Validating cell-free DNA from supernatant for molecular diagnostics on cytology specimens

Liquid biopsy: Comprehensive overview of circulating tumor DNA (Review)

Traditional tumor diagnosis methods rely on tissue biopsy, which can be invasive and unsuitable for long-term monitoring of tumor dynamics. The advent of liquid biopsy has notably improved the overall management of patients with cancer. Liquid biopsy techniques primarily involve detection of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA). The present review focuses on ctDNA because of its significance in tumor diagnosis, monitoring and treatment. The use of ctDNA-based liquid biopsy offers several advantages, including non-invasive or minimally invasive collection methods, the ability to conduct repeated assessment and comprehensive insights into tumor biology. It serves crucial roles in disease management by facilitating screening of high-risk patients, dynamically monitoring therapeutic responses and diagnosis. Furthermore, ctDNA can be used to demonstrate pseudo-progression, monitor postoperative tumor status and guide adaptive treatment plans. The present study provides a comprehensive review of ctDNA, exploring its origins, metabolism, detection methods, clinical role and the current challenges associated with its application.

Pleural effusion supernatant: a reliable resource for cell-free DNA in molecular testing of lung cancer

INTRODUCTION

DNA extracted from malignant pleural effusion (PE) sediments is the traditional source of tumor DNA for predictive biomarker molecular testing (MT). Few recent studies have proposed the utility of cell-free DNA (cfDNA) extracted from effusion cytology centrifuged supernatants (CCS) in MT. The aim of this study was to assess the feasibility and utility of molecular testing on cfDNA extracted from PE CCS in lung cancer patients.

MATERIALS AND METHODS

The study was of prospective design. All PE CCS were collected and stored. Subsequently, in patients confirmed as primary lung adenocarcinoma (LUAD) and where patient matched effusion sediment/tissue biopsy/plasma was being tested for EGFR mutations, cfDNA extraction and EGFR MT by real-time polymerase chain reaction (qPCR) were performed. Custom panel targeted next-generation sequencing (NGS) (Ion Torrent; Thermo Fisher, Carlsbad, CA) was also performed wherever feasible.

RESULTS

Out of 299 PE CCS collected, 20 CCS samples were included in the study. Concordant EGFR mutations were detected in pleural effusion CCS of 10 of 11 (91%) EGFR mutant cases as per qPCR performed on the matched sediment DNA (n = 8), lung biopsy (n = 2), and plasma (n = 1) samples. In 1 positive sample, CCS detected additional EGFR T790M mutation. Among 10 CCS samples also tested by NGS, additional EGFR mutations missed by qPCR were picked up in 2 (2 of 10). Success of mutation detection in CCS cfDNA did not correlate with cfDNA quantity or tumor fraction in sediment.

CONCLUSIONS

cfDNA from effusion CCS is a reliable and independent source of tumor DNA highly amenable for MT and complement results from other tumor DNA sources for comprehensive mutation profiling in LUAD patients.

Supernatant fluid from endobronchial ultrasound-guided transbronchial needle aspiration for rapid next-generation sequencing

INTRODUCTION

There is an increasing demand to optimize the workflow and maximize tissue available for next-generation sequencing (NGS) for non-small cell carcinoma. We looked at transbronchial needle endobronchial ultrasound-guided bronchoscopy with transbronchial needle aspiration samples and evaluated the performance of supernatant (SN) fluid processed from a dedicated aspirate collected for NGS testing.

MATERIALS AND METHODS

Nineteen samples were collected and processed using a new workflow. Five aspirates were collected in formalin. One additional dedicated pass was collected fresh and centrifuged. The resulting cell pellet was added to formalin for cell block (CB) processing. DNA and RNA were extracted from concentrated SN for targeted testing using the Oncomine Precision Assay (Thermo Scientific, Waltham, MA). NGS results from the corresponding CB samples were used as "controls" for comparison.

RESULTS

Thirty-one mutations were detected in SN (Table 1). The most frequently mutated genes were TP53 (35%), EGFR (23%), KRAS (13%), CTNNB1 (6%), and ERBB2 (6%). There was 100% concordance between the mutations detected in SN and corresponding CBs with comparable variant allele frequencies. Turnaround time of NGS results was 1 day for SN compared to 4-10 days for CB.

CONCLUSIONS

We were able to demonstrate the usefulness of SN for reliable rapid molecular results. We successfully incorporated the workflow for tissue handling and processing among 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.

Detection of Tumor DNA in Bronchoscopic Fluids in Peripheral NSCLC: A Proof-of-Concept Study

Introduction

DNA genotyping from plasma is a useful tool for molecular characterization of NSCLC. Nevertheless, the false-negative rate justifies the development of methods with higher sensitivity, especially in difficult-to-reach peripheral lung tumors.

