A Critical Evaluation of the PAXgene Tissue Fixation System

Mathieson, William; Marcon, Nathalie; Antunes, Laurent; Ashford, David A.; Betsou, Fay; Frasquilho, Sónia; Kofanova, Olga; McKay, Siobhan C.; Pericleous, Stephanos; Smith, Colleen; Unger, Kristian; Zeller, Constanze; Thomas, Geraldine

doi:10.1093/ajcp/aqw023

Cited by 39 publications

(37 citation statements)

References 45 publications

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“…Prospectively-collected tissues were fixed in PAXgene, which preserves RNA integrity as well as tissue architecture after embedding in paraffin, and these samples were used for RNA isolation (21). Informed consent was given by all patients, and all samples were de-identified per institutional policies.…”

Section: Methodsmentioning

confidence: 99%

Gleason Score 7 Prostate Cancers Emerge through Branched Evolution of Clonal Gleason Pattern 3 and 4

Sowalsky

Kissick

Gerrin

et al. 2017

Clinical Cancer Research

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Purpose The molecular features that account for the distinct histology and aggressive biological behavior of Gleason pattern 4 (Gp4) versus Gp3 prostate cancer (PCa), and whether Gp3 tumors progress directly to Gp4, remain to be established. Experimental Design Whole exome sequencing and transcriptome profiling of laser-capture microdissected adjacent Gp3 and cribiform Gp4 were used to determine the relationship between these entities. Results Sequencing confirmed that adjacent Gp3 and Gp4 were clonal based on multiple shared genomic alterations. However, large numbers of unique mutations in the Gp3 and Gp4 tumors showed that the Gp4 were not derived directly from the Gp3. Remarkably, the Gp3 tumors retain their indolent appearing morphology despite acquisition of multiple genomic alterations including tumor suppressor losses. Although there were no consistent genomic alterations that distinguished Gp3 from Gp4, pairwise transcriptome analyses identified increased c-Myc and decreased p53 activity in Gp4 versus adjacent clonal Gp3 foci. Conclusions These findings establish that at least a subset of Gp3 and aggressive Gp4 tumors have a common origin, and support a branched evolution model wherein the Gp3 and Gp4 tumors emerge early from a common precursor and subsequently undergo substantial divergence. Genomic alterations detectable in the Gp3 may distinguish these tumors from truly indolent Gp3. Screening for a panel of these genomic alterations in men who have prostate biopsies showing only Gp3 (Gleason score 6, Gs6) may allow for more precise selection of men who can be safely managed by active surveillance versus those who may benefit from further intervention.

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Section: Methodsmentioning

confidence: 99%

Gleason Score 7 Prostate Cancers Emerge through Branched Evolution of Clonal Gleason Pattern 3 and 4

Sowalsky

Kissick

Gerrin

et al. 2017

Clinical Cancer Research

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“…Ethanol is a frequently used tissue fixative [2,3]. The combination of ethanol with other fixatives has advantage to preserve the integrity of nucleic acids [2,[4][5][6]12] while improving the visibility of antigens [6].…”

Section: Discussionmentioning

confidence: 99%

“…Ethanol is a commonly used fixative and it can be used alone [2,3] or in combination with other fixatives [2,[4][5][6]. Fixation of the inner layers of tissues depends on the ability of the fixative to diffuse into the tissues.…”

Section: Introductionmentioning

confidence: 99%

The concentration of ethanol affects its penetration rate in bovine cardiac and hepatic tissues

Dunster-Jones

Steicke

Mackie

et al. 2018

Folia Histochem Cytobiol.

