Pathway Mutations Research Articles

A first-in-human, phase 1/2 trial of FOG-001, a β-catenin:TCF antagonist, in patients with locally advanced or metastatic solid tumors.

TPS3175 Background: The Wnt/β-catenin pathway is a frequently activated oncogenic pathway and a well-described driver of many cancers. FOG-001 is designed to be a first-in-class direct inhibitor of β-catenin that blocks β-catenin’s interaction with the T-cell factor (TCF) family of transcription factors. Preclinical studies have indicated FOG-001 can cause tumor growth inhibition and regression by disrupting β-catenin-dependent signaling. FOG-001 is unique from previously reported Wnt/β-catenin pathway modulators as it is designed to directly inhibit TCF transcription factor and β-catenin interaction, the most downstream node in the Wnt pathway. It is hypothesized FOG-001 will abrogate the hyperactivation of the Wnt pathway that is driven by most known pathway mutations. Methods: This first-in-human, Phase 1/2, multicenter, open-label, dose escalation (Parts 1a and 1b) and dose-expansion (Part 2) study is evaluating the safety/tolerability, pharmacokinetics (PK), pharmacodynamics (PD), and antitumor activity of FOG-001 in patients with advanced or metastatic solid tumors. Patients with the following tumor types are eligible: microsatellite stable (MSS) colorectal cancer (CRC) or any solid tumor with documented Wnt pathway activating mutation (WPAM) (Part 1a), MSS CRC only (Part 1b) and MSS CRC, gastric/gastroesophageal (GEJ) cancer, non-small cell lung cancer (NSCLC), and any solid tumors with documented WPAM in Part 2. Patients must have received ≥1 prior systemic anticancer therapy(ies) and be ineligible for curative surgery or curative chemoradiation. In Part 1, FOG-001 is administered at escalating doses via intravenous (IV) infusion on Days 1, 8, 15, and 22 of each 4-week cycle; additional dosing regimens may be explored. After selection of the preliminary recommended Phase 2 dose(s) (pRP2D) and regimen(s) in Part 1, the following cohorts will be enrolled to receive FOG-001 at the pRP2D in Part 2: (2a) MSS CRC; (2b) NSCLC with documented WPAM in adenomatous polyposis coli (APC) or β-catenin; (2c) gastric/GEJ cancer with documented WPAM in APC or β-catenin; and (2d) solid tumors with ≥1 documented WPAM in any predefined Wnt pathway genes. The primary endpoints are safety/tolerability (Parts 1 and 2), and also preliminary antitumor activity (objective response rate) (Part 2). Secondary endpoints are PK, PD, and additional antitumor activity assessments. Enrollment in Part 1 is ongoing. Clinical trial information: NCT05919264 .

Survey of actionable driver mutations KRAS and EGFR in non–small cell lung cancer to evaluate coexisting splicing gene and pathway mutations: A CBioportal database analysis.

8561 Background: Molecularly targeted therapies have advanced treatment for certain cancers, such as lung cancer with specific EGFR or KRAS mutations. However, oftentimes the tumor becomes eventually treatment resistant. This may be partly because cancers driven by EGFR/KRAS mutations may also harbor additional co-occurring genetic alterations. In non-small cell lung cancer (NSCLC), aberrations in RNA splicing pathways have shown substantial implications for tumor behavior and therapeutic responsiveness. Our study focuses on elucidating the interplay between RNA splicing defects and prominent NSCLC mutations. Methods: In this retrospective, cross-sectional study, we analyzed data from 20,719 NSCLC patients enrolled in participating institutions between 2017 and 2022. The data were sourced from the American Association for Cancer Research Genomics Evidence Neoplasia Information Exchange (version 13.0). EGFR L858R, EGFR E746_750del, KRAS G12C, KRAS G12D and other KRAS G12 mutations cases were identified and individually analyzed to abstract co-occurring RNA splicing genomic alterations. Results: Among 20,719 patients with NSCLC, we identified 1309 patients with EGFR L 858R mutation, 1121 patients with EGFR E746_750del mutation, 2446 with KRAS 12C, 852 with KRAS G12D, 1107 with KRAS G12V, 452 with KRAS G12A, 173 with KRAS G12F, and 109 with KRAS G12S. RBM 10 was the most common co-occurring RNA splicing gene for EGFR L 858R (178, 13.6%), followed by CDK12 (31, 2.3%) and SPEN (27, 2 %). Similarly, the most prevalent co-occurring RNA splicing genes with EGFR E746_750del were RBM 10 (38, 3.4%) and SPEN (23, 2 %). RBM 10 was the most prevalent co-existing RNA splicing gene for KRAS G12C (211, 8.6 %), KRAS G12D (63, 7.4 %), KRAS G12V (80, 7.2%), KRAS G12A (59, 13.1%), KRAS G12F (12, 7.0%), KRAS G12S (11, 10.1%) and KRAS G12R (6, 8%). Conclusions: Our study uncovers a crucial link between EGFR and KRAS mutations in NSCLC and RNA splicing gene dysregulation, particularly involving RBM10. Further research in this field is warranted as targeting RNA splicing, alone or alongside existing targeted inhibitors, could substantially enhance treatment efficacy for EGFR+ or KRAS+ NSCLC patients. [Table: see text]

Analysis of patch-based GCN risk score distribution corresponding to gene mutations in colorectal cancer using whole slide images.

