Formalin-fixed Paraffin-embedded Samples Research Articles

Molecular characterization of Pseudomyxoma peritonei with single-cell and bulk RNA sequencing

Pseudomyxoma peritonei (PMP), a rare condition characterized by mucinous ascites in the peritoneal cavity, often leads to a poor prognosis. However, omics profiling of this disease remains significantly underexplored. Here, we present single-cell transcriptomic profiling of five PMP cases to identify cell type-specific gene features associated with PMP pathogenesis. Additionally, we provide bulk RNA-seq datasets from two independent cohorts: 19 fresh frozen tissue samples (12 PMPs) and 34 formalin-fixed paraffin-embedded (FFPE) samples (25 PMPs). We also offer protein expression data from a tissue microarray (TMA) analysis of 90 samples (45 PMPs). Our single-cell and bulk transcriptomic profiles, along with TMA verifications, reveal the cellular diversity of PMP, highlighting the coexistence of epithelial and mesenchymal characteristics within PMP cells. These datasets enhance our understanding of PMP pathogenesis and provide a valuable resource for uncovering the intricate molecular landscape of PMP, with the potential to improve clinical utility through further research.

Detecting gene copy number alterations by Oncomine Comprehensive genomic profiling in a comparative study on FFPE tumor samples

Copy number alterations (CNAs) play a fundamental role in cancer development and constitute a potential tool for tailored treatments. The CNAs recognition in formalin fixed paraffin embedded (FFPE) material for diagnostic purposes has relied for years mainly on fluorescence in situ hybridization. The introduction of other procedures, such as Next-Generation Sequencing has dramatically improved CNAs discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. Herein, the CNAs detection by a widely used NGS assay (Oncomine Comprehensive Assay plus®, OCA+) were evaluated in 14 FFPE samples mirroring diagnostic daily practice and compared to a whole-genome assay. OCA+, a targeted DNA panel, showed lower CNAs detection sensitivity and equal specificity for gains and losses. According to proprietary software pipeline, OCA+ accurately identified gains characterized by CN ≥ 5,2. No significant threshold maximizing the difference between true and false positive losses was found. Orthogonal FISH tests validated seven CNAs characterized by CN gain ≥ 6 or complete loss. Considering the CNAs growing significance in precision medicine, our findings further prompt towards a robust validation of NGS detection in FFPE materials.

The Potential of Single-Transcription Factor Gene Expression by RT-qPCR for Subtyping Small Cell Lung Cancer

Complex RNA-seq signatures involving the transcription factors ASCL1, NEUROD1, and POU2F3 classify Small Cell Lung Cancer (SCLC) into four subtypes: SCLC-A, SCLC-N, SCLC-P, and SCLC-I (triple negative or inflamed). Preliminary studies suggest that identifying these subtypes can guide targeted therapies and potentially improve outcomes. This study aims to evaluate whether the expression levels of these three key transcription factors can effectively classify SCLC subtypes, comparable to the use of individual antibodies in immunohistochemical (IHC) analysis of formalin-fixed, paraffin-embedded (FFPE) tumor samples. We analyzed preclinical models of increasing complexity, including eleven human and five mouse SCLC cell lines, six patient-derived xenografts (PDXs), and two circulating tumor cell (CTC)-derived xenografts (CDXs) generated in our laboratory. RT-qPCR conditions were established to detect the expression levels of ASCL1, NEUROD1, and POU2F3. Additionally, protein-level analysis was performed using Western blot for cell lines and IHC for FFPE samples of PDX and CDX tumors, following our experience with patient tumor samples from the CANTABRICO trial (NCT04712903). We found that the analyzed SCLC cell line models predominantly expressed ASCL1, NEUROD1, and POU2F3, or showed no expression, as identified by RT-qPCR, consistently matching the previously assigned subtypes for each cell line. The classification of PDX and CDX models demonstrated consistency between RT-qPCR and IHC analyses of the transcription factors. Our results show that single-gene analysis by RT-qPCR from FFPE-extracted RNA simplifies SCLC subtype classification. This approach provides a cost-effective alternative to IHC staining or expensive multi-gene RNA sequencing panels, making SCLC subtyping more accessible for both preclinical research and clinical applications.

