Formalin-fixed Paraffin-embedded Tissue Blocks Research Articles

The diagnostic potentiality of the RNA aptamer against progesterone receptor isolated by crush and soak (CRUSOAK)-SELEX.

Aptamers are a class of molecular recognition elements that exhibit high binding affinity and specificity against their respective targets. In view of the many advantages aptamers harbor over their counterpart antibodies, we were impelled to isolate an RNA aptamer against progesterone receptor, particularly its DNA binding domain. A total of eight SELEX cycles were executed against the recombinant Progesterone Receptor DNA-binding domain (PR DBD). The RNA-protein complex in the gel shift assay was subjected to crush and soak method to elute the binders prior to conventional sequencing, the step of which was based upon to coin the term CRUSOAK-SELEX. The sequencing revealed three different classes of sequences, with one class termed, PRapt-3, showing the strongest binding against PR DBD. The dissociation constant of PRapt-3 RNA aptamer was estimated at 380nM ± 35nM. PRapt-3 was successfully used to develop aptamer-based diagnostic assays such as ELASA, aptamer-based dot blot, and aptamer-based western blot. The prominent highlight is the performance of the aptamer in aptacytostaining, which was unachievable with antibodies. Compared to its counterpart antibodies, PRapt-3 has a better penetration capacity in aptahistostaining using the formalin-fixed paraffin-embedded (FFPE) breast cancer cells and tissue blocks. This study represents the first ever demonstration of an aptamer against progesterone receptor and its diagnostic capacity.

Abstract PS11-07: High prevalence of HER2-Low and AR expression in breast cancer brain metastases provide novel therapeutic options

Abstract Background: Although survival rates for patients with advanced breast cancer (BC) have improved overall, rates of BC brain metastases (BCBM) have increased over the past two decades, occurring in up to 15% to 30% of patients. BCBM greatly reduce quality of life and overall survival (OS) and are now the leading cause of BC patient mortality. Patients with primary HER2+ and triple negative BC (TNBC) are at highest risk for BM. Locoregional therapy with surgery and radiation are currently standard of care (SOC), but these treatments have significant morbidity and BCBM progressing despite these interventions are hard to treat. Systemic therapies to reduce cognitive impairment and increase survival are desperately needed, particularly in HER2-negative patients. Currently, immune checkpoint inhibitors (ICIs) and small molecules such as PARP inhibitors are among the limited systemic options that have BCBM activity in HER2-negative BC. However, the benefit of these therapies is limited to a select group of patients. For example, androgen receptor (AR) is expressed in 60-80% of all BC and, in our recently completed clinical trial (NCT03206203), patients with AR+ metastatic TNBC treated with carboplatin +/- atezolizumab received no clinical benefit from the addition of atezolizumab. Alternatives to ICIs are needed for patients with AR+ TNBC. HER2-low (H2L) BC is a newly defined subset of HER2-negative BC with a HER2 immunohistochemical (IHC) score of 1+ ( >10%) or 2+/in situ hybridization (ISH) negative phenotype. Recent clinical trials have demonstrated significant clinical benefit from novel HER2 antibody-drug conjugates (ADCs) in treating H2L BC. Trastuzumab-deruxtecan (T-Dxd), a HER2-directing ADC (topoisomerase I inhibitor conjugated to a humanized HER2-targeted antibody) was recently FDA approved as the first targeted therapy to treat H2L BC and can penetrate the blood–brain barrier. DESTINY-Breast04 demonstrated notable PFS and OS benefit of T-DXd compared to SOC in patients with H2L metastatic BC and included 61 patients with BCBM (results anticipated shortly). The overall rates of AR and H2L expression in patients with BCBM is unknown. The goal of this study is to investigate the prevalence of AR and HER2-low expression in a large cohort of BCBM treated at our institution. Methods: We retrospectively assessed rates of H2L and AR positivity (AR+) among patients with BCBM whose treatment included surgery at our institution between 2005-2023. Results were correlated with clinical receptor status (HR+/HER2-, HER2+/HR+, HER2+/HR- and TNBC) and clinical characteristics. Results of ER, PR, and HER2 testing performed for clinical purposes on the brain metastases and primary tumors were obtained from pathology reports. We retrieved formalin-fixed paraffin-embedded tissue blocks of the brain metastases and performed IHC for AR (SP107) and prognostic markers for cases with missing data. Results: We identified 101 cases of BCBM. Based on clinical prognostic markers, BCBM subtypes were HR+/HER2- (22%), HR+/HER2+ (14%), HER2+/HR- (21%) and TNBC (43%). Forty-five percent of the BCBM (n=45) were AR+ ( >10%) and 24% (n=24) demonstrated > 50% AR+. Among tumors with >50% AR+, 42% (n=10) are H2L (7 HR+[30%] and 3 TNBC [13%]). Forty-two percent of BCBM were H2L. Among the HER2-negative BCBM (n= 66), 64% (n=42) were H2L, including 23 of 44 TNBC (52%) and 19 of 22 HR+ (86)%. Fifteen percent of BMBC changed clinical subtype from the primary, including conversion to TNBC and H2L. Conclusion: AR+ positive (24% > 50% expression) and HER2-Low expressing (42%) tumors represent a significant proportion of our BCBM cohort providing exciting new options for treatment. Trials re-evaluating AR antagonists in combination with SOC utilizing high AR+ thresholds may benefit patients with BCBM. At least 10% of BCBM are both H2L and demonstrate >50% AR positivity providing the rationale for the combination of ADCs such as T-DXd and AR-targeted therapies for BCBM. Citation Format: Guadalupe Garcia, Paula Gonzalez-Ericsson, Brian Lehmann, Bret Mobley, Jennifer Pietenpol, Laura Kennedy, Ben Park, Melinda Sanders. High prevalence of HER2-Low and AR expression in breast cancer brain metastases provide novel therapeutic options [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS11-07.

