Mutant Lung Adenocarcinoma Research Articles

Detecting Small Cell Transformation in Patients with Advanced EGFR Mutant Lung Adenocarcinoma through Epigenomic cfDNA Profiling.

Histologic transformation to small cell lung cancer (SCLC) is a mechanism of treatment resistance in patients with advanced oncogene-driven lung adenocarcinoma (LUAD) that currently requires histologic review for diagnosis. Herein, we sought to develop an epigenomic cell-free DNA (cfDNA)-based approach to noninvasively detect small cell transformation in patients with EGFR mutant (EGFRm) LUAD. To characterize the epigenomic landscape of transformed (t)SCLC relative to LUAD and de novo SCLC, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to profile the histone modifications H3K27ac, H3K4me3, and H3K27me3; methylated DNA immunoprecipitation sequencing (MeDIP-seq); assay for transposase-accessible chromatin sequencing; and RNA sequencing on 26 lung cancer patient-derived xenograft (PDX) tumors. We then generated and analyzed H3K27ac ChIP-seq, MeDIP-seq, and whole genome sequencing cfDNA data from 1 mL aliquots of plasma from patients with EGFRm LUAD with or without tSCLC. Analysis of 126 epigenomic libraries from the lung cancer PDXs revealed widespread epigenomic reprogramming between LUAD and tSCLC, with a large number of differential H3K27ac (n = 24,424), DNA methylation (n = 3,298), and chromatin accessibility (n = 16,352) sites between the two histologies. Tumor-informed analysis of each of these three epigenomic features in cfDNA resulted in accurate noninvasive discrimination between patients with EGFRm LUAD versus tSCLC [area under the receiver operating characteristic curve (AUROC) = 0.82-0.87]. A multianalyte cfDNA-based classifier integrating these three epigenomic features discriminated between EGFRm LUAD versus tSCLC with an AUROC of 0.94. These data demonstrate the feasibility of detecting small cell transformation in patients with EGFRm LUAD through epigenomic cfDNA profiling of 1 mL of patient plasma.

A comparative analysis indicates SLC7A11 expression regulate the prognostic value of KEAP1-NFE2L2-CUL3 mutations in human uterine corpus endometrial carcinoma

Uterine corpus endometrial cancer (UCEC) is a third most common malignancy in women with a poor prognosis in advanced stages. In this study, we performed an integrated comparative analysis of exome and transcriptome data from The Cancer Genome Atlas (TCGA) of Lung Adenocarcinoma (LUAD), and UCEC patients. Our multi-omics analysis shows that the UCEC patients carrying mutations in the KEAP1-NFE2L2-CUL3 genes were associated with better progression-free survival (PFS), whereas the KEAP1-NFE2L2-CUL3 mutation in LUAD showed poor outcomes. Functional annotations and correlative expression studies show that genes, particularly GCLC and GCLM related to glutathione synthesis are expressed at lower levels in the KEAP1-NFE2L2-CUL3 mutant UCEC compared to LUAD. This events result in glutathione deficiency and it may compromise to combat intracellular reactive oxygen species (ROS). However, the expression of genes involved in the glutathione recycling process was not affected. On the other hand, cellular import of cystine is high due to increased SLC7A11 expression in UCEC. Because glutathione synthesis is impaired, the unconverted cysteine accumulates in cells, leading to di-sulfite stress. Apart from NRF2, ARID1A is one of the positive regulators of SLC7A11. In support, UCEC patients with co-occurrence of KEAP1-NFE2L2-CUL3 and ARID1A mutation shows significantly decreased PFS with decline of SLC7A11 expression as compared to patients carrying only KEAP1-NFE2L2-CUL3 mutation. Thus, we hypothesize that the KEAP1-NFE2L2-CUL3 mutation in UCEC leads to uncontrollable ROS with di-sulfite stress, reflecting a favorable clinical outcome.

The efficacy of postoperative radiotherapy in resected pⅢA-N2 EGFR mutant and wild-type lung adenocarcinoma

The resected pⅢA-N2 non-small-cell lung cancer (NSCLC) patients who could benefit from postoperative radiotherapy (PORT) are not well-defined. The study explored the role of PORT on EGFR mutant and wild-type NSCLC patients. We retrospectively searched for resected pIIIA-N2 lung adenocarcinoma patients who underwent EGFR mutation testing. 80 patients with EGFR wild-type and 85 patients with EGFR mutation were included. 62 patients received PORT. In overall population, the median disease-free survival (DFS) was improved in PORT arm compared to non-PORT arm (22.9 vs. 16.1months; p= 0.036), along with higher 2-year locoregional recurrence-free survival (LRFS) rate (88.3% vs. 69.3%; p= 0.004). In EGFR wild-type patients, PORT was associated with a longer median DFS (23.3 vs. 17.2months; p= 0.044), and a higher 2-year LRFS rate (86.8% vs. 61.9%; p= 0.012). In EGFR mutant patients, PORT was not significantly correlated with improved survival outcomes. EGFR wild-type may a biomarker to identify the cohort that benefits from PORT.

Loss of heterozygosity (LOH) in KEAP1/STK11-mutated lung adenocarcinoma to characterize a new subgroup of hard-to-treat patients with unmet need in the real-world setting.

