Actionable Genetic Alterations Research Articles

Abstract A024: Genomic peroxisome proliferator-activated receptor gamma (PPARG) study: A sponsored testing program to identify patients harboring genetic alterations in advanced UC in support of the FX-909 Phase 1 study

Abstract The transcription factor PPARG is associated with the luminal lineage subtype representing ~65% of advanced urothelial cancer (UC) patients. Recurrent genetic alterations in PPARG, fibroblast growth factor receptor 3 (FGFR3), and the heterodimeric binding partner for PPARG, retinoid X receptor alpha (RXRA), are characteristic of this luminal subtype. FX-909, a covalent PPARG inverse agonist, represents a promising first-in-class therapy for patients with advanced UC. FX-909-CLINPRO-1 [NCT05929235] is an open-label Phase 1 study to evaluate the safety, tolerability, pharmacokinetics, biologic activity, and preliminary clinical activity of FX-909. This study includes a Phase 1b expansion cohort, which will enroll advanced UC patients with genetic alterations in PPARG, RXRA, and/or FGFR3. FlareTx is sponsoring a testing program called Genomic PPARG Study (GPS) to enable investigators to identify patients with these relevant genetic alterations. Tumors collected from patients with advanced UC were sequenced using the Tempus xT assay (DNA-seq of 648 genes at 500x coverage; RNA-seq). A clinical report is generated and returned to the physician to guide selection of approved therapies, and if appropriate to support eligibility for inclusion in the study. FlareTx is provided with de-identified genomic data, where assessment of the prevalence of genetic alternations such as copy number variation (CNV), fusions and mutations (single nucleotide variants) in PPARG, RXRA and FGFR3 are undertaken. Additionally, luminal molecular classification is performed using the Robertson method [1]. PPARG mean expression value are normalized by transcripts-per-million (TPM) and reported as Log2[TPM+1]. In the initial data set of 27 patients, 3 patients had PPARG amplification (CN >/= 3), 3 patients had RXRA hotspot mutation (S427F) [2], 6 patients had FGFR3 mutation(s), and 1 patient had both PPARG amplification and a FGFR3 mutation. Twenty of 27 patients tested had sufficient starting material of good quality to also perform whole transcriptome analysis. The mean mRNA expression level of PPARG was 6.77 Log2[TPM+1] (range 2.91 Log2[TPM+1] – 9.22 Log2[TPM+1]). Consistent with the Robertson subtype distribution, 65% of patients were luminal and 35% were non-luminal (basal-squamous and neuronal); 10 of 13 luminal patients had one or more genetic alteration in PPARG, RXRA and/or FGFR3. High PPARG expression was associated with luminal subtype compared to non-luminal subtype (7.90 Log2[TPM+1] vs 4.67 Log2[TPM+1]; p=0.00042). GPS is open at two active Phase 1 sites, with several more planned as the study advances towards the Phase 1B dose expansion stage. GPS runs concurrently with the FX-909 study and is a novel precision strategy to maximize identifying advanced UC patients with actionable genetic alterations to potentially enroll in the clinical study.

Pragmatic nationwide master observational trial based on genomic alterations in advanced solid tumors: KOrean Precision Medicine Networking Group Study of MOlecular profiling guided therapy based on genomic alterations in advanced Solid tumors (KOSMOS)-II study protocol KCSG AL-22–09

BackgroundNext-generation sequencing (NGS) has been introduced to many Korean institutions to support molecular diagnostics in cancer since 2017, when it became eligible for reimbursement by the National Health Insurance Service. However, the uptake of molecularly guided treatment (MGT) based on NGS results has been limited because of stringent regulations regarding prescriptions outside of approved indications, a lack of clinical trial opportunities, and limited access to molecular tumor boards (MTB) at most institutions. The KOSMOS-II study was designed to demonstrate the feasibility and effectiveness of MGT, informed by MTBs, using a nationwide precision medicine platform.MethodsThe KOSMOS-II trial is a large-scale nationwide master observational study. It involves a framework for screening patients with metastatic solid tumors for actionable genetic alterations based on local NGS testing. It recommends MGT through a remote and centralized MTB meeting held biweekly. MGT can include one of the following options: Tier 1, the therapeutic use of investigational drugs targeting genetic alterations such as ALK, EGFR, ERBB2, BRAF, FH, ROS1, and RET, or those with high tumor mutational burden; Tier 2, comprising drugs with approved indications or those permitted for treatment outside of the indications approved by the Health Insurance Review and Assessment Service of Korea; Tier 3, involving clinical trials matching the genetic alterations recommended by the MTB. Given the anticipated proportion of patients receiving MGT in the range of 50% ± 3.25%, this study aims to enroll 1,000 patients. Patients must have progressed to one or more lines of therapy and undergone NGS before enrollment.DiscussionThis pragmatic master protocol provides a mass-screening platform for rare genetic alterations and high-quality real-world data. Collateral clinical trials, translational studies, and clinico-genomic databases will contribute to generating evidence for drug repositioning and the development of new biomarkers.Trial registrationNCT05525858.

Immunohistochemistry of Lung Cancer Biomarkers.

