Formalin-fixed Paraffin-embedded Tissue Sections Research Articles

Multiplexed in situ RNA imaging by combFISH.

Multiplexed in situ RNA imaging offers new opportunities for gene expression profiling by providing high-throughput spatial information. In this work, we present a cyclic combinatorial fluorescent in situ hybridization (combFISH) assay to achieve multiplexed detection of RNA in cell cultures and tissues. Specifically, multiplexing is achieved through cyclic interrogation of barcode sequences on the rolling circle amplicons generated from the padlock probe assay by using sets of combinatorial detection probes. Theoretically, combFISH can detect 64 genes in three hybridization cycles by combinatorial barcoding using 12 fluorescently labeled detection probes. Our method eliminates sequencing-by-ligation (SBL) chemistry in the in situ sequencing protocol and directly uses RNA as targets for ligation, making it more straightforward. We showed that our method works in fresh-frozen and formalin-fixed paraffin-embedded tissue sections. With its straightforward protocols, we expect our method to be adopted by the scientific community and extended to clinical settings.

Exploring the Role of EZH2 and BCL2 in Demarcating Oral Verrucous Hyperplasia and Verrucous Carcinoma

Introduction Oral verrucous hyperplasia (OVH) and verrucous carcinoma (OVC) are precursors of oral squamous cell carcinoma exhibiting overlapping histopathological picture which warrants distinction. EZH2 is an epigenetic marker possessing multifaceted function in cellular proliferation, migration, and malignant transformation, whereas BCL2 is an integral part of the antiapoptotic mechanism regulating cellular homeostasis. Aim The aim was to distinguish OVH and OVC by analysis of immunohistochemical expression of EZH2 and BCL2. Material and Methods The study sample consisted of 79 formalin-fixed paraffin-embedded tissue sections of normal oral mucosa (10), OVH (10), oral OVC (27), and oral squamous cell carcinoma (32). Immunohistochemical analysis of EZH2 and BCL2 was done and labeling indices were calculated. Additionally, six histopathological parameters were assessed in OVH and OVC. Statistical analysis was done using Kruskal–Wallis test, Tukey honest significant difference test, and Spearman's correlation. Receiver operating characteristic curve was plotted and sensitivity, specificity, and cutoff score of each marker were calculated. Result and Discussion Labeling indices of EZH2 and BCL2 depicted a gradual incline from normal mucosa to oral squamous cell carcinoma. Significant difference of EZH2 and nonsignificant difference in BCL2 expression between OVH and OVC were noted. Out of the six histopathological parameters, keratin plugging, juxtaepithelial lymphocytic response, and frank endophytic growth yielded a significant difference. EZH2 serves as a superior marker than BCL2 to differentiate OVH and OVC. Juxtaepithelial lymphocytic response can also serve as a histopathological parameter in distinguishing OVH and OVC.

Abstract PO1-02-08: Comprehensive Molecular Profiling of Breast Cancer: A real-time PCR assay for identifying ESR1, PGR, ERBB2, MKI67 and a novel proliferative signature in core needle biopsies and resected invasive breast cancer tissues

Abstract Background: Accurate status determination of breast cancer (BC) biomarkers, including estrogen receptor (ER/ESR1), progesterone receptor (PR/PGR), human epidermal growth factor receptor 2 (HER2/ERBB2), and marker of proliferation Ki67 (MKI67), is crucial for guiding therapeutic decisions. However, current “gold standard” methods such as immunohistochemistry (IHC) for assessing these biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues face challenges in standardization and exhibit substantial inter- and intra-laboratory variability, particularly for Ki67. To address these limitations, APIS Breast Cancer Subtyping Kit has been developed, utilizing reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to evaluate the status of ER, PR, HER2, KI67, and a novel proliferative signature in breast cancer core needle biopsy (CNB) and resected specimens. The APIS Breast Cancer Subtyping Kit offers enhanced accuracy, improved reproducibility, and the ability to provide results in a timely manner. Herein we report the development and validation of the APIS Breast Cancer Subtyping Kit, assessing clinical performance using retrospective and prospective sample collection. Furthermore, reproducibility and reliability across three testing sites were evaluated. By comparing the results of the kit with those obtained through standard IHC, we demonstrate the reliability and utility of the APIS Breast Cancer Subtyping Kit for precise breast cancer subtyping and guiding personalized patient management decisions. Methods: FFPE tissue sections (n=652) taken by CNB or resection underwent histological analysis in accordance with laboratory’s standard of care methods. Samples with a HER2 score of 2+ were referred to fluorescence in situ hybridization (FISH) to determine ERBB2 amplification, with the FISH result replacing the IHC result in determining the HER2 status (positive/negative) of the sample. Tumors with greater than 1% positive stained nuclei for ER/PR were scored positive. A cut-off of 20% Ki67 staining was used for positive/negative status. The performance was assessed as the agreement with IHC/ISH status and reported as OPA (overall percent agreement) with corresponding 95% confidence intervals (95% CI). To assess the precision of the assay, a panel of RNA pools (samples) was repeatedly measured on different days across three independent laboratories. Reproducibility was evaluated using variance components analysis. Results: The APIS Breast Cancer Subtyping Kit showed high concordance (OPA) with IHC: 93.1% (95% CI: 90.9-94.8) for ER, 86.8% (95% CI: 84.0-89.2) for PR, 94.2% (95% CI: 92.2-95.8) for HER2 (IHC/FISH), 78.3% (95% CI: 75.0-81.3) for Ki67, and 80.1% (95% CI: 76.8-83.1) for proliferative signature (assessed against MKI67 IHC status). Inter-site reproducibility demonstrated excellent agreement in quantitative measurements, with a total SD ranging from 0.00 to 0.22. Binary single-marker status (positive/negative) calling achieved 100% reproducibility for ER, PR, and HER2 for all tested samples (negative/low positive/medium positive), as well as for most Ki67 samples (87% agreement for negative samples). Conclusions: APIS Breast Cancer Subtyping Kit demonstrated a high level of concordance with standard of care IHC/FISH in assessing breast cancer biomarker status. These findings suggest that the APIS Breast Cancer Subtyping Kit provides highly precise and reproducible quantitative assessment of BC biomarkers and molecular subtypes. Inclusion and exclusion criteria Citation Format: Anna Gasior, Joanna Gorniak, Sara Rollinson, Leanne Gough, Anne-Sophie Wegscheider, Axel Niendorf. Comprehensive Molecular Profiling of Breast Cancer: A real-time PCR assay for identifying ESR1, PGR, ERBB2, MKI67 and a novel proliferative signature in core needle biopsies and resected invasive breast cancer tissues [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 PO1-02-08.

