Quantitative assessment of glomerular basement membrane collagen IV α chains in paraffin sections from patients with focal segmental glomerulosclerosis and Alport gene variants.

Focal segmental glomerulosclerosis (FSGS) lesions have been linked to variants in COL4A3/A4/A5 genes, which are also mutated in Alport syndrome. Although it could be useful for diagnosis, quantitative evaluation of glomerular basement membrane (GBM) type IV collagen (colIV) networks is not widely used to assess these patients. To do so, we developed immunofluorescence imaging for collagen α5(IV) and α1/2(IV) on kidney paraffin sections with Airyscan confocal microscopy that clearly distinguishes GBM collagen α3α4α5(IV) and α1α1α2(IV) as two distinct layers, allowing quantitative assessment of both colIV networks. The ratios of collagen α5(IV):α1/2(IV) mean fluorescence intensities (α5:α1/2 intensity ratios) and thicknesses (α5:α1/2 thickness ratios) were calculated to represent the levels of collagen α3α4α5(IV) relative to α1α1α2(IV). The α5:α1/2 intensity and thickness ratios were comparable across all 11 control samples, while both ratios were significantly and markedly decreased in all patients with pathogenic or likely pathogenic Alport COL4A variants, supporting validity of this approach. Thus, with further validation of this technique, quantitative measurement of GBM colIV subtype abundance by immunofluorescence, may potentially serve to identify the subgroup of patients with FSGS lesions likely to harbor pathogenic COL4A variants who could benefit from genetic testing.

Hepatitis E virus infection of transplanted kidneys.

Immunocompromised patients are at risk of chronic hepatitis E (HEV) infection. Recurrent T cell and borderline rejections in a pediatric patient with high HEV copy numbers led us to study HEV infection within renal transplants. To investigate the frequency of renal HEV infection in transplanted patients, 15 samples from patients with contemporaneous diagnoses of HEV infection were identified at our center. Ten samples had sufficient residual paraffin tissue for immunofluorescence (IF) and RNA-fluorescence-in-situ-hybridization (RNA-FISH). The biopsy of the pediatric index patient was additionally sufficient for tissue polymerase chain reaction and electron microscopy. HEV RNA was detected in paraffin tissue of the index patient by tissue polymerase chain reaction. Subsequently, HEV infection was localized in tubular epithelial cells by IF, RNA-FISH, and electron microscopy. One additional biopsy from an adult was positive for HEV by RNA-FISH and IF. Focal IF positivity for HEV peptide was observed in 7 additional allografts. Ribavirin therapy was not successful in the pediatric index patient; after relapse, ribavirin is still administered. In the second patient, successful elimination of HEV was achieved after short-course ribavirin therapy. HEV infection is an important differential diagnosis for T cell rejection within transplanted kidneys. Immunostaining of HEV peptide does not necessarily prove acute infection. RNA-FISH seems to be a reliable method to localize HEV.

Optimization of PAS stain and similar Schiff's based methods for glycogen demonstration in liver tissue.

Demonstration of glycogen in tissue holds considerable diagnostic relevance across various pathological conditions, particularly in certain tumors. The histochemical staining of glycogen using methods utilizing Schiff's reagents is subject to influences arising from the type of fixative, fixation temperature, and oxidizing agents employed. This study aimed to assess diverse fixatives, fixation temperatures, and oxidizing agents, each with variable treatment durations, in conjunction with Schiff's reagent for optimal glycogen demonstration. Paraffin blocks derived from a rabbit's liver served as the experimental substrate, encompassing 340 paraffin sections subjected to different procedures. For tissues fixed at 4 °C, good staining outcomes, as determined by the periodic acid-Schiff (PAS) stain, were observed with 10% neutral buffered formalin (NBF), 80% alcohol, and Bouin's solution. Tissues fixed at room temperature (RT) demonstrated good PAS staining results with both 10% NBF and 80% alcohol. Notably, other oxidizing agents exhibited poor outcomes across all fixatives and fixation temperature, with two exceptions, as satisfactory staining results were obtained when using 5% chromic acid. Consequently, Both 10% NBF and 80% emerge as preferred fixatives of choice for glycogen demonstration when coupled with PAS stain. It is noteworthy that Bouin's solution could also provide good outcomes when fixation occurred at 4 °C.