Immunohistochemical (IHC) staining represents a comparatively inexpensive testing method that is attractive as a potential alternative to molecular sequencing methods or fluorescence in situ hybridization for pulmonary biomarker testing. While a variety of IHC tests directed at actionable genetic alterations have been developed and evaluated since the advent of targeted therapy, specific antibody clones for anaplastic lymphoma kinase, ROS-1, and potentially neurotrophic tropmyosin receptor kinase have been the primary antibodies that provide sufficiently robust results to be utilized as either a primary testing or screening method to direct targeted therapy. Antibodies for a variety of other targets such as epidermal growth factor receptors, for example, have lacked sufficient sensitivity and specificity to cover the range of mutations that may occur and are generally not recommended in lieu of molecular testing with the exception of limited resource settings. IHC is also used as a predictive marker for response to immunotherapy through evaluation of programmed death ligand 1 expression. In addition, multiple antibody-drug conjugates (ADCs) are under investigation, designed to deliver drugs directly to tumor cells through binding to specific target antigens. Some ADCs have already received accelerated FDA approval, and IHC was incorporated in many clinical trials evaluating ADC efficacy. As such, it is anticipated that ADCs may have a companion diagnostic IHC to guide patient selection.

Lymphangioleiomyomatosis as a potent lung cancer risk factor: Insights from a Japanese large cohort study.

Lymphangioleiomyomatosis (LAM) is a rare neoplastic disease associated with the functional tumour suppressor genes TSC1 and TSC2 and causes structural destruction in the lungs, which could potentially increase the risk of lung cancer. However, this relationship remains unclear because of the rarity of the disease. We investigated the relative risk of developing lung cancer among patients diagnosed with LAM between 2001 and 2022 at a single high-volume centre in Japan, using data from the Japanese Cancer Registry as the reference population. Next-generation sequencing (NGS) was performed in cases where tumour samples were available. Among 642 patients diagnosed with LAM (sporadic LAM, n = 557; tuberous sclerosis complex-LAM, n = 80; unclassified, n = 5), 13 (2.2%) were diagnosed with lung cancer during a median follow-up period of 5.13 years. All patients were female, 61.5% were never smokers, and the median age at lung cancer diagnosis was 53 years. Eight patients developed lung cancer after LAM diagnosis. The estimated incidence of lung cancer was 301.4 cases per 100,000 person-years, and the standardized incidence ratio was 13.6 (95% confidence interval, 6.2-21.0; p = 0.0008). Actionable genetic alterations were identified in 38.5% of the patients (EGFR: 3, ALK: 1 and ERBB2: 1). No findings suggested loss of TSC gene function in the two patients analysed by NGS. Our study revealed that patients diagnosed with LAM had a significantly increased risk of lung cancer. Further research is warranted to clarify the carcinogenesis of lung cancer in patients with LAM.

Agnostic Administration of Targeted Anticancer Drugs: Looking for a Balance between Hype and Caution.

Many tumors have well-defined vulnerabilities, thus potentially allowing highly specific and effective treatment. There is a spectrum of actionable genetic alterations which are shared across various tumor types and, therefore, can be targeted by a given drug irrespective of tumor histology. Several agnostic drug-target matches have already been approved for clinical use, e.g., immune therapy for tumors with microsatellite instability (MSI) and/or high tumor mutation burden (TMB), NTRK1-3 and RET inhibitors for cancers carrying rearrangements in these kinases, and dabrafenib plus trametinib for BRAF V600E mutated malignancies. Multiple lines of evidence suggest that this histology-independent approach is also reasonable for tumors carrying ALK and ROS1 translocations, biallelic BRCA1/2 inactivation and/or homologous recombination deficiency (HRD), strong HER2 amplification/overexpression coupled with the absence of other MAPK pathway-activating mutations, etc. On the other hand, some well-known targets are not agnostic: for example, PD-L1 expression is predictive for the efficacy of PD-L1/PD1 inhibitors only in some but not all cancer types. Unfortunately, the individual probability of finding a druggable target in a given tumor is relatively low, even with the use of comprehensive next-generation sequencing (NGS) assays. Nevertheless, the rapidly growing utilization of NGS will significantly increase the number of patients with highly unusual or exceptionally rare tumor-target combinations. Clinical trials may provide only a framework for treatment attitudes, while the decisions for individual patients usually require case-by-case consideration of the probability of deriving benefit from agnostic versus standard therapy, drug availability, associated costs, and other circumstances. The existing format of data dissemination may not be optimal for agnostic cancer medicine, as conventional scientific journals are understandably biased towards the publication of positive findings and usually discourage the submission of case reports. Despite all the limitations and concerns, histology-independent drug-target matching is certainly feasible and, therefore, will be increasingly utilized in the future.

