Abstract 4054: Gene expression difference (GED) revealed immune function gene down-regulation as tumor-associated inflammatory cell (TAIC) infiltration in microenvironment in non-small cell lung cancer (NSCLC)
Authors: Tang Ximing , Lu Wei , Zhang Jiexin , Berhens Carmen , Parra Edwin R. , Wineman John , Zhang Jianjun , Gibbons Don Lynn , Koeppel Mark , Kerns BJ , Stern Mark , Sepesi Boris , Lee Jack J. , Wistuba Ignacio I. 
Published: August 2018

Abstract
Background Advances in molecular analyses of tumor tissues based on high-throughput technologies can contribute to a better prediction of disease prognosis and the efficacy of immunotherapies. We investigated the GED related to immune response in a large cohort of NSCLC. Methods Using low-input, high-throughput HTG EdgeSeq assay, we examined expression of a panel of 549 immune response-related genes (28 are categorized as immune function genes) in FFPE tumor tissues of 226 surgically resected, stage I to III NSCLCs (137 adenocarcinomas [ADC] and 89 squamous cell carcinomas [SqCC]) with annotated clinical, pathological characteristics. Molecular data were available on mutations of EGFR and KRAS (cases=126), STK11, PIK3CA and TP53 by whole exome sequencing (n=180), and TAICs density detected by IHC (CD3, CD4, CD68, CD8, FOXP3, GZB, PD-L1 and PD-1) (n=145). We associated GED to 12 clinical, pathological or molecular characteristics including age, gender, smoking history, histology, stage, size, lymph node status and gene mutations of tumors and to patients' outcome (recurrence free survival [RFS] and overall survival [OS]). Results Univariate analysis showed upregulations of 82 genes in ADC and 89 in SqCC by comparing each other (P≤0.001). In ADC, 23 GEDs [FDR (false discover rate) ≤5%] associated with ever smoking history (8 up- and 15 down-regulated). Some genes were identified to be associated with mutations of EGFR, KRAS, STK11, PIK3CA and P53 genes. GEDs were identified in the tumors with TAIC high density by IHC. In ADC, 192 genes were down- and 191 up-regulated; while among the 28 immune function genes 21 down- and, only the gene APP (in all 8 high density TAICs) up-regulated. In SqCC, 121 genes down- and 112 up-regulated; while in the 28 genes 17 were down- and only the gene CAP up-regulated slightly in the high FOXP3 tumors. Cox proportional hazard model using FDR 5% in multi-testing showed that in ADC treated with adjuvant chemotherapy high-expression in 10 genes such as CD52, CD74 and HLA-DRA having a beneficial and 5 genes such as HRT2 and SERPINB2 having worse effect on OS; in the ADC patients who did not receive adjuvant therapy, high-expression of PIK3CD showed beneficial and, TTK and CXCL8 showed detrimental effect on OS; no gene was found to be associated with RFS in ADC and with OS and RFS in SqCC. Conclusion Gene expression profiling analysis of a panel of immune-related genes using low-input mRNA from FFPE tumor tissues revealed a number of genes associating to tumor characteristics, gene mutation patterns and TAIC infiltration in NSCLC. Interestingly, almost of immune function genes were down-regulated in the tumor with TAIC high density in NSCLC. (Supported in part by grant CPRIT RP160668)
Citation Format: Ximing Tang, Wei Lu, Jiexin Zhang, Carmen Berhens, Edwin R. Parra, John Wineman, Jianjun Zhang, Don Lynn Gibbons, Mark Koeppel, BJ Kerns, Mark Stern, Boris Sepesi, Jack J. Lee, Ignacio I. Wistuba. Gene expression difference (GED) revealed immune function gene down-regulation as tumor-associated inflammatory cell (TAIC) infiltration in microenvironment in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4054.