In vitro assessment of potential endocrine disrupting activities of chlorinated paraffins of various chain lengths.

The production of chlorinated paraffins (CPs) has risen in the past two decades due to their versatile industrial applications. Consequently, CPs are now widely detected in human food sources, the environment, and in human matrices such as serum, the placenta and breast milk. This raises concern about prenatal and postnatal exposure. While some studies suggest that certain short-chained CPs (SCCPs) may have endocrine disrupting properties, knowledge about potential endocrine disrupting potential of medium- (MCCP) and long-chained CPs (LCCPs) remains relativity sparse. Here, we used a panel of in vitro assays to investigate seven pure CPs and two technical mixtures of CPs. These varied in chain length and, chlorination degree. The in vitro panel covered androgen, estrogen, and retinoic acid receptor activities, transthyretin displacement, and steroidogenesis. One of the SCCPs inhibited androgen receptor (AR) activity. All SCCPs induced estrogen receptor (ER) activity. Some SCCPs and MCCPs increased 17ß-estradiol levels in the steroidogenesis assay, though not consistently across all substances in these groups. SCCPs exhibited the most pronounced effects in multiple in vitro assays, while the tested LCCPs showed no effects. Based on our results, some CPs can have endocrine disrupting potential in vitro. These findings warrant further examinations to ensure that CPs do not cause issues in intact organisms, including humans.

Gastrointestinal decontamination using oil-based solutions in patients with acute aluminum phosphide poisoning: a systematic review and meta-analysis.

Some studies suggested that gastrointestinal (GIT) decontamination with oil may improve the prognosis of patients who ingested aluminum phosphide (AlP). The aim of this study is to compare the efficacy and safety of gastric lavage with oil-based solutions to any method of gastric decontamination not using oils in patients presenting with acute AlP poisoning. The literature was searched for English-published randomized controlled trials (RCTs) from inception to 16 September 2023. The searched electronic databases included MEDLINE/PubMed, Cochrane Library, Web of Science, Egyptian Knowledge Bank, Scopus, and Google Scholar. Data were extracted and pooled by calculating the risk ratio (RR) for categorical outcomes and standardized mean difference (SMD) for numerical outcomes, with 95% confidence intervals (CI). Seven RCTs were included. Paraffin oil was significantly associated with a lower risk of mortality (RR = 0.59 [95% CI: 0.45, 0.76], p < .001), intubation (RR = 0.59 [95% CI: 0.46, 0.76], p < .001) and vasopressor need (RR = 0.71 [95% CI: 0.56, 0.91], p = .006). Survival time was significantly prolonged with paraffin oil (SMD = 0.72 [95% CI: 0.32, 1.13], p < .001). Coconut oil was significantly associated with prolonged survival time (SMD = 0.83 [95% CI: 0.06, 1.59], p = .03) as well as decreased risk of requiring intubation (RR = 0.78 [95% CI: 0.62, 0.99], p = .04). Oil-based GIT decontamination using paraffin oil showed benefits over conventional lavage regarding the incidence of in-hospital mortality and endotracheal intubation, and survival time. Coconut oil showed some benefits in terms of the intubation incidence and survival time. Decontamination using paraffin oil is recommended. Future clinical trials are warranted with larger sample sizes and focusing on cost-benefit and safety.

Are We Justified in Modeling Human Exposure to Chlorinated Paraffin Mixtures Using the Average Properties of Congeners and Homologues?

