Amplification Status Research Articles

GATA6 amplification is associated with improved survival in TP53-mutated unresectable pancreatic cancer

Abstract Objectives: GATA6 expression has been recently recognized as a favorable prognostic marker of pancreatic cancer whereas TP53 is recognized as a poor prognostic marker. We evaluated treatment outcomes by genetic alterations in TP53 and GATA6 to determine the prognostic and predictive impact of co-alterations. Methods A single institution retrospective analysis was performed on patients diagnosed with PDAC between 2014 to 2023. TP53 genotype and GATA6 amplification status were included in an analysis of overall survival (OS) and progression free survival (PFS). Previously published patient-derived organoids were used to investigate correlation between genetic status and drug sensitivity. Results Patients with TP53 mutations had worse OS compared to the wild type TP53 population. In general, patients with GATA6 amplification had better OS and a trend towards better PFS than the non-amplified population. Among patients with a TP53 mutation, patients with GATA6 co-alteration had longer OS compared to those who were not GATA6 amplified. In contrast, among patients who were TP53 wild type, the presence or absence of a GATA6 amplification did not impact OS or PFS. GATA6 genotype was not associated chemotherapy drug response in an organoid pharmacotyping model. Conclusions We found that GATA6 amplification appeared to attenuate poor prognosis observed in TP53-mutant patients regardless of the type of standard chemotherapy received, suggesting the GATA6 amplification is a prognostic biomarker but not a predictive biomarker of standard-of-care chemotherapy.

Computational approach for counting of SISH amplification signals for HER2 status assessment

The human epidermal growth factor receptor 2 (HER2) gene is a critical biomarker for determining amplification status and targeting clinical therapies in breast cancer treatment. This study introduces a computer-aided method that automatically measures and scores HER2 gene status from invasive tissue regions of breast cancer using whole slide images (WSI) through silver in situ hybridization (SISH) staining. Image processing and deep learning techniques are employed to isolate untruncated and non-overlapping single nuclei from cancer regions. The Stardist deep learning model is fine-tuned on our HER2-SISH data to identify nuclei regions, followed by post-processing based on identified HER2 and CEP17 signals. Conventional thresholding techniques are used to segment HER2 and CEP17 signals. HER2 amplification status is determined by calculating the HER2-to-CEP17 signal ratio, in accordance with ASCO/CAP 2018 standards. The proposed method significantly reduces the effort and time required for quantification. Experimental results demonstrate a 0.91% correlation coefficient between pathologists manual enumeration and the proposed automatic SISH quantification approach. A one-sided paired t-test confirmed that the differences between the outcomes of the proposed method and the reference standard are statistically insignificant, with p-values exceeding 0.05. This study illustrates how deep learning can effectively automate HER2 status determination, demonstrating improvements over current manual methods and offering a robust, reproducible alternative for clinical practice.

A DTI-based radiomics model for predicting epidermal growth factor receptor (EGFR) amplification in adult IDH1-wild glioblastomas.

Molecular alteration events are common in glioblastomas, the isocitrate dehydrogenase (IDH)-wild of which have had poor survival results so far. The progress of radiomics-based model provides novel sights for its preoperatively noninvasive prediction. To develop a radiomics-based model for predicting epidermal growth factor receptor (EGFR) amplification status in IDH1-wild glioblastomas of adults by pretreatment diffusion tensor imaging (DTI). A total of 124 patients with diagnosed glioblastomas were retrospectively collected. Six conventional magnetic resonance imaging (MRI) features of all the tumors were evaluated visually. Patients were divided into the training (n = 87) and the test set (n = 37) with a ratio of 7:3. Radiomics features were extracted from two regions of the glioblastomas, which were the total tumor (ROI_1) and the solid portion of tumor (ROI_2). The radiomics features extracted from the DTI and T1-contrast-enhanced (T1C) images were selected using the least absolute shrinkage and selection operator (LASSO) regression algorithm. Logistic regression analysis was conducted to develop models for EGFR amplification prediction in the training set. The radiomics model based on ROI_1 demonstrated favorable discrimination in both the training (area under the curve [AUC] = 0.86) and the test set (AUC = 0.82) (P < 0.05). Combining the radiomics features and the conventional feature tumor location, no significant improvement of AUCs was achieved (AUC = 0.86 and 0.81). The radiomics model derived from pretreatment DTI may have potential in differentiating the EGFR mutation status in glioblastomas.

