Deparaffinization of formalin-fixed paraffin-embedded tissue blocks using hot water instead of xylene

Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

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.

Exposure and health risk assessment of indoor volatile organic compounds in a medical university

Many volatile organic compounds (VOCs) are used for experiments at universities, and most of them contain benzene, toluene, ethylbenzene, xylene, and an extraction solvent of dichloromethane. This study aimed to investigate the indoor concentrations of these five compounds in different locations on campus and to evaluate possible health risks for faculty members and students in a medical university. We selected 10 locations as sampling sites to conduct 4-h monitoring sessions on weekdays each season during 2019-2020. We used a 6-liter canister to collect air samples and analyzed these five VOCs via gas chromatography with a flame ionization detector. Monte Carlo simulation was performed to evaluate the carcinogenic and noncarcinogenic risks of these five VOCs. We found that dichloromethane was the most highly detected compound (median: 621.07 μg/m³; range: 44.01-8523.91 μg/m³), and the Department of Medicine had the highest concentration of the total of these VOCs among all of the locations (median: 5595.29 μg/m³; range: 1565.67-7398.66 μg/m³). The median carcinogenic risks of dichloromethane and benzene were 6.36 × 10^-5 (95% confidence interval [CI]: 6.83 × 10^-6-7.37 × 10^-4) and 5.47 × 10^-6 (95% CI: 4.03 × 10^-7-2.42 × 10^-5), respectively, for faculty members, and the lower risks of 3.14 × 10^-5 (95% CI: 3.39 × 10^-6-3.64 × 10^-4) and 2.69 × 10^-6 (95% CI: 1.97 × 10^-7-1.19 × 10^-5) were estimated for the students. The chronic noncarcinogenic risks of four VOCs were less than one, except for dichloromethane with a median hazard index of 1.92 (95% CI: 2.11 × 10^-1-2.22 × 10¹). This study observed the spatial variation in the concentrations of the total of five VOCs and dichloromethane. The carcinogenic risks were classified as being at the possible level, and the noncarcinogenic risk of dichloromethane was greater than the acceptable level. Increasing local exhaust ventilation during the experiment and reducing the using amount of dichloromethane are recommended actions to reduce VOCs exposures in the medical university.

Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples

Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated VIM, AHNAK, and CLU from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.

Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens

Objectives

Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins.

Methods

Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS).

Results

Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval.

Conclusions

Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12014-022-09346-0.

A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens

Most human tumor tissues that are obtained for pathology and diagnostic purposes are formalin-fixed and paraffin-embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to proteolytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a 'green' xylene-free protocol for accelerated sample preparation of FFPE tissues based on paraffin-removal with hot water. Combined with tissue homogenization using disposable micropestles and a modified protein aggregation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label-free quantitation of FFPE cores from human ductal breast carcinoma in situ (DCIS) xenografts with a volume of only 0.79 mm³ showed a high correlation between replicates (r² = 0.992) with a median %CV of 16.9%. Importantly, this small volume is already compatible with tissue micro array (TMA) cores and core needle biopsies, while our results and its ease-of-use indicate that further downsizing is feasible. Finally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.

Mummified embalmed head skin: SR-FTIR microspectroscopic exploration

This case report details the examination of the skin of an Egyptian mummified head with a possible skin disorder. The head, thought to be dated in the first half of the 18th Dynasty, New Kingdom (1570-1400 BCE) belongs to the Museum of Forensic Anthropology, University of Madrid. Initial histological examination demonstrated evidence of chronic inflammation, which was confirmed by immunohistochemistry and Transmission Electron Microscopy (TEM). However, confirmation of pathology could be confounded by both the age of the specimen and the process of preservation by mummification. In this case report, Synchrotron Radiation Fourier Transform Microspectroscopy (SR-µFTIR) was used to add novel insights into embalmed mummified tissue. More precisely, FTIR is used for the first time on the specific specimens, while no other similar studies have been performed on these samples priorly. Additionally, modern skin tissue was examined too, in order to compare the amount of degradation to the mummified one. Whilst the FTIR results confirmed the results from the initial histological study, they also showed a biochemical modification of the mummified skin that could be indicative of tissue degradation. The latter was supported by comparing it to FTIR results of the modern tissue used.

