Alterations In Oncogenic Pathways Research Articles

Abstract PO4-15-05: Genomic characterization and molecular predictive biomarkers for chemotherapy in a real-world population with metastatic triple-negative breast cancer

Abstract Background: The genomic landscape of metastatic triple-negative breast cancer (mTNBC) in a real-world population is poorly defined and despite recent advances in precision oncology, molecular biomarkers for chemotherapy are largely lacking. The presence of specific genomic alterations and alterations in oncogenic pathways have the potential to provide prognostic as well as predictive information for chemotherapy, which remains the backbone treatment strategy for mTNBC. Methods: We conducted next-generation sequencing (NGS) with the FoundationOne CDx panel on tissue from the primary tumor and/or metastasis of 112 consecutive patients with mTNBC that were treated between 1998 and 2019 at 4 different Swedish hospitals. Every genomic alteration was, if applicable, subdivided into 1 of 10 canonical oncogenic pathways and noted for its involvement in the homologous recombination pathway (HRP). Frequently altered genes and pathways were then correlated with overall survival (OS) and evaluated regarding their association with progression-free survival (PFS) and response rate (RR) in patients treated with different chemotherapy agents. Tumor samples of patients with rapid progression or exceptional response to chemotherapy underwent exploratory comparison with regards to frequently altered genes and pathways and known clinical prognostic factors were compared between the two patient groups. Results: After excluding 15 patients due to insufficient quantity/quality of tumor tissue or absence of clinical data, 97 patients were analyzed. The median age at diagnosis of metastatic disease was 61 (range: 28-90), 80 % had visceral disease and 26 % received platinum-based chemotherapy in the first line setting. The most frequently altered genes were: TP53 (82 %), RAD21 (25 %), PIK3CA (23 %), MYC (22 %) and BRCA 1 or 2 (16 %). The most frequently altered pathways were TP53 (86 %), PI3K (60 %), RTK/RAS (47 %) and cell cycle (36 %). In total, 26 % of patients had an alteration in the HRP. None of the most frequently occurring genomic alterations were associated with OS. Variants of clinical significance in the HRP and BRCA1/BRCA2 genes were associated with a longer PFS in patients treated with platinum-based chemotherapy in the first line setting (HR 0.12-0.84 and 0.12-0.92). Exceptional responders to chemotherapy exhibited a more favorable clinical profile than rapid progressors (median age 51.5 vs 66.5, median Charlson comorbidity index 0.5 vs 3) whereas some numerical difference in the genomic profiling in terms of genomic alterations in MYC and RAS/RTK pathways (more often in exceptional responders) could be observed. Conclusions: We found no genomic alteration with prognostic significance in a cohort of mTNBC patients treated with chemotherapy in a real-world setting. Somatic variants of clinical significance in BRCA 1 and 2 and other HRP-related genes seem to define subgroups of patients with mTNBC that respond favorably to platinum-based chemotherapy. Further research into the genomic landscape of tumors from patients with rapid progression or exceptional response to specific treatment strategies can provide insights into mechanisms of resistance and identify new predictive biomarkers. Citation Format: Erik Olsson, Henrik Lindman, Evangelos Digkas, Viktoria Thurfjell, Haidar Mir Ali, Ute Krüger, Anna-Karin Wennstig, Marie Sundqvist, Antonis Valachis. Genomic characterization and molecular predictive biomarkers for chemotherapy in a real-world population with metastatic triple-negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-15-05.

Clinical relevance of somatic mutations in Chinese lung adenocarcinoma and their prognostic implications for survival.

To comprehensively elucidate the genomic and mutational features of lung cancer cases, and lung adenocarcinoma (LUAD), it is imperative to conduct ongoing investigations into the genomic landscape. In this study, we aim to analyze the somatic mutation profile and assessed the significance of these informative genes utilizing a retrospective LUAD cohort. A total of 247 Chinese samples were analyzed to exhibit the tumor somatic genomic alterations in patients with LUAD. The Cox regression analysis was employed to identify prognosis-related genes and establish a predictive model for stratifying patients with LUAD. In the Dianjiang People's Hospital (DPH) cohort, the top five frequent mutated genes were (Epidermal growth factor receptor) EGFR (68%), TP53 (30%), RBM10 (13%), LRP1B (9%), and KRAS (9%). Of which, EGFR is a mostly altered driver gene, and most mutation sites are located in tyrosine kinase regions. Oncogene pathway alteration and mutation signature analysis demonstrated the RTK-RAS pathway alteration, and smoking was the main carcinogenic factor of the DPH cohort. Furthermore, we identified 34 driver genes in the DPH cohort, including EGFR (68%), TP53 (30.4%), RBM10 (12.6%), KRAS (8.5%), LRP1B (8.5%), and so on, and 45 Clinical Characteristic-Related Genes (CCRGs) were found to closely related to the clinical high-risk factors. We developed a Multiple Parameter Gene Mutation (MPGM) risk model by integrating critical genes and oncogenic pathway alterations in LUAD patients from the DPH cohort. Based on publicly available LUAD datasets, we identified five genes, including BRCA2, Anaplastic lymphoma kinase (ALK), BRAF, EGFR, and Platelet-Derived Growth Factor Receptor Alpha (PDGFRA), according to the multivariable Cox regression analysis. The MPGM-low group showed significantly better overall survival (OS) compared to the MPGM-high group (p < 0.0001, area under the curve (AUC) = 0.754). The robust performance was validated in 55 LUAD patients from the DPH cohort and another LUAD dataset. Immune characteristics analysis revealed a higher proportion of primarily DCs and mononuclear cells in the MPGM-low risk group, while the MPGM-high risk group showed lower immune cells and higher tumor cell infiltration. This study provides a comprehensive genomic landscape of Chinese LUAD patients and develops an MPGM risk model for LUAD prognosis stratification. Further follow-up will be performed for the patients in the DPH cohort consistently to explore the resistance and prognosis genetic features.

