Formalin-fixed Paraffin-embedded Cell Research Articles

Xpert Breast Cancer STRAT4 Assay using fine-needle aspiration biopsy samples in a resource-constrained setting: a prospective diagnostic accuracy study

Use of fine-needle aspiration biopsy (FNAB) specimens on Xpert Breast Cancer STRAT4 Assay (STRAT4; Cepheid, Sunnyvale, CA, USA), a CE-marked in-vitro diagnostic medical device, could potentially increase access to breast cancer biomarker testing in resource-constrained settings. We aimed to assess the performance of a research use-only version of STRAT4 using FNAB specimens in Tanzania. In this prospective diagnostic accuracy study, patients aged 18 years or older with palpable breast masses presenting to the FNAB Clinic at Muhimbili National Hospital (Dar es Salaam, Tanzania) were recruited consecutively. Patients who were pregnant, lactating, or had a previous diagnosis of breast cancer were excluded. STRAT4 testing was performed on off-label FNAB samples using four protocols: the 1 × protocol (using the standard lysate method) on FNAB smears (1 × FNAB), quick lysis and Maui protocols (both on FNAB smears), and the 1 × protocol on formalin-fixed paraffin-embedded (FFPE) cell block material (1 × cell block). For 1 × FNAB and 1 × cell block, tissue was processed using FFPE lysis reagent, incubated at 80°C with proteinase K, and followed by addition of 95% or higher ethanol. Quick lysis was processed using FFPE lysis reagent and 95% or higher ethanol, whereas Maui was processed using a proprietary research-use only lysis reagent. The primary outcomes were overall concordance, sensitivity, specificity, and area under the receiver operating characteristic curve (AUC) of STRAT4 as compared with immunohistochemistry or immunohistochemistry plus fluorescence in-situ hybridisation performed on cell blocks using clinically validated protocols in a Clinical Laboratory Improvement Amendments-accredited laboratory at the University of California, San Francisco (San Francisco, CA, USA). Between Nov 29, 2017, and Dec 17, 2020, 208 patients were enrolled. Of 208 cases, 51 (25%) were excluded from analysis because of insufficient tissue in the cell block or absent cell blocks, leaving 157 participants (all female) for analysis. For oestrogen receptor, 1 × FNAB had the best performance, with an overall concordance of 95% (95% CI 90-100), sensitivity of 94% (85-100), specificity of 97% (90-100), and AUC of 0·96 (0·81-1·00). For progesterone receptor, 1 × cell block had the best overall performance (overall concordance 89% [95% CI 84-95], sensitivity 91% [82-99], and specificity 89% [81-97], with an AUC of 0·93 [0·89-0·99]) and 1 × FNAB performed the best among the smear protocols, with a concordance of 84% (95% CI 74-93), sensitivity of 63% (43-82), specificity of 97% (92-100), and AUC of 0·91 (0·72-0·97). For HER2, Maui had the highest agreement, with an overall concordance of 93% (95% CI 89-98), sensitivity of 96% (88-100), specificity of 92% (87-98), and AUC of 0·95 (0·98-1·00). For Ki67, Maui had the best performance of smear protocols, with a concordance of 73% (95% CI 64-82), sensitivity of 70% (58-81), specificity of 81% (66-96), and AUC of 0·80 (0·54-0·82). Processing FNAB samples with STRAT4 is feasible in Tanzania, and performance for the oestrogen receptor is robust. Further optimisation of STRAT4 for FNAB has the potential to improve timely access to breast cancer diagnostics in resource-constrained settings. US National Institutes of Health; UCSF Global Cancer Program, Helen Diller Family Comprehensive Cancer Center; UCSF Department of Pathology; and Cepheid.

Genetic profiles of oligometastatic non-small-cell lung cancer and corresponding brain metastases.

In patients with oligometastatic non-small-cell lung cancer (NSCLC), systemic therapy in combination with local ablative treatment of the primary tumour and all metastatic sites is associated with improved prognosis. For patient selection and treatment allocation, further knowledge about the molecular characteristics of the oligometastatic state is necessary. Here, we performed a genetic characterization of primary NSCLC and corresponding brain metastases (BM). We retrospectively identified patients with oligometastatic NSCLC and synchronous (<3 months) or metachronous (>3 months) BM who underwent surgical resection of both primary tumour and BM. Mutation profiling of formalin-fixed paraffin-embedded tumour cell blocks was performed by targeted next-generation sequencing using the Oncomine Focus Assay panel. Sequencing was successful in 46 paired samples. An oncogenic alteration was present in 31 primary tumours (67.4%) and 40 BM (86.9%). The alteration of the primary tumours was preserved in the corresponding BM in 29 out of 31 cases (93.5%). The most prevalent oncogenic driver in both primary tumours and BM was a KRAS (Kirsten rat sarcoma viral oncogene) mutation (s = 21). In 16 patients (34.8%), the BM harboured additional oncogenic alterations. The presence of a private genetic alteration in the BM was an independent predictor of shorter overall survival. In oligometastatic NSCLC, BM retain the main genetic alterations of the primary tumours. Patients may profit from targeted inhibition of mutated KRAS. Additional private genetic alterations in the BM are dismal.

