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Humphries EM, Loudon C, Craft GE, Hains PG, Robinson PJ. Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics. Anal Chem 2024. [PMID: 39102789 DOI: 10.1021/acs.analchem.3c04479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs). Using this, five extraction methods from the literature were modified and evaluated for their performance using kidney, leg muscle, lung, and testicular rat organs. All methods performed well, except for SP3 due to insufficient tissue lysis. Heat n' Beat was the fastest and most reproducible method with the highest digestion efficiency and lowest CVs. S-Trap produced the highest peptide yield, while TFE produced the best phosphopeptide enrichment efficiency. The quantitation of FFPE-derived peptides remains an ongoing challenge with bias in UV and fluorescence assays across methods, most notably in SPEED. Functional enrichment analysis demonstrated that each method favored extracting some gene ontology cellular components over others including chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, and nucleoplasm protein groups. The outcome is a set of recommendations for choosing the most appropriate method for different settings.
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Affiliation(s)
- Erin M Humphries
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Clare Loudon
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - George E Craft
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
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Kim D, Vanderbilt C, Yang SR, Nandakumar S, Nafa K, Feratovic R, Rekhtman N, Rijo I, Casanova J, Yun A, Brannon AR, Berger M, Ladanyi M, Lin O, Arcila M. Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling - A report on the impact of process optimization through the analysis of 4,871 cytology samples profiled by MSK-IMPACT. RESEARCH SQUARE 2024:rs.3.rs-4746484. [PMID: 39108489 PMCID: PMC11302697 DOI: 10.21203/rs.3.rs-4746484/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Comprehensive molecular profiling by next generation sequencing (NGS) has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACT™. Special emphasis is given to the use of residual supernatant cell free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples were similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples had excellent performance overall, low-level cross-contamination was identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples had negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy delivered successful results in 71% of cases where tumor tissue from CB was depleted.
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Affiliation(s)
- David Kim
- Memorial Sloan Kettering Cancer Center
| | | | | | | | | | | | | | | | | | - Anita Yun
- Memorial Sloan Kettering Cancer Center
| | | | | | | | - Oscar Lin
- Memorial Sloan Kettering Cancer Center
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Ivorová S, Kopčaková A, Pristaš P, Kišidayová S. Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus. Life (Basel) 2023; 13:2350. [PMID: 38137951 PMCID: PMC10744686 DOI: 10.3390/life13122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
An important feature of ruminal ciliates is their phenotypic plasticity, which makes their identification difficult. The common manifestation of the phenotypic plasticity in rumen ciliates is a change in their cell size and caudal spination. We analyzed various morphotypes of Epidinium with five caudal processes (spines) taken from the rumen of European bison (Bison bonasus). In the study, the cluster analysis and K-means analysis of morphometric data could not distinguish very similar morphotypes of Epidinium with five caudal processes. However, the morphotype of E. parvicaudatum prevailed (70%). The DNA of four individual E. parvicaudatum was isolated successfully from formaldehyde-preserved samples. The partial 18S rDNA gene sequences (about 350-400 bp) were identical to Epidinium sequences in GenBank (E. caudatum, a one-spine morphotype, and E. cattanei, a five-spine morphotype). It can be assumed that these short sequences cannot distinguish the differences between the Epidinium morphospecies. Complete gene sequences from various hosts and various molecular markers are necessary to reveal the validity of the Epidinium five-spine species. In conclusion, classical morphology should be supplemented with molecular data when more morphotypes of the rumen ciliate species are present in samples.
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Affiliation(s)
| | | | | | - Svetlana Kišidayová
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Košice, Slovakia; (S.I.); (A.K.); (P.P.)
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Ashton M, Czado N, Harrel M, Hughes S. Genotyping strategies for tissues fixed with various embalming fluids for human identification, databasing, and traceability. J Forensic Sci 2023. [PMID: 37904606 DOI: 10.1111/1556-4029.15414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023]
Abstract
Within anatomical willed body programs and skeletal collections, whole bodies and their disassociated limbs and organs are identified and tracked. However, if these tracking mechanisms fail, DNA recovered from the formalin-fixed tissues/organs could provide an additional layer of quality assurance. Embalming fluids preserve biological tissues; however, they also damage, fragment, and cross-link DNA and protein molecules. This project investigated the success of STR-typing from various soft tissue and bone samples that were fixed with embalming solutions with a range of formaldehyde concentrations. Formalin-fixed samples dissected from five cadavers, including skin, muscle, bone, heart, and kidney were used in Phase 1 of this study. In Phase 2, an additional 57 tissue samples from various embalmed organs and body parts were collected to demonstrate long-term fixation and direct applicability within a body donor program. DNA was extracted from the samples using the QIAamp® FFPE Tissue Kit (QIAGEN), quantified with the Investigator® QuantiPlex® Pro RGQ qPCR Kit (QIAGEN), and amplified using the Investigator® 24plex and 26plex QS Kits and the Investigator® DIPplex Kit (QIAGEN). The results show the DNA was severely damaged, degraded, and often in low amounts (after one year post-embalming). Sampling from skin and muscle tissues embalmed with ~2.5%-5% formaldehyde solutions appears to be the best strategy for identification, while also maintaining the preservation of the tissues. The results of this project can provide informative data when determining which genotyping strategy may be best suited for the identification, re-association, and establishment of a database for the provenance of formalin-fixed human remains.
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Affiliation(s)
- Madeline Ashton
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Sheree Hughes
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
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Vitošević K, Todorović D, Slović Ž, Varljen T, Radaković I, Radojević D, Čanović V, Todorović M. The quality of DNA isolated from autopsy formalin-fixed and formalin-fixed paraffin-embedded tissues: study of 1662 samples. Mol Biol Rep 2023; 50:6323-6336. [PMID: 37310548 DOI: 10.1007/s11033-023-08491-5] [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: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There are enormous formalin-fixed paraffin-embedded tissue archives and a constantly growing number of methods for molecular analyses but, the isolation of DNA from this tissue is still challenging due to the damaging effect of formalin on DNA. To determine the extent to which DNA purity, yield and integrity depend on the process of fixation in formalin, and to what extent on the process of tissue paraffin embedding, we compared the quality of DNA isolated from fixed tissues and DNA isolated from tissues embedded in paraffin blocks after fixation. METHODS AND RESULTS Heart, liver and brain tissues obtained from healthy people who suddenly died a violent death were fixed in 10% buffered formalin as well as in 4% unbuffered formalin for 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months. Additionally, the same tissues were fixed in 4% unbuffered formalin embedded in a paraffin block and stored from a few months to 30 years. The yield and purity of the DNA samples isolated from these tissues were measured using spectrophotometry. PCR amplification of the hTERT gene was performed to evaluate the degree of DNA fragmentation. Although the purity of the DNA isolated from almost all tissue samples was satisfactory, the DNA yields changed significantly. There was a decrease in successful PCR amplification of the hTERT gene in DNA samples isolated from tissue fixed in buffered and unbuffered formalin for up to 2 months from 100% to 8.3%. Archiving the tissue in paraffin blocks for up to 30 years also impacts the integrity of DNA, so there was a decrease in PCR amplification of the hTERT gene from 91% success to 3%. CONCLUSION The largest decrease in DNA yield was observed after tissue formalin fixation after 14 days of fixation in buffered and unbuffered formalin. DNA integrity depends on the time of tissue formalin fixation, especially after 6 days for tissue fixed in unbuffered formalin, while for tissue fixed in buffered formalin the time is prolonged up to 28 days. The age of paraffin blocks also impacted DNA integrity, after 1 year and 16 years of archiving the paraffin blocks of tissues, there was a decrease in the success of PCR amplification.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia.
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia.
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Legal Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Radaković
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Dušan Radojević
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Vanja Čanović
- Faculty of Medical Sciences, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
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Molecular Phylogenetic Analysis of Paracoccidioides Species Complex Present in Paracoccidioidomycosis Patient Tissue Samples. Microorganisms 2023; 11:microorganisms11030562. [PMID: 36985136 PMCID: PMC10055015 DOI: 10.3390/microorganisms11030562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Paracoccidioidomycosis (PCM) is the main and most prevalent systemic mycosis in Latin America, that until recently, it was believed to be caused only by Paracoccidioides brasiliensis (P. brasiliensis). In 2006, researchers described three cryptic species: S1, PS2, PS3, and later, another one, PS4. In 2009, Paracoccidioides lutzii (Pb01-like) was described, and in 2017, a new nomenclature was proposed for the different agents: P. brasiliensis (S1), P. americana (PS2), P. restrepiensis (PS3), and P. venezuelensis (PS4). These species are not uniformly distributed throughout Latin America and, knowing that more than one cryptic species could coexist in some regions, we aimed to identify those species in patients’ biopsy samples for a better understanding of the distribution and occurrence of these recently described species in Botucatu region. The Hospital of Medical School of Botucatu—UNESP, which is a PCM study pole, is located in São Paulo State mid-west region and is classified as a PCM endemic area. Genotyping analyses of clinical specimens from these patients that have been diagnosed and treated in our Hospital could favor a possible correlation between genetic groups and mycological and clinical characteristics. For this, molecular techniques to differentiate Paracoccidioides species in these biopsies, such as DNA extraction, PCR, and sequencing of three target genes (ITS, CHS2, and ARF) were conducted. All the sequences were analyzed at BLAST to testify the presence of P. brasiliensis. The phylogenetic trees were constructed using Mega 7.0 software and showed that 100% of our positive samples were from S1 cryptic species, therefore P. brasiliensis. This is important data, demonstrating the predominance of this species in the São Paulo State region.