e15650 Background: Colorectal cancer (CRC) is one of the most common malignancies, with the third highest incidence and the second highest mortality in the world. Risk scores are typically employed to predict outcomes such as disease risk, prognosis, or treatment response. Risk scores are usually calculated by combining biomarkers or genetic variants with statistical models, such as logistic regression or Cox proportional hazards models, and then observe the relationship between genetic variations and survival time through survival analysis. We have constructed a deep learning model based on Graph Convolutional Networks (GCNs), which is capable of predicting risk scores using Whole Slide Images (WSIs). Statistical analyses were applied to explore the distribution of risk scores associated with different variants in colorectal cancer. Methods: We performed risk scores prediction on a total of 384 samples from TCGA-COAD and TCGA-READ using our patch-based GCN model. We analyzed the distribution of risk scores in colorectal cancer samples and investigated the effects of gene mutations in key pathways on these risk scores. Results: Risk score predictions by our patch-based GCN model were conducted on 384 samples, revealing that the maximum, minimum, median, mean, and standard deviation of risk scores were -0.78, -1.89, -1.34, -1.34, and 0.20, respectively. The data overall conformed to a normal distribution ( p < 0.05 ). We selected core genes in key pathways combined with top ten genes with the highest mutation frequency in colorectal cancer for statistical analysis to explore the correlation with the predicted risk scores. These gene mutations were found in a total of 346 patients. The results indicated that mutations in the TP53 and OBSCN genes led to significant differences in risk scores as predicted by our model ( p < 0.05 ). The risk scores based on gene mutations also have significant differences and consistent trend in these genes. Conclusions: Our results indicate the risk scores generated by the patch-based GCN model have the consistent trend with the risk scores generated by mutation information of core genes in colorectal cancer. Whether risk scores based on digital pathology prediction can replace mutation detection in predicting patient survival status requires further exploration.

Comprehensive whole genome and transcriptome analysis of patients with advanced solid tumor treated with immune checkpoint inhibitor therapy in the pan-cancer cohorts from the Marathon of Hope Cancer Centres Network Study (MOHCCN).

2645 Background: Immune checkpoint inhibitors (ICI) improve survival in multiple advanced solid tumors but many patients do not benefit. We conducted a comprehensive whole genome transcriptome sequencing (WGTS) analysis to identify predictors of immune sensitivity. Methods: Clinical and molecular data from archival or pre-treatment FFPE tumor tissue were available for analysis from The Marathon of Hope Cancer Centres Network Study (MOHCCN). It includes patients (Pts) with advanced solid tumors and ECOG PS 0 or 1 treated with ICIs targeting PD-1, PD-L1, or CTLA-4 in the INSPIRE (NCT02644369) and OCTANE (NCT02906943) cohorts. Response (R) to ICI was defined as radiological and clinical response without PFS event at 6 months; versus non-response (NR) as radiological or clinical progression within 6 months. Responders without evidence of progression for >12 months were categorized as durable responders (DR). Nucleic acids were sequenced using Illumina NovaSeq 6000 system targeting minimum coverage of 80X and 30X for tumour and normal WGS, respectively and 80M reads for tumour RNA-seq. WGTS data were integrated with clinical data to identify associations with response to ICIs. Also, an analysis of immune cell types was conducted using multiplexed IHC and RNA-Seq deconvolution (CIBERSORT). Results: 59 Pts were included in this analysis: 28 (R) and 31 (NR). The most common tumor types were head and neck (n = 19) and melanoma (n = 7). Median age was 62 years (range 24-81); male 58% and median follow-up was 58 months (range 11-280). The most frequent ICI was pembrolizumab 76%, with 90% of all pts receiving ICI monotherapy and 10% combination. 75% of pts received chemotherapy prior to ICI. Higher tumor mutation burden (TMB) was observed in R vs NR (median 13 vs 5 coding mut/Mb, p=0.001), with the highest TMB in patients with DR (median 14 mut/Mb ). Differential RNA gene expression analysis showed NR had increased expression of several oncogenic pathway signatures, including MYC targets, G2M checkpoint, and E2F targets. Differential abundance analysis of immune cell types did not yield any differences of immune cell populations amongst R versus NR after correction for multiple comparisons. Responders had significant enrichment in mutations in WNT/β-catenin pathway genes in both coding (APC, AMER1, LZTR1, TCF7L2) and promoter regions (CTNNB1). Notably, the 6 Pts with CTNNB1 promoter mutations had significantly increased CTNNB1 gene expression (p = 0.005). Conclusions: ICI responders showed enrichment in coding mutations of several negative regulators of the Wnt/β-catenin pathway and non-coding promoter mutations in CTNNB1 compared with non-responders. Further investigation is ongoing to biologically validate how these mutations in the Wnt/β-catenin pathway may lead to improved response to ICI.

Single-cell and bulk sequencing analysis to evaluate the oncogenic role of PDE3A in pan-cancer and validation in breast cancer.

e15128 Background: PDE3A is involved in critical physiological processes through the hydrolysis of cycle AMP (cAMP) and GMP (cGMP). Its role in the occurrence and progression of cancer has recently attracted attention, but carcinogenic mechanism in pan-cancer has not been fully elucidated. Methods: We explored the expression, prognostic and diagnostic value, mutation, methylation, immune infiltration, and signaling pathway enrichment analysis of PDE3A in pan-cancer by combining multiple bioinformatics databases and single-cell sequencing analysis. Furthermore, we verified the protein and mRNA expression levels of PDE3A and investigated its oncogenic role in the progression of breast cancer (BRCA). Results: PDE3A was expressed at lower levels than normal tissues in most cancers and showed a wonderful prognostic value. PDE3A was strongly correlated with immune cells, especially cancer-associated fibroblast (CAF), and was involved in various vital signaling pathways. Furthermore, PDE3A could facilitate BRCA progression by promoting cells invasion and migration, and it may be associated with the efficacy of endocrine therapy in ER+ BRCA. Conclusions: We provided new insights into the carcinogenic effect of PDE3A in pan-cancer. PDE3A may be a potential biomarker for cancer diagnosis and prognosis, and it is also a promising target for cancer immunotherapy.