Abstract 1032: Development of a novel companion diagnostic immunohistochemistry antibody for claudin 18.2-targeted therapies

Abstract Background: CLDN18.2, the isoform 2 of CLDN18, is physiologically confined to gastric mucosa tight junctions, the epitopes of which would be exposed on the cancer cell surface upon malignant transformation and is highly expressed in a significant proportion of cancers, e.g., gastric and pancreatic adenocarcinomas, which makes it a promising drug target for cancer therapy. Currently, multiple drug modalities, such as monoclonal antibodies, ADCs, and CARTs targeting CLDN18.2 are being evaluated in clinical trials. A substantial correlation exists between the expression of CLDN18.2 and the efficacy of the these therapies. However, to date, no companion diagnostic (CDx) antibodies that are specific to CLDN18.2 have been approved. Therefore, it is important to promptly develop an anti-CLDN18.2 CDx antibody with a high specificity, sensitivity, and suitability for immunohistochemistry (IHC). In this study, we present the discovery and validation of a novel, highly sensitive IHC antibody that selectively identifies CLDN18.2. Methods: 3 CLDN18.2 specific peptide fragments from extracellular domain of human CLDN18.2 were conjugated with KLH. Antibodies were discovered by immunizing BALB/c and SJL mice with these peptides-KLH conjugates. Screening and selection process was relied on positive ELISA results against the immunogen, as well as FACS and Acumen Explorer Microplate staining of CLDN18.2-experssing cells. Hit antibodies were evaluated for IHC on formalin-fixed paraffin-embedded CHOK1 cells expressing full-length CLDN18.2 or CLDN18.1. The antibodies were further validated on human gastric cancer tissue samples to establish the analytical sensitivity and specificity of the IHC assay. Results: The mAb clone 43F11 exhibited binding to a fusion polypeptide comprising the first extracellular loop of human CLDN18.2 (aa32-53) at a half maximal effective concentration (EC50) of 0.212 nM. 43F11 showed positive cell surface IHC staining on CLDN18.2-experssing cells after fixation but demonstrated no staining on CLDN18.1-experssing cells. The IHC test method was established by utilizing clinical tumor tissues and PDX samples that had predetermined expression levels of CLDN18.2. The 43F11 antibody accurately identified the expression level of CLDN18.2 in the IHC assay, with a minimum concentration of 0.25 μg/mL. When compared to the commercial CLDN18.2 IHC antibody EPR19202, 43F11 demonstrated greater sensitivity, allowing for positive staining on cancer tissues that have significantly lower levels of CLDN18.2 expression. Conclusion: 43F11 exhibits specific recognition of human CLDN18.2 in IHC assays, while showing no reactivity towards CLDN18.1. It demonstrated superior sensitivity compared to the benchmark antibody. These data suggest that 43F11 has the capacity to serve as an effective diagnostic tool for identifying patients who positively express CLDN18.2. Citation Format: Jishun Chen, Suya Bai, Yu Bai, Zaoshun Hu, Peng Chen, Jay Mei, Bo Shan, Bing Hou. Development of a novel companion diagnostic immunohistochemistry antibody for claudin 18.2-targeted therapies [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 1032.

Diagnostic utility of immunocytochemistry by using liquid-based cytology (LBC) slides.

Cytological specimens, such as fine needle aspirations (FNAs) and exfoliative cytology samples, are minimally invasive options for diagnostic purposes. Liquid-based cytology (LBC), originally designed for cervical cytology, has gained prominence as an alternative technique for non-gynecological cytology. Immunocytochemistry (ICC) is an ancillary method used when diagnosis becomes challenging due to morphological overlap or the need for cellular origin clarification. This study aims to assess the diagnostic utility of ICC when applied to LBC slides and evaluate its effectiveness in relation to the waiting (lag) time of residual material. A total of 74 cases in which ICC was applied to LBC slides were studied over one year in a reference pathology laboratory (Prof. Dr. Cemil Tascioglu, Pathology Laboratory, City Hospital, Istanbul, Turkey). Cases in which immunohistochemistry (IHC) was performed on formalin-fixed paraffin-embedded cell blocks were excluded. The SurePath PAP method was used for the main LBC cytology slides. For the ICC study, 1-4 PAP-stained LBC slides were obtained from each case's residual material and stained with a primary antibody. The positive immunostaining was obtained in 81% of cases. The samples were categorized into groups based on the waiting time of residual LBC material for ICC analysis: 1-5 days, 6-10 days, 11-20 days, and 21-38 days. Comparative analysis revealed a decline in ICC efficacy as the waiting (lag) time increased. Additionally, a statistically significant difference was observed between the 11-20 days and 21-38 days groups (P < 0.05). An analysis of 142 LBC slides stained by ICC revealed that nuclear markers exhibited higher positivity compared to non-nuclear markers, although no significant difference was detected between the two groups. High positivity rates can be obtained in ICC studies performed on additional slides obtained from residual LBC material within the first 20 days. ICC applied to LBC slides is an important and useful alternative for diagnostic and prognostic markers in cases without a cell block or with a cell block without sufficient number of cells.

