Co-occurring Genomic Alterations Research Articles

Targeting focal adhesion kinase boosts immune response in KRAS/LKB1 co-mutated lung adenocarcinoma via remodeling the tumor microenvironment

BackgroundKRAS mutation is one of the most common oncogenic drivers in NSCLC, however, the response to immunotherapy is heterogeneous owing to the distinct co-occurring genomic alterations. KRAS/LKB1 co-mutated lung adenocarcinoma displays poor response to PD-1 blockade whereas the mechanism remains undetermined.MethodsWe explored the specific characteristics of tumor microenvironment (TME) in KL tumors using syngeneic KRASG12DLKB1−/− (KL) and KRASG12DTP53−/− (KP) lung cancer mouse models. The impact of focal adhesion kinase (FAK) inhibitor on KL lung tumors was investigated in vitro and in vivo through evaluation of both KL cell lines and KL lung cancer mouse models.ResultsWe identified KL tumors as “immune-cold” tumors with excessive extracellular matrix (ECM) collagen deposition that formed a physical barrier to block the infiltration of CD8+T cells. Mechanistically, abundant activated cancer-associated fibroblasts (CAFs) resulted from FAK activation contributed to the formation of the unique TME of KL tumors. FAK inhibition with a small molecular inhibitor could remodel the TME by inhibiting CAFs activation, decreasing collagen deposition and further facilitating the infiltration of anti-tumor immune cells, including CD8+ T cells, DC cells and M1-like macrophages into tumors, hence, converting “immune-cold” KL tumors into “immune-hot” tumors. The combined FAK inhibitor and PD-1 blockade therapy synergistically retarded primary and metastatic tumor growth of KL tumors.ConclusionsOur study identified FAK as a promising intervention target for KL tumors and provided basis for the combination of FAK inhibitor with PD-1 blockade in the management of KL lung cancers.

Characteristics and Survival Outcomes of Patients With Metastatic RET Fusion-Positive Solid Tumors Receiving Non-RET Inhibitor Standards of Care in a Real-World Setting.

RET fusions are oncogenic drivers across different solid tumors. However, the genomic landscape and natural history of patients with RET fusion-positive solid tumors are not well known. We describe the clinical characteristics of RET tyrosine kinase inhibitor (TKI)-naïve patients with RET fusion-positive solid tumors (excluding non-small-cell lung cancer [NSCLC]), treated in a real-world setting and assess the prognostic effect of RET fusions. Data for RET TKI-naïve patients with metastatic solid tumors (excluding NSCLC) who had ≥one Foundation Medicine comprehensive genomic profiling test (January 1, 2011-March 31, 2022) were obtained from a deidentified nationwide (US-based) clinicogenomic database. The primary objective of this study was to compare the overall survival (OS) of patients with RET fusion-positive tumors versus matched patients with RET wild-type (RET-WT) tumors. Patients with RET-WT solid tumors were matched (4:1) to patients with RET fusion-positive tumors on the basis of preselected covariates. The study population included 26 patients in the RET fusion-positive cohort, 7,220 patients in the RET-WT cohort (before matching), and 104 patients in the matched RET-WT cohort. Co-occurring genomic alterations were rare in the RET fusion-positive cohort. Median OS was consistently lower in patients with RET fusion-positive tumors versus those with RET-WT tumors, using three different analyses (hazard ratios, 2.0, 1.7, and 2.2). These data suggest that RET fusions represent a negative prognostic factor in patients with metastatic solid tumors and highlight the need for wider genomic testing and use of RET-specific TKIs that could improve patient outcomes. Our study also highlights the value of real-world data when studying rare cancers or cancers with rare genomic alterations.

Comprehensive Genomic Analysis of Patients With Non-Small-Cell Lung Cancer Using Blood-Based Circulating Tumor DNA Assay: Findings From the BFAST Database of a Single Center in Taiwan.