Abstract CT283: Phase 3 MK-2870-007 study: MK-2870 (SKB264) plus pembrolizumab vs pembrolizumab alone as first-line treatment for metastatic non-small-cell lung cancer with PD-L1 tumor proportion score (TPS) ≥50%

Abstract Background: Pembrolizumab (anti-PD-1) monotherapy is a standard of care first-line treatment for advanced or metastatic non-small-cell lung cancer (NSCLC) with PD-L1 TPS ≥50% without actionable genetic alterations; however, some patients do not respond to therapy or experience disease progression. Trophoblast cell-surface antigen 2 (TROP2) is another candidate for anticancer treatment and overexpression of TROP2 is associated with poor prognosis in patients with NSCLC. MK-2870 (SKB264) is an antibody-drug conjugate (ADC) composed of the humanized TROP2 monoclonal antibody, a hydrolytically cleavable linker, and the cytotoxic drug KL610023. In patients with relapsed or refractory locally advanced or metastatic NSCLC, MK-2870 monotherapy showed encouraging antitumor activity with a manageable safety profile. The complementary mechanisms of action of MK-2870 and pembrolizumab may provide more potent antitumor activity when given in combination compared with each therapy alone. To investigate this further, the MK-2870-007 study will evaluate the efficacy and safety of the addition of MK-2870 to pembrolizumab vs pembrolizumab alone in patients with previously untreated metastatic NSCLC with PD-L1 TPS ≥50%. Trial Design: Approximately 614 eligible patients aged ≥18 y with previously untreated histologically or cytologically confirmed stage IV (per American Joint Committee on Cancer v8.0) NSCLC, PD-L1 TPS ≥50% and no EGFR, ALK, or ROS1 alterations (nonsquamous only); ECOG PS 0 or 1; and measurable disease per RECIST v1.1 will be enrolled. Patients with well-controlled HIV are permitted. Patients will be randomized 1:1 to receive either pembrolizumab 400 mg Q6W for up to 18 cycles plus MK-2870 4 mg/kg Q2W or pembrolizumab 400 mg IV Q6W alone until progressive disease, intercurrent illness, patient withdrawal, unacceptable toxicity, prolonged interruption of study drug, or until maximum number of cycles (18 cycles for pembrolizumab). Randomization stratification factors include ECOG PS (0 vs 1), histology (squamous vs nonsquamous), TROP2 expression (low vs medium vs high), and geographic region (East Asia vs North America/Western Europe/Australia vs Rest of World). The primary endpoint is OS. Secondary endpoints include PFS, ORR, and duration of response per RECIST v1.1 by blinded independent central review, patient-reported outcomes, and safety. Tumor imaging will occur at baseline, Q6W until wk 48, and Q12W thereafter until PD, start of new anticancer treatment, or withdrawal of consent. PD-L1 TPS will be assessed centrally using PD-L1 IHC 22C3 pharmDx (Agilent Technologies, Carpinteria, CA). AEs will be graded according to National Cancer Institute Common Terminology Criteria for Adverse Events v5.0. Enrollment began in December 2023 and is currently ongoing. Citation Format: Nikolaj Frost, Razi Ghori, Ananya Roy, Ana Tablante Nunes, James Chih-Hsin Yang. Phase 3 MK-2870-007 study: MK-2870 (SKB264) plus pembrolizumab vs pembrolizumab alone as first-line treatment for metastatic non-small-cell lung cancer with PD-L1 tumor proportion score (TPS) ≥50% [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT283.

Real-world analysis of patients with advanced gastrointestinal (GI) cancers harboring inactivating TSC1 and TSC2 alterations using the Foundation Medicine genomic database.

558 Background: Genomic profiling of GI tumors can identify potentially actionable genetic alterations, ultimately leading to better outcomes in patients who currently have few treatment options. In exploratory biomarker analyses of patients with perivascular epithelioid cell tumors treated with the mTOR inhibitor nab-sirolimus (AMPECT, NCT02494570), those with inactivating alterations in the tumor suppressor genes TSC1 or TSC2 (critical negative regulators of mTOR activity) had confirmed responses (8/9 patients with inactivating TSC2 alterations and 1/5 patients with inactivating TSC1 alterations). PRECISION 1, a currently enrolling tumor-agnostic study, will evaluate nab-sirolimus in patients with TSC1 or TSC2 alterations. To enumerate the frequency of these alterations in GI cancers, we analyzed data from a real-world genomic database. Methods: Next-generation sequencing (NGS) data from Foundation Medicine’s genomic database of patients with advanced cancer were analyzed using the FoundationInsights web-based platform to identify patients with GI cancers who had inactivating TSC1 or TSC2 alterations (short variants [base substitutions, insertions and deletions], rearrangements, and copy number deletions). Tumor mutational burden (TMB), microsatellite instability status and other mutations were also characterized in this group of patients. Results: As of 29 March 2022, tumor tissue NGS data were available for 5816 patients with GI cancers bearing alterations in TSC1 or TSC2. Of these, 1642 patients had at least one inactivating alteration. The GI tumor types that most frequently expressed inactivating alterations in TSC1 or TSC2 were hepatocellular carcinoma (alterations in 6.5%); colorectal adenocarcinoma (1.7%); gastrointestinal stromal tumors (1.7%); and cholangiocarcinoma (1.6%). Of all 1642 patients, 688 were female, and most (74%) were 51–80 years of age when the sample was obtained. Of patients with inactivating TSC1 and TSC2 alterations, 37.6% were in TSC1 and 62.9% were in TSC2 and included short variants (31.3% and 48.4%), rearrangements (2.7% and 6.6%), and copy number deletions (3.5% and 7.4%), respectively. TMB was low (<6 mutations/megabase) in 58% of patients, and most patients had microsatellite stable (MSS; 71.3%) tumors. Other commonly mutated genes in this cohort were TP53 (62.7%), APC (38.5%) and KRAS (30.4%). Conclusions: TSC1 and/or TSC2 alterations were commonly observed in GI cancers. These cancers were frequently microsatellite stable and of low TMB suggesting that these are actionable alterations that may be candidates for targeted therapy. This hypothesis is being tested in the PRECISION 1 (NCT05103358) trial which is open for enrollment or just-in-time clinical trial sites and available to patients with GI cancers harboring TSC1 or TSC2 alterations.