Interplay between ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype in patients with metastatic breast cancer (MBC): comprehensive circulating tumor DNA (ctDNA) analysis

Backgroundalthough being central for the biology and druggability of hormone-receptor positive, HER2 negative metastatic breast cancer (MBC), ESR1 and PIK3CA mutations are simplistically dichotomized as mutated or wild type in current clinical practice.MethodsThe study analyzed a multi-institutional cohort comprising 703 patients with luminal-like MBC characterized for circulating tumor DNA through next generation sequencing (NGS). Pathway classification was defined based on previous work (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Single nucleotide variations (SNVs) were annotated for their oncogenicity through OncoKB. Only pathogenic variants were included in the models. Associations among clinical characteristics, pathway classification, and ESR1/PIK3CA codon variants were explored.ResultsThe results showed a differential pattern of associations for ESR1 and PIK3CA codon variants in terms of co-occurring pathway alterations patterns of metastatic dissemination, and prognosis. ESR1 537 was associated with SNVs in the ER and RAF pathways, CNVs in the MYC pathway and bone metastases, while ESR1 538 with SNVs in the cell cycle pathway and liver metastases. PIK3CA 1047 and 542 were associated with CNVs in the PI3K pathway and with bone metastases.ConclusionsThe study demonstrated how ESR1 and PIK3CA codon variants, together with alterations in specific oncogenic pathways, can differentially impact the biology and clinical phenotype of luminal-like MBC. As novel endocrine therapy agents such as selective estrogen receptor degraders (SERDS) and PI3K inhibitors are being developed, these results highlight the pivotal role of ctDNA NGS to describe tumor evolution and optimize clinical decision making.

Oncogenic pathways refine a new perspective on the classification of hepatocellular carcinoma

BackgroundGenetic alterations in oncogenic pathways are critical for cancer initiation, development, and treatment resistance. However, studies are limited regarding pathways correlated with prognosis, sorafenib, and transcatheter arterial chemoembolization (TACE) in hepatocellular carcinoma (HCC). MethodsIn this study, 1928 patients from 11 independent datasets and a clinical in-house cohort were screened to explore the relationships among canonical pathway alterations in HCC patients. The molecular mechanisms, biological functions, immune landscape, and clinical outcomes among three heterogeneous phenotypes were further explored. ResultsWe charted the detailed landscape of pathway alterations in the TCGA-LIHC cohort, screened three pivotal pathways (p53, PI3K, and WNT), identified co-occurrence patterns and mutual exclusively, and stratified patients into three altered-pathway dominant phenotypes (ADPs). P53|PI3K ADP characterized by genomic instability (e.g., highest TMB, FGA, FGG, and FGL) indicated an unfavorable prognosis. While, patients in WNT ADP suggested a median prognosis, enhanced immune activation, and sensitivity to PD-L1 therapy. Remarkably, sorafenib and TACE exhibited efficacy for patients in WNT ADP and low frequent alteration phenotype (LFP). Additionally, ADP could work independently of common clinical traits (e.g., AJCC stage) and previous molecular classifications (e.g., iCluster, serum biomarkers). ConclusionsADP provides a new perspective for identifying patients at high risk of recurrence and could optimize precision treatment to improve the clinical outcomes in HCC.

Dexamethasone enhances venetoclax-induced apoptosis in acute myeloid leukemia cells.

Acute myeloid leukemia (AML) therapies have been significantly improved by the development of medicines that can target BCL-2. On the other hand, non-recurrent alterations in oncogenic pathways and gene expression patterns have already been linked to therapeutic resistance to venetoclax therapy. Bone marrow mesenchymal stromal cells (BM-MSCs) support leukemic cells in preventing chemotherapy-induced apoptosis by mitochondrial transfer in leukemic microenvironment. In this study, we investigated the enhancement of the antitumor effect of BCL-2 inhibitor venetoclax by dexamethasone. In particular, dexamethasone had no significant effect on the viability of AML cells, but dexamethasone combined with venetoclax could significantly increase the apoptosis of AML cells induced by venetoclax. When AML cells were co-cultured with BM-MSCs, dexamethasone combined with venetoclax showed additional anti-tumor effect compared to venetoclax alone. Venetoclax increased reactive oxygen species level in co-cultured AML cells, contributed to transfer more mitochondria from BM-MSCs to AML cells and protect AML cells from apoptosis. Dexamethasone combined with venetoclax induced more apoptosis, but dexamethasone reduced the venetoclax-induced reactive oxygen species level in AML cells and reduced the transfer of mitochondria from BM-MSCs to AML cells. This may lead to a diminished protective effect of BM-MSCs on AML cells. Together, our findings indicated that venetoclax in combination with dexamethasone could be a promising therapy in AML.

The Next Frontier in Sarcoma: Molecular Pathways and Associated Targeted Therapies.