The Blood First Assay Screening Trial (BFAST) is a prospective study using next-generation sequencing (NGS) of circulating tumor DNA (ctDNA) in treatment-naïve advanced/metastatic non-small-cell lung cancer (NSCLC). We compared liquid biopsy to tissue testing and analyzed genomic alterations in Taiwanese patients with NSCLC using the BFAST database. A total of 269 patients underwent FoundationOne Liquid Companion Diagnostic (F1LCDx) assay at the National Taiwan University Hospital, of whom 264 underwent tissue-based genetic testing also. We analyzed the actionable mutations and the concordance between tissue-based genetic testing, which was limited to EGFR, ALK, ROS1, and BRAF, in a real-life clinical setting and blood-based NGS in the clinical trial. Additionally, we analyzed the co-occurring genomic alterations from the blood-based ctDNA assay. A total of 76.2% patients showed actionable mutations. Standard tissue testing did not detect known driver alterations in about 22.7% of the patients (sensitivity, 70.24%). Liquid NGS detected additional mutations (RET, KRAS, MET, and ErbB2) in 14% of the patients, which went undetected by the standard-of-care testing. The complementary use of ctDNA NGS increased the detection rate by 42%. The F1LCDx assay had a sensitivity of 83.41%. Lower tumor and metastasis stages predicted nondetected blood-based NGS ctDNA results. Common co-occurring mutations in the blood-based NGS ctDNA assay were TP53, DNMT3A, TET2, PIK3CA, CTNNB1, and RB1. Among the patients with EGFR-mutated NSCLC, TET2 co-occurring alterations correlated with shorter progression-free survival of EGFR tyrosine kinase inhibitor treatment. NGS ctDNA analysis in comprehensive genetic testing improves actionable mutation identification, vital for treating Asian NSCLC cases with high actionable mutation rates. Lower stages correlated with undetected blood-based NGS ctDNA assay results.

The spectrum and significance of secondary (co-occurring) genetic alterations in sarcomas: the hallmarks of sarcomagenesis.

Bone and soft tissue tumors are generally classified into complex karyotype sarcomas versus those with recurrent genetic alterations, often in the form of gene fusions. In this review, we provide an overview of important co-occurring genomic alterations, organized by biological mechanisms and covering a spectrum of genomic alteration types: mutations (single-nucleotide variations or indels) in oncogenes or tumor suppressor genes, copy number alterations, transcriptomic signatures, genomic complexity indices (e.g. CINSARC), and complex genomic structural variants. We discuss the biological and prognostic roles of these so-called secondary or co-occurring alterations, arguing that recognition and detection of these alterations may be significant for our understanding and management of mesenchymal tumors. On a related note, we also discuss major recurrent alterations in so-called complex karyotype sarcomas. These secondary alterations are essential to sarcomagenesis via a variety of mechanisms, such as inactivation of tumor suppressors, activation of proliferative signal transduction, telomere maintenance, and aberrant regulation of epigenomic/chromatin remodeling players. The use of comprehensive genomic profiling, including targeted next-generation sequencing panels or whole-exome sequencing, may be incorporated into clinical workflows to offer more comprehensive, potentially clinically actionable information. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

PD-23 Comprehensive survey of AACR GENIE cBioPortal database of receptor tyrosine kinase fusion in colorectal carcinoma identified high co-occurring genomic alterations in NTRK1 & RET fusion-positive CRC

PD-23 Comprehensive survey of AACR GENIE cBioPortal database of receptor tyrosine kinase fusion in colorectal carcinoma identified high co-occurring genomic alterations in NTRK1 & RET fusion-positive CRC

Abstract P2-23-10: Gene expression and mutation profiles in HER2-mutated metastatic breast cancer