Comparison of Confirmed Cytology Smears and Cell Blocks for Epidermal Growth Factor Receptor Mutation Testing in Non-Small Cell Lung Cancer.

Various cytologic specimens have been used to diagnose epidermal growth factor receptor (EGFR) gene mutations in non-small cell lung cancer (NSCLC). However, insufficient samples and lengthy DNA extraction procedures have led to inconsistent diagnostic results. To reduce manipulation losses and improve DNA extraction quality, we provide an improved procedure for DNA extraction from smear samples containing rare tumor cells in NSCLC. The effectiveness of this new method for DNA extraction and diagnosis was validated in 8 patients with pleural effusion smears and formalin-fixed paraffin-embedded cell blocks, and another with 2 smears. Smear samples with <5% tumor cells were collected, and visible particles were selected for DNA extraction after centrifugation. Qiagen formalin-fixed paraffin-embedded DNA extraction kit (Qiagen) was used for DNA extraction and the procedure was modified. The EGFR mutation analysis in both types of material used the EGFR mutation analysis kit (Therascreen EGFR RGQ PCR) and real-time polymerase chain reaction (Rotor-Gene Q). The DNA extraction amount of the smear was 2.6 to 258.8 ng/μL, and that of the cell block was 1.4 to 139.9 ng/μL. The DNA quantity and purity of DNA extracts isolated from both sample sources were sufficient for subsequent EGFR mutation detection, where mutation rates were similar and diagnostic results were consistent when smears or cell blocks were used. This improved method demonstrates that cytology smears can be used as a test material for the detection of EGFR mutations in patients with NSCLC with sparse cells.

Description of technique for endoscopic ultrasound-guided tissue acquisition in pancreatic cancer for comprehensive molecular profiling: Results of a randomized trial.

e16306 Background: As theoretically actionable genomic lesions are found in almost 50% of pancreatic cancers which can impact clinical management in up to 30% of patients, there is increased focus on molecular profiling. Although EUS-FNB is an established method for achieving pathological diagnosis in pancreatic cancers, the technique of tissue acquisition for comprehensive molecular profiling (CMP) has not been described. Methods: Patients proven to have pancreatic adenocarcinoma using rapid onsite evaluation (ROSE) at EUS were randomized to undergo two or three dedicated FNB passes for CMP. Tissue was procured using 22G Franseen needle adopting the fanning technique and stylet-retraction maneuver. Genomic DNA and total RNA were extracted from formalin-fixed paraffin-embedded (FFPE) cell blocks (Qiagen AllPrep). Next-generation sequencing (NGS) was performed (Archer Panels) for analyzing 69 gene DNA mutations (single nucleotide variants, insertions, and deletions) and 53 RNA somatic oncogenic gene fusions. Main outcome measure was the proportion of specimens in which adequate DNA and RNA were extracted for CMP. Results: 33 patients (mean age 77.0 years [SD 7.7], female = 20) with pancreatic cancer (location = head/uncinate 22; other 11) were randomized to two (n = 17) or three (n = 16) FNB passes. While sufficient DNA was extracted from all 33 FFPE cell blocks, adequate RNA was extracted from 15 of 16 in the three pass (93.8%) vs. 16 of 17 in the two pass cohort (94.1%) (p = 0.99). There was no significant difference in the mean concentration of DNA (two passes 10.7 ng/ul [SD 7.1] vs. three passes 7.9 ng/ul [SD 4.4]; p = 0.19) or RNA (two passes 37.1 ng/ul [SD 26.5] vs. three passes 28.9 ng/ul [SD 13.2]; p = 0.29) between the groups. While somatic oncogene RNA fusion (LDAH-ETV1) predictive of metastatic disease was identified in one specimen, DNA mutations were identified in all 33 specimens that included one BRCA1 mutation that warranted Oxaliplatin-based chemotherapy. Conclusions: Specimens of adequate quantity and of high quality for comprehensive molecular profiling in pancreatic cancer can be procured in nearly 95% of patients by performing two dedicated passes using the 22G Franseen needle, adopting the fanning maneuver and stylet-retraction technique. Clinical trial information: NCT05043532 .