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Kirkegaard MK. Ocular adnexal lymphoma: Subtype‐specific clinical and genetic features. Acta Ophthalmol 2022; 100 Suppl 270:3-37. [DOI: 10.1111/aos.15248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marina Knudsen Kirkegaard
- Department of Pathology, Eye Section, Copenhagen University Hospital Rigshospitalet Copenhagen Denmark
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Viljoen R, Reid KM, Mole CG, Rangwaga M, Heathfield LJ. Towards molecular autopsies: Development of a FFPE tissue DNA extraction workflow. Sci Justice 2022; 62:137-144. [DOI: 10.1016/j.scijus.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 08/02/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022]
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Luiz RLF, Menezes RC, Pereira SA, de Oliveira RDVC, Oliveira MME. Nested PCR for the Diagnosis of Feline Sporotrichosis From Formalin-Fixed and Paraffin-Embedded Samples Using Different DNA Extraction Protocols. Front Vet Sci 2022; 8:755897. [PMID: 35071377 PMCID: PMC8766819 DOI: 10.3389/fvets.2021.755897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/13/2021] [Indexed: 12/25/2022] Open
Abstract
Sporotrichosis is a chronic, cosmopolitan granulomatous mycosis that affects humans and animals. The infection is caused by the dimorphic fungi Sporothrix sp. The aims of the present study were to evaluate, standardize and validate a nested PCR technique using two DNA purification kits for the extraction of DNA from formalin fixed and paraffin-embedded tissues (FFPE) for Sporothrix sp. detection. FFPE mycological culture pellet samples of different Sporothrix species (S. chilensis, S. mexicana, S. pallida, S. globosa, S. brasiliensis and S. schenckii) were used as positive controls and clinical FFPE tissue samples of animals positive for Cryptococcus sp., Leishmania infantum and Histoplasma sp. were used as negative controls. Ten clinical FFPE skin samples from cats with sporotrichosis were used to validate the nested PCR. These samples were cut into two distinct paraffin sectioning protocols (5 and 16 μm thick). The paraffin sections were subjected to two different DNA extraction kits (chemical and thermal extractions). A nested PCR was performed on the extracted DNA to identify the genus Sporothrix. The chemical extraction protocol with the 5 μm thick paraffin section was more effective in extracting DNA from Sporothrix sp. from FFPE samples and the nested PCR technique showed the highest sensitivities (100% in the positive controls and of 50% in the skin samples of cats) and specificity (100%). Therefore, the nested PCR using this protocol has great potential to be applied in Sporothrix sp. diagnosis in FFPE samples of cats.
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Affiliation(s)
- Raul Leal Faria Luiz
- Laboratory of Taxonomy, Biochemistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rodrigo Caldas Menezes
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Sandro Antonio Pereira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Oba U, Kohashi K, Sangatsuda Y, Oda Y, Sonoda KH, Ohga S, Yoshimoto K, Arai Y, Yachida S, Shibata T, Ito T, Miura F. An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections. Biol Methods Protoc 2022; 7:bpac014. [PMID: 35937639 PMCID: PMC9351614 DOI: 10.1093/biomethods/bpac014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction" (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.
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Affiliation(s)
- Utako Oba
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
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Nascimento Araujo CD, Amorim AT, Barbosa MS, Alexandre JCPL, Campos GB, Macedo CL, Marques LM, Timenetsky J. Evaluating the presence of Mycoplasma hyorhinis, Fusobacterium nucleatum, and Helicobacter pylori in biopsies of patients with gastric cancer. Infect Agent Cancer 2021; 16:70. [PMID: 34949212 PMCID: PMC8705184 DOI: 10.1186/s13027-021-00410-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gastric cancer is the third leading cause of cancer-related deaths worldwide and has been associated with infections that may promote tumour progression. Accordingly, we analysed the presence of Mollicutes, Mycoplasma hyorhinis, Fusobacterium nucleatum and Helicobacter pylori in gastric cancer tissues and evaluated their correlation with clinicopathological factors. METHODS Using a commercial kit, DNA were extracted from 120 gastric samples embedded in paraffin: 80 from patients with gastric cancer and 40 from cancer free patients, dating from 2006 to 2016. Mollicutes and H. pylori were detected by PCR; F. nucleatum and M. hyorhinis were detected by qPCR, together with immunohistochemistry for the latter bacteria. RESULTS Mollicutes were detected in the case and control groups (12% and 2.5%) and correlated with the papillary histologic pattern (P = 0.003), likely due to cell transformation promoted by Mollicutes. M. hyorhinis was detected in the case and control group but was not considered a cancer risk factor. H. pylori was detected at higher loads in the case compared to the control group (8% and 22%, P = 0.008) and correlated with metastasis (P = 0.024), lymphatic invasion (P = 0.033), tumour of diffused type (P = 0.028), and histopathological grading G1/G2 (P = 0.008). F. nucleatum was the most abundant bacteria in the case group, but was also detected in the control group (26% and 2.5%). It increased the cancer risk factor (P = 0.045, OR = 10.562, CI95% = 1.057-105.521), and correlated with old age (P = 0.030) and tumour size (P = 0.053). Bacterial abundance was significantly different between groups (P = 0.001). CONCLUSION Our findings could improve the control and promote our understanding of opportunistic bacteria and their relevance to malignant phenotypes.
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Affiliation(s)
- Camila do Nascimento Araujo
- Department of Microbiology, Institute of Biomedical Sciences, ICB/USP, University of São Paulo, São Paulo, Brazil
| | - Aline Teixeira Amorim
- Department of Microbiology, Institute of Biomedical Sciences, ICB/USP, University of São Paulo, São Paulo, Brazil
| | - Maysa Santos Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, ICB/USP, University of São Paulo, São Paulo, Brazil
| | | | - Guilherme Barreto Campos
- Department of Microbiology, Institute of Biomedical Sciences, ICB/USP, University of São Paulo, São Paulo, Brazil.,Multidisciplinary Health Institute /Campus Anísio Teixeira, IMS/CAT - UFBA, Federal University of Bahia, Vitória da Conquista, Brazil
| | - Cláudia Leal Macedo
- Micro - Pathological Anatomy and Cytopathology Service, Vitória da Conquista, Brazil
| | - Lucas Miranda Marques
- Department of Microbiology, Institute of Biomedical Sciences, ICB/USP, University of São Paulo, São Paulo, Brazil. .,Multidisciplinary Health Institute /Campus Anísio Teixeira, IMS/CAT - UFBA, Federal University of Bahia, Vitória da Conquista, Brazil.
| | - Jorge Timenetsky
- Department of Microbiology, Institute of Biomedical Sciences, ICB/USP, University of São Paulo, São Paulo, Brazil
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Lam SY, Ioannou A, Konstanti P, Visseren T, Doukas M, Peppelenbosch MP, Belzer C, Fuhler GM. Technical challenges regarding the use of formalin-fixed paraffin embedded (FFPE) tissue specimens for the detection of bacterial alterations in colorectal cancer. BMC Microbiol 2021; 21:297. [PMID: 34715774 PMCID: PMC8555202 DOI: 10.1186/s12866-021-02359-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Formalin-fixed paraffin embedded (FFPE) tissues may provide an exciting resource to study microbial associations in human disease, but the use of these low biomass specimens remains challenging. We aimed to reduce unintentional bacterial interference in molecular analysis of FFPE tissues and investigated the feasibility of conducting quantitative polymerase chain reaction (qPCR) and 16S rRNA amplicon sequencing using 14 colorectal cancer, 14 normal adjacent and 13 healthy control tissues. Results Bacterial contaminants from the laboratory environment and the co-extraction of human DNA can affect bacterial analysis. The application of undiluted template improves bacterial DNA amplification, allowing the detection of specific bacterial markers (Escherichia coli and Faecalibacterium prausnitzii) by qPCR. Nested and non-nested PCR-based 16S rRNA amplicon sequencing approaches were employed, showing that bacterial communities of tissues and paired paraffin controls cluster separately at genus level on weighted Unifrac in both non-nested (R2 = 0.045; Pr(> F) = 0.053) and nested (R2 = 0.299; Pr(> F) = 0.001) PCR datasets. Nevertheless, considerable overlap of bacterial genera within tissues was seen with paraffin, DNA extraction negatives (non-nested PCR) or PCR negatives (nested PCR). Following mathematical decontamination, no differences in α- and β diversity were found between tumor, normal adjacent and control tissues. Conclusions Bacterial marker analysis by qPCR seems feasible using non-normalized template, but 16S rRNA amplicon sequencing remains challenging. Critical evaluation of laboratory procedures and incorporation of positive and negative controls for bacterial analysis of FFPE tissues are essential for quality control and to account for bacterial contaminants. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02359-z.
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Affiliation(s)
- Suk Yee Lam
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Athanasia Ioannou
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH , Wageningen, The Netherlands
| | - Prokopis Konstanti
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH , Wageningen, The Netherlands
| | - Thijmen Visseren
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Maikel Petrus Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH , Wageningen, The Netherlands
| | - Gwenny Manel Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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13
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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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14
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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15
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Shidham VB. Cell-blocks and other ancillary studies (including molecular genetic tests and proteomics). Cytojournal 2021; 18:4. [PMID: 33880127 PMCID: PMC8053490 DOI: 10.25259/cytojournal_3_2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/28/2023] Open
Abstract
Many types of elective ancillary tests may be required to support the cytopathologic interpretations. Most of these tests can be performed on cell-blocks of different cytology specimens. The cell-block sections can be used for almost any special stains including various histochemistry stains and for special stains for different microorganisms including fungi, Pneumocystis jirovecii (carinii), and various organisms including acid-fast organisms similar to the surgical biopsy specimens. Similarly, in addition to immunochemistry, different molecular tests can be performed on cell-blocks. Molecular tests broadly can be divided into two main types Molecular genetic tests and Proteomics.
