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Gignac PM, Valdez D, Morhardt AC, Lynch LM. Buffered Lugol's Iodine Preserves DNA Fragment Lengths. Integr Org Biol 2024; 6:obae017. [PMID: 38887427 PMCID: PMC11182668 DOI: 10.1093/iob/obae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 04/05/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Museum collections play a pivotal role in the advancement of biological science by preserving phenotypic and genotypic history and variation. Recently, contrast-enhanced X-ray computed tomography (CT) has aided these advances by allowing improved visualization of internal soft tissues. However, vouchered specimens could be at risk if staining techniques are destructive. For instance, the pH of unbuffered Lugol's iodine (I2KI) may be low enough to damage deoxyribonucleic acid (DNA). The extent of this risk is unknown due to a lack of rigorous evaluation of DNA quality between control and experimental samples. Here, we used formalin-fixed mice to document DNA concentrations and fragment lengths in nonstained, ethanol-preserved controls and 3 iodine-based staining preparations: (1) 1.25% weight-by-volume (wt/vol.) alcoholic iodine (I2E); (2) 3.75% wt/vol. I2KI; and (3) 3.75% wt/vol. buffered I2KI. We tested a null hypothesis of no significant difference in DNA concentrations and fragment lengths between control and treatment samples. We found that DNA concentration decreases because of staining-potentially an effect of measuring intact double-stranded DNA only. Fragment lengths, however, were significantly higher for buffered I2KI and control samples, which were not, themselves, significantly different. Our results implicate buffered I2KI as the appropriate choice for contrast-enhanced CT imaging of museum wet collections to safely maximize their potential for understanding genetic and phenotypic diversity.
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Affiliation(s)
- P M Gignac
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - D Valdez
- Department of Anatomy, Midwestern University, Glendale, AZ 85308, USA
| | - A C Morhardt
- Department of Neuroscience, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - L M Lynch
- Department of Anatomy, Midwestern University, Glendale, AZ 85308, USA
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2
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Radojevic DN, Todorovic MS, Vitosevic KM, Canovic V, Pavicevic M, Slovic ZS, Andric IM, Matic S, Todorovic DV. The changes in tissue histomorphology and quality of DNA in healthy human autopsied tissues stored at -20 °C and -150 °C. Leg Med (Tokyo) 2024; 67:102396. [PMID: 38237382 DOI: 10.1016/j.legalmed.2024.102396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 03/01/2024]
Abstract
The aim of this study was to compare the changes in tissue histomorphology and DNA quality in six different healthy tissues (brain, heart, lung, liver, spleen and kidney) exempted during autopsy of healthy individuals and storage at -20 °C and -150 °C three month. Tissue samples were obtained, divided by tissue and temperature group, and for each sample, tissue histomorphology and DNA (isolated from all tissues in duplicated - 72 samples of DNA) quality were analysed. Morphology of tissue samples was studied using H&E staining. DNA was isolated using the phenol-chloroform-isoamyl alcohol method. To assess the concentration and purity of the DNA samples, we used a spectrophotometer to measure absorbance at wavelengths of 280 nm and 260 nm. The fragments of human telomerase reverse transcriptase (hTERT) gene were amplified from the DNA using PCR reaction and then visualised using the 2 % agarose gel. Samples stored at -150 °C sustained the highest degree of histomorphological damage, while samples stored at -20 °C were less degraded, compared to control. The liver samples stored at -20 °C had a mean DNA concentration (1030.4 ± 51.5 ng/μl) higher than the samples of liver tissue stored at -150 °C (497.4 ± 167.1 ng/μl) (p < 0.001). Other tissues did not have statistically significantly different DNA concentration at both temperatures. Liver samples at -20 °C had degraded DNA, showed as the absence of hTERT gene in most of samples. Other tissue samples in both temperature groups had unfragmented DNA. Storing tissue samples at -20 °C is not inferior in terms of DNA yield and integrity, and possibly superior for tissue histomorphology, comparing with samples stored at -150⁰C.