Time to Deliver on Promises: The Role of ERBB2 Alterations as Treatment Options for Colorectal Cancer Patients in the Era of Precision Oncology.

Receptor tyrosine kinase erythroblastic oncogene B2 (ERBB2), also known as human epidermal growth factor receptor 2 (HER2), represents an oncogenic driver and has been effectively targeted in breast and gastric cancer. Recently, next-generation sequencing (NGS) discovered ERBB2 as a promising therapeutic target in metastatic colorectal cancer (mCRC), where it is altered in 3-5% of patients, but no therapies are currently approved for this use. Herein, we present the experience of a single center in diagnosing actionable genetic ERBB2 alterations using NGS and utilizing the latest therapeutic options. Between October 2019 and December 2022, a total of 107 patients with advanced CRC underwent molecular analysis, revealing actionable ERBB2 mutations in two patients and ERBB2 amplifications in two other patients. These findings correlated with immunohistochemical (IHC) staining. Of these four patients, two were treated with trastuzumab-deruxtecan (T-DXd). We present two exemplary cases of patients with actionable ERBB2 alterations to demonstrate the effectiveness of T-DXd in heavily pretreated ERBB2-positive mCRC patients and the need for early molecular profiling. To fully exploit the potential of this promising treatment, earlier molecular profiling and the initiation of targeted therapies are essential.

Latest trends in cancer clinical trials using genomics

Background: Recent advances in molecular biology and genomics have revolutionized the understanding of the intricate molecular underpinnings of cancer. Next-generation sequencing analysis now allows identification of specific actionable genetic alterations. This breakthrough has paved the way for precision medicine in oncology, redefining the conventional clinical trial landscape and enabling personalized approaches to cancer treatment.Current Concepts: The shift toward precision medicine involves a fundamental departure from the traditional Phases 1–4 clinical trial protocols. Instead of using uniform treatment pathways, personalized therapies are designed based on the genetic profiles of individual patients. Tumor-agnostic clinical trials are becoming as a prominent concept, encompassing innovative adaptive designs that adapt treatments to specific genetic variations. Master protocols such as umbrella studies, basket trials, platform studies, and master observational trials exemplify this transformation.Discussion and Conclusion: International precision medicine research is characterized by exemplar studies such as the NCI-MATCH study in the United States, the Drug Rediscovery Protocol study in the Netherlands, and the Targeted Agent and Profiling Utilization Registry study in the United States. Korean oncology research also contributed to the international effort in precision medicine through initiatives like K-MASTER and the Korean Precision Medicine Networking Group, which is making commendable contributions to the global precision medicine movements.

Clinical Practice Recommendations for the Use of Next-Generation Sequencing in Patients with Solid Cancer: A Joint Report from KSMO and KSP.

In recent years, next-generation sequencing (NGS)-based genetic testing has become crucial in cancer care. While its primary objective is to identify actionable genetic alterations to guide treatment decisions, its scope has broadened to encompass aiding in pathological diagnosis and exploring resistance mechanisms. With the ongoing expansion in NGS application and reliance, a compelling necessity arises for expert consensus on its application in solid cancers. To address this demand, the forthcoming recommendations not only provide pragmatic guidance for the clinical use of NGS but also systematically classify actionable genes based on specific cancer types. Additionally, these recommendations will incorporate expert perspectives on crucial biomarkers, ensuring informed decisions regarding circulating tumor DNA panel testing.

Real-World Outcomes of Immunotherapy in Second- or Later-Line Non-Small Cell Lung Cancer with Actionable Genetic Alterations.

While the efficacy of immune checkpoint inhibitors (ICIs) in treating non-small cell lung cancer (NSCLC) patients with actionable genetic alterations (AGAs) is modest, certain patients demonstrate improved survival. Thus, this study aimed to evaluate the benefits of ICIs in NSCLC patients with diverse AGAs and verify the predictive biomarkers of ICI efficacy. From January 2018 to July 2022, this study compared the progression-free survival (PFS) of NSCLC patients with different AGAs treated with ICI monotherapy as second- or later-line therapy at Samsung Medical Center. To ascertain the predictors of ICIs efficacy, we adjusted ICIs' effects on PFS in terms of clinical and molecular biomarkers. EGFR (46.0%) was the most prevalent mutation in 324 patients. In multivariate analysis, PD-L1 positivity (tumor proportion score (TPS) ≥ 1%) (HR = 0.41) and the use of steroids for immune-related adverse events (HR = 0.46) were positive factors for ICI therapy in the AGAs group. Co-existing mutation of STK11 with KRAS mutation (HR = 4.53) and TP53 with MET mutation (HR = 9.78) was negatively associated with survival. The efficacy of ICI treatment varied across AGA subtypes, but patients with KRAS, MET, and BRAF mutations demonstrated relatively long-duration benefits of ICI therapy. PD-L1 was a significant positive predictive biomarker in all AGA groups.