Soft tissue sarcomas (STS) are a rare, complex, heterogeneous group of mesenchymal neoplasms with over 150 different histological subtypes. Treatments for this malignancy have been especially challenging due to the heterogeneity of the disease and the modest efficacy of conventional chemotherapy. The next frontier lies in discerning the molecular pathways in which these mesenchymal neoplasms arise, metastasize, and develop drug-resistance, thereby helping guide new therapeutic targets for the treatment of STS. This comprehensive review will discuss the current understanding of tumorigenesis of specific STS subtypes, including oncogenic pathway alterations involved in cell cycle regulation, angiogenesis, NOTCH signaling, and aberrant genetic rearrangements. It will then review current therapies that have been recently developed to target these pathways, including a review of ongoing clinical studies for targeted sarcoma treatment, as well as discuss new potential avenues for therapies against known molecular pathways of sarcomagenesis.

Abstract IA01: Molecular drivers in hepatocellular carcinoma: The story of what we know and what are we missing

Abstract Hepatocellular carcinoma (HCC) is a highly heterogeneous cancer, both at the molecular and histological level. High-throughput sequencing and gene expression profiling have identified distinct transcriptomic subclasses and recurrently altered cancer driver genes. Several HCC subtypes characterized by histological features have also been identified. HCC phenotype appears to be closely related to particular gene mutation and driven by various oncogenic pathway alterations. Identification of the origin of HCC development and their trajectory of progression is important to understand tumor evolution and to identify the mechanisms of tumor response or resistance to therapies. We will review the early and late molecular alterations driving HCC occurrence and progression of tumors in the context of patient lifespan and exposure to environmental factors. Several questions remain to be answered, in particular on the identification of the cells at the origin of the malignant transformation into HCC and the mechanism of escape to the immunological monitoring. Citation Format: Jessica Zucman-Rossi. Molecular drivers in hepatocellular carcinoma: The story of what we know and what are we missing [abstract]. In: Proceedings of the AACR Special Conference: Advances in the Pathogenesis and Molecular Therapies of Liver Cancer; 2022 May 5-8; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(17_Suppl):Abstract nr IA01.

Abstract PD6-08: Exploring the interplay among ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype of metastatic breast cancer (MBC) through circulating tumor DNA (ctDNA) next-generation sequencing (NGS)

Abstract Background: High throughput genomic technologies such as NGS are enhancing the ability to dynamically characterize MBC but their role in describing biological evolution of multiple mutations together remains unclear. ESR1 and PIK3CA are central mutations related to the biology and druggability of hormone-receptor positive, HER2 negative (luminal-like) MBC. The aim of this study was to explore the interplay between oncogenic pathway alterations and ESR1 and PIK3CA codon variants on the impact and clinical phenotype of luminal-like MBC. Methods: The study retrospectively analyzed a multi-institutional cohort comprising 1047 MBC patients (pts) characterized for ctDNA through NGS before treatment start at Northwestern University (Chicago, IL), Massachusetts General Hospital (Boston, MA) and Washington University in St. Louis between 2015-2020. The analysis was then focused on luminal-like MBC. Pathway classification was defined based on previous work (Sanchez-Vega F et al, Cell. 2018) (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Single nucleotide variations (SNVs) were annotated for their oncogenicity through OncoKB and ClinVar. Only pathogenic variants were included in the models. Associations among, pathway classification, and ESR1/PIK3CA codon variants were explored through stepwise logistic regression. Overall survival (OS) was tested through Cox regression. Results: The luminal-like cohort comprised 702 pts. ESR1 mutations were detected in 166 pts (24%) and PIK3CA in 214 pts (31%). The most common ESR1 gene mutations were found in codons 537 (31%), 538 (21%), 536 (8%) and 380 (7%), while alterations in codons 1047 (38%), 545 (25%), and 542 (20%) were the most common for PIK3CA. Other pathogenic SNVs were observed in 33% and 17% of pts for ESR1 and PIK3CA, respectively with the former being polyclonal. SNVs alterations were mainly observed in the PI3K (35%), P53 (32%), ER (28%), RAS (8%), RTK (8%) and cell cycle (5%) pathways, while copy number variations (CNVs) were detected in the RTK (15%), cell cycle (11%), MYC (7%) PI3K (6%) and RAF (5%) pathways. ESR1 537 variants were associated with alterations in the ER and WNT pathways, 538 with cell cycle, 380 with P53 and ER, 536 with RTK. PIK3CA 1047 variants were associated with alterations in the RTK and P53 pathways, 542 with RTK, RAS and RAF, E545 with PI3K, RAS, cell cycle and P53. 1047 and 542 were also associated with CNVs in the PI3K pathway. Independent prognostic factors in terms of OS were ESR1 537/380 codon variants (HR 1.94 P = 0.001 and HR 2.29 P = 0.047), SNVs in the RAS, cell cycle, and P53 pathways (HR 1.74 P = 0.003 HR 1.84 P = 0.009 and HR 1.56 P &amp;lt; 0.001) and CNVs in the cell cycle pathway (HR 1.96 P &amp;lt; 0.001). Conclusions: This study demonstrated how ESR1 and PIK3CA codon variants, together with alterations in specific oncogenic pathways, can differentially impact the biology and clinical phenotype of luminal-like MBC. As novel endocrine therapy agents such as selective estrogen receptor degraders (SERDs) and PI3K inhibitors are being developed, these results highlight the pivotal role of ctDNA NGS to describe tumor evolution and optimize clinical decision making. Odds Ratio95% Confidence IntervalPESR1 Y537ER SNVs3.341.487.530.004WNT SNVs6.251.4127.740.016ESR1 D538cell cycle SNVs5.221.7915.230.003ESR1 E380P53 SNVs4.801.4116.310.012ER SNVs5.331.3321.400.018ESR1 L536RTK CNVs4.511.1517.690.031PIK3CA H1047RTK SNVs3.751.708.290.001P53 SNVs2.611.584.34&amp;lt; 0.001PI3K CNVs6.082.4515.08&amp;lt; 0.001PIK3CA E542RTK SNVs5.001.9412.880.001RAS SNVs3.651.369.770.01RAF SNVs6.011.0733.870.042PI3K CNVs6.302.2917.36&amp;lt; 0.001PIK3CA E545PI3K SNVs2.881.276.530.011RAS SNVs2.871.186.980.02cell cycle SNVs3.071.088.740.035NRF2 SNVs21.431.29356.520.033P53 SNVs3.752.046.89&amp;lt; 0.001 Citation Format: Lorenzo Gerratana, Andrew A Davis, Marko Velimirovic, Katherine Clifton, Whitney L Hensing, Ami N Shah, Charles S Dai, Carolina Reduzzi, Paolo D’Amico, Qiang Zhang, Firas Wehbe, Seth Wander, William J Gradishar, Amir Behdad, Fabio Puglisi, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli. Exploring the interplay among ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype of metastatic breast cancer (MBC) through circulating tumor DNA (ctDNA) next-generation sequencing (NGS) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-08.

