(s)
- Thien Ngoc Le
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia
| | - Oliva Handt
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia
- Forensic Science SA, PO Box 2790, Adelaide, SA, 5001, Australia
| | - Julianne Henry
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia
- Forensic Science SA, PO Box 2790, Adelaide, SA, 5001, Australia
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia.
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Seidlova V, Syrova E, Minarova H, Zukal J, Balaz V, Nemcova M, Papezikova I, Pikula J, Schmidt‐Posthaus H, Mares J, Palikova M. Comparison of diagnostic methods for Tetracapsuloides bryosalmonae detection in salmonid fish. JOURNAL OF FISH DISEASES 2021; 44:1147-1153. [PMID: 33837562 PMCID: PMC8360006 DOI: 10.1111/jfd.13375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/26/2021] [Indexed: 05/24/2023]
Abstract
Diagnostic accuracy of pathogen detection depends upon the selection of suitable tests. Problems can arise when the selected diagnostic test gives false-positive or false-negative results, which can affect control measures, with consequences for the population health. The aim of this study was to compare sensitivity of different diagnostic methods IHC, PCR and qPCR detecting Tetracapsuloides bryosalmonae, the causative agent of proliferative kidney disease in salmonid fish and as a consequence differences in disease prevalence. We analysed tissue from 388 salmonid specimens sampled from a recirculating system and rivers in the Czech Republic. Overall prevalence of T. bryosalmonae was extremely high at 92.0%, based on positive results of at least one of the above-mentioned screening methods. IHC resulted in a much lower detection rate (30.2%) than both PCR methods (qPCR32: 65.4%, PCR: 81.9%). While qPCR32 produced a good match with IHC (60.8%), all other methods differed significantly (p < .001) in the proportion of samples determined positive. Both PCR methods showed similar sensitivity, though specificity (i.e., the proportion of non-diseased fish classified correctly) differed significantly (p < .05). Sample preservation method significantly (p < .05) influenced the results of PCR, with a much lower DNA yield extracted from paraffin-embedded samples. Use of different methods that differ in diagnostic sensitivity and specificity resulted in random and systematic diagnosis errors, illustrating the importance of interpreting the results of each method carefully.
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Affiliation(s)
- Veronika Seidlova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Zoology, Fisheries, Hydrobiology and ApicultureMendel University in BrnoBrnoCzech Republic
| | - Eva Syrova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Infectious Diseases and Preventive MedicineVeterinary Research InstituteBrnoCzech Republic
| | - Hana Minarova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Infectious Diseases and Preventive MedicineVeterinary Research InstituteBrnoCzech Republic
| | - Jan Zukal
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
| | - Vojtech Balaz
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
| | - Monika Nemcova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Zoology, Fisheries, Hydrobiology and ApicultureMendel University in BrnoBrnoCzech Republic
| | - Ivana Papezikova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Zoology, Fisheries, Hydrobiology and ApicultureMendel University in BrnoBrnoCzech Republic
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Zoology, Fisheries, Hydrobiology and ApicultureMendel University in BrnoBrnoCzech Republic
| | - Heike Schmidt‐Posthaus
- Department of PathobiologyCentre for Fish and Wildlife HealthUniversity of BernBernSwitzerland
| | - Jan Mares
- Department of Zoology, Fisheries, Hydrobiology and ApicultureMendel University in BrnoBrnoCzech Republic
| | - Miroslava Palikova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and BeesFaculty of Veterinary Hygiene and EcologyUniversity of Veterinary and Pharmaceutical Sciences BrnoBrnoCzech Republic
- Department of Zoology, Fisheries, Hydrobiology and ApicultureMendel University in BrnoBrnoCzech Republic
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11
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Nicolás-Párraga S, Torres M, Alemany L, Félix A, Cruz E, de Sanjosé S, Bosch FX, Bravo IG. Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning 85 years. Virol J 2021; 18:65. [PMID: 33781303 PMCID: PMC8008572 DOI: 10.1186/s12985-021-01529-9] [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: 12/03/2020] [Accepted: 03/05/2021] [Indexed: 12/01/2022] Open
Abstract
Background Quality of the nucleic acids extracted from Formalin Fixed Paraffin Embedded (FFPE) samples largely depends on pre-analytic, fixation and storage conditions. We assessed the differential sensitivity of viral and human double stranded DNA (dsDNA) to degradation with storage time. Methods We randomly selected forty-four HPV16-positive invasive cervical cancer (ICC) FFPE samples collected between 1930 and 1935 and between 2000 and 2004. We evaluated through qPCR the amplification within the same sample of two targets of the HPV16 L1 gene (69 bp, 134 bp) compared with two targets of the human tubulin-β gene (65 bp, 149 bp). Results Both viral and human, short and long targets were amplified from all samples stored for 15 years. In samples archived for 85 years, we observed a significant decrease in the ability to amplify longer targets and this difference was larger in human than in viral DNA: longer fragments were nine times (CI 95% 2.6–35.2) less likely to be recovered from human DNA compared with 1.6 times (CI 95% 1.1–2.2) for viral DNA. Conclusions We conclude that human and viral DNA show a differential decay kinetics in FFPE samples. The faster degradation of human DNA should be considered when assessing viral DNA prevalence in long stored samples, as HPV DNA detection remains a key biomarker of viral-associated transformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01529-9.
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Affiliation(s)
- Sara Nicolás-Párraga
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Montserrat Torres
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.
| | - Laia Alemany
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ana Félix
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Lisbon), Lisbon, Portugal
| | - Eugenia Cruz
- Pathology Unit, Portuguese Institute of Oncology Francisco Gentil (IPO Coimbra), Coimbra, Portugal
| | - Silvia de Sanjosé
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Sexual and Reproductive Health, PATH, Seattle, USA.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francesc Xavier Bosch
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Biomedical Research Networking Centre On Cancer (CIBERONC), Madrid, Spain.,Universitat Oberta de Catalunya, Barcelona, Spain
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain.,Laboratory MIVEGEC (CNRS IRD Univ Montpellier), French National Center for Scientific Research (CNRS), Montpellier, France.,Center for Research On the Ecology and Evolution of Diseases (CREES), Montpellier, France
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12
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Weisbrod TC, Jeon AB, Childress A, Pouder DB, Castellanos-Gell J, Stacy NI, Walden HDS, Garner MM, Yanong RPE, Ossiboff RJ. Gastrointestinal entamoebiasis in captive anurans in North America. DISEASES OF AQUATIC ORGANISMS 2021; 143:109-118. [PMID: 33570044 DOI: 10.3354/dao03560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Infections with Entamoeba spp. are recognized as a cause of clinical disease in many species including humans and reptiles; however, cases in amphibians are under-reported. Investigation of a mortality event among a captive population of Cranwell's horned frogs Ceratophrys cranwelli at a production facility in Florida, USA, revealed that deaths were due to the newly described Entamoeba species CT1. Infection caused severe necroulcerative gastroenterocolitis with a predilection for the colon. To date, this Entamoeba species has only been described in invasive cane toads Rhinella marina in Australia. Retrospective screening of archived anuran cases from a zoological pathology service identified 8 cases from captive populations that had histological evidence of gastrointestinal entamoebiasis. Molecular characterization was positive in 3 cases. Two cases, 1 in a Puerto Rican crested toad Peltophryne lemur and 1 in an Amazon milk frog Trachycephalus resinifictrix, showed 100% homology to E. ranarum and 1 case in a White's tree frog Litoria caerulea showed 100% homology to Entamoeba sp. CT1. This is the first report of novel Entamoeba sp. CT1 being associated with clinical disease in anurans within North America and also the first report of this Entamoeba species causing disease within managed collections as far back as 2003.
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Affiliation(s)
- Tatiana C Weisbrod
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32610, USA
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13
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Gastrointestinal Mucormycosis in a two-year-old child: A clinical and radiological enigma. Med Mycol Case Rep 2019; 26:5-9. [PMID: 31667050 PMCID: PMC6811992 DOI: 10.1016/j.mmcr.2019.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 01/15/2023] Open
Abstract
Mucormycosis is a rare, fatal angioinvasive infection occurring in immunocompromised individuals. Gastrointestinal mucormycosis is rare variety with high mortality rate. We present a case of GI mucormycosis in a 2-year-old male child who presented with abdominal mass with no underlying risk factors. The aim of this case report is to emphasize on its etiopathogenesis and keeping mucormycosis high in the differential diagnosis in a child presenting with abdominal mass.