THU510 The Frequency Of Mutations In Advanced Thyroid Cancer In Japan: A Real Clinical Setting

Abstract Disclosure: S. Toda: None. A. Takahashi: None. K. Masudo: None. H. Iwasaki: None. Background: Thyroid cancer has a high incidence of actionable genetic alterations, but the frequency of mutations in advanced thyroid cancer that requires drug therapy is unknown. Therefore, we examined the outcomes of genetic testing performed in a real clinical setting for the purpose of pharmacotherapy. Methods: In Japan, Oncomine Dx is approved for thyroid cancer that requires drug therapy, and comprehensive genomic profiling is approved for anaplastic thyroid carcinoma and other thyroid carcinomas after the induction of tyrosine kinase inhibitors. We retrospectively reviewed the cases of those who had their tests performed between 2020 and 2022. Results: The study included 65 patients, and the testing methods used were Oncomine Dx in 36 cases, FoundationOne in 25 cases, and FoundationOne Liquid in 4 cases. With a median age of 74 years (range 17–86), 42 were female and 23 were male. Moreover, 13 cases had anaplastic thyroid carcinoma (ATC), 4 follicular thyroid carcinoma (FTC), 42 papillary thyroid carcinoma (PTC), and 6 poorly differentiated thyroid carcinoma (PDTC). Of the PTC examined by Oncomine Dx, 96.8% (30/31) were RAI-refractory; all comprehensive genomic profiling testing cases except ATC had previously been treated with tyrosine kinase inhibitors. In the following cases, actionable mutations were observed. Among 13 ATC cases, 46.2% (6) had BRAF mutation and 7.7% (1) had RET fusion. Of 42 PTC cases, 85.7% (36) had BRAF mutation and 7.1% (3) had RET fusion. Of 6 PDTC cases, 33.3% (2) had BRAF mutation and 16.7% (1) had RET fusion. No actionable mutations were observed in FTC (0/4). We found one case each of ATC and PTC with tumor mutation burden of 10 or higher, both with BRAF mutation. NTRK fusion was not observed in any of the 65 patients studied. There were four PTC cases (9.5%) with iodine accumulation in metastases, two with BRAF mutations, one with RET fusion, and one without detectable mutations. Comparing mutations in ATC and non-ATC, TERT promoter mutations were found in 84.6% of ATC (11/13) vs. 56.2% of non-ATC (9/16), whereas TP53 mutations were found in 76.9% of ATC (10/13) vs. 12.5% of non-ATC (2/16). ATC has a significantly higher prevalence of TP53 mutations. Conclusion: Advanced thyroid cancer is more likely to have actionable mutations. BRAF mutations in advanced PTC may be more common than those previously reported in standard PTC. Moreover, ATC has a higher rate of TP53 mutation than other thyroid carcinomas. Presentation: Thursday, June 15, 2023

Comprehensive genomic profiling of Japanese patients with thoracic malignancies: A single-center retrospective study

BackgroundFew studies have been conducted on comprehensive genomic profiling (CGP) panels in Japanese patients with thoracic malignancies after completing standard treatment. Consequently, its value in clinical practice remains unclear. MethodsWe conducted a retrospective study of Japanese patients with thoracic malignancies who underwent CGP between June 2019 and November 2022 at our hospital. We evaluated the detection rate of actionable genetic alterations and percentage of patients who received genomically-matched therapy. Furthermore, we examined the value of the CGP panel in patients who underwent multiplex gene-panel testing prior to their initial treatment. This study was performed in accordance with the principles of the Declaration of Helsinki. ResultsThe study included 56 patients, of whom 47 (83.9%) had actionable genetic alterations and 8 (14.3%) received genomically-matched therapy. Of these, four patients were treated with approved drugs and three patients were treated with investigational agents. In addition, one patient was treated with approved drugs using the patient-directed care system. Of the 17 patients who had multiplex gene-panel testing performed at the start of their initial therapy, two (11.8%) were newly identified by the CGP panel and subsequently received genomically-matched therapy. EGFR L718Q and MET amplification were observed in two of the seven patients with epidermal growth factor receptor-tyrosine kinase inhibitor resistance. ConclusionsThe CGP panel could identify genetic alterations, thereby facilitating genomically-matched therapy, even in patients with thoracic malignancies who could not be identified using multiplex gene-panel testing.

