Tumor Mutation Status Research Articles

Anti–Programmed Death Ligand 1 Plus Targeted Therapy in Anaplastic Thyroid Carcinoma

Anaplastic thyroid carcinoma (ATC) is a rare and lethal cancer. Although progress has been made in recent years in patients with mutated BRAF tumors, those who respond initially eventually die of their disease; furthermore, there are no approved therapies for non-BRAF mutated tumors. To determine whether treatment with matched-targeted therapy plus immune checkpoint inhibitors were associated with improved overall survival (OS). A phase 2 trial at a single center, tertiary institution with parallel cohorts, assigning treatment with targeted therapy according to the tumor mutation status. Patients with mutated BRAF V600E tumors received vemurafenib/cobimetinib plus atezolizumab (cohort 1); those with mutated RAS (NRAS, KRAS, or HRAS) or NF1/2 tumors received cobimetinib plus atezolizumab (cohort 2). Patients without any of these variants were assigned to receive bevacizumab plus atezolizumab (cohort 3). Patients were enrolled from August 3, 2017, to July 7, 2021. All consecutive, systemic therapy-naive patients with ATC with active disease and who met eligibility criteria were considered for participation. The analysis was conducted in September 2023. Patients were assigned to targeted therapy based on the driver mutation as follow: BRAF V600E (cohort 1, vemurafenib plus cobimetinib), RAS/NF (cohort 2, cobimetinib), or non-BRAF/RAS/NF (cohort 3, bevacizumab). All received atezolizumab. The primary outcome of the study was median OS of the entire targeted therapy cohort, compared with historical median OS of 5 months. Forty-three patients with ATC were enrolled in the targeted therapy cohorts, of which 42 were included in the primary analysis. The median OS in patients across these 3 cohorts was 19 months (95% CI, 7.79-43.24). Median OS and progression-free survival per cohort were as follows: cohort 1: 43 months (95% CI, 16-not estimable [NE]), 13.9 months (6.6-64.1); cohort 2: 8.7 months (95% CI, 5.1-37.0) and 4.8 months (1.8-14.7); cohort 3 (vascular endothelial growth factor inhibitor group): 6.21 months (4.1-NE) and 1.3 months (1.3-NE), respectively. In this nonrandomized clinical trial, atezolizumab combined with targeted therapy resulted in a longer median OS than historical landmark, achieving the study's primary end point, with cohort 1 achieving the longest OS. ClinicalTrials.gov Identifier: NCT03181100.

Consensus on drivers of maintenance treatment choice and patterns of care in advanced ovarian cancer

ObjectivesMaintenance therapies, including poly (ADP-ribose) polymerase (PARP) inhibitors and/or bevacizumab, have substantially improved the prognosis of patients with advanced ovarian cancer. Owing to the variability in treatment strategies across Europe,...

The Prognostic Impact of Tumor Size and BRAF Mutational Status in Middle Eastern Differentiated Thyroid Cancer.

Tumor size at diagnosis has been widely used as a major mortality risk factor in risk stratification of DTC. The current study was designed to analyze whether tumor size at diagnosis is a major prognostic factor in Middle Eastern DTC. We conducted a comparative study of the relationship between tumor size at diagnosis and event free survival (EFS) with respect to BRAF status in 1709 consecutive patients treated surgically for DTC. Patients were divided into four groups according to the size of tumor and BRAF mutation status: Group 1 (≤4 cm without BRAF mutation), Group 2 (≤4 cm with BRAF mutation), Group 3 (>4 cm without BRAF mutation) and Group 4 (>4 cm with BRAF mutation). Predictors of EFS were compared using the Log-rank test and Cox proportional hazards models. Tumor size >4cm was associated with adverse clinico-pathologic characteristics, such as older age, male gender, bilateral tumors, extrathyroidal extension, lymphovascular invasion, advanced tumor stage and persistent/recurrent disease. Tumor size was also inversely associated with BRAF mutation. Both tumor size (> 4cm) and BRAF mutation were associated with EFS on univariate analysis. On subgroup analysis, larger tumor size was an independent predictor of EFS (Group 3 vs. Group 1), irrespective of BRAF mutation status. Also, within the BRAF mutant tumors, larger tumor size was still an independent predictor of EFS (Group 4 vs. Group 2). Tumor size is an independent predictor of EFS in Middle Eastern DTC patients, regardless of BRAF mutational status.

Evaluation of an Image-based Classification Model to Identify Glioma Subtypes Using Arterial Spin Labeling Perfusion MRI On the Publicly Available UCSF Glioma Dataset.