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Affiliation(s)
- Dusan N Radojevic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Genetics
| | - Milos S Todorovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia.
| | - Katarina M Vitosevic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Vanja Canovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Milena Pavicevic
- University of Kragujevac, Serbia, Faculty of Science and Mathematics
| | - Zivana S Slovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine; University Clinical Center Kragujevac, Department of Forensic Medicine and Toxicology, Kragujevac, Serbia
| | - Ivana M Andric
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Forensic medicine
| | - Stevan Matic
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Danijela V Todorovic
- University of Kragujevac, Serbia, Faculty of Medical Sciences, Department of Genetics
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3
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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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4
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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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Devyatov AA, Davydova EE, Luparev AR, Karseka SA, Shuryaeva AK, Zagainova AV, Shipulin GA. Design of a Protocol for Soil-Transmitted Helminths (in Light of the Nematode Toxocara canis) DNA Extraction from Feces by Combining Commercially Available Solutions. Diagnostics (Basel) 2023; 13:2156. [PMID: 37443549 DOI: 10.3390/diagnostics13132156] [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: 05/04/2023] [Revised: 06/02/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
One of the main challenges for the mass introduction of the molecular diagnostics of soil-transmitted helminths (STHs) into clinical practice is the lack of a generally recognized effective method for isolating parasitic DNA from fecal samples. In the present study, we assessed the effects of various pretreatment procedures on the efficiency of removing PCR inhibitors and extracting Toxocara canis DNA from feces. We evaluated the effectiveness of four destructive methods (bead beating, the action of temperature-dependent enzymes, freeze-heat cycles, and incubation in a lysis buffer) on the integrity of T. canis eggs and the efficiency of DNA extraction. Also, we evaluated the effects of prewashes and the use of commercial concentrators on DNA extraction from fecal samples contaminated with T. canis eggs. A bead beating procedure was sufficient to destroy the T. canis eggs, while the effects of enzymes and freeze-heat cycles did not lead to a significant destruction of the eggs or the release of Toxocara DNA. Helminth DNA isolation protocols that do not include a bead beating step are not preferred. The preconcentration of STH eggs from feces using a commercial concentrator and subsequent washing can significantly increase the yield of DNA from STHs and reduce PCR inhibition.
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Affiliation(s)
- Alexander A Devyatov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Ekaterina E Davydova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Andrey R Luparev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Sofia A Karseka
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Anna K Shuryaeva
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - Angelica V Zagainova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
| | - German A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 10 bld 1, Pogodinskaya Str., 119121 Moscow, Russia
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6
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Matic S, Milovanovic D, Mijailovic Z, Djurdjevic P, Sazdanovic P, Stefanovic S, Todorovic D, Popovic S, Vitosevic K, Vukicevic V, Vukic M, Vukovic N, Milivojevic N, Zivanovic M, Jakovljevic V, Filipovic N, Baskic D, Djordjevic N. IFNL3/4 polymorphisms as a two-edged sword: An association with COVID-19 outcome. J Med Virol 2023; 95:e28506. [PMID: 36655749 DOI: 10.1002/jmv.28506] [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: 10/08/2022] [Revised: 12/14/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
Coronavirus Disease 2019 (COVID-19) has been ranked among the most fatal infectious diseases worldwide, with host's immune response significantly affecting the prognosis. With an aim to timely predict the most likely outcome of SARS-CoV-2 infection, we investigated the association of IFNL3 and IFNL4 polymorphisms, as well as other potentially relevant factors, with the COVID-19 mortality. This prospective observational case-control study involved 178 COVID-19 patients, hospitalized at Corona Center or Clinic for Infectious Diseases of University Clinical Centre Kragujevac, Serbia, followed up until hospital discharge or in-hospital death. Demographic and clinical data on all participants were retrieved from the electronic medical records, and TaqMan assays were employed in genotyping for IFNL3 and IFNL4 single nucleotide polymorphisms (SNPs), namely rs12980275, rs8099917, rs12979860, and rs368234815. 21.9% and 65.0% of hospitalized and critically ill COVID-19 patients, respectively, died in-hospital. Multivariable logistic regression analysis revealed increased Charlson Comorbidity Index (CCI), N/L, and lactate dehydrogenase (LDH) level to be associated with an increased likelihood of a lethal outcome. Similarly, females and the carriers of at least one variant allele of IFNL3 rs8099917 were almost 36-fold more likely not to survive SARS-CoV-2 infection. On the other hand, the presence of at least one ancestral allele of IFNL4 rs368234815 decreased more than 15-fold the likelihood of mortality from COVID-19. Our results suggest that, in addition to LDH level, N/L ratio, and CCI, IFNL4 rs368234815 and IFNL3 rs8099917 polymorphisms, but also patients' gender, significantly affect the outcome of COVID-19.