Examination of genomic profile of true single circulating tumor cells (sCTC) from hepatocellular carcinoma and its effect on mutational features.

e15039 Background: Hepatocellular carcinoma (HCC) is the fifth leading cause of cancer-related deaths worldwide. Despite numerous NGS studies unveiling diverse mutational patterns through tissue biopsies, the absence of tissue for biopsy and distinct biomarkers complicates both diagnosis and treatment. The utilization of sCTC genomics holds promise in furnishing clinically relevant and actionable insights to tailor personalized diagnostics and therapy for HCC. We present a comparative analysis of sCTC and paired ctDNA obtained from primary HCC patients for better Tx possibilities. Methods: Genomic profile from 24 sCTCs/CTC clusters (19 sCTCs, 79%; 5 CTC clusters, 21 %) revealed distinct mutational patterns compared to paired ctDNA. Live sCTCs/CTC clusters were isolated from peripheral blood of treatment naïve 12 Hepatobiliary Cancer with advanced and metastatic disease patients using OncoRadar technology. Whole genomes from sCTCs/CTC clusters were amplified, target enriched with hybridization capture using a comprehensive 1080 gene panel-OncoIndx to obtain sequencing libraries, and sequenced on Illumina NextSeq2000 platform in paired end mode (depth 500x). The raw sequence alignment and variant calling was performed using iCare software. Paired ctDNA samples were sequenced the same way, except at the depth of 5500x. Results: Pathogenic (P)/likely pathogenic (LP) variants were detected from all sCTCs, while ctDNA was negative for 40% samples. sCTCs showed at least twice as many P variants compared to paired ctDNA. ATM (50%), PIK3CA (42%), ARID1A /1B (42%), TP53/RB1 (34%), and IDH1 (34%) were among the most frequently mutated genes, while 42% sCTCs showed amplified CCND1/2 variants. In comparison, paired ctDNA had no distinct mutational pattern. Genomic profile of sCTC showed concordance with paired ctDNA for at least one gene mutation when compared at patient level. At pathway level, all sCTCs were mutated for at least one HRR pathway component, while 60% sCTCs had at least one mutation in receptor tyrosine kinase (RTK) pathway (FGFR1, ERBB, ALK, ROS1). sCTC population showed a strong cooccurrence of HRR mutation and epigenetic regulatory pathway mutations (OR =4, CI=0.4-60). At individual mutation level, 30 % concordance was observed in sCTC population, suggesting high mutational heterogeneity. Besides actionable targets, 50% sCTC were enriched with resistance conferring variants such as STK11, NF1, STAT5B, and RB1. Conclusions: The genomic profile of sCTCs in primary HCC pts revealed a complex mutational landscape, offering complementarity to ctDNA for clinical insights. sCTCs exhibited more actionable targets and greater heterogeneity compared to paired ctDNA, making sCTC genomics valuable for pts ineligible for tissue biopsy or lacking clinically relevant information from ctDNA.

Alliance EAY191-A6: FOLFOX in combination with binimetinib as second-line therapy for patients with advanced biliary tract cancers (BTCs) with MAPK pathway alterations: A ComboMATCH treatment trial.

TPS4196 Background: Advanced BTC patients have poor prognosis. Up to 40% of BTCs have KRAS mutations and are associated with worse overall survival (OS). With a median OS of 7.7 months in KRAS wild-type compared to 1.7 months in KRAS mutated disease, these alterations are independent poor prognostic factors in BTC. Gemcitabine and cisplatin (GC) with or without immunotherapy are often used as 1st-line therapies. However, there is a lack of data on best 2nd-line regimens. mFOLFOX6 (5-fluorouracil [5-FU], leucovorin [LV], oxaliplatin) or liposomal irinotecan+5-FU+LV are options when no biomarkers are found (e.g., MSI-H, BRAFV600E, FGFR-fusions, IDH1-mutation, HER2-overexpression). Prior studies do not demonstrate benefit with MEK inhibitors (MEKi), but none of the studies had biomarker selection. Pre-clinical studies in BTC cell lines suggest synergy between MEKi and 5-FU. Thymidylate synthase (TS )levels induced by 5-FU are downregulated by addition of binimetinib. Early clinical studies show safety and tolerance of this combination. In this study, we will evaluate if the combination of mFOLFOX6+binimetinib improves OS for patients with BTC and MAPK mutations compared to mFOLFOX6 alone in 2nd-line therapy. Methods: EAY191-A6 is a treatment study arm of the NCI ComboMATCH master registration trial EAY191. The A6 trial has a randomized phase II design, enrolling a maximum of 66 patients. Patients with any MAPK pathway mutations except those with available therapies will be eligible. Patient must first enroll to the EAY191 master trial. Local molecular results may be used for enrollment. Submission of tissue at baseline is mandatory. Eligible patients will be randomized 1:1 to mFOLFOX6 vs mFOLFOX6 + binimetinib (45 mg oral twice a day every 14 days). Stratification factors include location and stage of disease. Primary efficacy analysis will compare OS in the intent-to-treat population. If the observed hazard ratio (HR) of experimental arm vs standard of care is < 0.545 (corresponding to an observed increase in OS by 5 months or longer), experimental treatment will be considered superior. An interim futility analysis at 50% of expected events will be conducted. If the observed HR is ≥ 1, experimental treatment will not be considered superior, and accrual maybe suspended. Secondary endpoints include progression-free survival, objective response rate, duration of response, disease control rate and toxicity of treatments. Exploratory objectives include prognostic modeling, correlations of genomic alterations with response or resistance and use of machine learning for outcome prediction. This study is active and open to accrual. Clinical trial information: NCT05564403 .

Tumor evolution of brain-specific tropism in metastatic renal cell carcinoma.

