Blood-based Tumour Mutational Burden Assay Predicts Clinical Benefit in NSCLC Patients Treated with Atezolizumab

Results based on retrospective analysis of two large randomised trials

A group of investigators led by Drs David Gandara, Tony Mok and David Shames described in an article published online on 6 August 2018 in the Nature Medicine a novel, technically robust, blood-based assay to measure tumour mutational burden (TMB) in plasma (bTMB) that is distinct from tissue-based approaches. Using a retrospective analysis of two large randomised trials as test and validation studies, they showed that bTMB reproducibly identifies patients who derive clinically significant improvements in progression-free survival (PFS) from atezolizumab in second-line and higher advanced non-small cell lung cancer (NSCLC). The data show that high bTMB is a clinically actionable biomarker for atezolizumab in NSCLC. 

Immune checkpoint inhibitors that target the PD-L1–PD-1 pathway have demonstrated significant overall survival (OS) benefit in advanced NSCLC. In patients with previously treated, advanced NSCLC, an OS benefit is evident in unselected patients treated with atezolizumab and nivolumab. For example, the randomised phase III OAK trial demonstrated a median OS of 13.8 months in the atezolizumab arm versus 9.6 months in the docetaxel arm (hazard ratio (HR): 0.73; p= 0.0003). 

Although patients with PD-L1-positive tumours derive greater clinical benefit, PD-L1 expression alone does not fully explain the OS benefit in patients treated with these drugs. PD-L1 expression is rapidly becoming the first among many actionable biomarkers that are tested in the first-line setting. As a result, the availability of adequate tissue for subsequent molecular tests, including EGFR and ALK mutations and the TMB, is increasingly limited, the authors explained in study background. In addition, up to 30% of patients with NSCLC do not have adequate tissue available at diagnosis for standard biomarker testing. Thus, there is an urgent need to develop non-invasive diagnostic methods that can identify patients who are more likely to benefit from anti-PD-L1–PD-1 monotherapy in NSCLC. 

Multiple recent studies have shown that TMB may be a surrogate for overall neoantigen load. TMB, as measured by whole-exome sequencing, is associated with clinical benefit from multiple checkpoint inhibitors. An exploratory analysis from the CheckMate-026 trial showed an association between high tissue-based TMB (tTMB) count and greater clinical benefit with nivolumab in NSCLC in the first-line setting. Targeted next-generation sequencing (NGS) accurately measures tTMB when compared with whole-exome sequencing and also enriches for patients who are likely to receive clinical benefit from anti-PD-L1–PD-1 therapies in advanced NSCLC, metastatic melanoma and metastatic urothelial carcinoma. 

The ability to analyze tumour genomes through a simple blood draw has distinct advantages compared to tissue biopsy collection. As a result, interest in the field of blood-based detection of DNA has rapidly increased, and multiple technologies are available that reliably detect mutations in cell-free DNA (cfDNA. To date, most blood-based assays used for predictive biomarker detection are based on PCR; however, several recent publications have shown that NGS is a valid approach. 

Owing to the cost of sequencing, most of these panels have relatively limited genomic content and have not been analytically or clinically validated. Although calculation of TMB from blood has been suggested, robust, validated assays to measure TMB using cfDNA have yet to be developed. Therefore, it prompted the investigators in this study to development, testing and validation of a novel assay to measure bTMB. In particular, they tested the clinical utility of the assay using samples collected prospectively from two randomised trials, which included more than 1,000 plasma samples from second-line or higher patients with advanced NSCLC. 

Based on the samples from the POPLAR trial, the researchers identified a range of bTMB cut-points that correlate to clinically meaningful outcomes, which were confirmed in the OAK study. The study team demonstrated that TMB measured from the blood is a predictive biomarker for PFS in patients receiving atezolizumab monotherapy in NSCLC. This is the first demonstration that TMB can be accurately and reproducibly measured in plasma and that bTMB is associated with clinical benefit from immune checkpoint inhibitor therapy. 

Analyses performed in POPLAR samples and then confirmed in OAK samples demonstrate that bTMB ≥ 16 is a clinically meaningful and technically robust cut-point in NSCLC. The bTMB is not associated with high PD-L1 expression and is independently predictive of the PFS benefit. The use of plasma instead of tissue as a DNA source makes the bTMB assay a particularly attractive alternative for patients with metastatic NSCLC who are not amenable to biopsy or whose tumour tissue is otherwise unavailable. 

An important limitation of the bTMB assay is that it requires a minimum amount of ctDNA to be present in the blood for optimal assay performance, meaning that tumours must shed DNA into the blood and that this ctDNA must contain mutations with an allele frequency of ≥ 1% for a bTMB score to be valid. In addition, the likelihood of detecting ctDNA is also dependent on the overall tumour burden. Another limitation of the bTMB assay is that the TMB calculation is based only on single nucleotide variants (SNVs). Although this did not affect the concordance between bTMB and tTMB in this study, it is conceivable that, in certain rare cases, the assay may miss a patient whose tumour has a large number of indels but relatively few SNVs. Future versions of the assay will incorporate indels into the bTMB calling algorithm.

In summary, the data from this study show that measuring bTMB is feasible and that using a cut-point of ≥ 16 reproducibly identifies patients who obtained an increased PFS benefit from atezolizumab. Additional work is needed to better understand the dynamics and biology of bTMB and its relevance to other indications beyond NSCLC. The integration of this bTMB assay into the molecular diagnostic and therapeutic algorithms for patients who have progressed on first-line therapy for advanced NSCLC may be warranted. Prospective validation of the bTMB assay in first-line NSCLC is ongoing in the randomised phase III BFAST trial. 

Reference 

Gandara DR, Paul SM, Kowanetz M, et al. Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumabNature Medicine 2018 Aug 6. doi: 10.1038/s41591-018-0134-3. [Epub ahead of print]