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da Silva DL, Valladão R, Beraldo-Neto E, Coelho GR, Neto OBDS, Vigerelli H, Lopes AR, Hamilton BR, Undheim EAB, Sciani JM, Pimenta DC. Spatial Distribution and Biochemical Characterization of Serine Peptidase Inhibitors in the Venom of the Brazilian Sea Anemone Anthopleura cascaia Using Mass Spectrometry Imaging. Mar Drugs 2023; 21:481. [PMID: 37755094 PMCID: PMC10532579 DOI: 10.3390/md21090481] [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: 07/20/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
Sea anemones are known to produce a diverse array of toxins with different cysteine-rich peptide scaffolds in their venoms. The serine peptidase inhibitors, specifically Kunitz inhibitors, are an important toxin family that is believed to function as defensive peptides, as well as prevent proteolysis of other secreted anemone toxins. In this study, we isolated three serine peptidase inhibitors named Anthopleura cascaia peptide inhibitors I, II, and III (ACPI-I, ACPI-II, and ACPI-III) from the venom of the endemic Brazilian sea anemone A. cascaia. The venom was fractionated using RP-HPLC, and the inhibitory activity of these fractions against trypsin was determined and found to range from 59% to 93%. The spatial distribution of the anemone peptides throughout A. cascaia was observed using mass spectrometry imaging. The inhibitory peptides were found to be present in the tentacles, pedal disc, and mesenterial filaments. We suggest that the three inhibitors observed during this study belong to the venom Kunitz toxin family on the basis of their similarity to PI-actitoxin-aeq3a-like and the identification of amino acid residues that correspond to a serine peptidase binding site. Our findings expand our understanding of the diversity of toxins present in sea anemone venom and shed light on their potential role in protecting other venom components from proteolysis.
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Affiliation(s)
- Daiane Laise da Silva
- Programa de Pós-Graduação em Ciências-Toxinologia, Instituto Butantan, Av. Vital Brasil 1500, Butantã, São Paulo 05503-900, Brazil; (E.B.-N.); (G.R.C.); (H.V.); (A.R.L.)
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
- Centre for Advanced Imaging, University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Rodrigo Valladão
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
| | - Emidio Beraldo-Neto
- Programa de Pós-Graduação em Ciências-Toxinologia, Instituto Butantan, Av. Vital Brasil 1500, Butantã, São Paulo 05503-900, Brazil; (E.B.-N.); (G.R.C.); (H.V.); (A.R.L.)
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
| | - Guilherme Rabelo Coelho
- Programa de Pós-Graduação em Ciências-Toxinologia, Instituto Butantan, Av. Vital Brasil 1500, Butantã, São Paulo 05503-900, Brazil; (E.B.-N.); (G.R.C.); (H.V.); (A.R.L.)
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
| | - Oscar Bento da Silva Neto
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
| | - Hugo Vigerelli
- Programa de Pós-Graduação em Ciências-Toxinologia, Instituto Butantan, Av. Vital Brasil 1500, Butantã, São Paulo 05503-900, Brazil; (E.B.-N.); (G.R.C.); (H.V.); (A.R.L.)
- Laboratório de Genética, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil
| | - Adriana Rios Lopes
- Programa de Pós-Graduação em Ciências-Toxinologia, Instituto Butantan, Av. Vital Brasil 1500, Butantã, São Paulo 05503-900, Brazil; (E.B.-N.); (G.R.C.); (H.V.); (A.R.L.)
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
| | - Brett R. Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Eivind A. B. Undheim
- Centre for Advanced Imaging, University of Queensland, St. Lucia, QLD 4072, Australia;
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Juliana Mozer Sciani
- Laboratório de Farmacologia Molecular e Compostos Bioativos, Universidade São Francisco, Av. São Francisco de Assis, 218, São Paulo 12916-900, Brazil;
| | - Daniel Carvalho Pimenta
- Programa de Pós-Graduação em Ciências-Toxinologia, Instituto Butantan, Av. Vital Brasil 1500, Butantã, São Paulo 05503-900, Brazil; (E.B.-N.); (G.R.C.); (H.V.); (A.R.L.)