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Affiliation(s)
- Sanja Matic
- Department of Pharmacy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Dragan Milovanovic
- Department of Pharmacology and Toxicology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Department of Clinical Pharmacology, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Zeljko Mijailovic
- Department of Infectious Diseases, Serbia, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Infectious Diseases Clinic, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Predrag Djurdjevic
- Department of Internal medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Clinic for Haematology, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Predrag Sazdanovic
- Department of Anatomy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Gynecology and Obstetrics Clinic, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Srdjan Stefanovic
- Department of Pharmacy, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Danijela Todorovic
- Department of Genetics, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Suzana Popovic
- Centre for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Katarina Vitosevic
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Vukicevic
- Corona Centre, University Clinical Centre Kragujevac, Kragujevac, Serbia
| | - Milena Vukic
- Department of Chemistry, Faculty of Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Nenad Vukovic
- Department of Chemistry, Faculty of Sciences, University of Kragujevac, Kragujevac, Serbia
| | - Nevena Milivojevic
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia.,Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Marko Zivanovic
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia.,Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Jakovljevic
- Department of Physiology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Deprtment of Human Pathology, 1st Moscow Medical Unuversity "I. M. Sechenov", Moscow, Russia
| | - Nenad Filipovic
- Bioengineering Research and Development Center (BioIRC), Kragujevac, Serbia.,Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia
| | - Dejan Baskic
- Centre for Molecular Medicine and Stem Cell Research, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia.,Institute of Public Health Kragujevac, Kragujevac, Serbia
| | - Natasa Djordjevic
- Department of Pharmacology and Toxicology, Faculty of Medical Sciences, University of Kragujevac, Kragujevac, Serbia
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7
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Gilson Sena IF, Fernandes LL, Lorandi LL, Santana TV, Cintra L, Lima IF, Iwai LK, Kramer JM, Birbrair A, Heller D. Identification of early biomarkers in saliva in genetically engineered mouse model C(3)1-TAg of breast cancer. Sci Rep 2022; 12:11544. [PMID: 35798767 PMCID: PMC9263110 DOI: 10.1038/s41598-022-14514-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022] Open
Abstract
Breast cancer is one of leading causes of death worldwide in the female population. Deaths from breast cancer could be reduced significantly through earlier and more efficient detection of the disease. Saliva, an oral fluid that contains an abundance of protein biomarkers, has been recognized as a promising diagnostic biofluid that is easy to isolate through non-invasive techniques. Assays on saliva can be performed rapidly and are cost-effective. Therefore, our work aimed to identify salivary biomarkers present in the initial stages of breast cancer, where cell alterations are not yet detectable by histopathological analysis. Using state-of-the-art techniques, we employed a transgenic mouse model of mammary cancer to identify molecular changes in precancerous stage breast cancer through protein analysis in saliva. Through corroborative molecular approaches, we established that proteins related to metabolic changes, inflammatory process and cell matrix degradation are detected in saliva at the onset of tumor development. Our work demonstrated that salivary protein profiles can be used to identify cellular changes associated with precancerous stage breast cancer through non-invasive means even prior to biopsy-evident disease.
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Affiliation(s)
| | | | | | | | | | - Ismael Feitosa Lima
- Laboratory of Applied Toxicology, Center of Toxins, Immune-Response and Cell Signaling (LETA/CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Leo Kei Iwai
- Laboratory of Applied Toxicology, Center of Toxins, Immune-Response and Cell Signaling (LETA/CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Jill M Kramer
- Department of Oral Biology, School of Dental Medicine, The University of Buffalo, State University of New York, Buffalo, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil. .,Department of Dermatology, Medical Sciences Center, University of Wisconsin-Madison, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
| | - Débora Heller
- Post Graduate Program in Dentistry, Cruzeiro do Sul University, São Paulo, Brazil. .,Hospital Israelita Albert Einstein, São Paulo, Brazil. .,Department of Periodontology, University of Texas Health Science Center San Antonio, San Antonio, TX, USA.
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8
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Mielonen OI, Pratas D, Hedman K, Sajantila A, Perdomo MF. Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation. Viruses 2022; 14:v14010133. [PMID: 35062338 PMCID: PMC8779449 DOI: 10.3390/v14010133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/04/2023] Open
Abstract
Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.