Glioma is acomplex cancer comprising various subtypes and mutations, which may have different metabolic characteristics that can potentially be investigated and identified using perfusion imaging. Therefore, the aim of this work was to use radiomics and machine learning analysis of arterial spin labeling MRI data to automatically differentiate glioma subtypes and mutations. Atotal of 495 Arterial Spin Labeling (ASL) perfusion imaging datasets from the UCSF Glioma database were used in this study. These datasets were segmented to delineate the tumor volume and classified according to tumor grade, pathological diagnosis, and IDH status. Perfusion image data was obtained from a3T MRI scanner using pseudo-continuous ASL. High level texture features were extracted for each ASL dataset using PyRadiomics after tumor volume segmentation and then analyzed using amachine learning framework consisting of ReliefF feature ranking and logistic model tree classification algorithms. The results of the evaluation revealed balanced accuracies for the three endpoints ranging from 55.76% (SD = 4.28, 95% CI: 53.90-57.65) for the tumor grade using 25.4 ± 37.21 features, 62.53% (SD = 2.86, 95% CI: 61.27-63.78) for the mutation status with 23.3 ± 29.17 picked features, and 80.97% (SD = 1.83, 95% CI: 80.17-81.78) for the pathological diagnosis which used 47.3 ± 32.72 selected features. Radiomics and machine learning analysis of ASL perfusion data in glioma patients hold potential for aiding in the diagnosis and treatment of glioma, mainly for discerning glioblastoma from astrocytoma, while performance for tumor grading and mutation status appears limited.

543P Tumor mutational burden (TMB), BRAF status, and C-reactive protein (CRP) predict response to first-line alternating oxaliplatin-based chemotherapy and nivolumab in metastatic microsatellite-stable (MSS) colorectal cancer (CRC)

543P Tumor mutational burden (TMB), BRAF status, and C-reactive protein (CRP) predict response to first-line alternating oxaliplatin-based chemotherapy and nivolumab in metastatic microsatellite-stable (MSS) colorectal cancer (CRC)

Next-generation sequencing-based evaluation of the actionable landscape of genomic alterations in solid tumors: the "MOZART" prospective observational study.

The identification of the most appropriate targeted therapies for advanced cancers is challenging. We performed a molecular profiling of metastatic solid tumors utilizing a comprehensive next-generation sequencing (NGS) assay to determine genomic alterations' type, frequency, actionability, and potential correlations with PD-L1 expression. A total of 304 adult patients with heavily pretreated metastatic cancers treated between January 2019 and March 2021 were recruited. The CLIA-/UKAS-accredit Oncofocus assay targeting 505 genes was used on newly obtained or archived biopsies. Chi-square, Kruskal-Wallis, and Wilcoxon rank-sum tests were used where appropriate. Results were significant for P < .05. A total of 237 tumors (78%) harbored potentially actionable genomic alterations. Tumors were positive for PD-L1 in 68.9% of cases. The median number of mutant genes/tumor was 2.0 (IQR: 1.0-3.0). Only 34.5% were actionable ESCAT Tier I-II with different prevalence according to cancer type. The DNA damage repair (14%), the PI3K/AKT/mTOR (14%), and the RAS/RAF/MAPK (12%) pathways were the most frequently altered. No association was found among PD-L1, ESCAT, age, sex, and tumor mutational status. Overall, 62 patients underwent targeted treatment, with 37.1% obtaining objective responses. The same molecular-driven treatment for different cancer types could be associated with opposite clinical outcomes. We highlight the clinical value of molecular profiling in metastatic solid tumors using comprehensive NGS-based panels to improve treatment algorithms in situations of uncertainty and facilitate clinical trial recruitment. However, interpreting genomic alterations in a tumor type-specific manner is critical.

Single-nucleus and spatial transcriptome reveal adrenal homeostasis in normal and tumoural adrenal glands.

