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Pathologica Oct 2023COVID-19 identification is routinely performed on fresh samples, such as nasopharyngeal and oropharyngeal swabs, even if, the detection of the virus in formalin-fixed... (Review)
Review
COVID-19 identification is routinely performed on fresh samples, such as nasopharyngeal and oropharyngeal swabs, even if, the detection of the virus in formalin-fixed paraffin-embedded (FFPE) autopsy tissues could help to underlie mechanisms of the pathogenesis that are not well understood. The gold standard for COVID-19 detection in FFPE samples remains the qRT-PCR as in swab samples, contextually other methods have been developed, including immunohistochemistry (IHC), and in situ hybridization (ISH). In this manuscript, we summarize the main data regarding the methods of COVID-19 detection in pulmonary and extra-pulmonary post-mortem samples, and especially the sensitivity and specificity of these assays will be discussed.
Topics: Humans; COVID-19; Polymerase Chain Reaction
PubMed: 38054901
DOI: 10.32074/1591-951X-933 -
Molecular & Cellular Proteomics : MCP Nov 2023The NFE2L2 (NRF2) oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion, and...
The NFE2L2 (NRF2) oncogene and transcription factor drives a gene expression program that promotes cancer progression, metabolic reprogramming, immune evasion, and chemoradiation resistance. Patient stratification by NRF2 activity may guide treatment decisions to improve outcome. Here, we developed a mass spectrometry-based targeted proteomics assay based on internal standard-triggered parallel reaction monitoring to quantify 69 NRF2 pathway components and targets, as well as 21 proteins of broad clinical significance in head and neck squamous cell carcinoma (HNSCC). We improved an existing internal standard-triggered parallel reaction monitoring acquisition algorithm, called SureQuant, to increase throughput, sensitivity, and precision. Testing the optimized platform on 27 lung and upper aerodigestive cancer cell models revealed 35 NRF2 responsive proteins. In formalin-fixed paraffin-embedded HNSCCs, NRF2 signaling intensity positively correlated with NRF2-activating mutations and with SOX2 protein expression. Protein markers of T-cell infiltration correlated positively with one another and with human papilloma virus infection status. CDKN2A (p16) protein expression positively correlated with the human papilloma virus oncogenic E7 protein and confirmed the presence of translationally active virus. This work establishes a clinically actionable HNSCC protein biomarker assay capable of quantifying over 600 peptides from frozen or formalin-fixed paraffin-embedded archived tissues in under 90 min.
Topics: Humans; Squamous Cell Carcinoma of Head and Neck; Carcinoma, Squamous Cell; NF-E2-Related Factor 2; Head and Neck Neoplasms; Proteomics; Papillomavirus Infections; Biomarkers, Tumor; Cyclin-Dependent Kinase Inhibitor p16; Formaldehyde
PubMed: 37716475
DOI: 10.1016/j.mcpro.2023.100647 -
Nature Communications Sep 2023For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material....
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
Topics: Animals; Mice; Epigenomics; Paraffin Embedding; Retrospective Studies; Chromatin; Formaldehyde
PubMed: 37739938
DOI: 10.1038/s41467-023-41666-z -
Revista Espanola de Enfermedades... Dec 2023An 83-year-old female, suffering from abdominal pain, nausea, and vomiting, was admitted to our hospital. Gas-liquid level and tumor was not seen on the abdominal...
An 83-year-old female, suffering from abdominal pain, nausea, and vomiting, was admitted to our hospital. Gas-liquid level and tumor was not seen on the abdominal computed tomography scan. Instead, two high density balloon which were 2.7cm(distal) and 3.3cm(proximal) in diameter separately were shown (Figure A) in small intestine. The balloons proved to be part of ileus tube and iohexol which was incorrectly injected into the balloons caused a blockage in the tube. During colonoscopy, we were surprised to find that the distal balloon had passed through the ileocecal valve and we punctured it easily (Figure B). However, affected by the broken distal balloon, we could not reach another one. Finally, we cut off the connector fixed to the face and instructed the patient to take some oral paraffin oil and exercise appropriately. The next day, the balloons were discharged with the symptoms alleviated. It is rare for iatrogenic foreign body to cause ileal obstruction).
Topics: Female; Humans; Aged, 80 and over; Intestinal Obstruction; Ileus; Intestine, Small; Tomography, X-Ray Computed; Iatrogenic Disease
PubMed: 36263808
DOI: 10.17235/reed.2022.9225/2022 -
Nucleic Acids Research Aug 2023In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day... (Review)
Review
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
Topics: DNA; Formaldehyde; Paraffin Embedding; Sequence Analysis, DNA; Tissue Fixation
PubMed: 37351572
DOI: 10.1093/nar/gkad519