8641 Background: Recent research suggests that loss of heterozygosity (LOH) in KEAP1/STK11 mutated lung adenocarcinoma (LUAD) may present a new immunological and biological aggressive subtype unresponsive to current standard of care treatment options. Currently, there is limited data on the clinical impact of LOH in KEAP1/STK11 co-alterations in real-world settings. Methods: From November 1st, 2021, to October 1st, 2023, patients with LUAD and mutations detected by FoundationOne CDx in any of the genes KEAP1, STK11, KRAS were enrolled in the study. Clinical data, including overall survival (OS), duration of response to different treatment lines (DOR), and real-world progression-free survival (rwPFS) according to the treatment lines, were retrospectively assessed in patients who had given informed general consent. Multivariate Cox regression models included patient characteristics, selected two-way interactions, OS, LOH, PD-L1 status and rwPFS for patients with STK11, KEAP1, KRAS mutations. Results: A total of 104 patients were included, 63 (60.6%) males with a median age of 64.4 years; [range: 38-90]). 23 (22.1%) patients with STK11/KEAP1/KRASmutations, 15 (14.4%) patients with KEAP1/LOH mutations, 10 (10.4%) patients with STK11/KRAS mutations and six (5.8%) patients with STK11/KEAP1. In the KEAP1/LOH mutated subgroup, median OS (mOS) was 14 months (ms), whereas in the subgroup with KEAP1/KRASmutations mOS was 13 ms. Across all groups mOS was 14 ms. Compared to Keynote 189 with a PFS of 8.8 ms, rwPFS for the first treatment line (rwPFS1) was shorter in patients with KEAP1/LOH status and KRAS/STK11 mutations at 3.5 ms and 3 ms respectively. Additionally, DOR and rwPFS for further treatment lines were analyzed according to PD-L1 and TMB status, as well as the treatment lines patients received. Conclusions: Patients with mutations on STK11/KEAP1/KRAS or with LOH presented an mOS inferior to what is currently expected from historic data for metastatic LUAD, with a worse prognosis and shorter rwPFS1 for the subgroup of K EAP1/LOH, KEAP1/KRAS and KRAS/STK11. Surprisingly, the percentage of patients carrying concurrent mutations of interest was much higher in the analyzed population than previously described, emphasizing the importance of broad NGS panel testing, including STK11 and KEAP1 mutations. Our findings based on real-world data indicate that in addition to the already known STK11/KEAP1/KRASconcomitant mutations, KEAP1/LOH mutations define a new subset of hard-to-treat genetic alterations. These patients represent a subgroup associated with primary therapy resistance, highlighting a new unmet need for tailored therapeutic strategies. Furthermore, our data emphasizes the benefit of upfront panel sequencing, including STK11/KEAP1 mutations and LOH, to identify at-need patients.

CASTOR1 phosphorylation as a predictor of survival in male patients with KRAS-mutated lung adenocarcinoma.

e20015 Background: Lung cancer, a leading global cause of cancer-related mortality, necessitates enhanced prognostic markers for improved treatment outcomes. This study focuses on the predictive value of phosphorylated cytosolic arginine sensor for mTORC1 subunit 1 at S14 (pCASTOR1) in lung adenocarcinoma (LUAD) patients, specifically in males with KRAS mutations. Methods: This retrospective study, approved by University of Pittsburgh IRB, utilized formaline-fixed paraffin embedded primary tissues from two independent cohorts of patients who underwent thoracic surgical procedures at the University of Pittsburgh Medical Center (UPMC) from 2002 to 2011. Comprehensive clinical, demographical and pathological information was obtained from UPMC Cancer Registry, with cases lacking incomplete information excluded from analysis. Study endpoints included overall survival (OS) and relapse-free survival (RFS). An antibody targeting pCASTOR1 was employed to analyze LUAD tumor and adjacent non-tumor lung tissues from both cohorts. A pathologist, blinded to patient information and survival outcomes, conducted scoring in 5% increments. Scores were categorized as low or high pCASTOR1 based on second or third quartile. Correlations between pCASTOR1 scores and OS/RFS were examined, stratifying by clinical, pathological, demographic, or genotype data. Univariate OS and RFS analyses were conducted using the Kaplan-Meier method and log-rank test, while multivariate survival significance was assessed via Cox regression analysis. Additionally, unpaired T-tests were utilized to compare pCASTOR1 levels between non-tumor and tumor cells. A significance threshold of p < 0.05 was applied for all analyses. Results: Tumor cells exhibited significantly elevated pCASTOR1 scores compared to non-tumor cells in both cohorts (P < 0.05). High pCASTOR1 scores predicted poor OS (HR = 3.3, P = 0.0008) and RFS (HR = 3.0, P = 0.0035) in male patients with KRAS mutations in Cohort 1. pCASTOR1 remained an independent predictor for OS (HR = 4.1, P = 0.0047) and RFS (HR = 3.5, P = 0.0342) after controlling for other factors. Cohort 2, comprised solely of smokers with incomplete genotype information, validated these findings, with high pCASTOR1 scores correlating with worse OS (HR = 4.8, P = 0.0363). Notably, in early-stage LUAD, elevated pCASTOR1 scores were associated with significantly worse OS (HR = 3.3, P = 0.0176) and RFS (HR = 3.1, P = 0.0277) in male patients with KRAS mutations in Cohort 1, and worse OS (HR = 5.0, P = 0.0069) and RFS (HR = 5.0, P = 0.0069) in Cohort 2, akin to late-stage patients. Conclusions: Elevated pCASTOR1 score serves as a robust biomarker predicting poor OS and RFS in male LUAD patients with KRAS mutations, offering potential clinical utility in optimizing treatment strategies for this subgroup.

