scholarly journals Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Leah C. Wehmas ◽  
Susan D. Hester ◽  
Charles E. Wood
Keyword(s):  
Formalin Fixation ◽  
Tissue Samples ◽  
Archival Tissue

scholarly journals Influence of prolonged formalin fixation of tissue samples on the sensitivity of chromogenic in situ hybridization

2011 ◽  
Vol 23 (6) ◽  
pp. 1212-1216 ◽  
Author(s):  
Meike M. Mostegl ◽  
Barbara Richter ◽  
Nora Dinhopl ◽  
Herbert Weissenböck
Keyword(s):  
In Situ Hybridization ◽  
Nucleic Acid ◽  
Signal Intensity ◽  
Formalin Fixation ◽  
Proteinase K ◽  
Cross Linking ◽  
Fixation Time ◽  
Tissue Samples ◽  
Chromogenic In Situ Hybridization

Chromogenic in situ hybridization (ISH) is a commonly used tool in diagnostic pathology to detect pathogens in formalin-fixed, paraffin-embedded (FFPE) tissue sections. Prolonged formalin fixation time was identified to be a limiting factor for the successful detection of nucleic acid from different pathogens, most probably due to the cross-linking activity of formalin between RNA, DNA, and proteins. Therefore, in the current study, the influence of formalin fixation time on ISH signal intensity of 2 viral ( Porcine circovirus-2 [PCV-2] and Porcine respiratory and reproductive virus [PRRSV]) and 2 protozoal agents ( Cryptosporidium serpentis and Tritrichomonas sp.) was evaluated. Tissue samples were fixed in 7% neutral buffered formaldehyde solution, and at defined intervals, pieces were embedded in paraffin wax and subjected to pathogen-specific ISH. For all 4 pathogens, the signal intensity remained comparable with the starting ISH signal for different periods of fixation (PCV-2: 6 weeks, PRRSV: 23 weeks, C. serpentis: 55 weeks, Tritrichomonas sp.: 53 weeks). Thereafter, the signal started to decline until loss of nucleic acid detection. The influence of increased proteinase K concentrations for inverting the formalin-induced cross-linking activity was examined compared with the standard protocol. With all 4 infectious agents, a 4-fold proteinase K concentration restored the ISH signals to a level comparable with 1 day of fixation. In conclusion, the influence of prolonged formalin fixation on the intensity of detected ISH signal highly depends on the analyzed infectious agent and the pretreatment protocol.

Immunoelectron microscopic localization of elastic tissue components in archival tissue samples

1991 ◽  
Vol 162 (3) ◽  
pp. 355-367 ◽  
Author(s):  
Joseph C. Fanning ◽  
Jacinta F. White ◽  
Roman Polewski ◽  
Edward G. Cleary
Keyword(s):  
Elastic Tissue ◽  
Tissue Samples ◽  
Archival Tissue ◽  
Microscopic Localization

A method to isolate DNA from small archival tissue samples for p53 gene analysis

1993 ◽  
Vol 2 (2) ◽  
pp. 123-126 ◽  
Author(s):  
Elizabeth L. Schubert ◽  
Farideh Z. Bischoff ◽  
Laura L. Whitaker ◽  
Lisa M. Pleasants ◽  
Marc F. Hansen
Keyword(s):  
P53 Gene ◽  
Gene Analysis ◽  
Tissue Samples ◽  
Archival Tissue

Effect of formalin fixation on thermal conductivity of the biological tissue

2014 ◽  
Author(s):  
Steven C. Bauserman ◽  
Jonathan W. Valvano
Keyword(s):  
Thermal Conductivity ◽  
Biological Tissues ◽  
Formalin Fixation ◽  
Fatty Tissue ◽  
Fresh Tissue ◽  
Fixed Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Tissue ◽  
Formalin Fixed

Effect of formalin fixation on thermal conductivity of the biological tissues is presented. A self-heated thermistor probe was used to measure the tissue thermal conductivity. The thermal conductivity of muscle and fatty tissue samples was measured before the formalin fixation and then 27 hours after formalin fixation. The results indicate that the formalin fixation does not cause a significant change in the tissue thermal conductivity of muscle and fatty tissues. In the clinical setting, tissues removed surgically are often fixed in formalin for subsequent pathological analysis. These results suggest that, in terms of thermal properties, it is equally appropriate to perform in vitro studies in either fresh tissue or formalin-fixed tissue.

scholarly journals Will PAXgene substitute formalin? A morphological and molecular comparative study using a new fixative system

2012 ◽  
Vol 66 (2) ◽  
pp. 124-135 ◽  
Author(s):  
Benedetta Belloni ◽  
Chiara Lambertini ◽  
Paolo Nuciforo ◽  
Jay Phillips ◽  
Eric Bruening ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Mutational Analysis ◽  
Staining Intensity ◽  
Formalin Fixation ◽  
Pathology Laboratory ◽  
Tissue Samples ◽  
Dna And Rna ◽  
Immunohistochemical Markers ◽  
Fresh Frozen ◽  
Ffpe Tissues