Mutant Kras and mTOR crosstalk drives hepatocellular carcinoma development via PEG3/STAT3/BEX2 signaling.

Background & Aims: Abnormal activation of mTOR through loss of tuberous sclerosis complex (Tsc) frequently occurs in hepatocellular carcinoma (HCC). Mutant Kras could induce aggressive HCCs. Here, we aim to identify the predictive or prognostic biomarkers for HCC patients with Kras mutant and mTOR hyperactivation, and to provide potential therapeutic approaches for this subtype of HCCs. Methods: We generated transgenic mice in which hepatocytic mTOR was hyperactivated through Tsc1 insufficiency with or without oncogenic KrasG12D. Bioinformatics and gain- or loss-of-function studies were used to illustrate the mechanisms underlying oncogenic pathway alterations. Transcriptional profiling was used to identify biomarker for the subtype of HCC. The therapeutic efficacy of targeting mTOR was tested in a liver orthotropic homogeneous murine model. Results: Oncogenic KrasG12D facilitated mTOR activation via the Mek/Erk/ROS axis, leading to HCC tumorigenesis and metastasis. Inhibition of Mek/Erk enhanced the anticancer effect of mTOR inhibitor via reduction of mTOR activity. Paternally expressed 3 (PEG3) was responsible for Kras/Erk- and mTOR-driven HCC. Elevated PEG3 protein interacted with STAT3 and promoted its transcriptional activity, resulting in the upregulation of proliferation- and metastasis-related proteins. Targeting mTOR significantly inhibited these actions in vitro and in vivo. Moreover, in clinical samples, PEG3 was identified as a new poor prognostic marker for HCC patients with Kras/Erk and mTOR hyperactivation. Conclusion: These findings reveal the underlying mechanism of hepatocytic Kras/Erk-driven mTOR activation and its downstream targets (PEG3 and STAT3) in HCC, identify PEG3 as a new prognostic biomarker for HCC with Kras/Erk and mTOR hyperactivation, and provide a potential therapeutic strategy for this subset of HCC patients.

Abstract LBA021: Immune resistance interrogation study (IRIS): Initial report of next generation sequencing (NGS) results in patients with primary versus acquired resistance to anti-PD1/L1 antibodies

Abstract Background: The molecular mechanisms underlying primary versus acquired resistance to anti-PD-1/L1 antibodies have not been comprehensively evaluated across different tumor types. Methods: The Immune Resistance Interrogation Study (IRIS; NCT04243720) is a prospective, investigator-initiated study at the Princess Margaret Cancer Centre, aimed to perform extensive multi-omic characterization of solid tumors with primary resistance (disease progression on first imaging; or stable disease &amp;lt;6 months) versus acquired resistance (partial or complete response; or stable disease ≥6 months) to antiPD-1/L1 agents. A one-time fresh tumor biopsy is collected from patients (pts) who have progressed on anti-PD1/L1 antibody-based treatment as their most recent line of therapy; liquid biopsy or archived FFPE tissue is allowed as alternates when fresh biopsy is insufficient. NGS was performed using Foundation One (324 genes) or Foundation Liquid (309 genes) panels. Frequencies of disrupted genes and variants were compared in pts with primary versus acquired resistance using Fisher’s exact test. The planned samples size of IRIS is 100 pts. Results: Among the first 35 pts enrolled, 22 (63%) had primary resistance and 13 (37%) had acquired resistance. The most common diagnosis was melanoma (17 pts; 49%); followed by head and neck squamous cell carcinoma (13 pts; 37%); endometrial cancer (2 pts; 6%); pleural mesothelioma, gastroesophageal junction and colorectal cancer (1 pt each; 3%). Foundation One was performed in 23 pts (66%), 22 of them (63%) had biopsies with sufficient quality for NGS, and 1 (3%) had the analysis performed using archival FFPE tissue. The remaining 12 pts (34%) had Foundation Liquid testing done using liquid biopsy. Thirty-three pts (94%) had at least one oncogenic alteration. Genes most frequently altered included: TP53 in 16 patients (46%), TERT promoter in 12 pts (34%), CDKN2A in 9 pts (26%), PIK3CA in 6 pts (17%), and PTEN in 5 pts (14%). At the variant level, the most frequent alterations were: TERT promoter -146C&amp;gt;T mutation in 6 patients (17%), followed by TERT promoter -124C&amp;gt;T mutation in 5 patients (14%), FGF19/FGF4/FGF3 and CCND1 amplifications in 4 pts each (11%), and MDM2 amplification, CDK4 amplification and CDKN2A loss, detected in 3 pts each (9%). Pts with acquired resistance had a higher frequency of TP53 mutations (9/13 = 69%) compared to primary resistance pts (7/22 = 32%), p=0.04; however this was not significant when corrected for multiple testing. Interestingly, amplifications in CDK4, CCND1, FGF 19/FGF 3/FGF 4, MDM2 and mutations in NF1 were only identified in pts with primary resistant tumors. Conclusions: No significant differences in disrupted genes and variants were observed in the current analysis. However, this can be due to the small number of pts analyzed thus far. Accrual to this study is ongoing. A comparison of alterations in oncogenic pathways is planned to further define the genomic landscape of pts with primary versus acquired resistance to anti-PD1/PDL1 blockade. Citation Format: Sofia Genta, Farnoosh Abbas Aghababazadeh, Ming S Tsao, Aaron R Hansen, Marcus O Butler, Albiruni R Razak, Philippe L Bedard, Ben X Wang, Pugh J Trevor, Sevan Hakgor, Jeffrey Woo, Benjamin Haibe-Kains, Lillian L Siu, Anna Spreafico. Immune resistance interrogation study (IRIS): Initial report of next generation sequencing (NGS) results in patients with primary versus acquired resistance to anti-PD1/L1 antibodies [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr LBA021.

