Targeted molecular profiling of epithelial ovarian cancer from Italian BRCA wild-type patients with a BRCA and PARP pathways gene panel.

Ovarian cancer (OC) is the fifth most common type of cancer in women and the fourth most common cause of cancer death in women. Identification of pathogenic variants in OC tissues has an important clinical significance for therapeutic and prevention purposes. This study aims to evaluate the mutational profile of a patient cohort, negative for BRCA1/2 germinal variants and Mismatch Repair defects, using next-generation sequencing (NGS) approach on DNA from formalin-fixed paraffin-embedded samples. We used a custom NGS panel, targeting 34 cancer-related genes, mainly of the BRCA and PARP pathways, and analyzed NGS data to identify somatic and germline variants in Italian patients affected by primary epithelial ovarian cancer. We analyzed 75 epithelial ovarian cancer tissues and identified 54 pathogenic variants and 56 variants of unknown significance. TP53 was characterized by the highest mutational rate, occurring in 55% of tested epithelial ovarian cancers (EOCs). Interestingly, a subset of 8 EOCs showed pathogenic variants of homologous recombination pathway, which could be sensitive to PARP-inhibitor therapies. Germline analysis of actionable genes revealed 4 patients carrier of pathogenic germline variants respectively of RAD51C (2 patients), RAD51D, and PALB2. Molecular profiling of EOCs using our custom NGS panel has enabled the detection of both somatic and germline variants, allowing the selection of patients suitable for targeted therapies, and the identification of high-risk OC families that can benefit from genetic counseling and testing.

Unveiling the risks of ChatGPT in diagnostic surgical pathology.

ChatGPT, an AI capable of processing and generating human-like language, has been studied in medical education and care, yet its potential in histopathological diagnosis remains unexplored. This study evaluates ChatGPT's reliability in addressing pathology-related diagnostic questions across ten subspecialties and its ability to provide scientific references. We crafted five clinico-pathological scenarios per subspecialty, simulating a pathologist using ChatGPT to refine differential diagnoses. Each scenario, aligned with current diagnostic guidelines and validated by expert pathologists, was posed as open-ended or multiple-choice questions, either requesting scientific references or not. Outputs were assessed by six pathologists according to. (1) usefulness in supporting the diagnosis and (2) absolute number of errors. We used directed acyclic graphs and structural causal models to determine the effect of each scenario type, field, question modality, and pathologist evaluation. We yielded 894 evaluations. ChatGPT provided useful answers in 62.2% of cases, and 32.1% of outputs contained no errors, while the remaining had at least one error. ChatGPT provided 214 bibliographic references: 70.1% correct, 12.1% inaccurate, and 17.8% non-existing. Scenario variability had the greatest impact on ratings, and latent knowledge across fields showed minimal variation. Although ChatGPT provided useful responses in one-third of cases, the frequency of errors and variability underscores its inadequacy for routine diagnostic use and highlights the need for discretion as a support tool. Imprecise referencing also suggests caution as a self-learning tool. It is essential to recognize the irreplaceable role of human experts in synthesizing images, clinical data, and experience for the intricate task of histopathological diagnosis.

Immunohistochemical and molecular pattern of p53 in epithelial ovarian cancers negative for germline BRCA1/2 variants.

Epithelial ovarian cancers (EOC) associated with germline or somatic BRCA pathogenetic variants have a significantly higher rate of TP53aberrations. The majority of TP53 mutations are detectable by immunohistochemistry and several studies demonstrated that an abnormal p53 pattern characterized high-grade EOCs. An abnormal p53 immunohistochemical staining in fallopian tube (serous tubal intraepithelial carcinoma (STIC) and "p53 signature" is considered as a precancerous lesion of high-grade EOCs and it is often found in fallopian tube tissues of BRCA germline mutated patients suggesting that STIC is an early lesion and the TP53 mutation is an early driver event of BRCA mutated high-grade EOCs. No relevant data are present in literature about the involvement of p53 abnormal pattern in EOC carcinogenesis of patients negative for germline BRCA variants. We describe TP53 mutation results in relationship to the immunohistochemical pattern of p53 expression in a series of EOCs negative for BRCA1 and BRCA2 germline mutations. In addition, we also investigated STIC presence and "p53 signature" in fallopian tube sampling of these EOCs. Our results demonstrate that TP53 alterations are frequent and early events in sporadic EOCs including also low-grade carcinomas. Also in this series, STIC is associated with an abnormal p53 pattern in fallopian tubes of high-grade EOCs. In summary, TP53 aberrations are the most frequent and early molecular events in EOC carcinogenesis independently from BRCA mutation status.

Similarities and differences in gene expression profiles of BRCA1 methylated and mutated epithelial ovarian cancers.

