Single Circulating-Tumor-Cell-Targeted Sequencing to Identify Somatic Variants in Liquid Biopsies in Non-Small-Cell Lung Cancer Patients

Applications of single-cell analysis in immunotherapy for lung cancer: Current progress, new challenges and expectations

BACKGROUND

Lung cancer is a prevalent form of cancer worldwide, presenting a substantial risk to human well-being. Lung cancer is classified into two main types: non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). The advancement of tumor immunotherapy, specifically immune checkpoint inhibitors and adaptive T-cell therapy, has encountered substantial obstacles due to the rapid progression of SCLC and the metastasis, recurrence, and drug resistance of NSCLC. These challenges are believed to stem from the tumor heterogeneity of lung cancer within the tumor microenvironment.

AIM OF REVIEW

This review aims to comprehensively explore recent strides in single-cell analysis, a robust sequencing technology, concerning its application in the realm of tumor immunotherapy for lung cancer. It has been effectively integrated with transcriptomics, epigenomics, genomics, and proteomics for various applications. Specifically, these techniques have proven valuable in mapping the transcriptional activity of tumor-infiltrating lymphocytes in patients with NSCLC, identifying circulating tumor cells, and elucidating the heterogeneity of the tumor microenvironment.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review emphasizes the paramount significance of single-cell analysis in mapping the immune cells within NSCLC patients, unveiling circulating tumor cells, and elucidating the tumor microenvironment heterogeneity. Notably, these advancements highlight the potential of single-cell analysis to revolutionize lung cancer immunotherapy by characterizing immune cell fates, improving therapeutic strategies, and identifying promising targets or prognostic biomarkers. It is potential to unravel the complexities within the tumor microenvironment and enhance treatment strategies marks a significant step towards more effective therapies and improved patient outcomes.

Detection of Circulating Tumor Cells and EGFR Mutation in Pulmonary Vein and Arterial Blood of Lung Cancer Patients Using a Newly Developed Immunocytology-Based Platform

BACKGROUND

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors are powerful molecular targeted therapeutic agents for lung cancer. We recently developed an original immunocytology and glass slide-based circulating tumor cell (CTC) detection platform for both CTC enumeration and EGFR mutation analysis with DNA extracted from CTCs.

METHODS

Using this platform, we conducted a pilot clinical study for CTC enumeration in peripheral blood (PB), pulmonary arterial blood (PA), and pulmonary venous blood (PV) from 33 patients with lung cancer (Stage I-III) who underwent surgery, followed by digital PCR-based EGFR mutation analysis of CTCs in PV from 12 patients.

RESULTS

The results showed that CTC levels were significantly higher in PV and PA than in PB (p < 0.05, p < 0.01. respectively), with a notably greater number of small and large CTC clusters (p < 0.01). Genetic analysis of EGFR mutations of CTCs from PV (n = 12) revealed six mutations, including three Exon19del and three L856R, in CTCs and eight EGFR mutations, including five Exon19del and three L856R, in lung tumor tissue. CTC mutation status matched that of tissue samples in nine patients, was unmatched in two patients, and controversial in one patient, indicating a sensitivity of 0.75 (6/8) and specificity of 1.0 (4/4) with some false-negative results for the mutation analysis of CTCs.

CONCLUSIONS

This immunocytology-based CTC detection platform is a convenient method for detecting both CTC number and EGFR mutation status under microscopy, suggesting its potential as a liquid biopsy tool in the hospital for patients with lung cancer in some clinical settings.

Circulating Tumor Cells: How Far Have We Come with Mining These Seeds of Metastasis?

Circulating tumor cells (CTCs) are cancer cells that slough off from the tumor and circulate in the peripheral blood and lymphatic system as micro metastases that eventually results in macro metastases. Through a simple blood draw, sensitive CTC detection from clinical samples has proven to be a useful tool for determining the prognosis of cancer. Recent technological developments now make it possible to detect CTCs reliably and repeatedly from a simple and straightforward blood test. Multicenter trials to assess the clinical value of CTCs have demonstrated the prognostic value of these cancer cells. Studies on CTCs have filled huge knowledge gap in understanding the process of metastasis since their identification in the late 19th century. However, these rare cancer cells have not been regularly used to tailor precision medicine and or identify novel druggable targets. In this review, we have attempted to summarize the milestones of CTC-based research from the time of identification to molecular characterization. Additionally, the need for a paradigm shift in dissecting these seeds of metastasis and the possible future avenues to improve CTC-based discoveries are also discussed.

Integrated "lab-on-a-chip" microfluidic systems for isolation, enrichment, and analysis of cancer biomarkers

The liquid biopsy has garnered considerable attention as a complementary clinical tool for the early detection, molecular characterization and monitoring of cancer over the past decade. In contrast to traditional solid biopsy techniques, liquid biopsy offers a less invasive and safer alternative for routine cancer screening. Recent advances in microfluidic technologies have enabled handling of liquid biopsy-derived biomarkers with high sensitivity, throughput, and convenience. The integration of these multi-functional microfluidic technologies into a 'lab-on-a-chip' offers a powerful solution for processing and analyzing samples on a single platform, thereby reducing the complexity, bio-analyte loss and cross-contamination associated with multiple handling and transfer steps in more conventional benchtop workflows. This review critically addresses recent developments in integrated microfluidic technologies for cancer detection, highlighting isolation, enrichment, and analysis strategies for three important sub-types of cancer biomarkers: circulating tumor cells, circulating tumor DNA and exosomes. We first discuss the unique characteristics and advantages of the various lab-on-a-chip technologies developed to operate on each biomarker subtype. This is then followed by a discussion on the challenges and opportunities in the field of integrated systems for cancer detection. Ultimately, integrated microfluidic platforms form the core of a new class of point-of-care diagnostic tools by virtue of their ease-of-operation, portability and high sensitivity. Widespread availability of such tools could potentially result in more frequent and convenient screening for early signs of cancer at clinical labs or primary care offices.