Abstract PO3-08-08: Basal-Luminal (BL) Cells in Histologically Normal and Malignant Breast Tissue from BRCA1 and BRCA2 Carriers

Abstract Background Single-cell studies of normal breast tissue in BRCA mutation carriers have led to the identification of a candidate cancer precursor cell, the basal-luminal (BL) cell. The localization of BL cells within normal, pre-malignant and malignant breast tissue architecture is not well characterized. Here, using cyclic immunofluorescence (CyCIF), we quantify and localize BL cells within normal and malignant breast tissues from BRCA1 and BRCA2 carriers. Methods Formalin-fixed paraffin-embedded breast tissue sections from 9 BRCA1 and 9 BRCA2 consented patients treated at Dana Farber Cancer Institute (2001-2019) were retrieved from the clinical archives and subjected to CyCIF for luminal and basal markers including CK5, CK14 and CK19. Using one section/case, cells co-expressing basal and luminal cytokeratins (CK14/CK19 and/or CK5/CK19) were visually identified in invasive carcinoma, ductal carcinoma in situ (DCIS) and in adjacent normal breast tissue. In histologically normal tissue, regions of interest (ROIs) with co-expressing cells were classified as terminal duct lobular units (TDLUs) or isolated ducts. Within each ROI, the quantity of BL cells was scored as low (1-5 cells), moderate (6-10 cells), or high ( >10 cells). Results The 9 BRCA1 tumors included 8 invasive ductal carcinomas/no special type and 1 tubular carcinoma. The 9 BRCA2 tumors included 4 invasive ductal carcinomas/no special type and 5 invasive carcinomas with ductal and lobular features. 496 ROIs were evaluated in histologically normal tissue: 297 from BRCA1 cases and 199 from BRCA2 cases. BL cells co-expressing CK14/CK19 and/or CK5/CK19 were identified in normal TDLUs and isolated ducts in both BRCA1 and BRCA2 cases. BL cells were more frequently identified in BRCA2 cases, with at least one BL cell present in 97/297 ROIs (33%) in BRCA1 cases and in 133/199 ROIs (67%) in BRCA2 cases (p< 0.01). 55% of BRCA2 ROIs had >10 BL cells each versus 42% of BRCA1 ROIs; however, this difference was not significant. Four BRCA1 cases showed a diffuse BL cell phenotype within the invasive carcinoma with either a diffuse or scattered BL cell phenotype within the DCIS. The BL cell phenotype was not seen diffusely in invasive carcinoma or DCIS in the other 14 cases; however individual tumor cells or small cell clusters with the BL cell phenotype were occasionally found. Conclusions BL cells are found in histologically normal TDLUs and isolated ducts in breast tissue from BRCA1 and BRCA2 carriers, with greater prevalence in BRCA2 carriers. The BL cell phenotype is present diffusely within tumor cells in almost half of BRCA1-associated cancers and none of the BRCA2-associated cancers in this small cohort. Further study of this interesting cell population is warranted in efforts to understand early changes in epithelium at high risk for the development of cancer. Citation Format: Rodrigo Fonseca Abreu, Tabata Alves Domingos, Roberto Bonfim Pimenta Peixoto, Ashka Patel, Krishan Taneja, McKenna Moore, Alicia Pollaci, Judy Garber, Nomeda Girnius, Deborah Dillon. Basal-Luminal (BL) Cells in Histologically Normal and Malignant Breast Tissue from BRCA1 and BRCA2 Carriers [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 PO3-08-08.

Abstract PO3-01-05: Enhancing HER2 Evaluation: Correlation between APIS Breast Cancer Subtyping Kit and IHC/ISH for Accurate HER2 Quantification

