Detection of EGFR and KRAS gene mutations using suspension liquid-based cytology specimens in metastatic lung adenocarcinoma

Optimal Preservations of Cytological Materials Using Liquid-Based Cytology Fixatives for Next-Generation Sequencing Analysis

INTRODUCTION

Molecular targeted therapies have been established for various diseases, including cancers, and there is an increasing need for molecular testing on cytology specimens. The aim of this study was to determine the optimal preservation methods of liquid-based cytology (LBC) materials for molecular testing.

METHODS

Cytological samples from 35 surgical resected non-small cell lung carcinoma specimens were obtained between June 2016 and June 2021. The samples were fixed in CytoRich™ red Preservative and stored at 4°C. One week later, three tubes were prepared from each specimen sample and divided into the following groups: the SurePath™ group (continued storage at 4°C), Frozen (Fr) group (stored at -80°C after centrifugation), and LBC-Cell Block (LBC-CB) group (generation of paraffin-embedded CB and storage at 4°C). Samples from 5 patients were used for the time course analysis, and we performed evaluations on these samples at 1, 3, 6, 12, 24, and 36 months. The concentrations and purities of extracted DNA and RNA were measured. The double-stranded DNA (dsDNA) and RNA concentrations were also measured by a fluorometer. The DNA and RNA integrities were quantified by the DNA and RNA integrity number.

RESULTS

Evaluation of samples was performed at baseline and the six timepoints. In the LBC-CB group, DNA and dsDNA concentrations were higher rather than those in the other groups. The RNA concentration of the LBC-CB group was relatively high compared with those of the other groups at the 36-month timepoint. The Fr group maintained higher DNA quality compared with the other groups over 3 years. The LBC-CB group maintained a higher RNA quality than the other groups until 24 months.

CONCLUSION

LBC-CB preparation is an effective method to maintain DNA/RNA quality and quantity in long-duration preservation for eventual molecular testing. Therefore, LBC-CB may have applications on preanalytical stage for molecular genomic testing such as next-generation sequencing.

Kras Gene Analysis Using Liquid-Based Cytology Specimens Predicts Therapeutic Responses and Prognosis in Patients with Pancreatic Cancer

Simple Summary

New therapeutic strategies are needed to improve the prognosis of pancreatic ductal adenocarcinoma (PDAC) and developing biomarkers that can guide individualized treatment decisions is an important part of these strategies. In this study, we found that unresectable PDAC patients harboring wild-type Kras had significantly longer progression-free survival (PFS) and overall survival (OS) than those harboring mutant Kras after undergoing first-line gemcitabine and nab-paclitaxel (GA) therapy and that wild-type Kras was a significant predictor of longer PFS and OS. This is the first report suggesting that Kras gene analysis has the potential to predict therapeutic responses to GA and the prognosis of unresectable PDAC.

Abstract

Background: Although several molecular analyses have shown that the Kras gene status is related to long-term survival of patients with pancreatic ductal adenocarcinoma (PDAC), the results remain controversial. Here, we examined the Kras gene status in a cohort of unresectable PDAC patients who underwent first-line therapy with gemcitabine and nab-paclitaxel (GA) and assessed differences in chemotherapy responses and survival. Methods: Patients with a histological diagnosis of PDAC (based on EUS-guided fine-needle aspiration) from 2017 to 2019 were enrolled. Tumor genomic DNA was extracted from residual liquid-based cytology specimens and Kras mutations were assessed using the quenching probe method. The relationships between the Kras status and progression-free survival (PFS) and overall survival (OS) were assessed. Results: Of the 110 patients analyzed, 15 had wild-type Kras. Those with the wild-type gene showed significantly longer PFS and OS than those with mutant Kras (6.9/5.3 months (p = 0.044) vs. 19.9/11.8 months (p = 0.037), respectively). Multivariate analyses identified wild-type Kras as a significant independent factor associated with longer PFS and OS (HR = 0.53 (p = 0.045) and HR = 0.35 (p = 0.007), respectively). Conclusions: The analysis of the Kras gene status could be used to predict therapeutic responses to GA and prognosis in unresectable PDAC patients.