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Affiliation(s)
- Vinod B Shidham
- Department of Pathology, Wayne State University School of Medicine, Karmanos Cancer Center, and Detroit Medical Center, Detroit, Michigan, United States
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16
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Vitošević K, Todorović M, Slović Ž, Varljen T, Matić S, Todorović D. DNA isolated from formalin-fixed paraffin-embedded healthy tissue after 30 years of storage can be used for forensic studies. Forensic Sci Med Pathol 2020; 17:47-57. [PMID: 33159288 DOI: 10.1007/s12024-020-00327-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2020] [Indexed: 11/30/2022]
Abstract
Tissue formalin fixation and paraffin embedding (FFPE) is a standard method for long-term preservation and morphological and molecular analysis. The aim of this study was to analyze the effect of storage time on the integrity of DNA isolated from three different healthy FFPE tissues. DNA was isolated from FFPE heart, liver and brain tissues obtained from autopsy and archived from 1988 to 2017 using two different methods of DNA isolation: phenol-chloroform-isoamyl alcohol (PCI) and PureLink Genomic DNA Kit. The quantification and purity of DNA was measured spectrophotometrically at 260 nm and 280 nm. The quality of isolated DNA was evaluated by PCR amplification of GPD1 (150 bp), ACTB (262 bp) and RPL4 (407 bp) genes. The histomorphological characteristics of FFPE tissues were not significantly changed during 30 years of storage. Higher yield (272.9 ± 10.3 µg) and purity (A260/280 = 2.05) of DNA was obtained using the PCI method for DNA isolation from FFPE liver tissue. The PCI extraction method showed reproducible and consistent results in PCR amplification of all of three examined genes. The GPD1 gene can be amplified up to 30 years, the ACTB gene in the same samples up to 26 years and the RPL4 gene up to 6 years of storage in FFPE blocks. Although the best yield and purity of isolated DNA (using both isolation methods) was obtained from FFPE liver tissue, the DNA with the most preserved integrity was obtained from brain tissue archived up to 30 years. This is the first report using long-term archived healthy FFPE tissues (up to 30 years) that shows that the DNA isolated from these tissues is of preserved integrity and can be used in molecular autopsy.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Forensic Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Stevan Matić
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Kragujevac, Serbia.
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17
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Hakin-1, a New Specific Small-Molecule Inhibitor for the E3 Ubiquitin-Ligase Hakai, Inhibits Carcinoma Growth and Progression. Cancers (Basel) 2020; 12:cancers12051340. [PMID: 32456234 PMCID: PMC7281109 DOI: 10.3390/cancers12051340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/22/2022] Open
Abstract
The requirement of the E3 ubiquitin-ligase Hakai for the ubiquitination and subsequent degradation of E-cadherin has been associated with enhanced epithelial-to-mesenchymal transition (EMT), tumour progression and carcinoma metastasis. To date, most of the reported EMT-related inhibitors were not developed for anti-EMT purposes, but indirectly affect EMT. On the other hand, E3 ubiquitin-ligase enzymes have recently emerged as promising therapeutic targets, as their specific inhibition would prevent wider side effects. Given this background, a virtual screening was performed to identify novel specific inhibitors of Hakai, targeted against its phosphotyrosine-binding pocket, where phosphorylated-E-cadherin specifically binds. We selected a candidate inhibitor, Hakin-1, which showed an important effect on Hakai-induced ubiquitination. Hakin-1 also inhibited carcinoma growth and tumour progression both in vitro, in colorectal cancer cell lines, and in vivo, in a tumour xenograft mouse model, without apparent systemic toxicity in mice. Our results show for the first time that a small molecule putatively targeting the E3 ubiquitin-ligase Hakai inhibits Hakai-dependent ubiquitination of E-cadherin, having an impact on the EMT process. This represents an important step forward in a future development of an effective therapeutic drug to prevent or inhibit carcinoma tumour progression.
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18
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Ramesh PS, Madegowda V, Kumar S, Narasimha S, S R P, Manoli NN, Devegowda D. DNA extraction from archived hematoxylin and eosin-stained tissue slides for downstream molecular analysis. World J Methodol 2019; 9:32-43. [PMID: 31799154 PMCID: PMC6885493 DOI: 10.5662/wjm.v9.i3.32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/27/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Histopathologically stained archived tissue slides are stored in hospital archives for years to decades. They are the largest available source of biological materials and are a potentially useful resource that can be used for retrospective epidemiological studies. DNA recovered from the slides can be used for several downstream molecular processes including polymerase chain reaction, single nucleotide polymorphism analysis, and whole genome sequencing. The DNA from these slides can be utilized to compare gene signatures of normal and diseased tissues. However, extraction of high-quality DNA from archived stained hematoxylin and eosin (H&E) slides remains challenging.
AIM To standardize a new protocol for extracting DNA from archived H&E-stained tissue slides for further molecular assays.
METHODS A total of 100 archived H&E-stained cancer slides were subjected to a total of five methods of DNA extraction. Methods were varied in the deparaffinization step, tissue rehydration, duration of lysis, and presence or absence of proteinase K. The extracted DNA was quantified using a NanoDrop spectrophometer and the quality was analyzed by agarose gel electrophoresis. Then each sample was subjected to polymerase chain reaction (PCR) to amplify the internal control gene GAPDH, thereby confirming the DNA intactness, which could be further utilized for other downstream applications.
RESULTS Of the five different methods tested, the third method wherein xylene was used for tissue deparaffinization followed by 72 h of digestion and without proteinase K inactivation yielded the highest amount of DNA with good purity. The yield was significantly higher when compared to other methods. In addition, 90% of the extracted DNA showed amplifiable GAPDH gene.
CONCLUSION Here we present a step-by-step, cost-effective, and reproducible protocol for the extraction of PCR-friendly DNA from archived H&E-stained cancer tissue slides that can be used for further downstream molecular applications.
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Affiliation(s)
- Pushkal Sinduvadi Ramesh
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Venkatesh Madegowda
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Suprith Kumar
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Shailashree Narasimha
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Parichay S R
- CIPHER Healthcare Pvt Ltd., Hyderabad 500034, India
| | - Nandini Nandish Manoli
- Department of Pathology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
| | - Devananda Devegowda
- Center of Excellence in Molecular Biology and Regenerative Medicine, Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India
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19
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Lloyd J, Copaciu R, Yahyabeik A, DeWit C, Cummings K, Lacey M, Su Q. Characterization of polyclonal antibodies to Herpes Simplex Virus types 1 and 2. J Histotechnol 2019; 42:202-214. [PMID: 31680648 DOI: 10.1080/01478885.2019.1683132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Infections with herpes simplex virus (HSV) types 1 and 2 have been linked to oral, facial, genital lesions, as well as some visceral organ changes in patients under immunosuppressed conditions. Immunohistochemistry (IHC) with HSV antibodies is used for identification of the viruses in tissue samples. In this study, two polyclonal antibodies, prepared separately with HSV-1 and HSV-2 immunogens, were characterized in comparison to a monoclonal antibody to HSV-1 (10A3). The polyclonal anti-HSV-1 and monoclonal antibody 10A3 were shown to be reactive to viral proteins of both HSV-1 and HSV-2 on Western blots, while the polyclonal anti-HSV-2 was reactive to HSV-2 proteins, but not to those of HSV-1. Cross-reactivity was not observed to proteins of six other frequently encountered herpes viruses. IHC characterization was performed on 29 cases of HSV-infected tissue samples, 61 samples infected with other herpes viruses and 35 samples without known infection. By IHC, the polyclonal anti-HSV-1 and a monoclonal antibody 10A3 exhibited a signal, mainly in a nuclear pattern, in all of the HSV-infected samples and not in other tissue types. A positive signal, mainly in the cytoplasm, was identified with the polyclonal anti-HSV-2 in 21 of the 29 HSV-infected samples. Genotyping analysis was successful in 14 of the HSV-infected samples, with IHC HSV-2 positivity correlative to the HSV-2 genotype. The results demonstrate that these antibodies are useful tools for identification of HSV-1 and HSV-2, and their combinatorial application may help to distinguish between these two types of infection.
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Affiliation(s)
| | | | | | | | | | - Mike Lacey
- Cell Marque, MilliporeSigma, Rocklin, CA, USA
| | - Qin Su
- Cell Marque, MilliporeSigma, Rocklin, CA, USA
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20
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Singh H, Narayan B, Urs AB, Kumar Polipalli S, Kumar S. A novel approach for extracting DNA from formalin-fixed paraffin-embedded tissue using microwave. Med J Armed Forces India 2019; 76:307-311. [PMID: 32773934 DOI: 10.1016/j.mjafi.2019.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/12/2019] [Indexed: 10/26/2022] Open
Abstract
Background Formalin-fixed paraffin-embedded (FFPE) tissue is the gold standard procedure for tissue preservation. However, the extraction of DNA is a cumbersome procedure as the extracted DNA is fragmented because of the cross-linking effect of formalin. Hence, the aim of the present study is to extract DNA from FFPE tissues using different techniques with a specific objective of comparing the extracted DNA, both quantitatively and qualitatively. Method Ten samples of FFPE tissues were retrieved from the archives of the Department of Oral Pathology. Total genomic DNA was extracted by different methods which included QIAamp DNA FFPE Tissue Kit, Norgen DNA FFPE Tissue Kit, phenol-chloroform method, mineral oil-based extraction, M/10 NaOH solution method, and microwave method. A 280-base pair sequence was selected for evaluation of downstream amplification. Results The statistical analysis was performed using unpaired student's t-test to compare the DNA yields and quality obtained by microwave methods with other methods using SPSS software. Total genomic DNA retrieved by the microwave method was superior to other methods both qualitatively and quantitatively. Conclusion DNA extraction from FFPE tissues is an onerous task as irreversible bonds form between the nucleic acid during fixation which are difficult to break during DNA retrieval. Hence, the microwave method provides good total genomic DNA which gives better downstream results when compared with other methods.
