Direct next-generation sequencing analysis using endometrial liquid-based cytology specimens for rapid cancer genomic profiling

Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling - A report on the impact of process optimization through the analysis of 4,871 cytology samples profiled by MSK-IMPACT

Comprehensive molecular profiling by next generation sequencing (NGS) has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACT™. Special emphasis is given to the use of residual supernatant cell free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples were similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples had excellent performance overall, low-level cross-contamination was identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples had negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy delivered successful results in 71% of cases where tumor tissue from CB was depleted.

Immunoreactivity of TTF-1, GATA-3, CEA, and p16/Ki67 cocktail in Cellprep®-processed control samples: Comparison of long-term storage in vials and slides

INTRODUCTION

Cellprep® (CP) is a novel liquid-based cytology (LBC) system. This study aimed to assess the immunoreactivity of control samples stored long-term under two storage conditions using CP.

METHODS

The immunoreactivity in control samples was evaluated under two sample storage conditions: CP vial storage at room temperature (RT: 20-25°C) and CP slide storage in a refrigerator (2-6°C). Clinical samples as controls (total: positive/negative) were immunostained using thyroid transcription factor-1 (TTF-1) (20: 14/6), GATA binding protein 3 (GATA-3) (13: 10/3), carcinoembryonic antigen (CEA) (23: 15/8), and the p16/Ki67 cocktail (20: 12/8) markers. The first immunocytochemistry (ICC) was performed within 1 month using CP vials stored at RT. Samples stored in CP vials and on CP slides were used for the second (within 3-6 months) and third (within 6-11 months) ICCs. Compared with the first ICC, the concordance of immunoreactivity for the second and third ICCs was evaluated using the weighted kappa coefficient.

RESULTS

For TTF-1, CEA, and the p16/Ki67 cocktail markers, ICC controls had stable immunoreactivity for a minimum of 6 months when samples were stored in CP vials (kappa coefficients >0.8), whereas for GATA-3, they were for 3 months. On CP slides, only for the p16/Ki67 cocktail, ICC controls had stable immunoreactivity for at least 3 months (kappa coefficient >0.8).

CONCLUSION

Clinical samples as ICC controls revealed consistently more stable immunoreactivity in CP vials than on CP slides for TTF-1, GATA-3, CEA, and the p16/Ki67 cocktail markers.

Cancer gene analysis of liquid-based cytology specimens using next-generation sequencing: A technical report of bimodal DNA- and RNA-based panel application

BACKGROUND

As liquid-based cytology (LBC) specimens harbor high-quality DNA, genomic analysis using LBC specimens is beneficial for integrative diagnosis. This study aimed to clarify the feasibility of LBC specimens for a bimodal application of DNA- and RNA-based next-generation sequencing (NGS) panels.

METHODS

LBC specimens were prepared from cultured human cancer HEC59 cells using commercially available fixatives (Cellprep, CytoRich Red, and SurePath solutions), and were subjected to NGS for a feasibility study. Clinical LBC specimens of thyroid and salivary gland tumors were prepared using CytoRich Red solution. After DNA and RNA extraction, NGS analyses were performed in a single run using combined DNA- and RNA-based custom-made cancer panels for the detection of gene mutations and fusions.

RESULTS

High-quality DNA and RNA were obtained, and the expected gene mutations and fusions were detected in HEC59 cells using all types of LBC fixatives. Most available clinical cases (18 out of 20) exhibited pathogenic gene mutations (15 cases) and fusion genes (3 cases) using the bimodal DNA- and RNA-based panels. Overall, 18 cases (90%) showed oncogenic mutations or fusion genes of diagnostic values.

CONCLUSION

Simultaneous application of bimodal DNA- and RNA-based gene panels was useful in NGS analysis using residual LBC specimens for integrative diagnosis. Residual LBC specimens for genomic analysis, including fusion gene analysis, are particularly useful for obtaining genomic information before surgical resection.