Abstract Background: HER2 activating mutations occur in 2-5% of metastatic breast cancer (MBC) patients. These mutations cluster in the kinase domains and at amino acids 309-310 in the extracellular domain. The MutHER, SUMMIT, and PlasmaMATCH clinical trials have shown neratinib monotherapy or neratinib plus fulvestrant combination produce clinical benefit in 28% to 46% in HER2-mutated MBC patients, but median progression-free survival was only 3.6 to 5.4 months. In order to improve the knowledge and outcomes for patients with HER2-mutated MBC, we compared the mutational landscape and gene expression of HER2-mutated MBC patients to HER2-amplified and HER2-wild type MBC patients. Methods: De-identified data from a cohort of stage 4 breast cancer patients (n=1,834) sequenced with the Tempus xT (DNA-seq of 595-648 genes, whole exome-capture RNA-seq) solid tumor assay was retrospectively analyzed. The most recent sample of the patient was used for analyses. Patients were stratified by HER2 mutational status: HER2-wild type (HER2-wt), HER2-amplifications (HER2-amps), or HER2-mutants (HER2-muts). Additionally, a sub-analysis was conducted among HER2-mutants to compare kinase domain mutations to other HER2 mutations. Patient demographic characteristics were compared between groups along with the prevalence of individual gene alterations (pathogenic/likely pathogenic short variants and copy number alterations), adjusted for false-discovery. Results: Within the cohort, 62 (3.4%) patients harbored HER2-muts tumors and 125 (6.8%) patients had HER2-amps tumors. Three patients, whose tumors had both HER2 mutation and amplification, were classified among the HER2-muts. Relative to the HER2-wt cohort (median = 53 yo), HER2-muts patients were older (median = 55 yo) while HER2-amps patients were younger (median = 49 yo) (P< 0.001). Significant differences were observed in genomic alterations co-occurring with HER2-muts compared to HER2-wt and HER2-amps, including CDK12 (4.8% vs 0.2% vs 74%), CDH1 (44% vs 11% vs 4.8%), ESR1 (4.8% vs 21% vs 8.8%), TOP2A (3.2% vs 0.5% vs 14%), and ERBB3 (11% vs 0.9% vs 0.8%). Of note, the majority of CDK12 mutations are amplifications (96%). Median HER2 mRNA log10 gene expression differed among the three cohorts (HER2-muts (3.79), HER2-wt (3.56), HER2-amps (4.54); P< 0.001). Among HER2-muts patients, 46 (74.2%) patients had HER2 kinase domain mutations (HER2-kinase). Relative to other HER2-muts patients, HER2-kinase patients displayed a lower prevalence of CDH1 mutations (35% vs 69%; P = 0.018). No significant differences were noted in ERBB3 co-mutations, however all 7 were missense variants (5 of which are p.E928G variants) and occurred among HER2-kinase patients. Conclusions: Real-world data show increased HER2 mRNA expression in both HER2-mut and HER2-amps MBC patients. Co-occurring genomic alterations were different among all three groups. Notably, ERBB3 and CDH1 alterations co-occurred commonly in HER2-mut MBC patients, while ESR1 alterations co-occurred in only 4.8%. All ERBB3 co-mutations occurred with HER2 kinase domain mutations, while CDH1 co-mutations were less prevalent in the HER2-kinase group. Understanding the frequency and spectrum of HER2 mutations in MBC, as well as co-mutations, will help to guide combination treatment strategies and improve the clinical benefit of targeted therapy in HER2-mutated MBC. Citation Format: Whitney L. Hensing, Shana N. Thomas, Sherif El-Refai, Elizabeth Mauer, Cynthia Ma, Ron Bose. Gene expression and mutation profiles in HER2-mutated metastatic breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-10.

Clinical implications of Wnt signaling alterations in patients (pts) with advanced prostate cancer (aPC).

229 Background: Aberrant Wnt signaling has been implicated in prostate cancer tumorigenesis, progression, and metastasis in preclinical models. While studies have identified recurrent molecular alterations in the Wnt signaling components in about 20% of aPC pts, the clinical significance of these alterations has been incompletely characterized. Methods: PROMISE is a multi-institutional, retrospective, clinical-genomic database - inclusive of aPC pts who had tissue and/or blood-based genomic testing by commercially available CLIA-certified platforms. We evaluated outcomes in pts with alterations leading to the activation of the canonical Wnt pathway, specifically activating mutations in CTNNB1 or RSPO2 or inactivating mutations in APC, RNF43, or ZNRF3 (Wnt altered), compared to those lacking such alterations (Wnt wild type). Multiple endpoints were evaluated, including the frequency of metastatic disease to different sites and co-occurring alterations. Results: 1596 pts with aPC were included with a median age of 63 years at diagnosis. Wnt pathway alterations were identified in 12.4% (198/1596). Wnt altered pts had a statistically significant increase in liver and lung metastases compared with Wnt wild type pts at diagnosis (4.5% vs 2.1%, p=0.0438; 6.1% vs 2.9%, p=0.0292), at first metastatic disease (11.6% vs 5.4%, p= 0.0015; 14.8% vs 6.6%, p<0.0001), and at diagnosis of CRPC (14.2% vs 7.9%, p=0.01436; 16.1% vs 6.8%, p=0.0003). Fewer Wnt altered pts had bone metastases at CRPC compared with wild type pts (67.7% vs 75.2%, p=0.04948) without significant difference of bone metastases at the time of diagnosis or at the time of first metastatic disease. The frequency of metastases to other sites was similar between the cohorts. More Wnt altered pts had ductal features on histology at diagnosis compared with Wnt wild type pts (4.0% v 1.6%, p=0.02415) without difference in PSA, Gleason score, TNM stage, or presence of neuroendocrine or intraductal features. Co-occurring genomic alterations that were more common in Wnt altered pts included PTEN loss/mutation (25.3% vs 18.3%, p=0.0270), RB1 loss/mutation (10.6% vs 5.8%, p=0.0079), AR mutations or gain (37.9% vs 24.0%, p< 0.0001), and SPOP mutations (14.1% vs 3.9%, p< 0.0001) as compared with Wnt wild type pts. Conclusions: Wnt pathway alterations were associated with ductal histology, an increase in visceral metastases at all time points evaluated, and an increase in co-occurring PTEN, RB1, AR, and SPOP alterations. The clinical heterogeneity of aPC and differences in co-occurring mutations between the cohorts make isolating the effect of alterations in a single pathway challenging. Analysis of overall survival outcomes is currently in process, and future multivariable analysis is planned to adjust for established clinical factors and co-occurring mutations to identify the independent contributions of Wnt alterations to clinical outcomes.