Prognostic value of circulating tumor DNA for progression-free survival in patients with locally advanced dMMR/MSI-H colorectal cancer managed without surgery.

256 Background: Immunotherapy has shown the ability to induce a high rate of pathologic and clinical complete response in patients with deficient mismatch repair (dMMR)/microsatellite instability-high (MSI-H) colorectal cancer (CRC). The role of circulating tumor DNA (ctDNA) as a prognostic biomarker for survival in patients who receive non-operative management (NOM) is unknown. Among patients enrolled in a phase II trial (NCT04082572) that evaluated the efficacy of pembrolizumab in patients with locally advanced dMMR/MSI-H solid tumors, we evaluated the impact of ctDNA on progression-free survival (PFS) among 12 patients with locally advanced dMMR/MSI-H CRC who received NOM. Methods: ctDNA testing was performed in the CLIA-certified laboratory at MD Anderson using a 70-gene liquid biopsy panel (LBP-70), which used digital sequencing of cell-free DNA. Formalin-fixed paraffin-embedded tumor samples and germline peripheral blood mononuclear cells were profiled using next-generation sequencing. Mutations in ctDNA were considered tumor-specific if they were confirmed with matched tumor tissue profiling. The lower limit of detection of the LBP-70 assay was a mutational variant allele frequency of <0.3%. "ctDNA clearance" and “ctDNA(-)” status were defined as the absence of any detectable tumor-specific mutations in ctDNA. Two-year progression-free survival (PFS) was estimated using Kaplan-Meier techniques and compared with log-rank tests. Results: The median follow-up between the first cycle of pembrolizumab and last radiographic assessment was approximately three years (36.7 mo; range (range 1.2 – 51.0 mo). Forty-nine LBP-70 assays were performed among the 12 patients over the course of treatment with pembrolizumab. The median number of cycles was 16 (range 1 – 16 cycles). Six patients were ctDNA(-) prior to pembrolizumab, all of whom remained ctDNA(-) after. None of these six patients experienced disease progression (PD) at their last follow-up. The other six patients were ctDNA(+) prior to pembrolizumab (median baseline VAF 0.4%, range 0.3%–4.0%). Of these six patients, three experienced ctDNA clearance while receiving pembrolizumab. None of the three patients who cleared ctDNA experienced PD as of their last follow-up. Of the three patients who did not clear ctDNA, two experienced PD in their primary tumor (at two and six months after their first cycle, respectively), while the third patient remains without PD at their last follow-up. The two-year PFS rate was 100% among the nine patients who were ctDNA(-) after pembrolizumab compared to 33% among the three patients who were ctDNA(+) after pembrolizumab (p = 0.03). Conclusions: ctDNA may be a valuable tool for assessing treatment response and improving the ability to tailor organ-sparing, curative strategies to patients with locally advanced dMMR/MSI-H CRC.

Importance of circulating tumor DNA analysis at diagnosis in early triple-negative breast cancer patients.

Circulating tumor DNA (ctDNA) enables non-invasive evaluation and is considered a promising tool for diagnosis, treatment selection, risk stratification, and disease monitoring. However, while the utility of ctDNA has been demonstrated in advanced-stage cancers, its detection in early breast cancer (EBC) remains limited. This study investigated the characteristics of EBC patients associated with higher ctDNA detectability. A total of 101 patients with EBC were enrolled. Formalin-fixed paraffin-embedded samples (FFPEs) were obtained from biopsy tissue, and plasma samples were collected before and after neoadjuvant chemotherapy (NAC). Forty-seven breast cancer-related genes were analyzed using next-generation sequencing. The diagnostic performance of ctDNA was evaluated, and logistic regression analyses were conducted to assess the impact of clinical and molecular factors on ctDNA status. The most frequently identified gene was TP53 (FFPE, 66.7%; ctDNA, 46.4%), followed by PIK3CA (FFPE, 36.2%; ctDNA, 17.4%). The diagnostic performance of the three most common genes showed a sensitivity range of 11.1-58.7%, specificity of 78.3-100%, and diagnostic accuracy of 65.2-78.3%. The triple-negative breast cancer (TNBC) subtype exhibited the strongest association with ctDNA detection (odds ratio [OR] 209.50, p = 0.005) in multivariate analysis. Also, those who exhibited ctDNA clearance after NAC had a higher pathological complete response rate compared to those without clearance (38.5% vs. 11.1%, p = 0.238). Our study highlights that ctDNA analysis can complement genetic testing from a single tissue biopsy in breast cancer patients. Furthermore, ctDNA analysis may be particularly important in patients with TNBC.