4530 Background: Brain metastases (BMets) pose a clinical challenge in the management of patients (pts) with metastatic renal cell carcinoma (RCC), leading to significant morbidity and mortality. Herein, we sought to comprehensively characterize the molecular landscape of BMets in RCC. Methods: We performed panel-based DNA (DNAseq) and whole transcriptome (RNAseq) sequencing to analyze BMets, matched non-Brain metastases (nBMets), and matched primary renal tumors (PRT) from pts who underwent surgical resection of BMet(s) from RCC at our institution. Results: Our cohort consisted of 95 samples from 53 patients (BMets = 54, nBMets = 14, PRT = 27) with clear cell histology in 45 pts (84.9%). DNAseq was available 85 samples (50 pts). Patient-level mutations revealed recurring mutations in VHL(18 pts, 36%), TP53 (n = 12 pts, 24%), PBRM1(12 pts, 24%), SETD2(12 pts, 24%), and BAP1(4 pts, 8%). Mutations within the MTOR signaling pathway were enriched, with 25 pts (50%) having at least one mutation in PTEN (12 pts, 24%), TSC1 (4 pts, 8%), TSC2 (5 pts, 10%), or MTOR (9 pts, 18%). Copy number analyses revealed frequent deletions in chr14q21 (34 pts, 68%) and chr9p21 (35 pts, 70%) and gains in chr20q13 (n = 31, 62%) and chr7p15 (n = 31, 62%). At the sample-level, PTEN mutations were more common in BMets (11 pts, 22.9%) vs nBMets (0 pts) and PRTs (3 pts, 12%, p = 0.124), as were deletions in chr13q22 (BMets = 13pts [26.5%], nBMet = 1pts [8.3%], PRT = 1 [4%]; p = 0.036) and gains in chr20q13 (BMets = 30pts [61.2%], nBMet = 4pts [33.3%], PRT = 8 [32%]; p = 0.03). Deletions in chr9p21 were enriched in BMets (32, 65.3%) and nBMets (8, 66.7%) relative to PRTs (7, 28%, p = 0.006), whereas other copy number alterations and somatic mutations exhibited similar proportions across specimen sites. Differential expression analysis performed on 86 samples (51 pts) identified 806 differentially expressed genes (DEGs) between BMets and PRT (adjusted [adj.] p < 0.05) and 399 DEGs between BMet and nBMets (adj. p < 0.05). Gene set enrichment analysis of MSigDB Hallmark gene sets revealed upregulation of MTORC1 signaling, glycolysis, and MYC targets in BMets comparted to PRT and nBMETs (adj. p <0.0001). In contrast, immune-related gene sets, such as interferon-alpha, interferon-gamma, and tumor necrosis factor-alpha, were enriched in PRT relative BMets (adj. p <0.0001), but not nBMETs (adj. p > 0.05). CIBERSORT cellular deconvolution analysis comparing BMets with PRT revealed decreased proportions of M1 macrophages (p = 0.0003) and CD8+ T-cells (p = 0.0106), but an increase proportion of M2 macrophages (p = 0.0009). Conclusions: RCC with brain metastases are characterized by distinct copy number alterations, enrichment of MTOR pathway mutations, MTOR pathway hyperactivation, and an immunosuppressive tumor milieu. These findings may hold therapeutic implications of MTOR pathway inhibition and immune modulators in treating RCC BMets.

Interim analysis (IA) of the giredestrant (G) + everolimus (EVERO) arm in MORPHEUS Breast Cancer (BC): A phase I/II study of G treatment (tx) combinations in patients (pts) with estrogen receptor-positive (ER+), HER2-negative, locally advanced/metastatic BC (LA/mBC).

1059 Background: Endocrine therapy (ET) + a cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) is a therapeutic mainstay for first-line tx of ER+ mBC. Finding effective ET combinations after progression remains a challenge; however, targeting the Akt/mTOR pathway is a promising approach. G is a highly potent, non-steroidal, oral (PO), selective ER antagonist and degrader that is well tolerated and achieves robust ER occupancy. EVERO is an approved mTOR inhibitor. Here, we present a 16-week IA of the G + EVERO arm in MORPHEUS BC (NCT04802759). Methods: Eligible pts with disease progression on 1–2 lines of ET (including a CDK4/6i) for LA/mBC were randomized 1:6 to receive G (30 mg PO daily [QD]) or G + EVERO (10 mg PO QD) until disease progression (PD)/unacceptable toxicity. The study was not designed to make explicit power and type I error considerations for a hypothesis test. Primary endpoints were safety and objective response rate (ORR); other endpoints included progression-free survival (PFS), overall survival, clinical benefit rate, disease control rate (DCR), duration of response, and pharmacokinetics. Steroid mouthwash was recommended for prophylaxis or treatment. Genetic alterations were defined using baseline circulating tumor DNA. Results: Results for the G arm have been presented previously and are not included here. As of July 24, 2023, 15 pts were enrolled in the G + EVERO arm: 66.7% and 33.3% received 1–2 prior lines of therapy for LA/mBC, respectively; 26.7% had prior fulvestrant, and 73.3% had liver metastasis at enrollment. One pt had prior capecitabine. Safety data are in the table. Confirmed ORR in the G + EVERO arm was 26.7% (n = 4). Partial responses were reported in 26.7% of pts (n = 4; all had ESR1 mutations, 1 also had an Akt pathway mutation), 46.7% of pts (n = 7) had stable disease, and the DCR was 53.3% (n = 8). Median PFS was not reached at data cutoff. No clinically relevant drug–drug interactions were observed. Conclusions: Safety of G + EVERO was aligned with the individual safety profile of each drug with no overlapping toxicities or new safety signals seen. An encouraging efficacy signal was observed with G + EVERO in pts with PD on 1–2 lines of ET (including a CDK4/6i). G + EVERO is being further investigated in the Phase III evERA BC trial (NCT05306340). Clinical trial information: NCT04802759 . [Table: see text]

Study of single live circulating tumor cells capture and their genomic profile and enriched mutations of PIK3CA and HRR pathway in patients with breast cancer.