A high number of co-occurring genomic alterations detected by NGS is associated with worse clinical outcomes in advanced EGFR-mutant lung adenocarcinoma: Data from LATAM population

BackgroundCo-occurring genomic alterations identified downstream main oncogenic drivers have become more evident since the introduction of next-generation sequencing (NGS) analyses at diagnosis and progression. Emerging evidence has stated that co-occurring genomic alterations at diagnosis might represent de novo and primary resistance mechanisms to tyrosine kinase inhibitors (TKIs) in advanced EGFR-mutant (EGFRm) non-small lung cancer (NSCLC). In this study, we assessed the prognostic role of co-occurring genomic alterations in advanced EGFRm NSCLC. MethodsA cohort of 111 patients with advanced NSCLC harboring EGFR-sensitive mutations detected by PCR was analyzed in 5 Latin American oncological centers from January 2019 to December 2020. All eligible patients received upfront therapy with EGFR-TKI. Co-occurring genomic alterations were determined at diagnosis in every patient by the NGS (FoundationOneCDx) comprehensive platform, which evaluates 324 known cancer-related genes. ResultsEGFR exon19 deletion was the most frequent oncogenic driver mutation (60.4 %) detected by NGS. According to the NGS assay, 31 % and 68.3 % of patients had 1–2 and ≥ 3 co-occurring genomic alterations, respectively. The most frequent co-occurring genomic alterations were TP53 mutations (64.9 %) followed by CDKN2AB alterations (13.6 %), BRCA2 (13.6 %), and PTEN (12.7 %) mutations. Baseline central nervous system disease was present in 42.7 % of patients. First- or second-generation EGFR TKIs (gefitinib, afatinib, or erlotinib) were the most common treatment in 67.5 % of patients, while osimertinib was administered in 27.9 % of cases. The median PFS in all evaluated patients was 13.63 months (95 %CI: 11.79–15.52). Using ≥ 3 co-occurring alterations as the cut-off point, patients with ≥ 3 co-occurring genomic alterations showed a median PFS, of 12.7 months (95 %CI: 9.92–15.5) vs 21.3 months (95 %CI: 13.93-NR) in patients with 2 or less co-occurring genomic alterations [HR 3.06, (95 %CI: 1.55–5.48) p = 0.0001]. Also, patients with a TP53 mutation had a shorter PFS, 13.6 (95 %CI: 10.7–15.5) vs 19.2 months (95 %CI: 12.8-NR); in wild type TP53 [HR 2.01 (95 %CI: 1.18–3.74) p = 0.12]. In the multivariate analysis, the number (≥3) of concurrent genomic alterations and ECOG PS of 2 or more were related to a significant risk factor for progression [HR 2.79 (95 %CI: 1.49–5.23) p = 0.001 and HR 2.42 (95 %CI: 1.22–4.80) p = 0.011 respectively]. ConclusionEGFR-mutant NSCLC is not a single oncogene-driven disease in the majority of cases, harboring a higher number of co-occurring genomic alterations. This study finds the number of co-occurring genomic alterations and the presence of TP53 mutations as negative prognostic biomarkers, which confers potentially earlier resistance mechanisms to target therapy.

RET fusions as primary oncogenic drivers and secondary acquired resistance to EGFR tyrosine kinase inhibitors in patients with non-small-cell lung cancer