Primary lung cancer in women after previous breast cancer.

BackgroundBreast cancer is the most common malignancy among women in the USA. Improved survival has resulted in increasing incidence of second primary malignancies, of which lung cancer is the most common. The United States Preventive Services Task Force (USPSTF) guidelines for lung-cancer screening do not include previous malignancy as a high-risk feature requiring evaluation. The aim of this study was to compare women undergoing resection for lung cancer with and without a history of breast cancer and to assess whether there were differences in stage at diagnosis, survival and eligibility for lung-cancer screening between the two groups.MethodsWomen who underwent lung-cancer resection between 2000 and 2017 were identified. Demographic, clinicopathological, treatment and outcomes data were compared between patients with a history of breast cancer (BC-Lung) and patients without a history of breast cancer (P-Lung) before lung cancer.ResultsOf 2192 patients included, 331 (15.1 per cent) were in the BC-Lung group. The most common method of lung-cancer diagnosis in the BC-Lung group was breast-cancer surveillance or work-up imaging. Patients in the BC-Lung group had an earlier stage of lung cancer at the time of diagnosis. Five-year overall survival was not statistically significantly different between groups (73.3 per cent for both). Overall, 58.4 per cent of patients (1281 patients) had a history of smoking, and 33.3 per cent (731 patients) met the current criteria for lung-cancer screening.ConclusionDifferences in stage at diagnosis of lung cancer and treatment selection were observed between patients with and without a history of breast cancer. Overall, there were no statistically significant differences in genomic or oncogenic pathway alterations between the two groups, which suggests that lung cancer in patients who previously had breast cancer may not be affected at the genomic level by the previous breast cancer. The most important finding of the study was that a high percentage of women with lung cancer, regardless of breast-cancer history, did not meet the current USPSTF criteria for lung-cancer screening.

In vivo CRISPR inactivation of Fos promotes prostate cancer progression by altering the associated AP-1 subunit Jun.

Prostate cancer is a major global health concern with limited treatment options for advanced disease. Its heterogeneity challenges the identification of crucial driver genes implicated in disease progression. Activating protein-1 (AP-1) transcription factor is associated with cancer since the first identification of its subunits, the proto-oncogenes JUN and FOS. Whereas both JUN and FOS, have been implicated in prostate cancer, this study provides the first functional evidence that FOS acts as a tumor suppressor during prostate cancer progression and invasion. Data mining revealed decreased FOS expression in prostate cancer and a further downregulation in metastatic disease, consistent with FOS expression in cell lines derived from different prostate cancer stages. FOS deficiency in prostate cancer cell lines increases cell proliferation and induces oncogenic pathway alterations. Importantly, in vivo CRISPR/Cas9-mediated Fos and Pten double mutation in murine prostate epithelium results in increased proliferation and invasiveness compared to the abrogation of Pten alone. Interestingly, enhanced Jun expression is observed in the murine prostatic intraepithelial neoplasia lacking Fos. CRISPR/Cas9-mediated knockout of Jun combined with Fos and Pten deficiency diminishes the increased proliferation rate in vivo, but not the ability to form invasive disease. Overall, we demonstrate that loss of Fos promotes disease progression from clinical latent prostate cancer to advanced disease through accelerated proliferation and invasiveness, partly through Jun.

Baseline SUVmax is related to tumor cell proliferation and patient outcome in follicular lymphoma.

