Non-small Cell Lung Cancer Cohort Research Articles

P1.15-04 Dynamic Profiling of Blood Immunophenotypes and Radiomic Features to Predict Immunotherapy Response in Advanced Non-small Cell Lung Cancer

Up to date, no predictive biomarkers can robustly identify patients with non-small cell lung cancer (NSCLC) who will benefit from immune checkpoint inhibitors (ICIs). Thus, we sought to non-invasively decode tumor-immune interactions implicated in ICI response by exploring the dynamic of blood immune-inflammatory markers and radiomic features in a cohort of advanced NSCLC treated with ICIs.

EP16.03-021 Developing of EGFR resistant mutations to Tyrosine Kinase Inhibitors (TKI) in Non-Small Cell Lung Cancer (NSCLC)

Tyrosine kinase inhibitors (TKIs) are effective in EGFR mutant non-small cell lung cancer (NSCLC), but acquired resistance is virtually inevitable. Known resistance mechanisms include acquired EGFR mutations (e.g, 718V, c797x, 724s, 721s or T790M); copy number amplifications in MET, ERBB2, and PIK3CA; gene fusion events; and histological transformation. We herein present the prevalence of resistance mutations in the largest reported cohort of EGFR mutant NSCLC.

1107P BRAF mutations and fusions in a real-world cohort of NSCLC patients

BRAF V600E (class I) mutant non-small cell lung cancer (NSCLC) is well characterized. However, less is known about other classes of BRAF mutations or BRAF fusions in this population. Previous studies have suggested that different classes of BRAF mutations may have varied clinical implications, motivating further study to guide therapeutic options in clinical practice. In this work, we set out to characterize the class of BRAF and co-occurring mutations as well as BRAF fusions in a real-world NSCLC cohort using comprehensive genomic profiling (CGP).

Adjuvant chemotherapy is not a decisive factor in improving the overall survival of pulmonary sarcoma: A population-based study.

ObjectiveThis study aimed to investigate the impact of adjuvant chemotherapy on overall survival (OS) for pulmonary sarcomatoid carcinoma (PSC) and non-small-cell lung cancer (NSCLC) cohorts and to identify its potential risk factors.MethodsA retrospective analysis was performed by querying the Surveillance, Epidemiology, and End Results (SEER) database for patients diagnosed as having PSC (n=460) and NSCLC (n=140,467) from 2004 to 2015. The demographics, tumor characteristics, treatment modes, and survival were included in the scope of statistical analysis. Confounding factors were controlled by propensity score matching (PSM) analysis. Kaplan–Meier survival curves were performed to compare the effects of adjuvant chemotherapy on OS of the patients in the two cohorts (PSC vs. NSCLC). A multivariable Cox regression model was constructed, and Kaplan–Meier analysis on each variate was applied to predict risk factors associated with OS.ResultsWhen adjuvant chemotherapy approach was applied in the treatment of patients with PSC or adjusted NSCLC, respectively, an improved OS could be observed in the NSCLC cohort (p=0.017). For the entire PSC cohort, 1-, 3-, and 5-year OS were 25.43%, 13.04%, and 6.96%, respectively, compared with 41.96%, 17.39%, and 10.00%, respectively, for the new adjusted NSCLC cohort after PSM, which were statistically significant difference (p<0.001). Multivariable Cox regression analysis was performed on OS covering prognostic factors such as primary site (p=0.036), first malignant indicator (p<0.001), age at diagnosis (p<0.001), marital status at diagnosis (p=0.039), and high school education (p=0.045). Additionally, patients with the following parameters had the worse impact on OS: a poorly differentiated pathology (Grade III/IV, p=0.023), older age (p<0.001), liver or lung metastasis (p=0.004, p=0.029), and the number of lymph nodes removed <4 (p<0.001).ConclusionsAdjuvant chemotherapy did not play a decisive role in improving the OS of PSC, while it was associated with improved OS of NSCLC.

O13-6 Japanese subgroup analysis of datopotamab deruxtecan in NSCLC cohort of TROPION-PanTumor01, a phase 1 study

Datopotamab deruxtecan (Dato-DXd) is an antibody drug conjugate composed of a humanized anti-TROP2 IgG1 monoclonal antibody conjugated to a topoisomerase I inhibitor via a tetrapeptide-based cleavable linker. Dato-DXd demonstrated encouraging antitumor activity in patients (pts) with advanced/metastatic non-small cell lung cancer (NSCLC) from primary analysis results of TROPION-PanTumor01 (Garon E et al., WCLC2021). Here we report Japanese subgroup data from the NSCLC cohort of TROPION-PanTumor01.

Quantitative tissue analysis and role of myeloid cells in non-small cell lung cancer

BackgroundDespite the prominent role of innate immunity in the antitumor response, little is known about the myeloid composition of human non-small cell lung cancer (NSCLC) with respect to histology and...