Evaluation of stromal myofibroblasts in oral submucous fibrosis and its malignant transformation: An immunohistochemical study.

Oral submucous fibrosis (OSF) is a precancerous lesion, with oral squamous cell carcinoma (OSCC) being the most prevalent malignancy affecting the oral mucosa. The malignant transformation of OSF into OSCC is estimated to occur in 7-13% of cases. Myofibroblasts (MFs) play pivotal roles in both physiological and pathological processes, such as wound healing and tumorigenesis, respectively. This study aimed to explore the involvement of MFs in the progression of OSF and its malignant transformation. In total, 94 formalin-fixed paraffin-embedded tissue blocks were collected, including normal oral mucosa (NOM; n = 10), early-moderate OSF (EMOSF; n = 29), advanced OSF (AOSF; n = 29), paracancerous OSF (POSF; n = 21), and OSCC (n = 5) samples. Alpha-smooth muscle actin was used for the immunohistochemical identification of MFs. NOM exhibited infrequent expression of MFs. A higher staining index of MFs was found in AOSF, followed by EMOSF and NOM. Additionally, a significant increase in the staining index of MFs was found from EMOSF to POSF and OSCC. The staining index of MFs in NOM, EMOSF, AOSF, POSF, and OSCC was 0.14 ± 0.2, 1.69 ± 1.4, 2.47 ± 1.2, 3.57 ± 2.6, and 8.86 ± 1.4, respectively. All results were statistically significant (P < 0.05). The expression of MFs exhibited a gradual increase as the disease progressed from mild to malignant transformation, indicating the contributory role of MFs in the fibrogenesis and potential tumorigenesis associated with OSF.

Abstract 3623: Quantifying pharmacodynamic markers of radioligand therapies in tumor by multiplex immunofluorescence and automated quantitative analysis (AQUA) algorithms

Abstract Purpose: Due to profound clinical successes observed with radioligand therapies (RLT) across multiple cancers coupled with advances in drug handling and delivery logistics recently, clinical trials investigating RLTs are on the rise. Ionizing radiation produced by radioisotopes linked to antibodies causes double-stranded breaks either directly or via generation of reactive oxygen species. This type of DNA damage is associated with an increase in proteins mediating cell cycle arrest (e.g., p21/CIP1) and repairing damaged DNA (e.g., CHK2 and γH2Ax). Additionally, proliferating cells (identifiable by Ki67) are most susceptible to ionizing radiation as DNA is exposed during the mitotic phase of the cell cycle. We incorporated these biologically verified markers into a multiplexed fluorescence immunohistochemistry (mFIHC) assay for robust quantitation of the pharmacodynamic activity of RLTs and gain insights into the DNA damage response in on-treatment tumor core biopsies. Study Design: We designed a novel mFIHC assay incorporating antibodies to p21, pCHK2, γH2Ax, Ki67, CK to quantitatively characterize DNA damage across five tumor indications of commercially available ovarian cancer, colorectal cancer, gastric cancer, endometrial (uterine) cancer, and breast cancer formalin-fixed paraffin-embedded (FFPE) tissue blocks. We successfully validated this mFIHC assay using automated staining (Bond RX), imaging (PhenoImager HT), and combined with hypothesis-driven spatial profiling algorithms (e.g., AQUA Technology). Results: Sensitivity and specificity were confirmed on known positive and negative controls. Reproducibility and precision were observed across instruments, operators, and independent experiments for all markers The frequency of p21 ranged from 5% - 8%, pCHK2 from 3% - 36%, pH2Ax from 0% - 8%, Ki67 from 4% - 61%, and CK cells ranged from 25% to 87%. Over 56 unique parameters were evaluated. The prevalence of p21, pCHK2, and γH2Ax ranged from 0% to &amp;gt;30% across five tumor indications tested and were highly concordant. Conclusion: The validated mFIHC assay examines the expression of proteins mediating cell cycle arrest and DNA damage in tumor and stromal cells. This panel may be used to further understand the complexity of DNA damage response pathways in tumor and non-tumor areas in the context of RLT clinical trials. Citation Format: James Santos, Virginia Nyanchama, Vincent Romanet, Ernesta Dammassa, Lisa Kattenhorn, Ying Huang, Jimmie Lim, Xun Li, James Deeds, Lori Iaconis, Emmanuel Pacia, Margaret McLaughlin, Naveen Dakappagari, Jennifer Bordeaux. Quantifying pharmacodynamic markers of radioligand therapies in tumor by multiplex immunofluorescence and automated quantitative analysis (AQUA) algorithms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3623.