Chemical risk in hospital settings: Overview on monitoring strategies and international regulatory aspects

Chemical risk in hospital settings is a growing concern that health professionals and supervisory authorities must deal with daily. Exposure to chemical risk is quite different depending on the hospital department involved and might origin from multiple sources, such as the use of sterilizing agents, disinfectants, detergents, solvents, heavy metals, dangerous drugs, and anesthetic gases. Improving prevention procedures and constantly monitoring the presence and level of potentially toxic substances, both in workers (biological monitoring) and in working environments (environmental monitoring), might significantly reduce the risk of exposure and contaminations. The purpose of this article is to present an overview on this subject, which includes the current international regulations, the chemical pollutants to which medical and paramedical personnel are mainly exposed, and the strategies developed to improve safety conditions for all healthcare workers.

The potential role of fatty acids in prostate cancer determined by GC-MS analysis of formalin-fixed paraffin-embedded tissue samples

Prostate cancer (PCa) is one of the leading types of cancer in men. Although the diagnosis of this disease is currently quite effective, there is still a need to search for noninvasive diagnostic and monitoring methods. Consequently, identifying the mechanisms underlying the development and progression of PCa is crucial. It has been confirmed that the hallmarks of PCa include changes in metabolism, particularly that of fatty acids. Therefore, the application of lipidomics with an accurate histopathological assessment can provide the necessary information and reveal the metabolites that are characteristic of the disease. The use of formalin-fixed, paraffin-embedded (FFPE) tissue samples as an alternative matrix in retrospective research makes this approach highly innovative. The main goal of this study was to perform an untargeted lipidomic analysis of FFPE PCa tissue samples (n = 52) using gas chromatography coupled with mass spectrometry (GC-MS), in comparison to controls (n = 50). To our knowledge, this study is the first to simultaneously conduct a metabolic analysis and histopathological assessment. In the latter, the samples were evaluated based on Gleason grading score and pTNM stage. The obtained results were evaluated by univariate (Student's t-test or Mann-Whitney U-test) as well as multivariate statistical analysis (principal component analysis, partial least squares-discriminant analysis, variable importance into projection, and selectivity ratio) in order to select the metabolites with the most discriminative power. Additionally, the correlation between the level of metabolites and pathological characteristics was determined. The results of the analyses confirmed the changes in the lipid metabolism pathway in PCa. It can be assumed that PCa is linked with elevated de novo biosynthesis of steroid hormone-related fatty acids and beta-oxidation of fatty acids. An increased level of three fatty acids, namely 9-octadecanoic acid, 9,12-octadecadienoic acid, and 5, 8, 1,14-eicosatetraenoic acid, was observed in the PCa samples. These fatty acids were assigned as metabolites with the best discriminative power for the two tested groups. In practice, these compounds could be considered as specific biochemical factors that may be implemented in the diagnosis of PCa, but their significance should be validated on a more extensive set of samples. Undoubtedly, these results are valuable as they provide important information on prostate cancerogenesis in the context of a metabolic switch.

A Novel Nanoproteomic Approach for the Identification of Molecular Targets Associated with Thyroid Tumors

A thyroid nodule is the most common presentation of thyroid cancer; thus, it is extremely important to differentiate benign from malignant nodules. Within malignant lesions, classification of a thyroid tumor is the primary step in the assessment of the prognosis and selection of treatment. Currently, fine-needle aspiration biopsy (FNAB) is the preoperative test most commonly used for the initial thyroid nodule diagnosis. However, due to some limitations of FNAB, different high-throughput “omics” approaches have emerged that could further support diagnosis based on histopathological patterns. In the present work, formalin-fixed paraffin-embedded (FFPE) tissue specimens from normal (non-neoplastic) thyroid (normal controls (NCs)), benign tumors (follicular thyroid adenomas (FTAs)), and some common types of well-differentiated thyroid carcinoma (follicular thyroid carcinomas (FTCs), conventional or classical papillary thyroid carcinomas (CV-PTCs), and the follicular variant of papillary thyroid carcinomas (FV-PTCs)) were analyzed. For the first time, FFPE thyroid samples were deparaffinized using an easy, fast, and non-toxic method. Protein extracts from thyroid tissue samples were analyzed using a nanoparticle-assisted proteomics approach combined with shotgun LC-MS/MS. The differentially regulated proteins found to be specific for the FTA, FTC, CV-PTC, and FV-PTC subtypes were analyzed with the bioinformatic tools STRING and PANTHER showing a profile of proteins implicated in the thyroid cancer metabolic reprogramming, cancer progression, and metastasis. These proteins represent a new source of potential molecular targets related to thyroid tumors.