The human adrenal gland is a complex endocrine tissue. Studies on adrenal renewal have been limited to animal models or human foetuses. Enhancing our understanding of adult human adrenal homeostasis is crucial for gaining insights into the pathogenesis of adrenal diseases, such as adrenocortical tumours. Here, we present a comprehensive cellular genomics analysis of the adult human normal adrenal gland, combining single-nuclei RNA sequencing and spatial transcriptome data to reconstruct adrenal gland homeostasis. As expected, we identified primary cells of the various zones of the adrenal cortex and medulla, but we also uncovered additional cell types. They constitute the adrenal microenvironment, including immune cells, mostly composed of a large population of M2 macrophages, and new cell populations, including different subpopulations of vascular-endothelial cells and cortical-neuroendocrine cells. Utilizing spatial transcriptome and pseudotime trajectory analysis, we support evidence of the centripetal dynamics of adrenocortical cell maintenance and the essential role played by Wnt/β-catenin, sonic hedgehog, and fibroblast growth factor pathways in the adult adrenocortical homeostasis. Furthermore, we compared single-nuclei transcriptional profiles obtained from six healthy adrenal glands and twelve adrenocortical adenomas. This analysis unveiled a notable heterogeneity in cell populations within the adenoma samples. In addition, we identified six distinct adenoma-specific clusters, each with varying distributions based on steroid profiles and tumour mutational status. Overall, our results provide novel insights into adrenal homeostasis and molecular mechanisms potentially underlying early adrenocortical tumorigenesis and/or autonomous steroid secretion. Our cell atlas represents a powerful resource to investigate other adrenal-related pathologies.

Clinicopathological significance of mutation profile detected by next generation sequencing in different metastatic organs of non-small cell lung cancers

BackgroundThe primary tumor and it’s metastases show heterogeneity in molecular studies for targeted therapies in Non-Small Cell Lung Cancer(NSCLC), the leading cause of cancer-related deaths worldwide. The study aimed to identify somatic mutations in biopsies from NSCLC patients’ metastatic organs using Next-Generation Sequencing(NGS) and examine their association with clinicopathological parameters. Materials and methodsThe study included 128 NSCLC patients and, NGS was performed on tumor biopsies from different metastatic organs at Molecular Pathology laboratory of the Department of Medical Pathology in Aydın Adnan Menderes University Faculty of Medicine. The age, gender, histopathological diagnoses, metastatic organs, smoking and mutation status were all recorded, along with the analysis results of 72 genes and 4149 primers in the panel of the NGS system. Results53.9 % of the cases had a history of smoking and patients with brain metastases had a higher smoking rate(p=0.000). The most common occurrence(39.8 %) was lymph node metastasis, followed by brain(19.5 %). There was a strong correlation between mutation presence and metastasis in the liver(p=0.012), bone(p=0.002), and pleura(p=0.008). Smokers had a higher frequency of KRAS(p=0.000) and TP53(p=0.001) mutations. Brain metastases showed a statistically significant NF1 mutation(p=0.001), while the liver exhibited a significant BRAF mutation(p=0.000). NF1-TP53, PTEN-TP53 and NF1-PTEN were the most common concomitant mutations and, the brain was the most common metastatic organ in which they occurred. ConclusionOur results suggest prizing assessing detected mutations, in the prediction, follow-up and management of metastases, especially in patients with lung adenocarcinoma. The assessment also needs to consider the tumor's mutation status in metastatic organs. New therapeutic agents targeting NF1 mutations will be available in the future to treat NSCLC, especially in metastases.

Comprehensive analysis of EphA2 in pan-cancer: A prognostic biomarker associated with cancer immunity.

Several studies have reported a significant relationship between Ephrin receptor A2 (EphA2) and malignant progression in numerous cancers. However, there is a lack of comprehensive pan-cancer analysis on the prognostic value, mutation status, methylation landscape, and potential immunological function of EphA2. Using The Cancer Genome Atlas, Genotype Tissue Expression Database and GEO data, we analysed the differences in EphA2 expression between normal and tumour tissues and the effects of EphA2 on the prognosis of different tumours. Furthermore, using GSCALite, cBioPortal, TISDB, ULCLAN and TIMER 2.0 databases or platforms, we comprehensively analysed the potential oncogenic mechanisms or manifestations of EphA2 in 33 different tumour types, including tumour mutation status, DNA methylation status and immune cell infiltration. The correlation of EphA2 with immune checkpoints, tumour mutational burden, DNA microsatellite instability and DNA repair genes was also calculated. Finally, the effects of EphA2 inhibitors on the proliferation of human glioma and lung cancer cells were verified in cellular experiments. EphA2 is differentially expressed in different tumours, and patients with overexpression have poorer overall survival. In addition, gene mutations, gene copy number variation and DNA/RNA methylation of EphA2 have been identified in various tumours. Moreover, EphA2 is positively associated with immune infiltration involving macrophages and CD8+ T cells. Further, EphA2 mRNA expression is significantly associated with immune checkpoint in various cancers, especially programmed death-ligand 1. Finally, the EphA2 inhibitor ALW-II-41-27 shows potent anti-tumour activity. Our first pan-cancer study of EphA2 provides insight into the prognostic and immunological roles of EphA2 in different tumours, suggesting that EphA2 might be a potential biomarker for poor prognosis and immune infiltration in cancer.