- Laboratório de Bioquímica, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil; (R.V.); (O.B.d.S.N.)
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2
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Verdes A, Taboada S, Hamilton BR, Undheim EAB, Sonoda GG, Andrade SCS, Morato E, Isabel Marina A, Cárdenas CA, Riesgo A. Evolution, expression patterns and distribution of novel ribbon worm predatory and defensive toxins. Mol Biol Evol 2022; 39:6580756. [PMID: 35512366 PMCID: PMC9132205 DOI: 10.1093/molbev/msac096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ribbon worms are active predators that use an eversible proboscis to inject venom into their prey and defend themselves with toxic epidermal secretions. Previous work on nemertean venom has largely focused on just a few species and has not investigated the different predatory and defensive secretions in detail. Consequently, our understanding of the composition and evolution of ribbon worm venoms is still very limited. Here, we present a comparative study of nemertean venom combining RNA-seq differential gene expression analyses of venom-producing tissues, tandem mass spectrometry-based proteomics of toxic secretions, and mass spectrometry imaging of proboscis sections, to shed light onto the composition and evolution of predatory and defensive toxic secretions in Antarctonemertes valida. Our analyses reveal a wide diversity of putative defensive and predatory toxins with tissue-specific gene expression patterns and restricted distributions to the mucus and proboscis proteomes respectively, suggesting that ribbon worms produce distinct toxin cocktails for predation and defense. Our results also highlight the presence of numerous lineage-specific toxins, indicating that venom evolution is highly divergent across nemerteans, producing toxin cocktails that might be finely tuned to subdue different prey. Our data also suggest that the hoplonemertean proboscis is a highly specialized predatory organ that seems to be involved in a variety of biological functions besides predation, including secretion and sensory perception. Overall, our results advance our knowledge into the diversity and evolution of nemertean venoms and highlight the importance of combining different types of data to characterize toxin composition in understudied venomous organisms.
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Affiliation(s)
- Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain.,Department of Life Sciences, Natural History Museum, London, UK
| | - Sergi Taboada
- Department of Life Sciences, Natural History Museum, London, UK.,Departament of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Brett R Hamilton
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia.,Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Gabriel G Sonoda
- Departmento de Genética e Biología Evolutiva, University of Sao Paulo, Sao Paulo, Brazil
| | - Sonia C S Andrade
- Departmento de Genética e Biología Evolutiva, University of Sao Paulo, Sao Paulo, Brazil
| | - Esperanza Morato
- CBMSO Protein Chemistry Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Isabel Marina
- CBMSO Protein Chemistry Facility, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN), CSIC, Madrid, Spain.,Department of Life Sciences, Natural History Museum, London, UK
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3
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Jensen PSH, Johansen M, Bak LK, Jensen LJ, Kjær C. Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures. Neurochem Res 2020; 46:447-454. [PMID: 33249516 DOI: 10.1007/s11064-020-03183-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 11/28/2022]
Abstract
Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental findings. Here we investigate the impact of four pre-analytical factors on brain-derived RNA: time-before-collection, tissue specimen size, tissue collection method, and RNA isolation method. We report no significant differences in RNA yield or integrity between 20 mg and 60 mg tissue samples collected in either liquid nitrogen or the RNAlater stabilizing solution. Isolation of RNA employing the TRIzol reagent resulted in a higher yield compared to isolation via the QIAcube kit while the latter resulted in RNA of slightly better integrity. Keeping brain tissue samples at room temperature for up to 160 min prior to collection and isolation of RNA resulted in no significant difference in yield or integrity. Our findings have significant practical and financial consequences for clinical genomic departments and other laboratory settings performing large-scale routine RNA expression analysis of brain samples.