Comparison of HPV detection rate in formalin-fixed paraffin-embedded tissues of head and neck carcinoma using two DNA extraction kits and three amplification methods

The potential problems of DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples and amplification efficiency of Human papilloma virus (HPV) may occur in the molecular studies of head and neck squamous carcinoma (HNSCC). The aim of this study was to compare HPV detection rate in FFPE tissues of oral, oropharyngeal, hypopharyngeal, and laryngeal cancers using two silica-based extraction kits and three amplification methods. A total of 50 FFPE specimens from HNSCC tissues were analyzed. The quality and quantity of the extracted DNA were tested by spectrophotometry. HPV DNA was detected using a single polymerase chain reaction (PCR), a nested PCR, and a Real-time PCR kit. Statistically significantly higher DNA quality and quantity was observed using the QIAamp DNA FFPE Tissue Kit than when using the QIAamp DNA Mini Kit. There was not HPV amplification in any of the 50 FFPE samples using the single PCR and Real-time PCR kits, whereas HPV DNA was detected in 22% of samples using nested PCR. Comparing results of the three different methods showed that HPV DNA was detected only with nested PCR. The results presented imply that nested PCR is the most appropriate method for the detection of HPV DNA in FFPE samples, along with adequate DNA extraction methods.

PCR Amplifiable DNA from Breast Disease FFPE Section for Mutational Analysis

Formalin-fixed paraffin-embedded (FFPE) tissue specimens have been a staple of research, providing precious resources for molecular and genomic studies. However, the biggest challenge is the extraction of high-quality DNA from FFPE tissues, given that the integrity of DNA is critically affected by formalin fixation. Formaldehyde induces crosslinks in DNA that renders single or double-stranded DNA breaks. Such breaks cause extensive fragmentation that directly influences the quality of DNA purified and the number of templates available for PCR amplification. Thus, protocol for DNA purification from FFPE tissues must effectively extract highly fragmented DNA and reverse cross-linking caused by formalin fixation. DNA extraction methods available in the literature were selected and modified at different stages to optimize a protocol that extracts DNA of sufficient quality and fragment size to be detectable by PCR. Archived FFPE tissues belonged to patients with triple negative breast cancer (TNBC) and benign breast disease were used for the protocol optimization. The best optimized protocol was then used to amplify Exon 4 region of Proviral integration site for Moloney murine leukemia virus1 (Pim1) kinase gene to analyze any probable somatic mutations both in TNBCs and benign breast diseases. Of the 12 different protocols developed, best quality DNA in terms of fragment size and purity was obtained when Tween20 lysis buffer was used for both deparaffinization and overnight digestion along with high salt precipitation. Optimized protocol was then validated by extracting DNAs from 10 TNBCs and 5 benign breast disease specimens with consistent purity and fragment size. PCR amplification and subsequent Sanger's sequencing revealed the presence of mutations in the Exon 4 region of Pim1 kinase. Deparaffinization and overnight digestion in Tween20 lysis buffer along with high salt precipitation yielded the best quality PCR amplifiable DNA for mutational analysis.

Indoor air-related symptoms and volatile organic compounds in materials and air in the hospital environment

In this case study, hospital workers did suffer from symptoms related to the poor indoor air quality. To investigate reasons for symptoms MM40-survey and house inspection methods were performed. The study consisted of 49 operating rooms and 470 employees. MM-40 survey revealed that over 40% of the staff suffered from skin reactions, over 50% had upper respiratory tract symptoms and 25% suffered headaches. No reason for the staff's symptom could be found in the structural studies of workplaces. The mean air exchange rate of the rooms was 5.51/h. In total 61 materials and 49 indoor air samples were taken. The most frequently found compounds in the material samples were 2-ethyl-1-hexanol and aliphatic hydrocarbons. VOC emissions were high in some of the material samples and they presumably were the one reason for the workers' symptoms observed in some in of the rooms. However, indoor air VOC concentrations were low in most of the cases. According to the linear regression model emissions from flooring material couldn't explain the indoor air concentration of the VOCs. One reason for that was the high ventilation rates of the rooms, which presumably kept VOC levels in indoors low. In addition, VOC concentrations indoors were strongly related to the ongoing healthcare activities in the hospital.

