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Nguyen T, Camins BC, Butler DA. Taurolidine and Heparin as Catheter Lock Solution for Central Venous Catheters in Hemodialysis. Am J Ther 2024; 31:e398-e409. [PMID: 38710029 DOI: 10.1097/mjt.0000000000001736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
BACKGROUND Chronic kidney disease can lead to end-stage renal disease, and the prevalence is increasing. Many patients starting hemodialysis require central venous catheters (CVCs). Catheter-related bloodstream infections (CRBSIs) are a common complication and lead to significant morbidity and mortality. Interventions to prevent CRBSI include antimicrobial lock therapy but concern for the development of antimicrobial resistance and adverse effects. Nonantimicrobial antiseptics as catheter lock solutions have also been used. Taurolidine and heparin catheter lock solution is first approved by the Food and Drug Administration for the prevention of CRBSI in patients on hemodialysis. Taurolidine has a unique mechanism of action and favorable safety profile. MECHANISM OF ACTION, PHARMACODYNAMICS, AND PHARMACOKINETICS Taurolidine and heparin catheter lock solution have both antimicrobial and anticoagulant properties. Taurolidine is derivative of the amino acid taurine, and heparin is derived from porcine intestinal mucosa. Taurolidine not only damages microbial cell walls but also prevents the adherence of microorganisms to biological surfaces, preventing biofilm formation. Taurolidine and heparin catheter lock solution is intended to be used intraluminally within the catheter and should be aspirated. Because it is used locally, limited pharmacokinetic and pharmacodynamic data are available. CLINICAL TRIALS The LOCK-IT-100 trial is a randomized, double-blind, phase 3 study, which included 795 end-stage renal disease patients on hemodialysis with CVC. Taurolidine and heparin was compared with the control heparin alone. The results of the study showed a 71% risk reduction in CRBSI for taurolidine and heparin arm (95% confident interval, 38%-86%, P = 0.0006). Other studies have also shown that taurolidine lock solution leads to decreased CRBSI episodes. Several systematic reviews and meta-analysis consisted of taurolidine in adult, and pediatric populations also showed reduction in the incidence of CRBSIs. THERAPEUTIC ADVANCE Taurolidine and heparin lock solution represents a novel preventive strategy for those undergoing hemodialysis through a CVC by reducing the risk of CRBSI. This is significant progress because there are no other similar options available for patients for whom catheters are the only options for their life-saving treatment.
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Affiliation(s)
- Timothy Nguyen
- Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, NY
| | - Bernard C Camins
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; and
| | - David A Butler
- Department of Pharmacy Practice, Albany College of Pharmacy & Health Sciences, Albany, NY
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2
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Kobayashi G, Ito R, Taga M, Koyama K, Yano S, Endo T, Kai T, Yamamoto T, Hiratsuka T, Tsuruyama T. Proteomic profiling of FFPE specimens: Discovery of HNRNPA2/B1 and STT3B as biomarkers for determining formalin fixation durations. J Proteomics 2024; 301:105196. [PMID: 38723849 DOI: 10.1016/j.jprot.2024.105196] [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: 03/26/2024] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Recent advancements in proteomics technologies using formalin-fixed paraffin-embedded (FFPE) samples have significantly advanced biomarker discovery. Yet, the effects of varying sample preparation protocols on proteomic analyses remain poorly understood. We analyzed mouse liver FFPE samples that varied in fixatives, fixation duration, and storage temperature using LC/MS. We found that variations in fixation duration significantly affected the abundance of specific proteins, showing that HNRNPA2/B1 demonstrated a significant decrease in abundance in samples fixed for long periods, whereas STT3B exhibited a significant increase in abundance in samples fixed for long durations. These findings were supported by immunohistochemical analysis across liver, spleen, and lung tissues, demonstrating a significant decrease in the nuclear staining of HNRNPA2/B1 in long-duration acid formalin(AF)-fixed FFPE samples, and an increase in cytoplasmic staining of STT3B in long-duration neutral buffered formalin-fixed liver and lung tissues and granular staining in all long-duration AF-fixed FFPE tissue types. Similar trends were observed in the long-duration fixed HeLa cells. These results demonstrate that fixation duration critically affects the proteomic integrity of FFPE samples, emphasizing the urgent need for standardized fixation protocols to ensure consistent and reliable proteomic data. SIGNIFICANCE: The quality of FFPE samples is primarily influenced by the fixation and storage conditions. However, previous studies have mainly focused on their impact on nucleic acids and the extent to which different fixation conditions affect changes in proteins has not been evaluated. In addition, to our knowledge, proteomic research focusing on differences in formalin fixation conditions has not yet been conducted. Here, we analyzed FFPE samples with different formalin fixation and storage conditions using LC/MS and evaluated the impact of different fixation conditions on protein variations. Our study unequivocally established formalin fixation duration as a critical determinant of protein variation in FFPE specimens and successfully identified HNRNPA2/B1 and STT3B as potential biomarkers for predicting formalin fixation duration for the first time. The study findings open new avenues for quality assessment in biomedical research and diagnostics.
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Affiliation(s)
- Go Kobayashi
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Reiko Ito
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan; Department of Functions of Biological-defense Genome, Hiroshima University Graduate School, Hiroshima, Japan
| | - Masataka Taga
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Kazuaki Koyama
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Shiho Yano
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Tatsuya Endo
- Department of Physics, Graduate school of Science, Tohoku University, Miyagi, Japan
| | | | - Takushi Yamamoto
- Kyoto Applications Development Center, Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Takuya Hiratsuka
- Department of Drug Discovery Medicine, Pathology Division, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tatsuaki Tsuruyama
- Laboratory of Molecular Pathology, Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Japan; Department of Functions of Biological-defense Genome, Hiroshima University Graduate School, Hiroshima, Japan; Department of Physics, Graduate school of Science, Tohoku University, Miyagi, Japan; Department of Drug Discovery Medicine, Pathology Division, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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3
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Pruszkowska-Przybylska P, Dupont ME, Jacobsen SB, Smerup M, Tfelt-Hansen J, Morling N, Andersen JD. Evaluation of DNAmAge in paired fresh, frozen, and formalin-fixed paraffin-embedded heart tissues. PLoS One 2024; 19:e0299557. [PMID: 38718072 PMCID: PMC11078437 DOI: 10.1371/journal.pone.0299557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 05/12/2024] Open
Abstract
The continued development in methylome analysis has enabled a more precise assessment of DNA methylation, but treatment of target tissue prior to analysis may affect DNA analysis. Prediction of age based on methylation levels in the genome (DNAmAge) has gained much interest in disease predisposition (biological age estimation), but also in chronological donor age estimation in crime case samples. Various epigenetic clocks were designed to predict the age. However, it remains unknown how the storage of the tissues affects the DNAmAge estimation. In this study, we investigated the storage method impact of DNAmAge by the comparing the DNAmAge of the two commonly used storage methods, freezing and formalin-fixation and paraffin-embedding (FFPE) to DNAmAge of fresh tissue. This was carried out by comparing paired heart tissue samples of fresh tissue, samples stored by freezing and FFPE to chronological age and whole blood samples from the same individuals. Illumina EPIC beadchip array was used for methylation analysis and the DNAmAge was evaluated with the following epigenetic clocks: Horvath, Hannum, Levine, Horvath skin+blood clock (Horvath2), PedBE, Wu, BLUP, EN, and TL. We observed differences in DNAmAge among the storage conditions. FFPE samples showed a lower DNAmAge compared to that of frozen and fresh samples. Additionally, the DNAmAge of the heart tissue was lower than that of the whole blood and the chronological age. This highlights caution when evaluating DNAmAge for FFPE samples as the results were underestimated compared with fresh and frozen tissue samples. Furthermore, the study also emphasizes the need for a DNAmAge model based on heart tissue samples for an accurate age estimation.
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Affiliation(s)
| | - Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Jeong YJ, Seo MJ, Sung BH, Kim JS, Yeom SJ. Biotransformation of 2-keto-4-hydroxybutyrate via aldol condensation using an efficient and thermostable carboligase from Deinococcus radiodurans. BIORESOUR BIOPROCESS 2024; 11:9. [PMID: 38647973 PMCID: PMC10992282 DOI: 10.1186/s40643-024-00727-x] [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: 08/10/2023] [Accepted: 01/03/2024] [Indexed: 04/25/2024] Open
Abstract
The bioconversion of 4-hydroxy-2-keto acid derivatives via aldol condensation of formaldehyde and pyruvate has received substantial attention as potential source of chemicals for production of amino acids, hydroxy carboxylic acids, and chiral aldehydes. We developed an environmentally friendly biocatalyst consisting of a novel thermostable class II pyruvate aldolase from Deinococcus radiodurans with maltose-binding protein (MBP-DrADL), which has specific activity of 46.3 µmol min-1 mg-1. Surprisingly, MBP-DrADL maintained over 60% of enzyme activity for 4 days at 50 to 65 °C, we used MBP-DrADL as the best candidate enzyme to produce 2-keto-4-hydroxybutyrate (2-KHB) from formaldehyde and pyruvate via aldol condensation. The optimum reaction conditions for 2-KHB production were 50 °C, pH 8.0, 5 mM Mg2+, 100 mM formaldehyde, and 200 mM pyruvate. Under these optimized conditions, MBP-DrADL produced 76.5 mM (8.94 g L-1) 2-KHB over 60 min with a volumetric productivity of 8.94 g L-1 h-1 and a specific productivity of 357.6 mg mg-enzyme-1 h-1. Furthermore, 2-KHB production was improved by continuous addition of substrates, which produced approximately 124.8 mM (14.6 g L-1) of 2-KHB over 60 min with a volumetric productivity and specific productivity of 14.6 g L-1 h-1 and 583.4 mg mg-enzyme-1 h-1, respectively. MBP-DrADL showed the highest specific productivity for 2-KHB production yet reported. Our study provides a highly efficient biocatalyst for the synthesis of 2-KHB and lays the foundation for large-scale production and application of high-value compounds from formaldehyde.