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Affiliation(s)
- Pernille Søs Hovgaard Jensen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Maja Johansen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark
| | - Lasse K Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Christina Kjær
- Department of Technology, Faculty of Health and Technology, University College Copenhagen, 2200, Copenhagen, Denmark. .,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
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4
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Walker AA, Robinson SD, Hamilton BF, Undheim EAB, King GF. Deadly Proteomes: A Practical Guide to Proteotranscriptomics of Animal Venoms. Proteomics 2020; 20:e1900324. [PMID: 32820606 DOI: 10.1002/pmic.201900324] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/07/2020] [Indexed: 11/11/2022]
Abstract
Animal venoms are renowned for their toxicity, biochemical complexity, and as a source of compounds with potential applications in medicine, agriculture, and industry. Polypeptides underlie much of the pharmacology of animal venoms, and elucidating these arsenals of polypeptide toxins-known as the venom proteome or venome-is an important step in venom research. Proteomics is used for the identification of venom toxins, determination of their primary structure including post-translational modifications, as well as investigations into the physiology underlying their production and delivery. Advances in proteomics and adjacent technologies has led to a recent upsurge in publications reporting venom proteomes. Improved mass spectrometers, better proteomic workflows, and the integration of next-generation sequencing of venom-gland transcriptomes and venomous animal genomes allow quicker and more accurate profiling of venom proteomes with greatly reduced starting material. Technologies such as imaging mass spectrometry are revealing additional insights into the mechanism, location, and kinetics of venom toxin production. However, these numerous new developments may be overwhelming for researchers designing venom proteome studies. Here, the field of venom proteomics is reviewed and some practical solutions for simplifying mass spectrometry workflows to study animal venoms are offered.
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Affiliation(s)
- Andrew A Walker
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Samuel D Robinson
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Brett F Hamilton
- Centre for Microscopy and Microanalysis, The University of Queensland, St. Lucia, Queensland, 4072, Australia.,Centre for Advanced Imaging, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, Queensland, 4072, Australia.,Department of Biology, Centre for Biodiversity Dynamics, NTNU, Trondheim, 7491, Norway.,Department of Bioscience, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindern, Oslo, 0316, Norway
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia
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5
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Three-dimensional single-cell imaging for the analysis of RNA and protein expression in intact tumour biopsies. Nat Biomed Eng 2020; 4:875-888. [PMID: 32601394 DOI: 10.1038/s41551-020-0576-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/21/2020] [Indexed: 12/20/2022]
Abstract
Microscopy analysis of tumour samples is commonly performed on fixed, thinly sectioned and protein-labelled tissues. However, these examinations do not reveal the intricate three-dimensional structures of tumours, nor enable the detection of aberrant transcripts. Here, we report a method, which we name DIIFCO (for diagnosing in situ immunofluorescence-labelled cleared oncosamples), for the multimodal volumetric imaging of RNAs and proteins in intact tumour volumes and organoids. We used DIIFCO to spatially profile the expression of diverse coding RNAs and non-coding RNAs at the single-cell resolution in a variety of cancer tissues. Quantitative single-cell analysis revealed spatial niches of cancer stem-like cells, and showed that the niches were present at a higher density in triple-negative breast cancer tissue. The improved molecular phenotyping and histopathological diagnosis of cancers may lead to new insights into the biology of tumours of patients.
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6
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Gallion LA, Anttila MM, Abraham DH, Proctor A, Allbritton NL. Preserving Single Cells in Space and Time for Analytical Assays. Trends Analyt Chem 2020; 122:115723. [PMID: 32153309 PMCID: PMC7061724 DOI: 10.1016/j.trac.2019.115723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Analytical assays performed within clinical laboratories influence roughly 70% of all medical decisions by facilitating disease detection, diagnosis, and management. Both in clinical and academic research laboratories, single-cell assays permit measurement of cell diversity and identification of rare cells, both of which are important in the understanding of disease pathogenesis. For clinically utility, the single-cell assays must be compatible with the clinical workflow steps of sample collection, sample transportation, pre-analysis processing, and single-cell assay; therefore, it is paramount to preserve cells in a state that resembles that in vivo rather than measuring signaling behaviors initiated in response to stressors such as sample collection and processing. To address these challenges, novel cell fixation (and more broadly, cell preservation) techniques incorporate programmable fixation times, reversible bond formation and cleavage, chemoselective reactions, and improved analyte recovery. These technologies will further the development of individualized, precision therapies for patients to yield improved clinical outcomes.