Formalin fixation and paraffin embedding present the standard procedures for conserving clinical tissues for histological analysis. However, molecular analysis is impaired by the cross linking properties of formalin. The PAXgene tissue system (PreAnalytix, Switzerland) is a new formalin-free tissue collection device.AimsIn this study we aimed to evaluate this new tissue preservation technique in comparison with formalin fixation and fresh frozen tissue samples.Methods12 melanoma biopsy samples were divided and fixed simultaneously with formalin, PAXgene or fresh frozen in liquid nitrogen and analysed with regard to morphology, immunohistochemistry,  DNA and RNA content and quality. Markers of melanocytic differentiation and tumour cell proliferation were used.ResultsMorphology was well preserved in PAXPE samples. However, 5 out of 11 immunohistochemical markers showed significantly lower overall staining and staining intensity with PAXPE tissues in comparison with formalin-fixed, paraffin-embedded (FFPE). Increasing membrane permeability through adding a detergent did proportionally increase staining intensity in PAXPE samples. Amplification of different mRNA amplicons showed a direct relationship with the size of the amplicon with greater template integrity observed in PAXPE samples. Sequencing and mutational analysis of DNA samples were comparable for all the different fixation methods, while the level of DNA fragmentation seemed to be lower in PAXPE compared with FFPE tissues.ConclusionsThe switch from formalin to PAXgene fixation would require a re-evaluation of immunohistochemical markers and staining procedures originally developed for FFPE tissues. Our data demonstrate that PAXPE fixation offers some advantages concerning molecular analysis. However, these advantages would not justify substituting formalin fixation in any routine pathology laboratory.

scholarly journals Formalin Fixation of Human Healthy Autopsied Tissues: The Influence of Type of Tissue, Temperature and Incubation Time on the Quality of Isolated DNA

2019 ◽  
Vol 0 (0) ◽  
Author(s):  
Danijela Todorovic ◽  
Katarina Vitosevic ◽  
Milos Todorovic ◽  
Zivana Slovic
Keyword(s):  
Incubation Time ◽  
Formalin Fixation ◽  
Tissue Temperature ◽  
Dna Molecules ◽  
Healthy Human ◽  
Tissue Samples ◽  
The Impact ◽  
The Brain ◽  
Integrity Of Dna

Abstract Formalin fixation is a widely used method in histopathology that has certain limits. Formalin often leads to the degradation of DNA molecules in cancer tissues, which makes tissues unusable for molecular analysis. The other factors may also affect the quality of DNA isolated from fixed tissues. The aim of this study is to determine the impact of the incubation time and temperature on the quality of DNA molecules isolated from various healthy human tissues. The brain, lung and kidney tissues, excluded during the forensic autopsies of people who died of violent death, were fixed in phosphate-buffered formalin from 24h to two months. After the completion of the incubation period, the DNA was isolated using phenol-chloroform-isoamyl alcohol extraction method and the concentration and purity of the samples were determined spectrophotometrically. The degree of degradation of DNA was assessed by PCR reaction, by amplification of gene fragments which lengths were 150bp (GPD1) and 262bp (β-actin). The highest concentration, purity and preserved integrity of DNA were obtained from the brain samples. With prolonged tissue incubation times in formalin, the concentration and integrity of DNA decreased in all tissue samples, especially in the brain tissue, while the purity of DNA remained unchanged. Also, tissue fixation at +4°C contributed to a better quality of isolated DNA compared to DNA isolated from tissue fixed at room temperature. We can conclude that the type of human healthy tissue, temperature and the incubation time of formalin fixation have important influence on the concentration, purity and integrity of DNA during fixation of tissues excluded in the course of forensic autopsy.

scholarly journals In-silico performance, validation, and modeling of the Nanostring Banff Human Organ transplant gene panel using archival data from human kidney transplants

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
R. N. Smith
Keyword(s):  
Gene Expression ◽  
Microarray Data ◽  
In Silico ◽  
Organ Transplant ◽  
Human Kidney ◽  
Gene Panel ◽  
Gene Expressions ◽  
Tissue Samples ◽  
Human Organ ◽  
Archival Tissue

Abstract Background RNA gene expression of renal transplantation biopsies is commonly used to identify the immunological patterns of graft rejection. Mostly done with microarrays, seminal findings defined the patterns of gene sets associated with rejection and non-rejection kidney allograft diagnoses. To make gene expression more accessible, the Molecular Diagnostics Working Group of the Banff Foundation for Allograft Pathology and NanoString Technologies partnered to create the Banff Human Organ Transplant Panel (BHOT), a gene panel set of 770 genes as a surrogate for microarrays (~ 50,000 genes). The advantage of this platform is that gene expressions are quantifiable on formalin fixed and paraffin embedded archival tissue samples, making gene expression analyses more accessible. The purpose of this report is to test in silico the utility of the BHOT panel as a surrogate for microarrays on archival microarray data and test the performance of the modelled BHOT data. Methods BHOT genes as a subset of genes from downloaded archival public microarray data on human renal allograft gene expression were analyzed and modelled by a variety of statistical methods. Results Three methods of parsing genes verify that the BHOT panel readily identifies renal rejection and non-rejection diagnoses using in silico statistical analyses of seminal archival databases. Multiple modelling algorithms show a highly variable pattern of misclassifications per sample, either between differently constructed principal components or between modelling algorithms. The misclassifications are related to the gene expression heterogeneity within a given diagnosis because clustering the data into 9 groups modelled with fewer misclassifications. Conclusion This report supports using the Banff Human Organ Transplant Panel for gene expression of human renal allografts as a surrogate for microarrays on archival tissue. The data modelled satisfactorily with aggregate diagnoses although with limited per sample accuracy and, thereby, reflects and confirms the modelling complexity and the challenges of modelling gene expression as previously reported.

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