Implications of EGFR expression in MAPK dependency and adaptive immunity status of EGFR-mutated lung adenocarcinoma.

Implications of EGFR expression in MAPK dependency and adaptive immunity status of <i>EGFR</i>-mutated lung adenocarcinoma.

Gene expression correlates of adagrasib response in KRASG12C mutated non-small cell lung cancer (NSCLC).

8529 Background: KRASG12C inhibitors such as adagrasib and sotorasib have shown clinical promise in targeting KRASG12C-mutated lung cancers; however, most patients develop primary or secondary resistance. A biomarker of response to KRASG12C inhibitor is needed for better patient stratification and to understand the resistance mechanism. Methods: We analyzed transcriptional correlates of adagrasib treatment outcome in 68 patients in the KRYSTAL-1 trial, a phase 1/2 clinical trial of adagrasib monotherapy in the second line and beyond treatment for NSCLC. We also treated KRAS-mutated lung cancer mouse models and organoids with a KRAS inhibitor for the long term and characterized the resistant tumors’ transcriptional profile to identify resistance mechanisms. We also performed serial gene expression analysis of KrasG12D mutated lung organoids undergoing squamous transformation to identify transcription factor involved in the resistance process. Results: In patients with lung adenocarcinoma with KRASG12C and STK11/ LKB1 co-mutations, we find an enrichment of the squamous cell carcinoma gene signature in pre-treatment biopsies correlates with a poor response to adagrasib. Studies of Lkb1-deficient KRASG12C and KrasG12D lung cancer mouse models and organoids, treated with KRAS inhibitors adagrasib and MRTX1133, respectively, reveal that tumors invoke a lineage plasticity program, adeno-to-squamous transition (AST), that enables resistance to KRAS inhibition. We identify TP63 to be a transcription factor whose expression correlated with squamous transformation. The analysis of lineage plasticity program, adagrasib resistant tumors, and p63 regulon revealed KRT6A to be a common biomarker whose expression correlated with overall survival in the KRYSTAL-1 cohort. Conclusions: KRASG12C mutated lung adenocarcinoma patients with a higher expression of squamous cell carcinoma gene expression signature respond poorly to adagrasib treatment. Expression of the AST plasticity signature and KRT6A at baseline correlates with poor adagrasib responses. These data indicate the role of AST in KRAS inhibitor resistance and provide predictive biomarkers for KRAS-targeted therapies in lung cancer.

The clinicopathological features and possible physiological mechanisms of only the EGFR-T790M primary mutation in patients with lung adenocarcinoma

BackgroundThe treatment of non-small cell lung cancer (NSCLC) patients can be complicated by the presence of the EGFR-T790M mutation. Although primary or secondary EGFR-T790M mutations have been extensively studied worldwide, there are few reports on the clinicopathological characteristics and physiological mechanisms of lung adenocarcinoma (LUAD) with only the EGFR-T790M primary mutation. MethodsThe clinical data of all LUAD patients with only the EGFR-T790M primary mutation were collected. Immunohistochemical staining was performed on cell cycle-related proteins, targeted therapy indicators, and prognosis-related proteins in the specimens obtained from puncture biopsies or surgeries. ObjectivesThe aim of this study is to analyze the clinicopathological features and possible physiological mechanisms of only the EGFR-T790M primary mutation in LUAD, and to offer recommendations for clinical management. ResultsTwo patients who have only the T790M de novo mutation were both female (2/12,928, 0.02%). β-catenin and Cyclin D1 were both highly expressed. In case 1, IHC results showed a positive Ki67 and mutant P53 and there was a significant increase in serum CYFRA 21–1. Third-generation of EGFR TKIs resulted in a partial response (PR) time of less than 8 months in case 1. In case 2, the patient underwent surgical resection and adjuvant chemotherapy, resulting in a progression-free survival (PFS) time of 25 months. ConclusionThe results suggest that abnormal activation of the Wnt signaling pathway may be specifically associated with the EGFR-T790M primary mutation in LUAD. Furthermore, it has been observed that patients with significant Ki67, mutant P53, and CYFRA 21–1 expression tend to have a poor prognosis.

Ubiquitin-specific protease 54 regulates GLUT1-mediated aerobic glycolysis to inhibit lung adenocarcinoma progression by modifying p53 degradation.