Concern over human exposure to chlorinated paraffin (CP) mixtures keeps increasing. The absence of a comprehensive understanding of how human exposure varies with the physicochemical properties of CP constituents has hindered the ability to determine at what level of aggregation exposure to CPs should be assessed. We answer this question by comparing exposure predicted with either a "complex" method that utilizes isomer-specific properties or "simplified" methods that rely on median properties of congener, homologue, or short-/medium-/long-chain CP groups. Our results demonstrate the wide range of physicochemical properties across CP mixtures and their dependence on molecular structures. Assuming unit emissions in the environment, these variances translate into an extensive disparity in whole-body concentrations predicted for different isomers, spanning ∼11 orders of magnitude. CPs with 13-19 carbons and 6-10 chlorines exhibit the highest human exposure potential, primarily owing to moderate to high hydrophobicity and slow environmental degradation and biotransformation. Far-field exposure is dominant for most CP constituents. Our study underscores that using average properties of congener, homologue, or S/M/LCCP groups yields results that are consistent with those derived from isomer-based modeling, thus offering an efficient and practical framework for future risk assessments and human exposure studies of CPs and other complex chemical mixtures.

Remarkable Contamination of Short- and Medium-Chain Chlorinated Paraffins in Free-Range Chicken Eggs from Rural Tibetan Plateau.

Rapid social-economic development introduces modern lifestyles into rural areas, not only bringing numerous modern products but also new pollutants, such as chlorinated paraffins (CPs). The rural Tibetan Plateau has limited industrial activities and is a unique place to investigate this issue. Herein we collected 90 free-range chicken egg pool samples across the rural Tibetan Plateau to evaluate the pollution status of CPs. Meanwhile, CPs in related soils, free-range chicken eggs from Jiangxi, and farmed eggs from markets were also analyzed. The median concentrations of SCCPs (159 ng g-1 wet weight (ww)) and MCCPs (1390 ng g-1 ww) in Tibetan free-range chicken eggs were comparable to those from Jiangxi (259 and 938 ng g-1 ww) and significantly higher than those in farmed eggs (22.0 and 81.7 ng g-1 ww). In the rural Tibetan Plateau, the median EDI of CPs via egg consumption by adults and children were estimated to be 81.6 and 220.2 ng kg-1 bw day-1 for SCCPs and 483.4 and 1291 ng kg-1 bw day-1 for MCCPs, respectively. MCCPs might pose potential health risks for both adults and children in the worst scenario. Our study demonstrates that new pollutants should not be ignored and need further attention in remote rural areas.

Exposure to Short- and Medium-Chain Chlorinated Paraffins and the Risk of Gestational Diabetes Mellitus: A Nested Case-Control Study in Eastern China.

Toxicological studies have indicated that exposure to chlorinated paraffins (CPs) may disrupt intracellular glucose and energy metabolism. However, limited information exists regarding the impact of human CP exposure on glucose homeostasis and its potential association with an increased risk of developing gestational diabetes mellitus (GDM). Here, we conducted a prospective study with a nested case-control design to evaluate the link between short- and medium-chain CP (SCCPs and MCCPs) exposures during pregnancy and the risk of GDM. Serum samples from 102 GDM-diagnosed pregnant women and 204 healthy controls were collected in Hangzhou, Eastern China. The median (interquartile range, IQR) concentration of SCCPs was 161 (127, 236) ng/mL in the GDM group compared to 127 (96.9, 176) ng/mL in the non-GDM group (p < 0.01). For MCCPs, the GDM group had a median concentration of 144 (117, 174) ng/mL, while the control group was 114 (78.1, 162) ng/mL (p < 0.01). Compared to the lowest quartile as the reference, the adjusted odds ratios (ORs) of GDM were 7.07 (95% CI: 2.87, 17.40) and 3.34 (95% CI: 1.48, 7.53) in the highest quartile of ∑SCCP and ∑MCCP levels, respectively, with MCCPs demonstrating an inverted U-shaped association with GDM. Weighted quantile sum regression evaluated the joint effects of all CPs on GDM and glucose homeostasis. Among all CP congeners, C13H23Cl5 and C10H16Cl6 were the crucial variables driving the positive association with the GDM risk. Our results demonstrated a significant positive association between CP concentration in maternal serum and GDM risk, and exposure to SCCPs and MCCPs may disturb maternal glucose homeostasis. These findings contribute to a better understanding of the health risks of CP exposure and the role of environmental contaminants in the pathogenesis of GDM.