Abstract 196: In vitro modeling of pediatric solid tumor lung metastases

Abstract Metastasis remains the main cause of death in pediatric cancer patients with the lung being one of the most common affected organs. Our inability to cure these patients is largely due to insufficient knowledge about tumor and metastatic niche plasticity, while existing models are not fully effective in mirroring the response seen in clinical setting. Our goal is to overcome these limitations by establishing in vitro lung metastasis models using tumor/lung organoid co-cultures to study lung infiltration of pediatric solid tumors. We successfully established patient-derived lung organoids from pediatric lung tissue and characterized them according to the presence and the localization of the respective lung epithelial cell types. Co-culture conditions of lung organoids with PDX-derived Ewing sarcoma and osteosarcoma cells were optimized and models established, while the establishment of models for other pediatric solid tumor entities is ongoing. We have observed infiltration of the lung organoids by tumor cells, and our preliminary findings suggest distinct patterns of infiltration among different tumor entities. Furthermore, we have performed single-cell RNA sequencing analysis on these co-cultures in comparison to the parental lung organoids and tumor cells, aiming to uncover the specific signaling pathways activated in the lung metastatic niche in response to tumor cell invasion. Additionally, experiments using conditioned medium suggest that the lung organoid secretome is sufficient to induce homing of osteosarcoma and Ewing sarcoma cells to the organoids, with the CXCL12/CXCR4 signaling axis as a prime candidate driver. To ascertain the extent to which our in vitro model recapitulates the in vivo lung metastatic niche, we performed spatial transcriptomics (using VISIUM/10X Genomics) on formalin-fixed paraffin-embedded (FFPE) tissue blocks of paired primary tumors and lung metastasis samples for Ewing sarcoma and osteosarcoma. Comprehensive data analysis is currently ongoing, which will instruct a stepwise incorporation of additional factors into our modular organoid co-culture model, resulting in a better representation of the lung metastatic niche. Further, the analysis of patient-derived material will elucidate the spatial organization of solid tumor lung metastases and contribute to the identification of signaling pathways implicated in lung infiltration. In conclusion, our study not only unravels the complexities of pediatric solid tumor metastasis, but also lays the foundation for exploring the anti-metastatic potential of pathway-specific compounds targeting tumor/lung interactions using the established in vitro lung metastasis models. This study is supported by grant 35353-B of the Austrian Science Fund. Citation Format: Martha Zylka, Christoph Hafemeister, Lukas Watzke, Ulrike Mann, Didier Surdez, E. Alejandro Sweet-Cordero, Bernadette Liegl-Atzwanger, Matthias Dettmer, Matthias Farlik, Florian Halbritter, Martin Metzelder, Heinrich Kovar, Branka Radic-Sarikas. In vitro modeling of pediatric solid tumor lung metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 196.

High rate of high-risk human papillomavirus among benign and breast cancer patients in Ethiopia.

There have been numerous studies that showed the presence of human papillomavirus (HPV) in breast cancer; nonetheless, there is ongoing debate regarding their association. Given few studies in Ethiopia, we aimed to investigate the magnitude of HPV infection in Ethiopian breast cancer patients. A total of 120 formalin-fixed paraffin-embedded (FFPE) tissue blocks were obtained, and basic demographic, clinical, and histological data were collected from medical records. DNA was extracted from archived FFPE breast tissue specimens using GeneRead DNA FFPE Kit. The AnyplexTM II HPV28 Detection Kit (Seegene, Korea) was used to detect HPV by following the manufacturer's instructions. The SPSS Version 25 was used to enter and analyze data. Among the 120 study participants; HPV (both high-risk and low-risk) was detected in 20.6% of breast cancer and 29.6% of non-malignant breast tumors. The most common genotype was the high-risk HPV 16 genotype. The frequency of HPV was nearly 10-fold higher in estrogen receptor-positive than ER-negative breast cancer. The percentage of HPV in the luminal (luminal A and luminal B) breast cancer subtypes was also much higher than in the non-luminal subtypes (HER-2 enriched and triple-negative breast cancer). This study did not find a significant difference in HPV expression between breast cancer and non-malignant breast tumors; however, the higher percentage of HPV in ER-positive compared to ER-negative breast cancer warrants further attention.