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14
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Muscarella LA, Fabrizio FP, De Bonis M, Mancini MT, Balsamo T, Graziano P, Centra F, Sparaneo A, Trombetta D, Bonfitto A, Scagliusi V, Larizza P, Capoluongo ED, Fazio VM. Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics. Cancers (Basel) 2019; 11:cancers11111691. [PMID: 31671666 PMCID: PMC6896097 DOI: 10.3390/cancers11111691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/27/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
Thanks to personalized medicine trends and collaborations between industry, clinical research groups and regulatory agencies, next generation sequencing (NGS) is turning into a common practice faster than one could have originally expected. When considering clinical applications of NGS in oncology, a rapid workflow for DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples, as well as producing high quality library preparation, can be real challenges. Here we consider these targets and how applying effective automation technology to NGS workflows may help improve yield, timing and quality-control. We firstly evaluated DNA recovery from archived FFPE blocks from three different manual extraction methods and two automated extraction workstations. The workflow was then implemented to somatic (lung/colon panel) and germline (BRCA1/2) library preparation for NGS analysis exploiting two automated workstations. All commercial kits gave good results in terms of DNA yield and quality. On the other hand, the automated workstation workflow has been proven to be a valid automatic extraction system to obtain high quality DNA suitable for NGS analysis (lung/colon Ampli-seq panel). Moreover, it can be efficiently integrated with an open liquid handling platform to provide high-quality libraries from germline DNA with more reproducibility and high coverage for targeted sequences in less time (BRCA1/2). The introduction of automation in routine workflow leads to an improvement of NGS standardization and increased scale up of sample preparations, reducing labor and timing, with optimization of reagents and management.
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Affiliation(s)
- Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Maria De Bonis
- Department of Laboratory Medicine of the 'Agostino Gemelli' Foundation in Rome, 00168 Rome, Italy.
| | | | - Teresa Balsamo
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Paolo Graziano
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Flavia Centra
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Angelo Sparaneo
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Domenico Trombetta
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Antonio Bonfitto
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | | | | | - Ettore Domenico Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II-CEINGE, 80145 Naples, Italy.
| | - Vito Michele Fazio
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
- Department of Medicine, R.U. in Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy.
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15
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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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16
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Feucherolles M, Poppert S, Utzinger J, Becker SL. MALDI-TOF mass spectrometry as a diagnostic tool in human and veterinary helminthology: a systematic review. Parasit Vectors 2019; 12:245. [PMID: 31101120 PMCID: PMC6525464 DOI: 10.1186/s13071-019-3493-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/06/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a widely used technique for the rapid and accurate identification of bacteria, mycobacteria and certain fungal pathogens in the clinical microbiology laboratory. Thus far, only few attempts have been made to apply the technique in clinical parasitology, particularly regarding helminth identification. METHODS We systematically reviewed the scientific literature on studies pertaining to MALDI-TOF MS as a diagnostic technique for helminths (cestodes, nematodes and trematodes) of medical and veterinary importance. Readily available electronic databases (i.e. PubMed/MEDLINE, ScienceDirect, Cochrane Library, Web of Science and Google Scholar) were searched from inception to 10 October 2018, without restriction on year of publication or language. The titles and abstracts of studies were screened for eligibility by two independent reviewers. Relevant articles were read in full and included in the systematic review. RESULTS A total of 84 peer-reviewed articles were considered for the final analysis. Most papers reported on the application of MALDI-TOF for the study of Caenorhabditis elegans, and the technique was primarily used for identification of specific proteins rather than entire pathogens. Since 2015, a small number of studies documented the successful use of MALDI-TOF MS for species-specific identification of nematodes of human and veterinary importance, such as Trichinella spp. and Dirofilaria spp. However, the quality of available data and the number of examined helminth samples was low. CONCLUSIONS Data on the use of MALDI-TOF MS for the diagnosis of helminths are scarce, but recent evidence suggests a potential role for a reliable identification of nematodes. Future research should explore the diagnostic accuracy of MALDI-TOF MS for identification of (i) adult helminths, larvae and eggs shed in faecal samples; and (ii) helminth-related proteins that are detectable in serum or body fluids of infected individuals.
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Affiliation(s)
- Maureen Feucherolles
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, Belvaux, Luxembourg
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany.
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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17
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Makulović S, Vitošević K, Slović Ž, Todorović M, Todorović D. Formalin fixation at low temperature provides better yield and integrity of DNA. MEDICINSKI PODMLADAK 2019. [DOI: 10.5937/mp70-18949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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18
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Effect of formalin fixation on pcr amplification of DNA isolated from healthy autopsy tissues. Acta Histochem 2018; 120:780-788. [PMID: 30224244 DOI: 10.1016/j.acthis.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Abstract
The aim of this study is to investigate the effects of formalin fixation on the degradation of DNA molecules in five different healthy tissues exempted during the autopsy, as well as the selection of the method that is most suitable for the DNA isolation. Heart muscle, liver, brain, lung and kidney tissue obtained from the healthy people who suddenly died from a violent death were used. The parts of tissue were fixed in 10% phosphate-buffered formalin as well as in 4% unbuffered formalin at room temperature. Morphology of tissue was studied using H&E staining. The DNA was isolated 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months after fixation using two different methods: extraction with phenol-chloroform-isoamyl alcohol as well as with PureLink Genomic DNA Kit. Yield and purity of the DNA samples were measured spectrophotometrically at 260 nm and 280 nm. The PCR amplifications of the glycerol-3-phosphate dehydrogenase 1 (GPD1, 150 bp), ß actin (ACTB, 262 bp) and ribosomal protein L4 (RPL4, 407 bp) genes were performed to evaluate the degree of DNA fragmentation. The RPL4 gene was amplified up to 72 h, ACTB gene up to 14 days and GPD1 gene up to 28 days from tissue fixed in phosphate-buffered formalin using phenol-chloroform-isoamylalcohol protocol for DNA isolation. Liver and kidney gave better results of PCR amplification, but statistical significance between tissues was not found. Preserving period, fixative and DNA extracting method are important factors for successful PCR amplification. The healthy tissue, fixed in phosphate-formalin up to 28 days, can be useful source in molecular studies. Tissues fixed in unbuffered formalin are suitable for molecular analysis up to 7 days.
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19
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Gholinejad-Ghadi N, Shokohi T, Seifi Z, Aghili SR, Roilides E, Nikkhah M, Pormosa R, Karami H, Larjani LV, Ghasemi M, Haghani I. Identification of Mucorales in patients with proven invasive mucormycosis by polymerase chain reaction in tissue samples. Mycoses 2018; 61:909-915. [PMID: 30091261 DOI: 10.1111/myc.12837] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 07/14/2018] [Accepted: 08/01/2018] [Indexed: 01/17/2023]
Abstract
BACKGROUND Accurate diagnosis of mucormycosis, a life-threatening fungal infection, remains a challenge for physicians. OBJECTIVES To identify the causative Mucorales in fresh clinical samples and formalin-fixed paraffin-embedded (FFPE) samples of patients with proven mucormycosis by molecular method. PATIENTS/METHODS Fresh clinical samples of patients with proven mucormycosis according to the EORTC/MSG criteria admitted between 2015 and 2017 and histopathologically proven FFPE archives collected during 2004-2007 and 2015-2017 from Mazandaran University-affiliated hospitals of northern Iran were included. Seminested PCR targeting the 18S rDNA of Mucorales and ITS region was performed, and PCR products were then sequenced. RESULTS While culture was positive only in 5 of 9 (56%) of fresh specimen cases, PCR was positive in all 9 (100%) histologically proven mucormycosis. Ten of 18 (56%) FFPE samples were PCR-positive. Overall, Mucorales PCR was positive in 19 of 27 (70%) samples. Mucorales species were Rhizopus arrhizus in 16 (84%) cases, R. arrhizus/Amylomyces rouxii in 2 (10.5%) cases and Rhizopus stolonifer in one case (5.5%). Among 27 mucormycosis cases, 25 (93%) cases were rhinocerebral, and 2 (7%) cases were disseminated. Diabetes mellitus (74%) and neutropaenia (63%) were the main risk factors. CONCLUSIONS Seminested PCR targeting 18S rDNA region of Mucorales is useful for identification of the causative agents of mucormycosis.