Chlorinated paraffins in takeout food and its packaging in Beijing, China and dietary exposure risk.

Chlorinated paraffins (CPs) are hazardous to humans, and dietary intake acts as the primary pathway for human exposure to CPs. Takeout food is popular worldwide, but the presence of CPs in takeout food and its packaging is unclear. In this study, the concentrations and distributions of short- and median-chain CPs (SCCPs and MCCPs, respectively) were measured in 97 samples of four categories of takeout food and 33 samples of three types of takeout packaging. The SCCP and MCCP median concentrations for the takeout food samples were 248 and 339, 77.2 and 98.2, 118 and 258, 42.9 and 64.4 ng/g wet weight in meat, starch, half meat/half starch, and vegetables, respectively. Takeout food contained higher concentrations of SCCPs than MCCPs. The dominant SCCP and MCCP congener groups in takeout food were C10Cl6-7 and C14Cl7-8, respectively. The CP concentrations in takeout food were lower than those in packaging. The SCCP and MCCP median concentrations, respectively, in packaging were 9750 and 245 ng/g in polypropylene, 2830 and 135 ng/g in paper, and 2060 and 119 ng/g in aluminum foil. The concentrations of SCCPs and MCCPs were comparable in aluminum foil, whereas the concentrations of SCCPs were higher than those of MCCPs in polypropylene and paper. Correlations between CP concentrations in the takeout food and packaging indicated that CPs in packaging were potentially an important source of CPs in the takeout food. A dietary exposure risk assessment showed the takeout food posed a low risk for human exposure to CPs; however, high-frequency consumption may pose a health risk. This study clarified the current contamination situation in takeout food in Beijing, China. The resulting data could be used to prevent human exposure to CPs through dietary intake and to facilitate the market's control over the quality of takeout food.

A preliminary study on short- and medium-chain chlorinated paraffins in duck farms: Concentrations, distribution, and dietary exposure risks.

Chlorinated paraffins (CPs) in poultry feed and the farm environment might bioaccumulate in poultry eggs. Unlike chickens, which are mostly raised in cages, ducks are commonly raised free range. This would expose ducks to CPs in the environment. However, information on the presence of CPs on duck farms is scarce. In the present study, samples of duck eggs, duck feathers, poultry feed, and soil were collected from 25 duck farms in South China. Forty-eight congener groups of short- and medium-chain CPs (SCCPs and MCCPs) were detected in the samples. Interestingly, relatively high concentrations of SCCPs and MCCPs were found in the duck feathers. The median concentrations of SCCPs and MCCPs in the duck eggs, feathers, feed and soil were: 46 and 18 ng/g wet weight, 2460 and 992 ng/g, 103 and 47 ng/g, and 24 and 10 ng/g dry weight, respectively. The dominant groups of SCCPs and MCCPs were C10Cl6-7 and C14Cl7-8, respectively. The close relationship between duck feathers and poultry feed indicated that the duck feathers might act as a bioindicator for the exposure of ducks to CPs. The margin of exposure approach was used to assess the health risk, with the results showing that the consumption of duck eggs posed a low risk to different age groups from exposure to SCCPs and MCCPs.

Effects of environmentally relevant concentration of short-chain chlorinated paraffins on BV2 microglia activation and lipid metabolism, implicating altered neurogenesis.