Establishing clinical performance characteristics for Duoseq, a new assay for DNA and RNA sequencing.

e15059 Background: Despite advances in genomics and next generation sequencing (NGS), clinical implementation of NGS remains challenging. This challenge is critical in hematologic malignancies where NGS has become an essential part of the clinical workup. Many clinical labs resort to send-out testing that can delay appropriate treatment and drive up the cost of care. To address these issues, we have developed Duoseq as a unified approach for DNA and RNA NGS. Duoseq assesses mutations (single nucleotide variants [SNVs], insertions/deletions [indels] and splice site variants [SSVs]), structural variants, and gene expression using a panel of over 400 genes. It is supplied as a kit that enables preparation of DNA and RNA sequencing libraries in a single workflow performed at the point-of-care. It includes complete bioinformatics support that enables a clinical laboratory with an NGS instrument to perform the assay with a turn-around time of 2-3 days. Duoseq is optimized to work with formalin-fixed, paraffin embedded (FFPE) samples that are the standard fixation practice. Methods: We evaluated Duoseq on four dimensions critical to clinical performance: reproducibility, precision, analytical sensitivity (limit of detection, LoD), and analytical specificity. Identical experiments were run at clinical laboratories of two different institutions. Analytical validation samples included 4 FFPE cell lines and 2 synthetic DNA samples designed to harbor variants of interest at known allele frequencies. Results: We determined the LoD to be 5% mutant allele fraction (MAF) for SNVs, 10% MAF for indels/SSVs, and 10% tumor purity for SVs. Duoseq achieved 100% precision and reproducibility for each variant class for events at or above the LoD. Analytical specificity was 100%, indicating no instances of cross-contamination of samples within or across runs. We further evaluated Duoseq performance in 54 clinical cases of myeloid and lymphoid malignancies compared against clinical results provided by FoundationOne Heme NGS panel. Collectively, we assessed 119 SNVs and 49 indels/SSVs. Duoseq performed with 100% specificity for both SNVs and indels/SSVs. Duoseq achieved 98% sensitivity for SNVs and 96% for indels/SSVs. For example, Duoseq detected TP53 variants in 6 cases of myeloid neoplasms, which has relevance for the 2022 WHO and ICC classifications. Duoseq also identified therapeutically relevant variants in IDH1/2, EZH2, FLT3, KRAS and TET2. Conclusions: This study demonstrates performance characteristics that suggest Duoseq would perform well as a clinical-grade assay. Local laboratory factors that include staffing, case volumes, and reimbursement affect adoption and turnaround times in the individual clinical laboratory. However, we anticipate that Duoseq implementation will accelerate the diagnosis of hematologic malignancies and facilitate rapid, more cost-effective care to improve patient outcomes.

An Italian Multicenter Perspective Harmonization Trial for the Assessment of MET Exon 14 Skipping Mutations in Standard Reference Samples

Lung cancer remains the leading cause of cancer deaths worldwide. International societies have promoted the molecular analysis of MET proto-oncogene, receptor tyrosine kinase (MET) exon 14 skipping for the clinical stratification of non-small cell lung cancer (NSCLC) patients. Different technical approaches are available to detect MET exon 14 skipping in routine practice. Here, the technical performance and reproducibility of testing strategies for MET exon 14 skipping carried out in various centers were evaluated. In this retrospective study, each institution received a set (n = 10) of a customized artificial formalin-fixed paraffin-embedded (FFPE) cell line (Custom METex14 skipping FFPE block) that harbored the MET exon 14 skipping mutation (Seracare Life Sciences, Milford, MA, USA), which was previously validated by the Predictive Molecular Pathology Laboratory at the University of Naples Federico II. Each participating institution managed the reference slides according to their internal routine workflow. MET exon 14 skipping was successfully detected by all participating institutions. Molecular analysis highlighted a median Cq cut off of 29.3 (ranging from 27.1 to 30.7) and 2514 (ranging from 160 to 7526) read counts for real-time polymerase chain reaction (RT-PCR) and NGS-based analyses, respectively. Artificial reference slides were a valid tool to harmonize technical workflows in the evaluation of MET exon 14 skipping molecular alterations in routine practice.

Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing.