Concordance of Cytological Specimens with Histological Tissue for Detection of Epidermal Growth Factor Receptor Mutation in Non-Small Cell Lung Cancer: A Systematic Review

INTRODUCTION

There is increasing need for more testing in non-small cell lung cancer given the introduction of newer targeted therapies. Cytological specimens including conventional smears (CS), cell blocks (CB), and liquid-based cytology (LBC) are an alternative to histologic tissue (HT) specimens in detecting EGFR mutations, but the concordance of these 2 specimens is yet to be determined. The aim of the present systematic review is to determine the concordance rates between different cytologic specimens with HT in detecting EGFR mutations.

METHODS

PubMed, Cochrane Library, and Google Scholar were utilized in the primary search, along with reference lists of electronically retrieved full-text articles. Concordance rates were pooled together if 2 or more studies reporting the same type of cytologic specimen were available.

RESULTS

Overall, 15 studies were included in this review, with 13 studies included in the pooled analysis. There was an overall concordance rate of 92.8% in 593 paired cytologic and HT specimens, with LBC having the highest concordance rate of 96.0%, followed by CS and CB, each with a concordance rate of 95.8%, although the concordance rate of CS and/or CB was lower at 90.6% with a larger pool of studies. LBC was found to have a significantly higher concordance rate than CS and/or CB.

CONCLUSION

Cytological specimens have a high concordance rate in detecting EGFR mutations, when compared to HT. LBC has shown superior concordance rates compared to CS and CB. Cytological specimens should be considered as an additional and alternative source of diagnostic material for EGFR testing.

Testing EGFR with Idylla on Cytological Specimens of Lung Cancer: A Review

The current standard of care for advanced non-small-cell lung cancer is based on detecting actionable mutations that can benefit from targeted therapy. Comprehensive genetic tests can have long turn-around times, and because EGFR mutations are the most prevalent actionable mutation, a quick detection would enable a prompt initiation of targeted therapy. Furthermore, the scarcity of diagnostic material means that sometimes only cytologic material is available. The Idylla™ EGFR assay is a real-time PCR–based method able to detect 51 EGFR mutations in 2.5 h. Idylla is validated for use only on FFPE sections, but some researchers described their experiences with cytological material. We reviewed the relevant literature, finding four articles describing 471 cases and many types of cytological input material: smears, cell-block sections, suspensions, and extracted DNA. The sensitivity, specificity, and limit of detection appear comparable to those obtained with histological input material, with one exception: the usage of scraped stained smears as input may reduce the accuracy of the test. In conclusion, usage of cytological material as input to the Idylla EGFR test is possible. A workflow where common mutations are tested first and fast, leaving rarer mutations for subsequent comprehensive profiling, seems the most effective approach.

Evaluation of liquid based cytology in detection of EGFR mutation in NSCLC by large samples

Background

Cytology samples are the main resources to detect driver oncogene alterations for advanced lung cancer patients. To explore the value of liquid-based cytology in the detection of epidermal growth factor receptor (EGFR) mutation in non-small cell lung cancer (NSCLC), we analyzed data from a large cohort of EGFR mutation-positive patients.

Methods

We analyzed the clinicopathological characteristics of 8,029 NSCLC cases tested for EGFR mutation by liquid-based cytology specimens and 1,934 NSCLC cases tested by formalin-fixed and paraffine-embedded (FFPE) samples in the Shanghai Pulmonary Hospital from September 2015 to December 2019. Before detection, we evaluated the number of tumor cells in the liquid-based cytology slide, and samples with more than 50 tumor cells and visible sediment were selected for DNA extraction after centrifugation.

Results

The positive rate of EGFR mutation in liquid-based cytology-tested cases was 47.18%, higher than the 41.37% tested through FFPE sample (P<0.01). Accordingly, the mutation rate of EGFR in adenocarcinoma (AC) and NSCLC was higher than that of the FFPE sample (60.01% vs. 54.15%, P<0.01; 30.54% vs. 21.99%, P<0.01). The positive rate of EGFR mutation in pleural effusion was 62.67%, which was the highest rate among liquid-based cytology sample t (P<0.01).

Conclusions

Using quality control and standard procedure, it was found that liquid-based cytology specimen testing is a convenient and reliable method of EGFR detection, as validated by analysis of a large cohort. EGFR mutation detection should also be carried out in NSCLC patients diagnosed by cytology more than in AC patients.

