Search results for "Formalin fixed"

Dissection of DLBCL microenvironment provides a gene expression-based predictor of survival applicable to formalin-fixed paraffin-embedded tissue

2018

Abstract Background Gene expression profiling (GEP) studies recognized a prognostic role for tumor microenvironment (TME) in diffuse large B-cell lymphoma (DLBCL), but the routinely adoption of prognostic stromal signatures remains limited. Patients and methods Here, we applied the computational method CIBERSORT to generate a 1028-gene matrix incorporating signatures of 17 immune and stromal cytotypes. Then, we carried out a deconvolution on publicly available GEP data of 482 untreated DLBCLs to reveal associations between clinical outcomes and proportions of putative tumor-infiltrating cell types. Forty-five genes related to peculiar prognostic cytotypes were selected and their expression …

Detection of human papillomavirus DNA in formalin-fixed, paraffin-embedded squamous papillomas of the oral cavity

2018

Background Squamous papillomas are exophytic proliferations of surface oral epithelium. Human papillomavirus (HPV) infection is widely accepted as the etiology of squamous papillomas however the virus cannot be detected in a significant percentage of lesions. Material and methods Using polymerase chain reaction (PCR), we tested 35 formalin-fixed paraffin-embedded (FFPE) squamous papillomas for the presence of HPV DNA. Results Six papillomas (17%) tested positive for HPV DNA; four contained HPV-6 and two contained HPV-11. Given that β-globin DNA was only identified in half of the samples, DNA degradation appears to have significantly impacted the results. Conclusions The results likely repre…

Kupffer Cell and Monocyte-Derived Macrophage Identification by Immunofluorescence on Formalin-Fixed, Paraffin-Embedded (FFPE) Mouse Liver Sections

2020

Kupffer cells are the liver-resident macrophages and represent the first line of defense between the pathogens circulating from the intestines through the portal vein and systemic circulation. Recent works have highlighted the complex heterogeneity of macrophage functions and origins, thus raising awareness on the need for a better characterization of macrophage populations. The immunohistochemistry method here described, allows for a rapid distinction between Kupffer cells and monocyte-derived macrophages present on formalin-fixed, paraffin-embedded mouse liver samples. This protocol has been optimized for its reproducibility, reliability, and simplicity.

Targeted mRNA sequencing of small formalin-fixed and paraffin-embedded breast cancer samples for the quantification of immune and cancer-related genes

2017

Fluorescence In Situ Hybridization (FISH) on Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Sections

2011

Fluorescence In Situ Hybridization (FISH) is a powerful technique for localizing specific DNA targets directly in the fixed tissue or cells. Bacterial artificial chromosome (BAC) as well as commercial probes, which could be supplied ready for use or concentrated and must be diluted following the manufacturers instructions, can be used. The technique requires 2 days, as an overnight incubation of the FISH probes is needed for optimal hybridization. The critical steps include deparaffinization of tissue sections, optimal pretreatment (target retrieval and protein digestion), and probe hybridization. In this chapter, the described FISH protocol provides a methodology for analyzing the cytogene…

Influence of formalin fixation on the biomechanical properties of human diaphyseal bone.

2010

Owing to the lack of fresh human bones, formalin-fixed specimens are frequently used in biomechanical testing. However, formalin fixation is assumed to affect the biomechanical properties of bone. The aim of this study was to compare axial and torsional stiffness and bone mineral density in fresh and embalmed human bones. The subtrochanteric regions of 12 pairs of fresh human femora were randomised into two groups for paired comparison. After bone mineral density measurement, one group was preserved in 4% formalin. After 6 weeks, bone mineral density was remeasured and each specimen underwent axial and torsional loading. The formalin group showed significant higher stiffness values for tors…

Histophotometry: a new method for automated histological examination of solid tissue samples demonstrated on bladder cancer.

1979

The purpose of this study was to demonstrate the ability of a new method to discriminate between benign and malignant tissue. Tissue samples from three patients with bladder tumours and one patient with bladder diverticula have been examined by histophotometry. This method, based on the correlation of nuclear volume and nucleic acid contents per cell uses thick formalin fixed samples. The results are obtained by measurements averaging more than one hundred thousand cells per sample. By this histophotometric examination a clear differentiation between malignant and benign tissue could be achieved. It was also possible to determine the degree of malignancy and to differentiate between infiltr…