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Affiliation(s)
- Yeon-Ju Jeong
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Min-Ju Seo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Soo-Jin Yeom
- School of Biological Sciences and Biotechnology, Graduate School, Chonnam National University, Gwangju, Republic of Korea.
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea.
- Institute of Synthetic Biology for Carbon Neutralization, Chonnam National University, Gwangju, 61186, Republic of Korea.
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5
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Arya CK, Maurya S, Ramanathan G. Insight into the metabolic pathways of Paracoccus sp. strain DMF: a non-marine halotolerant methylotroph capable of degrading aliphatic amines/amides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:125947-125964. [PMID: 38010547 DOI: 10.1007/s11356-023-30858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N,N-dimethylformamide (DMF). The work presented here elaborates on the metabolic pathways involved in the degradation of C1 compounds, many of which are well-known pollutants and toxic to the environment. Investigations on microbial growth and detection of metabolic intermediates corroborate the outcome of the functional genome analysis. Several classes of C1 compounds, such as methanol, methylated amines, aliphatic amides, and naturally occurring quaternary amines like glycine betaine, were tested as growth substrates. The detailed growth and kinetic parameter analyses reveal that P. DMF can efficiently aerobically degrade trimethylamine (TMA) and grow on quaternary amines such as glycine betaine. The results show that the mechanism for halotolerant adaptation in the presence of glycine betaine is dissimilar from those observed for conventional trehalose-mediated halotolerance in heterotrophic bacteria. In addition, a close genomic survey revealed the presence of a Co(I)-based substrate-specific corrinoid methyltransferase operon, referred to as mtgBC. This demethylation system has been associated with glycine betaine catabolism in anaerobic methanogens and is unknown in denitrifying aerobic heterotrophs. This report on an anoxic-specific demethylation system in an aerobic heterotroph is unique. Our finding exposes the metabolic potential for the degradation of a variety of C1 compounds by P. DMF, making it a novel organism of choice for remediating a wide range of possible environmental contaminants.
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Affiliation(s)
- Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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6
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Wang K, Kumar T, Wang J, Minussi DC, Sei E, Li J, Tran TM, Thennavan A, Hu M, Casasent AK, Xiao Z, Bai S, Yang L, King LM, Shah V, Kristel P, van der Borden CL, Marks JR, Zhao Y, Zurita AJ, Aparicio A, Chapin B, Ye J, Zhang J, Gibbons DL, Sawyer E, Thompson AM, Futreal A, Hwang ES, Wesseling J, Lips EH, Navin NE. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell 2023; 186:3968-3982.e15. [PMID: 37586362 DOI: 10.1016/j.cell.2023.07.024] [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: 01/08/2023] [Revised: 05/09/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.
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Affiliation(s)
- Kaile Wang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tapsi Kumar
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junke Wang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Emi Sei
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianzhuo Li
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tuan M Tran
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Hu
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anna K Casasent
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenna Xiao
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shanshan Bai
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Yang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Lorraine M King
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK
| | - Petra Kristel
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Carolien L van der Borden
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Yuehui Zhao
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amado J Zurita
- Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Aparicio
- Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Brian Chapin
- Department of Urology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Ye
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ellinor Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK
| | - Alastair M Thompson
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Jelle Wesseling
- Department of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Esther H Lips
- Department of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Nicholas E Navin
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Bioinformatics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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7
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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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8
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Dupont ME, Christiansen SN, Jacobsen SB, Kampmann ML, Olsen KB, Tfelt-Hansen J, Banner J, Morling N, Andersen JD. DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis. Sci Rep 2023; 13:2004. [PMID: 36737451 PMCID: PMC9898234 DOI: 10.1038/s41598-023-29120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue from autopsied individuals represents an important resource for investigating the DNA methylation of heart tissue of deceased individuals. The DNA quality of FFPE tissue from autopsies may be decreased, affecting the DNA methylation measurements. Therefore, inexpensive screening methods for estimating DNA quality are valuable. We investigated the correlation between the DNA quality of archived FFPE heart tissue examined with the Illumina Infinium HD FFPE QC assay (Infinium QC) and Thermo Fisher's Quantifiler Trio DNA Quantification kit (QuantifilerTrio), respectively, and the amount of usable DNA methylation data as measured by the probe detection rate (probe DR) obtained with the Illumina Infinium MethylationEPIC array. We observed a high correlation (r2 = 0.75; p < 10-11) between the QuantifilerTrio degradation index, DI, and the amount of usable DNA methylation data analysed with SeSAMe, whereas a much weaker correlation was observed between the Infinium QC and SeSAMe probe DR (r2 = 0.17; p < 0.05). Based on the results, QuantifilerTrio DI seems to predict the proportion of usable DNA methylation data analysed with the Illumina Infinium MethylationEPIC array and SeSAMe by a linear model: SeSAMe probe DR = 0.80-log10(DI) × 0.25.
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Affiliation(s)
- Mikkel E Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Steffan N Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine B Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine B Olsen
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jytte Banner
- Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Jeppe D Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Van Haver D, Dendooven A, Impens F. Proteomics-Based Analysis and Diagnosis of Formalin-Fixed Paraffin-Embedded Amyloidosis Samples. Methods Mol Biol 2023; 2718:213-233. [PMID: 37665462 DOI: 10.1007/978-1-0716-3457-8_12] [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] [Indexed: 09/05/2023]
Abstract
Amyloidosis is a group of rare pathologies characterized by abnormal folding and deposition of susceptible proteins in tissues and organs. Diagnosis of amyloidosis often relies on immunohistochemistry of formalin-fixed paraffin-embedded (FFPE) patient samples; however, dependency on antibodies for protein staining is one of the major pitfalls of this approach, especially for the detection of rare amyloidosis types. In recent years, mass spectrometry-based proteomics has emerged as a promising alternative for adequate detection and amyloid typing, despite the fact that preparing FFPE samples for proteomics remains a challenging task. Major hurdles are removal of formalin-induced protein cross-links and water-insoluble paraffin prior to mass spectrometry analysis. With the recent development of the suspension trapping protocol, enabling the use of high concentrations of SDS, these obstacles can be overcome. In this chapter, we describe the implementation of suspension trapping for FFPE sample processing and its application to analyze human amyloidosis samples, comparing a standard procedure with probe sonication with a more advanced workflow based on ultrasonication.
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Affiliation(s)
- Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- Laboratory for Experimental Medicine and Pediatrics, Antwerp University, Edegem, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB Proteomics Core, Ghent, Belgium.
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Wegat V, Fabarius JT, Sieber V. Synthetic methylotrophic yeasts for the sustainable fuel and chemical production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:113. [PMID: 36273178 PMCID: PMC9587593 DOI: 10.1186/s13068-022-02210-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/25/2022] [Indexed: 11/13/2022]
Abstract
Global energy-related emissions, in particular carbon dioxide, are rapidly increasing. Without immediate and strong reductions across all sectors, limiting global warming to 1.5 °C and thus mitigating climate change is beyond reach. In addition to the expansion of renewable energies and the increase in energy efficiency, the so-called Carbon Capture and Utilization technologies represent an innovative approach for closing the carbon cycle and establishing a circular economy. One option is to combine CO2 capture with microbial C1 fermentation. C1-molecules, such as methanol or formate are considered as attractive alternative feedstock for biotechnological processes due to their sustainable production using only CO2, water and renewable energy. Native methylotrophic microorganisms can utilize these feedstock for the production of value-added compounds. Currently, constraints exist regarding the understanding of methylotrophic metabolism and the available genetic engineering tools are limited. For this reason, the development of synthetic methylotrophic cell factories based on the integration of natural or artificial methanol assimilation pathways in biotechnologically relevant microorganisms is receiving special attention. Yeasts like Saccharomyces cerevisiae and Yarrowia lipolytica are capable of producing important products from sugar-based feedstock and the switch to produce these in the future from methanol is important in order to realize a CO2-based economy that is independent from land use. Here, we review historical biotechnological applications, the metabolism and the characteristics of methylotrophic yeasts. Various studies demonstrated the production of a broad set of promising products from fine chemicals to bulk chemicals by applying methylotrophic yeasts. Regarding synthetic methylotrophy, the deep understanding of the methylotrophic metabolism serves as the basis for microbial strain engineering and paves the way towards a CO2-based circular bioeconomy. We highlight design aspects of synthetic methylotrophy and discuss the resulting chances and challenges using non-conventional yeasts as host organisms. We conclude that the road towards synthetic methylotrophic yeasts can only be achieved through a combination of methods (e.g., metabolic engineering and adaptive laboratory evolution). Furthermore, we presume that the installation of metabolic regeneration cycles such as supporting carbon re-entry towards the pentose phosphate pathway from C1-metabolism is a pivotal target for synthetic methylotrophy.
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Affiliation(s)
- Vanessa Wegat
- grid.469831.10000 0000 9186 607XFraunhofer Institute for Interfacial Engineering and Biotechnology, Straubing branch Biocat, Schulgasse 11a, 94315 Straubing, Germany ,grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
| | - Jonathan T. Fabarius
- grid.469831.10000 0000 9186 607XFraunhofer Institute for Interfacial Engineering and Biotechnology, Straubing branch Biocat, Schulgasse 11a, 94315 Straubing, Germany
| | - Volker Sieber
- grid.469831.10000 0000 9186 607XFraunhofer Institute for Interfacial Engineering and Biotechnology, Straubing branch Biocat, Schulgasse 11a, 94315 Straubing, Germany ,grid.6936.a0000000123222966Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
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11
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Köhler SA, Brandl L, Strissel PL, Gloßner L, Ekici AB, Angeloni M, Ferrazzi F, Bahlinger V, Hartmann A, Beckmann MW, Eckstein M, Strick R. Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping. Int J Mol Sci 2022; 23:ijms231810267. [PMID: 36142180 PMCID: PMC9499321 DOI: 10.3390/ijms231810267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.