BackgroundRET fusions are rare oncogenic drivers in non-small cell lung cancer (NSCLC). While activating RET rearrangements are found in NSCLC patients harboring epidermal growth factor receptor (EGFR) genetic alterations at resistance to EGFR inhibitors, the extent to which co-occurring genomic alterations exist and how they might affect prognosis or therapy response is poorly understood.MethodsTargeted next-generation sequencing (NGS) was used to assess 380 baseline patients with primary RET fusions and 71 EGFR-mutated NSCLC patients who acquired RET fusions after developing resistance to EGFR-tyrosine kinase inhibitors (EGFR-TKIs).ResultsPrimary RET fusions were more likely associated with females and younger age, with KIF5B being the predominant fusion partner. In baseline patients, both SMAD4 (5.3% vs. 0.0%, P = 0.044) and MYC copy-number gain variants (6.9% vs. 0.0%, P = 0.009) were more frequently co-mutated with KIF5B-RET than CCDC6-RET. By contrast, CDKN2A (11.3% vs. 2.4%, P = 0.003) mutations were significantly enriched in CCDC6-RET-rearranged baseline patients. A significant increase in the proportion of CCDC6-RET was observed in acquired RET-rearranged patients (47.3% vs. 22.5%, P < 0.001). The median progression-free survival (PFS) of patients harboring RB1 and TP53 double-mutations (5.5 vs. 10.0 months, P = 0.020) or ERBB2 amplification (5.6 vs. 10.0 months, P = 0.041) was significantly shorter than the wild-type counterparts. Moreover, we identified that RET fusions were more likely associated with acquired resistance (AR) to third-generation EGFR-TKIs than previous generations of EGFR-TKIs.ConclusionsIn conclusion, we depicted the mutational profiles of NSCLC patients who harbor RET fusions at baseline or after resistance to EGFR-TKIs. Furthermore, our results suggest that RET fusions mediate secondary resistance to third-generation EGFR-TKIs and might be associated with poor prognosis in patients with NSCLC.

Abstract 5403: Genetic, immunologic and prognostic heterogeneity in CRC patients with KRAS mutations

Abstract Genetic, immunologic and prognostic heterogeneity in CRC patients with KRAS mutations Background Currently, most patients with mCRC are treated with a combination of a cytotoxic and a biologic agent. Several factors should be put into account which influencing the treatment strategy for patients with mCRC. including tumor resectability, prior systemic therapy; tumor location (left or right), and molecular characteristics such as mutation in gene Kirsten rat sarcoma viral oncogene homolog (KRAS). It has been demonstrated to be a tightly associated with poor response to anti-EGFR treatment, and even poor response to immune checkpoint inhibitors for patients with colorectal cancer. Therefore, KRAS mutational status testing has been highlighted in recent years. Methods This study queried the data from Formalin-Fixed Paraffin-Embedded (FFPE) tissues of 2,294 CRC patients which underwent a targeted next-generation sequencing assay performed by 3DMed Clinical Laboratory Inc., a College of American Pathologists (CAP) certified and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory of 3D Medicines Inc. between January, 2017 and June, 2020 in China, to obtain a comprehensive molecular profile of KRAS mutations. Co-occurring genomic alterations, tumor mutational burden (TMB), microsatellite instability (MSI) status and PD-L1 expression (Dako 22C3 or VentanaSP263, TPS score) were analyzed. High TMB was defined as TMB ≥10 muts/Mb. Postoperative follow-up data for 27 patients were collected and analyzed. Results KRAS mutation account for 48.7% Chinese CRC patients. In addition, proportions of KRAS mutation in different exons were counted. KRAS mutation in CRC mainly occurred in exon2 (84.0%), exon3 (6.1%), exon4 (7.4%), and exon5 (0.7%). KRAS mutation in exon2, the main mutations were G12D (35.4%), G12V (20.8%), G13D (21.9%), G12C (5.9%) ad G12S (5.8%). while in exon3 and exon4, the main mutations were Q61H (50.7%) and A146T (73.2%), respectively. The proportion of MSI-H in CRC patients with and without KRAS mutation were very close. While it seemed that there were more MSI-H patients in KRAS exon3 and exon4 mutation. In addition, PD-L1 expression was detected in 1220 tumor samples by means of IHC. Among these available tumor samples, level of PD-L1expression were similar among patients without KRAS mutation, KRAS mutation in different exons, but it reveled that there were very small part of patient with strong positive PD-L1 level (TPS≥50). In addition, different prognosis were found among different mutations of KRAS exon2, in detail, worse PFS was showed in CRC patients with KRAS mutation in exon2 G12D than G12V and G13D. Conclusions CRC patients with KRAS mutations in different exons and different site have different genetic and prognostic characteristics, these patients should be managed differently in clinical practice. Citation Format: Zhengqi Wen, Hushan Zhang, Ruize Zhou, Xihong Liu, Wenliang Li. Genetic, immunologic and prognostic heterogeneity in CRC patients with KRAS mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5403.