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Affiliation(s)
- Hanspal Singh
- Senior Research Associate (Oral Pathology & Microbiology), Maulana Azad Institute of Dental Sciences, New Delhi, India
| | - Bhaskar Narayan
- Post Graduate Student (Oral Pathology & Microbiology), Maulana Azad Institute of Dental Sciences, New Delhi, India
| | - Aadithya B Urs
- Professor & Head (Oral Pathology & Microbiology), Maulana Azad Institute of Dental Sciences, New Delhi, India
| | - Sunil Kumar Polipalli
- Cytogeneticist (Pediatrics Research & Genetics Laboratory), Maulana Azad Medical College, New Delhi, India
| | - Somesh Kumar
- Ph.D Scholar (Pediatrics Research & Genetics Laboratory), Maulana Azad Medical College, New Delhi, India
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21
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Gornjec A, Novakovic S, Stegel V, Hocevar M, Pohar Marinsek Z, Gazic B, Krajc M, Skof E. Cytology material is equivalent to tumor tissue in determining mutations of BRCA 1/2 genes in patients with tubo-ovarian high grade serous carcinoma. BMC Cancer 2019; 19:296. [PMID: 30940100 PMCID: PMC6444857 DOI: 10.1186/s12885-019-5535-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/27/2019] [Indexed: 01/09/2023] Open
Abstract
Background High-grade serous ovarian cancer is a detrimental disease. Treatment options in patients with a recurrent disease are dependent on BRCA1/2 mutation status since only patients with known BRCA mutation are eligible for treatment with poly(ADP-ribose) polymerase inhibitors (PARPi). The aim of this study was to compare concordance of BRCA mutation analyses from cytological samples (CS) with BRCA mutation analyses from histological formalin fixed paraffin embedded (FFPE) samples. Methods Mutation analysis of BRCA1 and BRCA2 genes was performed in 44 women diagnosed with primary or recurrent high-grade ovarian cancer from three different samples: blood, cytological sample (ascites, pleural effusion and enlarged lymph nodes) and tumor tissue. Results from all three samples were compared. Results Among 44 patients, there were 15 germline mutations and two somatic mutations. A 100% concordance was found between cytological and histologic samples. Conclusion There is a 100% concordance in BRCA mutation testing between cytological and histologic samples. BRCA mutation testing from CS could replace testing from FFPE tissue in clinical decision making in ovarian cancer patients. Trial registration The study was retrospectively registered at ISRCTN registry on 24/11/2015 - ISRCTN42408038.
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Affiliation(s)
- Andreja Gornjec
- Department of Gynecologic Oncology, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Srdjan Novakovic
- Department of Molecular diagnostics, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Vida Stegel
- Department of Molecular diagnostics, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Marko Hocevar
- Department of Surgical Oncology, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Ziva Pohar Marinsek
- Department of Cythopathology, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Barbara Gazic
- Department of Pathology, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Mateja Krajc
- Department of Genetic counselling, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia
| | - Erik Skof
- Department of Medical oncology, Institute of Oncology Ljubljana, Zaloška cesta 2, 1000, Ljubljana, Slovenia.
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22
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Lee MF, Lindo JF, Auer H, Walochnik J. Successful extraction and PCR amplification of Giardia DNA from formalin-fixed stool samples. Exp Parasitol 2019; 198:26-30. [PMID: 30710500 DOI: 10.1016/j.exppara.2019.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 12/14/2018] [Accepted: 01/20/2019] [Indexed: 01/31/2023]
Abstract
Extracting genomic DNA of pathogenic agents from formalin-fixed specimens is inherently difficult. Storage of samples in formalin results in nucleic acid cross-linking and DNA fragmentation. In this study, DNA was extracted from 45 Giardia-positive stool samples stored in formalin and subjected to PCR amplification targeting the triose phosphate isomerase (tpi), beta gardin (bg) and glutamate dehydrogenase (gdh) genes. Samples were rehydrated by using a descending alcohol series before DNA extraction using a commercial kit. This was followed by EDTA-mediated inhibition of DNase activity and prolonged treatment with proteinase K to digest contaminating proteins. DNA was amplified at rates of 64.4% (29/45) at the tpi, 40% (18/45) at the bg and 20% (9/45) at the gdh loci as seen on nested PCR. DNA quality was subsequently tested in a genotyping experiment which produced high-quality sequences at the tpi (41.2%; 12/29) bg (50%; 9/18), and gdh (22.2%; 2/9) loci and enabled differentiation of Giardia strains at the subtype level. The modified extraction protocol was effective at removing inhibitors and reversing cross-linking of DNA. However, PCR amplification was limited to short fragments of DNA which resulted in highest success rate on amplification of the shortest (334 bp) gene fragment tested.
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Affiliation(s)
- Mellesia F Lee
- Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria; Department of Microbiology, The University of the West Indies Mona, Kingston, Jamaica
| | - John F Lindo
- Department of Microbiology, The University of the West Indies Mona, Kingston, Jamaica.
| | - Herbert Auer
- Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
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23
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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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24
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Hutson HN, Kujawa C, Eliceiri K, Campagnola P, Masters KS. Impact of tissue preservation on collagen fiber architecture. Biotech Histochem 2018; 94:134-144. [PMID: 30354688 DOI: 10.1080/10520295.2018.1530373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Microarchitectural features of collagen-rich extracellular matrices provide the mechanical foundation for tissue function and exhibit topographical cues that influence cellular behavior including proliferation, migration and protein expression. Preservation of tissue microarchitecture is required for accurate evaluation of tissue characteristics and pathology. It is unclear whether common tissue preservation methods possess equal ability to preserve microarchitecture. We investigated collagen microarchitecture in samples that had been flash frozen, fixed in formalin or preserved in RNAlater®, and which contained both collagen-rich and collagen-sparse regions. Fibrillar collagen organization was characterized using picrosirius red staining and second harmonic generation (SHG) microscopy. Maintenance of collagen fiber characteristics compared to the gold standard of flash freezing depended on both the method of preservation and the local collagen content of the tissue. Both formalin fixation and RNAlater® preserved collagen fiber characteristics similar to flash freezing in collagen-rich areas of the tissue, but not in collagen-sparse regions. Analysis using picrosirius red staining indicated preservation-dependent changes in overall tissue architecture and suprafibrillar organization. Together with considerations of cost, ease of use, storage conditions and ability to use the preserved tissue for RNA or protein analysis, our quantitative characterization of the effects of preservation method on collagen microarchitecture may help investigators select the most appropriate preservation approach for their needs.
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Affiliation(s)
- H N Hutson
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - C Kujawa
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K Eliceiri
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA.,b Laboratory for Optical and Computational Instrumentation, Laboratory of Cell and Molecular Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - P Campagnola
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
| | - K S Masters
- a Department of Biomedical Engineering , University of Wisconsin-Madison , Madison , WI , USA
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25
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Prieto-Potin I, Montagut C, Bellosillo B, Evans M, Smith M, Melchior L, Reiltin W, Bennett M, Pennati V, Castiglione F, Bürrig KF, Cooper U, Dockhorn-Dworniczak B, Rossenbach C, Luna-Aguirre CM, Barrera-Saldaña HA, Machado JC, Costa JL, Yacobi R, Tabibian-Keissar H, Buglioni S, Ronchetti L, Douglas-Berger L, Dubbink HJ, Alorini M, Sabourin JC, Rojo F. Multicenter Evaluation of the Idylla NRAS-BRAF Mutation Test in Metastatic Colorectal Cancer. J Mol Diagn 2018; 20:664-676. [PMID: 29959022 DOI: 10.1016/j.jmoldx.2018.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/01/2018] [Accepted: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
Treatment of colorectal cancer (CRC) with monoclonal antibodies against epidermal growth factor receptor requires the assessment of the mutational status of exons 2, 3, and 4 of the NRAS and KRAS oncogenes. Moreover, the mutational status of exon 15 of the BRAF oncogene is a marker of poor prognosis in CRC. The Idylla NRAS-BRAF Mutation Test is a reliable, simple (<2 minutes hands-on time), and quick (<2 hours turnaround time) sample-to-result solution, enabling the detection of clinically relevant mutations in NRAS (18 mutations) and BRAF (5 mutations). A multicenter study was conducted in 14 centers using the Idylla NRAS-BRAF Mutation Test to assess the NRAS and BRAF mutational status of 418 formalin-fixed, paraffin-embedded tissue samples from CRC patients. Results were compared with those obtained earlier by routine reference methods, including next-generation sequencing, pyrosequencing, mass spectrometry-based assays, PCR-based assays, and Sanger sequencing. In case of discordance, additional tests were performed by digital droplet PCR. Overall, after testing confirmation and excluding invalids/errors by design, concordances between the Idylla NRAS-BRAF Mutation Test and the reference test results were found in almost perfect agreement. In conclusion, the Idylla NRAS-BRAF Mutation Test enables the routine detection of all NRAS and BRAF mutations deemed clinically relevant according to the latest clinical guidelines, without necessitating molecular expertise or infrastructure.
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Affiliation(s)
- Iván Prieto-Potin
- Molecular Diagnostics Laboratory, Department of Pathology, CIBERONC, The Fundación Jiménez Díaz University Hospital Health Research Institute, Autonomous University of Madrid, Madrid, Spain
| | - Clara Montagut
- Oncology Department, Hospital del Mar, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Matthew Evans
- Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Matthew Smith
- Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Linea Melchior
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | | | - José C Machado
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - José L Costa
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | | | | | - Simonetta Buglioni
- Department of Pathology, Regina Elena National Cancer Institute, Rome, Italy
| | - Livia Ronchetti
- Department of Pathology, Regina Elena National Cancer Institute, Rome, Italy
| | - Lotte Douglas-Berger
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Federico Rojo
- Molecular Diagnostics Laboratory, Department of Pathology, CIBERONC, The Fundación Jiménez Díaz University Hospital Health Research Institute, Autonomous University of Madrid, Madrid, Spain.
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Kumarapeli AR, Bellamy W, Olgaard E, Massoll N, Korourian S. Short-Duration Rapid Chilling of Mastectomy Specimens Does Not Interfere With Breast Cancer Biomarker and Molecular Testing. Arch Pathol Lab Med 2018; 143:92-98. [PMID: 29932859 DOI: 10.5858/arpa.2017-0377-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— A thorough gross examination of specimens for breast cancer requires the tissue to be very thinly sectioned, which is often difficult in large mastectomy samples. We have implemented rapid chilling of mastectomy specimens before formalin fixation. OBJECTIVE.— To evaluate the effects of rapid chilling of breast tissue on subsequent biomarker and molecular testing. DESIGN.— Mastectomy specimens were chilled at -80°C for 20 minutes to facilitate uniform sectioning of tissue at 4-mm intervals and enhance proper fixation and identification of small lesions. The integrity of chilled tissue for ancillary and molecular testing was assessed. We identified patients who were diagnosed with breast cancer on biopsy at outside institutions and subsequently underwent mastectomy at our institution during 2010-2014. We compared the results of biomarker testing performed on biopsy tissue with those performed on mastectomy tissue. The quantity and quality of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) mastectomy tissue with invasive carcinoma were assessed by using spectrophotometry and polymerase chain reaction. All Oncotype DX reports from 2011-2014 were reviewed to identify any documented evidence of assay interference caused by rapid chilling of tissue. RESULTS.— We found essentially 100% concordances in estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 gene ERBB2 (HER2/neu) studies. Extracted tumor DNA showed suitable purity and concentration that produced amplified fragments of 300 to 400 base pair lengths by polymerase chain reaction of FFPE tissue. No documented assay interferences were found in the Oncotype DX reports. CONCLUSIONS.— Short-duration rapid chilling of mastectomy tissue improves gross examination, optimally preserves DNA, allows for molecular testing, and does not interfere with biomarker assessment.