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Affiliation(s)
- Stefanie A. Köhler
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Lisa Brandl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Pamela L. Strissel
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Laura Gloßner
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Miriam Angeloni
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Veronika Bahlinger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Markus Eckstein
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Reiner Strick
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Correspondence: ; Tel.: +49-91318536671
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Biswas P, Adhikari A, Pal U, Mondal S, Mukherjee D, Ghosh R, Obaid RJ, Moussa Z, Choudhury SS, Ahmed SA, Das R, Pal SK. A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative. Front Chem 2022; 10:978668. [PMID: 36118312 PMCID: PMC9473634 DOI: 10.3389/fchem.2022.978668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.
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Affiliation(s)
- Pritam Biswas
- Department of Microbiology, St. Xavier’s College, Kolkata, India
| | - Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Rami J. Obaid
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Sudeshna Shyam Choudhury
- Department of Microbiology, St. Xavier’s College, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Saleh A. Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
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Influence of moisture content of frozen and embalmed human cadavers for identification of dentinal microcracks using micro-computed tomography. J Mech Behav Biomed Mater 2022; 133:105310. [PMID: 35696968 DOI: 10.1016/j.jmbbm.2022.105310] [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: 04/24/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 10/18/2022]
Abstract
The aim of this study was to investigate the influence of moisture content in frozen and embalmed human cadavers on the detection of dentinal microcracks using micro-computed tomography (micro-CT). The group of embalmed specimens included three mandibular and two maxillary segments each containing one tooth. The group of frozen cadavers consisted of two frozen mandibular bone-blocks with two teeth and one mandibular segment containing one tooth. The final number of teeth for each preservation method was n = 5. All specimens were scanned with eight different moisture conditions: 48 h wet, 2 h dry, 48 h wet, 24 h dry, 48 h wet, 1 wk dry, 48 h wet, 1 wk dry. Micro-CT images were screened for the presence of dentinal microcracks. Statistical analysis was performed by nonparametric analysis of variance (α = 5%). Only few microcracks were observed in wet and in 2 h dried bone-blocks with no significant differences (p = 0.63 and p = 0.23, respectively). There was a significant and steady increase of microcracks within the groups of dried specimens as follows: 2 h dry < 24 h dry < first wk dry < second wk dry (all p < 0.008). Preservation method had no significant influence on the visibility of microcracks (p = 0.98). Identification of dentinal microcracks on micro-CT images is influenced by moisture content of cadaveric bone-blocks irrespective of the preservation method.
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Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma. Diagnostics (Basel) 2022; 12:diagnostics12051219. [PMID: 35626372 PMCID: PMC9139996 DOI: 10.3390/diagnostics12051219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Recovery and amplification of nucleic acids from archived formalin-fixed tissue samples is the most developing field in retrospective genetic studies. We compared different deparaffinization methods and DNA isolation techniques, and intergroup comparisons were performed to evaluate the effectiveness of different storing methods for archival OSCC samples based on obtained mean DNA quantity, quality, and PCR amplification of the P53 gene. The study comprised 75 archival histologically diagnosed OSCC samples which were divided into Group I: Formalin-fixed paraffin-embedded tissue blocks and Group II: Long-term formalin-fixed tissue. A comparison of different deparaffinization methods showed that xylene deparaffinization is an efficient method to obtain suitable DNA. Comparing different DNA isolation techniques illustrated that the conventional phenol–chloroform method gives better integrity to DNA in contrast with the kit method. Comparison between FFPET and long-term FFT samples demonstrated that samples fixed in formalin overnight and embedded in wax yield better quality and quantity DNA in comparison with long-term samples fixed in formalin. To obtain suitable integrity of DNA, tissue samples should be stored by fixing in formalin overnight followed by preparation of paraffin tissue blocks, deparaffinization by xylene, and subjecting them to the conventional phenol–chloroform DNA isolation protocol.
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15
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Acuña Hidalgo B, Armitage SAO. Host Resistance to Bacterial Infection Varies Over Time, but Is Not Affected by a Previous Exposure to the Same Pathogen. Front Physiol 2022; 13:860875. [PMID: 35388288 PMCID: PMC8979062 DOI: 10.3389/fphys.2022.860875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Immune priming describes the phenomenon whereby after a primary pathogen exposure, a host more effectively fights a lethal secondary exposure (challenge) to the same pathogen. Conflicting evidence exists for immune priming in invertebrates, potentially due to heterogeneity across studies in the pathogen species tested, the antigen preparation for the primary exposure, and the phenotypic trait used to test for priming. To explore these factors, we injected Drosophila melanogaster with one of two bacterial species, Lactococcus lactis or Providencia burhodogranariea, which had either been heat-killed or inactivated with formaldehyde, or we injected a 1:1 mixture of the two inactivation methods. Survival and resistance (the inverse of bacterial load) were assessed after a live bacterial challenge. In contrast to our predictions, none of the primary exposure treatments provided a survival benefit after challenge compared to the controls. Resistance in the acute phase, i.e., 1 day post-challenge, separated into a lower- and higher-load group, however, neither group varied according to the primary exposure. In the chronic phase, i.e., 7 days post-challenge, resistance did not separate into two groups, and it was also unaffected by the primary exposure. Our multi-angled study supports the view that immune priming may require specific circumstances to occur, rather than it being a ubiquitous aspect of insect immunity.
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Lee M, Shin J, Kim S, Gandla S. Whey Protein Isolate Film and Laser-Ablated Textured PDMS-Based Single-Electrode Triboelectric Nanogenerator for Pressure-Sensor Application. SENSORS 2022; 22:s22062154. [PMID: 35336324 PMCID: PMC8953929 DOI: 10.3390/s22062154] [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] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/31/2022]
Abstract
The use of biopolymers for realizing economical and eco-friendly triboelectric nanogenerators (TENGs) widens the application prospects of TENGs. Herein, an animal-sourced whey protein isolate (WPI) film, processed and prepared by a simple aqueous solution preparation and drop-casting technique, is applied to demonstrate its potential use in bio-TENGs. With the addition of formaldehyde in WPI, the films result in a free-standing and flexible film, whereas the pure WPI films are difficult to handle and lack flexibility. A TENG device based on the WPI and the laser-ablated textured polydimethylsiloxane (PDMS) for pressure-sensor application were developed. The output voltage of the TENG comprising WPI increased nearly two-fold compared to the TENG without WPI. A simple single-electrode TENG device configuration was adopted so that it could be easily integrated into a wearable electronic device. Moreover, WPI film exhibited tribo-negative-like material characteristics. This study provides new insights into the development of biocompatible and eco-friendly biopolymers for various electronic devices and sensors.
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Paramasivam P, Stöter M, Corradi E, Dalla Costa I, Höijer A, Bartesaghi S, Sabirsh A, Lindfors L, Yanez Arteta M, Nordberg P, Andersson S, Baudet ML, Bickle M, Zerial M. Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining. RNA (NEW YORK, N.Y.) 2022; 28:433-446. [PMID: 34949721 PMCID: PMC8848937 DOI: 10.1261/rna.078895.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Detection of nucleic acids within subcellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is particularly important for the delivery of nucleic acid therapeutics, which depends on endocytic uptake and endosomal escape. However, the current protocols fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization, and immunostaining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels that escape detection using conventional procedures. The optimized protocol proved effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids in cultured cells.
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Affiliation(s)
- Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eloina Corradi
- Department CIBIO, University of Trento, Trento 38123, Italy
| | | | - Andreas Höijer
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Stefano Bartesaghi
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Marianna Yanez Arteta
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Peter Nordberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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Nishikaku K, Noguchi T, Murakami S, Torii Y, Kobayashi T. Molecular analysis of bovine leukemia virus in early epidemic phase in Japan using archived formalin fixed paraffin embedded histopathological specimens. J Vet Med Sci 2022; 84:350-357. [PMID: 35046241 PMCID: PMC8983278 DOI: 10.1292/jvms.21-0570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bovine leukemia virus (BLV) is an important pathogen associated with enzootic bovine leukosis. In this study, we performed PCR and sequencing analysis to characterize BLVgp51 sequences from
formalin-fixed paraffin-embedded (FFPE) specimens made from 1974 to 2000 and successfully obtained BLV proviral genome sequences from 94% of the analyzed samples. Furthermore, from these
samples, we reconstructed eight full-length and nearly full-length BLVgp51 sequences. These sequences were classified as BLV genotype 1, implying that genotype1 has already been circulating
in Japan since the 1970s. In our results, the proviral DNA was detected in the 1970s, 1980s, and 1990s in the same manner, indicating that the detection of BLV proviral genome depends on
storage conditions rather than storage period. The sequences obtained in this study provide direct insights into BLV sequences before 2000, which serves as a good calibrator for inferring
ancient BLV diversity.
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Affiliation(s)
- Kohei Nishikaku
- Department of Animal Science, Faculty of agriculture, Tokyo University of Agriculture
| | - Tatsuo Noguchi
- Department of Animal Science, Faculty of agriculture, Tokyo University of Agriculture
| | - Satoshi Murakami
- Department of Animal Science, Faculty of agriculture, Tokyo University of Agriculture
| | - Yasushi Torii
- Department of Animal Science, Faculty of agriculture, Tokyo University of Agriculture
| | - Tomoko Kobayashi
- Department of Animal Science, Faculty of agriculture, Tokyo University of Agriculture
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Griffin CP, Paul CL, Alexander KL, Walker MM, Hondermarck H, Lynam J. Postmortem brain donations vs premortem surgical resections for glioblastoma research: viewing the matter as a whole. Neurooncol Adv 2022; 4:vdab168. [PMID: 35047819 PMCID: PMC8760897 DOI: 10.1093/noajnl/vdab168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There have been limited improvements in diagnosis, treatment, and outcomes of primary brain cancers, including glioblastoma, over the past 10 years. This is largely attributable to persistent deficits in understanding brain tumor biology and pathogenesis due to a lack of high-quality biological research specimens. Traditional, premortem, surgical biopsy samples do not allow full characterization of the spatial and temporal heterogeneity of glioblastoma, nor capture end-stage disease to allow full evaluation of the evolutionary and mutational processes that lead to treatment resistance and recurrence. Furthermore, the necessity of ensuring sufficient viable tissue is available for histopathological diagnosis, while minimizing surgically induced functional deficit, leaves minimal tissue for research purposes and results in formalin fixation of most surgical specimens. Postmortem brain donation programs are rapidly gaining support due to their unique ability to address the limitations associated with surgical tissue sampling. Collecting, processing, and preserving tissue samples intended solely for research provides both a spatial and temporal view of tumor heterogeneity as well as the opportunity to fully characterize end-stage disease from histological and molecular standpoints. This review explores the limitations of traditional sample collection and the opportunities afforded by postmortem brain donations for future neurobiological cancer research.