Lung adenocarcinoma (LUAD) is one of the most prevalent types of cancer. Ubiquitination is crucial in modulating cell proliferation and aerobic glycolysis in cancer. The frequency of TP53 mutations in LUAD is approximately 50%. Currently, therapeutic targets for wild-type (WT) p53-expressing LUAD are limited. In the present study, we systemically explored the expression of ubiquitin-specific protease genes using public datasets. Then, we focused on ubiquitin-specific protease 54 (USP54), and explored its prognostic significance in LUAD patients using public datasets, analyses, and an independent cohort from our center. We found that the expression of USP54 was lower in LUAD tissues compared with that in the paracancerous tissues. Low USP54 expression levels were linked to a malignant phenotype and worse survival in patients with LUAD. The results of functional experiments revealed that up-regulation of USP54 suppressed LUAD cell proliferation in vivo and in vitro. USP54 directly interacted with p53 protein and the levels of ubiquitinated p53 were inversely related to USP54 levels, consistent with a role of USP54 in deubiquitinating p53 in p53-WT LUAD cells. Moreover, up-regulation of the USP54 expression inhibited aerobic glycolysis in LUAD cells. Importantly, we confirmed that USP54 inhibited aerobic glycolysis and the growth of tumor cells by a p53-mediated decrease in glucose transporter 1 (GLUT1) expression in p53-WT LUAD cells. Altogether, we determined a novel mechanism of survival in the p53-WT LUAD cells to endure the malnourished tumor microenvironment and provided insights into the role of USP54 in the adaptation of p53-WT LUAD cells to metabolic stress.

Prognostic value of combining clinical factors, 18F-FDG PET-based intensity, volumetric features, and deep learning predictor in patients with EGFR-mutated lung adenocarcinoma undergoing targeted therapies: a cross-scanner and temporal validation study.

To investigate the prognostic value of 18F-FDG PET-based intensity, volumetric features, and deep learning (DL) across different generations of PET scanners in patients with epidermal growth factor receptor (EGFR)-mutated lung adenocarcinoma receiving tyrosine kinase inhibitor (TKI) treatment. We retrospectively analyzed the pre-treatment 18F-FDG PET of 217 patients with advanced-stage lung adenocarcinoma and actionable EGFR mutations who received TKI as first-line treatment. Patients were separated into analog (n = 166) and digital (n = 51) PET cohorts. 18F-FDG PET-derived intensity, volumetric features, ResNet-50 DL of the primary tumor, and clinical variables were used to predict progression-free survival (PFS). Independent prognosticators were used to develop prediction model. Model was developed and validated in the analog and digital PET cohorts, respectively. In the analog PET cohort, female sex, stage IVB status, exon 19 deletion, SUVmax, metabolic tumor volume, and positive DL prediction independently predicted PFS. The model devised from these six prognosticators significantly predicted PFS in the analog (HR = 1.319, p < 0.001) and digital PET cohorts (HR = 1.284, p = 0.001). Our model provided incremental prognostic value to staging status (c-indices = 0.738 vs. 0.558 and 0.662 vs. 0.598 in the analog and digital PET cohorts, respectively). Our model also demonstrated a significant prognostic value for overall survival (HR = 1.198, p < 0.001, c-index = 0.708 and HR = 1.256, p = 0.021, c-index = 0.664 in the analog and digital PET cohorts, respectively). Combining 18F-FDG PET-based intensity, volumetric features, and DL with clinical variables may improve the survival stratification in patients with advanced EGFR-mutated lung adenocarcinoma receiving TKI treatment. Implementing the prediction model across different generations of PET scanners may be feasible and facilitate tailored therapeutic strategies for these patients.

DEP domain containing 1 as a biomarker for poor prognosis in lung adenocarcinoma

ObjectiveThe DEP domain-containing 1 (DEPDC1) gene is essential in the development and advancement of different types of cancer. This study is to examine the levels of DEPDC1 in lung adenocarcinoma (LUAD), and to determine its relationship with clinical results and immune response. The goal is to assess its potential as a biomarker and therapeutic target for LUAD. MethodsBy comprehensively utilizing the Cancer Genome Atlas (TCGA), gene Expression Synthesis (GEO), UALCAN, cBioPortal, TISIDB databases and online platforms, we conducted a bioinformatics analysis to investigate DEPDC1 gene survival analysis, prognostic diagnosis, prognostic survival, immune cell infiltration, DNA methylation, and the correlation of genetic mutations in LUAD. The results were validated through cell assay and immunohistochemical staining. ResultsDEPDC1 shows high levels of expression in the majority of tumors, with its expression being notably elevated in LUAD compablue to normal tissues. The expression of DEPDC1 varies based on the clinical characteristics of patients with LUAD. DEPDC1 expression affects the survival prognosis and prognostic model construction of LUAD patients. In addition, the presence of DEPDC1 is linked to immune infiltration. Various chemokines and chemokine receptors, immunoinhibitors and immune-stimulators in LUAD are significantly correlated with DEPDC1 methylation levels. Cell experiments confirmed through qPCR that the mRNA expression of DEPDC1 in LUAD was markedly elevated in comparison to the normal population, and immunohistochemistry showed positive DEPDC1 expression in LUAD pathological sections. ConclusionSystematic analysis and experiments have verified that DEPDC1 serves as a biomarker for detecting early, prediction of survival, and evaluation of immune cell infiltration in LUAD.