18F]F-Poly(ADP-Ribose) Polymerase Inhibitor Radiotracers for Imaging PARP Expression and Their Potential Clinical Applications in Oncology.

Including poly(ADP-ribose) polymerase (PARP) inhibitors in managing patients with inoperable tumors has significantly improved outcomes. The PARP inhibitors hamper single-strand deoxyribonucleic acid (DNA) repair by trapping poly(ADP-ribose)polymerase (PARP) at sites of DNA damage, forming a non-functional "PARP enzyme-inhibitor complex" leading to cell cytotoxicity. The effect is more pronounced in the presence of PARP upregulation and homologous recombination (HR) deficiencies such as breast cancer-associated gene (BRCA1/2). Hence, identifying HR-deficiencies by genomic analysis-for instance, BRCA1/2 used in triple-negative breast cancer-should be a part of the selection process for PARP inhibitor therapy. Published data suggest BRCA1/2 germline mutations do not consistently predict favorable responses to PARP inhibitors, suggesting that other factors beyond tumor mutation status may be at play. A variety of factors, including tumor heterogeneity in PARP expression and intrinsic and/or acquired resistance to PARP inhibitors, may be contributing factors. This justifies the use of an additional tool for appropriate patient selection, which is noninvasive, and capable of assessing whole-body in vivo PARP expression and evaluating PARP inhibitor pharmacokinetics as complementary to the currently available BRCA1/2 analysis. In this review, we discuss [18F]Fluorine PARP inhibitor radiotracers and their potential in the imaging of PARP expression and PARP inhibitor pharmacokinetics. To provide context we also briefly discuss possible causes of PARP inhibitor resistance or ineffectiveness. The discussion focuses on TNBC, which is a tumor type where PARP inhibitors are used as part of the standard-of-care treatment strategy.

Genome-wide DNA methylation in relation to ARID1A deficiency in ovarian clear cell carcinoma

BackgroundThe poor chemo-response and high DNA methylation of ovarian clear cell carcinoma (OCCC) have attracted extensive attentions. Recently, we revealed the mutational landscape of the human kinome and additional cancer-related genes and found deleterious mutations in ARID1A, a component of the SWI/SNF chromatin-remodeling complex, in 46% of OCCC patients. The present study aims to comprehensively investigate whether ARID1A loss and genome-wide DNA methylation are co-regulated in OCCC and identify putative therapeutic targets epigenetically regulated by ARID1A.MethodsDNA methylation of ARID1Amt/ko and ARID1Awt OCCC tumors and cell lines were analyzed by Infinium MethylationEPIC BeadChip. The clustering of OCCC tumors in relation to clinical and mutational status of tumors were analyzed by hierarchical clustering analysis of genome-wide methylation. GEO expression profiles were used to identify differentially methylated (DM) genes and their expression level in ARID1Amt/ko vs ARID1Awt OCCCs. Combining three pre-ranked GSEAs, pathways and leading-edge genes epigenetically regulated by ARID1A were revealed. The leading-edge genes that passed the in-silico validation and showed consistent ARID1A-related methylation change in tumors and cell lines were regarded as candidate genes and finally verified by bisulfite sequencing and RT-qPCR.ResultsHierarchical clustering analysis of genome-wide methylation showed two clusters of OCCC tumors. Tumor stage, ARID1A/PIK3CA mutations and TP53 mutations were significantly different between the two clusters. ARID1A mutations in OCCC did not cause global DNA methylation changes but were related to DM promoter or gene-body CpG islands of 2004 genes. Three pre-ranked GSEAs collectively revealed the significant enrichment of EZH2- and H3K27me3-related gene-sets by the ARID1A-related DM genes. 13 Leading-edge DM genes extracted from the enriched gene-sets passed the expression-based in-silico validation and showed consistent ARID1A-related methylation change in tumors and cell lines. Bisulfite sequencing and RT-qPCR analysis showed promoter hypermethylation and lower expression of IRX1, TMEM101 and TRIP6 in ARID1Amt compared to ARID1Awt OCCC cells, which was reversed by 5-aza-2′-deoxycytidine treatment.ConclusionsOur study shows that ARID1A loss is related to the differential methylation of a number of genes in OCCC. ARID1A-dependent DM genes have been identified as key genes of many cancer-related pathways that may provide new candidates for OCCC targeted treatment.