Follicular lymphoma (FL) is the most common indolent lymphoma. Despite the clear benefit of CD20-based therapy, a subset of FL patients still progress to aggressive lymphoma. Thus, identifying early biomarkers that incorporate positron emission tomography metrics could be helpful to identify patients with a high risk of treatment failure with rituximab. We retrospectively included a total of 132 untreated FL patients separated into training and validation cohorts. Optimal threshold of baseline whole-body maximum standardized uptake (SUVmax) was first determined in the training cohort (n=48) to predict progression-free survival (PFS). The PET results were investigated along with the tumor and immune microenvironment, which were determined by immunochemistry and transcriptome studies involving gene set enrichment analyses and immune cell deconvolution, together with the tumor mutation profile. We report that baseline SUVmax>14.5 was associated with poorer PFS than baseline SUVmax≤14.5 (hazard ratio =0.28; P=0.00046). Neither immune T-cell infiltration nor immune checkpoint expression were associated with baseline PET metrics. By contrast, FL samples with Ki-67 staining ≥10% showed enrichment of cell cycle/DNA genes (P=0.013) and significantly higher SUVmax values (P=0.007). Despite similar oncogenic pathway alterations in both SUVmax groups of FL samples, four out of five cases harboring the infrequent FOXO1 transcription factor mutation were seen in FL patients with SUVmax>14.5. Thus, high baseline SUVmax reflects FL tumor proliferation and, together with Ki-67 proliferative index, can be used to identify patients at risk of early relapse with rituximab chemotherapy.

Abstract 1308: CDK12 alterations define a distinct molecular subtype of prostate cancers with unique genomic and clinical characteristics

Abstract Background: CDK12 alterations are present in several tumor types but little is known regarding their oncogenic role and their clinical significance. Here we sought to describe the landscape of CDK12 alterations across solid cancers and the clinical features of CDK12-altered prostate cancer. Methods: A total of 26,743 patients across 25 solid tumor types with available targeted sequencing data from MSK-IMPACT as part of their clinical care were included. Clinicopathological features and outcomes were assessed in prostate cancer. CDK12 alterations and association with genomic characteristics are described. For prostate cancer patients, overall survival from the date of metastasis and time to castration-resistance from the start of androgen deprivation therapy were assessed using univariable and multivariable Cox regression analysis. Results: CDK12 alterations were identified in 404/26,743 (1.5%) patients overall, but were most frequent in prostate (100/1875, 5.3%) and ovarian cancer (43/1034, 4.2%) where they were associated with a high prevalence of truncating variants and biallelic inactivation. CDK12 alterations defined a distinct subtype of prostate cancer with more aggressive clinical features, a unique copy number alteration profile and involvement of distinct oncogenic pathway alterations, including cell cycle pathway genes. Independent of standard clinical factors and genomic instability, CDK12-altered prostate cancer patients were associated with shorter overall survival (median 64.4 vs 74.9 months, adjusted hazard ratio [aHR] 1.65, 95% CI 1.07-2.53, p = 0.03) and shorter time to the development of castration-resistant disease (median 10.8 months vs 13.1, aHR 1.43, 95%CI 1.07-1.8, p = 0.02). Conclusions: CDK12 loss of function is a rare event across solid cancers but defines a distinct molecular subtype of prostate cancer that is associated with more aggressive clinical features and unique genomic alterations. Citation Format: Bastien Nguyen, Jose Mauricio Mota, Subhiksha Nandakumar, Konrad H. Stopsack, Emily Weg, Dana Rathkopf, Michael J. Morris, Howard Scher, Philip W. Kantoff, Anuradha Gopalan, Dmitriy Zamarin, David B. Solit, Nikolaus Schultz, Wassim Abida. CDK12 alterations define a distinct molecular subtype of prostate cancers with unique genomic and clinical characteristics [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1308.

Pan-cancer Analysis of CDK12 Alterations Identifies a Subset of Prostate Cancers with Distinct Genomic and Clinical Characteristics

BackgroundCDK12 genomic alterations occur in several tumor types, but little is known about their oncogenic role and clinical significance. ObjectiveTo describe the landscape of CDK12 alterations across solid cancers and the clinical features of CDK12-altered prostate cancer. Design, setting, and participantsA single-center retrospective study of 26743 patients across 25 solid tumor types who underwent tumor sequencing was performed. Clinicopathologic features and outcomes were assessed in prostate cancer. Outcome measurements and statistical analysisCDK12 alterations and their association with genomic characteristics are described. For prostate cancer patients, overall survival and time to castration resistance were assessed using univariable and multivariable Cox regression analysis. Results and limitationsCDK12 alterations were identified in 404/26743 patients (1.5%) overall, but were most frequent in prostate (100/1875, 5.3%) and ovarian cancer (43/1034, 4.2%), in which they were associated with a high prevalence of truncating variants and biallelic inactivation. CDK12 alterations defined a genomic subtype of prostate cancer with a unique copy-number alteration profile and involvement of distinct oncogenic pathway alterations, including cell-cycle pathway genes. CDK12-altered prostate cancer was associated with somewhat more aggressive clinical features and shorter overall survival (median 64.4 vs 74.9 mo; p=0.032) independent of standard clinical factors and tumor copy-number alteration burden (adjusted hazard ratio 1.80, 95% confidence interval 1.12–2.89; p=0.024). The study is limited by its retrospective nature. ConclusionsCDK12 alteration is a rare event across solid cancers but defines a clinically distinct molecular subtype of prostate cancer associated with unique genomic alterations and slightly more aggressive clinical features. Patient summaryCDK12 gene alterations occur rarely across tumor types, but more frequently in prostate cancer, where they are associated with genomic instability, cell-cycle pathway gene alterations, and somewhat worse clinical outcomes, warranting further investigation of therapeutic targeting of this disease subset.

