Associations between multimodal immune biomarkers and clinical outcomes in a real-world non-small cell lung cancer cohort

Authors Michelle M Stein, Mario Rosasco, Denise Lau, Yinjie Gao, Rotem Ben-Shachar, Justin Guinney, Halla Nimeiri and Nisha Mohindra

Background Established biomarkers of immune checkpoint inhibitor (ICI) response in metastatic non-small cell lung cancer (mNSCLC), such as PD-L1 and tumor mutational burden (TMB), do not identify all patients with durable response. While biomarkers spanning multiple data modalities have been proposed to address this unmet need, additional evidence is required for use in the clinic. Here, we performed a comparative study assessing the association between previously described biomarkers of ICI response and outcomes in a real-world mNSCLC cohort.

Methods Using the Tempus database, we analyzed de-identified records of non-squamous EGFR-negative and ALK fusion-negative mNSCLC patients treated with first-line ICI regimens and profiled with targeted-panel DNA-seq and whole-exome-capture RNA-seq. ICI-related biomarkers were calculated following published methods using the Tempus IO platform (table 1). Immune biomarkers included features describing tumor biology (including PD-L1 IHC, STK11 and KEAP1 mutations, APOBEC signature1), HLA (HLA-LOH, HLA A*03 genotype), neoantigens (TMB, neoantigen burden), and RNA-based signatures of immune activity such as IFNγ tumor inflammation signature,2 IMPRES,3 Cytotoxic score,4 NRS,5tertiary lymphoid structure (TLS),6 7 and others. Real-world time to progression (rwTTP) was defined as the interval from ICI start to the first progression event, censored on last known physician encounter. Cox proportional hazards (Cox PH) models were fitted to evaluate the relationship between each biomarker and rwTTP.

Results In this mNSCLC cohort (N=199), multiple RNA-based signatures related to immune infiltration, TLS, cytotoxic and cytolytic activity, and IFNγ tumor inflammation signature (TIS) were significantly associated with longer rwTTP (P < 0.001). HLA- and tumor-related biomarkers had no significant associations with longer rwTTP. As expected, TMB and PD-L1 IHC were significantly associated with longer rwTTP (P < 0.05). In multivariable Cox PH analyses controlling for PD-L1 IHC and TMB, several immune signatures remained significantly associated with rwTTP (table 1). Notably, many RNA-based signatures were highly correlated despite non-overlapping genes and functions, underscoring a broad profile of immune infiltration and activation is likely associated with ICI response.

Conclusions Here we demonstrate that RNA-based immune signatures are significantly associated with clinical benefit and may supplement well-established ICI biomarkers in therapy selection. These immune RNA-based signatures need to be prospectively validated in future studies.