Genomic ancestry and cancer among Latin Americans

Latin American populations, characterized by intricate admixture patterns resulting from the intermingling of ancestries from European, Native American (NA) Asian, and African ancestries which result in a vast and complex genetic landscape, harboring unique combinations of novel variants. This genetic diversity not only poses challenges in traditional population genetics methods but also opens avenues for a deeper understanding of its implications in health. In cancer, the interplay between genetic ancestry, lifestyle factors, and healthcare disparities adds a layer of complexity to the varying incidence and mortality rates observed across different Latin American subpopulations. This complex interdependence has been unveiled through numerous studies, whether conducted on Latin American patients residing on the continent or abroad, revealing discernible differences in germline composition that influence divergent disease phenotypes such as higher incidence of Luminal B and Her2 breast tumors, EGFR and KRAS mutated lung adenocarcinomas in addition to an enrichment in BRCA1/2 pathogenic variants and a higher than expected prevalence of variants in colorectal cancer associated genes such as APC and MLH1. In prostate cancer novel risk variants have also been solely identified in Latin American populations. Due to the complexity of genetic divergence, inputs from each individual ancestry seem to carry independent contributions that interplay in the development of these complex disease phenotypes. By understanding these unique population characteristics, genomic ancestries hold a promising avenue for tailoring prognostic assessments and optimizing responses to oncological interventions.

4 Clinical and molecular characteristics of BRAF mutant Lung Adenocarcinomas

4 Clinical and molecular characteristics of BRAF mutant Lung Adenocarcinomas

Abstract 1746: KRAS mutant lung adenocarcinoma is associated with distinct mutational signature profiles

Abstract Background: Lung cancer is the 3rd most common cancer in the UK and leading cause of cancer mortality worldwide. Somatic RAS mutations are the most common oncogenes in human cancer, and KRAS mutations are the largest molecular subset of lung adenocarcinoma (LUAD). Each cancer genome accumulates a unique combination of somatic mutations, and these mutational signatures provide a genetic imprint of mutational processes that have occurred during tumorigenesis. Mutational signatures provide information on tumor aetiology/maintenance and could highlight potential therapeutic targets. This is the largest study to date to profile KRAS mutant LUAD mutational signatures using whole genome sequencing (WGS) data. Methods: Paired tumor and germline WGS data were obtained through the 100 000 Genomes Project (Genomics England). KRAS mutations were profiled using Ensembl Variant Effect Predictor (VEP) v109.0. Single base substitution (SBS), doublet base substitution (DBS), small insertion and deletions (ID) and copy number (CN) mutational signature extraction was performed using SigProfiler (COSMIC version 3.3). Statistical analysis and plotting were performed in R; a two-tailed p-value &amp;lt;0.05 was considered statistically significant. Results: 680 LUAD patients were included; 301 KRAS mutant (44%), 379 KRAS wild type (63%). Common KRAS variants were present, including G12C (38.9%), G12V (15.9%) and G12D (14.0%). 17 SBS, 9 DBS, 10 ID and 9 CN signatures were extracted and present in both KRAS mutant and wild type cohorts. KRAS mutant samples were enriched in smoking related signatures (SBS4, DBS2, ID3; odds (OR) ratio 5.54, 3.80, 4.97 respectively, p &amp;lt;0.001) and diploid CN signature (CN1, OR 1.41, p = 0.03). Conversely, KRAS mutant samples were less likely to have clocklike (ID5, OR 0.61, p = 0.012; ID8, OR 0.44, p &amp;lt;0.001), APOBEC (SBS2, OR 0.49, p &amp;lt;0.001; SBS13; 0.50, p &amp;lt;0.001), chromosomal instability (CN9, OR 0.63, p = 0.019), loss of heterozygosity (CN14, OR 0.47, p = 0.015), or homologous recombination deficiency (CN17, OR 0.58, p &amp;lt;0.001) signatures. Discussion: These results show distinct mutational signature profiles between KRAS mutant and wild type LUAD. As previously described, KRAS mutant LUAD is dominated by smoking related signatures; however, the majority of remaining signatures were more common in the KRAS wild type cohort where there was a statistically significant difference. This data suggests different mutational processes are observed in KRAS mutant compared to wild type LUAD. KRAS mutations are commonly clonal and thought to initiate tumorigenesis: timing signatures relative to KRAS mutations is necessary to further our understanding of KRAS cancer evolution and the subject of future work. Combined with clinical data integration, mutational signatures could provide prognostic information and inform predictive models. Citation Format: Laura Woodhouse, Aliah Hawari, Andreas Gruber, Colin Lindsay, David Wedge. KRAS mutant lung adenocarcinoma is associated with distinct mutational signature profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1746.

Abstract 4047: Unraveling synergistic therapeutic strategies involving FAK inhibition and immunotherapy using anti-PD1 antibody in KRAS and LKB1-driven lung cancer