Co-occurring genomic alterations and immunotherapy efficacy in NSCLC

An oncogene-centric molecular classification paradigm in non-small cell lung cancer (NSCLC) has been established. Of note, the heterogeneity within each oncogenic driver-defined subgroup may be captured by co-occurring mutations, which potentially impact response/resistance to immune checkpoint inhibitors (ICIs). We analyzed the data of 1745 NSCLCs and delineated the landscape of interaction effects of common co-mutations on ICI efficacy. Particularly in nonsquamous NSCLC, KRAS mutation remarkably interacted with its co-occurring mutations in TP53, STK11, PTPRD, RBM10, and ATM. Based on single mutation-based prediction models, adding interaction terms (referred to as inter-model) improved discriminative utilities in both training and validation sets. The scores of inter-models exhibited undifferentiated effectiveness regardless of tumor mutational burden and programmed death-ligand 1, and were identified as independent predictors for ICI benefit. Our work provides novel tools for patient selection and insights into NSCLC immunobiology, and highlights the advantage and necessity of considering interactions when developing prediction algorithms for cancer therapeutics.

A High Number of Co-Occurring Genomic Alterations Detected by NGS is Associated with Worse Clinical Outcomes in Advanced EGFR-Mutant Lung Adenocarcinoma: Data from LATAM Population

A High Number of Co-Occurring Genomic Alterations Detected by NGS is Associated with Worse Clinical Outcomes in Advanced EGFR-Mutant Lung Adenocarcinoma: Data from LATAM Population

Characterization of KRAS Mutation Subtypes in Non-small Cell Lung Cancer.

KRAS is the most commonly mutated oncogene in NSCLC and development of direct KRAS inhibitors has renewed interest in this molecular variant. Different KRAS mutations may represent a unique biologic context with different prognostic and therapeutic impact. We sought to characterize genomic landscapes of advanced, KRAS-mutated non-small cell lung cancer (NSCLC) in a large national cohort to help guide future therapeutic development.Molecular profiles of 17,095 NSCLC specimens were obtained using DNA next-generation sequencing of 592 genes (Caris Life Sciences) and classified on the basis of presence and subtype of KRAS mutations. Co-occurring genomic alterations, tumor mutational burden (TMB), and PD-L1 expression [22C3, tumor proportion score (TPS) score] were analyzed by KRAS mutation type.Across the cohort, 4,706 (27.5%) samples harbored a KRAS mutation. The most common subtype was G12C (40%), followed by G12V (19%) and G12D (15%). The prevalence of KRAS mutations was 37.2% among adenocarcinomas and 4.4% in squamous cell carcinomas. Rates of high TMB (≥10 mutations/Mb) and PD-L1 expression varied across KRAS mutation subtypes. KRAS G12C was the most likely to be PD-L1 positive (65.5% TPS ≥ 1%) and PD-L1 high (41.3% TPS ≥ 50%). STK11 was mutated in 8.6% of KRAS wild-type NSCLC but more frequent in KRAS-mutant NSCLC, with the highest rate in G13 (36.2%). TP53 mutations were more frequent in KRAS wild-type NSCLC (73.6%).KRAS mutation subtypes have different co-occurring mutations and a distinct genomic landscape. The clinical relevance of these differences in the context of specific therapeutic interventions warrants investigation.

Landscape and Clonal Dominance of Co-occurring Genomic Alterations in Non–Small-Cell Lung Cancer Harboring MET Exon 14 Skipping

PURPOSEMET exon 14 skipping alterations (METex14) comprise a diverse set of actionable oncogene drivers in non–small-cell lung cancer (NSCLC). Recent studies have established the efficacy of tyrosine kinase inhibitors for this patient population. The landscape of co-occurring genetic alterations in METex14 NSCLC and their potential impact to therapeutic sensitivities has not yet been fully described.MATERIALS AND METHODSMETex14 NSCLC cases were collected from three cohorts: the VISION trial, and data sets from Guardant360 and GenePlus. Clinicopathologic characteristics and METex14 mutation sites were analyzed and compared across data sets. Co-occurring genetic alterations and the clonality relationships to METex14 were evaluated.RESULTSOf 40,824 NSCLCs, 692 METex14 cases (1.7%) were identified, including 332 in Guardant360, 188 in VISION, and 172 in GenePlus. The demographics and mutation type and/or sites were similar in the Asian versus Western cohorts. MET amplification, which were found to be associated with sensitivity to MET kinase inhibitors, co-occurs in 7.6%-13.8% of cases, whereas kinase domain secondary mutation of MET co-occurs in 5%-6%. When co-occurring with METex14, EGFR mutations were often identified as the dominant clone (78%, 7 of 9), whereas when co-occurring, METex14 (39%, 7 of 18) and KRAS (44%, 8 of 18) had similar rates of clonal dominance. PIK3CA and PTEN mutations were almost always subclones (89%, 16 of 18) to METex14. Moreover, RET-CCDC6 fusion and EGFR mutation were detected following crizotinib treatment in two patients, suggesting novel mechanisms of resistance.CONCLUSIONMETex14 mutations frequently co-occur with other potential driver oncogenes with differing patterns of clonal dominance observed among the drivers. This cellular context can provide insights into whether METex14 is acting as a primary oncogenic driver or resistance mechanism and help guide treatment choices.