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Affiliation(s)
- Cassandra P Griffin
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Biobank: NSW Regional Biospecimen and Research Services, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Christine L Paul
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- Priority Research Centre Cancer Research, Innovation and Translation, University of Newcastle, New South Wales, Australia
- Priority Research Centre Health Behaviour, University of Newcastle, New South Wales, Australia
| | - Kimberley L Alexander
- Neurosurgery Department, Chris O’Brien Lifehouse, Camperdown, New South Wales, Australia
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, New South Wales, Australia
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Marjorie M Walker
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Hubert Hondermarck
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Newcastle, New South Wales, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia
| | - James Lynam
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Cancer Research Alliance, University of Newcastle, Newcastle, New South Wales, Australia
- Department of Medical Oncology, Calvary Mater, Newcastle, New South Wales, Australia
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20
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Cazzato G, Caporusso C, Arezzo F, Cimmino A, Colagrande A, Loizzi V, Cormio G, Lettini T, Maiorano E, Scarcella VS, Tarantino P, Marrone M, Stellacci A, Parente P, Romita P, De Marco A, Venerito V, Foti C, Ingravallo G, Rossi R, Resta L. Formalin-Fixed and Paraffin-Embedded Samples for Next Generation Sequencing: Problems and Solutions. Genes (Basel) 2021; 12:genes12101472. [PMID: 34680867 PMCID: PMC8535326 DOI: 10.3390/genes12101472] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 02/05/2023] Open
Abstract
Over the years, increasing information has been asked of the pathologist: we have moved from a purely morphological diagnosis to biomolecular and genetic studies, which have made it possible to implement the use of molecular targeted therapies, such as anti-epidermal growth factor receptor (EGFR) molecules in EGFR-mutated lung cancer, for example. Today, next generation sequencing (NGS) has changed the approach to neoplasms, to the extent that, in a short time, it has gained a place of absolute importance and diagnostic, prognostic and therapeutic utility. In this scenario, formaldehyde-fixed and paraffin-embedded (FFPE) biological tissue samples are a source of clinical and molecular information. However, problems can arise in the genetic material (DNA and RNA) for use in NGS due to fixation, and work is being devoted to possible strategies to reduce its effects. In this paper, we discuss the applications of FFPE tissue samples in the execution of NGS, we focus on the problems arising with the use of this type of material for nucleic acid extraction and, finally, we consider the most useful strategies to prevent and reduce single nucleotide polymorphisms (SNV) and other fixation artifacts.
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Affiliation(s)
- Gerardo Cazzato
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
- Correspondence: or (G.C.); (G.I.)
| | - Concetta Caporusso
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Francesca Arezzo
- Section of Ginecology and Obstetrics, Department of Biomedical Science and Oncology (DIMO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (F.A.); (V.L.); (G.C.)
| | - Antonietta Cimmino
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Anna Colagrande
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Vera Loizzi
- Section of Ginecology and Obstetrics, Department of Biomedical Science and Oncology (DIMO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (F.A.); (V.L.); (G.C.)
| | - Gennaro Cormio
- Section of Ginecology and Obstetrics, Department of Biomedical Science and Oncology (DIMO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (F.A.); (V.L.); (G.C.)
| | - Teresa Lettini
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Eugenio Maiorano
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Vincenza Sara Scarcella
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Paola Tarantino
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Maricla Marrone
- Section of Legal Medicine, Interdisciplinary Department of Medicine, Bari Policlinico Hospital, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy; (M.M.); (A.S.)
| | - Alessandra Stellacci
- Section of Legal Medicine, Interdisciplinary Department of Medicine, Bari Policlinico Hospital, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy; (M.M.); (A.S.)
| | - Paola Parente
- UOC di Anatomia Patologica, Fondazione IRCCS Casa Sollievo Della Sofferenza, 71013 San Giovanni Rotondo, Italy;
| | - Paolo Romita
- Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy; (P.R.); (A.D.M.); (C.F.)
| | - Aurora De Marco
- Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy; (P.R.); (A.D.M.); (C.F.)
| | - Vincenzo Venerito
- Section of Reumathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy;
| | - Caterina Foti
- Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy; (P.R.); (A.D.M.); (C.F.)
| | - Giuseppe Ingravallo
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
- Correspondence: or (G.C.); (G.I.)
| | - Roberta Rossi
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
| | - Leonardo Resta
- Section of Molecular Pathology, Department of Emergency and Organ Transplantation (DETO), University of Bari “Aldo Moro”, 70124 Bari, Italy; (C.C.); (A.C.); (A.C.); (T.L.); (E.M.); (V.S.S.); (P.T.); (R.R.); (L.R.)
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21
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Löffler P. Review: Vaccine Myth-Buster - Cleaning Up With Prejudices and Dangerous Misinformation. Front Immunol 2021; 12:663280. [PMID: 34177902 PMCID: PMC8222972 DOI: 10.3389/fimmu.2021.663280] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022] Open
Abstract
Although vaccines have already saved and will continue to save millions of lives, they are under attack. Vaccine safety is the main target of criticism. The rapid distribution of false information, or even conspiracy theories on the internet has tremendously favored vaccine hesitancy. The World Health Organization (WHO) named vaccine hesitancy one of the top ten threats to global health in 2019. Parents and patients have several concerns about vaccine safety, of which the ubiquitous anxieties include inactivating agents, adjuvants, preservatives, or new technologies such as genetic vaccines. In general, increasing doubts concerning side effects have been observed, which may lead to an increasing mistrust of scientific results and thus, the scientific method. Hence, this review targets five topics concerning vaccines and reviews current scientific publications in order to summarize the available information refuting conspiracy theories and myths about vaccination. The topics have been selected based on the author's personal perception of the most frequently occurring safety controversies: the inactivation agent formaldehyde, the adjuvant aluminum, the preservative mercury, the mistakenly-drawn correlation between vaccines and autism and genetic vaccines. The scientific literature shows that vaccine safety is constantly studied. Furthermore, the literature does not support the allegations that vaccines may cause a serious threat to general human life. The author suggests that more researchers explaining their research ideas, methods and results publicly could strengthen the general confidence in science. In general, vaccines present one of the safest and most cost-effective medications and none of the targeted topics raised serious health concerns.
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Affiliation(s)
- Paul Löffler
- Institute for Environmental Sciences, University of Koblenz-Landau, Landau, Germany
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22
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Yazdi Z, Griffin MJ, Pierezan F, Eetemadi A, Shahin K, Soto E. Quantitative PCR for detection and quantification of Veronaea botryosa in fish and environmental samples. DISEASES OF AQUATIC ORGANISMS 2021; 144:175-185. [PMID: 33955855 DOI: 10.3354/dao03582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Systemic phaeohyphomycosis, aka 'fluid belly', is one of the most important emergent diseases in sturgeon Acipenser spp. aquaculture. The etiologic agent is the saprobic, dematiaceous fungus Veronaea botryosa. Effective vaccines and chemotherapeutic treatments are currently unavailable. Additionally, the fungus is a slow-growing organism, taking from 10-15 d for colonies to be observed in agar media. To this end, a specific quantitative PCR (qPCR) targeting the V. botryosa β-tubulin gene was developed and validated. The specificity of the assay to V. botryosa was initially confirmed in silico and in vivo against common fungal fish pathogens, including closely related members of the order Chaetothyriales (Exophiala spp.) and other black pigmented fungi (Alternaria spp. and Cladosporium spp.), as well as tissues from uninfected sturgeon. The assay possessed high clinical specificity (100%) and clinical sensitivity (74%) in detecting V. botryosa DNA in splenic tissues from laboratory-infected sturgeon. Using V. botryosa genomic DNA as a template, the limit of detection was equivalent to 10 conidia, and the method was found suitable for the detection of fungal DNA in fresh and formalin-fixed tissues. In addition, the presence of non-target DNA from white sturgeon did not influence assay sensitivity. The developed qPCR assay is a sensitive, specific, and rapid diagnostic method for the detection and quantification of V. botryosa DNA from white sturgeon tissues.