Abstract Lung cancer presents a global health challenge demanding innovative preclinical models forresearch and therapeutic advancement. Genetically engineered mouse models (GEMMs) have seenremarkable growth in complexity and application over the past two decades. Our work leveragesthese models and is specifically designed to address the pressing need for effectiveimmunochemotherapies in the context of KRAS and LKB1 (KL) mutant lung adenocarcinoma,which shows resistance to most immunotherapies. Our study centers around a preclinicalsyngeneic orthotopic mouse model we developed using mouse lung and metastatic tumor cell linesderived from KL-GEMM. This model, optimized to mimic human lung cancer closely, providesan ideal platform for exploring the intricate interplay between the immune system and tumorprogression. Furthermore, we have previously shown the LKB1 mutant cell lines and tumormodels are uniquely sensitive to FAK inhibitors, and therefore we wanted to test whether thecombination of a FAK inhibitor with anti-PD1 therapy can improve sensitivity. The combinatoryadministration of FAK inhibitor (VS-6063) with anti-PD1 mAb synergistically increased anti-tumor response and survival outcome compared with single-agent therapy in the KL-mediatedsyngeneic orthotopic lung cancer model. By using GEMM-derived syngeneic cell lines, we haveevaluated the potential for creating innovative immunochemotherapies, customized for KL co-mutant lung adenocarcinomas with promising clinical potential. Furthermore, using this modelenables a deeper understanding of the KL mutant disease's pathogenesis, the impact of sex-biasedcancer development, and the assessment of novel immunochemotherapy treatment strategies in theKL genetic sub-type of lung adenocarcinoma. Citation Format: Junghui Koo, Carol Tucker-Burden, Melissa Roy, Chunzi Huang, Wei Zhou, Melissa Gilbert-Ross, Haian Fu, Suresh S. Ramalingam, Adam I. Marcus. Unraveling synergistic therapeutic strategies involving FAK inhibition and immunotherapy using anti-PD1 antibody in KRAS and LKB1-driven lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4047.

Abstract 1221: Selective translational activation of PBK (PDZ- binding kinase) reveals a molecular vulnerability of drug-tolerant persister cells to targeted therapies in EGFR-mutant lung adenocarcinoma

Abstract In lung adenocarcinoma (LUAD), EGFR-targeted therapies often result in incomplete tumor responses followed by disease progression caused by acquired resistance. As EGFR mutations are truncal (i.e., present in every cell of a tumor), it remains unclear why a fraction of tumor cells can survive in the presence of drug treatment. It is increasingly recognized that drug-tolerant persister cells (DTPCs) can escape selective drug pressure and are important drivers of therapy failure and tumor relapse. The mechanisms underlying tumor cell adaptation and survival of DTPCs during therapy are not fully understood.Using EGFR-mutant LUAD cell lines treated with osimertinib, we unexpectedly observed that DTPCs display uncoupled mRNA and protein variations of PBK (PDZ Binding Kinase), a spindle assembly serine/threonine protein kinase. Mechanistically we discovered that although global protein synthesis is decreased upon osimertinib treatment, PBK translation is selectively maintained in DTPCs.The establishment and survival of DTPCs following EGFR inhibition is critically dependent on PBK, as genetic depletion of PBK reduces persistence to osimertinib treatment in vitro. PBK knockout leads to suppression of ERK1/2 reactivation following EGFR inhibition, and results in decreased expression of ZEB1 and Vimentin, key effectors of epithelial-to-mesenchymal transition (EMT), a hallmark of the DTPC phenotype. Consistently, combined treatment with osimertinib and OTS514 (PBK inhibitor) in vitro, reduces the DTPC fraction and decreases the enrichment of EMT-related transcriptional signatures. Similar results were obtained in LUAD patient-derived organoids, used to recapitulate the phenotype of residual disease in patients. In PDX treated with osimertinib, PBK is activated at both residual disease and acquired resistance. Concordantly, combined EGFR/PBK pharmacological inhibition was also effective in reverting osimertinib acquired resistance in vitro. Finally, in matched diagnosis and relapse samples from 7 EGFR-mutant LUAD patients treated with EGFR inhibitors, we observed increased PBK activation at the time of acquired resistance in 5 cases, including 3 EGFRT790M-positive cases, suggesting that PBK activation may co-occur with genetic resistant alterations.Our findings unveil a novel mechanism by which EGFR-mutant lung cancer DTPCs selectively translate PBK mRNA as an adaptive survival mechanism to persist during osimertinib treatment; and provide a therapeutic target of non-genetic drug resistance otherwise unlooked-for in routine transcriptomic analyses. A deeper understanding on the mRNA translational reprogramming in DTPCs is currently performed to uncover therapeutic vulnerabilities to reduce residual disease and delay or revert the emergence of acquired resistance. Citation Format: Camille Leonce, Anne-Laure Désage, Nour El-Houda Mourksi, Geneviève De Souza, Béatrice Vanbervliet, Camille Charrondière, Constance Nicq, Jérémy Néri, Aurélie Swalduz, Laurie Tonon, Eric Cumunel, Nicolas Gadot, Gabriel Ichim, Jean-Jacques Diaz, Christine Lovly, Julien Mazières, Mayeul Tabutin, Maurice Pérol, Sylvie Lantuejoul, Olivier Calvayrac, Fabien Forest, Virginie Marcel, Pierre Saintigny, Sandra Ortiz-Cuaran. Selective translational activation of PBK (PDZ- binding kinase) reveals a molecular vulnerability of drug-tolerant persister cells to targeted therapies in EGFR-mutant lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1221.