Genomic profiling, prognosis, and potential interventional targets in young and old patients with cholangiocarcinoma

ABSTRACT Molecular mechanisms behind potentially inferior prognosis of old cholangiocarcinoma (CCA) patients are unclear. Prevalence of interventional targets and the difference between young and old CCA patients are valuable for promising precision medicine. A total of 188 CCA patients with baseline tumor tissue samples were subgrouped into the young (≤45 years) and old (>45 years) sub-cohorts. Somatic and germline mutation profiles, differentially enriched genetic alterations, and actionable genetic alterations were compared. An external dataset was used for the validation of molecular features and the comparison of overall survival (OS). Compared to young patients, KRAS alterations were more common in old patients (P = .04), while FGFR2 fusions were less frequent (P = .05). TERT promoter mutations were exclusively detected in old patients. The external dataset (N = 392) revealed no significant difference in OS between young and old patients; however, old patient-enriched KRAS (hazard ratio [HR]: 1.96, 95% confidence interval [CI]: 1.37–2.80) and TERT alterations (HR: 2.03, 95% CI: 1.22–3.38) were associated with inferior OS. Approximately 38.3% of patients were identified of actionable oncogenic mutations indicative of a potential response to targeted therapy or immunotherapy. Actionable FGFR2 fusions (P = .01) and BRAFV600E (P = .04) mutations were more frequent in young females than old patients. The enrichment of KRAS/TERT alterations in CCA patients over 45 years resulted in inferior OS. Approximately one-third of CCA patients were eligible for targeted therapy or immunotherapy given the actionable mutations carried, especially young females.

Prostate cancer genetic alterations in Hispanic men.

Differences in DNA alterations in prostate cancer among White, Black, and Asian men have been widely described. This is the first description of the frequency of DNA alterations in primary and metastatic prostate cancer samples of self-reported Hispanic men. We utilized targeted next-generation sequencing tumor genomic profiles from prostate cancer tissues that underwent clinical sequencing at academic centers (GENIE 11th). We decided to restrict our analysis to the samples from Memorial Sloan Kettering Cancer Center as it was by far the main contributor of Hispanic samples. The numbers of men by self-reported ethnicity and racial categories were analyzed via Fisher's exact test between Hispanic-White versus non-Hispanic White. Our cohort consisted of 1412 primary and 818 metastatic adenocarcinomas. In primary adenocarcinomas, TMPRSS2 and ERG gene alterations were less common in non-Hispanic White men than Hispanic White (31.86% vs. 51.28%, p = 0.0007, odds ratio [OR] = 0.44 [0.27-0.72] and 25.34% vs. 42.31%, p = 0.002, OR = 0.46 [0.28-0.76]). In metastatic tumors, KRAS and CCNE1 alterations were less prevalent in non-Hispanic White men (1.03% vs. 7.50%, p = 0.014, OR = 0.13 [0.03, 0.78] and 1.29% vs. 10.00%, p = 0.003, OR = 0.12 [0.03, 0.54]). No significant differences were found in actionable alterations and androgen receptor mutations between the groups. Due to the lack of clinical characteristics and genetic ancestry in this dataset, correlation with these could not be explored. DNA alteration frequencies in primary and metastatic prostate cancer tumors differ among Hispanic-White and non-Hispanic White men. Notably, we found no significant differences in the prevalence of actionable genetic alterations between the groups, suggesting that a significant number of Hispanic men could benefit from the development of targeted therapies.

Biomarkers to predict the efficacy of immune checkpoint inhibitors in patients with non-small-cell lung cancer with actionable genetic alterations.

e21175 Background: Although the efficacy of immune checkpoint inhibitors (ICI) in patients with actionable genetic alterations (AGAs) in non-small-cell lung cancer (NSCLC) has been known to be modest, some patients demonstrated improved survival. Thus, this study aimed to find predictive biomarkers for ICI in patients with NSCLC with various AGAs and to identify the predictive biomarkers for ICI efficacy. Methods: We compared the progression-free survival (PFS) of 324 advanced NSCLC patients who received ICI monotherapy (as over second-line therapy) by different AGAs from January 2018 and July 2022 at the Samsung Medical Center. To identify predictive markers of ICI, we adjusted the impacts on PFS of ICI in smoking status, PD-L1 expression, TP53, KEAP, STK11 mutation status, and steroid use during ICI monotherapy. Results: The median age was 63.1 years (range, 27.8–84.8) and 53.1% of patients was male, and 46.3% of patients was an ex-/or current smoker. A total of 324 patients were included with the following AGAs: EGFR mutation (n = 149, 46.0%), ALK rearrangement, (n = 12, 3.7%), KRAS mutation (n = 72, 22.2%), HER2 mutation or amplification (n = 34, 10.5%), and MET ex14 skipping or amplification (n = 32, 9.9%), ROS1 rearrangement (n = 9, 2.8%), BRAF V600E (n = 9, 2.8%), and RET rearrangement (n = 7, 2.2%). The median PFS was 2.0 months (95% confidence interval, 1.8–2.2) in the total AGA group. The 6-month PFS rate was 25.8% (19.5–34.3) in the group with KRAS/ BRAF V600E/ MET/ HER2 and 12.8% (8.6–19.1) in the group with EGFR/ ALK/ ROS1/ RET (P < 0.01). In the group with KRAS/ BRAF V600E/ MET/ HER2, KEAP, or STK11 wild-type (P = 0.03), PD-L1 (≥1%) (P < 0.01) and steroid use during ICI monotherapy due to immune-related adverse events (IRAE) (P < 0.01) were related to a favorable PFS of ICI; however, no statistical significance was found for TP53 mutation and smoking status for PFS of ICI. In the group with EGFR/ ALK/ ROS1/ RET, PD-L1(≥ 50%) was the only factor that was related to a favorable PFS, and not TP53 mutation status, KEAP, or STK11. Conclusions: This study showed a difference in PFS among each type of AGAs. Although there are limitations due to the small number of patients, the KRAS/ BRAF V600E/ MET/ HER2 group had a favorable PFS compared with the EGFR/ ALK/ ROS1/ RET group . KEAP/STK11/PD-L1 status and steroid use due to IRAE predicted favorable PFS of ICI in the KRAS/ BRAF V600E/ MET/ HER2 group .