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Affiliation(s)
- Nahid Gholinejad-Ghadi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Tahereh Shokohi
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Invasive Fungi Research Centre (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Seifi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Reza Aghili
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Invasive Fungi Research Centre (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
| | - Emmanuel Roilides
- Infectious Diseases Section, 3rd Department of Pediatrics, Faculty of Medicine, Aristotle University School of Health Sciences, Thessaloniki, Greece
| | - Mehdi Nikkhah
- Department of Otolaryngology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Rostam Pormosa
- Department of Otolaryngology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hossein Karami
- Department of Pediatrics, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Laleh Vahedi Larjani
- Department of Pathology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Ghasemi
- Department of Pathology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Iman Haghani
- Department of Medical Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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20
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Chat-Uthai N, Vejvisithsakul P, Udommethaporn S, Meesiri P, Danthanawanit C, Wongchai Y, Teerapakpinyo C, Shuangshoti S, Poungvarin N. Development of ultra-short PCR assay to reveal BRAF V600 mutation status in Thai colorectal cancer tissues. PLoS One 2018; 13:e0198795. [PMID: 29879227 PMCID: PMC5991739 DOI: 10.1371/journal.pone.0198795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/25/2018] [Indexed: 02/06/2023] Open
Abstract
The protein kinase BRAF is one of the key players in regulating cellular responses to extracellular signals. Somatic mutations of the BRAF gene, causing constitutive activation of BRAF, have been found in various types of human cancers such as malignant melanoma, and colorectal cancer. BRAF V600E and V600K, most commonly observed mutations in these cancers, may predict response to targeted therapies. Many techniques suffer from a lack of diagnostic sensitivity in mutation analysis in clinical samples with a low cancer cell percentage or poor-quality fragmented DNA. Here we present allele-specific real-time PCR assay for amplifying 35- to 45-base target sequences in BRAF gene. Forward primer designed for BRAF V600E detection is capable of recognizing both types of BRAF V600E mutation, i.e. V600E1 (c.1799T>A) and V600E2 (c.1799_1800delTGinsAA), as well as complex tandem mutation caused by nucleotide changes in codons 600 and 601. We utilized this assay to analyze Thai formalin-fixed paraffin-embedded tissues. Forty-eight percent of 178 Thai colorectal cancer tissues has KRAS mutation detected by highly sensitive commercial assays. Although these DNA samples contain low overall yield of amplifiable DNA, our newly-developed assay successfully revealed BRAF V600 mutations in 6 of 93 formalin-fixed paraffin-embedded colorectal cancer tissues which KRAS mutation was not detected. Ultra-short PCR assay with forward mutation-specific primers is potentially useful to detect BRAF V600 mutations in highly fragmented DNA specimens from cancer patients.
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Affiliation(s)
- Nunthawut Chat-Uthai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Sutthirat Udommethaporn
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Puttarakun Meesiri
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chetiya Danthanawanit
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yannawan Wongchai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shanop Shuangshoti
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naravat Poungvarin
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
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21
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Monico J, Miller B, Rezeanu L, May W, Sullivan DC. Fibroblast growth factor receptor 1 amplification in laryngeal squamous cell carcinoma. PLoS One 2018; 13:e0186185. [PMID: 29351293 PMCID: PMC5774678 DOI: 10.1371/journal.pone.0186185] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/26/2017] [Indexed: 12/17/2022] Open
Abstract
Fibroblast growth factor receptor 1 (FGFR1) has been noted to be amplified in a variety of squamous cell carcinomas (SCCa) of the head, neck, and lung and increased copy number (CN) is a predictor of poor outcomes. FGFR1 is a therapeutic target for lung SCCa and inhibition therapy is currently in clinical trials. Absolute quantification of FGFR1 from formalin fixed paraffin embedded (FFPE) tissue of laryngeal SCCa was examined in this retrospective study. A droplet digital polymerase chain reaction (ddPCR) was used for absolute quantitation of the FGFR1 gene CN. Of the 74 samples analyzed, FGFR1 CN analysis revealed 54% of samples had CN greater than 2 copies/cell (1.8-2.2 copies/cell), and 38% had CN values greater than 3. The mean and standard deviation FGFR1 CN was 4.17 ± 1.46 CN for African American patients (n = 41) and 3.78 ±1.85 CN for Caucasian patients (n = 31). Further, 60.9% of specimens from African Americans demonstrated increased FGFR1 CN compared to 48.4% of Caucasians. Two SCCA samples from Native American demonstrated increased FGFR1 CN (4.19 and 3.01 CN). The level of FGFR1 amplification did not correlate with tumor stage, lymph node staging, or metastasis. In this population, the proportion of patient samples with an FGFR1 amplification was three times higher than in reported for SCCA of the head and neck. Further, increased FGFR1 CN was observed in two racial groups not previously reported: African Americans and Native Americans. However, FGFR1 amplification is not prognostic in laryngeal squamous cell carcinomas.
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Affiliation(s)
- Jesus Monico
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Brandon Miller
- Department of Otolaryngology and Communicative Sciences, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Luminita Rezeanu
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Warren May
- Department of Biostatistics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Donna C. Sullivan
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
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22
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Ludgate JL, Wright J, Stockwell PA, Morison IM, Eccles MR, Chatterjee A. A streamlined method for analysing genome-wide DNA methylation patterns from low amounts of FFPE DNA. BMC Med Genomics 2017; 10:54. [PMID: 28859641 PMCID: PMC5580311 DOI: 10.1186/s12920-017-0290-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/23/2017] [Indexed: 12/12/2022] Open
Abstract
Background Formalin fixed paraffin embedded (FFPE) tumor samples are a major source of DNA from patients in cancer research. However, FFPE is a challenging material to work with due to macromolecular fragmentation and nucleic acid crosslinking. FFPE tissue particularly possesses challenges for methylation analysis and for preparing sequencing-based libraries relying on bisulfite conversion. Successful bisulfite conversion is a key requirement for sequencing-based methylation analysis. Methods Here we describe a complete and streamlined workflow for preparing next generation sequencing libraries for methylation analysis from FFPE tissues. This includes, counting cells from FFPE blocks and extracting DNA from FFPE slides, testing bisulfite conversion efficiency with a polymerase chain reaction (PCR) based test, preparing reduced representation bisulfite sequencing libraries and massively parallel sequencing. Results The main features and advantages of this protocol are:An optimized method for extracting good quality DNA from FFPE tissues. An efficient bisulfite conversion and next generation sequencing library preparation protocol that uses 50 ng DNA from FFPE tissue. Incorporation of a PCR-based test to assess bisulfite conversion efficiency prior to sequencing.
Conclusions We provide a complete workflow and an integrated protocol for performing DNA methylation analysis at the genome-scale and we believe this will facilitate clinical epigenetic research that involves the use of FFPE tissue. Electronic supplementary material The online version of this article (10.1186/s12920-017-0290-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jackie L Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand
| | - James Wright
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.,School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Peter A Stockwell
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Ian M Morison
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, P.O. Box 56, Dunedin, 9054, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
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23
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Comparison of different methods for repairing damaged DNA from buffered and unbuffered formalin-fixed tissues. Int J Legal Med 2017; 132:675-681. [DOI: 10.1007/s00414-017-1666-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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24
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Patel PG, Selvarajah S, Guérard KP, Bartlett JMS, Lapointe J, Berman DM, Okello JBA, Park PC. Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores. PLoS One 2017. [PMID: 28640876 PMCID: PMC5480995 DOI: 10.1371/journal.pone.0179732] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer biomarker studies often require nucleic acid extraction from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissues, such as histologic sections or needle cores. A major challenge is low quantity and quality of extracted nucleic acids, which can limit our ability to perform genetic analyses, and have a significant influence on overall study design. This study was aimed at identifying the most reliable and reproducible method of obtaining sufficient high-quality nucleic acids from FFPE tissues. We compared the yield and quality of nucleic acids from 0.6-mm FFPE prostate tissue cores across 16 DNA and RNA extraction protocols, using 14 commercially available kits. Nucleic acid yield was determined by fluorometry, and quality was determined by spectrophotometry. All protocols yielded nucleic acids in quantities that are compatible with downstream molecular applications. However, the protocols varied widely in the quality of the extracted RNA and DNA. Four RNA and five DNA extraction protocols, including protocols from two kits for dual-extraction of RNA and DNA from the same tissue source, were prioritized for further quality assessment based on the yield and purity of their products. Specifically, their compatibility with downstream reactions was assessed using both NanoString nCounter gene expression assays and reverse-transcriptase real-time PCR for RNA, and methylation-specific PCR assays for DNA. The kit deemed most suitable for FFPE tissue was the AllPrep kit by Qiagen because of its yield, quality, and ability to purify both RNA and DNA from the same sample, which would be advantageous in biomarker studies.