RNA sequencing (RNAseq) analysis is emerging as a clinical research or diagnostic approach for cytologic samples, but there is need for formal comparison of different sample preparation methods in the cytology laboratory to identify which pre-analytic methods could provide alternatives to formalin-fixed paraffin-embedded (FFPE) sections. We prepared 13 malignant effusions (metastatic estrogen receptor-positive breast cancer) in the cytology laboratory using 6 routine cytologic methods: FFPE cell block, Carnoy's solution, 95% ethanol (EtOH), air-dried and Diff-Quik, ThinPrep, and SurePath preparations. Measurements of RNA quality, expression of 2 multigene expression signatures, molecular subtype, and 4 common activating mutation sites in each preparation were compared with fresh frozen (FF) cell pellet in RNA preservative using distribution of fragment length and concordance correlation coefficient (CCC). The fraction of RNA fragments measuring 200 bases or more (DV200) were 24% higher from cytospins fixed in Carnoy's solution or 95% EtOH than DV200 from FFPE cell blocks. SurePath samples failed RNAseq quality control. There was high concordance of gene expression measurements with FF samples using cytospins fixed in Carnoy's solution, 95% EtOH, Diff-Quik (CCC = 0.829, 0.812, 0.760, respectively), or ThinPrep (CCC = 0.736), but lower using FFPE cell block (CCC = 0.564). The proportion of mutant transcripts was concordant between FF and any cytologic preparation methods. Cytospin preparations fixed with Carnoy's or 95% ETOH then Papanicolaou stained produced RNAseq results that were equivalent to FF samples and superior to FFPE cell block sections.

Application of Immunohistochemistry in Cytology.

Immunohistochemistry (IHC), also referred to as immunocytochemistry in cytology literature, has revolutionized the practice of cytopathology. Because of the complexity of cytology preparation and limited diagnostic material, performing IHC remains a challenge. Formalin-fixed paraffin-embedded (FFPE) cell block (CB) is the optimal choice for IHC. In this review, the approaches for improving CB preparation will be discussed. When CB material is not available, various cytology specimens can also be used for IHC. With the utilization of Antigen Retrieval (AR) technique, these nonformalin-fixed cytology specimens can achieve successful IHC staining, comparable with the results from FFPE tissue sections. In the last part of this review, we will discuss the use of positive controls and the important role of AR in standardization of IHC in cytology.

External quality assessment (EQA) for tumor mutational burden: results of an international IQN path feasibility pilot scheme

Tumor mutational burden (TMB) has recently been approved as an agnostic biomarker for immune checkpoint inhibitors. However, methods for TMB testing have not yet been standardized. The International Quality Network for Pathology (IQNPath) organized a pilot external quality assessment (EQA) scheme for TMB testing. The aim of this program was the validation of the materials and the procedures for the EQA of this complex biomarker. Five formalin-fixed paraffin-embedded (FFPE) cell lines were selected to mimic the various TMB values observed in clinical practice. The FFPE samples were tested with the FoundationOne CDx (F1CDx) assay as the reference test and three commercially available targeted sequencing panels. Following this internal validation, the five cell lines were sent to 29 laboratories selected on the basis of a previous survey. Nineteen of the 23 laboratories that submitted results (82.6%) used targeted sequencing for TMB estimation. Only two laboratories performed whole exome sequencing (WES) and two assessed TMB by clinical exome. A high variability in the reported TMB values was observed. The variability was higher for samples with the highest TMB value according to the F1CDx test. However, good reproducibility of the TMB score was shown by laboratories using the same panel. The majority of laboratories did not indicate a TMB cut-off value for clinical interpretation. In conclusion, this pilot EQA scheme suggests that it is feasible to run such an EQA program for TMB assessment. However, the results of our pilot highlight the numerous challenges for the standardization of this test.

Supernatant Fluid from Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration for Rapid Next-Generation Sequencing

Abstract Introduction/Objective The aims of our study were to optimize the workflow of non-small cell carcinoma (NSCC) endobronchial ultrasound-guided bronchoscopy with transbronchial needle aspiration (EBUS-TBNA) samples to maximize tissue available for next-generation sequencing (NGS), preserve formalin-fixed paraffin-embedded (FFPE) cell blocks (CBs) for future testing, and shorten turnaround time (TAT) of NGS results. We evaluated the performance of supernatant fluid (SNF) processed from a dedicated aspirate for NGS testing. Methods/Case Report 20 EBUS-TBNA samples positive for NSCC on rapid on-site evaluation were collected and processed using a new workflow (Figure 1). Five aspirates were collected in formalin. One additional dedicated pass was collected fresh and centrifuged. The resulting cell pellet was added to the passes in formalin for FFPE CB processing. The SNF was recentrifuged. DNA and RNA were extracted from concentrated SNF for targeted testing using the Oncomine™ Precision Assay (Thermo Scientific™, Waltham, MA). NGS results from the corresponding FFPE CBs were used as “controls” for comparison. Results (if a Case Study enter NA) A total of 31 mutations were detected in SNF (Table 1). The most frequently mutated genes were TP53 (35%), EGFR (23%), KRAS (13%), CTNNB1 (6%), and ERBB2 (6%). EGFR and KRAS amplification, CDKN2A deletion, and SQSTM1-NTRK3 fusion alteration were also detected. There was 100% concordance between the mutations detected in SNF and corresponding FFPE CBs with comparable variant allele frequencies. TAT of NGS results was 1 day for SNF compared to 4 – 10 days for FFPE CB. Conclusion In our study, we were able to demonstrate the usefulness of NGS on SNF to provide reliable, rapid molecular results. This testing strategy was successfully incorporated into the workflow for tissue handling and processing between our clinical, cytopathology, and molecular teams. Molecular results were available at the same time as the cytologic diagnosis, allowing for timely reporting of a comprehensive diagnosis. This approach is particularly useful in patients with advanced disease requiring urgent management.