Short-chain chlorinated paraffins (SCCPs), a class of persistent organic pollutants, have been found to cause diverse organ and systemic toxicity. However, little is known about their neurotoxic effects. In this study, we exposed BV2, a mouse microglia cell line, to environmentally relevant concentration of SCCPs (1 µg/L, 10 µg/L, 100 µg/L) for 24 h to investigate their impacts on the nervous system. Our observations revealed that SCCPs induced the activation of BV2 microglia, as indicated by altered morphology, stimulated cell proliferation, enhanced phagocytic and migratory capabilities. Analysis at the mRNA level confirmed the activation status, with the downregulation of TMEM119 and Tgfbr1, and upregulation of Iba1 and CD11b. The upregulated expression of genes such as cenpe, mki67, Axl, APOE and LPL also validated alterations in cell functions. Moreover, BV2 microglia presented an M2 alternative phenotype upon SCCPs exposure, substantiated by the reduction of NF-κB, TNF-α, IL-1ß, and the elevation of TGF-ß. Additionally, SCCPs caused lipid metabolic changes in BV2 microglia, characterized by the upregulations of long-chain fatty acids and acylcarnitines, reflecting an enhancement of ß-oxidation. This aligns with our findings of increased ATP production upon SCCPs exposure. Intriguingly, cell activation coincided with elevated levels of omega-3 polyunsaturated fatty acids. Furthermore, activated microglial medium remarkably altered the proliferation and differentiation of mouse neural stem cells. Collectively, exposure to environmentally relevant concentrations of SCCPs resulted in activation and lipid metabolic alterations in BV2 microglia, potentially impacting neurogenesis. These findings provide valuable insights for further research on the neurotoxic effect of SCCPs.

Self-inflicted ingestion of harmful chemicals in adolescents and adults: risk factors and characteristics.

BACKGROUND: Injury due to ingestion of harmful chemicals has become an area of concern globally. In South Africa, paraffin has been widely implicated in multiple health outcomes, including severe ingestion injuries. A specific category of such injuries is those that are self-inflicted. A significant proportion of self-inflicted ingestion is reported to be intentional, although intentionality for self-infliction may be difficult to determine. Nonetheless, the identification of key explanatory risks and demographic factors of self-inflicted ingestion may contribute towards a better understanding of self-inflicted and harmful chemical ingestion injuries. METHODS: This study used secondary data that had been collected on burn injuries of all causes, including those due to the ingestion of harmful chemicals, from a sample of South Africans from low-income communities close to major metropolitan centres. The current analysis focused on the risks for self-inflicted ingestion injuries and used logistic regression to determine risks for self-inflicted ingestion as differentiated from ingestion due to the actions of another person (other-inflicted ingestion) by sex and age cohort of the victim, and the presence of alcohol, by examining paraffin ingestion versus that of other chemicals. RESULTS: The overwhelming majority of ingestion injuries (92.1%) were self-inflicted. The current findings indicate that sex (with females almost twice as likely to present with self-inflicted ingestion), age cohort (with those aged 18-29 and 30-44 years old four times more likely affected than older adults), presence of alcohol (twice as likely present than amongst individuals reporting ingestion injuries inflicted by others), and chemicals other than paraffin (three times more likely) are key explanatory factors for an increased risk for self-inflicted ingestion of harmful chemicals. CONCLUSIONS: The study empirically confirms the role of several key risk factors in what remains a relatively unreported and understudied phenomenon, but which appears to align with the demographic and risk profile reported for suicidal injuries through chemical ingestion, i.e. intentional self-inflicted ingestion. The findings may contribute towards improved safety policies on the availability and sale of chemical products and more focussed community interventions for at-risk individuals such as females and young people. It also flags the importance of assessing for alcohol use and alcohol use disorders at hospital admission of self-ingestion injuries.

Developmental toxicity of short-chain chlorinated paraffins on early-stage chicken embryos in a shell-less (ex-ovo) incubation system.

