Biomarkers in Non-Small Cell Lung Cancers: Indian Consensus Guidelines for Molecular Testing

Microfluidics-based EGFR mutation detection and its implication in the resource-limited clinical setting

Management of lung cancer today obligates a mutational analysis of the epidermal growth factor receptor (EGFR) gene particularly when Tyrosine Kinase Inhibitor (TKI) therapy is being considered as part of prognostic stratification. This study evaluates the performance of automated microfluidics-based EGFR mutation detection and its significance in clinical diagnostic settings. Formalin-fixed, paraffin-embedded (FFPE) samples from NSCLC patients (n = 174) were included in a two-phase study. Phase I: Validation of the platform by comparing the results with conventional real-time PCR and next-generation sequencing (NGS) platform. Phase II: EGFR mutation detection on microfluidics-based platform as part of routine diagnostics workup. The microfluidics-based platform demonstrates 96.5% and 89.2% concordance with conventional real-time PCR and NGS, respectively. The system efficiently detects mutations across the EGFR gene with 88.23% sensitivity and 100% specificity. Out of 144 samples analysed in phase II, the platform generated valid results in 94% with mutation detected in 41% of samples. This microfluidics-based platform can detect as low as 5% mutant allele fractions from the FFPE samples. Therefore the microfluidics-based platform is a rapid, complete walkaway, with minimum tissue requirement (two sections of 5 μ thickness) and technical skill requirement. The method can detect clinically actionable EGFR mutations efficiently and can be considered a reliable diagnostic platform in resource-limited settings. From receiving samples to reporting the results this platform provides accurate data without much manual intervention. The study helped to devise an algorithm that emphasizes effective screening of the NSCLC cases for EGFR mutations with varying tumour content. Thus it helps in triaging the cases judiciously before proceeding with multigene testing.

All EGFR mutations are (not) created equal: focus on uncommon EGFR mutations

PURPOSE

Most common EGFR mutations in NSCLC include del19 and exon 21 L858R. Approximately 10% of patients have uncommon EGFR mutations (indels, missense mutations involving G719, L861 and S768 codons, and exon 20 insertions) that do not respond to TKIs.

METHODS

Of 490 EGFR mutated NSCLC samples, 60 cases harboring uncommon/compound EGFR mutations were reviewed retrospectively, and 44 were included for survival analysis.

RESULTS

Sixty (12.2%) patients with a median age of 63 years (25-84 years) had uncommon/compound EGFR mutations. Majority had no history of smoking (52; 86.7%). Most common major uncommon mutations (G719X in exon 18, L861Q in exon 21 and S768I in exon 20) were identified in 19 (31.7%) patients. 17 (28.3%) cases demonstrated exon 20 insertions. De novo T790M was observed in 7 (11.7%) cases and 9 cases exhibited compound/dual mutations. Among the 12 patients who received first-line EGFR TKI, 7 received afatinib. Median progression-free survival of patients following first-line afatinib was 8.13 months, irrespective of mutation type exhibited. Overall response rate to first-line afatinib therapy was 57.1%.

CONCLUSION

The current study highlighted that rare/dual EGFR mutations are heterogeneous with distinct clinical features in a large Indian cohort of EGFR mutated patients with NSCLC.

Navigating patient journey in early diagnosis of lung cancer in India

Lung cancer (LC) is one of the leading causes of cancer deaths worldwide. In India, the incidence of LC is increasing rapidly, and a majority of the patients are diagnosed at advanced stages of the disease when treatment is less likely to be effective. Recent therapeutic developments have significantly improved survival outcomes in patients with LC. Prompt specialist referral remains critical for early diagnosis for improved patient survival. In the Indian scenario, distinguishing LC from benign and endemic medical conditions such as tuberculosis can pose a challenge. Hence, awareness regarding the red flags-signs and symptoms that warrant further investigations and referral-is vital. This review is an effort toward encouraging general physicians to maintain a high index of clinical suspicion for those at risk of developing LC and assisting them in refering patients with concerning symptoms to specialists or multidisciplinary teams as early as possible.

OUP accepted manuscript

Purpose

Lung cancer relapse may be associated with the presence of a small population of cancer stem cells (CSCs) with unlimited proliferative potential. Our study assessed the relationship between CSCs and the relapse rate in patients harboring adenocarcinoma (ADL) and squamous cell carcinoma of the lung (SCCL).

Experimental design

This is an observational prospective cohort study (NCT04634630) assessing the influence of CSC frequency on relapse rate after major lung resection in 35 patients harboring early (I-II) (n = 21) and locally advanced (IIIA) (n = 14) ADL and SCCL. There was a 2-year enrollment period followed by a 1-year follow-up period. Surgical tumor specimens were processed, and CSCs were quantified by cytofluorimetric analysis.