Optimization of RNA extraction protocol for long-term archived formalin-fixed paraffin-embedded tissues of horses

A suitable RNA extraction protocol was established to gain high quality RNA from formalin-fixed paraffin-embedded tissues to perform reliable molecular assays either applicable for using FFPE tissue archives or tissues with harsh formalin-fixation. Eighteen FFPE samples from the central nervous system of horses, stored up to 11 years, were used as archive cases. To test the influence of the fixation period, brain, liver, kidney, and skeletal muscle tissue fragments from another horse, were treated either with water or tris-acetate-EDTA buffer after fixation under different timepoints with 10% unbuffered formalin. Two deparaffinization methods and three proteinase K-based lysis step were tested and translated into three protocols. After detailed statistical analysis it was determined that a longer period and increase in volume of proteinase K incubation provide higher yields and purity of RNA (P < 0.01) of archived samples. Alongside, amplification of equid-housekeeping gene up to 298 bp was successful with the protocol adaptations. For different formalin-fixation timepoints, it was demonstrated that the right choice for treatment and formalin-fixation period is organ-related (P ≤ 0.05). Essentially, little alterations to pre-existing extraction protocols unwound the RNA of up to 11-year-old samples, enabling the use of FFPE tissue archives or e.g. harshly fixed material needed in infection research under high biosafety levels for a variety of molecular analysis.

Genotype characterization of livestock and human cystic echinococcosis in Mazandaran province, Iran

Echinococcus granulosus is a helminth from the family Taeniidae, which causes cystic echinococcosis (CE) in humans and diverse livestock around the world. The identification of existing genotypes in different regions is a major step towards the prevention and establishment of control programmes for the disease. This study aimed to detect CE genotypes using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer-1 (ITS1) gene and sequencing of the cytochrome c oxidase subunit 1 (Cox1) gene in isolates from the central part of Mazandaran province, northern Iran. Forty isolates were collected from sheep, 17 from cattle and 6 from human formalin-fixed paraffin-embedded tissues (FFPE). The ITS1 and Cox1 genes were successfully amplified by PCR in 41 and 42 samples, respectively. PCR-RFLP and sequencing showed that all isolates had the G1-G3 genotypes in this study. Out of 31 isolates subjected to sequencing for the Cox1 gene, 80.7% had the G1 genotype. G2 (16.1%) and G3 (3.2%) genotypes were observed in five sheep and one cattle samples, respectively. Five human isolates were also sequenced for the ITS1 gene, which showed that all samples belonged to the G1 genotype. Ten haplotypes were determined among the isolates by alignment analysis of the Cox1 gene. In summary, this study demonstrated that G1 was the dominant genotype circulating between humans and livestock in the studied region. Furthermore, high genotypic diversity among the CE isolates was observed.

Detection of Toxoplasma gondii DNA in Malignant Breast Tissues in Breast Cancer Patients

Breast cancer is the most prevalent malignancy in women throughout the world. Similar to other cancers, a strong relationship between breast cancer and environmental factors such as infectious agents has been reported. Toxoplasma gondii is a protozoan parasite which may play a role in cancer induction. The present study aimed to investigate a possible association between a history of T. gondii infection and breast cancer by detecting T. gondii DNA in malignant and non-malignant breast and lymph nodes tissues from breast cancer patients with latent toxoplasmosis. Formalin-fixed, paraffin-embedded (FFPE) tissue blocks from malignant/non-malignant breast and lymph nodes were obtained from twenty-nine breast cancer patients who were positive for anti-Toxoplasma antibodies (IgG). FFPE tissue blocks were deparaffinized using hot water method, and DNA was extracted. A conventional PCR analysis was performed to amplify partial regions of T. gondii B1 and REP-529 genes. Ninety-three samples from 29 patients were examined. All patients were negative for anti-T. gondii antibodies (IgM). T. gondii DNA was detected in 3 (10.3%) patients by PCR analysis of either B1 or REP-529 genes. These include two malignant breast and one normal lymph node samples. Sequence analysis of these genes showed a good similarity with previously published B1 and REP-529 sequences of T. gondii in NCBI GenBank. This study did not find any association between T. gondii infection and breast cancer. Furthermore, it is the first molecular identification of T. gondii in FFPE tissue samples obtained from breast cancer patients.

Volatile Organic Compounds in Anatomical Pathology Wards: Comparative and Qualitative Assessment of Indoor Airborne Pollution

The impact of volatile organic compounds (VOCs) on indoor air quality and on human health is widely recognized. However, VOC contamination in hospital indoor air is rarely studied and chemical compounds that singularly do not show high toxicity are not submitted to any regulation. This study aimed to compare VOC contamination in two different anatomical pathology wards in the same hospital. Hydrocarbons, alcohols, and terpenes were sampled by passive diffusive samplers. Analytical tests were performed by thermal desorption coupled with gas chromatography and mass spectrometry detector. Results highlighted a different VOC pollution in the two wards, due to the structural difference of the buildings and different organizational systems. The scarcity of similar data in the literature shows that the presence of VOCs in pathology wards is an underestimated problem. We believe that, because of the adverse effects that VOCs may have on the human health, this topic is worth exploring further.