P-2139. Evaluation of a Multiplex Real-time PCR for the Detection and Differentiation of Sporothrix schenckii and Sporothrix brasiliensis

Abstract Background Sporothrix spp is a thermally dimorphic fungi known to cause subacute or chronic subcutaneous lesions in humans and animals and is the cause of increasing public health concern due to spread of feline-associated cases.Figure 1.Limit of detection and genomic DNA standard curve of S. schenckii and S. brasiliensis Methods A recently described Real-time PCR assay targeting the β-tubulin gene to detect and differentiate two related species, S. schenckii and S. brasiliensis, was evaluated and adapted by adding lambda primers and probe for internal control amplification. Isolates, fresh tissues and suspected sporotrichosis Formalin-Fixed, Paraffin Embedded (FFPE) tissues from humans and animals were received in the Mycotic Diseases Branch laboratory at the U.S. Centers for Disease Control and Prevention (CDC) for the routine fungal identification by conventional PCR and sequencing, using the primers D1/D2, ITS5/ITS4 and ITS3/ITS4. Ten-fold serial dilutions from 1 ng/μl to 1 fg/μl of DNA were tested with 20 replicates to establish limit of detection (LOD), and DNA from four fresh tissues extracted on three different days was used to assess reproducibility.Table 1.Ct values and coefficient of variation (CV) of the reproducibility test using fresh tissues on three different days Results The assay was tested with 55 S. brasiliensis, 19 S. schenckii, and 85 isolates from other clinically relevant fungi, showing 100% concordance with sequencing methods. The test was also able to amplify S. schenckii DNA from 10 fresh tissues, which were previously confirmed by culture and sequencing as S. schenckii (100% sensitivity), with Ct values ranging from 19 to 38. Among 9 FFPE samples, S. schenckii was amplified in 6 samples (67% sensitivity) with Ct values ranging from 29 to 38. LOD was 1pg/μl of DNA. Results of the 20 replicates showed that at this concentration all the DNAs had a positive signal for both targets (fig 1). For reproducibility, the results showed consistent Ct values over the 3 days of the test with the four fresh tissue samples with a coefficient of variation (CV) of 4% (table 1). Conclusion This multiplex Real-time PCR assay successfully detected DNA from the S. brasiliensis and S. schenckii isolates as well as S. schenckii from fresh and FFPE tissues. Our results demonstrate this molecular assay performs well and could be a helpful molecular tool to support rapid identification and differentiation at species level from cultures and primary human and animal specimens. Disclosures All Authors: No reported disclosures

Research progress and perspectives on the application of tyramide signal amplification-based multiplex immunohistochemistry/immunofluorescence: a bibliometrics analysis

Background and aimsMultiplex immunohistochemistry/immunofluorescence (mIHC/IF), which uses the tyramide signal amplification (TSA) technique, enables sequential staining of multiple targets in formalin-fixed paraffin-embedded (FFPE) samples without worrying about cross-reactivity. This approach has received considerable attention from researchers over the past decades. This article aims to provide a bibliometric analysis of the research progress and perspectives on the application of TSA-based mIHC/IF.MethodsWe collected all the TSA-based mIHC/IF documents published between 2007 and 2023 from the Web of Science Core Collection (WoSCC) database. CiteSpace, VOSviewer and Bibliometrix R Package were used to perform the bibliometrics analysis, including details about annual publications, countries, institutions, authors, journals, and research topics and hotspots.ResultsA total of 873 relevant publications (811 articles and 62 reviews) with a time span of 17 years (2007-2023) were obtained. The number of annual publications started to increase rapidly since 2016. The United States (307, 35.17%) and the People’s Republic of China (297, 34.02%) are the top two listed countries for both the number of articles produced and the citations. The University of Texas System (53, 6.07%) was the most productive institution. Integrating these results of hotspot and frontier analysis, TSA-based mIHC/IF provides significant benefits, particularly in neurology, cancer and immunology.ConclusionThis study conducted a comprehensive bibliometric analysis for the use of TSA-based mIHC/IF. As TSA-based mIHC/IF and its associated imaging systems and analytic software progress, it will become the most promising tool for describing the variety of the whole tissue for a better understanding of pathological or physiological behavior.