Introduction: BRCA1 methylated (BRCA1met) epithelial ovarian cancer (EOC) is a recently defined and not well-investigated subset of neoplasms. To date, no studies have focused on the transcriptional profiles of BRCA1met cases, and, as a matter of fact, we still do not know if this subset of EOCs is similar, and to what extent, to BRCA1 mutated (BRCA1mut) cases. Methods: We compared a group of 17 BRCA1met cases against 10 BRCA1mut cases using a subset of carefully selected 17 BRCAwt EOCs as a control group. Results: First, BRCA1met cases showed a downregulation of the relative transcript, while this association was not observed for BRCA1mut EOCs. The BRCA1met group exhibited a general upregulation of homologous recombination (HR)-related genes, as well as BRCA1mut. Overall, BRCA1met had a different gene expression profile, characterized by diffuse downregulation, whereas BRCA1mut showed a general upregulation (p < 0.0001). Both BRCA1-defective groups showed a slightly activated immune response mediated by interferon (IFN) gamma pathways. Discussion: In conclusion, even if the expression profile of many genes related to DNA damage and repair system is shared between BRCA1mut and BRCA1met EOCs supporting that BRCA1met EOCs may benefit from PARPi therapies, our data demonstrate that BRCA1mut and BRCA1met EOCs show different expression profiles, suggesting a different mechanism of carcinogenesis that can be reflected in different responses to therapies and disease recovery.

Immunohistochemical and histomorphometric study of human uvula innervation: a comparative analysis of non-snorers versus apneic snorers.

OBJECTIVE: The objective of this study was to verify a possible correlation between the etiology of uvulopalatal ptosis and decrease in palatopharyngeal muscle tone, due to a reduction of the number of nerve fibers in surgical specimens obtained from snoring patients. DESIGN/SETTING OF THE STUDY: We have designed a comparative retrospective, case-control, double-blind, immunohistochemical and histomorphometric study of human uvula innervation in 51 apneic snoring patients who underwent uvulopalatopharyngoplasty (UPPP) and 47 normal subjects collected in a 5-year-long period in the Departments of Otolaryngology of Desio and Forlì Hospital, Italy. PATIENTS: Case study was chosen in patients who underwent UPPP, variably associated with other disobstructive surgical procedures for treatment of obstructive sleep apnea syndrome, classified according to current clinical, polysomnographic, endoscopic, and imaging criteria. Control subjects were recruited at the Institute of Legal Medicine, University of Milan, according to strong inclusion and exclusion criteria. The main outcome measure of the study was the number of nerve fibers in the patients' uvula evaluated histologically and repeated two times by two different people, in all the areas of the specimens. Finally, we correlated the area of the histological section with the number of fibers contained therein. RESULTS: The number of nerve fibers varied from a minimum of 58 to a maximum of 163 in normal subjects. In the snoring patient population, the number of nerve fibers varied from a minimum of 22 to a maximum of 126 (statistically significant difference, p < 0.0001). In conclusion, our results direct toward a clear neurogenetic predisposition to uvulopalatal ptosis, marked ab initio by a lower set of motor nerve fibers, which may be the initial stage of another subsequent morphological and functional abnormality.

IDH-wildtype lower-grade diffuse gliomas: the importance of histological grade and molecular assessment for prognostic stratification.

BACKGROUND: Isocitrate dehydrogenase (IDH) wildtype (wt) grade II gliomas are a rare and heterogeneous entity. Survival and prognostic factors are poorly defined. METHODS: We searched retrospectively all patients diagnosed with diffuse World Health Organization (WHO) grades II and III gliomas at our center (1989-2020). RESULTS: Out of 517 grade II gliomas, 47 were "diffuse astrocytomas, IDHwt." Tumors frequently had fronto-temporo-insular location (28/47, 60%) and infiltrative behavior. We found telomerase reverse transcriptase (TERT) promoter mutations (23/45, 51%), whole chromosome 7 gains (10/37, 27%), whole chromosome 10 losses (10/41, 24%), and EGFR amplifications (4/43, 9%), but no TP53 mutations (0/22, 0%). Median overall survival (OS) was 59 months (vs 19 mo for IDHwt grade III gliomas) (P < 0.0001). Twenty-nine patients (29/43, 67%) met the definition of molecular glioblastoma according to cIMPACT-NOW update 3. Median OS in this subset was 42 months, which was shorter compared with patients with IDHwt grade II gliomas not meeting this definition (median OS: 57 mo), but substantially longer compared with IDHwt grade III gliomas meeting the definition for molecular glioblastoma (median OS: 17 mo, P < 0.0001). Most patients with IDHwt grade II gliomas met cIMPACT criteria because of isolated TERT promoter mutations (16/26, 62%), which were not predictive of poor outcome (median OS: 88 mo). Actionable targets, including 5 gene fusions involving FGFR3, were found in 7 patients (24%). CONCLUSIONS: Our findings highlight the importance of histological grading and molecular profiling for the prognostic stratification of IDHwt gliomas and suggest some caution when assimilating IDHwt grade II gliomas to molecular glioblastomas, especially those with isolated TERT promoter mutation.