High dose bolus (HDB) interleukin-2 (IL2) and concurrent low dose ipilimumab followed sequentially by nivolumab in patients with advanced melanoma after failure of anti-PD1-based immunotherapy and BRAF-MEK inhibition.

9543 Background: Options are limited for patients with advanced metastatic melanoma who have disease progression following anti-PD1-based immunotherapy and BRAF-MEK inhibition (if BRAF V600 mutant). Evidence supports synergism between IL2 and CTLA4 blockade in enhancing the immunogenicity of the tumor microenvironment and therapeutic susceptibility to PD1 blockade. Methods: We conducted a phase II study of HDB IL2 in combination with LD ipilimumab followed sequentially by nivolumab in patients with advanced inoperable stage III or stage IV melanoma with progression after anti-PD1-based immunotherapy and BRAF-MEK inhibitors. Treatment consisted of up to 3 courses (One cycle is 21 days and one course is 4 cycles). HDB IL2 and concurrent ipilimumab 1 mg/kg were given during week 1 of the initial 2 cycles of each course. Nivolumab was given during week one of the 3rd cycle of each course. Patients without evidence of disease progression (RECIST v.1.1) or limiting toxicities (CTCAE v.5) were offered additional courses of treatment. A Simon two-stage minimax design (Simon, 1989) was followed. We report the outcomes for Stage I. Results: 12 pts (5 female, 7 male) with metastatic melanoma (2M1a, 1M1b, 6M1c, 3M1d) were treated. Median age 53 years (33 – 69), 11 cutaneous (including 1 acral) and 1 mucosal primary. Tumor mutation status: 4BRAF (V600E), 2NRAS (p.Q61K), 1NF1. The median number of prior regimens for metastatic melanoma was 3 (range 1 - 5). Eight patients previously received ipilimumab as monotherapy or in combination with anti-PD1. On study, the median number of doses of IL2 was 9 during cycle 1 and 7 during cycle 2. A median of 2 doses of ipilimumab and 1 dose of nivolumab were given as part of the combination regimen. Among the 11 evaluable patients (completed 1 course of systemic therapy), the response rate was 2/11 (18.2 %; 95% CI: 2.3% – 51.8%); 1CR, 1 PR, 5 SD, 4 PD and 1 NE as best response. After a median follow up of 39 months, both responses are ongoing (at 10+ and 37+ months), median progression free survival (PFS) was 3 months and median overall survival (OS) was 18.8 months. One-year PFS and OS were 17% (95% CI: 4.7% - 59%) and 83% (95% CI: 65% - 100%), respectively. The adverse event profile was consistent with the expected toxicity profile for each agent with no increase in frequency with the combination. Conclusions: Our combination regimen was relatively safe and well tolerated and demonstrated promising efficacy in a heavily pretreated patient population passing the prespecified efficacy criteria for Simon Stage I. The study has moved into Stage II testing. Clinical trial information: NCT04562129 .

Automatic prediction of isocitrate dehydrogenase mutation status of low-grade gliomas using radiomics and domain knowledge inspired features in magnetic resonance imaging

Aim: Most common and most deadly primary central nervous tumors, glial tumors harbor many heterogeneous clones of cells. Noninvasive determination of the genomic profiles of these tumors would have important implications regarding the classification, management, and prognostication of these tumors. Isocitrate dehydrogenase mutation is a key genomic signature that can downgrade the expected dismal course of these tumors. In this study we aimed to build a performant prediction model which can determine the Isocitrate Dehydrogenase (IDH) mutation status of glial tumors, using radiomics and leveraging automatic computation of domain knowledge-inspired features. Methods: Radiomics methods based on high throughput feature extraction and application of data science principles to these extracted features are promising tools for the noninvasive classification of lesions. Domain knowledge-inspired features besides radiomics features can contribute positively to the performance of the models. Some efforts particularly a joint approach to standardize the magnetic resonance imaging (MRI), reporting of glial tumors are mainstay for domain knowledge-inspired features. However, this requires active involvement and reporting of the radiologist which hampers automatization efforts. Additionally, this feature set evaluates a small subset of all possible signal and spatial-based computations. In this study, we combined domain knowledge-inspired features with radiomics features along with a multiparametric multihabitat comprehensive lesion description strategy. Results: Our best model which consisted of a combination of radiomics, and radiologist knowledge-inspired features reached a 0.93 f1 score (standard deviation (SD): 0.03), 0.93 accuracy (SD:0.03), and 0.98 area under curve (AUC), (SD:0.02). Conclusion: The multiparametric and multiregional approach employed in this study coupled with the integration of both radiomics and domain knowledge-inspired features resulted in a high-performance model emphasizing the contribution of each strategy to the outcome.