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Affiliation(s)
- Outi I. Mielonen
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
| | - Diogo Pratas
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Klaus Hedman
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Maria F. Perdomo
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Correspondence:
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9
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Mariya T, Sato T, Fujibe Y, Ishido M, Shimada H, Kubo T, Nagai Y, Arai W, Tanaka SE, Ashikawa K, Sakuraba Y, Ishioka S, Yokota SI, Saito T. Next-generation sequencing of 16S rRNA for identification of invasive bacterial pathogens in a formalin-fixed paraffin-embedded placental specimen: a case report of perinatal fulminant Streptococcus pyogenes infection. Med Mol Morphol 2021; 54:374-379. [PMID: 34287707 DOI: 10.1007/s00795-021-00298-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/18/2021] [Indexed: 11/27/2022]
Abstract
Intrauterine infection is one of the most important causes of maternal death. In perinatal emergency, we often miss an opportunity to obtain culture specimens. In this study, we tried to examine whether we investigated whether bacteria causing infection can be detected from a formalin-fixed paraffin-embedded (FFPE) placental specimen. We examined the placenta from a maternal invasive infection that resulted in infectious abortion at 18 weeks of gestation. The case was diagnosed by acute fever and abdominal pain, and the patient was cured after 3 weeks of intensive antimicrobial treatment. Four Streptococcus pyogenes strains were isolated from vaginal fluid and blood cultures of the patient. All of the strain types were emm1/ST28. We amplified the V1-V2 region of 16S rRNA from an FFPE placental specimen and sequencing was performed using a next-generation sequencer (NGS). Taxonomic analysis was then performed for sequenced data. We succeeded in detecting causative pathogens from the FFPE placenta: 69.1% of the predominantly identified bacteria were S. pyogenes and other small populations of bacteria were detected. Our results revealed the utility of NGS for 16S rRNA analysis of an FFPE placenta. This method may reveal previous perinatal invasive infections of unknown origin retrospectively.
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Affiliation(s)
- Tasuku Mariya
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan.
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yuya Fujibe
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Manami Ishido
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Hiroshi Shimada
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Terufumi Kubo
- Department of Pathology 1st, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | | | | | | | | | - Shinichi Ishioka
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tsuyoshi Saito
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, South 1 West 17, Chuo-ku, Sapporo, 060-8556, Japan
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10
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van Dijk MC, Kornegoor R, Mol S, Rodriguez M. Fetal and Perinatal Brain Autopsy: Useful Macroscopic Techniques Including Agar In-situ and Pre-Embedding Methods. Pediatr Dev Pathol 2021; 24:299-308. [PMID: 33734914 DOI: 10.1177/10935266211000036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fragile perinatal and fetal brains are the rule rather than the exception for developmental neuropathologists. Retrieving the fresh brain from the skull and examining early fetal, macerated or severely hydrocephalic brains after fixation can be a challenge. Textbooks on neurodevelopmental pathology mention these challenges to macroscopic examination of the developing central nervous system only in passing, but many perinatal pathologists recognize this diagnostic problem. We reviewed protocols and publications on the removal, fixation, slicing and sampling of these fetal- and perinatal brains. In addition, we describe a technique to facilitate the removal of severely hydrocephalic brains with very thin cerebral walls from the skull by replacing the intraventricular fluid with agar in-situ. Furthermore, we present a method for post-fixation pre-embedding in agar to facilitate slicing, macroscopic examination and sampling of fragile and macerated brains.
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Affiliation(s)
- Marcory Crf van Dijk
- Department of Pathology, Pathology-DNA, Rijnstate Hospital, Arnhem, the Netherlands
| | - Robert Kornegoor
- Department of Pathology, Pathology-DNA, Rijnstate Hospital, Arnhem, the Netherlands
| | - Suzanne Mol
- Department of Pathology, Pathology-DNA, Jeroen Bosch Hospital, Den Bosch, the Netherlands
| | - Michael Rodriguez
- Department of Pathology, Sydney Children's Hospital, Randwick, Australia.,Histopathology Department The Children's Hospital at Westmead, Westmead, Australia
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11
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Sena IFG, Rocha BGS, Picoli CC, Santos GSP, Costa AC, Gonçalves BOP, Garcia APV, Soltani-Asl M, Coimbra-Campos LMC, Silva WN, Costa PAC, Pinto MCX, Amorim JH, Azevedo VAC, Resende RR, Heller D, Cassali GD, Mintz A, Birbrair A. C(3)1-TAg in C57BL/6 J background as a model to study mammary tumor development. Histochem Cell Biol 2021; 156:165-182. [PMID: 34003355 DOI: 10.1007/s00418-021-01995-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2021] [Indexed: 02/06/2023]
Abstract
Diagnosis and prognosis of breast cancer is based on disease staging identified through histopathological and molecular biology techniques. Animal models are used to gain mechanistic insights into the development of breast cancer. C(3)1-TAg is a genetically engineered mouse model that develops mammary cancer. However, carcinogenesis caused by this transgene was characterized in the Friend Virus B (FVB) background. As most genetic studies are done in mice with C57BL/6 J background, we aimed to define the histological alterations in C3(1)-TAg C57BL/6 J animals. Our results showed that C3(1)-TAg animals with C57BL/6 J background develop solid-basaloid adenoid cystic carcinomas with increased fibrosis, decreased area of adipocytes, and a high proliferative index, which are triple-negative for progesterone, estrogen, and human epidermal growth factor receptor 2 (HER2) receptors. Our results also revealed that tumor development is slower in the C57BL/6 J background when compared with the FVB strain, providing a better model to study the different stages in breast cancer progression.