Abstract 1245: Comprehensive analysis of non-small cell lung cancer identifies molecular genotype-immunophenotype associations and candidate biomarkers predictive of response to immunotherapy

Abstract Lung cancer has the second highest incidence and leads cancer mortality worldwide, being Non-Small Cell Lung Cancer (NSCLC) the most prevalent subtype. Immunotherapy with checkpoint blockers has shown outstanding benefits in a subset of NSCLC patients, which are not accurately identified due to the lack of robust biomarkers of response. We hypothesize that specific molecular alterations of NSCLC tumor cells impact the immune microenvironment. Defining this association could improve the prediction of response to immunotherapy. This work aims to identify a multiparametric biomarker signature. We studied 178 tumor samples from a cohort of early stage NSCLC with complete clinical annotation. We analyzed their molecular aberrations, calculated their Tumor Mutational Burden and described their immune landscape by immunohistochemistry and a dedicated RNAseq panel. We defined novel subgroups of NSCLC tumors with specific immune, molecular and clinical features, showing an association between their molecular genotype and immune phenotype. Based on these data, subgroups were proposed as pro-immunogenic, pro-tumorigenic or mixed. Adenocarcinomas clustered in 4 groups. The pro-tumorigenic group had a significant higher proportion of alterations in ARID1A, FGF10, ROS1, TP53. One pro-immunogenic group had a significant higher proportion of MET alterations and lower proportion of EGFR alterations. An immune mixed group significantly accrued never smokers and had no alterations in FGF10. Squamous cell carcinomas clustered in 4 groups. The pro-tumorigenic group had a significant higher proportion of alterations in CCND1, FGF3, FGF10, FGF19, NOTCH1, PIK3CA, PIK3CB, TFRC. A pro-immunogenic group had a significant higher infiltration of T CD4+, T CD8+ and B cells and a higher overall survival. Another pro-immunogenic group had a significant absence of MYCN and NF1 alterations. Taken together we identified a set of candidate predictive biomarkers of response to immunotherapy in NSCLC. Genes overexpressed in pro-immunogenic tumors are related to adaptive immune response stimulation (CD28, FCRLA, JCHAIN, LY9, MS4A1, SLAMF7, TNFRSF9, TNFRSF17), antigen presentation (CD1C, CD1D, HLA-A), apoptosis (FAS), immune chemotaxis (CCL20, CCR4, CCR6), and immune regulation (CD53, PDCD1, SH2D1A, ZAP70). On the other hand, genes upregulated in pro-tumorigenic tumors are involved in angiogenesis (VEGFA), cell cycle regulation (BUB1, CCNB2, FOXM1, MAD2L1, TOP2A), cell growth/survival (IGF1R), DNA replication/repair (KIAA0101) and iron metabolism (HMBS, TFRC). These findings are being validated by Digital Spatial Profiling in a cohort of patients with advanced stage NSCLC that were treated with checkpoint blockers. If confirmed, these results could remarkably improve patient selection and the benefit upon immunotherapy. Citation Format: Javier Ramos-Paradas, David Gomez-Sanchez, Aranzazu Rosado, Alvaro Conrado Ucero, Nuria Carrizo, Ana Belen Enguita, Maria Teresa Muñoz, Esther Conde, Luis Paz-Ares, Eva Maria Garrido-Martin. Comprehensive analysis of non-small cell lung cancer identifies molecular genotype-immunophenotype associations and candidate biomarkers predictive of response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1245.

Abstract 5087: KDR mutation as novel biomarker for immune checkpoint inhibitors in pan-cancer

Abstract Purpose: Immune Checkpoint Inhibitors (ICIs) have marked important milestones in cancer treatment, while few patients experience clinical benefits from them. Therefore, reliable predictive markers for ICIs are urgently needed. Nowadays, the combination of antiangiogenic therapy and ICIs exhibits encouraging efficacy. As a key protein of VEGFR signaling, KDR may also function to regulate immune responses beyond its role in angiogenesis. Experimental Design: Pan-cancer immunotherapeutic patients from public cohorts including genomic data and clinical data were analyzed. Further analysis was performed on an internal validation data set including 67 non-small cell lung cancer (NSCLC). Investigation on underlying mechanism was performed in The Cancer Genome Atlas (TCGA) data via bioinformatics analysis. Results: We found better responses to ICIs in patients who harbored KDR mutation from pan-cancer public datasets (discovery cohort: n=662; validation cohort: n=1333). Our NSCLC cohort verified the value of KDR mutation in predicting better ICI outcomes, including objective response rate (70.0% vs 22.81%, P=0.0057) and progression-free survival (HR=0.158, 95% CI, 0.045-0.773; P=0.007). KDR mutation was associated with increased TMB level, neoantigen burden, immune cellular activities, and decreased VEGFR signaling. Meanwhile, KDR mutation was indicative of an immune-hot status, characterized by higher expression of PD-L1 and abundance of cytotoxic lymphocytes. Conclusions: Our work demonstrates that KDR mutation has the potential to become a predictive biomarker for ICIs. Citation Format: Renhua Guo, Yanan Cui, Pengpeng Zhang, Xiao Liang, Jiali Xu, Xinyin Liu, Yuemin Wu, Wei Wang, Fang Zhang, Junling Zhang, Mengli Huang. KDR mutation as novel biomarker for immune checkpoint inhibitors in pan-cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5087.