Association of ESR1 Germline Variants with TP53 Somatic Variants in Breast Tumors in a Genome-wide Study.

Emerging data show ancestry-specific differences in TP53 and PIK3CA mutation frequency in breast tumors suggesting that germline variants may influence somatic mutational processes. This study identified variants near ESR1 associated with TP53 mutation status and identified additional loci with suggestive association which may provide biological insight into observed differences.

Abstract PO4-22-02: pSmad2 as a marker of radiotherapy benefit in breast cancer- results from the randomized SweBCG91RT trial

Abstract Background: The TGF-beta pathway can have both pro- and antitumoral effects in breast cancer. Experimental studies further suggest that TGF-beta can mediate radioresistance, either through direct effects on tumor cells or indirectly by its immunomodulatory properties. However, the effect of TGF-beta signaling is highly depending on tumor stage, mutational status and microenvironmental cell composition. In order to explore TGF-beta signaling as a potential biomarker or therapeutical target it is therefore important to perform analyses in well-defined study populations. The purpose of this study was to study the effect of active TGF beta signaling in tumor cells, on the risk of ipsilateral breast tumor recurrence (IBTR) and benefit from radiotherapy (RT) in specifically early-stage breast cancer using nuclear, phosphorylated Smad2 (pSmad2) as a marker. Methods: The SweBCG91RT cohort included 1179 patients with stage I-IIA tumors randomized to breast-conserving surgery (BCS) with or without postoperative RT. Nuclear pSmad2 expression was assessed as for 987 available tumors on TMAs as the mean proportion of tumor cells with positive nuclear staining. Based on the distributions, tumors were categorized as having high (≥80%, n=344), medium (21-79%, n=428) or low (≤20%, n=161) pSmad2 staining. The primary endpoint was time to ipsilateral breast tumor recurrence as the first event within 10 years. Results: pSmad2Low tumors were more likely to be of grade III (p&amp;lt; 0.001) and tended to be larger than pSmad2Medium (p=0.002, median 15 vs 12 mm) and pSmad2High (p&amp;lt; 0.001, median 15 vs 12 mm) tumors. No associations between pSmad2 and subtype or age were found. Numerically, tumors with pSmad2low (HR 1.55, CI 95% 0.80-3.02, p=0.19) or pSmad2Medium (HR 2.53, CI 95% 1.52-4.22, p&amp;lt; 0.001) had a higher risk of IBTR than pSmad2high tumors (reference). These findings remained significant after adjustment for age, histological grade, and RT. The benefit from RT was similar for pSmad2High (HR0.41, CI 95% 0.15-1.07, p=0.068), pSmad2Medium (HR 0.36, CI 95% 0.21-0.63, p&amp;lt; 0.001), and pSmad2Low (HR 0.51, CI 95% 0.18-1.46, p=0.21) tumors (pinteraction=0.86). Conclusions: Early-stage breast tumors with high nuclear pSmad2 staining may be at a reduced risk of an IBTR. However, the relative benefit from RT does not seem to differ from tumors with medium or low pSmad2 staining. These results need to be confirmed in additional studies, but they provide initial evidence that tumoral TGF-beta signaling has rather tumor restraining functions in early-stage breast cancer. Next analytical steps should include the tumor mutation status (particularly for TGF-beta signaling components TGFBR2, SMAD4 and TP53), as well as the TGF-beta signaling status within the tumor microenvironment. Citation Format: Per Karlsson, Viktoria Thurfjell, Anikó Kovács, Fredrika Killander, Emma Niméus, Erik Holmberg, Carina Strell, Axel Stenmark Tullberg. pSmad2 as a marker of radiotherapy benefit in breast cancer- results from the randomized SweBCG91RT trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-22-02.

Keratin 17 is a prognostic and predictive biomarker in pancreatic ductal adenocarcinoma.