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Affiliation(s)
- Palak G. Patel
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - Shamini Selvarajah
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Karl-Philippe Guérard
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - John M. S. Bartlett
- Diagnostic Development Program, Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
| | - Jacques Lapointe
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David M. Berman
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - John B. A. Okello
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - Paul C. Park
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- * E-mail: ,
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25
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Bak ST, Staunstrup NH, Starnawska A, Daugaard TF, Nyengaard JR, Nyegaard M, Børglum A, Mors O, Dorph-Petersen KA, Nielsen AL. Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples. Mol Neurobiol 2016; 55:668-681. [PMID: 27995571 DOI: 10.1007/s12035-016-0345-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/05/2016] [Indexed: 01/14/2023]
Abstract
We here characterize the usability of archival formalin-fixed paraffin-embedded (FFPE) brain tissue as a resource for genetic and DNA methylation analyses with potential relevance for brain-manifested diseases. We analyzed FFPE samples from The Brain Collection, Aarhus University Hospital Risskov, Denmark (AUBC), constituting 9479 formalin-fixated brains making it one of the largest collections worldwide. DNA extracted from brain FFPE tissue blocks was interrogated for quality and usability in genetic and DNA methylation analyses by different molecular techniques. Overall, we found that DNA quality was inversely correlated with storage time and DNA quality was insufficient for Illumina methylation arrays; data from methylated DNA immunoprecipitation, clonal bisulfite sequencing, and pyrosequencing of BDNF and ST6GALNAC1 suggested that the original methylation pattern is indeed preserved. Proof-of-principle experiments predicting sex based on the methylation status of the X-inactivated SLC9A7 gene, or genotype differences of the Y and X chromosomes, showed consistency between predicted and actual sex for a subset of FFPE samples. In conclusion, even though DNA from FFPE samples is of low quality and technically challenging, it is likely that a subset of samples can provide reliable data given that the methodology used is designed for small DNA fragments. We propose that simple PCR-based quality control experiments at the genetic and DNA methylation level, carried out at the beginning of any given project, can be used to enrich for the best-performing FFPE samples. The apparent preservation of genetic and DNA methylation patterns in archival FFPE samples may bring along new perspectives for the identification of genetic and epigenetic changes associated with brain-manifested diseases.
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Affiliation(s)
- Stine T Bak
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark
| | - Nicklas H Staunstrup
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Tina F Daugaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark
| | - Jens R Nyengaard
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark
| | - Anders Børglum
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.,Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark.,Research Department P, Department of General Psychiatry, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karl-Anton Dorph-Petersen
- Translational Neuropsychiatric Unit, Department of Clinical Medicine, Aarhus University Hospital, Risskov, Denmark.,Centre for Stochastic Geometry and Advanced Bioimaging (CSGB), Aarhus University, Aarhus, Denmark.,Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, USA
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, Bartholin building, DK-8000, Aarhus C, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Aarhus, Denmark.
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26
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Rocha VCF, Figueiredo SCD, Rosales CAR, Porto CD, Sequeira JL, Neto JSF, Paes AC, Salgado VR. Infection by Mycobacterium bovis in a dog from Brazil. Braz J Microbiol 2016; 48:109-112. [PMID: 27914739 PMCID: PMC5220626 DOI: 10.1016/j.bjm.2016.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/25/2016] [Indexed: 11/01/2022] Open
Abstract
Tuberculosis (TB) is a chronic disease caused by bacteria belonging to the Mycobacterium tuberculosis complex (MtbC). This disease rarely affects dogs. Canine infections are usually caused by M. tuberculosis. Mycobacterium bovis infections are rare in dogs and associated with consumption of raw milk or contaminated products. Here, we report a Boxer dog who had a M. bovis infection and was admitted to a Brazilian veterinary hospital with a presumptive diagnosis of chronic ehrlichiosis. Despite receiving treatment for chronic ehrlichiosis, it progressed to death. TB was diagnosed during post-mortem examinations using histopathological analysis. Ziehl-Neelsen staining revealed acid-fast bacilli in the kidneys, liver, mesentery, and a mass adhered to the liver. Further, PCR-restriction analysis was performed to identify mycobacteria in the samples. A restriction profile compatible with MtbC was found in the lungs. In addition, PCR-based MtbC typing deletions at different loci of chromosome 9 enabled the identification of M. bovis in the lungs. Therefore, it is very essential to perform differential diagnosis of TB in dogs with non-specific clinical signs and who do not respond to treatment, particularly those who had been in contact with TB-infected cattle or owners. Further, we highlight the use of molecular methods for the identification of bacilli, improving the diagnosis and aiding epidemiological studies.
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Affiliation(s)
| | - Salomão Cambuí de Figueiredo
- Instituto Federal de Educação, Ciência e Tecnologia da Paraíba (IFPB), Faculdade de Medicina Veterinária, Sousa, PB, Brazil
| | | | | | - Julio Lopes Sequeira
- Universidade Estadual Paulista (UNESP), Faculdade de Medicina Veterinária e Zootecnia (FMVZ), Botucatu, SP, Brazil
| | - José Soares Ferreira Neto
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia (FMVZ), São Paulo, SP, Brazil
| | - Antônio Carlos Paes
- Universidade Estadual Paulista (UNESP), Faculdade de Medicina Veterinária e Zootecnia (FMVZ), Botucatu, SP, Brazil
| | - Vanessa Riesz Salgado
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia (FMVZ), São Paulo, SP, Brazil.
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27
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Nagai M, Minegishi K, Komada M, Tsuchiya M, Kameda T, Yamada S. Extraction of DNA from human embryos after long-term preservation in formalin and Bouin's solutions. Congenit Anom (Kyoto) 2016; 56:112-8. [PMID: 26662860 DOI: 10.1111/cga.12148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/03/2015] [Indexed: 01/05/2023]
Abstract
The "Kyoto Collection of Human Embryos" at Kyoto University was begun in 1961. Although morphological analyses of samples in the Kyoto Collection have been performed, these embryos have been considered difficult to genetically analyze because they have been preserved in formalin or Bouin's solution for 20-50 years. Owing to the recent advances in molecular biology, it has become possible to extract DNA from long-term fixed tissues. The purpose of this study was to extract DNA from wet preparations of human embryo samples after long-term preservation in fixing solution. We optimized the DNA extraction protocol to be suitable for tissues that have been damaged by long-term fixation, including DNA-protein crosslinking damage. Diluting Li2 CO3 with 70% ethanol effectively removed picric acid from samples fixed in Bouin's solution. Additionally, 20.0 mg/mL proteinase was valuable to lyse the long-term fixed samples. The extracted DNA was checked with PCR amplification using several sets of primers and sequence analysis. The PCR products included at least 295- and 838-bp amplicons. These results show that the extracted DNA is applicable for genetic analyses, and indicate that old embryos in the Kyoto Collection should be made available for future studies. The protocol described in this study can successfully extract DNA from old specimens and, with improvements, should be applicable in research aiming to understand the molecular mechanisms of human congenital anomalies.