Hierarchical identification of a transcriptional panel for the histological diagnosis of lung neuroendocrine tumors.

Background: Lung cancer is a complex disease composed of neuroendocrine (NE) and non-NE tumors. Accurate diagnosis of lung cancer is essential in guiding therapeutic management. Several transcriptional signatures have been reported to distinguish between adenocarcinoma (ADC) and squamous cell carcinoma (SCC) belonging to non-NE tumors. This study aims to identify a transcriptional panel that could distinguish the histological subtypes of NE tumors to complement the morphology-based classification of an individual. Methods: A public dataset with NE subtypes, including 21 small-cell lung cancer (SCLC), 56 large-cell NE carcinomas (LCNECs), and 24 carcinoids (CARCIs), and non-NE subtypes, including 85 ADC and 61 SCC, was used as a training set. In the training set, consensus clustering was first used to filter out the samples whose expression patterns disagreed with their histological subtypes. Then, a rank-based method was proposed to develop a panel of transcriptional signatures for determining the NE subtype for an individual, based on the within-sample relative gene expression orderings of gene pairs. Twenty-three public datasets with a total of 3,454 samples, which were derived from fresh-frozen, formalin-fixed paraffin-embedded, biopsies, and single cells, were used for validation. Clinical feasibility was tested in 10 SCLC biopsy specimens collected from cancer hospitals via bronchoscopy. Results: The NEsubtype-panel was composed of three signatures that could distinguish NE from non-NE, CARCI from non-CARCI, and SCLC from LCNEC step by step and ultimately determine the histological subtype for each NE sample. The three signatures achieved high average concordance rates with 97.31%, 98.11%, and 90.63%, respectively, in the 23 public validation datasets. It is worth noting that the 10 clinic-derived SCLC samples diagnosed via immunohistochemical staining were also accurately predicted by the NEsubtype-panel. Furthermore, the subtype-specific gene expression patterns and survival analyses provided evidence for the rationality of the reclassification by the NEsubtype-panel. Conclusion: The rank-based NEsubtype-panel could accurately distinguish lung NE from non-NE tumors and determine NE subtypes even in clinically challenging samples (such as biopsy). The panel together with our previously reported signature (KRT5-AGR2) for SCC and ADC would be an auxiliary test for the histological diagnosis of lung cancer.

Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

BackgroundClinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified.ResultsTissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to “edge effects” seen in histology, while the inner samples display no quality degradation related to fixation time.ConclusionsTo assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.

Application of the Milan system for reporting salivary gland cytopathology using cell blocks.

The Milan system for reporting salivary gland cytopathology (MSRSGC) is a novel standardized classification tool for salivary gland cytology specimens based on the use of direct smears. Formalin-fixed paraffin-embedded (FFPE) cell blocks facilitate the use of ancillary studies, leading to improved diagnostic accuracy. However, the application of the MSRSGC with only cell blocks has not been well established. Consecutive cohort of all parotid gland cytology specimens between 01/01/2018 and 30/06/2021 was performed. All cytology specimens were processed into cell blocks only. Cytologic diagnoses were classified prospectively according to the MSRSGC categories. The risk of malignancy (ROM) for each diagnostic category and the diagnostic performance were calculated. A total of 230 FNA samples from 221 patients were identified, including 47% and 78.4% with surgical or clinical follow-up, respectively. The ROMs based on surgical follow-up for the non-diagnostic, non-neoplastic, AUS, neoplasm: benign, SUMP, SFM and malignant categories were 21.4%,0%,50%,0%,30%,100% and 100%, respectively. The ROMs based on the clinical follow-up for these categories were 7.3%,0%,37.3%,0%,27.3%,100% and 100%, respectively. Following surgical excision, all Milan IVa category samples were confirmed as benign, and all Milan V and VI category samples were confirmed as malignant. This study validates the application of the MSRSGC with the sole use of FFPE cell blocks. The diagnostic accuracy of MSRSGC is high and compares favorably to other institutions using traditional cytology assessment methods. Furthermore, FNA results using this technique enabled to provide optimal patient management based on the ROM of the different Milan system categories.

