Subtype Of Lung Cancer Research Articles

Demographic bias in misdiagnosis by computational pathology models.

Despite increasing numbers of regulatory approvals, deep learning-based computational pathology systems often overlook the impact of demographic factors on performance, potentially leading to biases. This concern is all the more important as computational pathology has leveraged large public datasets that underrepresent certain demographic groups. Using publicly available data from The Cancer Genome Atlas and the EBRAINS brain tumor atlas, as well as internal patient data, we show that whole-slide image classification models display marked performance disparities across different demographic groups when used to subtype breast and lung carcinomas and to predict IDH1 mutations in gliomas. For example, when using common modeling approaches, we observed performance gaps (in area under the receiver operating characteristic curve) between white and Black patients of 3.0% for breast cancer subtyping, 10.9% for lung cancer subtyping and 16.0% for IDH1 mutation prediction in gliomas. We found that richer feature representations obtained from self-supervised vision foundation models reduce performance variations between groups. These representations provide improvements upon weaker models even when those weaker models are combined with state-of-the-art bias mitigation strategies and modeling choices. Nevertheless, self-supervised vision foundation models do not fully eliminate these discrepancies, highlighting the continuing need for bias mitigation efforts in computational pathology. Finally, we demonstrate that our results extend to other demographic factors beyond patient race. Given these findings, we encourage regulatory and policy agencies to integrate demographic-stratified evaluation into their assessment guidelines.

IBPGNET: lung adenocarcinoma recurrence prediction based on neural network interpretability.

Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer. Early-stage patients have a 30-50% probability of metastatic recurrence after surgical treatment. Here, we propose a new computational framework, Interpretable Biological Pathway Graph Neural Networks (IBPGNET), based on pathway hierarchy relationships to predict LUAD recurrence and explore the internal regulatory mechanisms of LUAD. IBPGNET can integrate different omics data efficiently and provide global interpretability. In addition, our experimental results show that IBPGNET outperforms other classification methods in 5-fold cross-validation. IBPGNET identified PSMC1 and PSMD11 as genes associated with LUAD recurrence, and their expression levels were significantly higher in LUAD cells than in normal cells. The knockdown of PSMC1 and PSMD11 in LUAD cells increased their sensitivity to afatinib and decreased cell migration, invasion and proliferation. In addition, the cells showed significantly lower EGFR expression, indicating that PSMC1 and PSMD11 may mediate therapeutic sensitivity through EGFR expression.

Construction of a prognostic model with CAFs for predicting the prognosis and immunotherapeutic response of lung squamous cell carcinoma.

Lung squamous cell carcinoma (LUSC) is one of the subtypes of lung cancer (LC) that contributes to approximately 25%-30% of its prevalence. Cancer-associated fibroblasts (CAFs) are key cellular components of the TME, and the large number of CAFs in tumour tissues creates a favourable environment for tumour development. However, the function of CAFs in the LUSC is complex and uncertain. First, we processed the scRNA-seq data and classified distinct types of CAFs. We also identified prognostic CAFRGs using univariate Cox analysis and conducted survival analysis. Additionally, we assessed immune cell infiltration in CAF clusters using ssGSEA. We developed a model with a significant prognostic correlation and verified the prognostic model. Furthermore, we explored the immune landscape of LUSC and further investigated the correlation between malignant features and LUSC. We identified CAFs and classified them into three categories: iCAFs, mCAFs and apCAFs. The survival analysis showed a significant correlation between apCAFs and iCAFs and LUSC patient prognosis. Kaplan-Meier analysis showed that patients in CAF cluster C showed a better survival probability compared to clusters A and B. In addition, we identified nine significant prognostic CAFRGs (CLDN1, TMX4, ALPL, PTX3, BHLHE40, TNFRSF12A, VKORC1, CST3 and ADD3) and subsequently employed multivariate Cox analysis to develop a signature and validate the model. Lastly, the correlation between CAFRG and malignant features indicates the potential role of CAFRG in promoting tumour angiogenesis, EMT and cell cycle alterations. We constructed a CAF prognostic signature for identifying potential prognostic CAFRGs and predicting the prognosis and immunotherapeutic response for LUSC. Our study may provide a more accurate prognostic assessment and immunotherapy targeting strategies for LUSC.

Abstract 2151: Additional impact of genetic ancestry over self-reported race/ethnicity to prevalence of KRAS mutations and allele-specific subtypes in non-small cell lung cancer