Evaluating HPV Viral Load and Multiple Infections for Enhanced Cervical Cancer Risk-Based Assessment

Human papillomavirus (HPV) is a major cause of cervical cancer, a significant health concern worldwide. Despite advances in screening methods, including the Pap test and the HPV DNA test, limitations remain in accurately predicting which HPV infections will progress to cervical intraepithelial neoplasia (CIN) and, eventually, invasive cancer. This study evaluates the usefulness in real life of assessing HPV viral load and the presence of multiple HPV genotypes in enhancing the diagnostic accuracy of triage in cervical cancer screening. A retrospective analysis was performed on 55 formalin-fixed paraffin-embedded cervical samples collected from women who underwent colposcopy with a biopsy or conization at San Martino Hospital, Genova, Italy, between January and June 2021. Histological diagnoses were compared with molecular analyses (HPV genotyping, viral load quantification and co-infection) using a multiplex real-time PCR platform. Of the samples analyzed, 56.4% were HPV DNA positive, while 40% tested negative. The molecular analysis identified more HPV-negative cases than the histological analysis (p < 0.05). Higher viral loads and HPV co-infections were more frequent in high-grade CIN lesions. These markers may help identify patients at an elevated risk for persistent infections and cancer progression. These findings support the potential of integrating HPV viral load and genotype co-infection assessments into routine cervical cancer screening protocols to improve early detection and reduce overtreatment and unnecessary interventions.

Weakly supervised pathological differentiation of primary central nervous system lymphoma and glioblastoma on multi-site whole slide images.

Differentiating primary central nervous system lymphoma (PCNSL) and glioblastoma (GBM) is crucial because their prognosis and treatment differ substantially. Manual examination of their histological characteristics is considered the golden standard in clinical diagnosis. However, this process is tedious and time-consuming and might lead to misdiagnosis caused by morphological similarity between their histology and tumor heterogeneity. Existing research focuses on radiological differentiation, which mostly uses multi-parametric magnetic resonance imaging. By contrast, we investigate the pathological differentiation between the two types of tumors using whole slide images (WSIs) of postoperative formalin-fixed paraffin-embedded samples. To learn the specific and intrinsic histological feature representations from the WSI patches, a self-supervised feature extractor is trained. Then, the patch representations are fused by feeding into a weakly supervised multiple-instance learning model for the WSI classification. We validate our approach on 134 PCNSL and 526 GBM cases collected from three hospitals. We also investigate the effect of feature extraction on the final prediction by comparing the performance of applying the feature extractors trained on the PCNSL/GBM slides from specific institutions, multi-site PCNSL/GBM slides, and large-scale histopathological images. Different feature extractors perform comparably with the overall area under the receiver operating characteristic curve value exceeding 85% for each dataset and close to 95% for the combined multi-site dataset. Using the institution-specific feature extractors generally obtains the best overall prediction with both of the PCNSL and GBM classification accuracies reaching 80% for each dataset. The excellent classification performance suggests that our approach can be used as an assistant tool to reduce the pathologists' workload by providing an accurate and objective second diagnosis. Moreover, the discriminant regions indicated by the generated attention heatmap improve the model interpretability and provide additional diagnostic information.