Short-chain chlorinated paraffins (SCCPs) are listed as a category of globally controlled persistent organic pollutants (POPs) by the Stockholm Convention in 2017. However, SCCP toxicity, particularly their developmental toxicity in avian embryos, has not been well studied. In this study, we observed the early development of chicken embryos (Gallus gallus domesticus) by applying a shell-less (ex-ovo) incubation system developed in our previous studies. After exposing embryos at Hamburger Hamilton stage (HHS) 1 to SCCPs (control, 0.1% DMSO; SCCPs-L, 200 ng/g; SCCPs-M, 2000 ng/g; SCCPs-H, 20,000 ng/g), we observed the development of embryos from the 3rd to 9th incubation day. Exposure to SCCPs-M and -H induced a significant reduction in survival, with an LD50 of 3100 ng/g on the 9th incubation day. Significant dose-dependent decreases in body length were observed from days 4-9. We also found that SCCPs-H decreased the blood vessel length and branch number on the 4th incubation day. Additionally, SCCPs-H significantly reduced the heart rate on the 4th and 5th incubation days. These findings suggest that SCCPs may have potential of developmental and cardiovascular toxicity during the early stages of chicken embryos. Quantitative PCR of the mRNA of genes related to embryonic development showed that SLC16A10 (a triiodothyronine transporter) level decreased in the SCCPs-H group, showing a significant positive correlation with the body length of embryos. THRA level, a thyroid hormone receptor, was significantly decreased in the SCCPs-H group, whereas that of DIO3 level, a deiodinase was significantly increased. These results suggest that SCCPs exposure induces developmental delays via the thyroxine signaling pathway. Analysis of thyroid hormones (THs) in blood plasma also indicated a significant reduction in thyroxine (T4) levels in the SCCPs-H group on the 9th incubation day of embryos. In conclusion, SCCPs induce developmental toxicity by disrupting thyroid functions at the early-life stage of chicken embryos.

[Conventional paraffin embedding technique and double-embedding technique for minute oral biopsies and delicate pulp tissue - a comparative study]. / Traditsionnyi metod zalivki v parafin i metod dvoinoi zalivki dlya malen'kikh bioptatov polosti rta i myagkikh tkanei pul'py ­ sravnitel'noe issledovanie.

BACKGROUND: Among oral biopsies, small incisional tissues, have to be preserved all through the processing and embedding to ensure optimal visualization of all the mucosal layers without compromise. Optimal tissue orientation is the most critical step in tissue processing for demonstration of definitive morphology in the sections, which is often more challenging in cases of minute/small or thinner sections using routine paraffin techniques to evaluate accurate diagnosis. Some modification is needed to handle these samples to get a better result. Double embedding technique with some modification has been widely used for small/ thin/ multiple biopsies and gives excellent results in many other fields like general pathology and biotechnology. The double embedding technique though produced excellent and significant results in mucosal biopsies yet, it is of minimal interest among oral pathologists. To best of our knowledge, this is the first study to use double embedding technique for pulp tissues. OBJECTIVE: The present study was aimed to evaluate and compare the ease of embedding and sectioning sections using Agar-Paraffin double embedding technique for small oral mucosal biopsies and thin pulp tissues. MATERIAL AND METHODS: A total of 40 oral tissue samples categorized into two groups were taken for the present study. Group I included 20 small oral mucosal biopsy samples of size ranging from 0.2 to 0.5 cm and Group II included 20 pulp tissues obtained from freshly extracted non carious tooth. 10 blocks were prepared by routine paraffin method and 10 blocks were prepared by modified double embedding method for each group. Scores were given by comparing all the criteria with that of the routine paraffin technique. Chi-square test was used for statistical analysis. RESULTS: The average ease score for the Agar-Paraffin double embedded small/minute biopsies showed better scores than the pulp tissue with that of the routine technique. However, no statistically significant difference was seen among embedding and sectioning sections between the two groups. CONCLUSION: Modified double embedding method is simple and reliable alternative technique that helps in better orientation, processing and sectioning especially for oral small or thin biopsies and delicate pulp tissues.

Construction and testing of a risk prediction classifier for cardia carcinoma.