To determine the role of keratin 17 (K17) as a predictive biomarker for response to chemotherapy by defining thresholds of K17 expression based on immunohistochemical tests that could be used to optimize therapeutic intervention for patients with pancreatic ductal adenocarcinoma (PDAC). We profiled K17 expression, a hallmark of the basal molecular subtype of PDAC, by immunohistochemistry in 2 cohorts of formalin-fixed, paraffin-embedded PDACs (n = 305). We determined a K17 threshold of expression to optimize prognostic stratification according to the lowest Akaike information criterion and explored the potential relationship between K17 and chemoresistance by multivariate predictive analyses. Patients with advanced-stage, low K17 PDACs treated using 5-fluorouracil (5-FU)-based chemotherapeutic regimens had 3-fold longer survival than corresponding cases treated with gemcitabine-based chemotherapy. By contrast, PDACs with high K17 did not respond to either regimen. The predictive value of K17 was independent of tumor mutation status and other clinicopathologic variables. The detection of K17 in 10% or greater of PDAC cells identified patients with shortest survival. Among patients with low K17 PDACs, 5-FU-based treatment was more likely than gemcitabine-based therapies to extend survival.

The Molecular Landscape of Gastric Cancers for Novel Targeted Therapies from Real-World Genomic Profiling.

Panel-based comprehensive genomic profiling is used in clinical practice worldwide; however, large real-world datasets of patients with advanced gastric cancer are not well known. We investigated what differences exist in clinically relevant alterations for molecularly defined or age-stratified subgroups. This was a collaborative biomarker study of a real-world dataset from comprehensive genomic profiling testing (Foundation Medicine, Inc.). Hybrid capture was carried out on at least 324 cancer-related genes and select introns from 31 genes frequently rearranged in cancer. Overall, 4634 patients were available for analyses and were stratified by age (≥40/<40 years), microsatellite instability status, tumor mutational burden status (high 10 ≥/low <10 Muts/Mb), Epstein-Barr virus status, and select gene alterations. We analyzed the frequency of alterations with a chi-square test with Yate's correction. Genes with frequent alterations included TP53 (60.1%), ARID1A (19.6%), CDKN2A (18.2%), KRAS (16.6%), and CDH1 (15.8%). Differences in comprehensive genomic profiling were observed according to molecularly defined or age-stratified subgroups. Druggable genomic alterations were detected in 31.4% of patients; ATM (4.4%), BRAF V600E (0.4%), BRCA1 (1.5%), BRCA2 (2.9%), ERBB2 amplification (9.2%), IDH1 (0.2%), KRAS G12C (0.7%), microsatellite instability-high (4.8%), NTRK1/2/3 fusion (0.13%), PIK3CA mutation (11.4%), and tumor mutational burden-high (9.4%). CDH1 alterations and MET amplification were significantly more frequent in patients aged <40 years (27.7 and 6.2%) than in those aged ≥40 years (14.7 and 4.0%). Real-world datasets from clinical panel testing revealed the genomic landscape in gastric cancer by subgroup. These findings provide insights for the current therapeutic strategies and future development of treatments in gastric cancer.

293 The Impact of Tumor Mutational Status on Protoporphyrin IX Accumulation in Tumor-Associated Macrophages in Glioblastoma Patients

INTRODUCTION: Immunotherapies provide promising new treatment options for lung cancer and melanoma, however success in glioblastoma (GBM) patients has been much rarer and uneven. Identifying candidates with GBM that are most likely to benefit from immunotherapy remains a challenge. The abundance of tumor-associated macrophages (TAMs) correlates response to immunotherapy in GBM patients. Here we leverage a new imaging technique for quantifying TAMs via tandem stimulated Raman histology (SRH) and two-photon excitation fluorescence microscopy (TPEF) to assess the impact of genetic classification on the abundance of TAMs. METHODS: We conducted tandem SRH and TPEF on specimens from 79 patients undergoing high-grade glioma resection with 5-ALA. We trained a MaskR-CNN deep neural network to identify TAMs and compute their density in each specimen. Corresponding clinical, demographic, genomic and methylomic data were collected for each patient. Independent sample t-tests were used to identify significant correlations between genetic markers, treatment, and TAM density. RESULTS: We analyzed 3,121,524 300 x 300 micron fields of view, from 151 fresh specimens, enabling segmentation of 611,789 TAMs. IDH-mutant tumors had significantly lower TAM density than IDH-wildtype tumors (p &lt; 0.01). The absence of MGMT promoter hypermethylation was associated with significantly higher TAM density (p = 0.03). Tumors with EGFR amplification averaged significantly lower TAM density than EGFR wildtype specimens (p &lt; 0.01). Recurrent tumors possessed 31.5% lower TAM density than primary resections. CONCLUSIONS: Tandem SRH and TPEF can estimate variations in TAM density in human GBMs. We found TAM density to be associated with IDH status, MGMT promoter methylation, and EGFR amplification. This imaging technique creates a new avenue for forecasting response to immunotherapy in GBM patients.