Abstract Background: The quantification of HER2-low in breast cancer (BC) has garnered considerable interest due to emerging evidence of the efficacy of targeted therapies in this patient subgroup. Trastuzumab deruxtecan (T-Dxd), an antibody-drug conjugate targeted at HER2, has recently gained approval in the USA and Europe for treating HER2-low BC, which is currently defined as immunohistochemical (IHC) scores of 1+ or 2+ without HER2/ERBB2 in situ hybridization (ISH) amplification. HER2 quantification using IHC/ISH was primarily designed to identify tumors overexpressing HER2, rather than differentiate between HER2-low and the absence of expression. Consequently, the adequacy of these assays in accurately detecting HER2- low remains uncertain. Improving the accuracy of HER2 evaluation is crucial to prevent the incorrect selection of patients for T-Dxd treatment. There is a clear need to develop HER2 testing methods that are more precise, reliable, and capable of detecting HER2-low expression with greater sensitivity and reproducibility. This is particularly important as the minimum threshold of HER2 expression required for T-Dxd efficacy is still under investigation, with clinical data suggesting the potential activity of T-Dxd even in patients with IHC 0 HER2 score. Here, we evaluated the correlation between HER2 mRNA expression levels, detected by APIS Breast Cancer Subtyping Kit, and IHC HER2 classification. Methods: Formalin-fixed paraffin-embedded (FFPE) tumour tissue sections (n=642) obtained by core needle biopsy or resection underwent histological analysis in accordance with laboratory’s standard of care methods. Samples with a HER2 score of 2+ were referred to ISH to determine ERBB2 amplification. To evaluate the diagnostic performance, the concordance between HER2 IHC score, and APIS Breast Cancer Subtyping Kit RNA expression level was reported in terms of Overall Percent Agreement (OPA), Negative Percent Agreement (NPA), and Positive Percent Agreement (PPA), along with their corresponding 95% confidence intervals (CI). Results: HER2 expression detected by APIS Breast Cancer Subtyping Kit showed strong correlation with IHC/ISH, with an OPA of 94.2% (95% CI: 92.2-95.8), PPA of 89.2% (95% CI: 80.1-94.4) and NPA of 94.9% (95% CI: 92.8-96.4). The expression of HER2 was detected by APIS Breast Cancer Subtyping Kit in a subset of patients with 0 and 1+ IHC HER2 scores, suggesting its potential as a more sensitive and reliable method for detection of HER2 expression, and providing the opportunity to enhance HER2 stratification. Conclusions: APIS Breast Cancer Subtyping Kit can accurately detect HER2 expression and has the potential to further stratify the HER2-low patients. Further studies examining the relationship between HER2 expression and the response to anti-HER2 therapies could yield valuable insights into treatment administration and identify patients who could benefit from such therapies. Incorporating continuous quantification of HER2 could optimize patient outcomes. Citation Format: Anna Gasior, Joanna Gorniak, Sara Rollinson, Leanne Gough, Anne-Sophie Wegscheider, Axel Niendorf. Enhancing HER2 Evaluation: Correlation between APIS Breast Cancer Subtyping Kit and IHC/ISH for Accurate HER2 Quantification [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 PO3-01-05.

Abstract PO4-16-01: EZH2 is Overexpressed in Invasive Carcinoma and DCIS in both BRCA1 and BRCA2 Mutation Carriers

Abstract Background The transcriptional repressor EZH2 (Polycomb Group Protein Enhancer of Zeste Homologue 2) is overexpressed in multiple neoplasms including breast cancer where it associates with high proliferation, aggressive features and poor prognosis and is of interest as a potential therapeutic target. EZH2 nuclear expression in breast cancer has been shown to correlate specifically with high tumor grade and basal-like histologic features but has not been well studied in cancers from BRCA carriers. Here we evaluate the expression of EZH2 protein in BRCA-associated invasive breast carcinomas and precursor lesions. Methods Eighteen cases of invasive breast cancer in consented BRCA carriers (8 BRCA1 and 10 BRCA2) treated at Dana Farber Cancer Institute from 2001-2019 were reviewed by two pathologists (TAD and RBPP). Histopathologic features (histologic subtype, nuclear grade, mitotic score) and presence of precursor lesions were recorded. Immunohistochemistry for EZH2 was performed on freshly cut formalin-fixed paraffin-embedded tissue sections (1-3 sections/case) using a monoclonal antibody against EZH2 (D2C9, Cell Signaling). Nuclear EZH2 expression was scored as negative (score=1, no staining); weak (score 2, < 25%); moderate (score=3, 25–75%); and strong (score=4, >75%), of any intensity following published criteria. EZH2 overexpression was defined as scores 3 and 4. Results The majority of the invasive carcinomas showed grade III histology (13/18, 72%), as expected. Of 8 BRCA1 cases, 6 were classified as grade III (75%), 1 as grade II, and 1 as grade I (7 cases of invasive ductal carcinoma and 1 case of invasive tubular carcinoma). Of 10 BRCA2 cases, 7 were classified as grade III (70%) and 3 as grade II (30%) (5 cases of invasive ductal carcinoma and 5 cases of invasive carcinoma with ductal and lobular features). The majority of cases (13 of 18, 72%) showed high expression of EZH2 in the invasive carcinoma (6 BRCA1 and 7 BRCA2 cases; 2 grade II and 11 grade III). Of 13 cases with EZH2 overexpression, 6 were ER+/PR+/HER2- and 7 were triple negative, with 9 invasive ductal carcinomas and 4 invasive carcinomas with ductal and lobular features. Of 5 cases with no/low EZH2 overexpression, 1 was ER+/PR+/HER2-, 3 were ER+/PR-/HER2- and 1 was triple negative, with 3 invasive ductal carcinomas, 1 invasive carcinoma with ductal and lobular features and 1 invasive tubular carcinoma. In all cases with adjacent ductal carcinoma in situ (DCIS) (n=14), the pattern of EZH2 expression in the DCIS was identical to that seen in the invasive carcinoma (11 high and 3 low expression). Overexpression of EZH2 was not observed in any other precursor lesions (LCIS, ADH, ALH) or in normal tissue. Conclusion EZH2 protein overexpression is seen in the majority of invasive carcinomas in BRCA carriers, both in BRCA1 and in BRCA2. In all cases, the associated DCIS shows the same pattern of expression as the invasive carcinoma, suggesting that overexpression occurs early in tumorigenesis, while tumor cells are still confined within the ducts. The high rate of overexpression of EZH2 in BRCA1- and BRCA2-associated tumors suggests a potential role for EZH2 as a target and/or a biomarker in these cancers. Citation Format: Tabata Alves Domingos, Roberto Bonfim Pimenta Peixoto, Rodrigo Fonseca Abreu, Ashka Patel, Krishan Taneja, McKenna Moore, Celina Kleer, Deborah Dillon. EZH2 is Overexpressed in Invasive Carcinoma and DCIS in both BRCA1 and BRCA2 Mutation Carriers [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 PO4-16-01.