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Affiliation(s)
- Momoko Nagai
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Katsura Minegishi
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Frontier Biosciences, Osaka University Graduate School, Osaka, Japan
| | - Munekazu Komada
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,School of dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Maiko Tsuchiya
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomomi Kameda
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shigehito Yamada
- Congenital Anomaly Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Human Health Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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28
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Zhang YA, Ma X, Sathe A, Fujimoto J, Wistuba I, Lam S, Yatabe Y, Wang YW, Stastny V, Gao B, Larsen JE, Girard L, Liu X, Song K, Behrens C, Kalhor N, Xie Y, Zhang MQ, Minna JD, Gazdar AF. Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers. J Thorac Oncol 2015; 11:346-360. [PMID: 26725182 DOI: 10.1016/j.jtho.2015.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The human secretin gene (SCT) encodes secretin, a hormone with limited tissue distribution. Analysis of the 450k methylation array data in The Cancer Genome Atlas (TCGA) indicated that the SCT promoter region is differentially hypermethylated in lung cancer. Our purpose was to validate SCT methylation as a potential biomarker for lung cancer. METHODS We analyzed data from TCGA and developed and applied SCT-specific bisulfite DNA sequencing and quantitative methylation-specific polymerase chain reaction assays. RESULTS The analyses of TCGA 450K data for 801 samples showed that SCT hypermethylation has an area under the curve (AUC) value greater than 0.98 that can be used to distinguish lung adenocarcinomas or squamous cell carcinomas from nonmalignant lung tissue. Bisulfite sequencing of lung cancer cell lines and normal blood cells allowed us to confirm that SCT methylation is highly discriminative. By applying a quantitative methylation-specific polymerase chain reaction assay, we found that SCT hypermethylation is frequently detected in all major subtypes of malignant non-small cell lung cancer (AUC = 0.92, n = 108) and small cell lung cancer (AUC = 0.93, n = 40) but is less frequent in lung carcinoids (AUC = 0.54, n = 20). SCT hypermethylation appeared in samples of lung carcinoma in situ during multistage pathogenesis and increased in invasive samples. Further analyses of TCGA 450k data showed that SCT hypermethylation is highly discriminative in most other types of malignant tumors but less frequent in low-grade malignant tumors. The only normal tissue with a high level of methylation was the placenta. CONCLUSIONS Our findings demonstrated that SCT methylation is a highly discriminative biomarker for lung and other malignant tumors, is less frequent in low-grade malignant tumors (including lung carcinoids), and appears at the carcinoma in situ stage.
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Potluri K, Mahas A, Kent MN, Naik S, Markey M. Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue. Anal Biochem 2015; 486:17-23. [DOI: 10.1016/j.ab.2015.06.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/05/2015] [Accepted: 06/23/2015] [Indexed: 02/06/2023]
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30
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Nicchia E, Benedicenti F, De Rocco D, Greco C, Bottega R, Inzana F, Faleschini M, Bonin S, Cappelli E, Mogni M, Stanzial F, Svahn J, Dufour C, Savoia A. Clinical aspects of Fanconi anemia individuals with the same mutation of FANCF identified by next generation sequencing. ACTA ACUST UNITED AC 2015; 103:1003-10. [PMID: 26033879 DOI: 10.1002/bdra.23388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Fanconi anemia (FA) is a rare genetic disease characterized by congenital malformations, aplastic anemia and increased risk of developing malignancies. FA is genetically heterogeneous as it is caused by at least 17 different genes. Among these, FANCA, FANCC, and FANCG account for approximately 85% of the patients whereas the remaining genes are mutated in only a small percentage of cases. For this reason, the molecular diagnostic process is complex and not always extended to all the FA genes, preventing the characterization of individuals belonging to rare groups. METHODS The FA genes were analyzed using a next generation sequencing approach in two unrelated families. RESULTS The analysis identified the same, c.484_485del, homozygous mutation of FANCF in both families. A careful examination of three electively aborted fetuses in one family and one affected girl in the other indicated an association of the FANCF loss-of-function mutation with a severe phenotype characterized by multiple malformations. CONCLUSION The systematic use of next generation sequencing will allow the recognition of individuals from rare complementation groups, a better definition of their clinical phenotypes, and consequently, an appropriate genetic counseling.
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Affiliation(s)
- Elena Nicchia
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Daniela De Rocco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Chiara Greco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | - Francesca Inzana
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | | | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Massimo Mogni
- Human Genetics Laboratory "E.O. Ospedali Galliera", Genoa, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Johanna Svahn
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Carlo Dufour
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Anna Savoia
- Department of Medical Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
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Deparaffinization with mineral oil: a simple procedure for extraction of high-quality DNA from archival formalin-fixed paraffin-embedded samples. Appl Immunohistochem Mol Morphol 2015; 22:623-6. [PMID: 24897067 DOI: 10.1097/pai.0b013e3182a77bfe] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Extracting DNA from formalin-fixed paraffin-embedded (FFPE) archival samples remains difficult. Successful polymerase chain reactions (PCR) with DNA extracted from FFPE samples is still very low. We extracted DNA from 12 recent and old archival FFPE bone marrow trephine biopsies by use of a simple protocol on the basis of deparaffinization with molecular biology-grade mineral oil followed by DNA extraction with the Qiagen FFPE kit. Comparison of this deparaffinization method with standard protocols, for example, xylene or Hemo-D with subsequent rehydration using graded ethanols, was investigated. The quality and quantity of extracted DNA were tested by a combination of ultraviolet spectroscopy, analysis on a Caliper LabChip GX, and real-time PCR combined with high-resolution melt analysis. Highest quality PCR-amplifiable DNA was obtained by deparaffinization with mineral oil, whereas more variable results were obtained for the other 2 deparaffinization procedures. This result was confirmed by real-time PCR and high-resolution melt analysis. Besides improvements in the quality of extracted DNA, use of mineral oil for deparaffinization has the added benefit of decreased time (20 vs. 75 min) and a significant reduction of hands-on labor (1 step vs. multiple hands-on centrifugation and decanting steps).
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32
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Yates RL, Esiri MM, Palace J, Mittal A, DeLuca GC. The influence ofHLA-DRB1*15on motor cortical pathology in multiple sclerosis. Neuropathol Appl Neurobiol 2015; 41:371-84. [DOI: 10.1111/nan.12165] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Richard L. Yates
- Nuffield Department of Clinical Neurosciences; University of Oxford; Oxford UK
| | - Margaret M. Esiri
- Nuffield Department of Clinical Neurosciences; University of Oxford; Oxford UK
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences; University of Oxford; Oxford UK
| | - Arunesh Mittal
- Department of Neuroscience; Johns Hopkins University; Baltimore MD USA
| | - Gabriele C. DeLuca
- Nuffield Department of Clinical Neurosciences; University of Oxford; Oxford UK
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33
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Kong H, Zhu M, Cui F, Wang S, Gao X, Lu S, Wu Y, Zhu H. Quantitative assessment of short amplicons in FFPE-derived long-chain RNA. Sci Rep 2014; 4:7246. [PMID: 25430878 PMCID: PMC5384205 DOI: 10.1038/srep07246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are important resources for molecular medical research. However, long-chain RNA analysis is restricted in FFPE tissues due to high levels of degradation. To explore the possibility of long RNA quantification in FFPE tissues, we selected 14 target RNAs (8 mRNAs and 6 long noncoding RNAs) from literatures, and designed short (~60 bp) and long (~200 bp) amplicons for each of them. Colorectal carcinomas with adjacent normal tissues were subjected to quantitative reverse-transcription PCR (quantitative RT-PCR) in 3 cohorts, including 18 snap-frozen and 83 FFPE tissues. We found that short amplicons were amplified more efficiently than long amplicons both in snap-frozen (P = 0.0006) and FFPE (P = 0.0152) tissues. Nonetheless, comparison of colorectal carcinomas with their adjacent normal tissues demonstrated that the consistency of fold-change trends in a single short amplicon between snap-frozen and FFPE tissues was only 36%. Therefore, we innovatively performed quantitative RT-PCR with 3 non-overlapping short amplicons for 14 target RNAs in FFPE tissues. All target RNAs showed a concordance of 100% of fold-change trends in at least two short amplicons, which offers sufficient information for accurate quantification of target RNAs. Our findings demonstrated the possibility of long-chain RNA analysis with 3 non-overlapping short amplicons in standardized-preserved FFPE tissues.