e13161 Background: Capturing live single circulating tumor cells (sCTC) for intra-cellular compressive genomic profiling and concordance with ctDNA is highly challenging. Utilization of single sCTC genomics holds promise for detecting clinically relevant, actionable insights to tailor personalized therapy, especially when No Mutations Detected (NMDs) using CfDNA. Despite numerous studies providing valuable insights on mutational landscapes from breast tumors, predicting cancer progression, metastasis, and relapse continue to pose major challenges. ctDNA is suboptimal for 30-40% population with disease relapse/progression after a primary therapy. We show comprehensive genetic profile (CGP) of live sCTCs and paired ctDNA from a diverse breast cancer population. Methods: 26 live sCTCs (2 CTC clusters) were isolated from 12 patients. Live sCTCs were isolated from 12 Breast Cancer patients using OncoRadar live sCTC capture method. Whole genomes were amplified using multiple displacement amplification, target enriched with hybridization capture using OncoIndx (CGP 1080 gene panel) to obtain sequencing libraries, and sequenced on Illumina platform in paired end mode (depth 500x). The raw sequence alignment and variant calling was performed using iCare software. Paired ctDNA samples were processed the same way, except for sequencing depth (5500x). Results: Compared to paired ctNDA, genomic profiling of sCTCs revealed complex mutational patterns. Whereas sCTCs showed least two pathogenic (P) or likely pathogenic (LP) variants, paired ctDNA was negative for 25% cases (3/12). 92% sCTCs showed mutations in the PIK3CA-MTOR pathway with PIK3CA being the most prevalent (73 %). A significant association was observed between co-occurrence of HER2 amplification and PIK3CA mutations (P =0.04, OR=10). Similarly, sCTCs showed a strong correlation between HRR pathway and PIK3CA pathway mutations (r=0.76, P =0.003, OR=3.43). Genomic profile of sCTCs and paired ctDNA showed concordance with at least one gene mutation when compared at individual patient level. Additionally, at individual mutation level, PIK3CA exon 10 mutations were most frequent (61.5%) along with BRCA2 pathway variants, followed by IDH1/2(54%), ARID1A (50%), NRAS (46%), FGFR2 (42%) and TP53 (42%). Interestingly, 70% sCTCs showed the presence of therapy resistance conferring variants (NF1, ARID1A, ESR1, RB1 and PTEN), compared to only 25 % observed in paired ctDNA. Conclusions: The genomic profile of sCTCs represents true tumor heterogeneity and can be combined with ctDNA for better clinical outcome. sCTCs exhibited high mutational heterogeneity compared to paired ctDNA. Therapy resistance signatures were more prevalent in sCTCs and may offer valuable clinical insights for patients unable to provide tissue biopsy or show negative ctDNA.

PAS-004: A novel macrocyclic MEK inhibitor to inhibit cancer cell growth in vitro and tumor growth in mouse xenograft studies.

3126 Background: Three MEK inhibitors have been approved to date to treat melanomas driven by RAS pathway mutations and a 4th compound (selumetinib) is approved to treat Neurofibromatosis type 1 (NF1) in pediatric patients. PAS-004 is the first macrocyclic MEK inhibitor in development for solid tumors and NF1. Methods: Ten NRAS mutant cancer cell lines were cultured for 48 hrs in the presence of the MEK inhibitor PAS-004, trametinib, binimetinib (bini) and selumetinib (selu) and cell proliferation was assayed using a Cell Titer Glo luminescence assay. The anti-tumor activity of PAS-004 was compared with selu and bini in two mouse xenograft studies using NRAS mutant human hepatocellular carcinoma (HCC) and lung carcinoma cell lines. Dose response was assessed with treatment initiated when the tumor reached a volume of 150 mm3 and mice treated for 20 days. Body weights and tumor volumes were measured twice weekly. Tumors were excised at the end of the study and pERK inhibition was assessed by Western blot. Terminal plasma was collected for PK analysis. Results: PAS-004 strongly inhibited 5/10 NRAS mutant cancer lines with IC50 values ranging from 0.024 to 0.306 µM. Maximal growth inhibition of >50% was achieved by PAS-004 in 8 cell lines and PAS-004 achieved greater maximal inhibition in 7/10 lines vs selu and bini. PAS-004 inhibition was comparable to trametinib in 5/10 cell lines tested. However, in contrast to trametinib PAS-004 did not reach a plateau at the highest dose tested in three of these lines. In the HCC xenograft study the highest dose of PAS-004 completely prevented tumor growth and the same dose caused a 69% reduction in tumor volume in the lung carcinoma xenograft study. The anti-tumor efficacy of PAS-004, when taken at equivalent doses, was shown to be superior to that of bini and selu. Specifically, PAS-004 at dose levels of 10 mg/kg and 5 mg/kg, once daily, exhibited higher efficacy compared to bini and selu at dose levels of 5 mg/kg and 2.5 mg/kg, when administered twice daily, respectively. No significant differences in body weight loss were seen between the compounds. Conclusions: The novel macrocyclic MEK inhibitorPAS-004 inhibited NRAS mutant tumor growth in mouse xenograft studies with similar activity as the approved MEK inhibitors selu and bini. In vitro, PAS-004 provided greater maximal growth inhibition of NRAS lines than selu and bini. These results support investigating PAS-004 further and a clinical trial in patients with advanced solid tumors carrying RAS pathway mutations, including NRAS variants, is ongoing.

Association between somatic mutation pathways and treatment response in patients with biliary tract cancers (BTCs).