OBJECTIVES: This research aimed to construct a prediction model for stages II and III cardia carcinoma (CC), and provide an effective preoperative evaluation tool for clinicians. METHODS: CC mRNA expression matrix was obtained from Gene Expression Omnibus and The Cancer Genome Atlas databases. Non-negative matrix factorization was used to cluster data to obtain subgroup information, and weighted gene co-expression network analysis was used to uncover key modules linked to different subgroups. Gene-set enrichment analysis analyzed biological pathways of different subgroups. The related pathways of multiple modules were scrutinized with Kyoto Encyclopedia of Genes and Genomes. Key modules were manually annotated to screen CC-related genes. Subsequently, quantitative real-time polymerase chain reaction assessed CC-related gene expression in fresh tissues and paraffin samples, and Pearson correlation analysis was performed. A classification model was constructed and the predictive ability was evaluated by the receiver operating characteristic curve. RESULTS: CC patients had four subgroups that were associated with brown, turquoise, red, and black modules, respectively. The CC-related modules were mainly associated with abnormal cell metabolism and inflammatory immune pathways. Then, 76 CC-elated genes were identified. Pearson correlation analysis presented that THBS4, COL14A1, DPYSL3, FGF7, and SVIL levels were relatively stable in fresh and paraffin tissues. The area under the curve of 5-gene combined prediction for staging was 0.8571, indicating good prediction ability. CONCLUSIONS: The staging classifier for CC based on THBS4, COL14A1, DPYSL3, FGF7, and SVIL has a good predictive effect, which may provide effective guidance for whether CC patients need emergency surgery.

A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples.

RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.

Unstained Tissue Imaging and Virtual Hematoxylin and Eosin Staining of Histologic Whole Slide Images.

Tissue structures, phenotypes, and pathology are routinely investigated based on histology. This includes chemically staining the transparent tissue sections to make them visible to the human eye. Although chemical staining is fast and routine, it permanently alters the tissue and often consumes hazardous reagents. On the other hand, on using adjacent tissue sections for combined measurements, the cell-wise resolution is lost owing to sections representing different parts of the tissue. Hence, techniques providing visual information of the basic tissue structure enabling additional measurements from the exact same tissue section are required. Here we tested unstained tissue imaging for the development of computational hematoxylin and eosin (HE) staining. We used unsupervised deep learning (CycleGAN) and whole slide images of prostate tissue sections to compare the performance of imaging tissue in paraffin, as deparaffinized in air, and as deparaffinized in mounting medium with section thicknesses varying between 3 and 20 µm. We showed that although thicker sections increase the information content of tissue structures in the images, thinner sections generally perform better in providing information that can be reproduced in virtual staining. According to our results, tissue imaged in paraffin and as deparaffinized provides a good overall representation of the tissue for virtually HE-stained images. Further, using a pix2pix model, we showed that the reproduction of overall tissue histology can be clearly improved with image-to-image translation using supervised learning and pixel-wise ground truth. We also showed that virtual HE staining can be used for various tissues and used with both 20× and 40× imaging magnifications. Although the performance and methods of virtual staining need further development, our study provides evidence of the feasibility of whole slide unstained microscopy as a fast, cheap, and feasible approach to producing virtual staining of tissue histology while sparing the exact same tissue section ready for subsequent utilization with follow-up methods at single-cell resolution.

Pathological characteristics of light chain crystalline podocytopathy.

Monoclonal immunoglobulin light chain (LC) crystalline inclusions within podocytes are rare, poorly characterized entities. To provide more insight, we now present the first clinicopathologic series of LC crystalline podocytopathy (LCCP) encompassing 25 patients (68% male, median age 56 years). Most (80%) patients presented with proteinuria and chronic kidney disease, with nephrotic syndrome in 28%. Crystalline keratopathy and Fanconi syndrome were present in 22% and 10%, respectively. The hematologic condition was monoclonal gammopathy of renal significance (MGRS) in 55% and multiple myeloma in 45%. The serum monoclonal immunoglobulin was IgG κappa in 86%. Histologically, 60% exhibited focal segmental glomerulosclerosis (FSGS), often collapsing. Ultrastructurally, podocyte LC crystals were numerous with variable effacement of foot processes. Crystals were also present in proximal tubular cells as light chain proximal tubulopathy (LCPT) in 80% and in interstitial histiocytes in 36%. Significantly, frozen-section immunofluorescence failed to reveal the LC composition of crystals in 88%, requiring paraffin-immunofluorescence or immunohistochemistry, with identification of kappa LC in 87%. The LC variable region gene segment, determined by mass spectrometry of glomeruli or bone marrow plasma cell sequencing, was IGKV1-33 in four and IGKV3-20 in one. Among 21 patients who received anti-plasma cell-directed chemotherapy, 50% achieved a kidney response, which depended on a deep hematologic response. After a median follow-up of 36 months, 26% progressed to kidney failure and 17% died. The mean kidney failure-free survival was 57.6 months and was worse in those with FSGS. In sum, LCCP is rare, mostly associates with IgG κappa MGRS, and frequently has concurrent LCPT, although Fanconi syndrome is uncommon. Paraffin-immunofluorescence and electron microscopy are essential to prevent misdiagnosis as primary FSGS since kidney survival depends on early diagnosis and subsequent clone-directed therapy.