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Affiliation(s)
- Zeinab Yazdi
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, California 95616-5270, USA
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23
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Klaric JA, Glass DJ, Perr EL, Reuven AD, Towne MJ, Lovett ST. DNA damage-signaling, homologous recombination and genetic mutation induced by 5-azacytidine and DNA-protein crosslinks in Escherichia coli. Mutat Res 2021; 822:111742. [PMID: 33743507 DOI: 10.1016/j.mrfmmm.2021.111742] [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: 10/27/2020] [Revised: 02/01/2021] [Accepted: 03/08/2021] [Indexed: 11/29/2022]
Abstract
Covalent linkage between DNA and proteins produces highly toxic lesions and can be caused by commonly used chemotherapeutic agents, by internal and external chemicals and by radiation. In this study, using Escherichia coli, we investigate the consequences of 5-azacytidine (5-azaC), which traps covalent complexes between itself and the Dcm cytosine methyltransferase protein. DNA protein crosslink-dependent effects can be ascertained by effects that arise in wild-type but not in dcmΔ strains. We find that 5-azaC induces the bacterial DNA damage response and stimulates homologous recombination, a component of which is Dcm-dependent. Template-switching at an imperfect inverted repeat ("quasipalindrome", QP) is strongly enhanced by 5-azaC and this enhancement was entirely Dcm-dependent and independent of double-strand break repair. The SOS response helps ameliorate the mutagenic effect of 5-azaC but this is not a result of SOS-induced DNA polymerases since their induction, especially PolIV, seems to stimulate QP-associated mutagenesis. Cell division regulator SulA was also required for recovery of QP mutants induced by 5-azaC. In the absence of Lon protease, Dcm-dependent QP-mutagenesis is strongly elevated, suggesting it may play a role in DPC tolerance. Deletions at short tandem repeats, which occur likewise by a replication template-switch, are elevated, but only modestly, by 5-azaC. We see evidence for Dcm-dependent and-independent killing by 5-azaC in sensitive mutants, such as recA, recB, and lon; homologous recombination and deletion mutations are also stimulated in part by a Dcm-independent effect of 5-azaC. Whether this occurs by a different protein/DNA crosslink or by an alternative form of DNA damage is unknown.
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Affiliation(s)
- Julie A Klaric
- Department of Biology and Rosentiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, 02454-9110, United States
| | - David J Glass
- Department of Biology and Rosentiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, 02454-9110, United States
| | - Eli L Perr
- Department of Biology and Rosentiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, 02454-9110, United States
| | - Arianna D Reuven
- Department of Biology and Rosentiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, 02454-9110, United States
| | - Mason J Towne
- Department of Biology and Rosentiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, 02454-9110, United States
| | - Susan T Lovett
- Department of Biology and Rosentiel Basic Medical Sciences Research Center Brandeis University, Waltham, MA, 02454-9110, United States.
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24
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Channathodiyil P, Houseley J. Glyoxal fixation facilitates transcriptome analysis after antigen staining and cell sorting by flow cytometry. PLoS One 2021; 16:e0240769. [PMID: 33481798 PMCID: PMC7822327 DOI: 10.1371/journal.pone.0240769] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/04/2021] [Indexed: 01/07/2023] Open
Abstract
A simple method for extraction of high quality RNA from cells that have been fixed, stained and sorted by flow cytometry would allow routine transcriptome analysis of highly purified cell populations and single cells. However, formaldehyde fixation impairs RNA extraction and inhibits RNA amplification. Here we show that good quality RNA can be readily extracted from stained and sorted mammalian cells if formaldehyde is replaced by glyoxal—a well-characterised fixative that is widely compatible with immunofluorescent staining methods. Although both formaldehyde and glyoxal efficiently form protein-protein crosslinks, glyoxal does not crosslink RNA to proteins nor form stable RNA adducts, ensuring that RNA remains accessible and amenable to enzymatic manipulation after glyoxal fixation. We find that RNA integrity is maintained through glyoxal fixation, permeabilisation with methanol or saponin, indirect immunofluorescent staining and flow sorting. RNA can then be extracted by standard methods and processed into RNA-seq libraries using commercial kits; mRNA abundances measured by poly(A)+ RNA-seq correlate well between freshly harvested cells and fixed, stained and sorted cells. We validate the applicability of this approach to flow cytometry by staining MCF-7 cells for the intracellular G2/M-specific antigen cyclin B1 (CCNB1), and show strong enrichment for G2/M-phase cells based on transcriptomic data. Switching to glyoxal fixation with RNA-compatible staining methods requires only minor adjustments of most existing staining and sorting protocols, and should facilitate routine transcriptomic analysis of sorted cells.
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Affiliation(s)
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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25
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Sandoval-Monzón RS, Arévalo-Rodriguez ICK, Carrillo-Torres AA, Ruiz-García LF. Efficacy of physical and chemical treatments on the inactivation of bovine leukosis virus present in milk. Clin Exp Vaccine Res 2021; 10:52-58. [PMID: 33628755 PMCID: PMC7892945 DOI: 10.7774/cevr.2021.10.1.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/03/2022] Open
Abstract
PURPOSE The objective of the present study was to evaluate the efficacy of pasteurization, freezing, the addition of formaldehyde and peroxymonosulfate on the inactivation of the bovine leukemia virus (BLV) present in milk. MATERIALS AND METHODS A sheep bioassay was carried out in 40 sheep, which were intraperitoneally inoculated with leukocytes from milk infected by the BLV previously treated with one of the virus inactivation methods. Five study groups were evaluated: (1) control group: milk without previous treatment, (2) pasteurization group: milk treated by pasteurization, (3) freezing group: milk treated by freezing for 36 hours, (4) formaldehyde group: 0.1% formaldehyde, and (5) peroxymonosulfate group: 0.05% peroxymonosulfate. The inoculated animals were followed for 10 weeks. RESULTS At week 10 post-inoculation, all the animals (8/8) of the control group and the peroxymonosulfate group were seropositive to BLV, while no animals were seropositive (0/8) to BLV in the remaining three groups. Statistically significant differences were found between the pasteurization, freezing and formaldehyde groups with respect to the control (p<0.001) and peroxymonosulfate groups (p<0.001). CONCLUSION The results indicate that pasteurization, freezing and formaldehyde processes are efficient in inactivating the BLV and can be used in milk to prevent the transmission of the virus.
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Affiliation(s)
| | | | | | - Luis Felipe Ruiz-García
- Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Perú
- Facultad de Ciencias Veterinarias y Biológicas, Universidad Científica del Sur, Lima, Perú
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26
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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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27
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Drew SC. Aldehyde Production as a Calibrant of Ultrasonic Power Delivery During Protein Misfolding Cyclic Amplification. Protein J 2020; 39:501-508. [PMID: 33011953 DOI: 10.1007/s10930-020-09920-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2020] [Indexed: 11/30/2022]
Abstract
The protein misfolding cyclic amplification (PMCA) technique employs repeated cycles of incubation and sonication to amplify minute amounts of misfolded protein conformers. Spontaneous (de novo) prion formation and ultrasonic power level represent two potentially interrelated sources of variation that frustrate attempts to replicate results from different laboratories. We previously established that water splitting during PMCA provides a radical-rich environment leading to oxidative damage to substrate molecules as well as the polypropylene PCR tubes used for sample containment. Here it is shown that the cross-linking agent formaldehyde is generated from buffer ions that are attacked by hydroxyl radicals. In addition, free radical damage to protein, nucleic acid, lipid, and detergent molecules produces a substantial concentration of aldehydes (hundreds of micromolar). The measurement of aldehydes using the Hantzsch reaction provides a reliable and inexpensive method for measuring the power delivered to individual PMCA samples, and for calibrating the power output characteristics of an individual sonicator. The proposed method may also be used to better account for inter-assay and inter-laboratory variation in prion replication and de novo prion generation, the latter of which may correlate with aldehyde-induced cross-linking of substrate molecules.
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Affiliation(s)
- Simon C Drew
- Department of Medicine (Royal Melbourne Hospital), The University of Melbourne, Victoria, 3010, Australia. .,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland.
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28
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Komatsu T, Kubo T, Kitou R, Kawamoto N, Mase M, Yamamoto Y, Shibahara T. Inclusion body hepatitis caused by Aviadenovirus in a tropical screech owl (Megascops choliba). J Vet Med Sci 2020; 82:1341-1345. [PMID: 32684609 PMCID: PMC7538312 DOI: 10.1292/jvms.20-0316] [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] [Indexed: 11/22/2022] Open
Abstract
In 2016, tropical screech owl (Megascops choliba) (Tso) chicks were suddenly found dead in a Japanese breeding facility. We autopsied a 9-day-old Tso and discovered white spots scattered on the liver surface. Multifocal necrosis was diffused, and macrophages had infiltrated the necrotic hepatic lesions. Hepatocytes contained numerous intranuclear inclusion bodies. Immunohistochemical staining detected Adenovirus antigen only in the liver. Next, PCR and sequencing (LC536616) identified Tso Adenovirus (TsoAd). Basic Local Alignment Search Tool (BLAST) and phylogenic analyzes suggested TsoAd is an owl Aviadenovirus. Our study contributes to an improved understanding of infectious disease among captive raptors.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Chuo Livestock Hygiene Service Center, 1-306 Jizono, Miaicho, Okazaki, Aichi 444-0805, Japan
| | - Takashi Kubo
- Aichi Prefectural Chuo Livestock Hygiene Service Center, 1-306 Jizono, Miaicho, Okazaki, Aichi 444-0805, Japan
| | - Rena Kitou
- Aichi Prefectural Chuo Livestock Hygiene Service Center, 1-306 Jizono, Miaicho, Okazaki, Aichi 444-0805, Japan
| | - Naomi Kawamoto
- Aichi Prefectural Chuo Livestock Hygiene Service Center, 1-306 Jizono, Miaicho, Okazaki, Aichi 444-0805, Japan
| | - Masaji Mase
- Division of Viral Disease and Epidemiology Research, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Yu Yamamoto
- Division of Pathology and Pathophysiology, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Tomoyuki Shibahara
- Division of Pathology and Pathophysiology, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.,Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
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29
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Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins. Nat Commun 2020; 11:3128. [PMID: 32561732 PMCID: PMC7305180 DOI: 10.1038/s41467-020-16935-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/02/2020] [Indexed: 12/17/2022] Open
Abstract
Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein–protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies. Formaldehyde (FA) is a popular cross-linking reagent, but applying it for cross-linking mass spectrometry (XLMS) has been largely unsuccessful. Here, the authors show that cross-links in structured proteins are the product of two FA molecules and identify hundreds of FA cross-links by XLMS in vitro and in situ.