Abstract 5795: Validation of FDA approved oncoReveal Dx lung and colon cancer assay (oRDx-LCCA)

Abstract Introduction: The oncoReveal™ Dx Lung and Colon Cancer Assay (oRDx-LCCA) is an amplicon-based targeted next generation sequencing (NGS), in vitro diagnostic test that detects DNA variants across 22 genes, including single nucleotide variants (SNVs) and insertions and deletions (INDELs) in KRAS and EGFR, from DNA isolated from formalin-fixed paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) tumor tissue specimens. It is approved by the FDA as a companion diagnostic (CDx) for identifying approved therapeutic treatments for KRAS G12/G13 wild-type variants in CRC, and EGFR L858R variants and exon 19 in-frame deletions for NSCLC. oRDx-LCCA can detect non-CDx variants such as EGFR T790M, G719X and exon 20 insertions in NSCLC and KRAS Q61X and A146T and BRAF V600E in CRC. Variants are detected using Pillar Biosciences’ proprietary PiVAT® (Pillar Variant Analysis Toolkit) software. Methods: DNA input range was evaluated at 6 concentrations between 5 - 160ng in duplicate using DNA extracted from 15 clinical FFPE samples containing SNVs and INDELs from representative targeted mutations. Accuracy was determined by comparing detected variants with an externally validated comparator (CompO) across 208 samples (84 CRC, 124 NSCLC). Limit of detection (LoD) was determined by serial dilution of KRAS, EGFR, or BRAF positive FFPE samples in normal DNA to detect variant allele frequency (VAF) between 1 - 10%. Reproducibility tests were performed across 3 sites, 9 runs, 6 operators, 3 reagent lots and 3 thermocyclers, resulting in a total of 360 libraries. The non-inferiority (NI) statistical test was used to compare the oRDx-LCCA with an FDA approved CDx assay for EGFR exon 19 deletions and L858R mutations (CompQ) and for KRAS G12/G13 mutations (CompC). Synthetic FASTQ files were created at VAFs above and below the variant detection threshold for CDx mutations and used to validate quality control parameters, mean coverage, and on-target rate. Results: Effective DNA input range was determined to be between 10 - 80ng. LoD’s for KRAS G12/G13, EGFR L858 and exon 19 deletion, and BRAF V600E were established at &amp;lt; 4%. Positive percent agreement (PPA) and negative percent agreement (NPA) between oRDx-LCCA and CompO were &amp;gt; 99% each. Across all variables tested for reproducibility, the average percent positive agreement (APA) and average percent negative agreement (ANA) were each &amp;gt; 95%. NI margin was calculated to be &amp;lt; 10% between oRDx-LCCA and CompQ across all NSCLC samples and between oRDx-LCCA and CompC across all CRC samples. A total of 61 synthetic FASTQ datasets were created to validate the functionality and accuracy of PiVAT including VAF thresholds for 126 SNV and INDEL CDx variants. Conclusion: oRDx-LCCA is a highly accurate FDA approved IVD assay and PiVAT is a powerful FDA approved software tool for the detection of clinically relevant KRAS variants in CRC and EGFR variants in NSCLC and determination of approved therapy. Citation Format: Gloria Chan Johnson, Jordan Aldersley, Nicholas Lodato, Jamie Lim, Ian Flockhart, Mark Urbin, Yue Ke, Sean Polvino, Martin Zillmann, Gang Song, Zhaohui Wang. Validation of FDA approved oncoReveal Dx lung and colon cancer assay (oRDx-LCCA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5795.

Molecular yield and cytomorphologic assessment of fine needle aspiration specimen supernatants.

Cytology samples are frequently relied upon for the diagnosis of advanced cancer such as lung cancer. As the recommendations for solid malignancies biomarker testing continue to expand, it becomes increasingly important to efficiently utilize limited specimens to minimize the need for additional sampling and its associated risks and costs. We performed molecular testing on fresh or CytoLyt-fixed supernatants derived from fine needle aspirates (FNAs) and compared its performance against the clinical specimen (including formalin-fixed paraffin-embedded cell blocks, residual PreservCyt and fresh samples). Supernatants were assessed for cellularity using Field-stained Cytospin (CS) preparations. There was overall almost perfect agreement (41/45 cases, K = 0.822) and substantial to almost perfect agreement in molecular testing results of clinically actionable variants between fresh (20/23 cases, Κ = 0.742) and CytoLyt-fixed (21/22 cases, Κ = 0.908) and its clinical specimen counterpart. Interestingly, CS examination of the supernatants revealed viable tumor cells. Centrifugation for 1 minute at 300 rpm is optimal for overall or tumor cellularity recovery. Delayed molecular testing after 3, 4 and 7 days at 4 degrees Celsius showed identical molecular results. We validated the use of supernatants derived from FNA cytology samples as a substrate for molecular testing using next-generation sequencing and other molecular techniques.

Crown-Cut Endobronchial Ultrasound Guided Transbronchial Aspiration Needle: First Real-World Experiences.