Preclinical models to study patient-derived circulating tumor cells and metastasis

Circulating tumor cells (CTCs) that are detached from the tumor can be precursors of metastasis. The majority of studies focus on enumeration of CTCs from patient blood to predict recurrence and therapy outcomes. Very few studies have managed to expand CTCs to investigate their functional dynamics with respect to genetic changes, tumorigenic potential, and response to drug treatment. A growing amount of evidence based on successful CTC expansion has revealed novel therapeutic targets that are associated with the process of metastasis. In this review, we summarize the successes, challenges, and limitations that collectively contribute to the better understanding of metastasis using patient-derived CTCs as blood-borne seeds of metastasis. The roadblocks and future avenues to move CTC-based scientific discoveries forward are also discussed.

Accurate isolation and detection of circulating tumor cells using enrichment-free multiparametric high resolution imaging

Introduction

The reliable and accurate detection of rare circulating tumor cells (CTCs) from cancer patient blood samples promises advantages in both research and clinical applications. Numerous CTC detection methods have been explored that rely on either the physical properties of CTCs such as density, size, charge, and/or their antigen expression profiles. Multiple factors can influence CTC recovery including blood processing method and time to processing. This study aimed to examine the accuracy and sensitivity of an enrichment-free method of isolating leukocytes (AccuCyte® system) followed by immunofluorescence staining and high-resolution imaging (CyteFinder® instrument) to detect CTCs.

Method

Healthy human blood samples, spiked with cancer cells from cancer cell lines, as well as blood samples obtained from 4 subjects diagnosed with cancer (2 pancreatic, 1 thyroid, and 1 small cell lung) were processed using the AccuCyte-CyteFinder system to assess recovery rate, accuracy, and reliability over a range of processing times.

Results

The AccuCyte-CyteFinder system was highly accurate (95.0%) at identifying cancer cells in spiked-in samples (in 7.5 mL of blood), even at low spiked-in numbers of 5 cells with high sensitivity (90%). The AccuCyte-CyteFinder recovery rate (90.9%) was significantly higher compared to recovery rates obtained by density gradient centrifugation (20.0%) and red blood cell lysis (52.0%). Reliable and comparable recovery was observed in spiked-in samples and in clinical blood samples processed up to 72 hours post-collection. Reviewer analysis of images from spiked-in and clinical samples resulted in high concordance (R-squared value of 0.998 and 0.984 respectively).

Discussion

The AccuCyte-CyteFinder system is as an accurate, sensitive, and clinically practical method to detect and enumerate cancer cells. This system addresses some of the practical logistical challenges in incorporating CTCs as part of routine clinical care. This could facilitate the clinical use of CTCs in guiding precision, personalized medicine.

Molecules at Play in Cancer

Despite its wide range of incidence, cancer can spontaneously occur in any part of the body and invade regions other than the originally affected tissue [...]

Targeting immune cell types of tumor microenvironment to overcome resistance to PD-1/PD-L1 blockade in lung cancer

Lung cancer is the common malignant tumor with the highest mortality rate. Lung cancer patients have achieved benefits from immunotherapy, including immune checkpoint inhibitors (ICIs) therapy. Unfortunately, cancer patients acquire adaptive immune resistance, leading to poor prognosis. Tumor microenvironment (TME) has been demonstrated to play a critical role in participating in acquired adaptive immune resistance. TME is associated with molecular heterogeneity of immunotherapy efficacy in lung cancer. In this article, we discuss how immune cell types of TME are correlated with immunotherapy in lung cancer. Moreover, we describe the efficacy of immunotherapy in driven gene mutations in lung cancer, including KRAS, TP53, EGFR, ALK, ROS1, KEAP1, ZFHX3, PTCH1, PAK7, UBE3A, TNF-α, NOTCH, LRP1B, FBXW7, and STK11. We also emphasize that modulation of immune cell types of TME could be a promising strategy for improving adaptive immune resistance in lung cancer.

Somatic mutation variant analysis in rural, resectable non-small cell lung carcinoma patients

Rural non-small cell lung cancer (NSCLC) patients do worse, largely related to lack of access to care. In this study, the mutational characteristics and potential for targeted therapy in rural, resectable NSCLC patients using whole exome sequencing (WES) were analyzed. WES was performed on tumor-adjacent normal pairs from rural patients undergoing resection for NSCLC. Sequencing alignment, variant-calling, annotation, and tumor mutational burden (TMB) calculations were performed using standard methods. cBioportal and OncoKB were used for comparisons of mutational frequencies and actionable targets. Thirty-four NSCLC patients underwent WES after surgical resection. The gene most frequently containing somatic variants was TP53. The median number of somatic variants was 188 (Range 11-1056), and median TMB was 3.30 (0.33-18.56) nonsynonymous mutations per Mb. Tumor stage and survival were not associated with number of variants, TMB or TP53 mutational status. Significant concordance among the most common mutations when cross-referenced to cBioportal (R = 0.78, p < 0.0001) was observed. 24% of patients had variants in actionable genes based on OncoKB annotation. In summary, we demonstrate baseline mutational frequency and establish foundations for targeted adjuvant trials in rural NSCLC patients with specific differences. Future studies must ensure to include rural patients to improve NSCLC patient outcomes.