Diagnostic markers and potential therapeutic agents for Sjögren's syndrome screened through multiple machine learning and molecular docking.

Primary Sjögren's syndrome (pSS) is a chronic inflammatory autoimmune disease, which mainly damages patients' exocrine glands. Sensitive early diagnostic indicators and effective treatments for pSS are lacking. Using machine learning methods to find diagnostic markers and effective therapeutic ways for pSS is of great significance. In our study, first, 1643 differentially expressed genes (DEGs; 737 were upregulated and 906 were downregulated) were ultimately screened out and analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes based on the datasets from the Gene Expression Omnibus. Then, support vector machine, least absolute shrinkage and selection operator regression, random forest, and weighted correlation network analysis were used to screen out feature genes from DEGs. Subsequently, the intersection of the feature genes was taken to screen 10 genes as hub genes. Meanwhile, the analysis of the diagnostic efficiency of 10 hub genes showed their good diagnostic value for pSS, which was validated through immunohistochemistry on the paraffin sections of the labial gland. Subsequently, a multi-factor regulatory network and correlation analysis of hub genes were performed, and the results showed that ELAVL1 and IGF1R were positively correlated with each other but both negatively correlated with the other seven hub genes. Moreover, several meaningful results were detected through the immune infiltration landscape. Finally, we used molecular docking to screen potential therapeutic compounds of pSS based on the hub genes. We found that the small molecules DB08006, DB08036, and DB15308 had good docking scores with ELAVL1 and IGF1R simultaneously. Our study might provide effective diagnostic biomarkers and new therapeutic ideas for pSS.

In situ sequence-specific visualization of single methylated cytosine on tissue sections using ICON probe and rolling-circle amplification.

Since epigenetic modifications differ from cell to cell, detecting the DNA methylation status of individual cells is requisite. Therefore, it is important to conduct "morphology-based epigenetics research", in which the sequence-specific DNA methylation status is observed while maintaining tissue architecture. Here we demonstrate a novel histochemical technique that efficiently shows the presence of a single methylated cytosine in a sequence-dependent manner by applying ICON (interstrand complexation with osmium for nucleic acids) probes. By optimizing the concentration and duration of potassium osmate treatment, ICON probes selectively hybridize to methylated cytosine on tissue sections. Since the elongation process by rolling-circle amplification through the padlock probe and synchronous amplification by the hyperbranching reaction at a constant temperature efficiently amplifies the reaction, it is possible to specifically detect the presence of a single methylated cytosine. Since the ICON probe is cross-linked to the nuclear or mitochondrial DNA of the target cell, subsequent elongation and multiplication reactions proceed like a tree growing in soil with its roots firmly planted, thus facilitating the demonstration of methylated cytosine in situ. Using this novel ICON-mediated histochemical method, detection of the methylation of DNA in the regulatory region of the RANK gene in cultured cells and of mitochondrial DNA in paraffin sections of mouse cerebellar tissue was achievable. This combined ICON and rolling-circle amplification method is the first that shows evidence of the presence of a single methylated cytosine in a sequence-specific manner in paraffin sections, and is foreseen as applicable to a wide range of epigenetic studies.