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Affiliation(s)
- Asangi R Kumarapeli
- From the Department of Pathology, University of Arkansas for Medical Sciences, Little Rock
| | - William Bellamy
- From the Department of Pathology, University of Arkansas for Medical Sciences, Little Rock
| | - Ericka Olgaard
- From the Department of Pathology, University of Arkansas for Medical Sciences, Little Rock
| | - Nicole Massoll
- From the Department of Pathology, University of Arkansas for Medical Sciences, Little Rock
| | - Soheila Korourian
- From the Department of Pathology, University of Arkansas for Medical Sciences, Little Rock
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Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach. Oncotarget 2018; 8:48126-48137. [PMID: 28611295 PMCID: PMC5564631 DOI: 10.18632/oncotarget.18296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/03/2017] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is altered in many types of disease, including metastatic colorectal cancer. However, the methylome has not yet been fully described in archival formalin-fixed paraffin embedded (FFPE) samples in the context of matched fresh-frozen (FF) tumor material at base-pair resolution using a targeted approach. Using next-generation sequencing, we investigated three pairs of matched FFPE and FF samples to determine the extent of their similarity. We identified a ‘bowing’ pattern specific to FFPE samples categorized by a lower CG proportion at the start of sequence reads. We have found no evidence that this affected methylation calling, nor concordance of results. We also found no significant increase in deamination, measured by C>T transitions, previously considered a result of crosslinking DNA by formalin fixation and a barrier to the use of FFPE in methylation studies. The methods used in this study have shown sensitivity of between 60-70% based on positions also methylated in colorectal cancer cell lines. We demonstrate that FFPE material is a useful source of tumor material for methylation studies using targeted sequencing.
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28
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Ayub Y, Mollel JT, Mbugi EV. Potential Value of Qiagen and PrepIT•MAX Kits in Extraction of Mycobacterial DNA From Presumptive Tuberculosis Archived Formalin-Fixed Paraffin-Embedded Tissues. East Afr Health Res J 2018; 2:18-25. [PMID: 34308170 PMCID: PMC8279293 DOI: 10.24248/eahrj-d-17-00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/28/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND DNA analysis has potential for screening for and diagnosing a variety of conditions as well as the characterization of various pathogens for many purposes including to identify genetic disorders and mutations, study genetic diversity, and establish evolutional trends. METHODS Our study compared the performance of 2 DNA extraction kits: Qiagen and prepIT•MAX. The study tested 160 formalin-fixed paraffin-embedded (FFPE) human tissue samples that had been collected at Muhimbili National Hospital (MNH) between 2010 and 2016. For each sample, DNA extraction was performed using both the Qiagen and prepIT•MAX kits followed by polymerase chain reaction (PCR) tests to target the RNA polymerase gene and gel electrophoresis. RESULTS The findings showed that the Qiagen was 3 times superior to the prepIT•MAX kit in successfully extracting mycobacterial DNA from presumptive tuberculosis (TB) FFPE tissues. Of the 160 previously Ziehl-Neelsen stain-negative Mycobacterium tuberculosis suspicious tissue samples, 12 (7.5%) tested positive with the PCR. Of the 12 PCR-detected positive samples, 8 (66.7%) yielded positive results with the Qiagen kit only and 4 (33.3%) yielded positive results with both Qiagen and prepIT•MAX kits. Additionally, 10 (83.3%) came from well-formed granuloma, 1 (8%) from caseous necrosis, and 1 (8.3%) Langhans-type giant cells endorsing their potential for housing infection such as TB adenitis. CONCLUSIONS A combination of molecular techniques, microscopy, and pathological features increases detection of M. tuberculosis from FFPE tissues. Both the Qiagen and the prepIT•MAX DNA extraction kits have shown a remarkable capability for extracting DNA from M. tuberculosis, although examination of FFPE tissues is not an intended use for the prepIT MAX, according to the manufacturer. In resource-limited countries, however, these kits may complement each other. We recommend further studies for validation and optimization, which includes the cost effectiveness of prepIT•MAX extraction kit to advocate for its use in extraction of mycobacterial DNA from FFPE tissues.
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Affiliation(s)
- Yunus Ayub
- Biochemistry Department, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Ministry of Health, Community Development, Gender, Elders & Children, Department of Human Resources Development, Singida Health Laboratory Assistants Training Centre, Singida, Tanzania
| | - Jackson T Mollel
- Department of Biological and Pre-Clinical studies, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Erasto V Mbugi
- Biochemistry Department, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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29
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Koo B, Jin CE, Park SY, Lee TY, Nam J, Jang YR, Kim SM, Kim JY, Kim SH, Shin Y. A rapid bio-optical sensor for diagnosing Q fever in clinical specimens. JOURNAL OF BIOPHOTONICS 2018; 11:e201700167. [PMID: 29024445 DOI: 10.1002/jbio.201700167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/15/2017] [Accepted: 10/06/2017] [Indexed: 05/16/2023]
Abstract
Recent zoonotic outbreaks, such as Zika, Middle East respiratory syndrome and Ebola, have highlighted the need for rapid and accurate diagnostic assays that can be used to aid pathogen control. Q fever is a zoonotic disease caused by the transmission of Coxiella burnetii that can cause serious illness in humans through aerosols and is considered a potential bioterrorism agent. However, the existing assays are not suitable for the detection of this pathogen due to its low levels in real samples. We here describe a rapid bio-optical sensor for the accurate detection of Q fever and validate its clinical utility. By combining a bio-optical sensor, that transduces the presence of the target DNA based on binding-induced changes in the refractive index on the waveguide surface in a label-free and real-time manner, with isothermal DNA amplification, this new diagnostic tool offers a rapid (<20 min), 1-step DNA amplification/detection method. We confirmed the clinical sensitivity (>90%) of the bio-optical sensor by detecting C. burnetii in 11 formalin-fixed, paraffin-embedded liver biopsy samples from acute Q fever hepatitis patients and in 16 blood plasma samples from patients in which Q fever is the cause of fever of unknown origin.
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Affiliation(s)
- Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and the Biomedical Engineering Research Center, Asan Institute of Life Sciences 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and the Biomedical Engineering Research Center, Asan Institute of Life Sciences 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Se Yoon Park
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University College of Medicine 59 Daesangwan-ro, Yongsan-gu, Seoul, Republic of Korea
| | - Tae Yoon Lee
- Department of Technology Education, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, School of Medicine, Korea University 145 Anam-ro, Seongbuk-gu, Seoul, Republic of Korea
| | - Young-Rock Jang
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
- Division of Infectious Disease, Department of Internal Medicine, Gil Medical Center, Gachon University College of Medicine, 21 Namdong-daero 774 beon-gil, Namdong-gu, Incheon, Republic of Korea
| | - Sun Mi Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine and the Biomedical Engineering Research Center, Asan Institute of Life Sciences 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
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30
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Lee JW, Shin JY, Seo JS. Identification of novel mutations in FFPE lung adenocarcinomas using DEPArray sorting technology and next-generation sequencing. J Appl Genet 2018. [PMID: 29525983 PMCID: PMC6060994 DOI: 10.1007/s13353-018-0439-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are utilized as the standard diagnostic method in pathology laboratories. However, admixture of unwanted tissues and shortage of normal samples, which can be used to detect somatic mutation, are considered critical factors to accurately diagnose cancer. To explore these challenges, we sorted the pure tumor cells from 22 FFPE lung adenocarcinoma tissues via Di-Electro-Phoretic Array (DEPArray) technology, a new cell sorting technology, and analyzed the variants with next-generation sequencing (NGS) for the most accurate analysis. The allele frequencies of the all gene mutations were improved by 1.2 times in cells sorted via DEPArray (tumor suppressor genes, 1.3–10.1 times; oncogenes, 1.3–2.6 times). We identified 16 novel mutations using the sequencing from sorted cells via DEPArray technology, compared to detecting 4 novel mutation by the sequencing from unsorted cells. Using this analysis, we also revealed that five genes (TP53, EGFR, PTEN, RB1, KRAS, and CTNNB1) were somatically mutated in multiple homogeneous lung adenocarcinomas. Together, we sorted pure tumor cells from 22 FFPE lung adenocarcinomas by DEPArray technology and identified 16 novel somatic mutations. We also established the precise genomic landscape for more accurate diagnosis in 22 lung adenocarcinomas with mutations detected in pure tumor cells. The results obtained in this study could offer new avenues for the treatment and the diagnosis of squamous cell lung cancers.
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Affiliation(s)
- Ji Won Lee
- Gongwu Genomic Medicine Institute (G2MI), Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea.,Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, 03080, Republic of Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Yeon Shin
- Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, 03080, Republic of Korea.,Macrogen Genome Institute, Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea
| | - Jeong-Sun Seo
- Gongwu Genomic Medicine Institute (G2MI), Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea. .,Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University, Seoul, 03080, Republic of Korea. .,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Macrogen Genome Institute, Medical Research Center, Seoul National University Bundang Hospital, Seongnamsi, 13605, Republic of Korea.