Abstract Background: KRAS mutation is the most common oncogenic driver in patients with non-small cell lung cancer (NSCLC). However, the interplay between self-reported race and/or ethnicity (SIRE) and genetically inferred ancestry (GIA) on KRAS mutations and allele-specific subtypes is largely unknown. Methods: A total of 3918 NSCLC patients from the Chinese OrigiMed (OM) cohort (n=2039) and Boston Lung Cancer Survival (BLCS) cohort (n=1879) were included, all of whom had baseline covariates including age, sex, clinical stage, SIRE, histology and smoking status. KRAS mutation and subtypes were determined by targeted NGS panels in each cohort, and KRAS mutation outcomes, including KRAS mutation, KRAS subtypes, and KRAS transversion and transition were analyzed. GIA was inferred from paired germline data for patients in the BLCS cohort. Multivariable and multinomial logistic regressions were employed to assess the associations between SIRE, GIA and KRAS outcomes. Results: In the entire cohort, 804 (20.5%) patients harbored KRAS mutation, with a considerably higher prevalence of 31.5% observed in BLCS compared to 10.4% in OM cohort. Patients with self-identified Asian was associated with a significantly lower rate of KRAS mutation (OR = 0.44, 95% CI:0.22 - 0.81, P = 0.01), transversion substitutions (OR = 0.24, 95% CI:0.10 - 0.62, P = 0.003) and KRASG12C (OR = 0.17, 95% CI:0.04 - 0.72, P = 0.02) compared to SIRE-White patients after adjusting for confounders including smoking status, sex and histology. The association of SIRE and KRAS driver mutation was further modified by sex, with Asian women demonstrating lower risk compared to Asian men, while the opposite trend was observed in SIRE-White patients. Increased European ancestry was associated with a higher risk of KRAS mutation (OR per 10% increase = 1.05, 95% CI:1.00 - 1.09, P = 0.03), particularly with more transition substitutions (OR per 10% increase = 1.10, 95% CI:1.01 - 1.21, P = 0.03) and KRASG12D (OR per 10% increase = 1.18, 95% CI:1.04 - 1.34, P = 0.01). This association was even more pronounced in patients of increased Northern European ancestry. Furthermore, even among SIRE-White patients, a 10% increase in European ancestry was associated with an additional 6% increase in the likelihood of KRAS mutations (OR = 1.06, 95% CI: 1.01 - 1.12, P = 0.03), while a 10% increase in Admixed American ancestry was associated with a 6% decreased likelihood of KRAS mutations (OR = 0.94, 95% CI: 0.88 - 0.99, P = 0.04). Results were validated in an independent cohort of 1450 patients. Conclusion: Self-reported race/ethnicity and genetic ancestry are both associated with KRAS driver mutations and allele-specific subtypes of NSCLC. This work highlights the significance of integrating both into population-based cancer research, aiming to refine clinical decision-making processes and mitigate health disparities. Citation Format: Xinan Wang, Kangcheng Hou, Biagio Ricciuti, Joao V. Alessi, Xihao Li, Federica Pecci, Rounak Dey, Jia Luo, Mark M. Awad, Alexander Gusev, Xihong Lin, Bruce E. Johnson, David C. Christiani. Additional impact of genetic ancestry over self-reported race/ethnicity to prevalence of KRAS mutations and allele-specific subtypes in non-small cell 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 2151.

Abstract 7567: In-depth mass cytometry analysis reveals different immune cell composition of unique molecular subtypes in extensive stage small-cell lung cancer

Abstract Background: A novel molecular subtype classification was fashionable for small cell lung cancer (SCLC). However, the distribution of SCLC molecular subtype classification in Chinese patients were unknown, especially extensive stage (ES)-SCLC. It should validate and define their associated microenvironments across subtypes in ES-SCLC. Method: We used immunohistochemical (IHC) to evaluate SCLC markers of the subtypes including ASCL1, NEUROD1, POU2F3, SCLC-A/N/P in 135 ES-SCLC tumors. Peripheral blood of 24 ES-SCLC patients was test by mass cytometry using time-of-flight (CyTOF) to evaluate the differences in immune subsets regard to the subtype tumor microenvironment (TME). Validation was performed using flow cytometry and multiplex IF. Results: ASCL1, NEUROD1, POU2F3, and Inflamed were account for 60.7%, 28.9%, 7.4%, and 18.5% of SCLC tumors, respectively. Significant intratumoral heterogeneity was observed with 15.6% of the tumors being both positive for SCLC-A and -N subtype markers, respectively. The SCLC-I type possessed more CD8+ T-cells infiltration and had higher frequency an ‘inflamed’ immunophenotyped. CyTOF data showed greater CD161+CD127+CD8+T cells proportion in SCLC-I than SCLC-N subtypes before and after anti-immunotherapy. Furthermore, we validated that lung tissue of SCLC-I were infiltrated more CD161+CD127+CD8+T cells compared to SCLC-N subpopulation(P=0.0281). Flow cytometry further showed the stronger immune activation of CD161+CD127+CD8+T cells in SCLC-I types induced higher expression of GZMB and GNLY and lower-expression of T-cell exhaustion markers PD-1,TIGIT and LAG3 in comparison with SCLC-N types. We further confirmed that the high level of CD161+CD127+CD8+T associated with a favorable treatment response and prolonged overall survival. Conclusion: The present study validated the molecular subtypes in ES-SCLC patients. Furthermore, SCLC-I subtype has longer PFS and OS than SCLC-A, -N and -P patients. Our research not only provides an insight into the immune landscape of ES-SCLC but also sheds light on a special subset of CD161+CD127+CD8+T cells with prognostic and therapeutic significance. Citation Format: Yuekang Li, Jingjing Qu, Binggen Wu, Qian Shen, Wenjia Sun, Lijun Chen, Bo Wang, Lixiong Ying, Jianya Zhou, Jianying Zhou. In-depth mass cytometry analysis reveals different immune cell composition of unique molecular subtypes in extensive stage small-cell 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 7567.

Abstract 7088: MALDI-IHC high-plex protein biomarker imaging for fast, non-iterative identification of lung carcinoma subtypes

