Background The rapid advancement of immunotherapies in oncology precipitates the need for clinicogenomic databases to verify published findings and to augment related discoveries. Growing bodies of real-world data (RWD) present such opportunities. We used one RWD source, Aster Insights’ ORIEN Avatar® database, to develop criteria for estimating real-world progression-free survival (rwPFS) endpoints and applied these criteria to a melanoma cohort, investigating association of rwPFS with a published, validated, prognostic, IFN-γ-related gene signature developed from clinical trial patients.1
Methods A cohort of 239 patients with melanoma and RNA-seq data were identified from the ORIEN Avatar® database (April 2023 release). This pan-cancer database is maintained by Aster Insights, which receives specimens and data submissions (comprised of whole-exome tumor/germline sequencing, RNA sequencing, and lifetime follow-up) from ORIEN members, a consortium research network of 18 U.S. cancer centers. Melanoma samples were collected from either the primary tumor site or a metastasis.
rwPFS endpoints were identified from normalized clinical data. The following were considered uncensored events: 1) annotated progression/recurrence in clinical records, 2) drug therapy annotated as stopped due to progression, 3) identification of new metastases, and 4) death. Patients without an event were right-censored at last follow-up.
RNA-seq analysis utilized a pipeline incorporating RSEM. Gene expression was quantified as Transcript Per Million (TPM), log2(TPM+1) transformed, and ComBat normalized to adjust for batch effects related to preservation method. A summary score was calculated for an 18 gene, IFN-γ-related signature previously reported to predict clinical response in PD-1 blockade.1
Results 112 patients in the melanoma cohort had immune-checkpoint inhibitor (ICI) therapy, RNA-seq prior to ICI therapy, and an evaluable rwPFS endpoint. Patient characteristics are shown in table 1. Median follow-up for the cohort was 4.4 years; median rwPFS was 1.5 years. Groups derived from a median cut of the IFN-γ-related signature demonstrated a marginally significant association with rwPFS (p=0.059). Higher expression of the signature associated with longer survival (figure 1). Identifying an optimal cutpoint for defining risk groups was outside the scope of this study, but stronger separation of groups was observed with lower cutpoints.
Conclusions The observation of longer rwPFS in the high IFN-γ-related signature group corresponds with the original report of the signature, in which high expression of the signature was associated with a favorable response to ICI treatment.1 Derivation of PFS endpoints from real-world data has recently been demonstrated2; the current study provides additional confirmation of the utility of rwPFS.
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Ethics Approval For this study, ORIEN members utilized a standard protocol, Total Cancer Care (TCC®; NCT03977402), to which patients provided an IRB-approved written informed consent at their participating institutions.
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