Pathological variants in HPV-independent vulvar tumours

Vulvar cancer is a rare gynaecological disease that can be caused by infection with human papillomavirus (HPV). The mutational frequencies and landscape for HPV-associated and HPV-independent vulvar tumor development are supposedly two distinctly different pathways and more detailed knowledge on target biological mechanisms for individualized future treatments is needed. The study included formalin-fixed paraffin-embedded (FFPE) samples from 32 cancer patients (16 HPV-negative and 16 HPV-associated), treated in Örebro, Sweden from 1988 to 2008. The Oncomine™ Comprehensive Assay v3 was used to detect variants across 161 different tumor relevant genes. Data analysis included quality assessment followed by variant analysis of DNA with the Oncomine Comprehensive v3 workflow and with a custom filter using the VarSome Clinical software. The RNA-analysis was performed with the Oncomine Comprehensive v3 workflow. Totally, 94% of DNA libraries and 81% of RNA libraries were of adequate quality for further downstream analysis. With the Oncomine™ filter chain there was an increased number of variants in the HPV-negative group (2.5 variants) compared to the HPV-associated group (1.5 variants). Using custom filter and the Varsome Clinical software; additional single nucleotide variants (SNV) were detected where the vast majority were classified as likely benign/benign. HPV-negative tumors had a larger fraction of variants of unknown significance (VUS), and likely pathogenic/pathogenic compared to the HPV-associated tumours. The top 10 frequently mutated genes in HPV-indepentent tumors were TP53, POLE, PTCH1, BRCA2, CREBBP, NOTCH2, ARID1A, CDKN2A, MSH2, and NOTCH1. Three fusion genes were detected; TBL1XR1(1)::PIK3CA(2) (n = 2) and NF1(5)::PSMD11(2) (n = 1). Copy number variations (CNV) were more common in HPV-associated tumors (n = 13/16, 81%) compared to HPV-negative tumors (n = 9/14, 64%). The most frequent CNV was found in the cMYC gene, followed by CDK2 (n = 5) and CDK4 (n = 4). The main outcome of this study show that vulvar cancer harbour genetic variations of different types and specifically, HPV-independent tumours are molecularly very heterogeneous and harboured more SNVs while HPV-associated tumors more frequently presented with gene amplifications. The PI3K/AKT/mTOR1 pathway was affected in both the groups as well as the cell cycle regulation pathway. Similarly, the DNA repair gene POLE was found mutated in both vulvar cancer groups.

Assessment of Exhaled Breath Condensate for ALK, RET, ROS1, and NTRK1 Fusion Transcript Detection in NSCLC: Comparison With Tissue and Liquid Biopsy Samples.

Lung cancer continues to be the primary cause of cancer-related deaths globally, with the majority of cases identified at advanced stages. Genetic alterations, including mutations and gene fusions, are central to its molecular pathogenesis. The discovery of therapeutically targetable gene fusions, such as ALK, RET, ROS1, and NTRK1, has significantly advanced lung cancer management. Conventional methods, such as tissue biopsies, are invasive and unsuitable for continuous molecular monitoring. Consequently, noninvasive approaches, such as liquid biopsies and exhaled breath condensate (EBC), offer promising options for real-time molecular surveillance. This study evaluates the feasibility of identifying fusion transcripts in 30 patients with lung adenocarcinoma by using next-generation sequencing (NGS) on formalin-fixed paraffin-embedded (FFPE) tissue, plasma, and EBC samples. Clinically significant fusion transcripts, including KIF5B-ALK, KIF5B-RET, and SQSTM1-ALK, were detected across different sample types. EBC samples showed strong concordance with tissue biopsy results, particularly in detecting ALK, ROS1, and RET fusions, and demonstrated greater sensitivity than plasma in detecting NTRK1 fusions. Additionally, 30 fusion transcripts of uncertain clinical significance were identified, highlighting the need for further research into their role in lung cancer pathogenesis. In conclusion, EBC samples provide a valuable, noninvasive medium for detecting clinically relevant and previously uncharacterized fusion transcripts in non-small cell lung cancer (NSCLC). The high concordance between EBC and tissue biopsies suggests that EBC could complement tissue biopsy for effective diagnosis and monitoring of NSCLC. These findings underscore the importance of comprehensive molecular profiling using multiple sample types to enhance diagnostic precision and optimize therapeutic outcomes in lung cancer management.