Abstract Lung cancer is the second most common cancer worldwide, with over 2.2 million new cases in 2020 and is the leading cause of cancer-related deaths worldwide. Most lung cancer (80-85%) is non-small cell (NSCLC), comprising mostly adenocarcinoma and squamous cell carcinoma, while roughly 10-15% of lung cancer is small cell lung cancer (SCLC), also termed neuroendocrine lung cancer. Subtype identification is critical for determining treatment, and with limited samples, it is critical to get the most data possible from each tissue section. NSCLC subtypes can be treated with chemotherapy or targeted drugs, whereas SCLC tends to respond best to a combination of chemotherapy and radiation. While there have been many improvements in the detection and treatment of lung carcinoma, the immuno-histochemical (IHC) confirmation of subtype remains a prolonged and often iterative process. To overcome this limitation, we have developed a new IHC approach which uses antibodies labeled with novel photocleavable mass-tags combined with matrix assisted laser desorption ionization (MALDI) mass spectrometry imaging. The approach, termed MALDI-IHC, provides fast (1 hr/cm2 imaging time) and highly multiplexed IHC (100+-plex) without the need for iterative cycling procedures. Here, we present a 20+-plex panel for the determination of subtype in lung cancer. An antibody panel comprised of established clinical biomarkers was developed to differentiate between the lung carcinoma subtypes and provide potentially prognostic information. This included markers for adenocarcinoma (TTF-1, Napsin A), squamous cell carcinoma (p40, CK5), and small cell lung cancer (CD56, Chromogranin A and Synaptophysin), as well as general carcinoma markers for t cells, b cells, macrophages, and fibroblasts These markers were first validated individually by immunofluorescence and then compared to MALDI-IHC on annotated tissues. Here we present an overview of the antibody validation for the 20+-plex lung carcinoma panel. Biomarker presence and peak signal intensity for the various subtypes was then determined using pathologist classified tissues for normal lung, adenocarcinoma, squamous cell carcinoma and small cell lung cancer. We report application of the MALDI-IHC approach to the simultaneous determination of lung carcinoma subtypes on a 99-core human lung tissue microarray (TMA) comprised of normal, normal adjacent, cancer adjacent, and cancerous tissues. Moreover, because MALDI-IHC is a non-destructive process, it can be followed by conventional H&E staining on the same tissue section for accurate co-registration of traditional pathology annotations with the highly multiplexed MALDI-IHC results. In the future, even larger, 100+-plex antibody panels can be used for precision medicine on a wide range of cancers, in order to determine the molecular subtypes and guide treatment paths. Citation Format: Catherine A. Kita, Kristina Schwamborn, Gargey Yagnik, Kenneth J. Rothschild, Mark J. Lim. MALDI-IHC high-plex protein biomarker imaging for fast, non-iterative identification of lung carcinoma subtypes [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 7088.

Abstract 4433: Secondary electrospray ionization mass spectrometry for volatile analysis of lung cancer

Abstract Lung cancer remains a leading cause of cancer-related mortality globally, necessitating innovative approaches for early detection and improved understanding of its metabolic landscape and consequences. Secondary Electrospray Ionization Mass Spectrometry (SESI-MS), an innovative analytical technique, has emerged as a powerful tool for the analysis of volatile organic compounds (VOCs) associated with various diseases, from metabolic disorders to bacterial infections. In this proof-of-concept study, we first utilized SESI-MS analyses of four representative lung cancer cells of both non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) to demonstrate its capability to profile VOCs released by lung cancer cells. The technique allows for real-time, non-invasive analysis of the headspace above cultured cells, enabling the detection of unique VOC signatures associated with different lung cancer subtypes. Meanwhile, SESI-MS also facilitated the discrimination specific cells based on distinct VOC patterns. Furthermore, we also performed cisplatin treatment experiments and observed the metabolic signature shift post drug treatment. These results collectively offered potential applications in early diagnosis and personalized treatment strategies. Next, we continued with in vivo investigations to further extend the utility of SESI-MS in lung cancer research. Animal models, mimicking human lung cancer pathophysiology, have been subjected to SESI-MS analysis to identify volatile biomarkers indicative of tumor development and progression. Several representative cancer drug treatments were performed to the lung cancer mice model, and the drug-induced responses were also monitored via SESI-MS breath analyses. The in vivo SESI-MS approach detected many interesting breath VOC features that could provide valuable insights into the dynamic changes in VOC profiles during various stages of lung cancer, and therefore has the potential to offer a deeper understanding of the disease's metabolic alterations and potential avenues for targeted therapeutic interventions. In conclusion, SESI-MS-based volatile analysis presents a robust and versatile approach for investigating lung cancer, and our ongoing work has the potential to bridge the gap between in vitro and in vivo models for better translational research outcomes. The detection of unique VOC signatures associated with lung cancer cells and tumors holds significant promise for early detection, subtype classification, and monitoring of treatment responses. As technology continues to advance, SESI-MS stands poised to play a pivotal role in transforming the landscape of lung cancer diagnostics and research. Citation Format: Jiangjiang (Chris) Zhu, Fouad Choueiry. Secondary electrospray ionization mass spectrometry for volatile analysis of 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 4433.

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 1463: Characterizing inflammation-induced epigenetic and transcriptomic alterations driving NSCLC using lung organoid models

Abstract Chronic inflammation is a major driver of lung cancer and contributes to its pathogenesis by inducing genetic and epigenetic alterations. These, in turn, modulate the microenvironment to facilitate emergence of tumor promoting immune evasive mechanisms. The evolution of epigenetic events and their role, both alone, and in association with lung cancer specific genetic drivers in initiation of lung cancer is not well delineated. Specific pathological subtypes of non-small cell lung cancer (NSCLC) have distinct cells of origin, suggestive of cell type-specific changes in driving their development. We employed lung organoid models with chronic exposure to cigarette smoke condensate (CSC) to elucidate sequential, cell type-specific epigenetic and transcriptomic alterations and their role in co-operating with genetic events to drive development of NSCLC. We examined epigenomic and transcriptomic alterations over a 6-month exposure period by DNA methylation arrays, ATAC-seq, and RNA-seq. We observe that CSC exposure causes distinct morphological changes in organoid structure and composition, accompanied by an increase in proliferative potential. Using flow cytometry and immunofluorescent staining approaches, we demonstrate a chronic inflammation-driven shift in stem cell populations accompanied by reduction in differentiated cell types. Bulk and single-cell RNA sequencing approaches identified distinct temporal changes in transcriptional signatures in CSC exposed organoids suggestive of evolution of an immune evasive and pro-tumorigenic phenotype. Gene set enrichment analysis revealed a downregulation of interferon signaling and upregulation of Myc targets and oxidative phosphorylation pathways in CSC treated organoids. Notably, co-culturing organoids with key immune cell populations, demonstrate the ability of the CSC exposed organoids to modulate shifts in immune cells from a pro- to anti- inflammatory state. In accordance with this shift in immune cell phenotype, CSC treated organoids secreted decreased levels of pro-inflammatory cytokines as measured by multiplex ELISA assays. Genome wide DNA methylation analysis reveal that CSC methylated genes were associated with differentiation and cell fate commitment as well as transcription factor activity. Finally, we demonstrate that introduction of key NSCLC-specific driver events at the 6-month time point sensitize only CSC treated organoids to tumor formation in vivo, leading to the development of distinct genetic driver-specific subtypes of NSCLC. Altogether, our results demonstrate the ability of chronic inflammation to drive key cell type-specific transcriptomic and epigenetic changes leading to the development of distinct subtypes of NSCLC. Our findings will help identify molecular correlates for early detection and aid development of novel therapeutic strategies for disease interception. Citation Format: Na Wang, Kara Lombardo, Raksha Padaki, Ray-Whay Chiu Yen, Malcolm V. Brock, Leslie Cope, Hariharan Easwaran, Stephen B. Baylin, Michelle Vaz. Characterizing inflammation-induced epigenetic and transcriptomic alterations driving NSCLC using lung organoid models [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 1463.