Distinct resistant mechanism and genomic evolution during TKI treatment in non-small cell lung cancer patients with or without acquired T790M mutation.

e20603 Background: EGFR-mutant non-small-cell lung cancer (NSCLC) patients inevitably develop drug resistance when treated with EGFR tyrosine kinase inhibitors (TKIs). Clonal and clinical analyses of genetic alterations at baseline and progressive disease (PD), as well as differences between acquired T790M and T790M-negative patients in drug-resistant mechanisms, have not been systematically studied. Methods: We performed targeted sequencing of pre-treatment and PD tumor samples from 54 EGFR-mutant NSCLC patients. Correlation between genomic features and patients’ progression-free survival (PFS) was evaluated. Ten additional patients were sequenced using whole exome sequencing to infer the clonal evolution patterns. Results: We observed new pathways limiting EGFR-inhibitor response, including NOTCH1/ STK11 co-deletion, and TGF-beta alterations. Besides acquired T790M mutation, chromosomal instability (CIN) related genes including AURKA and TP53 alterations were the most frequently acquired events. CIN significantly increased with TKI treatment in T790M-negative patients. Transcriptional regulators including HNF1A, ATRX and NKX2-1 acquired alterations were enriched in T790M-positive patients, and diverse oncogenic pathway alterations were more common in T790M-negative patients. T790M-positive patients had improved PFS compared to T790M-negative patients. We identified subgroups within T790M-positive or T790M-negative patients with distinct PFS. Interestingly, we observed a death-and-birth process of RTK-RAS mutations during TKI treatment, and baseline and acquired RTK-RAS mutations had opposite effects on PFS. Clonal evolution analysis indicated progression of T790M-positive patients depends on competition between T790M and non-T790M resistant subclones. Conclusions: T790M-positive and T790M-negative patients display divergent landscape of acquired somatic events. Subgroups of patients were identified within T790M-positive and T790M-negative patients with distinct survival. Our results point the importance of clonal competition between T790M and non-T790M resistant subclones.

Abstract PD9-06: Paired pre- and post-treatment DNA sequencing identifies genomic alterations mediating clinical resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer

Abstract Background: The combination of cyclin-dependent kinase 4 and 6 inhibitors (CDK 4/6 inh) and endocrine therapy have changed the treatment paradigm for hormone receptor-positive metastatic breast cancer (HR+ MBC). Three CDK 4/6 inhibitors (palbociclib, ribociclib, and abemaciclib) are now approved for HR+ MBC in combination with either an aromatase inhibitor (AI) or fulvestrant (a selective estrogen receptor degrader, SERD) after demonstrating significant improvement in progression-free survival compared to endocrine monotherapy. However, both primary and secondary resistance has been observed clinically, and the mechanisms of such resistance are not well understood. Here we describe emergence of molecular alterations following treatment with the combination of CDK 4/6 inhibitors and endocrine therapy. Methods: We evaluated molecular alterations by next-generation sequencing (NGS) prior to and following treatment with CDK 4/6 + endocrine therapy pre and post CDK inh among patients with HR+ MBC. We performed circulating tumor (ct) DNA analysis via the Guardant360 assay, an NGS-based assay that identifies potential tumor-related (somatic) genomic alterations through sequencing of the critical exons within 73 cancer-related genes, and/or tissue-based genomic analysis utilizing our institutional NGS platform (SNaPshot), which targets hotspots and exons in 89 genes. Results: A total of 33 HR+ MBC patients had paired pre/post CDK 4/6 tissue/liquid biopsies. 19 (57.6%) received palbociclib and 14 (42.4%) ribociclib, with 25 (75%) receiving an AI and 8 (24%) a SERD. Eight patients (24.2%) were first line. The median duration of response was 8 months (range 1-35 months). The most common acquired alterations at the time of progression that were not present in the pre-treatment specimens included mutations in ESR1 (30.3%), TP53 (30.3%), RB1 (12.1%) and PIK3CA (9.1%), and FGFR1 amplification (27.3%). We then evaluated these results in a subset of patients (N=17) who had paired pre/post liquid biopsies only and found similar results. We observed alterations in oncogenic pathways both upstream and downstream of CDK 4/6-cyclin-D complex (N=17), including upstream receptor tyrosine kinase alterations (29.4%), PI3K/AKT/mTOR alterations (5.9%), and MAPK alterations (17.6%), as well as downstream cell-cycle (35.3%) and DNA repair gene alterations (17.6%). Furthermore, 58.8% of patients had more than one acquired potential driver mutation, and 41.2% had both upstream and downstream alterations possibly reflecting emergence of different subclones and tumor heterogeneity under selective pressure from CDK 4/6 inhibitors. Conclusion: Both upstream and downstream genomic alterations may mediate acquired clinical resistance to CDK 4/6 inhibitors, reflecting genomic evolution and diversification after exposure to CDK 4/6 inhibitors. Additional studies are needed to confirm these findings and develop potential therapeutic strategies to overcome clinical resistance to CDK 4/6 inhibitors for patients with MBC. Citation Format: Spring LM, Haddad S, Malvarosa G, Vidula N, Juric D, Iafrate AJ, Ellisen LW, Moy B, Isakoff SJ, Bardia A. Paired pre- and post-treatment DNA sequencing identifies genomic alterations mediating clinical resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-06.