Results

Cancer stem cells were expressed in all patients with a median of 3.1% of the primary cell culture. Primary analysis showed no influence of CSC frequency on the risk of relapse (hazard ratio [HR] = 1.05, 95% confidence interval [CI] = 0.85-1.30). At secondary analysis, patients with locally advanced disease with higher CSC frequency had an increased risk of relapse (HR = 1.26, 95% CI = 1.14-1.39), whereas this was not observed in early-stage patients (HR = 0.90, 95% CI = 0.65-1.25).

Conclusion

No association was found between CSC and relapse rates after major lung resection in patients harboring ACL and SCCL. However, in locally advanced-stage patients, a positive correlation was observed between CSC frequency and risk of relapse. These results indicate a need for further molecular investigations into the prognostic role of CSCs at different lung cancer stages.

Clinical Trial Registration

NCT04634630.

EGFR detection by liquid biopsy: ripe for clinical usage

Introduction: With the International Association for the Study of Lung Cancer (IASLC) recommendations promoting liquid biopsy as a primary detection tool, a new era of research has begun. The authors aimed to study the concordance of plasma genotyping platforms against the tissue gold standard. Methods: 184 patients with non-small cell lung cancer underwent EGFR genotyping using Cobas, droplet digital polymerase chain reaction (ddPCR) and Therascreen assays from 2019-2020. Results: Of 184 cases, 70 were positive by Cobas, 51 by ddPCR and 69 by Therascreen. The sensitivity of Cobas was 97.1% and the sensitivity of ddPCR was 71%. Receiver operating characteristic analysis showed an area under the curve of 0.977 for Cobas and 0.846 for ddPCR. Conclusion: In line with the FLAURA trial of osimertinib making its way to first-line and given the IASLC recommendations, it is important to understand the attributes of these tests to initiate appropriate treatment.

Molecular testing in stage I-III non-small cell lung cancer: Approaches and challenges

Precision medicine in non-small cell lung cancer (NSCLC) is a rapidly evolving area, with the development of targeted therapies for advanced disease and concomitant molecular testing to inform clinical decision-making. In contrast, routine molecular testing in stage I-III disease has not been required, where standard of care comprises surgery with or without adjuvant or neoadjuvant chemotherapy, or concurrent chemoradiotherapy for unresectable stage III disease, without the integration of targeted therapy. However, the phase 3 ADAURA trial has recently shown that the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), osimertinib, reduces the risk of disease recurrence by 80% versus placebo in the adjuvant setting for patients with stage IB-IIIA EGFR mutation-positive NSCLC following complete tumor resection with or without adjuvant chemotherapy, according to physician and patient choice. Treatment with adjuvant osimertinib requires selection of patients based on the presence of an EGFR-TKI sensitizing mutation. Other targeted agents are currently being evaluated in the adjuvant and neoadjuvant settings. Approval of at least some of these other agents is highly likely in the coming years, bringing with it in parallel, a requirement for comprehensive molecular testing for stage I-III disease. In this review, we consider the implications of integrating molecular testing into practice when managing patients with stage I-III non-squamous NSCLC. We discuss best practices, approaches and challenges from pathology, surgical and oncology perspectives.

Testing for EGFR Mutations and ALK Rearrangements in Advanced Non-Small-Cell Lung Cancer: Considerations for Countries in Emerging Markets

The treatment of patients with advanced non-small-cell lung cancer (NSCLC) in recent years has been increasingly guided by biomarker testing. Testing has centered on driver genetic alterations involving the epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) rearrangements. The presence of these mutations is predictive of response to targeted therapies such as EGFR tyrosine kinase inhibitors (TKIs) and ALK TKIs. However, there are substantial challenges for the implementation of biomarker testing, particularly in emerging countries. Understanding the barriers to testing in NSCLC will be key to improving molecular testing rates worldwide and patient outcomes as a result. In this article, we review EGFR mutations and ALK rearrangements as predictive biomarkers for NSCLC, discuss a selection of appropriate tests and review the literature with respect to the global uptake of EGFR and ALK testing. To help improve testing rates and unify procedures, we review our experiences with biomarker testing in China, South Korea, Russia, Turkey, Brazil, Argentina and Mexico, and propose a set of recommendations that pathologists from emerging countries can apply to assist with the diagnosis of NSCLC.

An opportunity to emphasize the relevance of laboratory medicine

Objectives

Clinical practice guidelines (CPGs) are recommendations based on a systematic review of scientific evidence that are intended to help healthcare professionals and patients make the best clinical decisions. CPGs must be evidence-based and are designed by multidisciplinary teams. The purpose of this study is to assess the topics related to the clinical laboratory addressed in CPGs and evaluate the involvement of laboratory professionals in the CPG development process.