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Affiliation(s)
- Luke A. Gallion
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew M. Anttila
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David H. Abraham
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27695, USA
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7
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Chen L, Lu Y, Li W, Ren Y, Yu M, Jiang S, Fu Y, Wang J, Peng S, Bilyk KT, Murphy KR, Zhuang X, Hune M, Zhai W, Wang W, Xu Q, Cheng CHC. The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. Gigascience 2019; 8:5304890. [PMID: 30715292 PMCID: PMC6457430 DOI: 10.1093/gigascience/giz016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/26/2018] [Accepted: 01/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background The Southern Ocean is the coldest ocean on Earth but a hot spot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation, forming >120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and the rapid expansion of the Antarctic notothenioids remain poorly understood. Results We sequenced and compared 2 notothenioid genomes—the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus mawsoni and the basal Patagonian robalo Eleginops maclovinus, representing the temperate ancestor. We detected >200 protein gene families that had expanded and thousands of genes that had evolved faster in the toothfish, with diverse cold-relevant functions including stress response, lipid metabolism, protein homeostasis, and freeze resistance. Besides antifreeze glycoprotein, an eggshell protein had functionally diversified to aid in cellular freezing resistance. Genomic and transcriptomic comparisons revealed proliferation of selcys–transfer RNA genes and broad transcriptional upregulation across anti-oxidative selenoproteins, signifying their prominent role in mitigating oxidative stress in the oxygen-rich Southern Ocean. We found expansion of transposable elements, temporally correlated to Antarctic notothenioid diversification. Additionally, the toothfish exhibited remarkable shifts in genetic programs towards enhanced fat cell differentiation and lipid storage, and promotion of chondrogenesis while inhibiting osteogenesis in bone development, collectively contributing to the achievement of neutral buoyancy and pelagicism. Conclusions Our study revealed a comprehensive landscape of evolutionary changes essential for Antarctic notothenioid cold adaptation and ecological expansion. The 2 genomes are valuable resources for further exploration of mechanisms underlying the spectacular notothenioid radiation in the coldest marine environment.
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Affiliation(s)
- Liangbiao Chen
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Lu
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Wenhao Li
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Yandong Ren
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kuming, China
| | - Mengchao Yu
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Shouwen Jiang
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Yanxia Fu
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Jian Wang
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Sihua Peng
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Kevin T Bilyk
- Department of Animal Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Katherine R Murphy
- Department of Animal Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Xuan Zhuang
- Department of Animal Biology, University of Illinois at Urbana-Champaign, IL, USA
| | - Mathias Hune
- Fundación Ictiológica, Providencia, Santiago, Chile
| | - Wanying Zhai
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Wen Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kuming, China
| | - Qianghua Xu
- Internal Research Center for Marine Bioscience (Ministry of Science and Technology), Shanghai Ocean University, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education) and International Research Center for Marine Biosciences (Ministry of Science and Technology) at Shanghai Ocean University, Shanghai, China
| | - Chi-Hing Christina Cheng
- Department of Animal Biology, University of Illinois at Urbana-Champaign, IL, USA.,Fundación Ictiológica, Providencia, Santiago, Chile
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8
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Panzacchi S, Gnudi F, Mandrioli D, Montella R, Strollo V, Merrick BA, Belpoggi F, Tibaldi E. Effects of short and long-term alcohol-based fixation on Sprague-Dawley rat tissue morphology, protein and nucleic acid preservation. Acta Histochem 2019; 121:750-760. [PMID: 31277893 DOI: 10.1016/j.acthis.2019.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 12/11/2022]
Abstract
Safety concerns on the toxic and carcinogenic effects of formalin exposure have drawn increasing attention to the search for alternative low risk fixatives for processing tissue specimens in laboratories worldwide. Alcohol-based fixatives are considered some of the most promising alternatives. We evaluated the performance of alcohol-fixed paraffin-embedded (AFPE) samples from Sprague-Dawley (SD) rats analyzing tissue morphology, protein and nucleic acid preservation after short and extremely long fixation times (up to 7 years), using formalin-fixed paraffin-embedded (FFPE) samples as a comparator fixative. Following short and long-term alcohol fixation, tissue morphology and cellular details in tissues, evaluated by scoring stained sections (Hematoxylin-Eosin and Mallory's trichrome), were optimally preserved if compared to formalin fixation. Immunoreactivity of proteins (Ki67, CD3, PAX5, CD68), evaluated by immunohistochemistry, showed satisfactory results when the fixation period did not exceed 1 year. Finally, we confirm the superiority of alcohol fixation compared to formalin, in terms of quantity of nucleic acid extracted from paraffin blocks, even after an extremely long time of alcohol fixation. Our results confirm that alcohol fixation is a suitable and safe alternative to formalin for pathological evaluations. There is a need for standardization of formalin-free methods and harmonization of diagnosis in pathology department worldwide.