Abstract 2294: Customizable weighted DNA copy-number networks inform oncogenic pathway alterations and chemoresistance risk

Abstract Cancer is driven by mutations of many types: single nucleotide variants, insertion-deletion events within coding exons, and prolific DNA copy-number alterations (CNAs). CNAs have been often viewed as a passenger event due to seemingly inconsistent patterns between tumors and a large fraction of the genome altered, preventing traditional statistical analysis. Here, we present a tool which incorporates phenotypic data including haploinsufficiency and triploproficiency of genes and protein-protein interaction studies, which enables the identification of consistently altered pathways in cancer. This tool, HAPTRIG (for HAPloinsufficient and TRIplosensitive Gene) can be used with RNA, log2 CNA, absolute CNA data, or any other normalized gene-level data. As part of the pathway scoring process, control CNA networks are generated to provide a permuted-genome control, enabling detection of alterations in very heterogeneous cancer backgrounds. The customizable gene-scores which build these networks allow prioritization of altered network hubs: single genes which have exceptional influence within an altered pathway, facilitating hypothesis-testing in cell and animal models. A beta-version was validated in a recent publication from our lab to better predict tumor suppressor genes and oncogenes than Gene Set Enrichment Analysis, and additionally identified targetable pathway hubs which improved murine treatment in ovarian cancer chemo-resistant models. However, its applicability was limited in the beta. Now HAPTRIG can work with any user-supplied human dataset, not just TCGA samples, is an order of magnitude faster, able to run in parallel processors for unlimited speed improvement, and can produce pan-pathway outputs. The tool can use expected background rates from permuted data or compare to a second control dataset, which can be used to compare altered CNA pathways in tumor subtypes or unusual alterations of RNA compared to CNAs, among many other possibilities. We provide this tool for free community use online and in App form, so molecular biologists without bioinformatics training may produce well-informed hypotheses. We find that altered CNA pathways can predict chemoresistance risk groups within tumor types. A tumor suppressor gene hub was found to accelerate tumorigenesis upon deletion in a spontaneous mouse model. Overall, HAPTRIG represents a user-friendly tool to better understand a whole new landscape of tumor mutations: that of copy number alterations. Citation Format: Joe Ryan Delaney, Dwayne G. Stupack. Customizable weighted DNA copy-number networks inform oncogenic pathway alterations and chemoresistance risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2294.

Evolution and clinical impact of genomic alterations detectable in circulating tumor DNA of 1150 advanced EGFR-mutant (mt) lung cancer patients.

9009 Background: Advanced EGFR-mt lung adenocarcinomas (LUAD) frequently harbor additional genetic alterations. The clinical significance of these concurrent alterations and how they evolve with treatment are unclear. Methods: We performed next-generation sequencing (NGS) of ~70 cancer related genes from the circulating tumor DNA (ctDNA) of 1150 consecutive advanced LUAD patients (pts) with detectable EGFR mts. The analysis included 113 samples from 81 pts for whom clinical outcome data were known. Clinical response to EGFR TKI treatment was correlated to mutational status in 12 cancer-related pathways. Results: EGFR-mt cases contained an average of 3.6 genetic alterations (range 1-18). There was enrichment for co-alterations in TP53, CDK6, CTNNB1 and SMAD4 in EGFR-mt cases compared to a control cohort of 1008 EGFR WT cases. Enrichment for the EGFR T790M mutation was found upon progression to first-line EGFR TKI treatment, as expected. Analysis of 450 T790M-mt cases showed enrichment for co-alterations in genes controlling the cell cycle (28% vs. 21%, p = 0.01), DNA repair (12% vs. 8%, p = 0.03), and WNT (16% vs. 11%, p = 0.03) signaling. The number of genetic alterations increased during progression on each line of therapy in a manner unlinked to age, gender, or tobacco exposure (mean 3.2 pre-TKI vs. 6.4 after 2nd line, p = 0.001). Upon progression to second-line treatment, analysis revealed further selection for co-alterations in TP53, CCNE1, MYC and PIK3CA and the associated pathway-level classifications. We found an increased frequency of co-alteration in cell cycle genes in EGFR TKI non-responders versus responders (33% vs. 0%, p = 0.0005). Conclusions: Within the landscape of advanced EGFR-mt LUAD, we uncover features of evolutionary selection for multiple concurrent oncogenic pathway alterations including TP53, WNT, PI3K, MYC, and cell cycle genes. This large clinical and genetic dataset prompts a re-evaluation of the prevailing paradigm of monogenic-based molecular stratification to monotherapy, and highlights an alternative model of genetic collectives as a previously underappreciated determinant of lung cancer progression and therapy resistance.

Targeting the miR-200c/LIN28B axis in acquired EGFR-TKI resistance non-small cell lung cancer cells harboring EMT features

MicroRNA (miR)-200 family members (miR-200s) are frequently silenced in advanced cancer and have been implicated in the process of epithelial-to-mesenchymal transition (EMT). We previously reported that miR-200s were silenced through promoter methylation in acquired EGFR-tyrosine kinase inhibitor (TKI) resistant non-small cell lung cancer (NSCLC) cells harboring EMT features. In this study, we examined the functional role of miR-200s in NSCLC cells and investigated a novel approach to overcoming acquired EGFR-TKI resistance. In the analysis of NSCLC cell lines, each of the miR-200s expression-silenced cell lines showed promoter methylation. Significant correlations between miR-200c silencing and several oncogenic pathway alterations, including EMT-changes and LIN28B overexpression, were observed in the database analysis. In addition, EGFR-wild type cell lines had lower miR-200s expression levels than EGFR-mutant cell lines. The introduction of miR-200c using pre-miR-200c caused LIN28B suppression in cells with acquired EGFR-TKI resistance that harbored EMT features. Interestingly, both the introduction of miR-200c and the knockdown of LIN28B produced an antitumor effect in acquired EGFR-TKI resistance cells, whereas these manipulations were not effective in parental cells. The miR-200c/LIN28B axis plays an important role in cells with acquired resistance to EGFR-TKI that harbor EMT features and might be a useful therapeutic target for overcoming resistance.