Background ALK rearrangements are known drivers of a subset of lung adenocarcinomas (LAs), and ALK fusion-positive tumors are associated with reduced efficacy of PD-1/PD-L1 immune checkpoint inhibition. Precise knowledge of the molecular differences between ALK+ and ALK-normal LAs could provide important context when designing future clinical trials. The objective of this study was to compare biomarkers of from ALK+ and ALK-normal LAs.
Methods We searched our institutional records for cases of LAs that underwent comprehensive genomic and immune profiling (CGIP), which included panel-based next-generation sequencing of DNA (523 genes) and RNA (55 genes for fusions/splice site variants, 395 for immune gene expression). Tumor mutational burden (TMB) was calculated in mutations per megabase. PD-L1 expression was assessed by tumor proportion score (TPS) following 22C3 immunohistochemistry. LAs were categorized by the presence of ALK (ALK+), EGFR (EGFRm), KRAS alterations or absence of these alterations (AEKwt). Tumors harboring mutations in two or more of these genes were excluded from the analysis. Expression signatures for tumor immunogenicity (TIGS; 161 genes), cellular proliferation (CP; 10 genes including Ki-67), and cancer testis antigen burden (CTAB; 21 genes) were determined from rank gene expression scores by RNAseq. Statistical comparisons were preformed using the Mann-Whitney U test method.
Results We identified 3393 specimens with CGIP results, comprised of 66 ALK+ and 3327 ALK-wildtype (ALKwt) tumors. ALKwt tumors were composed of 497 EGFRm, 1087 KRASm, and 1743 AEKwt LAs. The entire patient cohort was comprised of 54.6% females and 45.4% males, with a median age of 71 y (range 26–90). ALK+ tumors were associated with a younger age at sequencing compared to ALKwt, EGFRm, and KRASm tumors (table 1, p<0.001). ALK+ tumors exhibited lower TMB compared to ALKwt, EGFRm, and KRASm LAs (p<0.001). ALK+ tumors displayed a greater number of tumor cells expressing PD-L1 compared to ALKwt and EGFRm (p<0.001). Regarding gene expression signatures, no significant differences were observed in TIGS and CP signatures among the different genetic subgroups. However, ALK+ tumors demonstrated a lower CTAB signature compared to ALKwt tumors (p=0.046). No significant difference in CTAB was found between ALK+ and KRASm tumors in the CTAB signature.
Conclusions The results highlight distinct features of ALK+ LAs compared to other driver mutations. Our results show that ALK rearrangements are associated with elevated levels of PD-L1 tumore expression. These findings support consideration for including patients with ALK+ LAs in appropriate clinical trials.
Ethics Approval For this study was obtained from WCG IRB (Study #1340120), an independent institutional review board, including waiver of informed consent.
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