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Affiliation(s)
- Isadora F G Sena
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bryan O P Gonçalves
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Paula V Garcia
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maryam Soltani-Asl
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Laboratory of Neuropharmacology and Neurochemistry, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of West Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Cellular and Molecular Genetics Laboratory, Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Debora Heller
- Hospital Israelita Albert Einstein, São Paulo, Brazil.,Cruzeiro Do Sul University, São Paulo, Brazil
| | - Geovanni D Cassali
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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12
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Watanabe N, Ohno SI, Sakuma M, Kuriwaki M, Miura M, Kuroda M. A case report on death from acute bacterial cholangitis accompanied by von Meyenburg complexes: Use of 16S rRNA gene sequencing to identify pathogenic microbes from postmortem formalin-fixed, paraffin-embedded tissue. Medicine (Baltimore) 2021; 100:e25526. [PMID: 33847675 PMCID: PMC8051965 DOI: 10.1097/md.0000000000025526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/25/2021] [Indexed: 01/04/2023] Open
Abstract
RATIONALE In some cases, autopsy is the first opportunity to find a previously unrecognized critical infection. Pathogens are identified by various methods, such as microscopic examination, special stains, culture tests, and immunohistochemistry. Here, we report a case of 16S ribosomal RNA (rRNA) gene sequencing using a postmortem formalin-fixed, paraffin-embedded (FFPE) tissue, which was useful for identifying pathogenic microbes. PATIENT CONCERNS Autopsy was performed on an 87-year-old man who had chronic renal failure and had developed sepsis from a central venous catheter infection 10 days before his death. Prior to these events, von Meyenburg complexes (VMCs) were also found during regular checkups. DIAGNOSIS Postmortem microscopic examination revealed acute purulent cholangitis with numerous microabscesses, accompanied by VMCs. Gram-negative rods were observed in some microabscesses, which were considered causative pathogens. INTERVENTIONS 16S rRNA gene sequencing using postmortem FFPE tissue. OUTCOMES Pseudomonas aeruginosa was identified, different from the one detected in the central venous catheter culture while alive. LESSONS 16S rRNA gene sequencing is a useful tool for identifying pathogenic microbes in postmortem FFPE tissues. This technique may be useful for amplicon sizes of approximately 100 bp or less.
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13
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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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14
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Flores Bueso Y, Walker SP, Tangney M. Characterization of FFPE-induced bacterial DNA damage and development of a repair method. Biol Methods Protoc 2020; 5:bpaa015. [PMID: 33072872 PMCID: PMC7548031 DOI: 10.1093/biomethods/bpaa015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/15/2020] [Accepted: 07/18/2020] [Indexed: 01/13/2023] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) specimens have huge potential as source material in the field of human microbiome research. However, the effects of FFPE processing on bacterial DNA remain uncharacterized. Any effects are relevant for microbiome studies, where DNA template is often minimal and sequences studied are not limited to one genome. As such, we aimed to both characterize this FFPE-induced bacterial DNA damage and develop strategies to reduce and repair this damage. Our analyses indicate that bacterial FFPE DNA is highly fragmented, a poor template for PCR, crosslinked and bears sequence artefacts derived predominantly from oxidative DNA damage. Two strategies to reduce this damage were devised – an optimized decrosslinking procedure reducing sequence artefacts generated by high-temperature incubation, and secondly, an in vitro reconstitution of the base excision repair pathway. As evidenced by whole genome sequencing, treatment with these strategies significantly increased fragment length, reduced the appearance of sequence artefacts and improved the sequencing readability of bacterial and mammalian FFPE DNA. This study provides a new understanding of the condition of bacterial DNA in FFPE specimens and how this impacts downstream analyses, in addition to a strategy to improve the sequencing quality of bacterial and possibly mammalian FFPE DNA.