Abstract 3817: Real-world clinical outcomes in patients with advanced ROS1+non-small cell lung cancer in the US

Abstract Introduction: ROS1 rearrangements define a rare molecular subtype of non-small cell lung cancer (NSCLC), occurring in 1-2% of patients (pts) with advanced NSCLC (aNSCLC). Crizotinib and entrectinib received US approval for ROS1+ aNSCLC in March 2016 and August 2019, respectively. Few studies have addressed temporal trends in first-line (1L) utilization since these drugs’ approval. This study describes treatment patterns and clinical outcomes in pts with ROS1+ aNSCLC in the US. Methods: This retrospective study used the nationwide Flatiron Health (FH) electronic health record-derived de-identified database and included adult pts with ROS1+ aNSCLC who received 1L (index) therapy between March 2015 and December 2022. Pts were followed until March 31, 2023, and had ≥ 3 months of follow-up post-index date. Treatment-related (sequence, time to treatment discontinuation [TTD], time to next treatment [TTNT]) and clinical (real-world progression-free survival [rwPFS], overall survival [OS]) outcomes of 1L therapy were assessed using descriptive statistics and Kaplan-Meier methods. Results: In the FH database, 87,784 pts had aNSCLC, and 242 were ROS1+. The median age was 65 years; most were female (64%), White (67%), non-squamous (91%) and had a history of smoking (52%), with most pts having ECOG performance status 0 (31%) or 1 (35%). 19% had brain metastases prior to or up to 30 days post-index. Median follow-up time was 14.2 months. In 1L treatment, only 59% received ROS1-sensitive TKI monotherapy (i.e. crizotinib, entrectinib, ceritinib), with 97 (40%) and 40 (17%) treated with crizotinib and entrectinib monotherapy, respectively. Median TTD and TTNT for 1L was 6.4 (95% CI: 5.0, 7.6) and 7.6 (95% CI: 6.5, 9.4) months, respectively. Among 1L crizotinib pts, 51% had 2L treatments and 57% of those initiated another ROS1-sensitive TKI (16% entrectinib). Among 1L entrectinib pts, 43% had 2L therapy; of these, 82% initiated another ROS1-sensitive TKI. Median rwPFS was 7.5 (95% CI: 6.2, 9.3) months (1L crizotinib, 8.6 [95% CI: 5.3, 13.0] months; 1L entrectinib, 8.0 [95% CI: 5.3, 13.6] months). Median OS was 29.0 (95% CI: 19.4, 35.9) months (1L crizotinib, 31 [95% CI: 19.4, not estimable [NE]] months; 1L entrectinib, NE). Patients initiated ROS1-sensitive TKIs (crizotinib, entrectinib or ceritinib) in 1L across each year of the study (2015: 67%, 2016: 58%, 2017: 51%, 2018: 47%, 2019: 63%, 2020: 81%, 2021: 52%, 2022: 68%). Overall, 5% received checkpoint-inhibitor (CPI) only, 17% chemotherapy alone, and 7% a chemotherapy/CPI combination. Conclusion: Compared to relevant clinical trials, ROS1+ aNSCLC pts in this real-world study were older, had greater smoking exposure, and worse overall survival. Only 59% of pts initiated 1L ROS1-sensitive TKI monotherapy. These results highlight potential disparities in the diagnosis and treatment of ROS1+ NSCLC and opportunities for improving clinical outcomes. Citation Format: Reginald Villacorta, Saurabh Ray, Yong Yuan, Sushupta Vijapur, Sonia Kim, Haiyan Sun, Sky Myers, Vincent Lam. Real-world clinical outcomes in patients with advanced ROS1+non-small cell lung cancer in the US [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 3817.

Abstract 2529: Comparison of small cell lung cancer transcriptional factor expression by immunohistochemistry, multiplex immunofluorescence, and a targeted RNA expression panel