Methods

A total of 16 CPGs recommended by the Spanish Society of Laboratory Medicine and/or retrieved from PubMed-Medline were included. A review of the information provided in CPGs about 80 topics related to the clinical laboratory was performed. The authorship of laboratory professionals was assessed.

Results

On average, the 16 CPGs addressed 49% (standard deviation [SD]: 11%) of the topics evaluated in relation to the clinical laboratory. By order of frequency, CPGs contained information about 69% of postanalytical variables (SD: 20%); 52% of preanalytical variables (SD: 11%); and 43% of the analytical variables studied (SD: 18%). Finally, half the CPGs included a laboratory professional among its authors.

Conclusions

CPGs frequently failed to provide relevant laboratory-related information. Laboratory professionals were co-authors in only half the CPGs. There is scope for improvement, and laboratory professionals should be included in multidisciplinary teams involved in the development of CPGs.

Evaluation of the reporting quality of clinical practice guidelines on lung cancer using the RIGHT checklist

BACKGROUND

In recent years, the number of clinical practice guidelines (CPGs) for lung cancer has increased, but the quality of these guidelines has not been systematically assessed so far. Our aim was to assess the reporting quality of CPGs on lung cancer published since 2018 using the International Reporting Items for Practice Guidelines in Health Care (RIGHT) instrument.

METHODS

We systematically searched the major electronic literature databases, guideline databases and medical society websites from January 2018 to November 2020 to identify all CPGs for small cell and non-small cell lung cancer (NSCLC). The search and extraction were completed using standardized forms. The quality of included guidelines was evaluated using the RIGHT statement. We present the results descriptively, including a stratification by selected determinants.

RESULTS

A total of 49 CPGs were included. The mean proportion across the guidelines of the 22 items of the RIGHT checklist that were appropriately reported was 57.9%. The items most common to be poorly reported were quality assurance (item 17) and description of the role of funders (item 18b), both of which were reported in only one guideline. The proportions of items within each of the seven domains of the RIGHT checklist that were correctly reported were Basic information 75.9%; background 83.2%; evidence 44.5%; recommendations 55.4%; review and quality assurance 12.2%; funding and declaration and management of interests 42.9%; and other information 38.1%. The reporting quality of guidelines did not differ between publication years. CPGs published in journals with impact factor >30 tended to be best reported.

CONCLUSIONS

Our results revealed that reporting in CPGs for lung cancer is suboptimal. Particularly the declaration of funding and quality assurance are poorly reported in recent CPGs on lung cancer.

EGFR and PDL1: A Match (Not) Made in Heaven-A Real-World Retrospective Analysis of PDL1 Expression in EGFR-Mutated NSCLC

INTRODUCTION

EGFR (epidermal growth factor receptor) mutant NSCLC (non-small cell lung carcinoma) comprises 35-40% of cases in the Asian NSCLC cohort, compared to 15-20% in the rest of the world. Improved response rates have been observed in terms of PFS (progression-free survival) and ORR (overall response rate) when treated with EGFR TKIs (tyrosine kinase inhibitors). However, resistance eventually ensues regardless of the generation of TKI used. Preclinical studies have reported that PDL1 (programmed death ligand 1) is a downstream target of EGFR and is interposed by IL-6/JAK/STAT3 (interleukin-6/Janus kinase/signal transducer and activator of transcription 3), NF-κB (nuclear factor kappa beta), and p-ERK1/2/p-c-Jun pathways. Hence, it may potentially be repressed by EGFR TKIs. In this retrospective exploratory analysis, we studied whether PDL1 expression affects efficacy of EGFR TKIs and clinical outcome in patients with untreated metastatic EGFR-mutated lung adenocarcinoma.

METHODS

This single-center retrospective, exploratory analysis was performed between January 2015 and December 2019. Among 1350 cases of NSCLC, 470 were EGFR mutant, of which PDL1 expression testing was done in 193 patients who were included in this study.

RESULTS

Median age was 60 years (range 24-87 years). A total of 116 patients (60.1%) had inframe deletion in exon 19, 52 (26.9%) had L858R, and 25 (13%) had uncommon mutations. The number of patients with PDL1 tumour proportion score (TPS) < 1% was 109 (56.5%); 1-49%, 57 (29.5%); and ≥ 50%, 27 (14%). Comparing clinical characteristics among various PDL1 groups, there were no statistically significant correlations obtained. However, patients with PDL1 > 50% were smokers, and showed a trend for higher disease burden at diagnosis. Median PFS of PDL1 < 1% was 10.14 months, compared to 9.4 months in the PDL1 > 1% group; however, the values did not reach statistical significance.