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31
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Castosa R, Martinez-Iglesias O, Roca-Lema D, Casas-Pais A, Díaz-Díaz A, Iglesias P, Santamarina I, Graña B, Calvo L, Valladares-Ayerbes M, Concha Á, Figueroa A. Hakai overexpression effectively induces tumour progression and metastasis in vivo. Sci Rep 2018; 8:3466. [PMID: 29472634 PMCID: PMC5823865 DOI: 10.1038/s41598-018-21808-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/12/2018] [Indexed: 12/31/2022] Open
Abstract
At early stages of carcinoma progression, epithelial cells undergo a program named epithelial-to-mesenchymal transition characterized by the loss of the major component of the adherens junctions, E-cadherin, which in consequence causes the disruption of cell-cell contacts. Hakai is an E3 ubiquitin-ligase that binds to E-cadherin in a phosphorylated-dependent manner and induces its degradation; thus modulating cell adhesions. Here, we show that Hakai expression is gradually increased in adenoma and in different TNM stages (I-IV) from colon adenocarcinomas compared to human colon healthy tissues. Moreover, we confirm that Hakai overexpression in epithelial cells drives transformation in cells, a mesenchymal and invasive phenotype, accompanied by the downregulation of E-cadherin and the upregulation of N-cadherin, and an increased proliferation and an oncogenic potential. More importantly, for the first time, we have studied the role of Hakai during cancer progression in vivo. We show that Hakai-transformed MDCK cells dramatically induce tumour growth and local invasion in nude mice and tumour cells exhibit a mesenchymal phenotype. Furthermore, we have detected the presence of micrometastasis in the lung mice, further confirming Hakai role during tumour metastasis in vivo. These results lead to the consideration of Hakai as a potential new therapeutic target to block tumour development and metastasis.
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Affiliation(s)
- Raquel Castosa
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain
| | - Olaia Martinez-Iglesias
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain
| | - Daniel Roca-Lema
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain
| | - Alba Casas-Pais
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain
| | - Andrea Díaz-Díaz
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain
| | - Pilar Iglesias
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain.,Pathology Department, INIBIC, CHUAC, Sergas, UDC, Spain
| | - Isabel Santamarina
- Clinical and Translational Oncology Group, INIBIC, CHUAC, Sergas, UDC, Spain
| | - Begoña Graña
- Clinical and Translational Oncology Group, INIBIC, CHUAC, Sergas, UDC, Spain
| | - Lourdes Calvo
- Clinical and Translational Oncology Group, INIBIC, CHUAC, Sergas, UDC, Spain
| | | | - Ángel Concha
- Pathology Department, INIBIC, CHUAC, Sergas, UDC, Spain
| | - Angélica Figueroa
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Universidade da Coruña (UDC), Sergas, Spain.
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Reid KM, Maistry S, Ramesar R, Heathfield LJ. A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting. Forensic Sci Int 2017; 280:181-187. [PMID: 29078160 DOI: 10.1016/j.forsciint.2017.09.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/15/2017] [Accepted: 09/26/2017] [Indexed: 11/26/2022]
Abstract
Molecular analyses in a post-mortem setting are becoming increasingly common, particularly in cases of sudden unexplained death, with the aim of identifying genetic mutations which may be responsible for causing death. In retrospective investigations, the access to suitable autopsy biological samples may be limited, and often formalin fixed paraffin embedded (FFPE) tissue is the only sample available. The preservation of tissue in formalin is known to damage DNA through crosslinking activity. This results in the extraction of severely fragmented DNA of variable yields, which subsequently reduces the ability to perform downstream molecular analyses. Numerous studies have investigated possible improvements to various aspects of the DNA extraction and amplification procedures from FFPE tissue and this review aims to collate these optimization steps in a cohesive manner. A systematic review was performed of three major databases, which identified 111 articles meeting the inclusion criteria. Five main areas for optimization and improvements were identified in the workflow: (1) tissue type, (2) fixation process, (3) post-fixation, (4) DNA extraction procedure and (5) amplification. It was found that some factors identified, for example tissue type and fixation process, could not be controlled by the researcher when conducting retrospective analyses. For this reason, optimization should be performed in other areas, within the financial means of the laboratories, and in accordance with the purposes of the investigation. Implementation of one or more of the optimization measures described here is anticipated to assist in the extraction of higher quality DNA. Despite the challenges posed by FFPE tissue, it remains a valuable source of DNA in retrospective molecular forensic investigations.
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Affiliation(s)
- Kate Megan Reid
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Sairita Maistry
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Raj Ramesar
- MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa.
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Arber DA, Borowitz MJ, Cessna M, Etzell J, Foucar K, Hasserjian RP, Rizzo JD, Theil K, Wang SA, Smith AT, Rumble RB, Thomas NE, Vardiman JW. Initial Diagnostic Workup of Acute Leukemia: Guideline From the College of American Pathologists and the American Society of Hematology. Arch Pathol Lab Med 2017; 141:1342-1393. [PMID: 28225303 DOI: 10.5858/arpa.2016-0504-cp] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - A complete diagnosis of acute leukemia requires knowledge of clinical information combined with morphologic evaluation, immunophenotyping and karyotype analysis, and often, molecular genetic testing. Although many aspects of the workup for acute leukemia are well accepted, few guidelines have addressed the different aspects of the diagnostic evaluation of samples from patients suspected to have acute leukemia. OBJECTIVE - To develop a guideline for treating physicians and pathologists involved in the diagnostic and prognostic evaluation of new acute leukemia samples, including acute lymphoblastic leukemia, acute myeloid leukemia, and acute leukemias of ambiguous lineage. DESIGN - The College of American Pathologists and the American Society of Hematology convened a panel of experts in hematology and hematopathology to develop recommendations. A systematic evidence review was conducted to address 6 key questions. Recommendations were derived from strength of evidence, feedback received during the public comment period, and expert panel consensus. RESULTS - Twenty-seven guideline statements were established, which ranged from recommendations on what clinical and laboratory information should be available as part of the diagnostic and prognostic evaluation of acute leukemia samples to what types of testing should be performed routinely, with recommendations on where such testing should be performed and how the results should be reported. CONCLUSIONS - The guideline provides a framework for the multiple steps, including laboratory testing, in the evaluation of acute leukemia samples. Some aspects of the guideline, especially molecular genetic testing in acute leukemia, are rapidly changing with new supportive literature, which will require on-going updates for the guideline to remain relevant.
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34
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Brusletto BS, Hellerud BC, Løberg EM, Goverud IL, Vege Å, Berg JP, Brandtzaeg P, Øvstebø R. Traceability and distribution of Neisseria meningitidis DNA in archived post mortem tissue samples from patients with systemic meningococcal disease. BMC Clin Pathol 2017; 17:10. [PMID: 28824331 PMCID: PMC5559868 DOI: 10.1186/s12907-017-0049-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 08/03/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The pathophysiology and outcome of meningococcal septic shock is closely associated with the plasma level of N. meningitidis lipopolysaccharides (LPS, endotoxin) and the circulating level of meningococcal DNA. The aim of the present study was to quantify the number of N. meningitidis in different formalin-fixed, paraffin-embedded (FFPE) tissue samples and fresh frozen (FF) tissue samples from patients with systemic meningococcal disease (SMD), to explore the distribution of N. meningitidis in the body. METHODS DNA in FFPE and FF tissue samples from heart, lungs, liver, kidneys, spleen and brain from patients with meningococcal shock and controls (lethal pneumococcal infection) stored at variable times, were isolated. The bacterial load of N. meningitidis DNA was analyzed using quantitative real-time PCR (qPCR) and primers for the capsule transport A (ctrA) gene (1 copy per N. meningitidis DNA). The human beta-hemoglobin (HBB) gene was quantified to evaluate effect of the storage times (2-28 years) and storage method in archived tissue. RESULTS N. meningitidis DNA was detected in FFPE and FF tissue samples from heart, lung, liver, kidney, and spleen in all patients with severe shock. In FFPE brain, N. meningitidis DNA was only detected in the patient with the highest concentration of LPS in the blood at admission to hospital. The highest levels of N. meningitidis DNA were found in heart tissue (median value 3.6 × 107 copies N. meningitidis DNA/μg human DNA) and lung tissue (median value 3.1 × 107 copies N. meningitidis DNA/μg human DNA) in all five patients. N. meningitidis DNA was not detectable in any of the tissue samples from two patients with clinical meningitis and the controls (pneumococcal infection). The quantity of HBB declined over time in FFPE tissue stored at room temperature, suggesting degradation of DNA. CONCLUSIONS High levels of N. meningitidis DNA were detected in the different tissue samples from meningococcal shock patients, particularly in the heart and lungs suggesting seeding and major proliferation of meningococci in these organs during the development of shock, probably contributing to the multiple organ failure. The age of archived tissue samples appear to have an impact on the amount of quantifiable N. meningitidis DNA.
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Affiliation(s)
- Berit Sletbakk Brusletto
- Blood Cell Research Group, Section for Research, Department of Medical Biochemistry, Oslo University Hospital HF, Ullevål Hospital, PO Box 4956 Nydalen, 0424 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Else Marit Løberg
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Ingeborg Løstegaard Goverud
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Åshild Vege
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section for Forensic Pediatric Pathology, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | - Jens Petter Berg
- Blood Cell Research Group, Section for Research, Department of Medical Biochemistry, Oslo University Hospital HF, Ullevål Hospital, PO Box 4956 Nydalen, 0424 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Petter Brandtzaeg
- Blood Cell Research Group, Section for Research, Department of Medical Biochemistry, Oslo University Hospital HF, Ullevål Hospital, PO Box 4956 Nydalen, 0424 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Reidun Øvstebø
- Blood Cell Research Group, Section for Research, Department of Medical Biochemistry, Oslo University Hospital HF, Ullevål Hospital, PO Box 4956 Nydalen, 0424 Oslo, Norway
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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Schlecht U, Mok J, Dallett C, Berka J. ConcatSeq: A method for increasing throughput of single molecule sequencing by concatenating short DNA fragments. Sci Rep 2017; 7:5252. [PMID: 28701704 PMCID: PMC5507877 DOI: 10.1038/s41598-017-05503-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/30/2017] [Indexed: 12/26/2022] Open
Abstract
Single molecule sequencing (SMS) platforms enable base sequences to be read directly from individual strands of DNA in real-time. Though capable of long read lengths, SMS platforms currently suffer from low throughput compared to competing short-read sequencing technologies. Here, we present a novel strategy for sequencing library preparation, dubbed ConcatSeq, which increases the throughput of SMS platforms by generating long concatenated templates from pools of short DNA molecules. We demonstrate adaptation of this technique to two target enrichment workflows, commonly used for oncology applications, and feasibility using PacBio single molecule real-time (SMRT) technology. Our approach is capable of increasing the sequencing throughput of the PacBio RSII platform by more than five-fold, while maintaining the ability to correctly call allele frequencies of known single nucleotide variants. ConcatSeq provides a versatile new sample preparation tool for long-read sequencing technologies.