Novel method for classification of prion diseases by detecting PrPres signal patterns from formalin-fixed paraffin-embedded samples

ABSTRACT Prion disease is an infectious and fatal neurodegenerative disease. Western blotting (WB)-based identification of proteinase K (PK)-resistant prion protein (PrPres) is considered a definitive diagnosis of prion diseases. In this study, we aimed to detect PrPres using formalin-fixed paraffin-embedded (FFPE) specimens from cases of sporadic Creutzfeldt–Jakob disease (sCJD), Gerstmann–Sträussler–Scheinker disease (GSS), glycosylphosphatidylinositol-anchorless prion disease (GPIALP), and V180I CJD. FFPE samples were prepared after formic acid treatment to inactivate infectivity. After deparaffinization, PK digestion was performed, and the protein was extracted. In sCJD, a pronounced PrPres signal was observed, with antibodies specific for type 1 and type 2 PrPres exhibited a strong or weak signals depending on the case. Histological examination of serial sections revealed that the histological changes were compatible with the biochemical characteristics. In GSS and GPIALP, prion protein core-specific antibodies presented as PrPres bands at 8–9 kDa and smear bands, respectively. However, an antibody specific for the C-terminus presented as smears in GSS, with no PrPres detected in GPIALP. It was difficult to detect PrPres in V180I CJD. Collectively, our findings demonstrate the possibility of detecting PrPres in FFPE and classifying the prion disease types. This approach facilitates histopathological and biochemical evaluation in the same sample and is safe owing to the inactivation of infectivity. Therefore, it may be valuable for the diagnosis and research of prion diseases.

NanoCMSer: a consensus molecular subtype stratification tool for fresh‐frozen and paraffin‐embedded colorectal cancer samples

Colorectal cancer (CRC) is a significant contributor to cancer‐related mortality, emphasizing the need for advanced biomarkers to guide treatment. As part of an international consortium, we previously categorized CRCs into four consensus molecular subtypes (CMS1‐CMS4), showing promise for outcome prediction. To facilitate clinical integration of CMS classification in settings where formalin‐fixed paraffin‐embedded (FFPE) samples are routinely used, we developed NanoCMSer, a NanoString‐based CMS classifier using 55 genes. NanoCMSer achieved high accuracy rates, with 95% for fresh‐frozen samples from the MATCH cohort and 92% for FFPE samples from the CODE cohort, marking the highest reported accuracy for FFPE tissues to date. Additionally, it demonstrated 96% accuracy across a comprehensive collection of 23 RNAseq‐based datasets, compiled in this study, surpassing the performance of existing models. Classifying with only 55 genes, the CMS predictions were still biologically relevant, recognizing CMS‐specific biology upon enrichment analysis. Additionally, we observed substantial differences in recurrence‐free survival curves when comparing CMS2/3 patients in stage III versus II. Probability of recurrence after 5 years increased by 21% in CMS2 and 31% in CMS3 for patients in stage III, whereas this difference was less pronounced for CMS1 and CMS4, with 11% and 10%, respectively. We posit NanoCMSer as a robust tool for subtyping CRCs for both tumor biology and clinical practice, accessible via nanocmser r package (https://github.com/LEXORlab/NanoCMSer) and Shinyapp (https://atorang.shinyapps.io/NanoCMSer).

Towards Reliable Methodology: Microbiome Analysis of Fresh Frozen vs. Formalin-Fixed Paraffin-Embedded Bladder Tissue Samples: A Feasibility Study.

Studies have shown that the human microbiome influences the response to systemic immunotherapy. However, only scarce data exist on the impact of the urinary microbiome on the response rates of bladder cancer (BC) to local Bacillus Calmette-Guérin instillation therapy. We launched the prospective SILENT-EMPIRE study in 2022 to address this question. We report the results of the pilot study of SILENT-EMPIRE, which aimed to compare the microbiome between fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) samples in the cancerous tissue and adjacent healthy tissue of BC patients. Our results show that alpha diversity is increased in FF samples compared to FFPE (coverage index p = 0.041, core abundance index p = 0.008). No significant differences concerning alpha diversity could be detected between cancerous and non-cancerous tissue in the same BC patients. This study demonstrates that microbiome analysis from both FF and FFPE samples is feasible. Implementing this finding could aid in the translation of research findings into clinical practice.