The spectrum of TP53 mutations in Rwandan patients with gastric cancer

BackgroundGastric cancer is the sixth most frequently diagnosed cancer and third in causing cancer-related death globally. The most frequently mutated gene in human cancers is TP53, which plays a pivotal role in cancer initiation and progression. In Africa, particularly in Rwanda, data on TP53 mutations are lacking. Therefore, this study intended to obtain TP53 mutation status in Rwandan patients with gastric cancer.ResultsFormalin-fixed paraffin-embedded tissue blocks of 95 Rwandan patients with histopathologically proven gastric carcinoma were obtained from the University Teaching Hospital of Kigali. After DNA extraction, all coding regions of the TP53 gene and the exon–intron boundary region of TP53 were sequenced using the Sanger sequencing. Mutated TP53 were observed in 24 (25.3%) of the 95 cases, and a total of 29 mutations were identified. These TP53 mutations were distributed between exon 4 and 8 and most of them were missense mutations (19/29; 65.5%). Immunohistochemical analysis for TP53 revealed that most of the TP53 missense mutations were associated with TP53 protein accumulation. Among the 29 mutations, one was novel (c.459_477delCGGCACCCGCGTCCGCGCC). This 19-bp deletion mutation in exon 5 caused the production of truncated TP53 protein (p.G154Wfs*10). Regarding the spectrum of TP53 mutations, G:C > A:T at CpG sites was the most prevalent (10/29; 34.5%) and G:C > T:A was the second most prevalent (7/29; 24.1%). Interestingly, when the mutation spectrum of TP53 was compared to three previous TP53 mutational studies on non-Rwandan patients with gastric cancer, G:C > T:A mutations were significantly more frequent in this study than in our previous study (p = 0.013), the TCGA database (p = 0.017), and a previous study on patients from Hong Kong (p = 0.006). Even after correcting for false discovery, statistical significance was observed.ConclusionsOur results suggested that TP53 G:C > T:A transversion mutation in Rwandan patients with gastric cancer is more frequent than in non-Rwandan patients with gastric cancer, indicating at an alternative etiological and carcinogenic progression of gastric cancer in Rwanda.

High Concordance of Different Assays in the Determination of Homologous Recombination Deficiency-Associated Genomic Instability in Ovarian Cancer.

Poly(ADP-ribose) polymerase inhibitors (PARPi) have shown promising clinical results in the treatment of ovarian cancer. Analysis of biomarker subgroups consistently revealed higher benefits for patients with homologous recombination deficiency (HRD). The test that is most often used for the detection of HRD in clinical studies is the Myriad myChoice assay. However, other assays can also be used to assess biomarkers, which are indicative of HRD, genomic instability (GI), and BRCA1/2 mutation status. Many of these assays have high potential to be broadly applied in clinical routine diagnostics in a time-effective decentralized manner. Here, we compare the performance of a multitude of alternative assays in comparison with Myriad myChoice in high-grade serous ovarian cancer (HGSOC). DNA from HGSOC samples was extracted from formalin-fixed paraffin-embedded tissue blocks of cases previously run with the Myriad myChoice assay, and GI was measured by multiple molecular assays (CytoSNP, AmoyDx, Illumina TSO500 HRD, OncoScan, NOGGO GISv1, QIAseq HRD Panel and whole genome sequencing), applying different bioinformatics algorithms. Application of different assays to assess GI, including Myriad myChoice, revealed high concordance of the generated scores ranging from very substantial to nearly perfect fit, depending on the assay and bioinformatics pipelines applied. Interlaboratory comparison of assays also showed high concordance of GI scores. Assays for GI assessment not only show a high concordance with each other but also in correlation with Myriad myChoice. Thus, almost all of the assays included here can be used effectively to assess HRD-associated GI in the clinical setting. This is important as PARPi treatment on the basis of these tests is compliant with European Medicines Agency approvals, which are methodologically not test-bound.