Association of ATM mutations in metastatic prostate cancer with differential genomic alteration profiles from homologous recombination deficient and proficient tumors.

5063 Background: ATM mutations, one of a family of DNA repair defects prevalent in prostate cancer, have been included in a list of actionable mutations for PARP inhibitor (PARPi) therapeutic trials. Despite preclinical evidence, PARPi have shown minimal clinical activity in ATM mutant prostate cancer (ATMmPCa). The present analysis explores co-occurring genomic alterations that may drive outcomes of metastatic PCa (mPCa) patients with tumors harboring ATM mutations and provide clues for understanding therapy resistance and potential targets. Methods: This study included molecular profiling analysis of 1375 cases of mPCa. Tumors were analyzed using next-generation sequencing (NGS), whole transcriptome sequencing (WTS), and immunohistochemistry (IHC) (Caris Life Sciences, Phoenix, AZ). dMMR/MSI-H status was determined by IHC, NGS, and fragment analysis and tumor mutational burden (TMB) was calculated based on somatic nonsynonymous missense mutations. We performed differential gene expression analysis of HR-associated transcripts such as ATR, PARP1-3, RAD50, RAD51A/B/C/D and RAD54. Significance was determined using the ꭓ2 test and Benjamini-Hochberg method. Results: Fifty-nine (4.2%) cases harbored pathogenic ATM mutations, 84 (6.2%) harbored BRCA2 mutations. 1018 tumors (74%) were deemed homologous recombination proficient (HRP) and 155 tumors (11.3%) were HR Deficient (HRD); harboring one or more mutation in HR-related genes excluding ATM and BRCA2. The mutation rate of TP53 was significantly lower in ATMmPCa (12.0%) compared to BRCA2mPCa (35%), HRD (35%) and HRP (46.6%) tumors. ATMmPCa showed higher rates of SMAD2 (3.7%/1%) and FLCN (5.2%/0.3%) alterations compared to HRP cases. PARP1 and RAD51D gene expression was reduced in ATMmPCa compared to HRP (p &lt; 0.05) and BRCA2mPCa ( p &lt; 0.05) tumors, respectively. No differences in gene expression levels were detected for ATR, PARP2, PARP3, RAD50, and RAD54. Chromosomal segments demonstrating differential CNA in ATMmPCa vs HRP, HRD, or BRCA2mPCa included FGF19, FGF4, PTPN11, ALDH2, DAXX, BCL7A, CCND1, BMPR1A and MEF2B (Q-value &lt; 0.05 determined by ꭓ2). The most common CNA in ATMmPCa was CCND1, present in approximately 13% (7/55) of cases. Compared to BRCA2mPCa and HRD cases, ATMmPCa cases are less likely to display markers of immunotherapy response such as dMMR/MSI-H or TMB ≥10 mutations/MB. Conclusions: ATMmPCa demonstrated several differences in co-occurring alterations compared to BRCA2mPCa, HRD and HRP mPCa. ATMmPCa tumors were less likely to harbor alterations in TP53 compared to BRCA2, HRD or HRP tumors. CNA in ATMmPCa occurred in 9 genes across distinct mPCa molecular subtypes and were enriched for those associated with the 11q13 amplicon harboring Cyclin D1. The FGF and PTPN11 related pathways are potentially targetable pathways in ATMmPC and may merit further study.

P76.43 Co-occurring genomic alterations and treatment outcomes in patients with EGFR exon 20 insertion positive NSCLC