RNA Polymerase II hypertranscription at histone genes in cancer FFPE samples.

Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our FFPE-CUTAC method for mapping RNA Polymerase II (RNAPII) genome-wide in formalin-fixed paraffin-embedded (FFPE) sections. We demonstrate global RNAPII elevations in mouse gliomas and assorted human tumors in small clinical samples and discover regional elevations corresponding to de novo HER2 amplifications punctuated by likely selective sweeps. RNAPII occupancy at replication-coupled histone genes correlated with WHO grade in meningiomas, accurately predicted rapid recurrence, and corresponded to whole-arm chromosome losses. Elevated RNAPII at histone genes in meningiomas and diverse breast cancers is consistent with histone production being rate-limiting for S-phase progression and histone gene hypertranscription driving overproliferation and aneuploidy in cancer, with general implications for precision oncology.

Clinicopathological significance of sulfite oxidase expression in surgically resected lung adenocarcinoma.

The coenzyme sulfite oxidase (SUOX), located in mitochondria, plays a role in redox and metabolism. Its expression has been associated with cancer progression and prognosis. Lung cancer has a high incidence rate and poor prognosis. We aim to clarify its expression in lung adenocarcinomas and investigated the utility of SUOX expression as a recurrence factor in operable lung adenocarcinoma. We used 60 formalin-fixed paraffin-embedded samples of operable primary lung adenocarcinoma between 2017 and 2018 to immunohistochemically assess SUOX expression levels. Patients were classified into a high or low SUOX expression group, and the associations of SUOX expression with clinicopathological findings and recurrence were analyzed. We revealed that high SUOX expression was significantly (p < 0.05) associated with sex, low Brinkman index, histological type, histological grade and positive for epidermal growth factor receptor (EGFR) mutation. High SUOX expression (HR = 10.218, 95% CI 1.758‒59.376, p = 0.0096) and pathological Stage (HR = 7.538, 95% CI 1.95‒29.14, p = 0.0034) were independently associated with relapse free survival. High SUOX expression may be a new indicator of recurrence risk in surgically resected lung adenocarcinomas.

The Roles of Vitamin D Receptor (VDR) and CD8+ T-Lymphocytes in Acral and Mucosal Melanoma Invasion Depth.

Acral and mucosal melanomas, the most common sun-shielded site melanoma subtypes in Asia and Indonesia, often yield poor prognoses. The invasion depth reflects their progressivity, and the pathogenesis is influenced by vitamin D receptor (VDR) status and CD8+ T-Lymphocyte amount. This study aims to determine the association between the invasion depth of acral and mucosal melanomas with their VDR and CD8+ immunoexpression. A cross-sectional observational study was conducted on 60 formalin-fixed paraffin-embedded (FPPE) samples, with equal representation in acral and mucosal melanoma groups from 2017 to 2021. The samples were assessed for the invasion depth and immunoexpression of VDR and CD8+. A chi-square test with an alternative Exact-Fisher analysis was used to determine the association between the variables in both subtype groups. An association between VDR and CD8+ immunoexpression and invasion depth in acral melanoma (p value = 0.0001 and 0.009, respectively) was observed, while only VDR immunoexpression was associated with the invasion depth in mucosal melanoma (p-value =0.004). Interestingly, no association was found between CD8+ immunoexpression and the invasion depth in mucosal melanoma (p = 0.640). The role of VDR and CD8+ T-lymphocytes are inversely associated with melanoma depth in acral melanoma, while only VDR is associated with melanoma depth in mucosal melanoma.

High frequency of HPV high-risk preventable genotypes in Ecuadorian women with invasive cervical cancer.