DETERMINING GOOD DNA QUALITY OF FFPE CRC TISSUES VIA A MACRODISSECTION-DNA EXTRACTION PROTOCOL

A good DNA quality and quantity from a formalin-fixed paraffin-embedded (FFPE) tissue sample is crucial for a better downstream genomic analysis. Previous research has focused on comparing FFPE DNA extraction kits, but the improvement in kit outcome has yet to be studied. This study aimed to make some modifications to a selected Qiagen DNA extraction manual protocol using a manual macrodissected FFPE colorectal cancer (CRC) tissue sample. A variety of DNA extraction protocol-related variables, such as washing steps, tissue sections, and FFPE tissue age have been investigated to determine the DNA quality and quantity of the FFPE tissues. The prechilled absolute ethanol washing step showed the highest DNA concentration with good purity ratios. One, two, or four tissue sections using the washing step were sufficient to obtain adequate DNA concentrations with acceptable DNA purity ratios. 1% or 2% agarose gel electrophoresis with the pre-casting method allowed better visualisation of FFPE DNA. Based on the ideal quality and quantity, we chose a manual macrodissected DNA extraction protocol employing 4 x 10 µm FFPE tissue sections generated in recent years with an optimised prechilled absolute ethanol washing step.

Abstract 2905: Spatial analysis of neuropilin 2 expression in the microenvironment of melanoma

Abstract Background: Neuropilin 2 (NRP2) is a co-receptor that enhances signaling of growth factor and cytokine receptors and is expressed in tumor and microenvironment (TME) cells in melanoma and other tumors. Neuropilin 2 expression in tumor cells is associated with more aggressive tumors. Expression in tumor associated macrophages enhances efferocytosis and immunologically silent tumor cell death. Methods: Whole excisional lymph node biopsies were obtained from 10 treatment naïve patients with metastatic cutaneous melanoma who subsequently received anti-PD1 treatment. A single 5mm formalin-fixed paraffin embedded tissue section was used to assess a panel of 39 analytes by cyclic multiplex immunofluorescence (MxIF). Fields of view (~1mm2, n=288) were selected from pathologist-annotated regions of the tumor core, tumor-immune interface and adjacent lymphoid tissue. Pixel-based single cell segmentation and a supervised classifier approach was applied to resolve 12 distinct tumor, stromal and immune cell phenotypes and functional states (NRP2 positive or negative) in 1.5 million cells. Results: Tumor recurrence was observed in 6 patients (relapsed), whereas 4 patients were recurrence-free (non-relapsed) during follow up. Among the different cell types, NRP2 expression was more frequent in macrophages (44%), tumor cells (40%), dendritic cells (40%), followed by Tregs (31%) and T helper cells (29%), and less frequent in neutrophils (24%), cytotoxic T cells (23%) and B cells (15%). In colocalization permutation analysis, NRP2 expressing macrophages clustered away from tumor cells in non-relapsed patients while a random spatial distribution of NRP2 expressing macrophages with respect to tumor cells was observed in relapsed patients. In comparing the odds of tumor cell interactions with NRP2-expressing macrophages to those with NRP2 non-expressing macrophages, we found in the tumor:stromal interface (10% tumor cells) that cells from both non-relapsed and relapsed patients were more likely to interact with NRP2 non-expressing macrophages (OR = 0.73, 95% CI = [0.71, 0.75] and OR = 0.56, 95% CI = [0.55, 0.58] for non-relapsed and relapsed patients, respectively). However, in the tumor core (90% tumor cells), tumor cells from relapsed patients had significantly higher odds of interacting with NRP2 expressing macrophages, (OR = 1.15, 95% CI = [1.12, 1.18]), and this was not seen for non-relapsed patients (OR = 0.68, 95% CI = [0.66, 0.71]). In FOVs dominated by tumor cells (75% tumor), tumor cells from relapsed patients had 4.97 times the odds of expressing NRP2 compared to tumor cells from non-relapsed patients (95% CI = [2.23, 11.09], p = 0.0001). Conclusions: These spatial analytics suggest complex interactions among NRP2 expression in tumor and TME of melanoma determining risk for relapse with anti-PD1 treatment. Citation Format: Anastasios Dimou, Raymond M. Moore, Caitlin Ward, Alexey Leontovich, Ruifeng Guo, Chen Wang, Shankar Suman, Betty Dicke, Jill M. Schimke, Noah A. Stueven, Chathu A. Atherton, Wendy Nevala, Svetomir N. Markovic. Spatial analysis of neuropilin 2 expression in the microenvironment of melanoma [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 2905.