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30
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Detection of Tetracycline Resistance Genes in European Hedgehogs (Erinaceus europaeus) and Crested Porcupines (Hystrix cristata). J Wildl Dis 2020. [DOI: 10.7589/2019-03-068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Desmons S, Fauré R, Bontemps S. Formaldehyde as a Promising C1 Source: The Instrumental Role of Biocatalysis for Stereocontrolled Reactions. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03128] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sarah Desmons
- LCC-CNRS, Université de Toulouse, CNRS, Toulouse, France
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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Gan J, Tang FMK, Su X, Lu G, Xu J, Lee HSS, Lee KKH. microRNA-1 inhibits cardiomyocyte proliferation in mouse neonatal hearts by repressing CCND1 expression. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:455. [PMID: 31700891 DOI: 10.21037/atm.2019.08.68] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background The functions of microRNA-1 (miR-1) in cardiac hypertrophy, and cardiomyocyte differentiation have been investigated. However, the mechanism on how miR-1 could repress cardiomyocyte proliferation has not been fully elucidated. Methods We address this issue by investigating whether miR-1 affected the proliferation of neonatal cardiomyocyte and identify some of the genes targeted by miR-1. miR-1 was over-expressed in neonatal cardiomyocytes and the effect on cell cycle and growth were analyzed by flow cytometry and Brdu-incorporation assay. Relevant vectors carrying the luciferase reporter were constructed for validation of miR-1 binding to its matching sites on the 3'-untranslated region of the predicated target mRNAs. Cardiomyocytes were co-transfected with the vectors and miR-1 mimics, then luciferase reporter assay was performed. Lastly, we examined the expression of target genes in cardiomyocytes after transfection with miR-1 mimics, as well as their normal expression pattern in 2- and 13-day-old mice hearts. Results We have demonstrated that miR-1 was the most significantly upregulated miRNA in 13-day-old mouse hearts compared with 2-day-old hearts. We also showed that miR-1 could repress cardiomyocyte G1/S phase transition, proliferation and viability. IGF1 and CCND1 were identified as candidate target genes regulated by miR-1. In addition, overexpression of miR-1 could suppress the expression of these two genes at the mRNA level. It could also correspondingly inhibit CCND1 expression at the protein level but not for IGF1. Conclusions Our results suggest that miR-1 plays an important role in inhibiting cardiomyocyte proliferation in the developing neonatal mouse heart by directly suppressing the cell-cycle regulator, CCND1.
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Affiliation(s)
- Jingyi Gan
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Basic Medicine, School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Florence Mei Kuen Tang
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xianwei Su
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jing Xu
- Department of Basic Medicine, School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Henry Siu Sum Lee
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
| | - Kenneth Ka Ho Lee
- MOE Key Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Chinese University of Hong Kong-University of Southampton Joint Laboratory for Regenerative Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
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Espadinha D, Sobral RG, Mendes CI, Méric G, Sheppard SK, Carriço JA, de Lencastre H, Miragaia M. Distinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of Staphylococcus epidermidis Clonal Lineages. Front Microbiol 2019; 10:1971. [PMID: 31507574 PMCID: PMC6719527 DOI: 10.3389/fmicb.2019.01971] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Staphylococcus epidermidis is a common skin commensal that has emerged as a pathogen in hospitals, mainly related to medical devices-associated infections. Noteworthy, infection rates by S. epidermidis have the tendency to rise steeply in next decades together with medical devices use and immunocompromized population growth. Staphylococcus epidermidis population structure includes two major clonal lineages (A/C and B) that present contrasting pathogenic potentials. To address this distinction and explore the basis of increased pathogenicity of A/C lineage, we performed a detailed comparative analysis using phylogenetic and integrated pangenome-wide-association study (panGWAS) approaches and compared the lineages's phenotypes in in vitro conditions mimicking carriage and infection. Results: Each S. epidermidis lineage had distinct phenotypic signatures in skin and infection conditions and differed in genomic content. Combination of phenotypic and genotypic data revealed that both lineages were well adapted to skin environmental cues. However, they appear to occupy different skin niches, perform distinct biological functions in the skin and use different mechanisms to complete the same function: lineage B strains showed evidence of specialization to survival in microaerobic and lipid rich environment, characteristic of hair follicle and sebaceous glands; lineage A/C strains showed evidence for adaption to diverse osmotic and pH conditions, potentially allowing them to occupy a broader and more superficial skin niche. In infection conditions, A/C strains had an advantage, having the potential to bind blood-associated host matrix proteins, form biofilms at blood pH, resist antibiotics and macrophage acidity and to produce proteases. These features were observed to be rare in the lineage B strains. PanGWAS analysis produced a catalog of putative S. epidermidis virulence factors and identified an epidemiological molecular marker for the more pathogenic lineage. Conclusion: The prevalence of A/C lineage in infection is probably related to a higher metabolic and genomic versatility that allows rapid adaptation during transition from a commensal to a pathogenic lifestyle. The putative virulence and phenotypic factors associated to A/C lineage constitute a reliable framework for future studies on S. epidermidis pathogenesis and the finding of an epidemiological marker for the more pathogenic lineage is an asset for the management of S. epidermidis infections.
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Affiliation(s)
- Diana Espadinha
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Rita G Sobral
- Laboratory of Molecular Microbiology of Bacterial Pathogens, UCIBIO/REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Costa de Caparica, Portugal
| | - Catarina Inês Mendes
- Molecular Microbiology and Infection Unit, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Guillaume Méric
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, University of Bath, Bath, United Kingdom.,MRC CLIMB Consortium, Bath, United Kingdom
| | - João A Carriço
- Molecular Microbiology and Infection Unit, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.,Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, United States
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Sabbaghi A, Miri SM, Keshavarz M, Zargar M, Ghaemi A. Inactivation methods for whole influenza vaccine production. Rev Med Virol 2019; 29:e2074. [PMID: 31334909 DOI: 10.1002/rmv.2074] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/16/2019] [Accepted: 06/19/2019] [Indexed: 12/16/2022]
Abstract
Despite tremendous efforts toward vaccination, influenza remains an ongoing global threat. The induction of strain-specific neutralizing antibody responses is a common phenomenon during vaccination with the current inactivated influenza vaccines, so the protective effect of these vaccines is mostly strain-specific. There is an essential need for the development of next-generation vaccines, with a broad range of immunogenicity against antigenically drifted or shifted influenza viruses. Here, we evaluate the potential of whole inactivated vaccines, based on chemical and physical methods, as well as new approaches to generate cross-protective immune responses. We also consider the mechanisms by which some of these vaccines may induce CD8+ T-cells cross-reactivity with different strains of influenza. In this review, we have focused on conventional and novel methods for production of whole inactivated influenza vaccine. As well as chemical modification, using formaldehyde or β-propiolactone and physical manipulation by ultraviolet radiation or gamma-irradiation, novel approaches, including visible ultrashort pulsed laser, and low-energy electron irradiation are discussed. These two latter methods are considered to be attractive approaches to design more sophisticated vaccines, due to their ability to maintain most of the viral antigenic properties during inactivation and potential to produce cross-protective immunity. However, further studies are needed to validate them before they can replace traditional methods for vaccine manufacturing.
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Affiliation(s)
- Ailar Sabbaghi
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran.,Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | | | - Mohsen Keshavarz
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohsen Zargar
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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35
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O'Cathail SM, Buffa FM. Science in Focus: Bioinformatics Part 1 - Lost in Translation. Clin Oncol (R Coll Radiol) 2019; 31:337-340. [PMID: 30975523 DOI: 10.1016/j.clon.2019.03.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 02/07/2023]
Affiliation(s)
- S M O'Cathail
- CRUK/MRC Oxford Institute of Radiation Oncology, University of Oxford, Oxford, UK.
| | - F M Buffa
- Department of Oncology, University of Oxford, Oxford, UK
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Gradinaru V, Treweek J, Overton K, Deisseroth K. Hydrogel-Tissue Chemistry: Principles and Applications. Annu Rev Biophys 2019; 47:355-376. [PMID: 29792820 PMCID: PMC6359929 DOI: 10.1146/annurev-biophys-070317-032905] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past five years, a rapidly developing experimental approach has enabled high-resolution and high-content information retrieval from intact multicellular animal (metazoan) systems. New chemical and physical forms are created in the hydrogel-tissue chemistry process, and the retention and retrieval of crucial phenotypic information regarding constituent cells and molecules (and their joint interrelationships) are thereby enabled. For example, rich data sets defining both single-cell-resolution gene expression and single-cell-resolution activity during behavior can now be collected while still preserving information on three-dimensional positioning and/or brain-wide wiring of those very same neurons-even within vertebrate brains. This new approach and its variants, as applied to neuroscience, are beginning to illuminate the fundamental cellular and chemical representations of sensation, cognition, and action. More generally, reimagining metazoans as metareactants-or positionally defined three-dimensional graphs of constituent chemicals made available for ongoing functionalization, transformation, and readout-is stimulating innovation across biology and medicine.
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Affiliation(s)
- Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Jennifer Treweek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - Kristin Overton
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA;
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA; .,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California 94305, USA.,H oward Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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37
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Min Y, Cao W, Xiong Y, Si Z, Khan D, Chen L. Formaldehyde assimilation through coordination of the glyoxylate pathway and the tricarboxylic acid cycle in broad bean roots. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 138:65-79. [PMID: 30852239 DOI: 10.1016/j.plaphy.2019.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Formaldehyde (HCHO) assimilation in broad bean (Vicia faba L. cv. YD) roots was investigated using 13C-labeled HCHO followed by 13C-NMR analysis. Results revealed that H13CHO was first oxidized to H13COOH in the roots treated with 2 mM H13CHO in a time-dependent manner. Subsequently, a massive signal peak of [2, 4-13C]citrate (Cit) and a signal peak of [2, 3-13C]succinate (Su) were observed in accompany with an enhancement in the signal intensity of [3-13C]Cit. The data suggested that the glyoxylate pathway and the tricarboxylic acid (TCA) cycle functioned simultaneously in the subsequent assimilation of H13COOH. The yield of [2, 4-13C]Cit accounted for more than 80% of the total metabolites. The activity of isocitrate lyase (ICL), a key enzyme in the glyoxylate pathway, was stimulated by HCHO in a dosage-dependent manner. As a result, [2, 4-13C]Cit production was increased significantly in YD roots treated with high concentrations (4 and 6 mM) of H13CHO. Moreover, induction of the ICL activity by methanol resulted in a simultaneous elevation in the production of [2, 4-13C]Cit and [3-13C]Cit in methanol-pretreated roots under 2 mM H13CHO stress. Pretreatment of roots with cyclosporin A, which hinders the transport of 13C-enriched compounds into mitochondria, caused a notable decline in the signal peak and yield of [2, 4-13C]Cit and consequently induced a notable accumulation of [2, 3-13C]Su and an increase in the HCO3- production (generated from H13COOH oxidation) in H13CHO-treated roots. These results suggested that the glyoxylate pathway and the TCA cycle function coordinately in HCHO assimilation in broad bean roots.