Abstract 5838: The landscape of EGFR exon 20 insertion mutations in Chinese patients with non-small cell lung cancer

Abstract Background: The epidermal growth factor receptor (EGFR) is one of the most commonly altered genes in non-small cell lung cancer(NSCLC). Of these, insertion mutation in 20 exon (Ex20ins) of the EGFR occurs less frequently. In comparison with the common EGFR mutations (19Del/L858R), the NSCLC patients with Ex20ins have a worse prognosis. Recently, the FDA approved targeted oral therapeutic agent for NSCLC patients with EX20ins mutation, which has markedly improved their survival. Here we carry out a complete analysis of the frequency and types of EGFR 20 Exon insertion mutations in the large-scale NSCLC cohort of the Chinese population. Methods: From January 2020 to October 2021, a total of 4,091 patients were confirmed as NSCLC were included in the study. The Next-generation sequencing was utilized for detecting genetic mutations. Results: Among the 4,091 NSCLC patients, 2,411 (58.9%) experienced EGFR mutations. In which we identified 90 patients(2.2%) with Ex20ins. All of the Ex20ins were localized between amino acids S767-V774, and after C-helix of the EGFR kinase domain. Different from the exon 19 deletion, we found that Ex20ins exhibits various types of mutations. A total of 34 Ex20ins types were detected, with the most common A767_V769dupASV and S768_D770dupSVD mutations, accounting for 26% and 22.2% respectively. In addition, H773dupH (6.67%), H773_V774dupHV(5.56%), H773_V774insAH (2.22%), D770_N771insG (2.22%), and N771_P772insG(2.22%) were also observed in the NSCLC patients. Conclusions: We described the landscape of EGFR Ex20ins in Chinese NSCLC patients cohort. Based on the large sample size, the frequency of the Ex20ins mutation in Chinese NSCLC patients was 2.2%, and the types of EGFR Ex20ins mutation were highly heterogeneous. Citation Format: shun xu, Zhichao Fu. The landscape of EGFR exon 20 insertion mutations in Chinese patients with non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5838.

Abstract 2028: Spatially resolved proteomic profiling identifies tumor cell CD44 as a novel indicative biomarker of sensitivity to PD-1 axis blockade in advanced non-small cell lung cancer (NSCLC)

Abstract Introduction: Most patients with advanced NSCLC fail to develop durable responses from PD-1 axis blockade, and more robust predictive biomarkers are needed. In this study, we aimed to discover and validate spatially resolved protein markers associated with sensitivity to PD-1 axis inhibition across multiple NSCLC cohorts. Methods: We first used the GeoMx Digital Spatial Profiling (DSP) system in a discovery cohort of 56 NSCLC patients treated with PD-1 axis inhibitors at Yale (USA). Pre-treatment tumors were represented in a tissue microarray (YTMA471) and analyzed using a 71-plex primary antibody panel. Proteins were measured from three molecularly defined tissue compartments: tumor (CK+), leukocytes (CD45+/CD68-), and macrophages (CD68+). We used quantitative immunofluorescence (QIF) to orthogonally validate candidate biomarkers. For external validation of identified predictors, we assessed pre-treatment whole tissue sections from a cohort of 128 NSCLC patients treated with single-agent PD-1 axis inhibitors at the Hospital 12 de Octubre (Madrid, Spain) using DSP (39-plex protein panel, measured from CK+ and CD45+ compartments). In addition, we analyzed two immunotherapy untreated cohorts to address prognostic significance: YTMA423 (Yale, USA; n = 252) and CIMA-CUN (UNAV, Spain; n = 124), using QIF and DSP respectively. Results: Using continuous log-scaled data, we found 5 markers independently associated with progression-free survival (PFS) in the tumor compartment (including PD-L1, p = 0.002). Among the novel candidate predictors, tumor cell CD44, a marker of pluripotency and stemness, was associated with longer PFS (multivariate HR = 0.63, p= 0.002). Using QIF, we orthogonally validated that CD44 expression in the tumor compartment was associated with longer PFS (p &amp;lt;0.001) and overall survival (OS) (p = 0.03). In the external validation cohort, CD44 expressed in the tumor compartment, but not in the immune compartment, was predictive of clinical benefit (OR 1.22, p = 0.018), and was significantly associated with longer PFS (first tertile cutpoint: HR 0.62, p = 0.03). In contrast, high CD44 expression was not associated with survival in the two untreated cohorts. Using DSP data from two cohorts, regions of interest with elevated expression of CD44 in tumor cells consistently showed prominent (Fold Change&amp;gt;1.5, p&amp;lt;0.05) upregulation of TIM-3, and PD-L1 and multiple co-stimulatory molecules (including CD40, ICOS, CD27). Conclusion: This work highlights CD44 as a novel indicative biomarker of sensitivity to PD-1 axis blockade in NSCLC. NSCLCs with high CD44 expression in epithelial cells may be associated with an immune contexture primed for higher response to immune checkpoint blockade. Further studies are needed to understand the interplay between CD44+ cancer stem cell phenotype and mechanisms of immune evasion. Citation Format: Myrto Moutafi, Magdalena Molero, Sandra Martinez-Morilla, Javier Baena, Ioannis Vathiotis, Niki Gavrielatou, Laura Castro, Gorka Ruiz de Garibay, Vera Adradas, Daniel Orive, Karmele Valencia, Alfonso Galvo, Luis M. Montuenga, Santiago Ponce, Kurt Schalper, Luis Paz-Ares, David L. Rimm, Jon Zugazagoitia. Spatially resolved proteomic profiling identifies tumor cell CD44 as a novel indicative biomarker of sensitivity to PD-1 axis blockade in advanced non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2028.