Abstract 5176: TIGIT expression increases with advancing clinical stages and does not differ across racial groups in resected pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) has a dismal 12% 5-year survival rate (SEER) due to a lack of early detection biomarkers and resistance to standard therapeutic options (surgery, chemotherapy, radiation). Black African Americans (BAA) have 20% increased incidence of PDAC compared to those with European Ancestry (EA). TIGIT, an immune checkpoint receptor, is a marker of T cell exhaustion and plays a key role in the inhibition of anti-tumor immune responses. Recent studies have demonstrated that immune checkpoint receptor expression (PD-1 and TIGIT) on specific T cell populations correlates to worse overall survival (OS). TIGIT inhibitors are being explored in clinical trials in pancreatic cancer due to implications of its ligand (CD155) promoting immune evasion. We hypothesize that targeted anti-TIGIT therapy, in conjunction with other therapies targeting the tumor microenvironment, could reverse the immune suppression that is characteristic of PDAC. We performed RNAscope in situ hybridization (ISH) with a probe specific for human TIGIT mRNA (combined with a nuclear counterstain) on 79 tissue samples. The cohort of tissue samples included 8 biopsies (endoscopic-guided fine needle biopsies at time of diagnosis), 66 primary (from surgical resection), and 5 metastatic (liver core biopsies from patients with a primary PDAC diagnosis) formalin-fixed paraffin-embedded (FFPE) tissue sections from patients with histologically confirmed PDAC. After cells were segmented based on nuclear recognition, the presence of TIGIT probe within the cytoplasm of each cell was determined and quantified. Percent positive cell values were then exported for statistical analysis in R. De-identified clinical metadata was obtained from REDCap, a cloud-based HIPAA-compliant database used to compile patient data for research purposes. We tested for associations between %TIGIT present and clinical covariates, using linear regression for continuous outcomes, and logistic regression for binary outcomes. ScRNAseq revealed that TIGIT mRNA is enriched in, but not exclusive to the T/NK cellular compartments in PDAC. Staining analysis showed that TIGIT expression did not differ significantly between racial groups (comparing BAA to non-BAA). The mean percentage of TIGIT positive cells was 64.0%. High expression of TIGIT was associated with clinical stage, where an increase in stage was associated with increasing %TIGIT (p < 0.05).The TIGIT biomarker assay can be conducted at time of diagnosis, time of surgical resection, and time of metastatic biopsy. If patients’ samples contain high levels of TIGIT expression, these patients may be candidates for anti-TIGIT drug therapy. Considering that TIGIT expression correlates with advancing clinical stage, patients with more advanced staging at diagnosis (stage IIB, III, IV) especially may benefit from anti-TIGIT therapy. Citation Format: Madison George, Julie Clark, Kendyll Gartrelle, Georges Nassif, Kailee Hartway, Daniel Long, Daniel Salas-Escabillas, Allison Wombwell, Thais Pichardo, Hui-Ju Wen, Simone Benitz, Samuel Zwernik, Rupen Shah, Hakmin Park, Philip, Gazala Khan, Howard Crawford, David Kwon, Brian Theisen, Nina Steele. TIGIT expression increases with advancing clinical stages and does not differ across racial groups in resected pancreatic cancer [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 5176.

The importance of novel histopathological classification and its association with outcomes of primary aldosteronism: What you need to know from a urologist’s perspective

Primary aldosteronism (PA), the most important cause of secondary endocrine hypertension, is hallmarked by excessive aldosterone secretion. There were 2 subtypes of PA—unilateral aldosterone-producing adenoma and bilateral adrenal hyperplasia, which are now outdated. Since conventional adrenal pathological reports only examined hematoxylin and eosin staining, the secretory function of the structural adenoma(s) could not be determined. Several enzymes produce aldosterone-related steroids, and 2 isoforms of 11β-hydroxylase, namely CYP11B1 and CYP11B2 (aldosterone synthase), are responsible for producing cortisol and aldosterone, respectively. Since the availability of specifically selective antibodies for targeting CYP11B1 and CYP11B2, the diagnosis/nomenclature of PA-related adrenal pathology has been revolutionized by using immunohistochemistry staining for CYP11B2 to identify the aldosterone production site in the human adrenal cortex. The significance of immunohistochemical staining of formalin-fixed paraffin-embedded adrenal tissue sections has become “mandatory” for precisely detecting the lesions responsible for PA. Recently, the histopathology of PA consensus, based on immunochemical findings, was established to define the nomenclature and adrenal histopathological features in unilateral PA. In this study, we further investigate the association between the pathological subtypes and the surgical outcomes of PA as per the criteria of the Primary Aldosteronism Surgery Outcome consensus. Unfortunately, a significant lag is seen in the adaptation of Taiwan’s pathologists to the histopathology of PA consensus. Furthermore, a strong push from all urologists across Taiwan and the governmental health care authorities is required to elevate the care level provided to all patients with PA in Taiwan to exceptional.

Evaluation of species-specific polyclonal antibodies to detect and differentiate between Neospora caninum and Toxoplasma gondii.

Neosporosis and toxoplasmosis are major causes of abortion in livestock worldwide, leading to substantial economic losses. Detection tools are fundamental to the diagnosis and management of those diseases. Current immunohistochemistry (IHC) tests, using sera raised against whole parasite lysates, have not been able to distinguish between Toxoplasma gondii and Neospora caninum. We used T. gondii and N. caninum recombinant proteins, expressed in Escherichia coli and purified using insoluble conditions, to produce specific polyclonal rabbit antisera. We aimed to develop species-specific sera that could be used in IHC on formalin-fixed, paraffin-embedded (FFPE) tissue sections to improve the diagnosis of ruminant abortions caused by protozoa. Two polyclonal rabbit sera, raised against recombinant proteins, anti-Neospora-rNcSRS2 and anti-Toxoplasma-rTgSRS2, had specificity for the parasite they were raised against. We tested the specificity for each polyclonal serum using FFPE tissue sections known to be infected with T. gondii and N. caninum. The anti-Neospora-rNcSRS2 serum labeled specifically only N. caninum-infected tissue blocks, and the anti-Toxoplasma-rTgSRS2 serum was specific to only T. gondii-infected tissues. Moreover, tissues from 52 cattle and 19 sheep previously diagnosed by lesion profiles were tested using IHC with our polyclonal sera and PCR. The overall agreement between IHC and PCR was 90.1% for both polyclonal anti-rNcSRS2 and anti-rTgSRS2 sera. The polyclonal antisera were specific and allowed visual confirmation of protozoan parasites by IHC, but they were not as sensitive as PCR testing.

Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction.

Signal amplification based on the mechanism of hybridization chain reaction (HCR) facilitates spatial exploration of gene regulatory networks by enabling multiplex, quantitative, high-resolution imaging of RNA and protein targets. Here, we extend these capabilities to the imaging of protein:protein complexes, using proximity-dependent cooperative probes to conditionally generate a single amplified signal if and only if two target proteins are colocalized within the sample. HCR probes and amplifiers combine to provide automatic background suppression throughout the protocol, ensuring that even if reagents bind nonspecifically in the sample, they will not generate amplified background. We demonstrate protein:protein imaging with a high signal-to-background ratio in human cells, mouse proT cells, and highly autofluorescent formalin-fixed paraffin-embedded (FFPE) human breast tissue sections. Further, we demonstrate multiplex imaging of three different protein:protein complexes simultaneously and validate that HCR enables accurate and precise relative quantitation of protein:protein complexes with subcellular resolution in an anatomical context. Moreover, we establish a unified framework for simultaneous multiplex, quantitative, high-resolution imaging of RNA, protein, and protein:protein targets, with one-step, isothermal, enzyme-free HCR signal amplification performed for all target classes simultaneously.

Abstract C012: TIGIT expression correlates to worse overall survival in primary and metastatic pancreatic ductal adenocarcinoma

Abstract Pancreatic Cancer has a 12% 5-year survival rate due to late-stage detection and lack of many chemotherapy or targeted therapy options. TIGIT is an immune checkpoint inhibitor being explored in clinical trials in pancreatic cancer due to the implications of its ligand (CD155) promoting immune evasion. TIGIT is a marker of T cell exhaustion and plays a key role in the inhibition of anti-tumor immune responses. We hypothesize that targeted anti-TIGIT therapy, in conjunction with other therapies targeting the tumor microenvironment, could reverse immune suppression that is characteristic of pancreatic ductal adenocarcinoma (PDAC). As such, here we aim to quantify TIGIT expression using automated RNAscope technology and to correlate it with overall patient survival. We performed RNAscope in situ hybridization and immunohistochemistry on 25 primary and 4 metastatic (liver) formalin-fixed paraffin-embedded (FFPE) tissue sections from patients with histologically confirmed PDAC. A nuclear counterstain combined with an RNAscope probe specific for the human TIGIT mRNA was utilized. Slides were scanned at 40X magnification with an automated slide scanner and quantified using the ISH-IHC module of the HALO-v3.5 software. After cells were segmented based on nuclear recognition, the presence of TIGIT probe within the cytoplasm of each cell was determined and quantified. Percent positive cell values were then exported for statistical analysis in SPSS. De-identified clinical metadata was obtained from REDCap, a cloud-based HIPAA-compliant database used to compile patient data for research purposes. Gender, survival months, ethnicity, race, tumor histology, stage, cancer history, treatment status, and comorbidities were evaluated. We analyzed a cohort of 29 histologically-confirmed surgically resected PDACs, comprised of 25 primary pancreatic tumor samples and 4 metastatic liver core biopsies. The mean percentage of TIGIT positive cells was 63%. From this, the TIGIT high versus low threshold was determined to be 70%. High TIGIT was associated with significantly lower overall survival (p=.013), suggesting that expression of TIGIT and T cell exhaustion may predict overall worse survival. The median overall survival months for the TIGIT low group was 321 months versus 106 months for the TIGIT high group. This data leads us to hypothesize that expression of TIGIT and T cell exhaustion may predict worse overall survival. Anti-TIGIT medications are currently in clinical trials for metastatic PDAC. Here we demonstrate that high TIGIT expression is associated with an overall worse prognosis and present a novel, automated TIGIT detection protocol that may be used to determine if patients are candidates for anti-TIGIT therapy. In a clinical setting, this novel, automated biomarker TIGIT detection protocol could be used to select candidates for anti-TIGIT therapy. This may lead to improved overall patient survival. Citation Format: Madison George, Julie Clark, Kendyll Gartrelle, Georges Nassif, Donald Rempinski, Daniel Long, Hui-Ju Wen, Simone Benitz, Samuel Zwernik, Rupen Shah, Hakmin Park, David Kwon, Philip Philip, Gazala Khan, Howard Crawford, Brian Theisen, Nina Steele. TIGIT expression correlates to worse overall survival in primary and metastatic pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C012.