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Affiliation(s)
- Yong Min
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong Campus, Chenggong, Kunming, 650500, China
| | - Wenjia Cao
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong Campus, Chenggong, Kunming, 650500, China
| | - Yun Xiong
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong Campus, Chenggong, Kunming, 650500, China
| | - Zhihao Si
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong Campus, Chenggong, Kunming, 650500, China
| | - Dawood Khan
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong Campus, Chenggong, Kunming, 650500, China
| | - Limei Chen
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong Campus, Chenggong, Kunming, 650500, China.
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Policastro RA, Zentner GE. Enzymatic methods for genome-wide profiling of protein binding sites. Brief Funct Genomics 2019; 17:138-145. [PMID: 29028882 DOI: 10.1093/bfgp/elx030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has played a central role in studying genome-wide protein binding, recent work has highlighted systematic biases in the technique that warrant technical and interpretive caution and underscore the need for orthogonal techniques to both confirm the results of ChIP-seq studies and uncover new insights not accessible to ChIP. Several such techniques, based on genetic or immunological targeting of enzymatic activity to specific genomic loci, have been developed. Here, we review the development, applications and future prospects of these methods as complements to ChIP-based approaches and as powerful techniques in their own right.
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Abstract
INTRODUCTION Among various human tissue identity testing platforms, short tandem repeat (STR) genotyping has emerged as the most powerful and cost-effective method. Beyond forensic applications, tissue identity testing has become increasingly important in modern medical practice, in areas such as diagnostic pathology. Areas covered: A brief overview of various molecular/genetic techniques for identity testing is provided. This includes restriction fragment length polymorphism, single nucleotide polymorphism array and STR genotyping by multiplex PCR. Diagnostic applications of STR genotyping are covered in greater details: genotyping diagnosis of gestational trophoblastic disease, resolving tissue specimen mislabeling or histologic contaminant or 'floaters', bone marrow engraftment/chimerism analysis and interrogation of the primary source of malignancy in patients receiving organ donation. Four clinical cases are then presented to further illustrate these important clinical applications along with discussion of the interpretation, limitations, and pitfalls of STR genotyping. Expert commentary: STR genotyping is currently the most applicable method of identity testing and has extended its role well into the practice of diagnostic pathology with novel and powerful applications beyond forensics.
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Affiliation(s)
- Ian Baine
- a Department of Pathology , Yale University School of Medicine , New Haven , CT , USA
| | - Pei Hui
- a Department of Pathology , Yale University School of Medicine , New Haven , CT , USA
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40
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Balla A, Hampel KJ, Sharma MK, Cottrell CE, Sidiropoulos N. Comprehensive Validation of Cytology Specimens for Next-Generation Sequencing and Clinical Practice Experience. J Mol Diagn 2018; 20:812-821. [DOI: 10.1016/j.jmoldx.2018.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/21/2018] [Indexed: 12/29/2022] Open
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Shishodia S, Zhang D, El-Sagheer AH, Brown T, Claridge TDW, Schofield CJ, Hopkinson RJ. NMR analyses on N-hydroxymethylated nucleobases - implications for formaldehyde toxicity and nucleic acid demethylases. Org Biomol Chem 2018; 16:4021-4032. [PMID: 29767200 PMCID: PMC5977384 DOI: 10.1039/c8ob00734a] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Formaldehyde is produced in cells by enzyme-catalysed demethylation reactions, including those occurring on N-methylated nucleic acids. Formaldehyde reacts with nucleobases to form N-hydroxymethylated adducts that may contribute to its toxicity/carcinogenicity when added exogenously, but the chemistry of these reactions has been incompletely defined. We report NMR studies on the reactions of formaldehyde with canonical/modified nucleobases. The results reveal that hydroxymethyl hemiaminals on endocyclic nitrogens, as observed with thymidine and uridine monophosphates, are faster to form than equivalent hemiaminals on exocyclic nitrogens; however, the exocyclic adducts, as formed with adenine, guanine and cytosine, are more stable in solution. Nucleic acid demethylase (FTO)-catalysed hydroxylation of (6-methyl)adenosine results in (6-hydroxymethyl)adenosine as the major observed product; by contrast no evidence for a stable 3-hydroxymethyl adduct was accrued with FTO-catalysed oxidation of (3-methyl)thymidine. Collectively, our results imply N-hydroxymethyled adducts of nucleic acid bases, formed either by reactions with formaldehyde or via demethylase catalysis, have substantially different stabilities, with some being sufficiently stable to have functional roles in disease or the regulation of nucleic acid/nucleobase activity.
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Affiliation(s)
- S. Shishodia
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - D. Zhang
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - A. H. El-Sagheer
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
- Chemistry Branch, Department of Science and Mathematics
, Faculty of Petroleum and Mining Engineering
, Suez University
,
43721 Suez
, Egypt
| | - T. Brown
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - T. D. W. Claridge
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - C. J. Schofield
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - R. J. Hopkinson
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
- Leicester Institute of Structural and Chemical Biology and Department of Chemistry
, University of Leicester
,
Henry Wellcome Building
, Lancaster Road
, Leicester
, LE1 7RH
, UK
.
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Nakagun S, Okazaki M, Toyotome T, Sugiyama N, Watanabe K, Horiuchi N, Kobayashi Y. Fatal Pulmonary and Cerebellar Zygomycosis due to Rhizomucor pusillus in a Ringed Seal (Pusa hispida). Mycopathologia 2018; 183:979-985. [PMID: 29789990 DOI: 10.1007/s11046-018-0268-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 04/25/2018] [Indexed: 11/25/2022]
Abstract
A 4-year-old captive ringed seal (Pusa hispida) was treated with subcutaneous antibacterial injections for pus exuding wounds in the skin and associated blubber following a bite attack. Three months after the incident, the animal presented nystagmus and died the following day. At necropsy, there was a 25 × 18 × 25 mm well-delineated, opaque nodular mass in the lung, besides the skin ulcers and localized areas of discoloration in the blubber correlating with the bite wound and injection sites. Histopathology of the pulmonary mass demonstrated severe eosinophilic inflammatory infiltration among numerous intralesional fungal hyphae. The hyphae were irregularly branched, broad and aseptate, consistent of zygomycosis. Magnetic resonance imaging was conducted on the head, which was initially frozen intact, revealing diffuse areas of hyperintensity in the cerebellum. Restricted histopathologic examination of the cerebellum showed severe granulomatous inflammation well spread within the neuroparenchyma, associated with abundant intralesional fungal hyphae similar to those appreciated in the pulmonary mass. Molecular analyses of the fungi in the pulmonary and cerebellar tissue identified the etiologic agent in both sites as Rhizomucor pusillus. The likely route of infection is through inhalation of R. pusillus spores or fragmented hyphae from the environment that developed into an initial pulmonary infection, becoming the source of hematogenous dissemination to the cerebellum. The skin and blubber lesions likely contributed to immunosuppression. Zygomycosis is uncommon in pinnipeds, and the present report emphasizes the importance of considering zygomycete dissemination even when the primary focus is highly confined.
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Affiliation(s)
- Shotaro Nakagun
- Laboratory of Veterinary Pathology, Obihiro University of Agriculture and Veterinary Medicine, W2-11, Inada, Obihiro, Hokkaido, 080-8555, Japan.
| | - Masako Okazaki
- Okhotsk Tokkari Center, 2 Kaiyokoen, Mombetsu, Hokkaido, 094-0031, Japan
| | - Takahito Toyotome
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, W2-11, Inada, Obihiro, Hokkaido, 080-8555, Japan
| | - Nobuki Sugiyama
- Uminonakamichi Animal Hospital, 6-2-31 Mitoma East Ward, Fukuoka, Fukuoka, 811-0201, Japan
| | - Kenichi Watanabe
- Laboratory of Veterinary Pathology, Obihiro University of Agriculture and Veterinary Medicine, W2-11, Inada, Obihiro, Hokkaido, 080-8555, Japan
| | - Noriyuki Horiuchi
- Laboratory of Veterinary Pathology, Obihiro University of Agriculture and Veterinary Medicine, W2-11, Inada, Obihiro, Hokkaido, 080-8555, Japan
| | - Yoshiyasu Kobayashi
- Laboratory of Veterinary Pathology, Obihiro University of Agriculture and Veterinary Medicine, W2-11, Inada, Obihiro, Hokkaido, 080-8555, Japan
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Wagner K, Springer B, Pires VP, Keller PM. Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture. Sci Rep 2018; 8:6964. [PMID: 29725065 PMCID: PMC5934447 DOI: 10.1038/s41598-018-25129-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/13/2018] [Indexed: 12/30/2022] Open
Abstract
The rising incidence of invasive fungal infections and the expanding spectrum of fungal pathogens makes early and accurate identification of the causative pathogen a daunting task. Diagnostics using molecular markers enable rapid identification of fungi, offer new insights into infectious disease dynamics, and open new possibilities for infectious disease control and prevention. We performed a retrospective study using clinical specimens (N = 233) from patients with suspected fungal infection previously subjected to culture and/or internal transcribed spacer (ITS) PCR. We used these specimens to evaluate a high-throughput screening method for fungal detection using automated DNA extraction (QIASymphony), fungal ribosomal small subunit (18S) rDNA RT-PCR and amplicon sequencing. Fungal sequences were compared with sequences from the curated, commercially available SmartGene IDNS database for pathogen identification. Concordance between 18S rDNA RT-PCR and culture results was 91%, and congruence between 18S rDNA RT-PCR and ITS PCR results was 94%. In addition, 18S rDNA RT-PCR and Sanger sequencing detected fungal pathogens in culture negative (N = 13) and ITS PCR negative specimens (N = 12) from patients with a clinically confirmed fungal infection. Our results support the use of the 18S rDNA RT-PCR diagnostic workflow for rapid and accurate identification of fungal pathogens in clinical specimens.