Abstract 1153: Using spatial transcriptomics to dissect cell to cell cooperation in lung adenocarcinoma

Abstract Lung cancer is the second most common cancer in the United States and the leading cause of cancer related deaths in this country. Unfortunately, efficacious treatments for lung cancer remain suboptimal. Lung cancer is characterized by several distinct subtypes of which lung adenocarcinoma is the most common, comprising about 40% of this malignancy. The hallmark gene mutations of lung adenocarcinoma include TP53, RAS, and STK11. LKB1 is a serine-threonine kinase (coded by the gene STK11) that largely functions as a tumor suppressor, and is mutated in 20-30% of non-small cell lung cancers (NSCLCs). The diversity between and within lung cancer subtypes, as well as within a patient (i.e. metastases vs primary tumor), makes treating this cancer very challenging. Lung adenocarcinoma, in particular, has collective invasion packs of cells adjacent to the primary tumor that correlate with metastatic disease in mouse models. We hypothesize that the transcriptomic profile of the collective invasion packs in lung adenocarcinoma patients varies significantly from the adjacent primary tumor and represents a targetable metastatic sub-population. This work will help to identify specific cell signaling pathways that have the translational potential to develop novel therapeutics for metastatic disease, ultimately improving patient outcomes through precision medicine. Utilizing patient lung adenocarcinoma samples with KRAS and KRAS+LKB1 mutations, we identified regions of interest including bulk tumor and surrounding invasion packs. Then, using GeoMx digital spatial profiling technology (by Nanostring) and next-gen sequencing, we generated transcriptomic profiles from bulk tumor and invasion packs. Preliminary results indicate region specific transcriptomic differences, highlighting the heterogeneity of these cell populations. More specifically, collective invasion packs exhibit upregulation of gene networks involving immune cell differentiation, function, oxidative phosphorylation, tumor invasiveness, and mitochondrial structure. To discern the metastatic potential, transcriptomic profiles and biological functions will be compared between invasion packs, tumor bulk vs invasion packs, and finally, inter-patient differences. Successful completion of this project will characterize transcriptomes of metastatic lung cancer and has the potential to ultimately identify biomarkers of aggressive disease. Lastly, this foundational study will pave the way for future studies on the transcriptomic landscape of metastatic pediatric cancers and cancer predisposition syndromes. Citation Format: Raehannah Jamshidi, Lyra Griffiths, Rich Johnston, Vaunita Parihar, Frank Schneider, Adam Marcus. Using spatial transcriptomics to dissect cell to cell cooperation in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1153.

Abstract 2667: Mucin 5AC inhibition via intratracheal RNAi delivery as an effective alternative strategy for prevention and treatment of Kras mutant lung cancer

Abstract Lung cancer, including lung adenocarcinoma (LUAD), is the leading cause of cancer-related deaths in the United States. KRAS mutations are the most prevalent oncogenic driver alteration in human LUAD. We have previously shown that high expression of Mucin 5 AC (MUC5AC), a main airway secretory mucin, is significantly associated with poor prognosis. Mucins are essential for mucociliary clearance and the maintenance of airway homeostasis, however, their overproduction could negatively affect the lung immune microenvironment and has been shown to promote airway diseases such as chronic obstructive pulmonary disease (COPD) and lung cancer. Previously, we have shown that genetic deletion of MUC5AC in a murine model of K-ras mutant lung adenocarcinoma (KM-LUAD) impedes tumor development and reduces pro-tumor inflammatory and immune phenotypes. These findings indicate that MUC5AC is a potential druggable target against KM-LUAD. In this study, we sought a translational approach and inhibited MUC5AC in our K-rasG12D mutant mouse model of LUAD via RNA interference (RNAi). Six-week-old mice were given RNAi (5mg/kg) or vehicle (saline) via biweekly intratracheal administration for 8 weeks. This approach led to a significant decrease in tumor burden (40%) and a trending increase in total white blood cell counts, predominantly macrophages in the lung tumor microenvironment which was associated with phenotypic changes in macrophages characterized by reduced expression of Fizz1, and M2 pro-tumor macrophage marker. Additionally, RNAi-treated mice had reduced expression of Siglec-E, a mucin receptor and known inhibitor of the TLR4 endocytosis and promoter of NF-ĸB signaling, as well as a significant decrease in IL-6, a product of the NF-ĸB pathway and promoter of STAT3 signaling which we have previously shown to have an essential role in promotion of KM-LUAD. In summary, these findings elucidate a potential mechanism by which MUC5AC protects tumor cells from apoptosis and immune-mediated cytotoxic activity but also highlights how MUC5AC RNAi is an effective indirect preventive and therapeutic strategy in high-risk individuals (smokers with COPD) and patients with early stage KM-LUAD, respectively. Citation Format: Melvin Zarghooni, Maria T. Grimaldo, Avantika Krishna, Michael J. Clowers, Linda Phan, Yasmina H. Rezai, Arnav Gaitonde, Carlos Rodriguez Reyna, Walter Velasco Torrez, Erik Bush, Seyed Javad Moghaddam. Mucin 5AC inhibition via intratracheal RNAi delivery as an effective alternative strategy for prevention and treatment of Kras mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2667.