Extrapulmonary tuberculosis - A cross-sectional study comparing the utility of Ziehl-Neelsen stain and immunohistochemistry

Background: Tuberculosis (TB) continues to be a significant global health issue despite known causes and effective treatments. Factors such as virulent strains, drug resistance, and the human immunodeficiency virus pandemic, especially in India, contribute to its prevalence. Mycobacterium tuberculosis, the TB agent, can evade immune responses, persisting within host cells. A distinct feature of TB, granuloma formation, can also appear in diseases such as leprosy, histoplasmosis, and non-infectious conditions like Crohn’s disease. Proper diagnosis is vital, as in resource-limited countries, TB treatment often relies on presumptive diagnoses based on imaging and symptoms, leading to high false positive rates. Aims and Objectives: This study aims to compare the utility of Ziehl-Neelsen (ZN) staining and immunohistochemistry (IHC) staining in suspected extrapulmonary TB lesions. Materials and Methods: This is a retrospective cross-sectional study conducted at the Institute of Pathology, Rajiv Gandhi Government General Hospital, Chennai, over a 2-year period from August 2015 to July 2017. Fifty cases out of the 198 suspected extrapulmonary TB lesions were selected for the study. Results: About 12% of cases were positive for acid-fast bacilli by ZN staining, whereas 82% of cases were positive for acid-fast bacilli by IHC staining. P value was found to be <0.001 by McNemar test which was statistically significant. Conclusion: Diagnosing extrapulmonary TB can be challenging because the disease presents with various clinical manifestations and the bacterial load may be low. Immunohistochemistry is superior to ZN staining for localization of the tubercle bacilli and thus can serve as an effective ancillary technique in diagnoses of extrapulmonary TB in formalin-fixed paraffin embedded tissue sections.

Multiplex Immunofluorescence Staining Protocol for the Dual Imaging of Hypoxia-Inducible Factors 1 and 2 on Formalin-Fixed Paraffin-Embedded Samples.

Hypoxia is a common condition in rapidly proliferating tumors and occurs when oxygen delivery to the tissue is scarce. It is a prevalent feature in ~90% of solid tumors. The family of HIF (hypoxia-inducible factor) proteins-HIF1α and HIF2α-are the main transcription factors that regulate the response to hypoxia. These transcription factors regulate numerous downstream gene targets that promote the aggressiveness of tumors and therefore have been linked to worse prognosis in patients. This makes them a potential biomarker to be tested in the clinical setting to predict patient outcomes. However, HIFs have been notoriously challenging to immunolabel, in part due to their fast turnover under normal oxygen conditions. In this work, we developed a multiplexed immunofluorescence (mIF) staining protocol for the simultaneous detection of HIF1α and HIF2α in the same formalin-fixed paraffin-embedded (FFPE) tissue section.

Expression of NKX2.2 in Non-Ewing Tumors With Round Cell Morphology.

Background Round cell sarcomas pose diagnostic challenges due to overlapping histopathological features, necessitating precise immunohistochemical markers for accurate categorization. NKX2.2 has emerged as a sensitive diagnostic tool, particularly in Ewing sarcoma. This study extends this understanding to various round-cell sarcomas, shedding light on the potential diagnostic utility of NKX2.2 beyond its established role. The nuanced exploration of NKX2.2 expression aims to enhance diagnostic strategies, prognostic assessments, and therapeutic developments in the landscape of sarcoma research. Methodology Cases were retrieved from the surgical pathology and consultation files of Shaukat Khanum Memorial Cancer Hospital and Research Center, Lahore, Pakistan. Representative hematoxylin and eosin-stained slides of six different types of already confirmed tumors, including lymphoblastic lymphoma, neuroblastoma, rhabdomyosarcoma, synovial sarcoma, Wilms tumor, and Ewing sarcoma, were reviewed by a panel of pathologists. Immunohistochemistry, utilizing a rabbit anti-NKX2.2 monoclonal antibody, was performed on formalin-fixed paraffin-embedded tissue sections. The presence of NKX2.2 was defined as moderate or high nuclear immunoreactivity in at least 5% of cells. Results The histopathological examination revealed characteristic features in each sarcoma subtype, aligning with established diagnostic criteria. In Lymphoblastic lymphoma, T-cell lineage was confirmed through TdT expression, while the atypical finding of focal NKX 2.2 expression hinted at genetic diversity. Neuroblastoma exhibited the expected salt and pepper chromatin pattern, with NKX 2.2 expression raising questions about its prognostic significance. Rhabdomyosarcoma presented primitive cells expressing desmin, and NKX 2.2 focal expression echoed previous subtype-associated studies. Synovial sarcoma displayed both monophasic and biphasic growth patterns and TLE1 expression, with NKX 2.2 variation suggesting tumor heterogeneity. In Wilms tumor, the characteristic WT1 expression was observed, while NKX2.2's absence reaffirmed its irrelevance in this context. Ewing sarcoma displayed the anticipated homogenous cell population, strong NKX2.2 expression, and CD99 positivity across various sites. Furthermore, age and gender impact on this range of sarcomas found no significant relation with an expression of NKX2.2. Conclusion In conclusion, the diverse expression profiles of diagnostic markers discovered in this study, particularly the atypical expression of NKX2.2 beyond its established role in Ewing sarcoma, signify a significant advancement. This unique finding accentuates the potential diagnostic importance of NKX2.2 in various sarcomas, presenting a novel dimension to our understanding of these malignancies.

Splenic B Cell Lymphoma Innate Immune Cells: Detection of Red Versus White Pulp Lymphoma Differences in NK Cell Populations By High-Parameter Flow Cytometry