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Affiliation(s)
- Hui Kong
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Mengou Zhu
- Harvard College, Harvard University, Cambridge, MA, 02138, USA
| | - Fengyun Cui
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuyang Wang
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xue Gao
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Shaohua Lu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ying Wu
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hongguang Zhu
- 1] Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, 200032, China [2] Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China [3] Institute of Biomedical Sciences, Fudan University, Shanghai, 200032, China
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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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Stanta G, Bonin S, Machado I, Llombart-Bosch A. Models of biobanking and tissue preservation: RNA quality in archival samples in pathology laboratories and "in vivo biobanking" by tumor xenografts in nude mice-two models of quality assurance in pathology. Biopreserv Biobank 2014; 9:149-55. [PMID: 24846260 DOI: 10.1089/bio.2011.0010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tissue banks represent essential resources and platforms for biomedical research serving basic, translational, and clinical research projects. In this article, we describe 2 models of biobanking and tissue preservation with different approaches and aims. Archive tissue biobanking is described here as a resource of residual pathology tissues for translational research, which represents the huge clinical heterogeneity. In this context, managing of tissues and RNA quality in archive tissue are discussed. The other model of tissue biobanking is referred to as xenograft tissue banking, which represents an alternative method for obtaining large amounts of tissue, over an indefinite period, in so far as the tumor can be transferred in vivo over generations, maintaining the histological and genetic particularities. A description of the method and examples of the application are given with particular emphasis on sarcomas (Ewing's sarcoma/primitive neuroectodermal sarcoma, synovial sarcomas, and rhabdomyosarcomas) and early stages of tumor angiogenesis in sarcomas.
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Affiliation(s)
- Giorgio Stanta
- 1 Department of Medical, Surgical and Health Sciences, University of Trieste , Cattinara Hospital, Trieste, Italy
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Dovgerd AP, Zharkov DO. Application of repair enzymes to improve the quality of degraded DNA templates for PCR amplification. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814030053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhi Y, Sasai D, Okubo Y, Shinozaki M, Nakayama H, Yamagata Murayama S, Wakayama M, Ide T, Zhang Z, Shibuya K. Comparison between the effectiveness of polymerase chain reaction and in situ hybridization in detecting the presence of pathogenic fungi by using the preserved DNA in formalin-fixed and paraffin-embedded tissues. Jpn J Infect Dis 2013; 66:173-9. [PMID: 23698476 DOI: 10.7883/yoken.66.173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In situ hybridization (ISH) has been recognized as an important technique for identifying the causative fungi in the foci of infection observed in histopathological specimens which was processed from formalin-fixed and paraffin-embedded (FFPE) tissues. However, few basic studies have conducted an evaluation of the DNA preservation for use in ISH in comparison to polymerase chain reaction (PCR). The latter is a DNA amplification-based modality. In the present study, we analyzed 65 FFPE lung tissue specimens collected from autopsy cases for comparing the usefulness of ISH and PCR analysis. As a result, the positive identification rates for PCR were strikingly low; a majority of these results can be assumed to be false negative because the presence of fungi had been confirmed by histopathological analysis. In contrast, panfungal ISH targeting of the 28S rRNA showed a higher sensitivity than the 230-bp panfungal PCR primers did (80.0% versus 4.6%, respectively). Furthermore, over 60% of the samples we examined showed a favorable intensity of the ISH signal. Therefore, in conventional postmortem FFPE tissues, the state of DNA preservation may be more favorable for ISH than PCR analysis.
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Affiliation(s)
- Yuzhu Zhi
- Department of Surgical Pathology, Toho University School of Medicine, Tokyo, Japan
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Badiee P, Arastefar A, Jafarian H. Comparison of histopathological analysis, culture and polymerase chain reaction assays to detect mucormycosis in biopsy and blood specimens. IRANIAN JOURNAL OF MICROBIOLOGY 2013; 5:406-10. [PMID: 25848513 PMCID: PMC4385169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND OBJECTIVES The aim of this study was to compare direct microscopic examination with culture and PCR for the diagnosis of Mucorales infection in blood and tissue specimens. MATERIAL AND METHODS Blood samples and tissue specimens were obtained from 28 patients (total 58 samples) with suspected invasive fungal infection and cultured on proper media. Direct smear of tissue samples was done with potassium hydroxide, hematoxylin and eosin, and methenamine silver staining. DNA extracted from blood and tissue specimens were used for semi-nested PCR targeting 18S rDNA of Mucorales species. RESULTS Mucormycosis was documented in 7/28 (25%) of tissue specimens with positive findings by direct smear, of which PCR and culture were positive in 6 (86%) and 5 (70%) specimens, respectively. The etiologic agents were Mucor spp. and Rhizopus spp. However, culture and PCR results for all blood specimens were negative. CONCLUSIONS As the orders of Mucorales do not have well growth in culture media, PCR with tissue specimens is more sensitive than tissue or blood culture methods. Unfortunately, there is no alternative method for direct smear, which is an invasive method. Molecular methods may be helpful in these cases.
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Affiliation(s)
- Parisa Badiee
- Corresponding author: Parisa Badiee Ph.D, Address: Prof. Alborzi Clinical Microbiology Research Center, Nemazi Hospital, Zand Ave, Shiraz, Iran, Tel: +98-711-6474292, Fax: +98-711 6474303
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Leong KJ, James J, Wen K, Taniere P, Morton DG, Bach SP, Matthews GM. Impact of tissue processing, archiving and enrichment techniques on DNA methylation yield in rectal carcinoma. Exp Mol Pathol 2013; 95:343-9. [PMID: 24161956 DOI: 10.1016/j.yexmp.2013.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Formalin fixation, duration of tissue storage and tissue enrichment techniques can affect DNA methylation yield but these effects have not been quantitatively measured. The aim is to investigate the relative impact of these conditions on DNA methylation in rectal cancer. METHODS 10 rectal cancers with matched undissected fresh frozen tissues, laser capture microdissected (LCM) formalin-fixed paraffin-embedded (FFPE) tissues, manual macrodissected FFPE tissues, adjacent normal mucosa and stromal tissues were analysed for APC and LINE-1 methylation using bisulphite pyrosequencing. RESULTS FFPE cancer tissues, which had been stored for at least 4 years showed similar APC and LINE-1 methylation changes to matched fresh frozen cancer tissues. Laser capture microdissection did not increase the degree of methylation detected compared to manual macrodissection. Analysis of stromal tissues showed that they had undergone significant methylation changes compared to adjacent macroscopically normal mucosa, but not to the same extent as cancer tissues. CONCLUSION Reliable DNA methylation results can be obtained from FFPE rectal cancer tissues, which have been in long-term storage. Because only minor differences in methylation between macrodissected and LCM cancer tissues were found, our results do not support the routine use of LCM to enrich for cancer cells for DNA methylation studies.
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Affiliation(s)
- Kai Juen Leong
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom.
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Dietrich D, Uhl B, Sailer V, Holmes EE, Jung M, Meller S, Kristiansen G. Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition. PLoS One 2013; 8:e77771. [PMID: 24155973 PMCID: PMC3796491 DOI: 10.1371/journal.pone.0077771] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/05/2013] [Indexed: 02/06/2023] Open
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissues represent a valuable source for biomarker studies and clinical routine diagnostics. However, they suffer from degradation of nucleic acids due to the fixation process. Since genetic and epigenetic studies usually require PCR amplification, this degradation hampers its use significantly, impairing PCR robustness or necessitating short amplicons. In routine laboratory medicine a highly robust PCR performance is mandatory for the clinical utility of genetic and epigenetic biomarkers. Therefore, methods to improve PCR performance using DNA from FFPE tissue are highly desired and of wider interest. The effect of template DNA derived from FFPE tissues on PCR performance was investigated by means of qPCR and conventional PCR using PCR fragments of different sizes. DNA fragmentation was analyzed via agarose gel electrophoresis. This study showed that poor PCR amplification was partly caused by inhibition of the DNA polymerase by fragmented DNA from FFPE tissue and not only due to the absence of intact template molecules of sufficient integrity. This PCR inhibition was successfully minimized by increasing the polymerase concentration, dNTP concentration and PCR elongation time thereby allowing for the robust amplification of larger amplicons. This was shown for genomic template DNA as well as for bisulfite-converted template DNA required for DNA methylation analyses. In conclusion, PCR using DNA from FFPE tissue suffers from inhibition which can be alleviated by adaptation of the PCR conditions, therefore allowing for a significant improvement of PCR performance with regard to variability and the generation of larger amplicons. The presented solutions to overcome this PCR inhibition are of tremendous value for clinical chemistry and laboratory medicine.
