The Challenges of Tumor Mutational Burden as an Immunotherapy Biomarker

Abstract

Tumor mutational burden (TMB) reflects cancer mutation quantity. Mutations are processed to neo-antigens and presented by major histocompatibility complex (MHC) proteins to T cells. To evade immune eradication, cancers exploit checkpoints that dampen T cell reactivity. Immune checkpoint inhibitors (ICIs) have transformed cancer treatment by enabling T cell reactivation; however, response biomarkers are required, as most patients do not benefit. Higher TMB results in more neo-antigens, increasing chances for T cell recognition, and clinically correlates with better ICI outcomes. Nevertheless, TMB is an imperfect response biomarker. A composite predictor that also includes critical variables, such as MHC and T cell receptor repertoire, is needed.

Keywords: biomarker; cancer therapy; genetics; immunotherapy; mutattional load.

Figure 1 –. Schematic representation of the main FDA-approved assays for TMB estimation as well as whole exome sequencing calculation.

Two of the NGS gene panels are FDA-approved tests (Foundation One (Frampton et al., 2013) and MSK-Impact) (Cheng et al., 2015). Symbols represent genetic alterations that are captured as mutations, while the denominator refers to the genome region that is considered for each test. The Foundation Medicine TMB assay examines a genomic region of approximately 1.1 Mb. For TMB estimation this test includes synonymous and non-synonymous mutations and short indels, while oncogenic drivers are excluded. In addition, germline alterations are excluded based on validated bioinformatics algorithms. The MSK IMPACT TMB assay examines approximately 1.5 Mb and, similar to WES, includes non-synonymous mutations in coding regions and oncogenic drivers. Germline alterations are excluded by subtracting matched normal samples. Examples of other commercial available assays include: Illumina TruSight 500 (~2Mb exome coverage [i.e region sequenced]), Thermo Fisher Scientific Oncomine (1.7 Mb exome coverage), Caris Molecular Intelligence (1.7 Mb exome coverage); NEO New Oncology NEOplus v2 RUO (1.1 Mb exome coverage); TruSight Tumor 170 (0.5 Mb exome coverage); Tempus Plataform (2.4 Mb exome cover) Abbreviations: Mb = megabase; WES: Whole exome sequencing

Figure 2 –. Environmental and host factors that influence TMB as a biomarker for anticancer immunotherapies.

Several different processes lead to gain of genomic alterations in tumors cells, whose number can be quantified by TMB. Environmental factors (e.g. UV) and DNA editing errors (MSI) cause patterns of mutations classified under different signatures.(Zehir et al., 2017) Each signature may influence not only the number of mutations, but also the quality and immunogenicity of the neo-antigens presented as a result of the mutanome burden. Host intrinsic characteristics also impact neo-antigen presentation and recognition. For instance, MHC diversity defines how well the neo-antigens can be presented, while TCR repertoire may define neo-antigen recognition.(Chowell et al., 2018; Weber et al., 2016) Epigenetic modulation (such as by histone modifications and DNA methylation) may also influence the host ability to generate an effective immune response.(Peng et al., 2015) Abbreviations: MHC, major histocompatibility complex; MSI, microsatellite instability; TCR, T-cell receptor; TMB: tumor mutational burden; UV, ultraviolet light