Abstract Recent studies have identified distinct molecular subtypes of small cell lung cancer (SCLC) (SCLC-A, SCLC-N, SCLC-P, and SCLC-Y) based on ASCL1, NEUROD1, POU2F3, and YAP1 expression. In this study, we investigated the correlation between immunohistochemistry (IHC), multiplex immunofluorescence (mIF), and RNA Salah Targeted Expression Panel (RNA STEP) for ASCL1, NEUROD1, POU2F3, and YAP1 in formalin-fixed-paraffin-embedded (FFPE) samples from 14 SCLC samples collected under an IRB-approved protocol (MCC19163). For the mIF evaluation, FFPE samples were immunostained using the AKOYA Biosciences OPAL TM 7-Color Automation IHC kit on the BOND RX autostainer. For RNA STEP, nanoString nCounter TagSet chemistry was used to measure gene expression levels of test FFPE samples relative to a reference pooled human normal mRNA control. All three methods demonstrated significant correlation for ASCL1 levels (Table 1). IHC and RNA STEP NEUROD1 results exhibited significant correlation. However, mIF NEUROD1 results did not correlate with the results of other methods likely due to non-specific positivity of the NEUROD1 mIF antibody. No strong correlation was observed between any of the methods for POU2F3 and YAP1. Only 2 of the 14 samples displayed positive POU2F3 protein expression by IHC; one of these also had elevated POU2F3 expression by RNA STEP. Importantly, the sample with the highest POU2F3 protein expression by IHC also had the highest values by mIF and RNA STEP. All samples were negative for YAP1 by IHC and RNA STEP. Notably, ASCL1 staining was primarily observed in CD56+ POU2F3- cells by mIF. These findings highlight the reliability and utility of IHC and RNA STEP in assessing transcriptional factors in SCLC. Also, mIF presents an innovative method for the simultaneous analysis of multiple markers using a single tissue section, enabling the concurrent detection of multiple markers within individual cells. Table 1. Statistical Significance (p-values) and Correlation Analysis (Spearman's Coefficients) IHC vs RNA STEP IHC vs mIF RNA STEP vs mIF p r P r p r ASCL1 0.021 0.62 <0.0001 0.91 0.010 0.67 NEUROD1 0.002 0.78 0.517 -0.14 0.671 0.12 POU2F3 0.201 0.36 0.422 0.18 0.045 0.55 YAP1 0.299 0.30 0.364 0.20 0.295 0.30 Citation Format: Hilal Ozakinci, Aileen Alontaga, Jonathan V Nguyen, Carlos M Moran Segura, Daryoush Saeed-Vafa, Jhanelle Gray, Eric Haura, Alberto A Chiappori, Theresa Boyle. Comparison of small cell lung cancer transcriptional factor expression by immunohistochemistry, multiplex immunofluorescence, and a targeted RNA expression panel [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 2529.

Abstract 3261: Improving targeted therapy in female patients with lung squamous cell carcinoma

Abstract Non-small cell lung cancer (NSCLC) will claim the lives of ~60,000 female patients in the US in 2023. Lung squamous cell carcinoma (LUSC) is a subtype of Non-Small Cell Lung Cancer (NSCLC) that comprises ~30% of NSCLC and is characterized by high metabolic activity. Specifically, LUSC typically exhibits elevated rates of both glucose and glutamine metabolism driven by the PI3K-AKT-mTOR and KEAP1/NRF2 pathways. Further, a paucity of identifiable genetic drivers in LUSC has resulted in a lack of effective targeted therapies for patients with this devastating disease. Despite recent advances in therapy, the 5-year survival rate for patients with advanced NSCLC is 6%, underscoring the need for better treatment options. Importantly, no significant sex bias is seen in the newly diagnosed cases of lung cancer (~50%M/~50%F) (American Cancer Society, 2023), yet there are no sex-specific therapeutic approaches in clinical use. We demonstrated that the catalytic mTOR kinase inhibitor TAK228 can be utilized to effectively treat LUSC tumors via inhibition of glycolysis, an approach that is currently being evaluated on two phase I/II clinical trials (NCT02417701, NCT04250545), launched as a direct result of our pre-clinical work. However, our pre-clinical data suggests that despite the potential benefit of TAK228 inhibition in LUSC, a subset of tumors are resistant to TAK228 despite on-target activity of mTOR inhibitor, leading to the rationale of the current hypothesis, namely the possibility that sex-specific differential effects of TAK228 may exist. To evaluate this hypothesis, we have generated preliminary data demonstrating that sex is a determinant of TAK228 response in LUSCs, whereby male mice are significantly more sensitive to mTOR inhibition than females. Follow-on experiments have demonstrated that the anti-estrogen therapy (Letrozole) sensitized previously resistant female mice bearing LUSCs to TAK228, suggesting an estrogen-related link to TAK228 resistance in females. Additionally, RNASeq and biochemical analyses identified pathways that are upregulated in TAK228 resistant female mice with LUSC tumors. These results suggest that the estrogen may play a key role in the observed pattern of female resistance to mTOR inhibition. As such, the goal of the current proposal is to evaluate the catalytic mTOR kinase inhibitor TAK228, in combination with anti-estrogen therapy as a therapeutic strategy to treat LUSC in females. Citation Format: Milica Momcilovic, David Shackelford. Improving targeted therapy in female patients with lung squamous cell carcinoma [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 3261.

Abstract 4312: KRAS oncogenic activation in Gramd2 + AT1 cells form lung adenocarcinoma with distinct transcriptomic and tumor microenvironment signatures

Abstract Lung adenocarcinoma (LUAD) is the most prevalent subtype of lung cancer and presents with a high degree of biological heterogeneity and distinct clinical outcomes. The current paradigm of LUAD etiology recognizes alveolar epithelial type II (AT2) cells as the primary cell of origin, while the role of AT1 cells in LUAD oncogenesis remains relatively unknown. Here, we examined transformation via activation of the oncogenic KRASG12D mutation in a Gram-domain containing 2 (Gramd2)+ AT1 cell lineage tracing model system, which resulted in multifocal LUAD, primarily of papillary histology. Spatial transcriptomic sequencing revealed significant differences of transcriptomic signatures and signaling activities between Gramd2+ AT1 cell-derived and Sftpc+ AT2 cell-derived LUAD. Single-cell RNA sequencing of macrodissected LUAD lesions demonstrated heterogeneous cell composition of the tumor microenvironment (TME), with Gramd2+ AT1 cell-derived LUAD fostering a proinflammatory, immunoreactive TME and Sftpc+ AT2-derived LUAD presenting with an immunosuppressive TME. Collectively, our study suggests that cell of origin for LUAD is associated with histologic subtype, transcriptomic aberrations, and immune cell composition within LUAD that may influence response to therapy. Citation Format: Minxiao Yang, Jonathan Castillo, Edgar Gonzalez, Chunli Yan, Evanthia Roussos Torres, Zea Borok, Crystal Marconett. KRAS oncogenic activation in Gramd2 + AT1 cells form lung adenocarcinoma with distinct transcriptomic and tumor microenvironment signatures [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 4312.