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Affiliation(s)
- Ulrich Schlecht
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA.
| | - Janine Mok
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Carolina Dallett
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Jan Berka
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
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Non-reproducible sequence artifacts in FFPE tissue: an experience report. J Cancer Res Clin Oncol 2017; 143:1199-1207. [PMID: 28314930 DOI: 10.1007/s00432-017-2399-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Recent advances in sequencing technologies supported the development of molecularly targeted therapy in cancer patients. Thus, genomic analyses are becoming a routine part in clinical practice and accurate detection of actionable mutations is essential to assist diagnosis and therapy choice. However, this is often challenging due to major problems associated with DNA from formalin-fixed paraffin-embedded tissue which is usually the primary source for genetic testing. OBJECTIVES Here we want to share our experience regarding major problems associated with FFPE DNA used for PCR-based sequencing as illustrated by the mutational analysis of ERBB4 in melanoma. We want to focus on two major problems including extensive DNA fragmentation and hydrolytic deamination as source of non-reproducible sequence artifacts. Further, we provide potential explanations and possible strategies to minimize these difficulties and improve the detection of targetable mutations. METHODS Genomic DNA from formalin-fixed paraffin-embedded tumor samples was isolated followed by PCR amplification, Sanger sequencing and statistical analysis. RESULTS Analysis of Sanger sequencing data revealed a total of 46 ERBB4 mutations in 27 of 96 samples including the identification of 11 mutations at three previously unknown mutational hotspots. Unfortunately, we were not able to confirm any assumed hotspot mutation within repeated sequencing of relevant amplicons suggesting the detection of sequence artifacts most likely caused by DNA lesions associated with FFPE tissues. CONCLUSION Since DNA from FFPE tissue is usually the primary source for mutational analyses, appropriate measures must be implemented in the workflow to assess DNA damage in formalin-fixed tissue to ensure accurate detection of actionable mutations and minimize the occurrence of sequence artifacts.
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Kikuchi A, Sawamura T, Daimaru O, Horie M, Sasaki K, Okita N. Improved protocol for extraction of genomic DNA from formalin-fixed paraffin-embedded tissue samples without the use of xylene. Clin Chem Lab Med 2017; 54:e375-e377. [PMID: 27171389 DOI: 10.1515/cclm-2016-0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/12/2016] [Indexed: 11/15/2022]
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Krishnappa P, Kong HM, Mohamad IB, Voon K, Somanath SD. CD40 polymorphism in cervical carcinoma in a subset of Malaysian population. J Obstet Gynaecol Res 2017; 43:923-928. [PMID: 28181356 DOI: 10.1111/jog.13277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 08/02/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022]
Abstract
AIM The aim of this study was to determine the allelic frequency of single nucleotide polymorphisms (SNPs) in the human CD40 gene in cervical cancer. METHODS A total of 200 cases were selected from the records of the Department of Pathology, Hospital Tuanku Jaafar, Seremban, Malaysia. The samples were collected in three separate groups: cervicitis (n = 61), cervical intraepithelial neoplasia (n = 69), and cervical carcinoma (n = 70). The patients' demographic data and the respective paraffin-embedded tissue samples from Hospital Tuanku Jaafar, Seremban were obtained upon consent. The sample tissues were submitted for DNA extraction using G-spin Total DNA Extraction Kit. DNA obtained was then submitted for nested PCR before restriction enzyme digestion. RESULTS SNP rs1883832 showed higher prevalence of T alleles in the cervical carcinoma group compared to the control groups and in rs3765459, a higher prevalence of G alleles in the cervical carcinoma group was noted. The results of rs1800686 and rs4810485 were insignificant. CONCLUSION The data from our study indicates a potential association between the rs1883832 and rs3765459 CD40 gene polymorphism and susceptibility to cervical cancer.
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Affiliation(s)
| | - Hong Mun Kong
- Department of Pathology, International Medical University, Kuala Lumpur, Malaysia
| | | | - Kenny Voon
- Department of Pathology, International Medical University, Kuala Lumpur, Malaysia
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40
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Tong YQ, Liu B, Fu CH, Zheng HY, Gu J, Liu H, Luo HB, Li Y. Genetic analysis of the PKHD1 gene with long-rang PCR sequencing. ACTA ACUST UNITED AC 2016; 36:758-766. [PMID: 27752906 DOI: 10.1007/s11596-016-1658-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/26/2016] [Indexed: 12/13/2022]
Abstract
PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease (ARPKD). However, it is inconvenient to detect the mutations by common polymerase chain reaction (PCR) because the open reading frame of PKHD1 is very long. Recently, long-range (LR) PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.
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Affiliation(s)
- Yong-Qing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Bei Liu
- Department of Pathology, Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, China
| | - Chao-Hong Fu
- Department of Clinical Laboratory, Dongfeng Hospital, Hubei University of Medicine, Shiyan, 442008, China
| | - Hong-Yun Zheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hang Liu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Hong-Bo Luo
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Yan Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
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HPV16 detection by qPCR method in relation to quantity and quality of DNA extracted from archival formalin fixed and paraffin embedded head and neck cancer tissues by three commercially available kits. J Virol Methods 2016; 236:157-163. [DOI: 10.1016/j.jviromet.2016.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/20/2022]
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Ayatollahi H, Sadeghian MH, Keramati MR, Ayatollahi A, Shajiei A, Sheikhi M, Bakhshi S. The effect of deoxyribonucleic acid extraction methods from lymphoid tissue on the purity, content, and amplifying ability. Niger Med J 2016; 57:199-203. [PMID: 27630381 PMCID: PMC4995809 DOI: 10.4103/0300-1652.188321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Nowadays, definitive diagnosis of numerous diseases is based on the genetic and molecular findings. Therefore, preparation of fundamental materials for these evaluations is necessary. Deoxyribonucleic acid (DNA) is the first material for the molecular pathology and genetic analysis, and better results need more pure DNA. Furthermore, higher concentration of achieved DNA causes better results and higher amplifying ability for subsequent steps. We aim to evaluate five DNA extraction methods to compare DNA intimacy including purity, concentration, and amplifying ability with each other. Materials and Methods: The lymphoid tissue DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue through five different methods including phenol-chloroform as the reference method, DNA isolation kit (QIAamp DNA FFPE Tissue Kit, Qiagen, Germany), proteinase K and xylol extraction and heat alkaline plus mineral oil extraction as authorship innovative method. Finally, polymerase chain reaction (PCR) and real-time PCR method were assessed to compare each following method consider to DNA purity and its concentration. Results: Among five different applied methods, the highest mean of DNA purity was related to heat alkaline method. Moreover, the highest mean of DNA concentration was related to heat alkaline plus mineral oil. Furthermore, the best result in quantitative PCR was in proteinase K method that had the lowest cycle threshold averages among the other extraction methods. Conclusion: We concluded that our innovative method for DNA extraction (heat alkaline plus mineral oil) achieved high DNA purity and concentration.
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Affiliation(s)
- Hossein Ayatollahi
- Department of Hematopathology and Blood Banking, Cancer Molecular Pathology Research Center, Faculty of Medicine, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Hadi Sadeghian
- Department of Hematopathology and Blood Banking, Cancer Molecular Pathology Research Center, Faculty of Medicine, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Keramati
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Ayatollahi
- Cancer Molecular Pathology Research Center, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arezoo Shajiei
- Cancer Molecular Pathology Research Center, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Sheikhi
- Cancer Molecular Pathology Research Center, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samane Bakhshi
- Cancer Molecular Pathology Research Center, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
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Tian SK, Killian JK, Rekhtman N, Benayed R, Middha S, Ladanyi M, Lin O, Arcila ME. Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience. Arch Pathol Lab Med 2016; 140:1200-1205. [PMID: 27588332 DOI: 10.5858/arpa.2016-0108-ra] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The value and suitability of cytology specimens for molecular diagnosis has been demonstrated by numerous studies. In practice, however, the success rates vary widely across institutions depending on the disease setting, institutional practices of acquisition, handling/processing, and testing methodologies. As the number of clinically relevant biomarkers continues to increase, more laboratories are turning to next-generation sequencing platforms for testing. Although amplicon-based next-generation sequencing assays, interrogating a limited genomic territory, can be performed with minimal input material, broader-based next-generation sequencing assays have higher DNA input requirements that may not be met if the small tissue samples are not acquired and handled appropriately. We briefly describe some of the process changes we have instituted in our laboratories when handling cytologic material to maximize the tissue available for broad hybrid-capture-based next-generation sequencing assays. Among the key changes established were the consolidation and preservation of previously discarded supernatant material in cytologic samples, the introduction of mineral oil for deparaffinization of cell blocks, and adjustments in the molecular laboratory process and bioinformatics pipelines. We emphasize that even minimal changes can have broad implications for test performance, highlighting the importance of a cohesive group-based approach among clinical, cytopathology, surgical pathology, molecular, and bioinformatics teams.
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Crozier C, Wood GA, Foster RA, Stasi S, Liu JHW, Bartlett JMS, Coomber BL, Sabine VS. KRAS Mutations in Canine and Feline Pancreatic Acinar Cell Carcinoma. J Comp Pathol 2016; 155:24-8. [PMID: 27290644 DOI: 10.1016/j.jcpa.2016.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/04/2016] [Accepted: 05/07/2016] [Indexed: 12/15/2022]
Abstract
Companion animals may serve as valuable models for studying human cancers. Although KRAS is the most commonly mutated gene in human ductal pancreatic cancers (57%), with mutations frequently occurring at codons 12, 13 and 61, human pancreatic acinar cell carcinomas (ACCs) lack activating KRAS mutations. In the present study, 32 pancreatic ACC samples obtained from 14 dogs and 18 cats, including seven metastases, were analyzed for six common activating KRAS mutations located in codons 12 (n = 5) and 13 (n = 1) using Sequenom MassARRAY. No KRAS mutations were found, suggesting that, similar to human pancreatic ACC, KRAS mutations do not play a critical role in feline or canine pancreatic ACC. Due to the similarity of the clinical disease in dogs and cats to that of man, this study confirms that companion animals offer potential as a suitable model for investigating this rare subtype of pancreatic carcinoma.