Abstract 5396: DNA damage repair gene mutations predict the efficacy of immunization combined with platinum chemotherapy in advanced non-small cell lung cancer: A retrospective cohort study

Abstract Purpose: DNA damage repair (DDR) mutations are known to predict response to platinum-based chemotherapy in multiple solid tumors, as well as immunotherapy in non-small cell lung cancer (NSCLC). However, the predictive value of DDR in immunization combined with platinum chemotherapy remains unclear. Methods: We retrospectively collected information from 495 patients with advanced NSCLC whose tumors were analyzed using next-generation sequencing (NGS) and analyzed the characteristics of DDR mutations. Among them, 64 patients with NSCLC who received platinum chemotherapy and 37 patients who received immunotherapy combined with platinum chemotherapy were included in the prognostic analysis. Results: The DDR genes was commonly mutated in Chinese NSCLC population (242/495, 48.89%). In Chinese NSCLC cohort, DDR mutations showed a strong association with high tumor mutational burden (TMB-H) (DDR mutant vs DDR wild-type: 7.26 muts/Mb vs 5.15 muts/Mb, P=0.001) and higher rates of strong PD-L1 (TPS≥50%) positivity (DDR mutant vs DDR wild-type: 28.74% vs 20.69). Sixty-four advanced NSCLC patients treated with platinum-based chemotherapy were analyzed, the ORRs were 16% for the patients with DDR mutations (DDRmut) and 2.70% for the DDR wild-type (DDRwt) subgroup (P&amp;lt;0.05), and the DCRs were 88% for the DDRmut group and 48.64% for the DDRwt group (P&amp;lt;0.05). The DDRmut patients had significantly improved median PFS than the DDRwt group (7.07 months vs 4.27 months, hazard ratio (HR) =0.57, 95%CI 0.33−0.97, P= 0.0303). Median OS was also significantly better among the DDRmut patients than in the DDRwt group (29.93 vs 20.7 months, HR=0.49, 95%CI 0.25−0.97, P= 0.0359). Moreover, in thirty-Seven advanced NSCLC patients treated with immunization combined with platinum chemotherapy, the ORRs were 45% for the patients with DDR mutations (DDRmut) and 11.76% for the DDR wild-type (DDRwt) subgroup (P&amp;lt;0.05), and the DCRs were 95% for the DDRmut group and 70.59% for the DDRwt group (P&amp;lt;0.05). The DDRmut patients had significantly improved median PFS than the DDRwt group (16.83 months vs 5.83 months, hazard ratio (HR) =0.34, 95%CI 0.12−0.973, P= 0.0079). For patients in the DDRmut group, PFS receiving immunization combined with platinum chemotherapy was significantly better than those receiving platinum-based chemotherapy (16.83 months vs 7.07 months, hazard ratio (HR) =0.48, 95%CI 0.24−0.97, P= 0.046). However, for patients in the DDRwt group, there was no significant difference in PFS between those who received immunization combined with platinum chemotherapy and those who received platinum-based chemotherapy (5.8 months vs 4.2 months, hazard ratio (HR) =0.76, 95%CI 0.394−1.495, P= 0.491). Conclusions: DDR mutations may serve as a positive predictor of immunization combined with platinum chemotherapy in patients with advanced NSCLC. Citation Format: Zhiwe Xiao, Lingling Sun, Yating Zheng, Hanrui Chen, Xinting Zheng, Jiamin Luo, Chuying Gu, Ruiting Lin, Xue Hu, Mengli Huang, Lizhu Lin. DNA damage repair gene mutations predict the efficacy of immunization combined with platinum chemotherapy in advanced non-small cell lung cancer: A retrospective cohort study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5396.

Abstract 1390: Immunotherapy boosts B cell responses in lung adenocarcinoma

Abstract Introduction: B cells constitute a major part of the lung tumour microenvironment where they are organised in tertiary lymphoid structures (TLS) that resemble antibody-producing germinal centres. The presence of TLS has been associated with improved patient outcome and response to immunotherapy, though the mechanisms remain unclear. Similarly, the contribution of B cells and TLS to anti-tumour immunity in non-small cell lung cancer (NSCLC) remains largely unexplored. Methods: We evaluated TRACERx and TCGA NSCLC cohorts to compare B cell and TLS signatures as well as BCR sequences from human adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). Using a novel immunogenic mouse model of LUAD, we applied lineage tracing, 3D IF, and single-cell sequencing to characterise the evolution of lung germinal centre and antibody responses over tumour progression and immunotherapy treatment. We validated immunotherapy observations in a cohort of melanoma patients with pre- and post-treatment samples. Results: We found that B cell and TLS gene set scores were significantly higher in LUAD compared to LUSC. We examined B cell signals in specific mutational backgrounds, and observed an increase in BCR CDR3 diversity and IgG class switch in the context of clonal TP53 mutation. We therefore investigated the mechanistic basis of B cells in LUAD using an immunogenic mouse model on a KRAS/TP53 background. We found that TLS organisation was triggered by CXCL13 and that exogenous CXCL13 treatment increased B cell infiltration and overall survival. Using serum transfer experiments, we demonstrated that tumour-binding class-switched antibodies played an anti-tumour role and increased survival. We found that immunotherapy increased germinal centre B cell responses and antibody quantity and quality. Using single-cell BCR sequencing of immunotherapy-treated mice, we showed clonal expansion of B cells reactive to re-expressed endogenous retroviral antigens. Furthermore, we found that KRAS G12C but not MEK inhibition boosted B cell and antibody responses. Finally, combined treatment with CXCL13 and checkpoint blockade improved survival, suggesting that boosting local B cell responses can improve immunotherapy outcome. In checkpoint blockade-treated melanoma patients, we found that BCR diversity and the number of unique antigen specificities was elevated in responders post-therapy. Non-responders showed a loss of expanded clones, suggesting that both maintenance of expanded clones and recruitment of new clones associate with successful response. Conclusions: Our work describes a novel role for B cells in the lung tumour microenvironment and establish that TLS directly contribute to anti-tumour immunity by producing class-switched protective antibodies. We demonstrate that selective boosting of anti-tumour B cells shows therapeutic potential in combination with targeted and immunotherapy. Citation Format: Katey Enfield, Kevin Ng, Jesse Boumelha, Kevin Litchfield, Oriol Pich, TRACERx Consortium, Charles Swanton, George Kassiotis, Julian Downward. Immunotherapy boosts B cell responses in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1390.