CONCLUSION

The current study was an exploratory retrospective study; however, the results add to the growing body of evidence that PDL1 expression in EGFR-mutated NSCLC does not have any prognostic significance. Also the efficacy of EGFR TKIs is not influenced by variations in PDL1 TPS.

Next generation sequencing for detection of EGFR alterations in NSCLC: is more better?

AIMS

The emergence of sophisticated next generation sequencing (NGS) based technologies in routine molecular diagnostics has paved the way for robust and accurate detection of variants which may otherwise be missed on single gene testing. This study aims at highlighting the same premise in EGFR mutated non-small cell lung carcinoma (NSCLC).

METHODS

1350 cases of NSCLC were screened, of which 490 EGFR mutated cases were taken. The clinical records and molecular features were evaluated retrospectively to determine those cases which were missed on single gene testing.

RESULTS

Among these 490 cases, there were 11 (2.2%) cases which tested negative on single gene testing using polymerase chain reaction (therascreen). These were then subjected to NGS based testing and were positive for 13 different EGFR mutations. Five out of the 11 cases received EGFR tyrosine kinase inhibitor (TKI) based on the NGS test outcome. Four cases with exon 20 insertion mutations were not offered TKI as these mutations are known to be intrinsically resistant to TKI therapy. The five patients who have been treated with TKI have shown fair response and have not progressed to date.

CONCLUSIONS

We demonstrated a potentially preferable way to profile treatment-naïve patients with NSCLC by NGS and from our early experience in EGFR mutant cases, the advantages of NGS over single gene testing is clearly evident.

A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation

Today, genomic data holds great potential to improve healthcare strategies across various dimensions – be it disease prevention, enhanced diagnosis, or optimized treatment. The biggest hurdle faced by the medical and research community in India is the lack of genotype-phenotype correlations for Indians at a population-wide and an individual level. This leads to inefficient translation of genomic information during clinical decision making. Population-wide sequencing projects for Indian genomes help overcome hurdles and enable us to unearth and validate the genetic markers for different health conditions. Machine learning algorithms are essential to analyze huge amounts of genotype data in synergy with gene expression, demographic, clinical, and pathological data. Predictive models developed through these algorithms help in classifying the individuals into different risk groups, so that preventive measures and personalized therapies can be designed. They also help in identifying the impact of each genetic marker with the associated condition, from a clinical perspective. In India, genome sequencing technologies have now become more accessible to the general population. However, information on variants associated with several major diseases is not available in publicly-accessible databases. Creating a centralized database of variants facilitates early detection and mitigation of health risks in individuals. In this article, we discuss the challenges faced by genetic researchers and genomic testing facilities in India, in terms of dearth of public databases, people with knowledge on machine learning algorithms, computational resources and awareness in the medical community in interpreting genetic variants. Potential solutions to enhance genomic research in India, are also discussed.

Non-amplification genetic alterations of HER2 gene in non-small cell lung carcinoma

AIMS

The present study investigated the incidence and spectrum of human epidermal growth factor receptor 2 (HER2) mutations, associated clinicopathological characteristics and the co-occurrence of HER2 gene amplification in the HER2 gene mutated cases in non-small cell lung cancer (NSCLC).

METHODS

All patients with advanced lung adenocarcinoma (LUAD) who underwent broad genomic profiling by next generation sequencing (NGS) from 2015 to 2019 were included in the study. HER2 gene amplification was checked in all the HER2 gene mutated cases. Tumour tissues of all the mutated cases were examined by fluorescent in situ hybridisation (FISH).

RESULTS

Fifty-four (37.2%) out of the 145 cases harboured tier 1 driver mutations comprising EGFR in 22.1%, ALK rearrangements in 7.6% cases, ROS1 rearrangements and BRAF ^V600E in 3.5% cases each, and NTRK fusion in 0.7% cases. Nine (6.2%) cases exhibited a significant genetic alteration in HER2 gene (tiers 2 and 3) on NGS. The most common alteration was exon 20 insertion of amino acid sequence AYVM in five cases (p.E770_A771insAYVM) followed by insertion of YVMA (p.A771_Y772insYVMA) in one case, insGSP (p.V777_G778insGSP) in one case and two missense mutations: p.G776C and p.QA795C (novel variant). The median copy number of the HER2 gene was 3.21 while on FISH, the median HER2/CEP17 ratio was 2.0.

CONCLUSIONS

There is a relatively higher occurrence of HER2 exon 20 mutations as primary oncogenic driver in NSCLC especially LUAD. Our cohort has demonstrated (p.E770_A771insAYVM) as the strikingly dominant insertion mutation against the most often globally reported (p.A771_Y772insYVMA).