A radiologic-pathologic study of the histopathologic variants of ameloblastomas and their proliferation indices

Objectives: This study aimed to analyze the clinicoradiologic features and Ki-67 proliferation indices between the histopathologic variants of ameloblastomas (ABs) for possible associations. Study design: The diagnosis and histopathologic variant were confirmed for all cases by experienced Oral and Maxillofacial Pathologists. Immunohistochemistry for Ki-67 was performed on the most representative formalin-fixed paraffin-embedded tissue block. Demographic, clinical data and radiologic features were analyzed from patient records and available radiographic examinations. The investigators were blinded to the histopathologic variant and proliferation index when the clinicoradiologic features were assessed. Results: The current study included 116 cases of AB in the final sample. The indolent behavior of the unicystic variant was supported by their low proliferation index and slow growth paired with low frequencies of cortical destruction, loss of teeth, root resorption, and encroachment on anatomical structures. In contrast, the comparatively high proliferation index of the plexiform variant correlated with their fast growth and pain. Furthermore, high radiologic frequencies of cortical destruction, loss of teeth, and encroachment of surrounding anatomical structures supported their more aggressive clinical course. Conclusion: Statistically significant differences were noted between certain variants and Ki-67, location, borders, locularity, and cortical destruction, providing better insight into their biological behavior.

Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study

BackgroundTongue squamous cell carcinoma (TSCC) is the most common oral cavity cancer, and p16 immunohistochemistry is an exact and available tool in the prognostic and predictive characterization of squamous cell cancers in the head and neck. Microorganisms have a close relationship with the development of TSCC. However, the association between oral bacteria and p16 status has not been well defined in the case of TSCC. Compared with traditional clinical microbial collection methods, formalin-fixed paraffin-embedded (FFPE) tissue samples have several advantages.MethodsTo compare the microbiota compositions between p16-positive and p16-negative patients with TSCC, we performed a small pilot study of microbiological studies of TSCC by paraffin tissue. DNA from FFPE tissue blocks were extracted and microbiomes were profiled by sequencing the 16 S-rRNA-encoding gene (V1–V2/V3-V4/V4 regions). Alterations in the functional potential of the microbiome were predicted using PICRUSt, Tax4Fun, and BugBase.ResultsA total of 60 patients with TSCC were enrolled in the study, however, some challenges associated with DNA damage in FFPE tissues existed, and only 27 (15 p16-positive and 12 p16-negative) passed DNA quality control. Nevertheless, we have tentatively found some meaningful results. The p16 status is associated with microbiota diversity, which is significantly increased in p16-positive patients compared with p16-negative patients. Desulfobacteria, Limnochordia, Phycisphaerae, Anaerolineae, Saccharimonadia and Kapabacteria had higher abundances among participants with p16-positive. Moreover, functional prediction revealed that the increase of these bacteria may enhance viral carcinogenesis in p16-positive TSCC.ConclusionsBacterial profiles showed a significant difference between p16-positive TSCC and p16-negative TSCC. These findings may provide insights into the relationship between p16 status and the microbial taxa in TSCC, and these bacteria may provide new clues for developing therapeutic targets for TSCC.

Robust detection of clinically relevant features in single-cell RNA profiles of patient-matched fresh and formalin-fixed paraffin-embedded (FFPE) lung cancer tissue.

Single-cell transcriptional profiling reveals cell heterogeneity and clinically relevant traits in intra-operatively collected patient-derived tissue. So far, single-cell studies have been constrained by the requirement for prospectively collected fresh or cryopreserved tissue. This limitation might be overcome by recent technical developments enabling single-cell analysis of FFPE tissue. We benchmark single-cell profiles from patient-matched fresh, cryopreserved and archival FFPE cancer tissue. We find that fresh tissue and FFPE routine blocks can be employed for the robust detection of clinically relevant traits on the single-cell level. Specifically, single-cell maps of fresh patient tissues and corresponding FFPE tissue blocks could be integrated into common low-dimensional representations, and cell subtype clusters showed highly correlated transcriptional strengths of signaling pathway, hallmark, and clinically useful signatures, although expression of single genes varied due to technological differences. FFPE tissue blocks revealed higher cell diversity compared to fresh tissue. In contrast, single-cell profiling of cryopreserved tissue was prone to artifacts in the clinical setting. Our analysis highlights the potential of single-cell profiling in the analysis of retrospectively and prospectively collected archival pathology cohorts and increases the applicability in translational research.

Identification of specific codon 201 mutation of the DCC Gene in the colonoscopic specimen of colorectal cancer.