Mutations in KMT2C, BCOR and KDM5C Predict Response to Immune Checkpoint Blockade Therapy in Non-Small Cell Lung Cancer.

Simple SummaryEfficient biomarkers are urgently needed to predict response to immune checkpoint blockade (ICB) therapy for non-small cell lung cancer (NSCLC), particularly NSCLC with low tumor mutational burden (TMB). Here, we show that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, are associated with the ICB response in NSCLC, including NSCLC with low TMB level. Furthermore, this association is further improved by a combined use of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 expression. These data suggest that KMT2C/BCOR/KDM5C mutation status has the potential to serve as a predictive biomarker for ICB therapy in NSCLC.Efficient predictive biomarkers are urgently needed to identify non-small cell lung cancer (NSCLC) patients who could benefit from immune checkpoint blockade (ICB) therapy. Since chromatin remodeling is required for DNA repair process, we asked whether mutations in chromatin remodeling genes could increase tumor mutational burden (TMB) and predict response to ICB therapy in NSCLC. Analysis of seven ICB-treated NSCLC cohorts revealed that mutations of three chromatin remodeling-related genes, including KMT2C, BCOR and KDM5C, were significantly associated with ICB response, and combined mutations of these three genes further enhance this association. NSCLC patients with KMT2C/BCOR/KDM5C mutations had comparable clinical outcomes to TMB-high patients in terms of objective response rate, durable clinical benefit and overall survival. Although KMT2C/BCOR/KDM5C mutations were positively correlated with TMB levels in NSCLC, the association of this mutation with better ICB response was independent of tumor TMB and programmed death-ligand 1 (PD-L1) level, and combination of KMT2C/BCOR/KDM5C mutations with TMB or PD-L1 further improve the prediction of ICB response in NSCLC patients. Cancer Genome Atlas (TCGA) pan-cancer analysis suggested that the association of KMT2C/BCOR/KDM5C mutations with ICB response observed here might not result from DNA repair defects. In conclusion, our data indicate that KMT2C/BCOR/KDM5C mutation has the potential to serve as a predictive biomarker, alone or combined with PD-L1 expression or TMB, for ICB therapy in NSCLC.

Spatial interplay patterns of cancer nuclei and tumor-infiltrating lymphocytes (TILs) predict clinical benefit for immune checkpoint inhibitors.

Immune checkpoint inhibitors (ICIs) show prominent clinical activity across multiple advanced tumors. However, less than half of patients respond even after molecule-based selection. Thus, improved biomarkers are required. In this study, we use an image analysis to capture morphologic attributes relating to the spatial interaction and architecture of tumor cells and tumor-infiltrating lymphocytes (TILs) from digitized H&E images. We evaluate the association of image features with progression-free (PFS) and overall survival in non–small cell lung cancer (NSCLC) (N = 187) and gynecological cancer (N = 39) patients treated with ICIs. We demonstrated that the classifier trained with NSCLC alone was associated with PFS in independent NSCLC cohorts and also in gynecological cancer. The classifier was also associated with clinical outcome independent of clinical factors. Moreover, the classifier was associated with PFS even with low PD-L1 expression. These findings suggest that image analysis can be used to predict clinical end points in patients receiving ICI.

Ancestry-based differences in gene alterations in non–small cell lung cancer: Real-world data using genetic ancestry analysis.