Advancements in personalized medicine have increased the demand for quantity and preservation of tissue architecture of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) samples. These demands may be addressed by the SonoTip TopGain® needle, which has a 3-point crown-cut design that contrasts with the standard single bevel design of the ViziShot 2®. The objective was to compare the SonoTip TopGain® and ViziShot 2® needles by considering biopsy sample characteristics, diagnostic accuracy, and patient safety. The primary endpoint of the study was the number of high-power fields (HPFs) in the center of the formalin-fixed paraffin-embedded cell block per sample. The lymph node with the highest probability for malignant infiltration based on size and sonographic appearance was chosen as the target lymph node for 20 patients. The same lymph node in each patient was sampled using both the ViziShot 2® and SonoTip TopGain® needles. The samples were measured, sliced, and analyzed by a pathologist. Sixteen patients were biopsied with both needles. Four patients could not be biopsied with the SonoTip TopGain® needle since it could not penetrate cartilage or be repositioned to bypass cartilage. HPFs and sample dimensions were significantly greater in the patients where sampling with the SonoTip TopGain® needle was possible (p = 0.007 and p = 0.005, respectively). Diagnostic accuracy and safety profiles were comparable. Significantly more material can be sampled using the SonoTip TopGain® needle when cartilage penetration can be avoided. This improves the yield for molecular workup in the era of personalized medicine.

Primary Tumor Suppression and Systemic Immune Activation of Macrophages through the Sting Pathway in Metastatic Skin Tumor.

PurposeAgonists of the stimulator of interferon genes (STING) play a key role in activating the STING pathway by promoting the production of cytokines. In this study, we investigated the antitumor effects and activation of the systemic immune response of treatment with DMXAA (5,6-dimethylxanthenone-4-acetic acid), a STING agonist, in EML4-ALK lung cancer and CT26 colon cancer.Materials and MethodsThe abscopal effects of DMXAA in the treatment of metastatic skin nodules were assessed. EML4-ALK lung cancer and CT26 colon cancer models were used to evaluate these effects after DMXAA treatment. To evaluate the expression of macrophages and T cells, we sacrificed the tumor-bearing mice after DMXAA treatment and obtained the formalin-fixed paraffin-embedded (FFPE) tissue and tumor cells. Immunohistochemistry and flow cytometry were performed to analyze the expression of each FFPE and tumor cell.ResultsWe observed that highly infiltrating immune cells downstream of the STING pathway had increased levels of chemokines after DMXAA treatment. In addition, the levels of CD80 and CD86 in antigen-presenting cells were significantly increased after STING activation. Furthermore, innate immune activation altered the systemic T cell-mediated immune responses, induced proliferation of macrophages, inhibited tumor growth, and increased numbers of cytotoxic memory T cells. Tumor-specific lymphocytes also increased in number after treatment with DMXAA.ConclusionThe abscopal effect of DMXAA treatment on the skin strongly reduced the spread of EML4-ALK lung cancer and CT26 colon cancer through the STING pathway and induced the presentation of antigens.

CISH and IHC for the Simultaneous Detection of ZIKV RNA and Antigens in Formalin-Fixed Paraffin-Embedded Cell Blocks and Tissues.

Zika virus is an arthropod-borne virus that has recently emerged as a significant public health emergency due to its association with congenital malformations. Serological and molecular tests are typically used to confirm Zika virus infection. These methods, however, have limitations when the interest is in localizing the virus within the tissue and identifying the specific cell types involved in viral dissemination. Chromogenic in situ hybridization (CISH) and immunohistochemistry (IHC) are common histological techniques used for intracellular localization of RNA and protein expression, respectively. The combined use of CISH and IHC is important to obtain information about RNA replication and the location of infected target cells involved in Zika virus neuropathogenesis. There are no reports, however, of detailed procedures for the simultaneous detection of Zika virus RNA and proteins in formalin-fixed paraffin-embedded (FFPE) samples. Furthermore, the chromogenic detection methods for Zika virus RNA published thus far use expensive commercial kits, limiting their widespread use. As an alternative, we describe here a detailed and cost-effective step-by-step procedure for the simultaneous detection of Zika virus RNA and proteins in FFPE samples. First, we describe how to synthesize and purify homemade RNA probes conjugated with digoxygenin. Then, we outline the steps to perform the chromogenic detection of Zika virus RNA using these probes, and how to combine this technique with the immunodetection of viral antigens. To illustrate the entire workflow, we use FFPE samples derived from infected Vero cells as well as from human and mouse brain tissues. These methods are highly adaptable and can be used to study Zika virus or even other viruses of public health relevance, providing an optimal and economical alternative for laboratories with limited resources. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of RNA probes conjugated with digoxigenin (DIG) Basic Protocol 2: Simultaneous detection of ZIKV RNA and proteins in FFPE cell blocks and tissues.