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Affiliation(s)
- Dimo Dietrich
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
- * E-mail:
| | - Barbara Uhl
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Verena Sailer
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Emily Eva Holmes
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Maria Jung
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Sebastian Meller
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Glen Kristiansen
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
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Wang JH, Gouda-Vossos A, Dzamko N, Halliday G, Huang Y. DNA extraction from fresh-frozen and formalin-fixed, paraffin-embedded human brain tissue. Neurosci Bull 2013; 29:649-54. [PMID: 23996594 DOI: 10.1007/s12264-013-1379-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 06/07/2013] [Indexed: 11/25/2022] Open
Abstract
Both fresh-frozen and formalin-fixed, paraffin-embedded (FFPE) human brain tissues are invaluable resources for molecular genetic studies of central nervous system diseases, especially neurodegenerative disorders. To identify the optimal method for DNA extraction from human brain tissue, we compared methods on differently-processed tissues. Fragments of LRRK2 and MAPT (257 bp and 483 bp/245 bp) were amplified for evaluation. We found that for FFPE samples, the success rate of DNA extraction was greater when using a commercial kit than a laboratory-based method (successful DNA extraction from 76% versus 33% of samples). PCR amplicon size and storage period were key factors influencing the success rate of DNA extraction from FFPE samples. In the fresh-frozen samples, the DNA extraction success rate was 100% using either a commercial kit (QIAamp DNA Micro) or a laboratory-based method (sample boiling in 0.1 mol/L NaOH, followed by proteinase K digestion, and then DNA extraction using Chelex-100) regardless of PCR amplicon length or tissue storage time. Although the present results demonstrate that PCR-amplifiable genomic DNA can be extracted from both fresh-frozen and FFPE samples, fresh brain tissue is recommended for DNA extraction in future neuropathological studies.
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Affiliation(s)
- Jian-Hua Wang
- Neuroscience Research Australia and the University of New South Wales, Sydney, 2031, Australia,
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Kizys MML, Cardoso MG, Lindsey SC, Harada MY, Soares FA, Melo MCC, Montoya MZ, Kasamatsu TS, Kunii IS, Giannocco G, Martins JRM, Cerutti JM, Maciel RMB, Dias-da-Silva MR. Optimizing nucleic acid extraction from thyroid fine-needle aspiration cells in stained slides, formalin-fixed/paraffin-embedded tissues, and long-term stored blood samples. ACTA ACUST UNITED AC 2012; 56:618-26. [DOI: 10.1590/s0004-27302012000900004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/22/2012] [Indexed: 11/22/2022]
Abstract
OBJECTIVE: Adequate isolation of nucleic acids from peripheral blood, fine-needle aspiration cells in stained slides, and fresh and formalin-fixed/paraffin-embedded tissues is crucial to ensure the success of molecular endocrinology techniques, especially when samples are stored for long periods, or when no other samples can be collected from patients who are lost to follow-up. Here, we evaluate several procedures to improve current methodologies for DNA (salting-out) and RNA isolation. MATERIALS AND METHODS: We used proteinase K treatment, heat shock, and other adaptations to increase the amount and quality of the material retrieved from the samples. RESULTS: We successfully isolated DNA and RNA from the samples described above, and this material was suitable for PCR, methylation profiling, real-time PCR and DNA sequencing. CONCLUSION: The techniques herein applied to isolate nucleic acids allowed further reliable molecular analyses. Arq Bras Endocrinol Metab. 2012;56(9):618-26
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Gisele Giannocco
- Universidade Federal de Sao Paulo, Brazil; Faculdade de Medicina do ABC, Brazil
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Funabashi KS, Barcelos D, Visoná I, e Silva MS, e Sousa MLAPO, de Franco MF, Iwamura ESM. DNA extraction and molecular analysis of non-tumoral liver, spleen, and brain from autopsy samples: The effect of formalin fixation and paraffin embedding. Pathol Res Pract 2012; 208:584-91. [DOI: 10.1016/j.prp.2012.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 05/29/2012] [Accepted: 07/05/2012] [Indexed: 10/28/2022]
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Use of formalin-fixed paraffin-embedded tumor tissue as a DNA source in molecular epidemiological studies of pediatric CNS tumors. ACTA ACUST UNITED AC 2012; 21:105-13. [PMID: 22555093 DOI: 10.1097/pdm.0b013e3182340a78] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Formalin-fixed paraffin-embedded tissue (FFPET) samples are a potential source of DNA for molecular epidemiological studies. However, the use of FFPET samples can be restricted by the yield and quality of DNA isolated. The aim of this study was to examine whether FFPET biopsies from pediatric central nervous system tumors were a feasible alternative to archival frozen tissue when characterizing common gene polymorphisms. DNA was isolated from 50 frozen pediatric central nervous system tumor biopsies and matched FFPET samples. Real-time polymerase chain reaction (PCR) was used to quantify DNA and characterize GSTT1, GSTM1, GSTP1, and MTHFR gene polymorphisms. The use of whole-genome amplification (WGA) to increase DNA yields was also investigated. The results showed that DNA isolated from FFPET samples was more fragmented and provided smaller yields than DNA isolated from frozen samples. Attempts to increase the DNA yield from FFPET using WGA were unsuccessful. DNA from FFPET samples was successfully genotyped for the GSTP1 Ile105Val and MTHFR 677 C>T polymorphisms in 98% of samples and was 100% concordant with the results from frozen tissue. However, DNA from FFPET performed poorly in real-time PCR assays for GSTM1 and GSTT1 deletion polymorphisms. Our investigations show that DNA extracted from FFPET is substantially fragmented and not readily amplified using WGA. In addition, careful validation of PCR assays should be carried out due to the variable amplification of fragmented FFPET DNA.
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Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses. Virchows Arch 2012; 460:131-40. [PMID: 22270699 DOI: 10.1007/s00428-011-1184-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/27/2011] [Accepted: 12/13/2011] [Indexed: 01/25/2023]
Abstract
Tissues used for clinical diagnostics are mostly formalin-fixed and paraffin-embedded (FFPE) which provides many advantages. However, the quality of the obtained nucleic acids (NA) is reduced and this turns out to be a challenge for further molecular analyses. Although the spectrum of analyses of NA extracted from FFPE tissue has increased, the standard operating procedures for NA isolation from old tissue blocks still need to be improved. Here, we compared the efficiency of different NA extraction methods, using FFPE tissues of variable age and origin, with respect to downstream analyses. Our study showed that the phenol-chloroform isoamyl alcohol (PCI) and the commercial Qiagen protocol yielded samples with highest purity. The PCI protocol delivered the longest amplicons even from samples from the 1970s. We developed a short (1 h) tissue lysis procedure that turned out to be highly time- and cost-effective when DNA quality was tested using single and multiplex PCR. Compared to a 1-day lysis-protocol, the amplicons were only 100 bp shorter. In addition, single-copy genes used in daily routine were successfully amplified from long-term stored FFPE samples following 1-h tissue-lysis. The RNA integrity numbers (RIN) determined on RNA isolated from FFPE tissues indicated degraded RNA; however, all RINs were above the generally agreed threshold of 1.4. We showed that, depending on the purpose of the analysis, NA retrieved from FFPE tissues older than 40 years may be successfully used for molecular analysis.
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Thunnissen E, Kerr KM, Herth FJF, Lantuejoul S, Papotti M, Rintoul RC, Rossi G, Skov BG, Weynand B, Bubendorf L, Katrien G, Johansson L, López-Ríos F, Ninane V, Olszewski W, Popper H, Jaume S, Schnabel P, Thiberville L, Laenger F. The challenge of NSCLC diagnosis and predictive analysis on small samples. Practical approach of a working group. Lung Cancer 2011; 76:1-18. [PMID: 22138001 DOI: 10.1016/j.lungcan.2011.10.017] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/20/2011] [Accepted: 10/22/2011] [Indexed: 12/17/2022]
Abstract
Until recently, the division of pulmonary carcinomas into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) was adequate for therapy selection. Due to the emergence of new treatment options subtyping of NSCLC and predictive testing have become mandatory. A practical approach to the new requirements involving interaction between pulmonologist, oncologist and molecular pathology to optimize patient care is described. The diagnosis of lung cancer involves (i) the identification and complete classification of malignancy, (ii) immunohistochemistry is used to predict the likely NSCLC subtype (squamous cell vs. adenocarcinoma), as in small diagnostic samples specific subtyping is frequently on morphological grounds alone not feasible (NSCLC-NOS), (iii) molecular testing. To allow the extended diagnostic and predictive examination (i) tissue sampling should be maximized whenever feasible and deemed clinically safe, reducing the need for re-biopsy for additional studies and (ii) tissue handling, processing and sectioning should be optimized. Complex diagnostic algorithms are emerging, which will require close dialogue and understanding between pulmonologists and others who are closely involved in tissue acquisition, pathologists and oncologists who will ultimately, with the patient, make treatment decisions. Personalized medicine not only means the choice of treatment tailored to the individual patient, but also reflects the need to consider how investigative and diagnostic strategies must also be planned according to individual tumour characteristics.