e16196 Background: Comprehensive somatic genomic profiling has become the standard of care for patients with BTCs, serving to identify targetable mutations and aiding in prognostication. While previous studies have identified individual somatic mutations such as TP53, CDKN1A, and KRAS as negative prognostic markers, little is known about their role as predictive biomarkers. This study aimed to investigate the predictive potential of somatic mutations and pathways using commercially available next-generation sequencing. Methods: We conducted a retrospective cohort study at Beth Israel Deaconess Medical Center (BIDMC) from January 2016 to January 2023, with data censoring in January 2024. Patient characteristics, including age, gender, race, stage, site of metastasis, performance status, and survival status, were collected. Somatic genomic alterations data were extracted from FoundationOneCDx, a commercially available NGS platform designed to capture 324 genetic alterations validated for therapy targets or unambiguous drivers of oncogenesis. Genetic alterations were classified into 14 oncogenic pathways constructed based on the TCGA and Reactome databases. Multivariate Cox proportional hazards regression analysis was performed between pathway alterations, progression-free survival and overall survival, accounting for selected covariates with p < 0.05 or potential known confounders. Results: Among 97 BTCs, 90 were successfully sequenced. Among these, 40 patients received gemcitabine and cisplatin, and 28 received fluorouracil and oxaliplatin (FOLFOX) therapy. Intrahepatic cholangiocarcinoma was present in 70% of cases, perihilar or distal cholangiocarcinoma in 27%, and gallbladder carcinoma in 3%. At presentation, 18% had stage I disease, and 44% had stage IV. The median follow-up time was 15 months. A total of 339 genomic alterations were identified, with 8% of samples harboring FGFR fusion or mutation, 9% IDH1 mutation, 6 % HER2 amplification, 30% KRAS mutation, and 32% with TP53 mutation. The most affected pathways were the cell cycle (66%) and DNA repair (50%). In multivariate regression analysis accounting for age, ECOG, and anatomical location, TP53 mutation was associated with shorter progression-free survival on gemcitabine and cisplatin treatment (n = 11, 2 vs. 6 months, HR 4.19, 95% CI 1.51 – 11.7, p < 0.01), whereas cell cycle pathway mutation was associated with longer progression-free survival (n = 14, 6 vs. 5 months, HR = 0.43, 95% CI 0.19-0.96, p < 0.05). No association was found between oncogenic pathways and treatment response to FOLFOX therapy. Conclusions: TP53 mutation is associated with a worse response, whereas cell cycle pathway mutations are associated with an improved response to gemcitabine and cisplatin therapy in patients with BTCs. Further research is needed to understand the mechanisms contributing to these observed effects.

Sequential use of PI3K/AKT/mTOR pathway inhibitors alpelisib and everolimus in patients with hormone receptor-positive (HR+) metastatic breast cancer.

1057 Background: Alpelisib (A), a PI3K inhibitor, is FDA-approved with fulvestrant for patients with PIK3CA-mutated HR+/HER2- MBC. Everolimus (E), an mTOR inhibitor, is FDA-approved with endocrine therapy (ET) regardless of PI3K/AKT/mTOR pathway mutation status. The efficacy and safety of sequential treatment with these pathway inhibitors is not well described. Methods: This single-center retrospective cohort study identified patients with HR+/HER2- MBC treated with both A and E sequentially, each in combination with ET, in either order from 2012-2023. We collected information on patient demographics, clinical and pathologic characteristics, treatment history, treatment adverse effects, and dates of disease progression (defined as radiographic or clinical progression leading to treatment change) from medical records. Patients treated first with E then A were categorized as Group 1 and those first with A then E as Group 2. Rates of prior CDK4/6i use were compared between groups with the chi-square test; differences in prior lines of therapy were assessed with the Wilcoxon rank sum test. Median PFS1 (PFS on 1st pathway inhibitor) and PFS2 (PFS on 2nd pathway inhibitor) were computed using the Kaplan-Meier method and the impact of prior treatment on PFS2 between groups was compared using Cox proportional hazards analysis. Results: 115 patients with HR+/HER2- MBC were included in this study. There were 62 (54%) patients in Group 1 and 53 (46%) patients in Group 2. Median prior lines of therapy in the metastatic setting for Group 1 was 4 (range 1-13) and for Group 2 was 3 (range 1-8; p=0.08). Median number of intervening therapies between E and A in Group 1 was 2 (range 0-8) and between A and E in Group 2 was 0 (range 0-4; p<0.001). 34/62 (55%) patients in Group 1 and 45/53 (85%) in Group 2 received prior CDK4/6i ( p<0.001). In Group 1, 49/62 (79%) of patients discontinued E for progression and 13 (21%) discontinued for toxicity. Median PFS1 was 9.2 months (95%CI 5.5-13.0) and PFS2 was 5.0 months (95%CI 4.6-7.9). In Group 2, 34/53 (64%) of patients discontinued A for progression and 19 (36%) discontinued for toxicity. Median PFS1 was 9.3 months (95%CI 7.0-14.0) and PFS2 was 3.5 months (95%CI 3.0-4.1). After adjusting for prior CDK4/6i use and prior lines of therapy (total and intervening), PFS2 was not significantly different between the groups. Genomic information will be included at the time of presentation. Conclusions: This is the largest retrospective study to-date of patients treated sequentially with PI3K/AKT/mTOR pathway inhibitors. PFS was longer with the 1st pathway inhibitor than with the 2nd regardless of sequence. This has implications for optimal integration of capivasertib, an AKT inhibitor, into HR+ MBC treatment. Prospective studies testing optimal sequencing are needed.

Phase 1 study of ERK inhibitor JSI-1187 for patients with advanced solid tumors with MAPK pathway mutations.

e15111 Background: Mitogen-activated protein kinase (MAPK) pathway is a key regulator of cellular proliferation and survival, it is highly correlated with the occurrence of many cancers, JSI-1187 is a potent and reversible small molecule inhibitor of ERK1/2. This study is designed to assess the safety and efficacy of ERK Inhibitor JSI-1187 for advanced MAPK-mutant tumors patients. Methods: This is a phase 1 study included dose escalation and expansion (NCT06239623). The dose escalation study was conducted using a 3+3 escalation design to assess JSI-1187 16, 24, 32, 48,72, 80 and 96 mg BID, and 80, 128 and 152mg QD, repeated q 28 days. Dose limiting toxicities (DLTs) were predefined in the protocol. MAPK-mutant tumor patients whose disease progressed after existing standard treatment were treated. RAS and BRAF-mutated solid malignant tumors were explored in the dose-escalation phase. Results: As of December 23, 2023, 26 patients were enrolled, including 23 from the BID group and 3 from the 80mg QD group. No DLT was observed in QD group, 1 DLT (1 macular edema) and 2 DLTs (1 macular edema and 1 pneumonia) were observed at 96 and 80 mg BID, respectively. The most common JSI-1187 16-96mg BID related AEs were hypoalbuminemia (69.6%), rash (62.5%), and anemia (43.5%), while the most common JSI-1187 80mg QD related AEs were rash (100%), leukopenia (100%) and neutropenia (66.7%). The most common Grade 3 JSI-1187 16-96mg BID treatment-related AEs were anemia (17.4%) and thrombocytopenia (8.7%). Tumor response was evaluated in 18 of the total 26 patients. SD was noted as best response at doses of 16 – 96 mg BID and 80 mg QD including 29.8% tumor shrinkage in 1 NRAS-mutant melanoma patient treated at 32mg BID and 21.6% tumor shrinkage in 1 MEK1 K57N-mutant lung cancer patient treated at 72mg BID. Conclusions: JSI-1187 monotherapy is well-tolerated in advanced solid tumor patients and demonstrated preliminary antitumor effect. Current evidence supports future exploration of JSI-1187 as monotherapy, and in combination, in patients with MAPK-mutant tumors. Research Sponsor: JS Innopharm Clinical trial information: NCT06239623 .