Methods

We aimed at comparing molecular analysis from the supernatant of guide sheath flush fluid collected during radial-EndoBronchial UltraSound (r-EBUS) bronchoscopy with plasma sampling and tumor biopsies in patients with peripheral NSCLC. The DNA was genotyped using high-throughput sequencing or the COBAS mutation test. There were 65 patients with peripheral lung tumors subjected to concomitant sampling of guide sheath flush supernatant, plasma tumor DNA, and tumor biopsy and cytology using r-EBUS. There were 33 patients (including 24 newly diagnosed with having NSCLC) with an identifiable tumor mutation in the primary lesion selected for the comparative analysis.

Results

Guide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17 of 24 mutated EGFR, one of two ERBB2, one of one KRAS, one of one MAP2K, one of four MET, and zero of one STK11), compared with 33% in plasma-based genotyping (p = 0.0151). Furthermore, in eight of 34 r-EBUS without tumor cells on microscopic examination, we were able to detect the mutation in four paired guide sheath flush supernatant, compared with only two in paired plasma.

Conclusion

The detection of tumor DNA in the supernatant of guide sheath flush fluid collected during r-EBUS bronchoscopy represents a sensitive and complementary method for genotyping NSCLC.

One procedure-one report: the Re-Imagine Cytopathology Task Force position paper on small tissue biopsy triage in anatomic pathology

INTRODUCTION

Endoscopic biopsy procedures increasingly generate multiple tissue samples from multiple sites, and frequently retrieve concurrent cytologic specimens and small core needle biopsies. There is currently lack of consensus in subspecialized practices as to whether cytopathologists or surgical pathologists should review such samples, and whether the pathology findings should be reported together or separately.

MATERIALS AND METHODS

In December 2021, the American Society of Cytopathology convened the Re-Imagine Cytopathology Task Force to examine various workflows that would facilitate unified pathology reporting of concurrently obtained biopsies and improve clinical care.

RESULTS AND CONCLUSIONS

This position paper summarizes the key points and highlights the advantages, challenges, and resources available to support the implementation of such workflows that result in "one procedure-one report".

The Value of Cell-Free Circulating DNA Profiling in Patients with Skin Diseases

Liquid biopsy, also known as fluid biopsy or fluid-phase biopsy, is the sampling and analysis of the blood, cerebrospinal fluid, saliva, pleural fluid, ascites, and urine. Compared with tissue biopsy, liquid biopsy technology has the advantages of being noninvasive, having strong repeatability, enabling early diagnosis, dynamic monitoring, and overcoming tumor heterogeneity. However, interest in cfDNA and skin diseases has not expanded until recently. In this review, we present an overview of the literature related to the basic biology of cfDNA in the field of dermatology as a biomarker for early diagnosis, monitoring disease activity, predicting progression, and treatment response.

Transcending Blood—Opportunities for Alternate Liquid Biopsies in Oncology

Simple Summary

Cell-free DNA—DNA that has been expelled from cells and can be isolated from blood plasma and other body fluids—is a useful tool in medicine, with applications as a biomarker in diagnosis, prognosis, disease profiling, and treatment selection. In oncology, the ease of access to the tumour genome is a major advantage of cell-free DNA, but while this has led to significant research in blood, other body fluids have not received equal attention. This review article summarises the current research into cell-free DNA in non-blood body fluids, highlighting its values and limitations, and suggesting the direction of future studies. We conclude that cell-free DNA from non-blood body fluids may provide additional information to supplement traditional biopsies, allowing informative and improved patient care across many cancer types.

Abstract

Cell-free DNA (cfDNA) is a useful molecular biomarker in oncology research and treatment, but while research into its properties in blood has flourished, there remains much to be discovered about cfDNA in other body fluids. The cfDNA from saliva, sputum, cerebrospinal fluid, urine, faeces, pleural effusions, and ascites has unique advantages over blood, and has potential as an alternative ‘liquid biopsy’ template. This review summarises the state of current knowledge and identifies the gaps in our understanding of non-blood liquid biopsies; where their advantages lie, where caution is needed, where they might fit clinically, and where research should focus in order to accelerate clinical implementation. An emphasis is placed on ascites and pleural effusions, being pathological fluids directly associated with cancer. We conclude that non-blood fluids are viable sources of cfDNA in situations where solid tissue biopsies are inaccessible, or only accessible from dated archived specimens. In addition, we show that due to the abundance of cfDNA in non-blood fluids, they can outperform blood in many circumstances. We demonstrate multiple instances in which DNA from various sources can provide additional information, and thus we advocate for analysing non-blood sources as a complement to blood and/or tissue. Further research into these fluids will highlight opportunities to improve patient outcomes across cancer types.