Immunotherapy response score (IRS) integrates tumor mutation burden (TMB) and quantitative expression biomarkers to predict anti-PD-1/PD-L1 [PD-(L)1] monotherapy benefit. Here, we evaluated IRS in additional cohorts. Patients from an observational trial (NCT03061305) treated with anti-PD-(L)1 monotherapy were included and assigned to IRS-High (-H) versus -Low (-L) groups. Associations with real-world progression-free survival (rwPFS) and overall survival (OS) were determined by Cox proportional hazards (CPH) modeling. Those with available PD-L1 IHC treated with anti-PD-(L)1 with or without chemotherapy were separately assessed. Patients treated with PD-(L)1 and/or chemotherapy (five relevant tumor types) were assigned to three IRS groups [IRS-L divided into IRS-Ultra-Low (-UL) and Intermediate-Low (-IL), and similarly assessed]. In the 352 patient anti-PD-(L)1 monotherapy validation cohort (31 tumor types), IRS-H versus IRS-L patients had significantly longer rwPFS and OS. IRS significantly improved CPH associations with rwPFS and OS beyond microsatellite instability (MSI)/TMB alone. In a 189 patient (10 tumor types) PD-L1 IHC comparison cohort, IRS, but not PD-L1 IHC nor TMB, was significantly associated with anti-PD-L1 rwPFS. In a 1,103-patient cohort (from five relevant tumor types), rwPFS did not significantly differ in IRS-UL patients treated with chemotherapy versus chemotherapy plus anti-PD-(L)1, nor in IRS-H patients treated with anti-PD-(L)1 versus anti-PD-(L)1 + chemotherapy. IRS associations were consistent across subgroups, including both Europeans and non-Europeans. These results confirm the utility of IRS utility for predicting pan-solid tumor PD-(L)1 monotherapy benefit beyond available biomarkers and demonstrate utility for informing on anti-PD-(L)1 and/or chemotherapy treatment.This study confirms the utility of the integrative IRS biomarker for predicting anti-PD-L1/PD-1 benefit. IRS significantly improved upon currently available biomarkers, including PD-L1 IHC, TMB, and MSI status. Additional utility for informing on chemotherapy, anti-PD-L1/PD-1, and anti-PD-L1/PD-1 plus chemotherapy treatments decisions is shown.
<p>Supplementary Table S2 shows the adjusted Cox proportional hazards models for real-world progression free survival and overall survival in the monotherapy validation cohort</p>
<p>Confirmation of the added utility of the IRS versus clinical PD-L1 IHC and TMB alone. <b>A,</b> Normalized PD-L1 (<i>CD274</i>) expression (and the other IRS expression components) by the qTP platform used to generate IRS were validated versus qRT-PCR in a validation cohort of 96 FFPE tumor tissue samples tested by clinical CGP and in parallel qTP. The Pearson correlation and linear range of each component is shown (<a href="#SMF1" target="_blank">Supplementary Fig. S1</a>). <b>B</b> and <b>C</b>, The Pearson correlation of normalized <i>PD-L1</i> expression by qTP [log<sub>2</sub> normalized reads per million (nRPM) units] versus clinical PD-L1 IHC score (in submitted pathology reports) was determined in two cohorts of clinical FFPE tumor tissues [regardless of TMB availability and anti-PD-(L)1 treatment]. <b>B,</b> PD-L1 expression by qTP (log<sub>2</sub> normalized units) versus PD-L1 IHC by TPS [using the 22C3 antibody clone (log<sub>2</sub> TPS) in 276 clinically tested FFPE NSCLC tumors with available TPS is plotted]. The linear fit, Pearson correlation (<i>r</i>), and <i>P</i> value are shown. <b>C,</b> PD-L1 expression by qTP versus PD-L1 IHC by CPS using the 22C3 antibody clone (log<sub>2</sub> CPS) in 221 clinically tested FFPE tumors (23 tumor types; most frequently EGC) with available TPS is plotted. The linear fit, Pearson correlation (<i>r</i>), and <i>P</i> value are shown. <b>D,</b> Using B and C, we identified a cohort of all 189 eligible NCT03061305 patients with IRS and PD-(L)1 IHC in accompanying pathology reports who were treated with anti-PD-(L)1 therapy (± chemotherapy). The association of biomarkers with anti-PD-(L)1 rwPFS was determined by Cox proportional hazards modeling [adjusting for age, sex assigned at birth, line of therapy, tumor type, therapy type (monotherapy vs. chemotherapy combination), and inclusion in IRS discovery status]. PD-L1 IHC score (continuous; log<sub>2</sub>) was included in the baseline model (Model 1), with the aHR, 95% CI, number (<i>n</i>) of patients and events, and <i>P</i> value shown for the biomarker term by forest plot. TMB status (-H vs. -L; pink) and IRS status (-H vs. -L; light blue) were separately added to this model (Models 2 and 3, respectively). The significance of each biomarker term is shown and the <i>P</i> value of the LRT comparing the full (Model 2 or 3) versus reduced (Model 1) model is shown. Model 4 includes PD-L1 IHC, TMB, and IRS. Significant biomarker terms are shown by filled in aHR estimates. <b>E,</b> Anti-PD-(L)1 rwPFS stratified by IRS group is shown by unadjusted Kaplan–Meier analysis, with the aHR from Model 4 in D shown. See <a href="#SMT7" target="_blank">Supplementary Table S7</a> for full subgroup analysis.</p>
Abstract Background Anti-PD-1 and PD-L1 (collectively PD-[L]1) therapies are approved for many advanced solid tumors. Biomarkers beyond PD-L1 immunohistochemistry, microsatellite instability, and tumor mutation burden (TMB) may improve benefit prediction. Methods Using treatment data and genomic and transcriptomic tumor tissue profiling from an observational trial (NCT03061305), we developed Immunotherapy Response Score (IRS), a pan-tumor predictive model of PD-(L)1 benefit. IRS real-world progression free survival (rwPFS) and overall survival (OS) prediction was validated in an independent cohort of trial patients. Results Here, by Cox modeling, we develop IRS—which combines TMB with CD274 , PDCD1 , ADAM12 and TOP2A quantitative expression—to predict pembrolizumab rwPFS (648 patients; 26 tumor types; IRS-High or -Low groups). In the 248 patient validation cohort (248 patients; 24 tumor types; non-pembrolizumab PD-[L]1 monotherapy treatment), median rwPFS and OS are significantly longer in IRS-High vs. IRS-Low patients (rwPFS adjusted hazard ratio [aHR] 0.52, p = 0.003; OS aHR 0.49, p = 0.005); TMB alone does not significantly predict PD-(L)1 rwPFS nor OS. In 146 patients treated with systemic therapy prior to pembrolizumab monotherapy, pembrolizumab rwPFS is only significantly longer than immediately preceding therapy rwPFS in IRS-High patients (interaction test p = 0.001). In propensity matched lung cancer patients treated with first-line pembrolizumab monotherapy or pembrolizumab+chemotherapy, monotherapy rwPFS is significantly shorter in IRS-Low patients, but is not significantly different in IRS-High patients. Across 24,463 molecularly-evaluable trial patients, 7.6% of patients outside of monotherapy PD-(L)1 approved tumor types are IRS-High/TMB-Low. Conclusions The validated, predictive, pan-tumor IRS model can expand PD-(L)1 monotherapy benefit outside currently approved indications.
<p>Supplementary Table S2 shows the adjusted Cox proportional hazards models for real-world progression free survival and overall survival in the monotherapy validation cohort</p>