Abstract 6278: Effect of tumor size and BRAF mutational status in Middle Eastern differentiated thyroid cancer

Abstract Background: Risk stratified treatment strategies have become a focus in the treatment of Differentiated Thyroid Cancer (DTC). Tumor size at diagnosis has been widely used as a major mortality risk factor in risk stratification of DTC, but whether this is generally applicable, particularly in patient with different BRAF genetic backgrounds, is unclear. The current study was designed to analyze whether tumor size at diagnosis is a major prognostic factor in Middle Eastern DTC. Methods: We conducted a comparative study of the relationship between tumor size at diagnosis and event free survival with respect to BRAF status in 1709 consecutive patients treated surgically for Middle Eastern DTC. Patients were divided into four groups according to the size of tumor (≤4 cm vs. &amp;gt;4 cm) and BRAF mutation status: Group 1 (≤4 cm without BRAF mutation, n = 587), Group 2 (≤4 cm with BRAF mutation, n = 765), Group 3 (&amp;gt;4 cm without BRAF mutation, n = 198) and Group 4 (&amp;gt;4 cm with BRAF mutation, n = 159). Predictors of event-free survival (EFS) were compared using the Log-rank test and Cox proportional hazards models. Results: Following multivariate analysis, patients with tumors &amp;gt;4cm did worse than patients with tumors &amp;lt;4cm with respect to EFS (Group 3 vs Group1 HRadjusted=1.38, 95% CI=1.02-1.86, p = 0.0359; Group 4 vs Group 2 HRadjusted=1.61, 95% CI=1.20-2.16, p = 0.0017). However, patients did not differ according to EFS, regardless of the presence of BRAF mutation within each size category (Group 2 vs Group 1 HRadjusted=0.98 CI=.78-1.23, p=0.8415 ; Group 4 vs Group 3 HRadjusted=1.17, 95% CI=0.84-1.62, p=0.3523] Conclusion: Tumor size is an independent predictor of EFS in Middle Eastern DTC patients, regardless of BRAF mutational status. Citation Format: Rong Bu, Abdul K. Siraj, Sandeep K. Parvathareddy, Kaleem Iqbal, Saud Azam, Zeeshan Qadri, Maha Al-Rasheed, Wael Haqawi, Allianah D. Benito, Khawla S. Al-Kuraya. Effect of tumor size and BRAF mutational status in Middle Eastern differentiated thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6278.

Abstract 6777: An ex-vivo organotypic culture platform of mucinous carcinomatosis peritonei identifies CDK4-6 inhibition as a novel treatment

Abstract Concomitant mutations in KRAS and GNAS have been linked to mucinous histology in gastrointestinal neoplasms of the appendix, colon, and pancreas (IPMN). Upon progression, these tumors are characterized by metastasis which favors the peritoneal surface, resulting in mucinous carcinomatosis peritonei (MCP). Recently we have described a novel technique which allows for long term culture and drug intervention of human MCP tumors ex-vivo. With evidence of durable clinical benefit of CDK4-6 inhibition in a single patient with chemo refractory MCP of appendiceal origin, we sought to further investigate anti-tumor responses using CDK4-6 inhibition in ex-vivo tumor slices, in order to identify candidates for a personalized clinical therapy trial. Here, in a comparison of ex-vivo patient tumor slices from 18 individual donors, treatment using CDK4-6 inhibitors revealed a significant reduction in cancer cell specific proliferation in mucinous GNAS-mut tumors compared to non-mucinous cancers. Anti-tumor responses of CDK4-6 were determined to be tumor-cell intrinsic, as CDK4-6 inhibition blocked proliferation of stromal cells in the TME independently of patient tumor mutational and mucin status. Based on these finding a personalized clinical trial was conducted where we report that 13 of 16 patients (81%) enrolled with MCP treated with palbociclib had at least a 10% decrease in CEA, as compared to historical chemotherapy responses rates reported from 14-30%. These results indicate that CDK4/6 inhibition is a novel and efficacious treatment for patients with MCP. Citation Format: Jonathan Weitz, Daisuke Nishizaki, Jay Patel, Isabella Ng, Siming Sun, Dana Ramms, Jingjing Zou, Joel Baumgartner, Kaitlyn Kelly, Hitendra Patel, Rebekah White, Jula Veerapong, Peter Vu, Silvio Gutkind, Herve Tiriac, Shumei Kato, Andrew Lowy. An ex-vivo organotypic culture platform of mucinous carcinomatosis peritonei identifies CDK4-6 inhibition as a novel treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6777.