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Affiliation(s)
- Erik Thunnissen
- Department of Pathology, VU Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Khokhar SK, Mitui M, Leos NK, Rogers BB, Park JY. Evaluation of Maxwell® 16 for automated DNA extraction from whole blood and formalin-fixed paraffin embedded (FFPE) tissue. Clin Chem Lab Med 2011; 50:267-72. [PMID: 22022984 DOI: 10.1515/cclm.2011.763] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 10/05/2011] [Indexed: 11/15/2022]
Abstract
BACKGROUND The aim of the study was to assess the performance of Promega, Maxwell® 16 for the extraction of genomic DNA from whole blood and FFPE tissue. METHODS DNA was extracted from 10 whole blood and 10 FFPE specimens using six different commercial kits. RESULTS For whole blood, the mean DNA concentration obtained by Maxwell® 16 was significantly greater than either easyMAG® (p<0.0001) or QIAamp® Blood DNA kit (p<0.001). For FFPE, the mean DNA concentration obtained by the AllPrep® FFPE specific DNA/RNA kit was significantly greater than either the Maxwell® 16 (p<0.0001) or the general AllPrep® DNA/RNA kit (p<0.0001). CONCLUSIONS Comparative evaluation of the six DNA extraction kits indicated that the semi-automated Maxwell® 16 was superior for whole blood extraction while the manual AllPrep® FFPE DNA/RNA kit (Qiagen) performed better for FFPE DNA extraction in terms of quantity of DNA obtained. All six extraction methods (blood and FFPE) performed well in terms of purity. Although there were variances in the quantity of DNA obtained, there were no significant differences in the efficiency of these methods in yielding amplifiable DNA extracts, as demonstrated by β-actin for whole blood specimens. In evaluation of FFPE DNA extraction methods, the Qiagen AllPrep® FFPE DNA/RNA Mini Kit was the best for applications requiring larger amplicons, but for smaller amplicons the Maxwell was most consistent.
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Turashvili G, Yang W, McKinney S, Kalloger S, Gale N, Ng Y, Chow K, Bell L, Lorette J, Carrier M, Luk M, Aparicio S, Huntsman D, Yip S. Nucleic acid quantity and quality from paraffin blocks: defining optimal fixation, processing and DNA/RNA extraction techniques. Exp Mol Pathol 2011; 92:33-43. [PMID: 21963600 DOI: 10.1016/j.yexmp.2011.09.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 09/10/2011] [Accepted: 09/13/2011] [Indexed: 01/01/2023]
Abstract
Although the extraction and analysis of nucleic acids from formalin-fixed paraffin-embedded tissues is a routine and growing part of pathology practice, no generally accepted recommendations exist to guide laboratories in their selection of tissue fixation, processing and DNA/RNA extraction techniques. The aim of this study was to determine how fixation method and length, paraffin embedding, processing conditions and nucleic acid extraction methods affect quality and quantity of DNA and RNA, and their performance in downstream applications. Nine tissue samples were subjected to freezing, fixation in formalin for <24 h and 7 days followed by conventional processing, and fixation in molecular fixative for <24 h and 7 days followed by rapid processing. DNA and RNA were isolated using in-house extraction and commercial kits, and assessed by PCR reactions for amplicons with varying sizes ranging from 268 to 1327 bp and one-step RT-PCR for 621 bp and 816 bp amplicons of housekeeping genes. Molecular fixative (MF) appeared to perform well under nearly all circumstances (extraction methods, fixation lengths and longer amplicons), often performing as well as frozen samples. Formalin fixation generally performed well only for shorter length amplicons and short fixation (<24 h). WaxFree kit showed consistently higher success rates for DNA and poorer rates for RNA. RecoverAll kit generally performed suboptimally in combination with prolonged formalin fixation. In conclusion, the Molecular Fixative regardless of fixation length, and the rapid tissue processing system were able to preserve large DNA and RNA fragments in paraffin blocks, making these techniques preferable for use in downstream molecular diagnostic assays.
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Affiliation(s)
- Gulisa Turashvili
- The Centre of Translation and Applied Genomics, BC Cancer Agency, Provincial Health Services Authority, Vancouver, BC, Canada V5Z 4E6.
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Fineschi V, Bafunno V, Bello S, De Stefano F, Margaglione M, Neri M, Riezzo I, Turillazzi E, Bonsignore A, Vecchione G, Ventura F, Grandone E. Fatal pulmonary thromboembolism. A retrospective autopsy study: searching for genetic thrombophilias (Factor V Leiden (G1691A) and FII (G20210A) gene variants) and dating the thrombus. Forensic Sci Int 2011; 214:152-8. [PMID: 21871746 DOI: 10.1016/j.forsciint.2011.07.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 06/26/2011] [Accepted: 07/25/2011] [Indexed: 10/17/2022]
Abstract
The accuracy of antemortem diagnosis of pulmonary embolism is within the range of just 10-30%, so representing one of the most frequent missed diagnosis in sudden, unexpected death. We describe 43 fatal cases of pulmonary embolism as confirmed by post-mortem examination. The aim of our study was to verify the systematic search for the most common genetic thrombophilias (Factor V Leiden (G1691A) and FII (G20210A) gene variants) and dating the thrombus. As a whole, 41 patients (95.3%) had at least one risk factor. Pre-existing symptoms are described just before fatal embolism in 18 (41.9%) out 43 patients. In 18 out of 43 (41.9%) it was not possible to find the thrombotic site. In 24 out of the remaining 25 cases the involvement of the deep veins of one leg was shown; in 1 case the thrombus was localised in the inferior caval vein. 10 (41.7%) were iliac vein thromboses, 7 (29.1%) femoral, 2 (8.3%) popliteal, 3 (12.6%) posterior-tibial, 1 (4.1%) anterior-tibial and 1 (4.1%) peroneal vein thromboses. In our cohort of patients, 4 (10%) out of 40 cases carried the 20210A prothrombin gene variant in heterozygosis. One (2.5%) out of 40 carried the Factor V Leiden (G1691A) gene variant in heterozygosis. Patients carrying these gene variants in homozygosis or carrying both were not present in our case-series. We strongly underline the relevance of a complete methodological approach, integrating clinical data by means of autopsy findings and histological study. On the contrary, investigating common inherited thrombophilia is not warranted.
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Affiliation(s)
- Vittorio Fineschi
- Department of Forensic Pathology, University of Foggia, Ospedale Colonnello D'Avanzo, Foggia, Italy.
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Awadin W, Hussein H, Elseady Y, Babiuk S, Furuoka H. Detection of lumpy skin disease virus antigen and genomic DNA in formalin-fixed paraffin-embedded tissues from an Egyptian outbreak in 2006. Transbound Emerg Dis 2011; 58:451-7. [PMID: 21699673 DOI: 10.1111/j.1865-1682.2011.01238.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An outbreak of lumpy skin disease (LSD) was reported in 2006 in Egypt affecting 16 provinces. Biopsies and post-mortem tissue samples were collected from calves that showed typical clinical signs of LSD and fixed in formalin. These samples were collected from a private dairy farm in the Damietta province of Egypt. Formalin-fixed paraffin-embedded tissue samples were assessed using histology, and skin lesions were classified as either acute or subacute/chronic. Both lumpy skin disease virus (LSDV) DNA detected by polymerase chain reaction and LSDV antigen detected by immunohistochemistry using a capripoxvirus-specific monoclonal antibody were observed in the acute skin lesions and in some subacute/chronic skin lesions.
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Affiliation(s)
- W Awadin
- Department of Pathology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
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