Endometrial Cytology in Diagnosis of Endometrial Cancer: A Systematic Review and Meta-Analysis of Diagnostic Accuracy

BACKGROUND

Because the incidence of endometrial cancer has been increasing every year, it is important to identify an effective screening method for it. The endometrial cytology test (ECT) is considered to be the more acceptable technique compared to invasive endometrial sampling.

METHODS

The study followed the Priority Reporting Project for Systematic Evaluation and Meta-Analysis (PRISMA-DTA) protocol. This systematic rating searched EMBASE and Web of Science databases for studies on ECT for endometrial cancer from the databases' dates of inception to 30 September 2022. All literature screening and data extraction were performed by two researchers, while the methodological quality of the included studies was assessed against defined inclusion criteria. And a third researcher resolves the disagreements.

RESULTS

Twenty-six studies were eventually included in this final analysis. Meta-analysis results showed that the diagnostic accuracy characteristics of ECT for endometrial cancer were as follows: combined sensitivity = 0.84 [95% confidence interval (CI) (0.83-0.86)], combined specificity = 0.98 [95% CI (0.98-0.98)], combined positive likelihood ratio = 34.65 [95% CI (20.90-57.45)], combined negative likelihood ratio = 0.21 [95% CI (0.15-0.30)], and area under the summary receiver operating characteristic curve = 0.9673.

CONCLUSIONS

ECT had the ability to detect endometrial cancer with strong specificity, although some studies have demonstrated significant differences in sensitivity.

Cytopathological features associated with POLE mutation in endometrial cancer

OBJECTIVE

For patients with endometrial cancer, the POLE (polymerase epsilon) mutation (POLEmut)-subtype, one of four molecular-analysis-based categories in the Cancer Genome Atlas (TCGA), has the best prognosis. The following histological characteristics are typically observed in endometroid carcinoma cases with the POLEmut-subtype: (1) the presence of tumour giant cells, (2) numerous tumour-infiltrating lymphocytes (TILs) and/or peri-tumoral lymphocytes, and (3) a high grade. However, in the context of cytology, the morphological characteristics of this subtype remain unknown.

METHODS

DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues was subjected to next-generation sequencing analysis and categorised according to the TCGA classifications. Genomic mutation, tumour mutation burden (TMB), and microsatellite instability were also assessed. Cytological specimens of resected uteri obtained using the Papanicolaou method were histologically separated into three types.

RESULTS

Seven out of 112 patients (6%) with endometrial cancer were diagnosed with the POLEmut-subtype between January 2019 and August 2021. Tumour giant cells were observed in three cases (43%) on histology and cytology. TIL and/or peritumoral lymphocytes with inflammatory cells were detected in five cases (71%) on histology and three cases (43%) on cytology. Cases in which these three characteristics were observed on both cytology and histology may have belonged to the POLEmut-subtype. There were no cases in which these characteristics were absent on histology but present on cytology. TMB tended to be higher in cases when the three characteristics were observed in both cytological and histological findings.

CONCLUSIONS

Preoperative endometrial cytology highlighted the characteristics of the POLEmut-subtype in the histological analysis of resected uterine specimens and has the potential to play an important role in treatment decisions.

Pelvic Carcinosarcoma Showing a Diverse Histology and Hierarchical Gene Mutation with a Common POLE Mutation to Endometrial Endometroid Carcinoma: A Case Report

POLE mutation-type endometrial cancer is characterized by an extremely high tumor mutation burden. Most POLE mutation-type endometrial cancers are histologically endometrioid carcinomas, and POLE mutation-type carcinosarcomas are rare among endometrial cancers. We report a case of endometrial and pelvic cancer in a 53-year-old woman who was analyzed using next-generating sequencing. The endometrial lesion harbored a p.T457del POLE mutation with an elevated tumor mutation burden and low microsatellite instability. The pelvic lesion showed divergent histological features, consisting of high-grade endometrioid carcinoma, neuroendocrine carcinoma, and chondrosarcoma. In addition to the common POLE mutation detected in the endometrial lesion, the pelvic lesion in each element showed additional gene mutations in a hierarchical manner. Therefore, it is indicated that the p.T457del POLE mutation is a pathogenic mutation and may be related to POLE mutation-induced carcinogenesis and divergent morphogenesis in endometrial cancer.