Abstract 7502: MCT1 and ΜCT4 on circulating tumor cells isolated from non small cell lung cancer patients

Abstract Background: Lung cancer is the leading cause of cancer-related deaths. Non-small-cell lung cancer (NSCLC) is the most common subtype of lung cancer and is characterized by poor prognosis and survival rate. This is associated with the fact that most patients are diagnosed at advanced stages of the disease and the possibility of recurrence after treatment remains high. Monocarboxylate transporters 1 and 4 (MCT1 and MCT4) play a crucial role in cellular metabolism, as they are responsible for the transport of lactate and other monocarboxylic acids across the plasma membrane. Their function can further regulate cell survival and proliferation, especially under hypoxic conditions. To elucidate the relationship between CTCs and the metabolic aspect of cancer, we aimed to investigate the expression of MCT1 and MCT4 in CTCs derived from NSCLC patients and its potential association with patients’ outcome. Methods: Fifty-three NSCLC patients at baseline were enrolled in the current study. CTCs were isolated using the ISET system and triple immunofluorescence experiments were performed, using CK, MCT1, MCT4, and CD45 antibodies. The expression of MCT1 and MCT4 in CTCs was assessed by confocal laser scanning microscopy and statistical analysis was performed using SPSS software. Results: CTCs were detected in 29 out of 53 (55%) NSCLC patients. CK expression was characterized as high or low, with the predominant phenotypes among CK-positive patients being the CKhigh/MCT1+/CD45-and CKlow/MCT4-/CD45- (63% and 66%, respectively). Whereas the phenotype CKhigh/MCT4+/CD45- was detected in 52% of the patients. The phenotypes with the lowest frequency were the CKlow/MCT4+/CD45- (7%), CKlow/MCT1+/CD45- (15%), and the CKhigh/MCT1-/CD45- (15%). Most of the isolated CTCs had the CKhigh/MCT1+/CD45- and CKlow/MCT4-/CD45- phenotypes with a mean percentage of 48% and 51% respectively, while only a small number of CTCs per patient were CKlow/MCT1+/CD45- or CKlow/MCT4+/CD45- (8%and 5%, respectively). The phenotype CKlow/MCT1-/CD45- was associated with poorer overall survival (OS) [p = 0.005, (15 vs 33 months respectively)], HR=0.351), while the presence of more than 3 CKhigh/MCT4+/CD45- CTCs was related to poorer progression-free survival (PFS) [p = 0.042 (4 vs 17 months respectively)]. Conclusions: MCT1 and MCT4 were expressed in a high proportion of NSCLC patients at baseline and may constitute interesting biomarkers relevant to cancer progression. However, further analysis in a larger cohort of patients is required to clarify their potential significance in clinical practice. Citation Format: Karolina Mangani, Evangelia Pantazaka, Evi Lianidou, Vassilis Gerogoulias, Athanasios Kotsakis, Athina Markou, Galaktia Kallergi. MCT1 and ΜCT4 on circulating tumor cells isolated from non small cell lung cancer patients [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 7502.

Abstract 4299: A lineage-specific role of oncogenic protein kinase Cι in lung adenocarcinoma

Abstract Lung adenocarcinoma (LUAD), the most prevalent subtype of lung cancer, can arise from two different cell populations: alveolar type 2 (AT2) cells and bronchiolar club cells. By utilizing genomic data from the cancer genome atlas program, human LUAD cell lines, and the well-characterized LSL-KrasG12D/Trp53-/- (KP) mouse model, we demonstrated that tumors arising from club cells are much more aggressive and follow a different trajectory of tumorigenesis when compared to those arising from AT2 cells. Intriguingly, our data strongly suggest that expression and signaling activity of protein kinase C iota (PKCι) can profoundly affect the cell of origin and oncogenic signaling pathways employed by resultant tumors. Specifically, KP-mediated transformation of club cells appears to be dependent on PKCι-ELF3-NOTCH3 and PKCι-YAP1 signaling axes, while AT2 cell malignancy is dependent on the PKCι-independent WNT signaling. In addition, club-cell-origin tumors exhibit an enrichment of cancer stem cells and increased infiltration of immunosuppressive myeloid cells in comparison to AT2-cell-origin tumors. This results in accelerated progression and increased likelihood of metastasis by LUAD tumors that originate from club cells. Taken together, our results indicate that PKCι expression and signaling activity can profoundly influence the cells of origin, tumor trajectories, and therapeutic vulnerabilities of LUAD tumors. Citation Format: Duy T. Nguyen, Ning Yin, Capella R. Weems, Lee Jamieson, Kayleah Meneses, Yi Liu, Nicole R. Murray, Alan P. Fields. A lineage-specific role of oncogenic protein kinase Cι 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 4299.

Abstract 3304: Modulation of enhancer accessibility by SMARCA2 PROTACs synergize with TEAD inhibitors to suppress growth of SMARCA4 mutant lung cancers