NSCLC harboring an EGFR exon 20 insertion (ex20ins) often has additional genomic aberrations, which may influence the underlying biology and predict outcomes. Clinical outcomes data overall remain limited in patients (pts) with ex20ins and comprehensive characterization of these tumors is lacking. NSCLC samples were profiled by targeted NGS (Caris Life Sciences, Phoenix, AZ). Mutations and copy number variations (CNV) were assessed. Gene amplification was defined as gene copy number ≥ 6 and copy number loss as gene copy number < -1.4. Clinical outcomes data were obtained through an IRB-approved retrospective chart review. Among 3,359 pts with NSCLC harboring an EGFR mutation, 250 (7.4%) had EGFR ex20ins. 170 (68%) were females with a mean age 65 (range 29-90). 60 different ex20ins variants were identified with the most common being A767_V769dup (25%), followed by S768_D770dup (18%), N771_H773dup (7%), H773_dup (6%) and A763_Y764insFQEA (3%). 4% had compound ex20ins mutations. The most common co-mutations included TP53 (56.6%), followed by CTNNB1 (6.6%), RB1 (5.1%), PIK3CA (4.7%) and CDKN2A (4.3%). Commonly amplified genes included EGFR (9.6%), FOXA1 (4%), MDM2 (3.6%) and CDK4 (3.5%). Copy number loss was observed in CDKN2A (4.6%), BRCA2 (1.1%), FANCL (1.1%), CTNNB1 (0.5%), and ATR (0.5%). PD-L1 expression by 22C3 was high (TPS ≥ 50%) in 16%, low (1-49%) in 27%, and negative in 57%. Clinical data were obtained from 26 pts with advanced NSCLC with ex20ins mutations from four institutions. In the first-line setting, 12 (46%) received chemotherapy, 10 (39%) received an EGFR-TKI and 4 (15%) received chemo-IO. Mean PFS was 9.3 months with chemotherapy-based regimens and 6 months with TKI therapy. One patient with P772_H773dup treated with TKI achieved a partial response. Across all treatments, mean PFS was 8 months and mean OS was 28.3 months. The diverse spectrum of EGFR ex20ins mutations demonstrates notable molecular heterogeneity within this uncommon EGFR mutation. PFS and OS in this population remain poor. Understanding the role of co-occurring genomic alterations and their impact on outcomes may have therapeutic implications on clinical trial development.

203P Characterization of renal cell carcinoma (RCC) with VHL mutation

VHL is one of the most commonly mutated oncogene in RCC. However, different co-mutated genes and VHL mutation types are associated with different prognoses and treatments. A more comprehensive understanding of the genomic landscape relative to different VHL variant subsets will help guide therapeutic development. Molecular profiles of 322 RCC samples were obtained using next-generation sequencing of 808 genes (Acornmed Corporation) and classified based on the presence and types of VHL variant. Incidence of VHL mutations was noted across the cohort. Co-occurring genomic alterations and tumor mutational burden (TMB) were analyzed by VHL mutation type. Across the entire cohort, 163 VHL mutations were detected among 154 patients(47.8%). Frameshift mutations were the most prevalent mutation type, accounting for the 42.9%(70/163), followed by missense, nonsense, splicing mutation, copy number loss(42.4%(69/163), 9.2%(15/163), 4.3%(7/163) and 1.2%(2/163) respectively). These mutations were classified into structural variant(58.4%) and non-structural variant(41.6%) based on the effects of variants on protein structure. PBRM1, SETD2, BAP1, KDM5C were commonly co-occurring with VHL(all p<0.05). SETD2 and KDM5C mutations were more common in VHL-nosv RCC, followed by VHL-sv and the VHL-wt. BAP1 has a similar mutation frequency in cases of VHL-sv and VHL-nosv, while VHL-wt had a lower frequency. PBRM1 was mutated in 10.1% of VHL wild type RCC but more frequently noted in both VHL subtype, with the higher rate in VHL-sv (43.3%) and lower in VHL-nosv(29.7%). TMB-H was defined by >12.8 mutations/Mb(upper quartile of the cohort). TMB-H varied across the different VHL mutation subset, most common in VHL-sv (31.1%) and least common in VHL wild type(VHL-wt) (22.2%). VHL mutations are relatively common in Renal cell Carcinoma and VHL structural variant is the most common type. The different VHL mutation has different co-occurring mutations and a different genomic landscape. VHL-sv was associated with the highest rate of TMB and PBRM1 frequency. These different clinical correlates in terms of therapeutic interventions need to be investigated.

305P Novel co-occurring genomic alterations associated with prediction and prognosis in lung adenocarcinoma

305P Novel co-occurring genomic alterations associated with prediction and prognosis in lung adenocarcinoma

Effects of Co-occurring Genomic Alterations on Survival in Patients with KRAS-Mutant Pancreatic Cancer

We report the case of a young patient with left breast cancer with stage IIB (T2N1M0), negative hormone receptors, HER2-positive and no particular medical history. The patient was particularly sensitive to the neurological and allergic-type toxicity of the adjuvant treatment she received and it required the stopping and successive change of the various prescribed protocols.

Effects of Co-occurring Genomic Alterations on Survival in Patients with KRAS-Mutant Pancreatic Cancer

The world is suffering from a pandemic of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which was ruined in Wuhan (China) and consequently spread worldwide...