Identifying mutations in ctDNA to predict antibody-drug conjugate response in breast cancer.

e13074 Background: Metastatic breast cancer (mBC) is a complex disease, and outcomes remain poor because new therapies are needed. A new class of drugs, antibody-drug conjugate (ADC), has shown effectiveness across all breast cancer subtypes. Yet FDA- approval for these therapies is restricted only to HER2 and triple-negative subtypes. Therefore, we urgently need to identify which patients, regardless of subtype, will respond to ADCs. The advent of circulating tumor DNA (ctDNA) offers a unique noninvasive method to capture breast cancer (BC) heterogeneity. Recently, ctDNA testing has been employed in clinical practice to guide targeted therapies for mBC, particularly in cases of hormone receptor positive (HR+) disease with mutations in PIK3CA and ESR1. The clinical implications to predict response to ADC therapy in BC remains unclear. Here we test the hypothesis that ctDNA can detect mutations that predict response to novel ADCs. Methods: We analyzed a subset of patients from the Dallas Metastatic Breast Cancer Study comprised of patients with mBC who underwent ctDNA testing using the Tempus xF liquid biopsy ctDNA sequencing panel. The data was analyzed from a single academic medical center between the initial year of ctDNA collection in 2019 to 2023. We identified detectable mutations from patients and addressed a relationship by using Metascape. Relevant signaling pathways were identified: APOBEC, ErbB signaling, p53 and Ras-MAPK pathway. Patients with triple negative, HER2, and HR BC were examined for ADC response and associated mutations. Survival analyses were estimated using Kaplan-Meier and Gehan Breslow Wilcoxon test for statistical analysis. Results: We identified 43 patients with HR+ mBC who had at least one mutation within the Ras-MAPK pathway and 10 of 43 received ADC therapy. Median survival of patients who received ADC therapy 58 months (n=10) vs not receiving ADC therapy 33 months (n=33) (p < 0.05). Of the ten patients who received ADC treatment, 60% had 1+ HER2 staining on tissue biopsy. 70% of patients received Trastuzumab deruxtecan (T-DXd) and 30% received Sacituzumab govitecan (SG). SG was given to patients with negative HER2 staining on biopsy. Patients with at least one mutation within ABOBEC, ErbB signaling, and p53 pathways did not have statistically significant differences in mOS. Conclusions: In HR+ mBC, detection of mutated genes associated with the Ras-MAPK pathway by ctDNA was associated with a more favorable response when treated with ADCs. These findings are exciting because HR+ BCs are being targeted with ADCs regardless of HER2 or TROP2 expression, highlighting the need for new biomarkers to distinguish which HR+ patients to treat. Our retrospective analysis findings are limited by the number of patients with ctDNA testing and also timing of testing. Further studies are needed to solidify the observed correlation between Ras-MAPK pathway mutations and favorable response to ADC treatment.

The GPI-anchor biosynthesis pathway is critical for syncytiotrophoblast differentiation and placental development

The glycosylphosphatidylinositol (GPI) biosynthetic pathway in the endoplasmic reticulum (ER) is crucial for generating GPI-anchored proteins (GPI-APs), which are translocated to the cell surface and play a vital role in cell signaling and adhesion. This study focuses on two integral components of the GPI pathway, the PIGL and PIGF proteins, and their significance in trophoblast biology. We show that GPI pathway mutations impact on placental development impairing the differentiation of the syncytiotrophoblast (SynT), and especially the SynT-II layer, which is essential for the establishment of the definitive nutrient exchange area within the placental labyrinth. CRISPR/Cas9 knockout of Pigl and Pigf in mouse trophoblast stem cells (mTSCs) confirms the role of these GPI enzymes in syncytiotrophoblast differentiation. Mechanistically, impaired GPI-AP generation induces an excessive unfolded protein response (UPR) in the ER in mTSCs growing in stem cell conditions, akin to what is observed in human preeclampsia. Upon differentiation, the impairment of the GPI pathway hinders the induction of WNT signaling for early SynT-II development. Remarkably, the transcriptomic profile of Pigl- and Pigf-deficient cells separates human patient placental samples into preeclampsia and control groups, suggesting an involvement of Pigl and Pigf in establishing a preeclamptic gene signature. Our study unveils the pivotal role of GPI biosynthesis in early placentation and uncovers a new preeclampsia gene expression profile associated with mutations in the GPI biosynthesis pathway, providing novel molecular insights into placental development with implications for enhanced patient stratification and timely interventions.