Use of an artificial intelligence (AI) –based pre-screening tool for patients with bladder cancer with fibroblast growth factor receptor (FGFR) alteration.

e13580 Background: Over 25% of urothelial carcinoma have actionable genetic alterations in FGFR. The clinical trial of the pan-FGFR inhibitor requires thousands of patients with FGFR alterations to be screened; however, the cost is prohibitively expensive. A deep learning model can help predict the occurrence of specific genetic alterations and effectively screen patients with FGFR actionable alterations in bladder cancer. Methods: The prediction model of FGFR oncogenic alterations was trained by using 440 H&E-stained bladder cancer diagnostic slides (from 373 patients) from the OrigiMed Database and validated with 448 slides (from 376 patients) from the additional TCGA-BLCA dataset. The model employs an attention-based, weakly supervised learning method to identify tissue subregions most likely to have the mutations of FGFR1-4, so as to classify the entire slide. Every patch is assigned an attention score, which represents the corresponding contribution to slide classification. The slide-level aggregation rule of attention-based pooling computes a final attention score by weighted average. Results: The FGFR oncogenic alteration predictive AI (FGFRonaP) model was trained, validated and tested on the OrigiMed real-world cohort. The FGFRonaP model could identify patients with FGFR1-4 gene oncogenic aberration on the test set accurately (Precision = 60.0%, Recall = 69.2%, AUROC = 0.839). When the model was tested on the additional TCGA independent cohort, 11 negative samples were included mistakenly while 323 true negative slide and 19 true positive slides were identified correctly. The FGFRonaP model showed an acceptable classification precision (63.3%), much higher than the occurrence rate (26.9%) of FGFR oncogenic alterations, in spite of an imperfect AUROC (0.636) and recall (0.167). Conclusions: FGFRonaP is feasible to serve as an in-house or monocentric application to pre-screen the potential FGFR-altered patients. It could be useful and efficient in preliminary screening to reduce workloads of genetic testing, and thus help pharmaceutical companies improve the proportion of candidates with FGFR-alterations in all patients who undergo genetic testing and cut expensive costs for enrolling patients.

CtDNA mutational profiles in luminal breast cancer with early vs late distant relapse: Geicam/2014-03.

1060 Background: Patients with hormone receptor-positive early breast cancer (BC) can develop resistance to endocrine therapies (ET) and face a continuous risk of relapse, which can occur anywhere from a few months (m) to several decades after surgery. The causes of early vs late relapses are not well understood. Our research examines the presence of oncogenic drivers in circulating tumor DNA (ctDNA) at the time of relapse in patients with luminal BC who have either an early or late distant recurrence. Methods: We identified pts included in the GEICAM/2014-03 study (NCT02819882) with: 1) HR-positive BC, 2) metastatic relapse either <36m (early relapse, [early-R]) or >120m (late relapse, [late-R]) from diagnosis, and 3) ctDNA obtained before first line treatment for advanced disease. The AVENIO ctDNA assay was used for identifying genomic aberrations in 77 cancer-related genes. Results: Eighty-four pts, 36 in early-R and 48 in late-R groups, were selected. Median time to relapse was 24.97m in early-R vs 151.84m in late-R. Median time from last dose of adjuvant ET to relapse was 0.03m for early-R vs 74.06m for late-R. Median PFS to first line treatment was 7.62m in early-R and 35.15m in late-R. With a median follow-up of 32.08m, median OS after diagnosis of metastatic disease was 27.74m for early-R and not reached for late-R. ctDNA analysis detected at least 1 mutation (mut) in 71/84 (85%) pts (89% in early-R vs 81% in late-R). Early-R pts were enriched in mut in TP53 (44% vs 19%), ESR1 (11% vs 4%), MAPK_ERK pathway (14% vs 6%), and ERBB2 copy number alterations (CNA) (25% vs 2%). PI3K/AKT pathway alterations had similar frequency in both recurrence groups (38% vs 42%) and they were not associated with OS. Seven ESR1 mut were detected in 6 pts. In the early-R group there were 5 ESR1 mut (71% of total ESR1 mut), median mutant allele frequency (mMAF): 0.64%; while in the late-R, 2 ESR1 mut (29%), mMAF: 0.4%. ESR1 mut were associated with worse OS (median OS 48.48m vs 12.84m wild-type vs mutant; p=0.0025). There were 10 pts with E RBB2 CNA at metastatic relapse; 9 (25%) in the early-R and 1 pts (2%) in the late-R. Seven pts (70%) had HER2-positive. Pts with ctDNA ERBB2 CNA had worse OS (median OS 48.48m vs 20.52m wild-type vs mutant; p-adj=0.025). Conclusions: In luminal breast cancer (BC), early and late distant relapse differ at both the clinical and genomic levels. Early relapse is a highly aggressive form of the disease and is enriched in TP53 mutations and actionable genetic alterations, such as mutations in the ESR1 and CNA in ERBB2, as detected by ctDNA analysis at the time of metastatic relapse diagnosis. Clinical trial information: NCT02819882 . [Table: see text]