To identify the mutation in codon 201 of the deleted in colorectal cancer gene in colorectal cancer, and to correlate that mutation to the histopathological grading of colorectal cancer. The cross-sectional study was conducted from February 2019 to February 2021 after approval from the ethics review board of the Dow University of Health Sciences, Karachi, and comprised biopsy-proven colorectal cancer patients regardless of age and gender. After histopathological reporting, formalin-fixed paraffin-embedded tissue blocks of colorectal cancer were used for deoxyribonucleic acid extraction, followed by polymerase chain reaction optimisation and deoxyribonucleic acid Sanger sequencing for mutational analysis. Data was analysed using SPSS 25. Of the 100 biopsy specimens assessed, 45(45%) were selected. Of them, 13(29%) samples failed to show any band on gel electrophoresis. The remaining 32(71%) samples were used for Sanger sequencing. Of these, 1(3%) sample did not sequence, while 31(97%) showed sequencing. All the sequenced samples identified a mutation in codon 201 of exon 3 in the deleted in colorectal cancer gene; 30(97%) showed homozygosity, and 1(3%) showed heterozygosity. No significant association of point mutation was noted with various demographic and clinicopathological parameters (p>0.05). The deleted in colorectal cancer gene's missense mutation in codon 201 was frequently observed in colorectal cancer patients.

Linking inflammation and angiogenesis with fibrogenesis: Expression of FXIIIA, MMP-9, and VEGF in oral submucous fibrosis

ObjectivesInterplay of Factor XIIIa (FXIIIa), a transglutaminase, responsible for cross-linking of matrix proteins, Matrix Metalloproteinase-9 (MMP-9), a gelatinase, and Vascular Endothelial Growth Factor (VEGF), an angiogenic inducer, were studied in relation to fibrogenesis and disease progression in oral submucous fibrosis (OSMF). Material and methodsImmunohistochemical expression of markers was studied in 60 formalin-fixed paraffin-embedded tissue blocks of OSMF and 20 normal oral mucosal tissues. FXIIIa was studied quantitatively while MMP-9 and VEGF were assessed semi-quantitatively. Expression was compared with histopathological grades of OSMF. ResultsFXIIIa expression significantly increased in OSMF (p-value 0.000). However, expression decreased and cells became quiescent with increasing grades (p-value 0.000). MMP-9 (p-value epithelium 0.011, p-value connective tissue 0.000) and VEGF expression (p-value epithelium 0.000, connective tissue 0.000) increased in OSMF. A negative correlation between FXIIIa and MMP-9 (−0.653) in early grade (p-value of 0.021) and a positive correlation between FXIIIa and VEGF (0.595) (p-value of 0.032) was found in the moderate grade OSMF. Regression analysis showed a significant association (p<0.01) of FXIIIa in OSMF and with increasing grades of OSMF. ConclusionFXIIIa may play a crucial role in initiation of fibrosis in OSMF. MMP-9 may have a diverse role to play in OSMF as a regulator of fibrosis. VEGF may show an angio-fibrotic switch and contribute to fibrosis in OSMF. These cytokines may show altered function and can contribute to fibrosis and chronicity of disease due to changes in the microenvironment. Tissue stiffness in OSMF itself creates an environment that enhances the chronicity of the disease.

Survivin as a potential biomarker for early diagnosis of the progression of precancerous lesions to gastric cancer.

Gastric cancer is a common cancer developed in a carcinogenesis process from precancerous lesions including chronic gastritis, intestinal metaplasia, and dysplasia. Survivin, an inhibitor-of-apoptosis protein, is associated with the initiation and progression of gastric cancer. The present study aimed to evaluate the immunohistochemical expression patterns of survivin and its relationship with early diagnosis of gastric cancer in Iranian patients. In this retrospective case-control study, immunoexpression of survivin was investigated on sections obtained from formalin-fixed paraffin-embedded tissue blocks of 38 chronic gastritis, 32 intestinal metaplasia, 20 dysplasia, 28 gastric adenocarcinoma, and 22 controls. Survivin immunoexpression in chronic gastritis was higher than controls, but this difference was not statistically significant (P > 0.05). However, survivin immunoexpression had a steady significant increase from control and chronic gastritis to intestinal metaplasia to dysplasia to gastric adenocarcinoma (P < 0.05). Sensitivity, specificity, and area under the curve of survivin immunohistochemical test for the diagnosis of gastric cancer were 87.5%, 74.4%, and 0.85, respectively. Males had a significantly higher survivin expression than females (P < 0.001). Also, survivin expression was significantly higher in older patients than in younger ones (P < 0.001). It seems that the steady increase in survivin expression from different precancerous lesions to gastric adenocarcinoma suggests that survivin can be used as a potential biomarker for the prevention and early diagnosis of gastric cancer.