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Affiliation(s)
- K Wagner
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - B Springer
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Graz, Austria
| | - V P Pires
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - P M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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44
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Bonnet E, Moutet ML, Baulard C, Bacq-Daian D, Sandron F, Mesrob L, Fin B, Delépine M, Palomares MA, Jubin C, Blanché H, Meyer V, Boland A, Olaso R, Deleuze JF. Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples. PLoS One 2018; 13:e0195471. [PMID: 29621323 PMCID: PMC5886566 DOI: 10.1371/journal.pone.0195471] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/25/2018] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.
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Affiliation(s)
- Eric Bonnet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marie-Laure Moutet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Céline Baulard
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Florian Sandron
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Lilia Mesrob
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Bertrand Fin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marc Delépine
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marie-Ange Palomares
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Hélène Blanché
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
- LabEx GenMed, Evry, France
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
- Centre de REFérence, d’Innovation, d’eXpertise et de transfert (CREFIX), Evry, France
- * E-mail:
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45
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Wang R, Zeng Z, Guo H, Tan H, Liu A, Zhao Y, Chen L. Over-expression of the Arabidopsis formate dehydrogenase in chloroplasts enhances formaldehyde uptake and metabolism in transgenic tobacco leaves. PLANTA 2018; 247:339-354. [PMID: 28988354 DOI: 10.1007/s00425-017-2790-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2017] [Indexed: 06/07/2023]
Abstract
MAIN CONCLUSION Over-expression of AtFDH controlled by the promoter of Rubisco small subunit in chloroplasts increases formaldehyde uptake and metabolism in tobacco leaves. Our previous study showed that formaldehyde (HCHO) uptake and resistance in tobacco are weaker than in Arabidopsis. Formate dehydrogenase in Arabidopsis (AtFDH) is a key enzyme in HCHO metabolism by oxidation of HCOOH to CO2, which enters the Calvin cycle to be assimilated into glucose. HCHO metabolic mechanism in tobacco differs from that in Arabidopsis. In this study, AtFDH was over-expressed in the chloroplasts of transgenic tobacco using a light inducible promoter. 13C-NMR analysis showed that the carbon flux from H13CHO metabolism was not introduced into the Calvin cycle to produce glucose in transgenic tobacco leaves. However, the over-expression of AtFDH significantly enhanced the HCHO metabolism in transgenic leaves. Consequently, the productions of [4-13C]Asn, [3-13C]Gln, [U-13C]oxalate, and H13COOH were notably greater in transgenic leaves than in non-transformed leaves after treatment with H13CHO. The increased stomatal conductance and aperture in transgenic leaves might be ascribed to the increased yield of oxalate in the guard cells with over-expressed AtFDH in chloroplasts. Accordingly, the transgenic plants exhibited a stronger capacity to absorb gaseous HCHO. Furthermore, the higher proline content in transgenic leaves compared with non-transformed leaves under HCHO stress might be attributable to the excess formate accumulation and Gln production. Consequently, the HCHO-induced oxidative stress was reduced in transgenic leaves.
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Affiliation(s)
- Ru Wang
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China
| | - Zhidong Zeng
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China
| | - Hongxia Guo
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China
| | - Hao Tan
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China
| | - Ang Liu
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China
| | - Yan Zhao
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China
| | - Limei Chen
- Faculty of Life Science and Biotechnology, Kunming University of Science and Technology, Chenggong, Kunming, 650500, China.
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46
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Meyers C, Milici J, Robison R. UVC radiation as an effective disinfectant method to inactivate human papillomaviruses. PLoS One 2017; 12:e0187377. [PMID: 29088277 PMCID: PMC5663507 DOI: 10.1371/journal.pone.0187377] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/18/2017] [Indexed: 12/15/2022] Open
Abstract
Endocavitary ultrasound probes are part of a commonly used procedure in the clinical arena. The cavities examined, vaginal canal and cervix, anal canal, and oral cavity are all areas commonly infected with the human papillomavirus (HPV), thus making them susceptible to contamination by HPV. It has been demonstrated that these probes can remain contaminated with high-risk HPV even when approved disinfection protocols have been performed. we have previously shown that HPV is resistant to some high-level disinfectant (HLD). In our present study we analyzed efficacy of using high-level ultra-violet C (UVC) radiation against HPV16 and HPV18 using a hard-surface carrier test. Stocks of infectious authentic HPV16 and HPV18 virions were dried onto carriers with a 5% (v/v) protein soil or 4ppm hard water. Efficacy testing were performed with the automated device, Antigermix S1 device (UVC radiation at 253.7nm) and 0.55% OPA in quadruplicate with matched input, neutralization, and cytotoxicity controls. Hypochlorite was included as a positive control for viral deactivation. Infectivity was determined by the abundance (qRT-PCR) of the spliced E1^E4 transcript in infected recipient cells. The automated Antigermix S1 device showed excellent efficacy against HPV16 and HPV18 whereas OPA showed minimal efficacy. While HPV is highly resistant to OPA, high-level UVC radiation offers an effective disinfection practice for ultrasound probes. Our results suggest that healthcare facilities using endocavitary ultrasound probes need to strongly consider disinfection methods that are effective against HPV.
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Affiliation(s)
- Craig Meyers
- Department of Microbiology and Immunology, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
- * E-mail:
| | - Janice Milici
- Department of Microbiology and Immunology, Pennsylvania State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Richard Robison
- Department of Microbiology & Molecular Biology, Brigham Young University, Provo, Utah, United States of America
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47
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Comparison of different methods for repairing damaged DNA from buffered and unbuffered formalin-fixed tissues. Int J Legal Med 2017; 132:675-681. [DOI: 10.1007/s00414-017-1666-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
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48
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Watanabe M, Hashida S, Yamamoto H, Matsubara T, Ohtsuka T, Suzawa K, Maki Y, Soh J, Asano H, Tsukuda K, Toyooka S, Miyoshi S. Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods. Exp Ther Med 2017; 14:2683-2688. [PMID: 28962212 DOI: 10.3892/etm.2017.4797] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/14/2017] [Indexed: 12/12/2022] Open
Abstract
Techniques for the extraction and use of nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissues, preserved over long time periods in libraries, have been developed. However, DNA extracted from FFPE tissues is generally damaged, and long-term storage may affect DNA quality. Therefore, it is important to elucidate the effect of long-term storage on FFPE tissues and evaluate the techniques used to extract DNA from them. In the present study, the yield, purity, and integrity of DNA in FFPE tissue samples was evaluated. Two DNA extraction techniques were used: A silica-binding DNA collection method using QIAamp DNA FFPE Tissue kit (QIA) and a total tissue DNA collection method using a WaxFree DNA extraction kit (WAX). A total of 25 FFPE tissues from lung adenocarcinomas were studied, which had been surgically resected and fixed at Okayama University Hospital prior to examination and subsequent storage at room temperature for 0.5, 3, 6, 9 and 12 years. Extracted DNA was quantified using ultraviolet absorbance, fluorescent dye, and quantitative polymerase chain reaction (qPCR). The quality of the DNA was defined by the absorbance ratio of 260 to 280 nm (A260/280) and Q-score, which is the quantitative value of qPCR product size ratio. The results demonstrated that the yield of total DNA extracted using WAX was significantly greater than when QIA was used (P<0.01); however, DNA extracted using WAX included more contaminants and was significantly more fragmented compared with DNA extracted using QIA (P<0.01). Aging had no significant effect on absolute DNA yield or DNA purity, although it did significantly contribute to increased DNA degradation for both QIA and WAX extraction (QIA P=0.02, WAX P=0.03; 0.5 years vs. 3 years, QIA P<0.01, WAX P=0.03; 9 years vs. 12 years). Both extraction methods are viable depending on whether high yield or high quality of extracted DNA is required. However, due to the increased degradation with age, storage time limits the available DNA in FFPE tissues regardless of the extraction method.
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Affiliation(s)
- Mototsugu Watanabe
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shinsuke Hashida
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan.,Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Hiromasa Yamamoto
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Takehiro Matsubara
- Okayama University Hospital Biobank, Okayama University Hospital, Okayama 700-8558, Japan
| | - Tomoaki Ohtsuka
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Ken Suzawa
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yuho Maki
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Junichi Soh
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Hiroaki Asano
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Kazunori Tsukuda
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shinichi Toyooka
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan.,Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shinichiro Miyoshi
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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49
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Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2017; 19:341-365. [PMID: 28341590 DOI: 10.1016/j.jmoldx.2017.01.011] [Citation(s) in RCA: 425] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics. The recommendations emphasize the role of laboratory director in using an error-based approach that identifies potential sources of errors that may occur throughout the analytical process and addressing these potential errors through test design, method validation, or quality controls so that no harm comes to the patient. The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results.
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Affiliation(s)
- Lawrence J Jennings
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois.
| | - Maria E Arcila
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Corless
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Pathology and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Suzanne Kamel-Reid
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ira M Lubin
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Pfeifer
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Washington University School of Medicine, St. Louis, Missouri
| | | | - Karl V Voelkerding
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Marina N Nikiforova
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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50
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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