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Affiliation(s)
- Yensi Flores Bueso
- CancerResearch@UCC, University College Cork, Cork, T12 XF62, Ireland.,SynBioCentre, University College Cork, Cork, T12 XF62, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Sidney P Walker
- CancerResearch@UCC, University College Cork, Cork, T12 XF62, Ireland.,SynBioCentre, University College Cork, Cork, T12 XF62, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Mark Tangney
- CancerResearch@UCC, University College Cork, Cork, T12 XF62, Ireland.,SynBioCentre, University College Cork, Cork, T12 XF62, Ireland.,APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
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15
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De la Cruz Pino JG, Morales Mávil JE, Sánchez García ADC, Hernandez-Baltazar D. Optimized technique to extract and fix Olive ridley turtle hatchling retina for histological study. Acta Histochem 2020; 122:151592. [PMID: 32778246 DOI: 10.1016/j.acthis.2020.151592] [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: 10/02/2019] [Revised: 06/06/2020] [Accepted: 07/03/2020] [Indexed: 10/23/2022]
Abstract
The efficient extraction and fixation of a tissue allows in preserving the cytoarchitecture, chemical composition and tissue organization, which is key in physiological and histopathological studies. The main goal of this study was to establish a microsurgery technique to obtain ocular tissue and provide an optimized immersion fixation protocol based on the 10 % formalin-intraocular injection on Olive ridley sea turtle hatchlings (Lepidochelys olivacea). To evaluate this optimized technique, a histological comparison between traditional immersion and intraocular/immersion protocols was done. The eyeball were processed into five protocols: Frozen eyes (Group 1), frozen eyes immersed in 10 % formalin (Group 2), fresh eyes immersed in 10 % formalin (Group 3), fresh eyes intraocularly injected with 0.1 M phosphate buffer solution (PBS) and then immersed in 10 % formalin (Group 4), and fresh eyes fixed by 10 % formalin-intraocular followed by 10 % formalin-immersion (Group 5). In comparison with all groups evaluated, the intraocular/immersion fixation protocol lead the conservation of eyeball shape, cell integrity and maintenance of the organization of the retina layers of sea turtle hatchlings. If this method will be the key in studying sea turtle, we suppose that this procedure, with minimal adjustments, could be useful in animals with similar eye anatomy.
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16
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Flores Bueso Y, Walker SP, Hogan G, Claesson MJ, Tangney M. Protoblock - A biological standard for formalin fixed samples. MICROBIOME 2020; 8:122. [PMID: 32828122 PMCID: PMC7443293 DOI: 10.1186/s40168-020-00901-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/24/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) tissue is the gold standard in pathology tissue storage, representing the largest collections of patient material. Their reliable use for DNA analyses could open a trove of potential samples for research and are currently being recognised as a viable source material for bacterial analysis. There are several key features which limit bacterial-related data generation from this material: (i) DNA damage inherent to the fixing process, (ii) low bacterial biomass that increases the vulnerability to contamination and exacerbates the host DNA effects and (iii) lack of suitable DNA extraction methods, leading to data bias. The development and systematic use of reliable standards is a key priority for microbiome research. More than perhaps any other sample type, FFPE material urgently requires the development of standards to ensure the validity of results and to promote reproducibility. RESULTS To address these limitations and concerns, we have developed the Protoblock as a biological standard for FFPE tissue-based research and method optimisation. This is a novel system designed to generate bespoke mock FFPE 'blocks' with a cell content that is user-defined and which undergoes the same treatment conditions as clinical FFPE tissues. The 'Protoblock' features a mix of formalin-fixed cells, of known number, embedded in an agar matrix which is solidified to form a defined shape that is paraffin embedded. The contents of various Protoblocks populated with mammalian and bacterial cells were verified by microscopy. The quantity and condition of DNA purified from blocks was evaluated by qPCR, 16S rRNA gene amplicon sequencing and whole genome sequencing. These analyses validated the capability of the Protoblock system to determine the extent to which each of the three stated confounding features impacts on eventual analysis of cellular DNA present in FFPE samples. CONCLUSION The Protoblock provides a representation of biological material after FFPE treatment. Use of this standard will greatly assist the stratification of biological variations detected into those legitimately resulting from experimental conditions, and those that are artefacts of the processed nature of the samples, thus enabling users to relate the outputs of laboratory analyses to reality. Video Abstract.