Genomic characterization reveals distinct mutational landscapes and therapeutic implications between different molecular subtypes of triple-negative breast cancer

Triple-negative breast cancer (TNBC) has high heterogeneity, poor prognosis, and limited treatment success. Recently, an immunohistochemistry-based surrogate classification for the “Fudan University Shanghai Cancer Center (FUSCC) subtyping” has been developed and is considered more suitable for clinical application. Seventy-one paraffin-embedded sections of surgically resected TNBC were classified into four molecular subtypes using the IHC-based surrogate classification. Genomic analysis was performed by targeted next-generation sequencing and the specificity of the subtypes was explored by bioinformatics, including survival analysis, multivariate Cox regression, pathway enrichment, Pyclone analysis, mutational signature analysis and PHIAL analysis. AKT1 and BRCA1 mutations were identified as independent prognostic factors in TNBC. TNBC molecular subtypes encompass distinct genomic landscapes that show specific heterogeneities. The luminal androgen receptor (LAR) subtype was associated with mutations in PIK3CA and PI3K pathways, which are potentially sensitive to PI3K pathway inhibitors. The basal-like immune-suppressed (BLIS) subtype was characterized by high genomic instability and the specific possession of signature 19 while patients in the immunomodulatory (IM) subtype belonged to the PD-L1 ≥ 1% subgroup with enrichment in Notch signaling, suggesting a possible benefit of immune checkpoint inhibitors and Notch inhibitors. Moreover, mesenchymal-like (MES) tumors displayed enrichment in the receptor tyrosine kinase (RTK)-RAS pathway and potential sensitivity to RTK pathway inhibitors. The findings suggest potential treatment targets and prognostic factors, indicating the possibility of TNBC stratified therapy in the future.

Immunotherapy-relevance of a candidate prognostic score for Acute Myeloid Leukemia

BackgroundAcute Myeloid Leukemia (AML) exhibits a wide array of phenotypic manifestations, progression patterns, and heterogeneous responses to immunotherapies, suggesting involvement of complex immunobiological mechanisms. This investigation aimed to develop an integrated prognostic model for AML by incorporating cancer driver genes, along with clinical and phenotypic characteristics of the disease, and to assess its implications for immunotherapy responsiveness. MethodsCritical oncogenic driver genes linked to survival were identified by screening primary effector and corresponding gene pairs using data from The Cancer Genome Atlas (TCGA), through univariate Cox proportional hazard regression analysis. This was independently verified using dataset GSE37642. Primary effector genes were further refined using LASSO regression. Transcriptomic profiling was quantified using multivariate Cox regression, and the derived prognostic score was subsequently validated. Finally, a multivariate Cox regression model was developed, incorporating the transcriptomic score along with clinical parameters such as age, gender, and French-American-British (FAB) classification subtype. The ‘Accurate Prediction Model of AML Overall Survival Score’ (APMAO) was developed and subsequently validated. Investigations were conducted into functional pathway enrichment, alterations in the gene mutational landscape, and the extent of immune cell infiltration associated with varying APMAO scores. To further investigate the potential of APMAO scores as a predictive biomarker for responsiveness to cancer immunotherapy, we conducted a series of analyses. These included examining the expression profiles of genes related to immune checkpoints, the interferon-gamma signaling pathway, and m6A regulation. Additionally, we explored the relationship between these gene expression patterns and the Tumor Immune Dysfunction and Exclusion (TIDE) dysfunction scores. ResultsThrough the screening of 95 cancer genes associated with survival and 313 interacting gene pairs, seven genes (ACSL6, MAP3K1, CHIC2, HIP1, PTPN6, TFEB, and DAXX) were identified, leading to the derivation of a transcriptional score. Age and the transcriptional score were significant predictors in Cox regression analysis and were integral to the development of the final APMAO model, which exhibited an AUC greater than 0.75 and was successfully validated. Notable differences were observed in the distribution of the transcriptional score, age, cytogenetic risk categories, and French-American-British (FAB) classification between high and low APMAO groups. Samples with high APMAO scores demonstrated significantly higher mutation rates and pathway enrichments in NFKB, TNF, JAK-STAT, and NOTCH signaling. Additionally, variations in immune cell infiltration and immune checkpoint expression, activation of the interferon-γ pathway, and expression of m6A regulators were noted, including a negative correlation between CD160, m6A expression, and APMAO scores. ConclusionThe combined APMAO score integrating transcriptional and clinical parameters demonstrated robust prognostic performance in predicting AML survival outcomes. It was linked to unique phenotypic characteristics, distinctive immune and mutational profiles, and patterns of expression for markers related to immunotherapy sensitivity. These observations suggest the potential for facilitating precision immunotherapy and advocate for its exploration in upcoming clinical trials.

Chordoma: Genetics and Contemporary Management.

Chordomas, arising from notochord remnants, are rare neoplasms with aggressive growth patterns despite their histologically low-grade nature. This review explores their embryological origins, molecular markers like brachyury, and genetic alterations driving pathogenesis. Diagnosis relies on advanced imaging and biopsy confirmation due to overlapping features with chondrosarcoma. The WHO classification distinguishes conventional, dedifferentiated, and poorly differentiated chordomas, each with distinct prognostic implications. Recent genomic analyses uncovered recurrent mutations in PI3K signaling pathways and chromatin remodeling genes, informing prognostic models. Surgery remains the cornerstone of treatment, though adjuvant radiation complements surgical resection. Although chordomas are generally considered refractory to medical therapy, emerging targeted molecular strategies show potential promise in ongoing trials. This review aims to provide a concise yet comprehensive overview of chordomas, guiding clinicians in diagnosis, treatment, and prognostication for improved patient outcomes.

Targeting MCL1-driven anti-apoptotic pathways overcomes blast progression after hypomethylating agent failure in chronic myelomonocytic leukemia

RAS pathway mutations, which are present in 30% of patients with chronic myelomonocytic leukemia (CMML) at diagnosis, confer a high risk of resistance to and progression after hypomethylating agent (HMA) therapy, the current standard of care for the disease. Here, using single-cell, multi-omics technologies, we seek to dissect the biological mechanisms underlying the initiation and progression of RAS pathway-mutated CMML. We identify that RAS pathway mutations induce transcriptional reprogramming of hematopoietic stem and progenitor cells (HSPCs) and downstream monocytic populations in response to cell-intrinsic and -extrinsic inflammatory signaling that also impair the functions of immune cells. HSPCs expand at disease progression after therapy with HMA or the BCL2 inhibitor venetoclax and rely on the NF-κB pathway effector MCL1 to maintain survival. Our study has implications for the development of therapies to improve the survival of patients with RAS pathway-mutated CMML.