Abstract 5326: Selective deletion of estrogen receptor β in lung epithelium suppresses K-ras mutant lung tumorigenesis

Abstract Although lung cancer is the most prolific cause of global cancer-related deaths, outcomes by sex have gained traction as a means to stratify patients and tailor therapies accordingly. In recent years, females have begun to shoulder a greater burden of lung cancer diagnoses, specifically within the lung adenocarcinoma (LUAD) subtype; conversely, mortality is worsened for males. However, other sex-dependent effects in lung cancer are harder to predict. For example, hormone replacement therapy for post-menopausal women has been shown to predict better survival in some cohorts while auguring worse outcomes in others. Similar controversy exists regarding menopausal status, gender affirming care, and castration/oophorectomy status. However, there is consensus that these differential effects relate to a patient’s sex hormone composition. Estrogen, a sex hormone abounding in females, boasts well-described pro-tumor signaling in breast cancer. Unfortunately, its role in lung cancer remains elusive. Estrogen is reported to exert inflammatory properties in the lung environment, to drive immune function, and to induce proliferation of lung cancer cells. This functional antagonism has led to questions about how these compartment-specific effects are balanced. In the lung, estrogen signaling occurs mainly via estrogen receptor beta (ERβ), a nuclear hormone receptor highly expressed in lung tissue and lung tumors. ERβ is understudied relative to its sibling ERα, a well-known oncogene in breast cancer. While it is tempting to analogize ERα oncogene function to ERβ, the literature lacks consensus on the role of ERβ in lung cancer, with some authors classifying it as an oncogene and others as a tumor suppressor. In LUAD, Kras mutations encompass a quarter of driver mutations, and interaction of Kras with ERβ is understudied. Here, we tested the effects of genetic ablation of ERβ in a murine model of Kras mutant LUAD (KM-LUAD) termed CCSPCre/LSL-KrasG12D (CC-LR). Esr2 floxed mice were crossed with CC-LR mice to create a lung epithelial-specific conditional knockout of ERβ (LR/Esr2Δ/Δ). LR/Esr2Δ/Δ mice show significant decrease in tumor burden and total lung immune infiltration, indicating reduced tumor development and tumor-promoting inflammation. Of note, this effect manifests regardless of sex. RNA and protein-level analysis further suggest that ERβ deletion alters the balance of inflammatory transcription factors, resulting in skewing from STAT3- to NF-κB-driven inflammation and a net anti-tumor response. These data suggest that ERβ offers a promising early target in nascent KM-LUAD tumors with therapeutic intervention possible regardless of sex-specific effects. Acknowledgement: supported by NIH/NCI grant awarded to Seyed Javad Moghaddam (R01 CA225977); Michael J Clowers partly supported by NIH/NCI (F31 CA261121); Annamarie L Thompson supported by CPRIT Research Training Award (RP210028). Citation Format: Michael Joseph Clowers, Annamarie L. Thompson, Carlos Ignacio Rodriguez Reyna, Shanshan Deng, Seyed Javad Moghaddam. Selective deletion of estrogen receptor β in lung epithelium suppresses K-ras mutant lung tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5326.

Abstract 4048: Comparative effects of SOS1 inhibitor with IL-6 blockade and their combination on Kras mutant lung cancer

Abstract Despite recent advances in treatment, lung adenocarcinoma (LUAD), particularly harboring Kras mutations, is still the leading cause of cancer mortality. We and others have previously shown that Kras mutant LUAD development and progression is associated with intrinsic inflammatory characteristics driven by epithelial NF-κB activation, increased levels of IL-6 (which is transcriptionally regulated by NF-κB), and activation of the IL-6-responsive transcription factor STAT3. We further demonstrated that IL-6 blockade suppresses lung tumorigenesis by reducing tumor-associated immunosuppressive myeloid populations and induction of a T cell-mediated anti-tumor response. The recent discovery of a novel SOS1-targeting compound (BI-3406) that selectively inhibits the KRAS-SOS1 interaction and leads to anti-proliferative activity has opened up the possibility to more efficiently inhibit Kras mutant lung cancer. Accordingly, in this study we used a mouse model of KRAS mutant LUAD (CC-LR) to compare the therapeutic effects of BI-3406, IL-6 blockade, and MEK inhibitor (trametinib). We also tested whether inhibiting IL-6 driven pro-tumor immune response would provide a synergistic/additive response and increase the tumor inhibitory effect of either BI-3406 or Trametinib. Eight cohorts of 14-week-old female mice were treated with either anti-IL-6 antibody, trametinib, or BI-3406, or their combinations for 4 weeks, and their tumor burden was compared at the end of study. We observed a significant reduction in tumor multiplicity and tumor area in response to all monotherapies, with the highest effect in the trametinib treated cohort. Neither combination therapy led to decreased tumor burden over either of the monotherapy regimens in our model. However, we observed an increase in T helper 1 and CD8 T expressing IFNγ cell populations in the cohort treated with Trametinib and anti-IL-6 Ab combination. In addition, using qPCR analysis of RNA extracted from the whole lung we found a higher expression of IFNγ along with a reduced expression of IL-10 in the cohort treated with BI-3406 and anti-IL-6 Ab combination. This suggests that these combinations may have the potential to improve the anti-tumor immune responses. Hence, we conclude that further adjustment of the treatment regimen (doses, interval, duration) may allow to obtain improved anti-tumor efficacy with these combinations. Overall, this study provides a new research perspective for the improvement of currently available treatment modalities for patients with Kras mutant lung cancer that could be further explored preclinically. Citation Format: Katherine E. Larsen, Maria J. Arredondo Sancristobal, Melody Zarghooni, Avantika Krishna, Maria T. Grimaldo, Nastaran Karimi, Arnav Gaitonde, Michael J. Clowers, Seyed Javad Moghaddam. Comparative effects of SOS1 inhibitor with IL-6 blockade and their combination on Kras mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4048.