9125 Background: Racial differences in morbidity and mortality of non-small cell lung cancer (NSCLC) have been demonstrated and some genomic alterations (e.g. EGFR) in NSCLC are known to differ according to race. However, studies have been limited in sample size and hence, limited in their capacity to detect discrepancies in less frequently altered genes. Here, we investigated alteration prevalence in a large real-world NSCLC cohort, stratified by genetic ancestry. Methods: 75,362 NSCLC patients from the United States, were profiled with comprehensive genomic profiling (CGP) of tissue biopsy, as part of routine clinical care (Foundation Medicine Inc., FMI; Frampton GM, et al. Nat Biotechnol 2013). 296 genes targeted across all assays were examined for known/likely pathogenic alterations of all classes. Predominant genetic ancestry was inferred using a SNP-based approach (Newberg J, et al. AACR 2019), and patients were categorized into European (EUR), African (AFR), East Asian (EAS), Admixed American (AMR), and South Asian (SAS) ancestry groups. Patients were additionally stratified by histological type, age (≥40/ &lt; 40), and sex. The prevalence of high tumor mutational burden (TMB-High), defined as ≥ 10 mutations/mb (Chalmers ZR, et al. Genome Med 2017), and microsatellite instability status (Trabucco, et al. J Mol Diagn 2019) was also calculated. Results: In this NSCLC cohort, ancestry was split 82.2% for EUR, 10.0% for AFR, 4.4% for EAS, 2.7% for AMR, and 0.8% for SAS. 50.4% were female (n = 37,972) and 49.6% male (n = 37,360). The most prevalent alterations in the overall cohort included TP53 (67.5%), KRAS (30.6%), CDKN2A (29.2%), CDKN2B (17.2%), STK11 (16.1%), and EGFR (15.3%). The prevalence of TMB-High status in the overall cohort was 34.6%. Stratified by ancestry, the prevalence of EGFR alterations was significantly enriched in EAS vs. other ancestry groups ( p &lt; 0.001). KRAS and STK11 were enriched in EUR and AFR vs. other groups ( p &lt; 0.001). TMB-High status was significantly enriched in AFR vs. all other groups ( p &lt; 0.001). In EAS and SAS, TMB-High was typically reduced vs. other ancestry groups (TMB-High AFR 41.6%, AMR 20.1%, EAS 14.1%, EUR 35.5%, SAS 11.7%). A similar analysis based on sex revealed differences in prevalence of 80 gene alterations and TMB-High with sex-specific enrichments (e.g., EGFR 19.0% female vs. 11.5% male; KRAS 34.6% vs. 26.6%). With respect to age, the prevalence of 41 gene alterations and TMB-High were significantly different between samples from patients age &lt; 40 and age ≥ 40 (e.g., ALK 21.1% age &lt; 40 vs. 2.7% age ≥ 40; KRAS 13.0% vs. 30.8%; TMB-High 14.4% vs. 34.8%). Conclusions: Comprehensive analysis of this real-world dataset, which includes the largest NSCLC patient cohort, revealed ancestry-associated differences in genomic alterations in NSCLC. Age and sex were also associated with differences in genomic alteration and TMB-High prevalence.

Glycoproteomics as a powerful liquid biopsy-based screening tool for non-small cell lung cancer.

e21148 Background: Protein glycosylation is the most abundant and complex form of post-translational protein modification. Glycosylation profoundly affects protein structure, conformation, and function. The elucidation of the potential role of differential protein glycosylation as biomarkers has so far been limited by the technical complexity of generating and interpreting this information. We have recently established a novel, powerful platform that combines liquid chromatography/mass spectrometry with a proprietary artificial-intelligence-based data processing engine that allows, for the first time, highly scalable interrogation of the glycoproteome. Methods: Using this platform, we interrogated 694 glycopeptide (GP) and non-glycosylated peptide transitions derived from 74 serum proteins in pre-treatment peripheral blood samples from a cohort of 316 individuals with non-small-cell lung cancer (NSCLC) (128 females, 187 males, 1 with unknown sex, median age 66 years, age range 31-89 years, stage 0-4 N’s: 1 / 99 / 80 / 84 / 49, 3 missing) and a comparison cohort of 194 healthy control samples (102 females, 92 males, median age 52 years, age range 30-63 years). Age- and sex-adjusted differential expression analysis for 596 normalized biomarkers were performed to evaluate statistically significant differential abundances using an FDR-adjusted q-value of 0.05 as a cutoff. Repeated five-fold cross-validated LASSO-regularized logistic regression was performed to create a multivariable classifier that predicts whether a serum sample belongs to the healthy or NSCLC cohort. Results: We identified 432 biomarkers with significant abundance differences at FDR ≤ 0.05 between samples with NSCLC and healthy controls. Using 70% of the complete cohort (balanced by case/control membership, NSCLC stage, sex, and age quartile) as a training set, we selected a total of 375 glycopeptide and non-glycosylated peptide biomarker features that remained differentially expressed at FDR-adjusted q-value ≤ 0.05 as input into a LASSO-regularized multivariable classifier. This resulting in a 19-biomarker model exhibiting an accuracy of 94.8% (96.9% sensitivity, 91.2% specificity) and AUC of 0.989. This classifier was validated in an independent test set comprising the remaining 30% of subjects, yielding an accuracy of 94.5% (95.5% sensitivity, 93.0% specificity) and AUC of 0.975. Sensitivity in the test set was 100% / 96% / 99% / 96% / 94% / 10%, in stages 0-4 and missing, respectively. Conclusions: Our results indicate that glycoproteomic biomarkers can be leveraged as a strong liquid biopsy-based screening tool for patients at high risk of NSCLC, as an alternative to imaging modalities.

Disparities in Biomarker Testing and Clinical Trial Enrollment Among Patients With Lung, Breast, or Colorectal Cancers in the United States.