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Affiliation(s)
- C Crozier
- Transformative Pathology Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - G A Wood
- Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - R A Foster
- Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - S Stasi
- Transformative Pathology Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - J H W Liu
- Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - J M S Bartlett
- Transformative Pathology Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - B L Coomber
- Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada.
| | - V S Sabine
- Transformative Pathology Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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45
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Comparison of DNA yield and STR success rates from different tissues in embalmed bodies. Int J Legal Med 2016; 131:61-66. [DOI: 10.1007/s00414-016-1405-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
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46
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Smiley Evans T, Gilardi KVK, Barry PA, Ssebide BJ, Kinani JF, Nizeyimana F, Noheri JB, Byarugaba DK, Mudakikwa A, Cranfield MR, Mazet JAK, Johnson CK. Detection of viruses using discarded plants from wild mountain gorillas and golden monkeys. Am J Primatol 2016; 78:1222-1234. [PMID: 27331804 DOI: 10.1002/ajp.22576] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 01/03/2023]
Abstract
Infectious diseases pose one of the most significant threats to the survival of great apes in the wild. The critically endangered mountain gorilla (Gorilla beringei beringei) is at high risk for contracting human pathogens because approximately 60% of the population is habituated to humans to support a thriving ecotourism program. Disease surveillance for human and non-human primate pathogens is important for population health and management of protected primate species. Here, we evaluate discarded plants from mountain gorillas and sympatric golden monkeys (Cercopithecus mitis kandti), as a novel biological sample to detect viruses that are shed orally. Discarded plant samples were tested for the presence of mammalian-specific genetic material and two ubiquitous DNA and RNA primate viruses, herpesviruses, and simian foamy virus. We collected discarded plant samples from 383 wild human-habituated mountain gorillas and from 18 habituated golden monkeys. Mammalian-specific genetic material was recovered from all plant species and portions of plant bitten or chewed by gorillas and golden monkeys. Gorilla herpesviral DNA was most consistently recovered from plants in which leafy portions were eaten by gorillas. Simian foamy virus nucleic acid was recovered from plants discarded by golden monkeys, indicating that it is also possible to detect RNA viruses from bitten or chewed plants. Our findings show that discarded plants are a useful non-invasive sampling method for detection of viruses that are shed orally in mountain gorillas, sympatric golden monkeys, and potentially other species. This method of collecting specimens from discarded plants is a new non-invasive sampling protocol that can be combined with collection of feces and urine to evaluate the most common routes of viral shedding in wild primates. Am. J. Primatol. 78:1222-1234, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tierra Smiley Evans
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California.
| | - Kirsten V K Gilardi
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California
| | - Peter A Barry
- California National Primate Research Center, Center for Comparative Medicine, University of California, Davis, California
| | | | | | - Fred Nizeyimana
- Gorilla Doctors, Mountain Gorilla Veterinary Project, Inc., Davis, California
| | - Jean Bosco Noheri
- Gorilla Doctors, Mountain Gorilla Veterinary Project, Inc., Davis, California
| | | | | | - Michael R Cranfield
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California
| | - Jonna A K Mazet
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California
| | - Christine K Johnson
- Gorilla Doctors, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, California
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Kalantari N, Bayani M, Ghaffari T. Deparaffinization of formalin-fixed paraffin-embedded tissue blocks using hot water instead of xylene. Anal Biochem 2016; 507:71-3. [PMID: 27287960 DOI: 10.1016/j.ab.2016.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 05/10/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
This study aimed to deparaffinize formalin-fixed paraffin-embedded (FFPE) tissues using hot water instead of xylene and measuring the quantity and quality of the extracted DNA from the respective tissues. To deparaffinize the tissue sections with hot water, small sections were exposed to 90 °C distilled sterile water. After 25 FFPE tissue samples were deparaffinized with the hot water method, DNA was then extracted. The mean of optical density and the ratio of absorbance of the DNA solution were 220.01 ± 36.1 ng/μl and 1.65 ± 0.1, respectively. Polymerase chain reaction (PCR) analysis of the toll-like receptor 4(TLR4) gene showed that the method can be used as a tool for different applications.
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Affiliation(s)
- Narges Kalantari
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Masomeh Bayani
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran.
| | - Taraneh Ghaffari
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
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48
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Abed FM, Dark MJ. Determining the utility of veterinary tissue archives for retrospective DNA analysis. PeerJ 2016; 4:e1996. [PMID: 27168995 PMCID: PMC4860330 DOI: 10.7717/peerj.1996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 04/11/2016] [Indexed: 11/29/2022] Open
Abstract
Histopathology tissue archives can be an important source of specimens for retrospective studies, as these include samples covering a large number of diseases. In veterinary medicine, archives also contain samples from a large variety of species and may represent naturally-occurring models of human disease. The formalin-fixed, paraffin-embedded (FFPE) tissues comprising these archives are rich resources for retrospective molecular biology studies and pilot studies for biomarkers, as evidenced by a number of recent publications highlighting FFPE tissues as a resource for analysis of specific diseases. However, DNA extracted from FFPE specimens are modified and fragmented, making utilization challenging. The current study examines the utility of FFPE tissue samples from a veterinary diagnostic laboratory archive in five year intervals from 1977 to 2013, with 2015 as a control year, to determine how standard processing and storage conditions has affected their utility for future studies. There was a significant difference in our ability to obtain large amplicons from samples from 2015 than from the remaining years, as well as an inverse correlation between the age of the samples and product size obtainable. However, usable DNA samples were obtained in at least some of the samples from all years tested, despite variable storage, fixation, and processing conditions. This study will help make veterinary diagnostic laboratory archives more useful in future studies of human and veterinary disease.
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Affiliation(s)
- Firas M Abed
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida , Gainesville, FL , United States
| | - Michael J Dark
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States; Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
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Piskorz AM, Ennis D, Macintyre G, Goranova TE, Eldridge M, Segui-Gracia N, Valganon M, Hoyle A, Orange C, Moore L, Jimenez-Linan M, Millan D, McNeish IA, Brenton JD. Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples. Ann Oncol 2016; 27:532-9. [PMID: 26681675 PMCID: PMC4769995 DOI: 10.1093/annonc/mdv613] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 10/29/2015] [Accepted: 12/01/2015] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) of tumour samples is a critical component of personalised cancer treatment, but it requires high-quality DNA samples. Routine neutral-buffered formalin (NBF) fixation has detrimental effects on nucleic acids, causing low yields, as well as fragmentation and DNA base changes, leading to significant artefacts. PATIENTS AND METHODS We have carried out a detailed comparison of DNA quality from matched samples isolated from high-grade serous ovarian cancers from 16 patients fixed in methanol and NBF. These experiments use tumour fragments and mock biopsies to simulate routine practice, ensuring that results are applicable to standard clinical biopsies. RESULTS Using matched snap-frozen tissue as gold standard comparator, we show that methanol-based fixation has significant benefits over NBF, with greater DNA yield, longer fragment size and more accurate copy-number calling using shallow whole-genome sequencing (WGS). These data also provide a new approach to understand and quantify artefactual effects of fixation using non-negative matrix factorisation to analyse mutational spectra from targeted and WGS data. CONCLUSION We strongly recommend the adoption of methanol fixation for sample collection strategies in new clinical trials. This approach is immediately available, is logistically simple and can offer cheaper and more reliable mutation calling than traditional NBF fixation.
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Affiliation(s)
- A M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
| | - D Ennis
- Institute of Cancer Sciences, University of Glasgow, Glasgow
| | - G Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
| | - T E Goranova
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
| | - M Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge
| | - N Segui-Gracia
- Cancer Molecular Diagnostics Laboratory, Department of Oncology, University of Cambridge, Cambridge
| | - M Valganon
- Cancer Molecular Diagnostics Laboratory, Department of Oncology, University of Cambridge, Cambridge
| | - A Hoyle
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow
| | - C Orange
- Institute of Cancer Sciences, University of Glasgow, Glasgow
| | - L Moore
- Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge Department of Histopathology, Addenbrooke's Hospital, Cambridge, UK
| | - M Jimenez-Linan
- Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge Department of Histopathology, Addenbrooke's Hospital, Cambridge, UK
| | - D Millan
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow
| | - I A McNeish
- Institute of Cancer Sciences, University of Glasgow, Glasgow
| | - J D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge
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50
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Troncoso-Palacios J, Elorza AA, Puas GI, Alfaro-Pardo E. A new species of Liolaemus related to L. nigroviridis from the Andean highlands of Central Chile (Iguania, Liolaemidae). Zookeys 2016:91-114. [PMID: 26877688 PMCID: PMC4740823 DOI: 10.3897/zookeys.555.6011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/26/2015] [Indexed: 11/12/2022] Open
Abstract
The Liolaemusnigroviridis group is a clade of highland lizards endemic to Chile. These species are distributed from northern to central Chile, and currently there are no cases of sympatric distribution. This study describes a new species, Liolaemusuniformissp. n., from this group, and provides a detailed morphological characterization and mitochondrial phylogeny using cytochrome-b. Liolaemusuniformis was found in sympatry with Liolaemusnigroviridis but noticeably differed in size, scalation, and markedly in the color pattern, without sexual dichromatism. This new species has probably been confused with Liolaemusmonticola and Liolaemusbellii, both of which do not belong to the nigroviridis group. The taxonomic issues of this group that remain uncertain are also discussed.
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Affiliation(s)
- Jaime Troncoso-Palacios
- Programa de Fisiologia y Biofisica, Instituto de Ciencias Biomedicas (ICBM), Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile
| | - Alvaro A Elorza
- Centro de Investigaciones Biomedicas, Facultad de Ciencias Biologicas y Facultad de Medicina, Universidad Andres Bello, Republica 239, Santiago, Chile; Instituto Milenio de Inmunologia e Inmunoterapia, Portugal 49, Santiago, Chile
| | - German I Puas
- Centro de Investigaciones Biomedicas, Facultad de Ciencias Biologicas y Facultad de Medicina, Universidad Andres Bello, Republica 239, Santiago, Chile; Instituto Milenio de Inmunologia e Inmunoterapia, Portugal 49, Santiago, Chile
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