Abstract The SWI/SNF chromatin remodeling complex is frequently mutated in non-small cell lung cancer with a frequency of 33% in advanced stage disease, making it the most commonly altered complex in lung cancer. Among the various subunits of the SWI/SNF complex, SMARCA4 and ARID1A are by far the most frequently mutated. Importantly, multiple clinical reports have shown that SMARCA4 mutant lung cancers have one of the worst prognosis among genetically defined lung cancer subtypes and lack response to both immunotherapy and KRAS G12C inhibitors. Recent reports, and our own data, have identified the paralogue SMARCA2 to be synthetic lethal to SMARCA4 suggesting SMARCA2 could be a high value therapeutic target. Unfortunately, the discovery of selective inhibitors of SMARCA2 has so far been challenging. To overcome this hurdle, we have recently developed novel, potent and selective SMARCA2 degrading small molecules based on proteolysis targeting chimera (PROTAC) technology. We demonstrated that YD23, our lead SMARCA2 PROTAC, potently and selectively induced degradation of SMARCA2. Importantly, we showed that YD23 selectively inhibits growth of SMARCA4 mutant lung cancer cells. Mechanistically, we demonstrated that YD23 decreased chromatin accessibility only in SMARCA4 deficient cells. In particular, SMARCA2 degradation profoundly decreased chromatin accessibility at enhancers of a number of genes with cell cycle and cell growth regulatory roles. Gene expression profiling and pathway analysis indicated that cell cycle genes were downregulated by YD23 consistent with the reduced chromatin accessibility at their cis-regulatory regions. We further showed that YD23 robustly inhibited growth of SMARCA4-mutant xenograft tumors. While this is promising, SMARCA2 degradation by itself does not induce regression of tumors highlighting the need for identification of efficacious combination strategies. Using integrative gene expression, ATAC-Seq and CUT&RUN assays, we uncover a critical role for YAP/TEAD transcription factor signaling axis in mediating pro-growth phenotypes in SMARCA4 mutant tumors. Finally, we show that the combination of TEAD inhibitors synergizes with YD23 to induce profound tumor growth inhibition. In conclusion, our study provides a mechanistic basis for the anti-tumor action of SMARCA2 degraders and introduces a novel combination strategy for future clinical development against a genetically defined subtype of lung cancer with dismal prognosis. Citation Format: Sasi Kotagiri, Nicholas Blazanin, Mohammad Qudrattulah, Yuanxin Xi, Jing Wang, Yonathan Lissanu. Modulation of enhancer accessibility by SMARCA2 PROTACs synergize with TEAD inhibitors to suppress growth of SMARCA4 mutant lung cancers [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 3304.

Abstract 5972: Therapeutic modulation of rock overcomes metabolic adaption to oxphos inhibition and suppresses tumor growth

Abstract Lung cancer is the top cause of cancer mortality. Despite recent advances, the majority of patients with lung cancer still lack effective therapeutic options, underscoring the dire need for additional treatment approaches. Genomic studies have identified frequent mutations in subunits of the SWI/SNF chromatin remodeling complex including SMARCA4 and ARID1A in non-small cell lung cancer with a frequency of up to 33% in advanced stage disease, making it the most frequently mutated complex in lung cancer. Previous work in our lab, as well as others, have identified a metabolic vulnerability in targeting oxidative phosphorylation (OXPHOS) in SMARCA4-mutant lung cancer. However, OXPHOS inhibitors are still not approved to treat cancer due to modest efficacy and adverse effects. This strongly suggests that novel, efficacious and tolerated agents that synergize with OXPHOS inhibition are urgently needed. To this end, we undertook a functional genomics screen by utilizing a focused CRISPR-Cas9 library targeting genes with available FDA approved therapeutics in genetically defined lung cancer cell lines. Importantly, we utilized low doses of the OXPHOS inhibitor IACS-10759 that are known to be well tolerated in patients. Among our top validated hits was ROCK1/2 kinases and we demonstrate that Belumasudil, a clinically approved ROCK inhibitor with a robust safety and tolerability profile, displays a synergistic combination with IACS-10759. Furthermore, low doses of IACS-10759 synergized with ROCK inhibition in vivo eliciting marked tumor growth inhibition. Mechanistically, we showed that the combination of Belumasudil and IACS-10759 induced a profound energetic stress. This was primarily due to ROCK inhibition-mediated suppression of the normally observed adaptive increase in glycolysis upon OXPHOS inhibition. Steady-state metabolomics and C13-glucose isotope tracing confirmed downregulation of multiple glycolytic metabolites and reduced glycolytic flux by the combination of ROCK inhibition and IACS-10759 and was associated with severe reduction in glucose uptake. In summary, our study identified a key role of ROCK kinases in metabolic adaptation of cancer cells and provides a strong rationale for pursuing ROCK inhibitors as novel combination agents with OXPHOS inhibition and lay the foundation for future clinical investigation in genetically defined subtypes of lung cancer. Citation Format: Nicholas Blazanin, Xiaobing Liang, Iqbal Mahmud, Eiru Kim, Lin Tan, Nazanin Esmaeili Anvar, Waikin Chan, Min Jin Ha, Rosalba Minelli, Michael Peoples, Philip Lorenzi, Travar Hart, Yonathan Lissanu, Nicholas Blazanin. Therapeutic modulation of rock overcomes metabolic adaption to oxphos inhibition and suppresses tumor growth [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 5972.

Abstract 5815: Next-generation RNAi therapeutics: siRNA-loaded exosomes targeting KRAS G12C in non-small cell lung cancer (NSCLC)

Abstract Background: NSCLC represents the predominant subtype of lung cancer, boasting an overall 5-year survival rate of 26%, a figure that fluctuates based on the disease stage. Within NSCLC, certain cancer gene mutations, notably KRAS G12C, are currently classified as 'undruggable targets,' creating hurdles in achieving effective treatment. The development of innovative anticancer drugs aimed at these challenging targets is expected to present a viable solution to these difficulties. Methods: Exosomes have garnered attention as an inventive drug delivery system for in vivo gene delivery through systemic injection. We used a new post-loading approach by actively loading KRAS G12C siRNA into exosomes using the shock waves (SWEET: shock wave exosome engineering technology ) in this study. The effect of in vitro and in vivo were tested in NCI-H358 (KRAS G12C mt NSCLC) cells and its xenograft mouse model. The tumor size and weight were measured twice a week. Results: We developed an exosome-based therapeutic using siRNA to effectively inhibit KRAS G12C, targeting NSCLC. The SWEET platform's post-loading method showed a high efficiency in loading KRAS G12C siRNA into exosomes. The KRAS G12C siRNA-loaded exosomes effectively silenced oncogenic KRAS G12C expression in cancer cells; they inhibited tumor growth when administered intravenously in a NSCLC xenograft mouse model. Remarkably, the anticancer effect of KRAS G12C-loaded exosome was similar to that of Sotorasib, a KRAS G12C mutation targeting anti-cancer drug. Conclusion: Our study showed KRAS G12C siRNA loaded exosomes were effectively delivered to NSCLC tumor tissue via intravenous (IV) administration. And its anti-cancer effects were very similar to sotorasib, showing potential as a treatment for KRAS G12C mutation-expressing cancer. The effective delivery of siRNA to tumor tissues through exosomes highlights the potential of this technology as a promising approach for developing new RNAi therapeutics for cancer. Citation Format: Hyo Kyeong Kim, Yujeong Choi, Kyoung Hwa Kim, Yeongju Byun, Tae Hee Kim, Jae Hwan Kim, Shung Hyun An, DaeHo Bae, MyeongKwan Choi, Jihwa Chung, Kihwan Kwon. Next-generation RNAi therapeutics: siRNA-loaded exosomes targeting KRAS G12C in non-small cell lung cancer (NSCLC) [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 5815.