Comprehensive tumor biomarker testing is a fundamental step in the selection of highly effective molecularly driven therapies for a variety of solid tumors. The primary objective of this study was to examine racial differences in biomarker testing and clinical trial participation in the United States using a real-world database. Patients in a real-world deidentified database diagnosed with advanced/metastatic non-small-cell lung cancer (NSCLC), metastatic colorectal cancer (CRC), or metastatic breast cancer were eligible. Biomarker testing and clinical trial participation was compared between Black and White racial groups using chi-squared test and stepwise logistic regression controlling for baseline covariates. A total of 23,488 patients met eligibility criteria. Next-generation sequencing (NGS) testing rates differed significantly between White versus Black race before first-line therapy (36.6% v 29.7%, P < .0001) and at any given time (54.7% v 43.8%, P < .0001) in the nonsquamous NSCLC cohort. Similar disparities in NGS testing rates at any time during the study were observed among patients with CRC (White 51.6%; Black 41.8%, P < .0001). No differences were observed in the breast cancer cohort. Patients of Black race were less likely to be treated in a clinical trial in the overall NSCLC cohort when compared with White counterparts (3.9% v 2.1%, P = .0002). A statistically significant relationship between biomarker/NGS testing and clinical trial enrollment was observed in all cohorts (P < .003) after adjusting for covariates. In a real-world database, significant disparities in NGS-based testing rates were observed between Black and White races in NSCLC and CRC. NGS and any biomarker testing were both associated with trial enrollment in all cohorts. There is a need for interventions to promote access to comprehensive testing for patients with advanced/metastatic tumors.

Newly updated activity results of alrizomadlin (APG-115), a novel MDM2/p53 inhibitor, plus pembrolizumab: Phase 2 study in adults and children with various solid tumors.

9517 Background: Alrizomadlin restores TP53 function, activating p53-mediated apoptosis in tumor cells with wild-type TP53 and/or MDM2 amplification. Alrizomadlin also functions as a host immunomodulator and may restore antitumor activity in pts with cancers that progressed on PD-1/PD-L1 inhibitors. Methods: This US/Australian multicenter trial evaluated alrizomadlin, an investigational MDM2-selective, small-molecule inhibitor, combined with pembrolizumab, in pts with unresectable/metastatic melanoma that progressed on I-O drugs; pts with malignant peripheral nerve sheath tumor (MPNST), well-differentiated/dedifferentiated liposarcoma, non-small cell lung cancer (NSCLC), or solid tumors with ATM mutations that progressed on available standard therapy; or pts for whom therapy was unavailable. Eligible pts had ECOG performance status of 0-2 and, if present, stable brain metastases. Alrizomadlin 150 mg PO was administered QOD for 2 consecutive weeks, with 1 week off, and pembrolizumab 200 mg IV over 30 minutes on Day 1 of a 21-day cycle. Results: As of November 3, 2021, preliminary and interim results are reported for 130 pts in 6 cohorts: melanoma (n = 44), NSCLC (n = 26), ATM mutation (n = 18), liposarcoma (n = 17), urothelial (n = 13), and MPNST (n = 12). In the melanoma cohort, confirmed ORR by RECIST, (PR + CR) was 13% (2 CRs + 3 PRs/38 efficacy evaluable [EE] pts). In cutaneous and uveal melanoma subcohorts, confirmed ORR was 24% (2 CRs + 2 PRs/17 EE pts) and 9% (1 PR/11 EE pts), respectively. In the MPNST cohort, the clinical benefit rate, defined by confirmed ORR + SD of &gt; 4 cycles, was 40% (4 SDs/10 EE pts). Additional confirmed PRs were reported in NSCLC, urothelial, and liposarcoma cohorts (1 each). Common treatment (alrizomadlin or pembrolizumab)-related adverse events (TRAEs; ≥ 10%) were nausea (62%), thrombocytopenia (39%), vomiting (38%), fatigue (38%), decreased appetite (29%), diarrhea (25%), neutropenia (15%), and anemia (12%). Grade 3+ TRAEs (≥ 5%) included thrombocytopenia (23%), neutropenia (10%), and anemia (7%). A total of 16 pts discontinued treatment due to AEs; 6 were treatment related, including grade 4 thrombocytopenia (n = 3), grade 2 vomiting (n = 1), grade 2 fatigue (n = 1), and grade 2 posterior reversible encephalopathy syndrome (PRES; n = 1). A total of 10 pts reported treatment-related SAEs: 1 each of abdominal pain, asthenia, colitis, febrile neutropenia, hypophysitis, peripheral edema, overdose, PRES, pulmonary embolism, pyrexia, and thrombocytopenia. Conclusions: Alrizomadlin, combined with pembrolizumab, is well tolerated and demonstrates preliminary antitumor activity in multiple tumor types and may restore antitumor effects in pts with cancer resistant or intolerant to I-O drugs. Internal study identifiers: APG-115-US-002; Keynote MK-3475-B66. Clinical trial information: NCT03611868.

Acquired EGFR-resistant mutations in non–small cell lung cancer (NSCLC).