Method for preservation of DNA stability of liquid-based cytology specimens from a lung adenocarcinoma cell line

Liquid-based cytology (LBC) specimens of lung adenocarcinoma have the potential to be widely used for genetic analysis. However, formaldehyde contained in some LBC preservation solutions can cause DNA fragmentation during specimen storage, rendering the samples unsuitable for molecular analysis. To investigate a novel preservation technique for improved DNA stability, which was evaluated by mutation analysis of epidermal growth factor receptor (EGFR) gene in human lung adenocarcinoma cell lines. Cells were fixed in CytoRich Red preservation solution. After 30 min of fixation, cells were either stored using the conventional method (suspended in preservation solution) or washed in phosphate-buffered saline and stored as a cell pellet (newly proposed method). The effect of storage was evaluated after 5, 7, and 9 days of storage at ambient temperature. The cell pellet group was also tested after 14 and 28 days. Specifically, we evaluated the DNA stability, DNA yield, and sample suitability for polymerase chain reaction (PCR), and EGFR mutation detection. The DNA yields and degree of stability from the cell pellet group were higher than those from the suspension group at every time point examined. PCR amplification from the cell pellet group was successful up to day 28. Mutation detection using the Cycleave PCR method indicated that the Ct values of the cell pellet group were significantly lower than those of the suspension group. Storing LBC specimens as a cell pellet post-fixation can maintain the DNA quality for a longer period than the conventional method, making it a promising strategy for molecular analysis.

ALK and ROS1 rearrangement tested by ARMS-PCR in non-small-cell lung cancer patients via cytology specimens: The experience of Shanghai Pulmonary Hospital

BACKGROUND

Cytology specimens are the main samples used for the diagnosis of advanced lung cancer. The objective of our study was to assess anaplastic lymphoma kinase (ALK) and c-ros oncogene 1 receptor tyrosine kinase (ROS1) genes by an amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR) using cytology specimens and to then evaluate the mutation frequency of ALK and ROS1 in non-small-cell lung cancer (NSCLC) patients.

METHODS

A large cohort that consisted of 8180 NSCLC patients who were genetically tested using cytology samples or formalin-fixed and paraffin-embedded (FFPE) samples (tumor tissue or biopsy) from January 2015 to December 2018 were screened. The gene rearrangement ratio and clinical characteristics of the two sample groups were analyzed by SPSS software.

RESULTS

In our hospital, cytology specimens are the main resource used for gene testing in NSCLC. In most cases, an abundant quantity of nucleic acid was extracted from the residual liquid-based cell pellet for testing the ALK and ROS1 genes. In certain cases, when the residual cell pellet was insufficient for the gene testing, the cell block and liquid-based cell smear served as alternative options. In addition, we retrospectively analyzed our previous data, and the mutation ratio of the ALK/ROS1 rearrangements obtained by using the cytology samples (4.98%/1.80%) and the FFPE samples (6.06%/1.62%) was almost the same (P-value = .09/.634).

CONCLUSIONS

This study demonstrated that AMRS-PCR method can effectively identify ALK and ROS1 gene rearrangements and cytology specimens might be an excellent source for routine molecular testing in patients with advanced NSCLC.

Subtyping and EGFR mutation testing from blocks of cytological materials, based on liquid-based cytology for lung cancer at bronchoscopic examinations

BACKGROUND

Liquid-based cytology (LBC) allows immunohistochemistry (IHC), fluorescence in situ hybridization, and molecular testing to be performed in fixed cell materials. We examined the feasibility of subtyping and EGFR mutation testing of bronchoscopic samples from patients with lung cancer using cell blocks (CB) based on LBC fixation (LBC-CB).

METHODS

We included 35 consecutive patients with peripheral lung nodules who underwent endobronchial ultrasonography with a guide sheath in our hospital. Thirty of these patients were diagnosed with lung cancer by obtaining cytological samples. Cytological subtyping was performed with IHC using LBC-CB, and the Cobas EGFR Mutation Test ver. 2 was performed using extracted genomic DNA from the LBC-CB, formalin-fixed paraffin-embedded (FFPE) tissue, and matched plasma.