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Introduction. Ethanol is a commonly used fixative. Fixation of the inner layers of the tissue depends on the ability of the fixative to diffuse into the tissue. It is unknown whether the concentration of ethanol affects its penetration into tissues. This study aimed to compare the penetration rates of 50% and 100% ethanol into bovine heart and liver tissues. Materials and methods. The penetration distance and tissue shrinkage or expansion were measured by analysing the digital images of the heart and liver tissues before and after immersion in ethanol at 20°C for 2, 6, 24 or 30 hours. The penetration coefficients were calculated as the slope of the regression line using the linear regression function between the penetration distance and square root of fixation time. Differences in tissue shrinkage or expansion and penetration distance at various time points between the two concentrations of ethanol were analysed using a mixed design ANOVA followed by Bonferroni's post-hoc test. Results. The penetration distance of 100% ethanol was significantly greater in both heart and liver tissues compared with that of 50% ethanol (n = 4, p < 0.05 for both). 100% ethanol shrank immersed liver tissue significantly more than 50% ethanol (p = 0.002), but the shrinkage of the heart tissue caused by two concentrations of ethanol did not significantly differ (p = 0.054). The greater penetration distance of 100% over 50% ethanol remained unchanged after normalising the penetration distance to the individual tissue's shrinkage (n = 4, p < 0.001). The mean penetration coefficient of 100% ethanol was significantly greater than 50% ethanol in the heart tissue (0.906 vs. 0.442, p = 0.003) and in the liver tissue (0.988 vs. 0.622, p = 0.028). Conclusions. It was proven that in two types of tissue that substantially differ in histological structures, 100% ethanol penetrated tissue significantly faster than 50% ethanol.

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“…In aquatic animal monitoring, tissues for microscopic analyses are generally fixed in the field using formalin-based fixatives. Neutral-buffered formalin is the preservation of choice within the medical and research communities due to the excellent preservation of morphology, ability for long periods of storage with few artifacts, minimal tissue shrinkage, ease of storage of paraffin-embedded blocks, and cost-effectiveness (Mathieson et al 2016). Zinc-based fixatives, such as Z-fix™ (Anatech LTD, Battle Creek, MI), are still formalin-based and share the same advantages but have been shown to improve the preservation of nucleic acids and proteins in human tissues (Wester et al 2003).…”

Section: Introductionmentioning

confidence: 99%

“…PAXgene, another tissue fixative, was created to eliminate the effects of cross-linking and to improve nucleic acid integrity for downstream molecular analyses (Viertier et al 2012). It is a two-step/two reagent process in which tissues are first placed in fixative for 2-4 hours and then in a stabilization reagent (Mathieson et al 2016). For mammalian tissues PAXgene-fixed paraffin embedded tissue sections are comparable to FFPE for morphologic quality and provides good quality RNA from paraffin-embedded tissue (Mathieson et al 2016;Staff et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Application of Molecular Pathology Techniques to Understand Mechanisms of Disease in Smallmouth Bass

Walsh¹

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In the Chesapeake Bay drainage, smallmouth bass Micropterus dolomieu are used as an indicator species of estrogenic contaminant exposure and have been implicated in fish kills and disease since 2005. In the Potomac River drainage, adult smallmouth bass have experienced mortality and disease and males have a high prevalence of intersex (testicular oocytes). Conversely, in the Susquehanna River drainage mortalities and disease of young-of-the-year smallmouth bass (YOY SMB) have occurred and resulted in a population shift to older and larger fish. The exact cause of these events remains unknown; however, factors such as poor water quality, contaminants, pathogens and parasites, increased temperatures, and nutrification have been assessed. In order to address this issue, the USGS Fish Health Branch, Leetown Science Center, and West Virginia Cooperative Fish and Wildlife Research Unit have ongoing assessment and monitoring projects throughout the Chesapeake Bay watershed. The use of routine histopathology has provided guidance for further research with molecular endpoints that may help explain the mechanisms involved in disease in smallmouth bass. The purpose of this dissertation research was to: 1.) Identify the prevalence of coinfections and risk factors of disease in YOY SMB; 2.) Use in situ hybridization to identify coinfections of bacteria with the myxozoan parasite Myxobolus inornatus in YOY smallmouth bass; 3.) Model liver helminths and coinfections of YOY SMB with land use at two spatial scales; 4.) Develop laser capture microdissection methods for nucleic acid extractions which could be used with smallmouth bass tissues; and 5.) Utilize Next-Generation Sequencing to develop a partial testes transcriptome to identify molecular markers that may help explain intersex development in male smallmouth bass. would like to thank the many people who have helped in the laboratory and in the field including Kathy Spring,

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A Critical Evaluation of the PAXgene Tissue Fixation System

Abstract: While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.

Cited by 39 publications

References 45 publications

Gleason Score 7 Prostate Cancers Emerge through Branched Evolution of Clonal Gleason Pattern 3 and 4

Gleason Score 7 Prostate Cancers Emerge through Branched Evolution of Clonal Gleason Pattern 3 and 4

The concentration of ethanol affects its penetration rate in bovine cardiac and hepatic tissues

Application of Molecular Pathology Techniques to Understand Mechanisms of Disease in Smallmouth Bass

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