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9
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The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space. Nat Med 2018; 24:1611-1624. [PMID: 30150718 DOI: 10.1038/s41591-018-0156-x] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 07/12/2018] [Indexed: 12/12/2022]
Abstract
Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the role of the epigenome in glioblastoma disease progression. Here, we present genome-scale maps of DNA methylation in matched primary and recurring glioblastoma tumors, using data from a highly annotated clinical cohort that was selected through a national patient registry. We demonstrate the feasibility of DNA methylation mapping in a large set of routinely collected FFPE samples, and we validate bisulfite sequencing as a multipurpose assay that allowed us to infer a range of different genetic, epigenetic, and transcriptional characteristics of the profiled tumor samples. On the basis of these data, we identified subtle differences between primary and recurring tumors, links between DNA methylation and the tumor microenvironment, and an association of epigenetic tumor heterogeneity with patient survival. In summary, this study establishes an open resource for dissecting DNA methylation heterogeneity in a genetically diverse and heterogeneous cancer, and it demonstrates the feasibility of integrating epigenomics, radiology, and digital pathology for a national cohort, thereby leveraging existing samples and data collected as part of routine clinical practice.
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10
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Sarot E, Carillo-Baraglioli MF, Duranthon F, Péquignot A, Pyronnet S. Assessment of alternatives to environmental toxic formalin for DNA conservation in biological specimens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:16985-16993. [PMID: 28580543 DOI: 10.1007/s11356-017-9349-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
One essential step of museum and clinical specimen preservation is immersion in a fixative fluid to prevent degradation. Formalin is the most largely used fixative, but its benefit is balanced with its toxic and carcinogenic status. Moreover, because formalin-fixation impairs nucleic acids recovery and quality, current museum wet collections and formalin-fixed, paraffin-embedded clinical samples do not represent optimal tanks of molecular information. Our study has been developed to compare formalin to two alternative fixatives (RCL2® and ethanol) in a context of molecular exploitation. Based on a unique protocol, we created mammalian fixed collections, simulated the impact of time on preservation using an artificial ageing treatment and followed the evolution of specimens' DNA quality. DNA extraction yield, purity, visual integrity and qualitative and quantitative ability to amplify the Cox1 gene were assessed. Our results show that both RCL2 and ethanol exhibit better performances than formalin. They do not impair DNA extraction yield, and more importantly, DNA alteration is delayed over the preservation step. The use of RCL2 or ethanol as fixative in biological collections may insure a better exploitation of the genetic resources they propose.
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Affiliation(s)
- Emeline Sarot
- INSERM-UMR1037, Université de Toulouse, Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer (LabEx TOUCAN), 31037, Toulouse, France
| | | | - Francis Duranthon
- Muséum d'Histoire Naturelle de Toulouse, 35 allées Jules Guesde, 31000, Toulouse, France
| | - Amandine Péquignot
- Patrimoine Locaux et Gouvernance, UMR208, Muséum national d'Histoire naturelle, 36 rue Geoffroy Saint Hilaire, 75005, Paris, France
| | - Stéphane Pyronnet
- INSERM-UMR1037, Université de Toulouse, Centre de Recherches en Cancérologie de Toulouse (CRCT), Equipe Labellisée Ligue Contre le Cancer, Laboratoire d'Excellence Toulouse Cancer (LabEx TOUCAN), 31037, Toulouse, France.
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