Burden of tumor mutations, neoepitopes, and other variants are dubious predictors of cancer immunotherapy response and overall survival

Abstract

Background: Tumor mutational burden (TMB, the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as a result. However, TMB harbors intrinsic variability across cancer types, and its assessment and interpretation are poorly standardized. Methods: Using a standardized approach, we quantify the robustness of TMB as a metric and its potential as a predictor of immunotherapy response and survival among a diverse cohort of cancer patients. We also explore the additive predictive potential of RNA-derived variants and neoepitope burden, incorporating several novel metrics of immunogenic potential. Results: We find that TMB is a partial predictor of immunotherapy response in melanoma and non-small cell lung cancer, but not renal cell carcinoma. We find that TMB is predictive of overall survival in melanoma patients receiving immunotherapy, but not in an immunotherapy-naive population. We also find that it is an unstable metric with potentially problematic repercussions for clinical cohort classification. We finally note minimal additional predictive benefit to assessing neoepitope burden or its bulk derivatives, including RNA-derived sources of neoepitopes. Conclusions: We find sufficient cause to suggest that the predictive clinical value of TMB should not be overstated or oversimplified. While it is readily quantified, TMB is at best a limited surrogate biomarker of immunotherapy response. The data do not support isolated use of TMB in renal cell carcinoma. KEYWORDStumor mutational burden, TMB, neoepitopes, neoepitope burden, neoantigens, splice junctions, retained introns, tumor variant burden, immunotherapy response BACKGROUNDThe advent of immunotherapy as a promising form of cancer treatment has been accompanied by a parallel effort to explore potential mechanisms and drivers of therapeutic response. For instance, tumor mutational burden (TMB, the overall quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy (1) and overall survival (2) . Similarly, the quantity of non-synonymous single nucleotide variants was shown to be associated with immunotherapy response in several independent clinical cohorts (3-6) . Other sources of sequence variation such as frameshifting insertions/deletions (7) and tumor-specific alternative splicing (e.g. intron retention (8) ) have also been found to correlate with immunotherapy response. These phenomena are widely accepted and appear to be particularly pronounced in patients harboring DNA repair deficiencies (9) . Indeed, the checkpoint inhibitor, pembrolizumab, was granted accelerated disease-agnostic approval by the FDA on this basis for any cancer patient harboring deficiencies in their capacity to perform DNA mismatch repair (10) . Moreover, an expanding cohort of clinical immunotherapy trials (e.g. NCT03668119, NCT03178552, NCT03519412) are actively utilizing TMB status as a k...

Putatively cancer-specific alternative splicing is shared across patients and present in developmental and other non-cancer cells

“…Previous studies have established the importance of alternative and aberrant splicing in cancer prognosis (Bjørklund et al, 2017;Li et al, 2017;Marcelino Meliso et al, 2017;Robertson et al, 2018;Zhu et al, 2018;Zong et al, 2018) and have begun to explore its potential relevance in cancer immunotherapy (Kahles et al, 2018;Wood et al, 2019). In this study, we explore "novel" exon-exon junction use among cancers with respect to a broad collection of normal tissues and cells.…”

Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification

“…The heterogeneity of C-terminal cleavage profiles seen in our study specific pepsickle application raises the question of whether cleavage prediction is universally helpful in target identification, or if specific study or design contexts are required to see benefit from cleavage predictions. In addition, whether or not there is an impact of using proteasomal prediction ad-hoc (via integration with existing neoepitope prediction pipelines 82,83 ) vs. post-hoc remains to be seen. Application of pepsickle to more patient derived data in the future will help us better understand the broader potential of applying cleavage prediction in this space, with the potential for broad implications in the research and clinical communities.…”

Low-dose ipilimumab plus nivolumab combined with IL-2 and hyperthermia in cancer patients with advanced disease: exploratory findings of a case series of 131 stage IV cancers – a retrospective study of a single institution

“…Low tumor mutational burden (TMB low ) and low microsatellite instability (MSI low ) was determined only in a small subgroup of patients. However, TMB low and MSI low can be expected in the majority based on published evidence [ 37 ]. In contrast, published meta-analyses included patients with high PD-L1 expression, TMB high , and MSI high [ 30 , 38 ].…”