9113 Background: EGFR mutations are present in more than 10% of patients (pts) with NSCLC in the US. While EGFR with tyrosine kinase inhibitors (TKIs) are effective, acquired resistance is expected. Known mechanisms include acquired EGFR mutations (e.g. 718V, c797x, 724s, 721s or T790M); copy number amplifications in MET, ERBB2, and PIK3CA; gene fusion events; and histological transformation. We herein present the prevalence of resistance mutations in the largest reported cohort of EGFR mutant NSCLC. Methods: Non-small cell lung cancer (NSCLC) tumor samples were submitted to Caris Life Sciences (Phoenix, AZ) for NextGen Sequencing (NextSeq, 592 Genes) and whole exome sequencing (NovaSeq, WES). PD-L1 expression was tested by IHC using 22c3 (Dako) and TPS scores were reported (cutoff &gt;1). TMB was measured by totaling somatic mutations (TMB-high cut-off &gt; 10 mutations per MB), genomic loss of heterozygosity (gLOH) was determined by WES. Patient treatment information was obtained from insurance claims data. Results: A total of 27,848 NSCLC tumors were evaluated and 3,223 (12%) had a EGFR sensitizing mutations. We found 60 tumors with common missense resistance mutations: 790 (n = 30, 0.9%), 797 (n = 38, 1.2 %), 718 (n = 11, 0.3%), 724 (n = 7, 0.2%) and 721 (n = 4, 0.1). Table 1 describes the frequencies, PD-L1 expression and the most common co-mutations. TMB-H (&gt; = 10) was found in 12.5% of the tumors and dMMR/MSI-H in 1.8%. The most prevalent co-alterations were TP53 54%), gLOH (28%), CTNNB1 (19%), NFKB1A (13%), APC (10%), PIK3CA (11%), SMAD4 (9%) and other 15 co-mutations in less than 7% were seen. In the 30 T790M mutants, in addition to TP53 mutations, other prevalent co-mutations were PIK3CA (14%) and CTNNB1 (17%). In 797-mutant tumors, in addition to T790M, the most prevalent co-mutations were TP53 (53%), CTNNB1 (22%), APC (16%) and PIK3CA (11%). L718 mutations co-occurred with either L858R (8/11), exon 19 (3/11) or T790M mutations (3/11). G724 mutations were found in 7 patients (0.02%) and G721 mutations in 4 patients (0.01%). Conclusions: Acquired resistance in EGFR mutant NSCLC is very heterogeneous and their frequency is still low most likely due to lack of enough sequencing of EGFR resistant tumors. While T790M and C797S mutations are well described, this report also notes a significant number of L718V mutations, primarily in osimertinib-treated pts with an original L858R. These data support the NGS evaluation of patients with resistant EGFR mutant lung cancers. [Table: see text]

Maximum somatic allele frequency-adjusted blood-based tumor mutational burden balances the effect of intratumor heterogeneity on response to immune checkpoint Inhibitors in non-small cell lung cancer patients.

e21137 Background: ctDNA abundance can influence the accuracy of blood-based tumor mutational burden (bTMB), driving a paradox of bTMB in predicting response and survival benefit of patients with non-small cell lung cancer (NSCLC) receiving immune checkpoint inhibitors (ICIs) therapy. However, the optimal algorithm of ctDNA adjusted bTMB remains largely unestablished. We aimed to develop a novel approach to optimize the calculation of bTMB by integrating maximum somatic allele frequency (MSAF) to better differentiate the ICI-beneficial NSCLC patients, as well as explore the correlated mechanism. Methods: A 1021-gene panel-based targeted capture sequencing was utilized to evaluate the correlation between MSAF and bTMB based on blood samples in 1679 Chinese NSCLC patients (GCGD database, N = 1679). The establishment of MSAF-adjusted bTMB (Ma-bTMB) was derived from three independent NSCLC cohorts treated with programmed death ligand 1 (PD-L1) or the programmed death 1 (PD-1) inhibitors, including POPLAR cohort (N = 231) as training set, and OAK (N = 642) and Wang (N = 81) cohorts as validation sets separately. PyClone was employed to estimate clonal and subclonal populations. Results: MSAF demonstrated a modest positive correlation between bTMB and MSAF (Spearman’s R = 0.41, P &lt; 0.001, GCGD cohort) and was negatively correlated with survival benefit (Spearman’s rank sum test, overall survival (OS): R = −0.39, P &lt; 0.001; progression-free survival (PFS): R = −0.41, P &lt; 0.001, Wang cohort). Patients with high Ma-bTMB (Ma-bTMB-H) demonstrated improved survival outcomes of anti-PD(L)-1 therapy compared to chemotherapy in POPLAR (PFS, hazard ratio (HR) = 0.63, interaction P = 0.030; OS, HR = 0.44, interaction P = 0.020), which was validated in OAK cohorts (PFS, HR = 0.72, interaction P = 0.040; OS, HR = 0.50, interaction P = 0.010). In addition, Ma-bTMB-H was associated with a better clinical benefit compared to low Ma-bTMB (Ma-bTMB-L) in Wang cohort (PFS, HR = 0.55, P = 0.012; OS, HR = 0.46, P = 0.036). Furthermore, there was a positive correlation between intratumor heterogeneity (ITH) and MSAF (R = 0.37, P &lt; 0.001) in GCGD database, and the effect of ITH on Ma-bTMB (subclones, P = 0.57; subclonal mutations, P = 0.8) was substantially reduced compared to traditional bTMB (subclones, P &lt; 0.001; subclonal mutations, P &lt; 0.001) in Wang cohort. Conclusions: We developed and validated Ma-bTMB, a convenient, readily available, non-invasive predictive biomarker, which reduced the confounding effect of ITH and could effectively differentiate beneficiaries of anti-PD(L)1 therapy, warranting investigation in future clinical trials. Clinical trial information: NCC2018-092.