Expression of Ki-67 and E-cadherin in patients with non-small cell lung cancer attending a tertiary care hospital

Background: E-cadherin and Ki-67 expressions may provide real-time insights into the tumor's status and can be utilized as targeted therapeutics for lung cancer. We aimed to explore the expression of Ki-67 and E-cadherin in non-small cell lung cancer (NSCLC) patients and to identify their association with clinicopathological features. Methods: In this cross-sectional study, forty formalin-fixed paraffin-embedded (FFPE) NSCLC tissue blocks were identified from January to October 2022, based on hospital records from the Department of Pathology of National Institute of Diseases of the Chest and Hospital, Dhaka Medical College and Hospital. Samples were reevaluated for tissue quality, diagnosis, and exclusion-inclusion criteria. Finally, twenty-five samples were analyzed, and relevant clinicopathological data were collected from patients or authorized representatives. Ki-67 and E-cadherin expression were analyzed by immunohistochemistry and their relationships with each other. Results: Ki-67 expression was positive in 40% of the NSCLC tissue, and E-cadherin was negative in 40% of the NSCLC tissue. No statistically significant relation was found between the expressions of Ki-67 and E-cadherin. No statistically significant association was found in Ki-67 and E-cadherin expressions with clinicopathological characteristics except E-cadherin with comorbidity. Conclusion: Positive expression of Ki-67 and negative expression of E-cadherin was found in two-fifths of NSCLC tissues but not significant. Simultaneous estimated of Ki-67 and E-cadherin may contribute to the treatment planning and predict prognosis of the NSCLC patients.

PATH-65. INTEGRATING DNA METHYLATION AND SEQUENCING TECHNOLOGIES FOR ADVANCED BRAIN TUMOR DIAGNOSIS

Abstract DNA methylation has emerged as an indispensable tool in neuropathological diagnostics, improving the diagnosis of various brain tumor entities. At our institution, methylation arrays as well as DNA and RNA sequencing from Formalin-Fixed Paraffin-Embedded (FFPE) tissue blocks have become routine diagnostic practices for several years. In this study, we present an integration of DNA methylation analyses with targeted gene panel sequencing and RNA sequencing data in an extensive cohort comprising 5749 cases. The cohort encompassing both adult and pediatric patients with central nervous system (CNS) tumors. Only those cases conclusively classified by the Heidelberg brain tumor classifier (v12.5, cutoff &amp;gt; 0.9) and possessing available sequencing data were included in the analyses. The study includes several rare and less characterized brain tumor entities, unveiling frequent mutations and gene fusions that will improve the diagnostic process. Our study offers an unparalleled comprehensive overview of the prevalence of genetic alterations in brain tumors, precisely defined by their unique methylation classes. The profound implications of our results extend far beyond diagnosis alone, significantly augmenting the evaluation of targeted treatment options for patients undergoing DNA methylation analyses.

Immunohistochemistry-derived subtypes of breast cancer distribution in four regions of Ethiopia.

Different biological characteristics, therapeutic responses, and disease-specific outcomes are associated with different molecular subtypes of breast cancer (BC). Although there have been different studies on BC in the Ethiopian capital city of Addis Ababa, there have been few studies in other parts of the nation, and none have evaluated biological characteristics in other locations in the context of the extensive ethnic and genetic diversity found in Ethiopia. This study was carried out to evaluate the distribution of immunohistochemistry (IHC) subtypes of BCs throughout four Ethiopian regions. A total of 227 formalin-fixed paraffin-embedded (FFPE) tissue blocks were collected from tertiary hospitals in four Ethiopian regions between 2015 and 2021. The IHC staining was performed for subtyping, ER, PR, HER2, and Ki-67 proliferation markers. The mean age at diagnosis was 43.9 years. The percentage of ER and PR-negative tumors were 48.3% and 53.2%, respectively. The IHC subtypes showed the following distribution: 33.1% triple-negative breast cancer (TNBC), 27.6% luminal B, 25.2% luminal A, and 14.1% HER2 enriched. In multiple logistic regression analysis, grade III and HER2 positivity were associated with larger tumor size, and also originating from Jimma compared to Mekele. Patients with ER-negative, PR-negative, and TNBC were found in 48.3%, 53.2%, and 33.1% of cases, respectively, showing that half the patients could potentially benefit from endocrine treatment. A considerably high prevalence of TNBC was reported in our study, demanding additional research that includes genetic predisposition factors. Additionally, aggressive tumors were found in a high percentage of younger age groups, which must be considered when planning personalized treatment strategies.

MTOR Pathway Somatic Pathogenic Variants in Focal Malformations of Cortical Development: Novel Variants, Topographic Mapping, and Clinical Outcomes.