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Affiliation(s)
- Yensi Flores Bueso
- CancerResearch@UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sidney P Walker
- CancerResearch@UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Glenn Hogan
- CancerResearch@UCC, University College Cork, Cork, Ireland
- SynBioCentre, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Mark Tangney
- CancerResearch@UCC, University College Cork, Cork, Ireland.
- SynBioCentre, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
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17
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Giovanoli Evack J, Schmidt RS, Boltryk SD, Voss TS, Batil AA, Ngandolo BN, Greter H, Utzinger J, Zinsstag J, Balmer O. Molecular Confirmation of a Fasciola gigantica × Fasciola hepatica Hybrid in a Chadian Bovine. J Parasitol 2020; 106:316-322. [PMID: 32330281 DOI: 10.1645/19-66] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Fascioliasis is a zoonotic infection of humans and, more commonly, ruminants. It is caused by 2 liver fluke species, Fasciola hepatica and Fasciola gigantica, which differ in size. The traditional morphological methods used to distinguish the 2 species can be unreliable, particularly in the presence of hybrids between the 2 species. The development of advanced molecular methods has allowed for more definitive identification of Fasciola species, including their hybrids. Hybrids are of concern, as it is thought that they could acquire advantageous traits such as increased pathogenicity and host range. In 2013, we collected flukes from Fasciola-positive cattle, sheep, and goats slaughtered in 4 Chadian abattoirs. DNA from 27 flukes was extracted, amplified, and analyzed to identify species using the ITS1+2 locus. Twenty-six of the 27 flukes were identified as F. gigantica, while the remaining fluke showed heterozygosity at all variable sites that distinguish F. hepatica and F. gigantica. Cloning and sequencing of both alleles confirmed the presence of 1 F. hepatica and 1 F. gigantica allele. To our knowledge, this is the first unambiguous, molecular demonstration of the presence of such a hybrid in a bovine in sub-Saharan Africa.
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Affiliation(s)
- Jennifer Giovanoli Evack
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Remo S Schmidt
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Sylwia D Boltryk
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Till S Voss
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Annour A Batil
- Institut de Recherche en Elevage pour le Développement, Boîte Postale 473, N'Djamena, Chad
| | - Bongo N Ngandolo
- Institut de Recherche en Elevage pour le Développement, Boîte Postale 473, N'Djamena, Chad
| | - Helena Greter
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Oliver Balmer
- Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland.,University of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
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18
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Formalin Fixation of Human Healthy Autopsied Tissues: The Influence of Type of Tissue, Temperature and Incubation Time on the Quality of Isolated DNA. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2020. [DOI: 10.2478/sjecr-2019-0020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Formalin fixation is a widely used method in histopathology that has certain limits. Formalin often leads to the degradation of DNA molecules in cancer tissues, which makes tissues unusable for molecular analysis. The other factors may also affect the quality of DNA isolated from fixed tissues. The aim of this study is to determine the impact of the incubation time and temperature on the quality of DNA molecules isolated from various healthy human tissues. The brain, lung and kidney tissues, excluded during the forensic autopsies of people who died of violent death, were fixed in phosphate-buffered formalin from 24h to two months. After the completion of the incubation period, the DNA was isolated using phenol-chloroform-isoamyl alcohol extraction method and the concentration and purity of the samples were determined spectrophotometrically. The degree of degradation of DNA was assessed by PCR reaction, by amplification of gene fragments which lengths were 150bp (GPD1) and 262bp (β-actin). The highest concentration, purity and preserved integrity of DNA were obtained from the brain samples. With prolonged tissue incubation times in formalin, the concentration and integrity of DNA decreased in all tissue samples, especially in the brain tissue, while the purity of DNA remained unchanged. Also, tissue fixation at +4°C contributed to a better quality of isolated DNA compared to DNA isolated from tissue fixed at room temperature. We can conclude that the type of human healthy tissue, temperature and the incubation time of formalin fixation have important influence on the concentration, purity and integrity of DNA during fixation of tissues excluded in the course of forensic autopsy.
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