Diagnostic value of endometrial cytology and related technology

BACKGROUND

Endometrial cytology is not much popular in the world, but is commonly used in a few countries. Although cytomorphological evaluation of endometrial cytology is complicating, recent advance in technology helps improve diagnostic accuracy. In addition, new reporting system, The Yokohama System, has been introduced as a standard reporting system resembling The Bethesda System of the uterine cervical cytology. Although sample standardization is one of the causes in diagnostic problem, it was solved by liquid-based cytology (LBC) technology. In addition, standardized diagnostic algorithm by cytomorphological assessment of LBC samples, the Osaki Study Group (OSG) method, was recently proposed as a reliable and reproducible method. LBC can be utilized for ancillary methods. Application of immunocytochemistry and molecular technology on endometrial cytology samples has been studied to improve diagnostic accuracy. Recent progress of molecular technology has revealed many driver gene mutations in endometrial cancer and its precursors. Surprisingly, many studies revealed that even normal endometrial tissue had driver gene mutations.

CONCLUSION

Based on the recent advance in knowledge of molecular profile of endometrial lesions and normal endometrial tissue, endometrial cytology will gain much power in clinical usefulness.

Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care

Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess the early experience and performance characteristics of a novel approach to biomarker testing at a large community center. This approach to NGS included an automated workflow utilizing the Genexus integrated sequencer, validated for clinical use. NGS testing was further integrated within a routine immunohistochemistry (IHC) service, utilizing histotechnologists to perform technical aspects of NGS, with results reported directly by anatomic pathologists. Results: Between October 2020 and October 2021, 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR: 2-5). Four hundred eighty-one (83%) of the cases were resulted in fewer than 5 business days, and 66 (11%) of the cases were resulted simultaneously with diagnosis. Tumor types included lung cancer (310), melanoma (97), and colorectal carcinoma (68), among others. NGS testing detected key driver alterations at expected prevalence rates: lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAF (67%), among others. Conclusion: This is the first study demonstrating clinical implementation of rapid NGS. This supports the feasibility of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry. This novel approach to biomarker testing offers considerable advantages to clinical cancer care.

Impact of LBC fixative type and fixation time on molecular analysis of pancreatic cancer cells: A comparative study of cell morphology, antigenicity and nucleic acids

Introduction:

Liquid-based cytology (LBC) has been widely used since 2000. Next-Generation Sequencing (NGS) analysis of residual specimens in LBC fixative may also be performed for pancreatic cancer in the near future. We examined cell morphology, antigenicity and nucleic acids in pancreatic cancer cells at different fixation times using two types of LBC fixatives.

Methods:

PANC-1 cells were fixed in 1 ml CytoRich Red (CR), CytoRich Blue (CB), 95% ethanol (95% AL) or 10% neutral buffered formalin (10% NBF) and evaluated for cell area, antigenicity and nucleic acids with fixation times of 1 hour and 1, 3, 9, and 14 days. Antigenicity was evaluated by immunocytochemical staining for p53 and CK20, and nucleic acid fragmentation was assessed by real-time PCR.

Results:

There was no difference in total cell area between 1 hour and 14 day fixation times for the CR group, but the CB group showed cell contraction with 9 days fixation. In immunocytochemical staining, the CR group showed high p53 and CK20 positivity even after 14 days fixation. The CB group had a lower p53 positive rate than the CR group from 1 hour fixation. For nucleic acid fragmentation, Ct values for the CR group increased with fixation time. The CB group had consistently low Ct values.

Conclusion:

Different LBC fixatives and fixation time can have varying effects on cell morphology, antigenicity and nucleic acids in pancreatic cancer cells. Therefore, fixative type and fixation time should be considered for molecular testing on residual samples in LBC fixatives.