Somatic and germline pathogenic variants in genes of the mammalian target of rapamycin (mTOR) signaling pathway are a common mechanism underlying a subset of focal malformations of cortical development (FMCDs) referred to as mTORopathies, which include focal cortical dysplasia (FCD) type II, subtypes of polymicrogyria, and hemimegalencephaly. Our objective is to screen resected FMCD specimens with mTORopathy features on histology for causal somatic variants in mTOR pathway genes, describe novel pathogenic variants, and examine the variant distribution in relation to neuroimaging, histopathologic classification, and clinical outcomes. We performed ultra-deep sequencing using a custom HaloPlexHS Target Enrichment kit in DNA from 21 resected fresh-frozen histologically confirmed FCD type II, tuberous sclerosis complex, or hemimegalencephaly specimens. We mapped the variant alternative allele frequency (AAF) across the resected brain using targeted ultra-deep sequencing in multiple formalin-fixed paraffin-embedded tissue blocks. We also functionally validated 2 candidate somatic MTOR variants and performed targeted RNA sequencing to validate a splicing defect associated with a novel DEPDC5 variant. We identified causal mTOR pathway gene variants in 66.7% (14/21) of patients, of which 13 were somatic with AAF ranging between 0.6% and 12.0%. Moreover, the AAF did not predict balloon cell presence. Favorable seizure outcomes were associated with genetically clear resection borders. Individuals in whom a causal somatic variant was undetected had excellent postsurgical outcomes. In addition, we demonstrate pathogenicity of the novel c.4373_4375dupATG and candidate c.7499T>A MTOR variants in vitro. We also identified a novel germline aberrant splice site variant in DEPDC5 (c.2802-1G>C). The AAF of somatic pathogenic variants correlated with the topographic distribution, histopathology, and postsurgical outcomes. Moreover, cortical regions with absent histologic FCD features had negligible or undetectable pathogenic variant loads. By contrast, specimens with frank histologic abnormalities had detectable pathogenic variant loads, which raises important questions as to whether there is a tolerable variant threshold and whether surgical margins should be clean, as performed in tumor resections. In addition, we describe 2 novel pathogenic variants, expanding the mTORopathy genetic spectrum. Although most pathogenic somatic variants are located at mutation hotspots, screening the full-coding gene sequence remains necessary in a subset of patients.

Protein expression and localization of ABC transporters in pancreatic adenocarcinoma: Prognostic role of ABCC8

BackgroundATP-binding cassette (ABC) transporters translocate various substances across cellular membranes. Their deregulation may cause cancer drug resistance or perturbations in the supply of building blocks for cancer cells and modify patients’ prognosis. This study investigated protein expression and cellular localization of the previously suggested putative prognostic biomarkers – ABCB2/TAP1, ABCC7/CFTR, ABCC8/SUR1, and ABCD4 in patients with pancreatic ductal adenocarcinoma (PDAC). MethodsProtein expression and localization were assessed by immunohistochemistry in formalin-fixed paraffin-embedded primary tumor tissue blocks of 61 PDAC patients and associated with clinical data and the survival of patients. ResultsNo CFTR protein expression was observed in PDAC, while TAP1 and ABCC8 were expressed predominantly in the cytoplasm of tumor cells. Most samples (81 %) had detectable both membranous and cytoplasmic ABCD4 staining and 42 % had ABCD4 expressed in the apical orientation. Negative membranous ABCD4 staining was significantly more frequent in advanced stage III or IV tumors (p = 0.022). Small or medium counts of individual ABCC8-positive cells in the stroma surrounding tumor tubules were also more often found in stage III or IV (p = 0.044). Patients with moderate or strong ABCC8 cytoplasmic staining intensity in tumor cells had a 3.5-fold higher risk of disease progression than those with weak staining (p = 0.002). ConclusionsThe study shows for the first time that the cytoplasmic ABCC8 protein expression has prognostic value in PDAC.

Prognostic value of APOBEC3A in patients with cervical squamous cell carcinoma in a major urban center in China: a retrospective study.

APOBEC3A (A3A) has been implicated to have vital prognostic value in several common cancers. This study aimed to investigate the prognostic value of A3A expression in cervical squamous cell carcinoma (CESC). This retrospective study enrolled 59 patients with CESC or cervical squamous intraepithelial neoplasia from January 2014 to January 2017 in Changhai Hospital, Naval Medical University. Then, A3A histoscores (H-scores) using immunohistochemistry (IHC) were analyzed in formalin-fixed paraffin-embedded archival tissue blocks. Moreover, overall survival was analyzed by the Kaplan-Meier method. The H-score of A3A protein expression was relatively higher in CESC than in squamous intraepithelial neoplasia, and the relative expression level of normal cervical tissues was lower than that of cervical squamous intraepithelial neoplasia (P<0.001). Moreover, the H-score of poorly differentiated cases was 6, which was higher than that of moderately differentiated cases (H-score =3), while the H-score of well-differentiated cases was 2, which was lower than that of moderately differentiated cases. Moreover, patients in the A3A low expression group had higher overall survival rates by prognostic analysis (P=0.027). A3A protein expression was increased during CESC progression. Moreover, A3A expression was tightly related to poor prognosis in CESC. Thus, these results showed that A3A overexpression may provide a marker for poor prognosis in CESC.