To determine the distribution of human papillomavirus (HPV) genotypes in invasive cervical cancer samples from Ecuadorian women who attended the Cancer Institute (Sociedad de Lucha Contra el Cáncer - SOLCA). Archived formalin-fixed paraffin-embedded (FFPE) cervical cancer tissue samples collected during 2017-2021 were deparaffinized, and nucleic acid extraction and purification was performed using silica columns. The obtained nucleic acids were analyzed using INNO-LiPA® HPV Genotyping Extra II per the manufacturer's specifications. Data were retrieved from records, and HPV genotypes were determined from the FFPE samples. The study included samples from 190 women diagnosed with invasive cervical cancer, with a median age of 52.78 years. Squamous cell carcinoma accounted for 78.94% of the cases, while 21.05% had adenocarcinoma. Among the 190 samples, 80.53% tested positive for HPV DNA, while 19.47% were negative. The most common genotypes detected were HPV 16 (64.05%), 18 (16.99%), and 58 (6.54%). HPV infection frequency was higher in samples from patients with elementary level education (p < 0.05). This study provides valuable insights into the distribution of HPV genotypes in invasive cervical cancer samples from Ecuadorian women. The results indicate an elevated presence of HPV 16, HPV 18, and HPV 58, which are vaccine-preventable genotypes.

Prevalence of SPOP and IDH Gene Mutations in Prostate Cancer in a Jordanian Population.

Speckle-type POZ (SPOP) is described as an essential tumor suppressor factor in gastric cancer, colorectal cancer, and prostate cancer (PCa). SPOP gene mutations were reported in primary human PCa. Isocitrate dehydrogenase-1 (IDH1) oncogene mutations were detected in gliomas, acute myeloid leukemia, some benign and malignant cartilaginous tumors, and only 1% of PCa. This study aimed to investigate the prevalence of mutations of SPOP and IDH1 genes in PCa in the Jordanian population. One hundred formalin-fixed paraffin-embedded tissue samples were collected from patients diagnosed with prostate adenocarcinoma. The obtained specimens were subjected to genomic DNA extraction, PCR amplification, and direct sequencing of exons 4, 5, 6, and 7 of the SPOP gene and exon 6 of the IDH1 gene. SPOP gene mutations were found in 17% of PCa cases, while no mutation was detected in the screened exon 6 of the IDH1 gene. Clinicopathological data demonstrated a strong correlation between prostate-specific antigen (PSA) levels and both Gleason score (GS) and the International Society of Urological Pathology (ISUP) grade group (GG). There was no significant correlation between PSA levels and age (p = 0.816) nor there were significant associations for SPOP mutational status with age (p = 0.659), PSA levels (p = 0.395), GS (p = 0.259), and ISUP GG (p = 0.424) in the tested population. The study found a strong correlation between PSA levels and both GS and ISUP GG. It also identified a high frequency (17%) of SPOP gene mutations in Jordanian Arab PCa patients, mainly in exon 7. No IDH1 mutations were detected in exon 6.

Identify characteristics of Vietnamese oral squamous cell carcinoma patients by machine learning on transcriptome and clinical-histopathological analysis

Background/purposeOral squamous cell carcinoma (OSCC) is notorious for its low survival rates, due to the advanced stage at which it is commonly diagnosed. To enhance early detection and improve prognostic assessments, our study harnesses the power of machine learning (ML) to dissect and interpret complex patterns within mRNA-sequencing (RNA-seq) data and clinical-histopathological features. Materials and methods206 retrospective Vietnamese OSCC formalin-fixed paraffin-embedded (FFPE) tumor samples, of which 101 were subjected to RNA-seq for classification based on gene expression. Then, learning models were built based on clinical-histopathological data to predict OSCC subtypes and propose potential biomarkers for the remaining 105 samples. Results2 distinct groups of OSCC with different clinical-histopathological characteristics and gene expression. Subgroup 1 was characterized by severe histopathologic features with immune response and apoptosis signatures while subgroup 2 was denoted by more clinical/pathological features, cell division and malignant signatures. XGBoost and SVM (Support Vector Machine) models showed the best performance in predicting subtype OSCC. The study also proposed 12 candidate genes as potential biomarkers for OSCC subtypes (6/group). ConclusionThe study identified characteristics of Vietnamese OSCC patients through a combination of mRNA sequencing and clinical-histopathological analysis. It contributes to the insight into the tumor microenvironment of OSCC and provides accurate ML models for biomarker prediction using clinical-histopathological features.