Introduction Splenic B-cell lymphomas, (SLs, total incidence ~1:100,000/year) comprise four distinct indolent B-cell non-Hodgkin lymphomas. Three predominantly involve the red pulp of the spleen (classical hairy cell leukemia (HCL), hairy cell leukemia variant (HCLv) and splenic diffuse red pulp small B-cell lymphoma (SDRPL)) and the fourth predominantly involves the white pulp (splenic marginal zone lymphoma (SMZL)). HCL is usually diagnosed by detection of an activation mutation in BRAF and responds well to treatment. We focused our study on the remaining three diseases, which have overlapping clinical presentations with only subtle differences in their morphology and phenotypes, but have considerable differences in prognosis, response to treatment and outcome. The white pulp lymphoma SMZL generally has good treatment responses and longer survival, whereas the red pulp SLs, HCLv and SDRPL are less responsive to treatments with shorter survival. Cells of the tumor microenvironment (TME) may have distinct characteristics between these three diseases. We hypothesized that TME innate immune cells from red pulp SLs (HCLv, and SDRPL) would be similar to each other and distinct from the white pulp SL, SMZL.In this study, we report that natural killer (NK) cells, which are important innate immune cells critical for immune surveillance, vary in proportions among red and white pulp SLs. Methods We studied splenectomy specimens from patients with SMZL (n=8), HCLv (n=8), SDRPL (n=7), and controls (healthy, post-trauma, n=8). Cryo-preserved bulk splenic suspension cell isolates from fresh (<4 hour) surgical specimens and intact formalin-fixed paraffin embedded (FFPE) tissue sections were used. Human specimen collection and usage was conducted with written informed consent after approval of the Institutional Research Subjects Review Board. FFPE tissue sections were studied by immunohistochemical (IHC) staining and splenic suspension cells were analyzed by high-parameter fluorescence flow cytometry using a Cytek Aurora spectral flow cytometer with a 25-color myeloid and a 28-color NK/B-cell panel. Results IHC characterization showed an extensive network of innate immune cells as reflected by CD163 + macrophages. Using high-parameter flow cytometry, we focused on innate immune cells in the non-B- non-T-cell (CD3 -CD19 -) population. The average proportions of this population were: NK cells 25-36%, monocyte/macrophages 20-34%, dendritic cells 5-11%, and granulocytes 2%. Among the patient groups, the median percentage of NK cells was greater for controls (34%) and SMZL (35%) as compared to red pulp lymphomas (HCLv (28%), SDRPL (24%)). Next, we examined NK subtypes: 1) cytotoxic NK cells (CD56 +CD16 +), 2) cytokine-secreting weakly cytotoxic NK cells (CD56 +CD16 -), and 3) undefined NK cells (CD56 -CD16 +) as a median percentage of total NK cells. The major subtype for control and SMZL was CD56 +CD16 - with values of 58 and 44%, respectively. This subtype comprises only 38%-40% of red pulp SLs. Proportionally the CD56 +CD16 + subtype was the largest for red pulp SLs at 52-57% as compared to 30% for control and 38% for SMZL. The remaining CD56 -CD16 + NK cell subtype was generally higher among red pulp SLs (HCLv (9%), SDRPL (12%)) as compared to control (6%) and SMZL (4%) patients. The increase in cytotoxic CD56 +CD16 + subtype among red pulp SLs was confirmed by measuring the percentage of granzymeB +perforin + cells among mature cytotoxic NK cells (CD56 +CD16 +/ CD57 +NKG2a -). SLs had higher proportions of this NK phenotype (78-86% compared to control 69%) and red pulp SLs had the most granzymeB +perforin + proportions with 82 and 86% for HCLv and SDRPL, respectively. Discussion In summary, spleens from patients with SMZL had similar percentages of total NK cells to controls, with lower percentages in red pulp SLs. All SLs had a higher percentage of cytotoxic NK cells than control, with the red pulp SLs having the most. These data suggest that monoclonal antibody treatments targeting SL antigen, such as anti-CD20, may be effective by activating cytotoxic NK cell to target lymphoma cells by antibody-dependent cellular cytotoxicity. Thus, uncovering the characteristics of the TME may aid the development of non-invasive diagnostic procedures and/or precision therapies.

The Expression of Mucin-4 (MUC4) in Sarcomas Apart From Sclerosing Epithelioid Fibrosarcoma and Low-Grade Fibromyxoid Sarcoma.

Background Low-grade fibromyxoid sarcoma (LGFMS) and sclerosing epithelioid fibrosarcoma (SEF) are two rare but aggressive soft tissue sarcomas that can be difficult to distinguish due to histopathological similarities. The present study examines the diagnostic capacities of mucin-4 (MUC4), a transmembrane mucin, in identifying different types of sarcomas and broadens its evaluation to include a wide range of sarcomas. Methods Immunohistochemical (IHC) examination of tissue samples from various sarcomas was performed using a mouse anti-MUC4 monoclonal antibody. IHC was conducted on 4-mm thick formalin-fixed paraffin-embedded tissue sections after pressure cooker antigen retrieval with a mouse anti-MUC4 monoclonal antibody. Results MUC4 was shown to be highly expressed in SEF (n=13) and LGFMS (n=10), while focal positivity in synovial sarcoma (n=1). Other sarcomas, such as malignant peripheral nerve sheath tumors, fibrosarcoma, leiomyosarcoma, liposarcoma, and myxofibrosarcoma, exhibited no expression (n=0). These findings are consistent with previous research and support MUC4 specificity as a SEF and LGFMS marker.This study provides information on the diagnostic efficacy of MUC4, particularly in the context of certain subtypes. It not only helps our understanding of these unique instances, but it also provides context for histopathological and IHC findings in soft tissue sarcoma. Furthermore, this study investigates the influence of age and gender on MUC4 expression in a range of sarcomas, which was typically understudied in the literature and found no relation with expression of MUC4. Conclusion In conclusion, this study adds to our understanding of soft tissue sarcomas by emphasizing the crucial role of MUC4 in certain sarcoma subtypes while acknowledging the complex variety of the sarcoma landscape. Further research is needed to understand the molecular mechanism that governs marker expression patterns, as well as the therapeutic implications.

MO15-6 A highly efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections

MO15-6 A highly efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections

Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections

Technologies to study localized host–pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host–pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.