Identification of SNVs via targeted comprehensive genome profiling in patients with brain cancer.

e14047 Background: Advanced brain tumors comprise an aggressive class of malignancies and are characterized by poor patient survival. In general, the 5-yr survival rate for people ≥40 years is about 21%. These tumors also appear to be recalcitrant to available SOC, hence the need for deeper insights to recognize actionable genetic alterations in order to make reliable assessments of diagnosis, prognosis, therapy response, and resistance. Comprehensive targeted Next Generation Sequencing (NGS) has allowed significant advances in precision oncology by pinpointing actionable alterations in oncogenes, tumor suppressor genes, and cellular signaling pathways. Methods: Retrospective NGS-based genome profiling was performed on ccfDNA (circulating cell-free DNA) and genomic DNA (FFPE/fresh tissue) samples from 8 brain tumor patients OncoIndx proprietary gene panel that targets exonic regions of 600 cancer related genes. Illumina compatible libraries were prepared by target hybridization method and sequenced on Nextseq 2000 platform in pair-end fashion. Variant calling was performed using an in-house developed bioinformatics pipeline. The 8 patients comprised 1 each for glioma, anaplastic astrocytoma, pilocytic astrocytoma and parietal SOL (Space Occupying Lesion) and 2 each for GBM and ependymoma. Results: Novel mutations such as GNASA366S, BRAFM590K and RAD54LD592V were observed in glioblastoma. Additionally, novel SNVs such as STK11G215V, CREBBPG1465E, GNA11G208C and SF3B1R549S were observed in ependymoma along with as yet unreported amplification of KIT, KDR and PDGFRA. NOTCH3 double mutation C428S and C455S was identified for the first time in this study in anaplastic astrocytoma. EGFRH835L, as yet unreported in glioma or ependymoma, was also identified here. Strikingly, some of these alterations are actionable: preclinical data links GNAS to MAPK and Wnt signaling creating a potential workspace for these targeted agents. Similarly, loss of STK11 sensitizes 3D gliomaspheres to metformin and mutations in SF3B1 are known to cause cellular sensitivity to PRMT5i. SF3B1 R549S mutation has not been reported yet and it will be crucial to assess the effect this alteration has on protein function. Furthermore, amplification of KIT, KDR and PDGFRA is known to create a sensitive niche for TKI in adenoid cystic carcinoma and may also have potential in ependymoma where these amplifications have been reported for the first time in this study. The EGFR H835L finding has clinical implication since L833V/H835L co-mutation has shown remarkable efficacy to Afatinib in LUAD. Conclusions: We report, for the first-time actionable mutations in key genes related to critical signaling pathways in a mixed population of brain tumor patients. The data highlights that comprehensive NGS-based deep assessment can lead to clinically viable insights in this population of patients with brain tumors.

Korean Precision Medicine Networking Group study of molecular profiling guided therapy based on genomic alterations in advanced solid tumors (KOSMOS) II (KCSG AL 22-09).

TPS1608 Background: Next-generation sequencing (NGS) has been introduced to many Korean institutions as molecular diagnostics for cancers since 2017, when it was reimbursed by the National Health Insurance Service. However, molecularly-guided treatment (MGT) options based on NGS results have been limited due to the strict regulation for prescribing outside of the approved indication, lack of clinical trial availability, and limited access to molecular tumor boards (MTB) in most institutions. Given our previous KOSMOS study results, which showed MGT was available for 54% (124/198) of patients based on local NGS (ESMO Open 2022;7(6, Suppl 1);100653), KOSMOS-II study was designed to demonstrate MGT would be feasible and effective via a nation-wide precision medicine platform. Methods: This national, prospective, pragmatic, multi-cohort study comprised of a framework to screen pts with metastatic solid tumors for actionable genetic alterations (GA) based on local NGS testing and to recommend MGT by a remote and centralized MTB held weekly or biweekly. MGT can be one of the following options: Tier 1, the therapeutic use of investigational drugs targeting GAs including ALK, EGFR, ERBB2, BRAF, FH, ROS1, RET, or high tumor mutational burden; Tier 2, drugs that are allowed for treatment outside of the approved indications by the National Health Insurance; Tier3, clinical trials matched for GA recommended by MTB. To estimate the proportion of patients receiving MGT to be 50±3.25% with 95% confidence interval, we will enroll 1,000 pts, considering 5% drop-out rate. The clinical benefit rate of MGT beyond 16±2 weeks is the second co-primary endpoint, which is expected to be 30% with type I error of 5% and 90% power. Pts must have progressed ≥ 1 or more lines of therapies; have undergone NGS testing; are able to provide the Variant Call Format (vcf) file of the NGS results. MTB determines clinical actionability of GA and recommends MGT if possible, according to Tier 1,2, or 3. The vcf files and matched clinical information will be deposited to the repository of National Center Center Korea and will be curated in a de-identified clinico-genomic database. As of Feb 2023, 139 of planned 1,000 have been enrolled. Clinical trial information: NCT05525858 .