The molecular landscape of glioma in patients with Neurofibromatosis 1.

Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome in which glioma is one of the prevalent tumors. Gliomagenesis in NF1 results in a heterogeneous spectrum of low- to high-grade neoplasms occurring during the entire lifespan of patients. The pattern of genetic and epigenetic alterations of glioma that develops in NF1 patients and the similarities with sporadic glioma remain unknown. Here, we present the molecular landscape of low- and high-grade gliomas in patients affected by NF1 (NF1-glioma). We found that the predisposing germline mutation of the NF1 gene was frequently converted to homozygosity and the somatic mutational load of NF1-glioma was influenced by age and grade. High-grade tumors harbored genetic alterations of TP53 and CDKN2A, frequent mutations of ATRX associated with Alternative Lengthening of Telomere, and were enriched in genetic alterations of transcription/chromatin regulation and PI3 kinase pathways. Low-grade tumors exhibited fewer mutations that were over-represented in genes of the MAP kinase pathway. Approximately 50% of low-grade NF1-gliomas displayed an immune signature, T lymphocyte infiltrates, and increased neo-antigen load. DNA methylation assigned NF1-glioma to LGm6, a poorly defined Isocitrate Dehydrogenase 1 wild-type subgroup enriched with ATRX mutations. Thus, the profiling of NF1-glioma defined a distinct landscape that recapitulates a subset of sporadic tumors.

Antigen Masking During Fixation and Embedding, Dissected.

Antigen masking in routinely processed tissue is a poorly understood process caused by multiple factors. We sought to dissect the effect on antigenicity of each step of processing by using frozen sections as proxies of the whole tissue. An equivalent extent of antigen masking occurs across variable fixation times at room temperature. Most antigens benefit from longer fixation times (>24 hr) for optimal detection after antigen retrieval (AR; for example, Ki-67, bcl-2, ER). The transfer to a graded alcohol series results in an enhanced staining effect, reproduced by treating the sections with detergents, possibly because of a better access of the polymeric immunohistochemical detection system to tissue structures. A second round of masking occurs upon entering the clearing agent, mostly at the paraffin embedding step. This may depend on the non-freezable water removal. AR fully reverses the masking due both to the fixation time and the paraffin embedding. AR itself destroys some epitopes which do not survive routine processing. Processed frozen sections are a tool to investigate fixation and processing requirements for antigens in routine specimens.

Disaccharides Protect Antigens from Drying-Induced Damage in Routinely Processed Tissue Sections.

Drying of the tissue section, partial or total, during immunostaining negatively affects both the staining of tissue antigens and the ability to remove previously deposited antibody layers, particularly during sequential rounds of de-staining and re-staining for multiple antigens. The cause is a progressive loss of the protein-associated water up to the removal of the non-freezable water, a step which abolishes the immunoavailability of the epitope. In order to describe and prevent these adverse effects, we tested, among other substances, sugars, which are known to protect unicellular organisms from freezing and dehydration, and stabilize drugs and reagents in solid state form in medical devices. Disaccharides (lactose, sucrose) prevented the air drying-induced antigen masking and protected tissue-bound antigens and antibodies from air drying-induced damage. Complete removal of the bound antibody layers by chemical stripping was permitted if lactose was present during air drying. Lactose, sucrose and other disaccharides prevent air drying artifacts, allow homogeneous, consistent staining and the reuse of formalin-fixed, paraffin-embedded tissue sections for repeated immunostaining rounds by guaranteeing constant staining quality in suboptimal hydration conditions.

HER2 status of gastric carcinoma and corresponding lymph node metastasis.

Our goal is to verify HER2 status variability between primary tumor and metastatic site. Our second intention is to identify the most reliable criteria for pathological HER2 status assessment in gastric cancer node metastases since, at present, there is not a validated standard. 3 independent pathologists evaluated HER2 immunohistochemical and gene status (for IHC 2+ cases) in 34 gastric carcinoma metastatic lymph nodes and in their corresponding primary tumors. For primary gastric cancers, we followed the current HER2 assessment guidelines and for nodal metastases, we applied two immunohistochemical scoring systems with different cut-offs. The immunohistochemical inter-pathologists mean agreement was 71.4 % (κ = 0.45); a final score for each case was defined after collegial revision. By applying the two immunohistochemical criteria, we found 2 discordant cases, which can imply different pathological management. Moreover, a significantly different HER2 status between lymph node metastasis and primary tumor was obtained in 4 cases (concordance ratio 87.5 %). None of the patients would have undergone a different therapeutic pathway despite the scoring method applied. On the other hand we also detected a subset of patients who could have their therapeutic management changed, according to the differences between HER2 status in lymph nodes metastases and primary tumor.