Abstract 1115: Enhancing lung cancer sensitivity to chemotherapy, radiation, and chemo-radiation through inhibition of a mitotic checkpoint kinase BUB1

Abstract Non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) represent two major subtypes of lung cancer, marked by challenging treatment resistance. Our study explores the inhibition of BUB1, a critical mitotic checkpoint kinase, in conjunction with radiotherapy and chemotherapy. This approach has the potential to overcome resistance, thus enhancing the efficacy of treatment and improving treatment outcomes for lung cancer patients. We analyzed BUB1 expression in lung cancer using TCGA datasets and patient tissue microarrays (TMAs). In vitro experiments used four NSCLC and two SCLC cell lines with BUB1 inhibitor (BAY1816032), Paclitaxel, Cisplatin and Olaparib. Cells were irradiated (2, 4, or 6 Gy), and assays measured proliferation, long-term effects, DNA damage, and repair. Bioinformatic analysis in NSCLC subtype, lung adenocarcinoma (LUAD) demonstrated marked overexpression of BUB1, correlated with cancer stage, tumor grade and survival. Lung cancer TMAs revealed elevated expression of BUB1 protein in SCLC that correlated with poorer survival. BUB1 inhibition (BUB1i) induced cytotoxicity in LUAD cell lines at micromolar concentrations, while nanomolar concentrations enhanced cell death significantly when combined with radiation. Furthermore, BUB1i sensitized LUAD cells to different classes of chemotherapy (Paclitaxel, Cisplatin), and PARP inhibitor (Olaparib) alone (chemo-sensitization) or with radiation therapy (chemo-radiosensitization). H2030 and H1975 demonstrated higher chemo-radiosensitization efficacy compared to A549, likely due to genetic differences, potentially including a p53 mutation that improves sensitivity by affecting DNA repair and cell cycle regulation. Preliminary investigations revealed DNA double-strand breaks, indicated by prolonged γH2AX foci, and the inhibition of the NHEJ DNA damage repair pathway after BUB1 ablation. Among SCLC cell lines, NCI-H1876 demonstrated higher radiosensitivity upon BUB1 ablation compared to NCI-H2198, potentially due to genetic differences/mutations affecting radiation response. The study highlights the potential of BUB1i in enhancing the sensitivity of NSCLC and SCLC cells to radiotherapy and chemotherapy and provide rationale to explore BUB1i as a novel approach to enhance lung cancer therapy in clinical trials. Citation Format: Shivani Thoidingjam, Sushmitha Sriramulu, Stephen L. Brown, Farzan Siddiqui, Benjamin Movsas, Shirish Gadgeel, Shyam Nyati. Enhancing lung cancer sensitivity to chemotherapy, radiation, and chemo-radiation through inhibition of a mitotic checkpoint kinase BUB1 [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 1115.

Abstract 1251: Tobacco smoke alters the adaptive landscape of lung adenocarcinoma and influences the strength of epistatic interactions

Abstract Tobacco smoke produces both mutagenic and physiological effects, altering the mutation rate of cells and the selection acting on them in the damaged lung environment, and facilitating its role in driving cancer progression. In addition to these gene-by-environment interactions, gene-by-gene epistatic interactions also shape the adaptive landscape, influencing the evolutionary trajectories of cancer. Understanding the influence of tobacco smoke on the epistatic trajectories of lung cancer progression would help guide the development of targeted therapies that are more effective for smoker or never-smoker populations. To address this need, we constructed a continuous-time Markov chain model for the evolutionary trajectories of lung adenocarcinoma (LUAD), the most common subtype of lung cancer and the most frequent subtype among never-smokers. Using thousands of tumor sample sequences aggregated across studies, we profiled the trajectories of LUAD in smokers and never-smokers and estimated the rates at which mutations are gained from each possible set of pre-existing mutations, or genetic states. We then accounted for differences in baseline mutation rates to quantify the selective benefit of mutations. We find that epistasis is prevalent in LUAD, with several strong synergistic interactions—such as between RB1 and EGFR mutations- and antagonistic interactions-such as between EGFR and KEAP1 or KRAS mutations. Additionally, we identify non-additive epistatic effects: STK11 mutations are synergistic with KEAP1 and KRAS mutations but do not experience additional selection when both are mutated. In contrast, GNAS mutations are not synergistic with KEAP1 or RBM10 mutations alone but are synergistic with their co-mutation. Smoking has a large influence on the adaptive landscape, with several common mutations being preferentially selected in never-smoker cancers, including EGFR, SMAD4, GNAS, and PIK3CA mutations. KEAP1, STK11, and KRAS mutations are preferentially selected in smoker cancers. Smoking’s physiological influence also affects the strength of certain epistatic interactions, such as between STK11 and KEAP1 mutations. Overall, we find that smoking not only increases the mutation rate of lung cells but also substantially alters the adaptive landscape of lung adenocarcinoma, leading to clinically relevant differences in selection on mutations between smoker and never-smoker cancers. We additionally detect frequent pairwise and higher-order epistatic effects in LUAD that may inform the personalized application of targeted therapies. Citation Format: Krishna Dasari, Jorge Alfaro-Murillo, Jeffrey Townsend. Tobacco smoke alters the adaptive landscape of lung adenocarcinoma and influences the strength of epistatic interactions [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 1251.