RESULTS

Of the 30 cases, 25 were classified cytomorphologically as adenocarcinoma (ADC, n = 17) and squamous-cell carcinoma (SQCC, n = 8). The remaining five cases were classified by IHC as favor ADC (n = 3) and favor SQCC (n = 2) according to the WHO criteria. In the final ADC group (n = 20), EGFR mutations on the LBC-CB were identified in eight cases (40%; 1 exon 19 deletion, 6 L858R, and 1 L861Q). Mutations in FFPE samples were identified in seven cases (35%) at the same site in each case. Plasma EGFR mutations were identified in four cases (20%) at the same site. The CB detection rate was higher than for FFPE and plasma.

CONCLUSION

LBC-CB is suitable for subtyping and EGFR mutation testing in lung cancers.

Molecular Analysis of Liquid-Based Cytological Specimen Using Virtually Positive Sputum with Adenocarcinoma Cells

Liquid-based cytology (LBC) analysis of sputum is a useful diagnostic and prognostic tool for detecting lung cancer. DNA and RNA derived from lung cancer cells can be used for this diagnosis. However, the quality of cytological material is not always adequate for molecular analysis due to the effect of formalin in the commercially available fixation kits. In this study, we examined DNA and RNA extraction methods for LBC analysis with formalin fixation, using lung carcinoma cell lines and sputum. The human non-small cell lung cancer cell lines were fixed with LBC fixation reagents, such as CytoRich red preservative. Quantification of thyroid transcription factor-1 (TTF-1) and actin mRNA, epidermal growth factor receptor (EGFR) DNA in HCC827, H1975, and H1299 cells, and mutation analysis of EGFR in HCC827 and H1975 cells were performed by quantitative PCR (qPCR) and fluorescence resonance energy transfer (FRET)-based preferential homoduplex formation assay (F-PHFA) method, respectively. mRNA and DNA extracted from cell lines using RNA and/or DNA extraction kits for formalin-fixed paraffin-embedded (FFPE) fixed with various LBC solutions were efficiently detected by qPCR. The detection limit of EGFR mutations was at a rate of 5% mutated positive cells in LBC. The detection limit of the EGFR exon 19 deletion in HCC827 was detected in more than 1.5% of the positive cells in sputum. In contrast, the detection limit of the T790M/L858R mutation in H1975 was detected in more than 13% of the positive cells. We also detected EGFR mutations using next generation sequencing (NGS). The detection limit of NGS for EGFR mutation was lower than that of the F-PHFA method. Furthermore, more than 0.1% of positive cells could be cytomorphologically detected. Our results demonstrate that LBC systems are powerful tools for cytopathological and genetic analyses. However, careful attention should be paid to the incidence of false negative results in the genetic analysis of EGFR mutations detected by LBC.

K-ras mutation analysis of residual liquid-based cytology specimens from endoscopic ultrasound-guided fine needle aspiration improves cell block diagnosis of pancreatic ductal adenocarcinoma

Background

Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) technology is widely used for the diagnosis of pancreatic masses. However, in some cases, inadequate tissue volume or difficulty of morphological diagnosis are constraining factors for adequate cytopathological evaluation. K-ras mutation is the most frequently acquired genetic abnormality, occurring in approximately 90% of all patients with pancreatic ductal adenocarcinoma (PDAC). In the present study, the clinical utility of residual liquid-based cytology (LBC) specimens obtained using EUS-FNA for K-ras mutation analysis was evaluated.

Methods

In this study, 81 patients with pancreatic lesions were examined. The cell block (CB) specimens separated from EUS-FNA samples were morphologically evaluated by hematoxylin–eosin (HE) staining. Final diagnoses were confirmed by CB specimens, surgical resection specimens, diagnostic imaging, and clinical follow-up. Genomic DNA of residual LBC specimens stored at 4°C for several months were extracted and assessed for K-ras mutations using a fluorescence resonance energy transfer-based preferential homoduplex formation assay.

Results

K-ras mutation analysis using residual LBC samples was successful in all cases. The sensitivity, specificity, and accuracy of CB examination alone were 77.4%, 100%, and 81.3%, respectively, and those of the combination of CB examination and K-ras mutation analysis were 90.3%, 92.3%, and 90.7%, respectively. Furthermore, K-ras mutations were detected in 8 (57.1%) of 14 PDAC samples for which the CB results were inconclusive.

Conclusion

These findings suggest that K-ras mutation analysis using residual LBC specimens improves the diagnostic accuracy of EUS-FNA.