Multi-center external validation of an automated method segmenting and differentiating atypical lipomatous tumors from lipomas using radiomics and deep-learning on MRI

As differentiating between lipomas and atypical lipomatous tumors (ALTs) based on imaging is challenging and requires biopsies, radiomics has been proposed to aid the diagnosis. This study aimed to externally and prospectively validate a radiomics model differentiating between lipomas and ALTs on MRI in three large, multi-center cohorts, and extend it with automatic and minimally interactive segmentation methods to increase clinical feasibility. Three study cohorts were formed, two for external validation containing data from medical centers in the United States (US) collected from 2008 until 2018 and the United Kingdom (UK) collected from 2011 until 2017, and one for prospective validation consisting of data collected from 2020 until 2021 in the Netherlands. Patient characteristics, MDM2 amplification status, and MRI scans were collected. An automatic segmentation method was developed to segment all tumors on T1-weighted MRI scans of the validation cohorts. Segmentations were subsequently quality scored. In case of insufficient quality, an interactive segmentation method was used. Radiomics performance was evaluated for all cohorts and compared to two radiologists. The validation cohorts included 150 (54% ALT), 208 (37% ALT), and 86 patients (28% ALT) from the US, UK and NL. Of the 444 cases, 78% were automatically segmented. For 22%, interactive segmentation was necessary due to insufficient quality, with only 3% of all patients requiring manual adjustment. External validation resulted in an AUC of 0.74 (95% CI: 0.66, 0.82) in US data and 0.86 (0.80, 0.92) in UK data. Prospective validation resulted in an AUC of 0.89 (0.83, 0.96). The radiomics model performed similar to the two radiologists (US: 0.79 and 0.76, UK: 0.86 and 0.86, NL: 0.82 and 0.85). The radiomics model extended with automatic and minimally interactive segmentation methods accurately differentiated between lipomas and ALTs in two large, multi-center external cohorts, and in prospective validation, performing similar to expert radiologists, possibly limiting the need for invasive diagnostics. Hanarth fonds.

Concordance of HER2 Expression in Paired Primary and Metastatic Sites of Endometrial Serous Carcinoma and the Effect of Intratumoral Heterogeneity

Primary endometrial serous carcinoma, known for its aggressive nature and poor prognosis, shares similarities with breast and gastric cancers in terms of potential HER2 overexpression as a therapeutic target. Assessing HER expression is complicated by tumor heterogeneity and discrepancies between primary and metastatic sites. In this study, we retrospectively analyzed HER amplification and expression in 16 pairs of primary endometrial serous carcinoma resections and corresponding metastases. HER2 status was determined using immunohistochemistry (IHC), with criteria based on the percentage and intensity of tumor cell staining. Confirmatory techniques, such as dual in situ hybridization (DISH) and fluorescence in situ hybridization (FISH), were also employed. This study reports on the concordance rates and the presence and pattern of HER2 heterogeneity. Our results showed an 87.5% concordance rate in HER2 amplification status between primary and metastatic sites, with 33% of cases scored as 2+ being amplified. Heterogeneity was observed in 100% of amplified cases and 95% of non-amplified cases on in situ testing, with variations in heterogeneity patterns between techniques. In conclusion, our findings emphasize the importance of testing both primary and metastatic sites or recurrences, with a concordance rate of 87.5%. In addition, a review of the literature and combining the results showed a concordance rate of up to 68%. The presence and pattern of heterogeneity, particularly in cases of mosaic or clustered heterogeneity in the primary tumor, may serve as reliable indicators of concordance, predicting a non-amplified HER2 status in corresponding metastases.

Current and Emerging Biomarkers: Impact on Risk Stratification for Neuroblastoma.

Neuroblastoma has heterogenous clinical presentations that are reflected by several well-defined clinical factors and biomarkers. Combinations of these clinical and biologic prognostic factors have been used for decades to generate classifiers to stratify patients into risk groups (low, intermediate, and high), which in turn are used to inform and tailor treatment as reported in the new NCCN Clinical Practice Guidelines in Oncology for Neuroblastoma. Risk classification uses clinical features, such as age and tumor stage, along with the most significant prognostic tumor biomarkers, including histologic features (differentiation and mitosis-karyorrhexis index), MYCN amplification status, chromosomal copy number alterations (segmental or numerical), and ploidy (DNA content). Recent next-generation sequencing approaches have identified additional tumor-specific genetic factors that have potential roles as prognostic and predictive biomarkers. These emerging biomarkers include telomerase maintenance mechanisms, such as telomerase reverse transcription (TERT) expression and alternative lengthening of telomeres (ALT) status. Somatic alterations of genes, including mutations in the anaplastic lymphoma kinase gene ALK, detected in >10% of patients with newly diagnosed disease, have both prognostic and predictive roles in determining eligibility for targeted therapies (eg, ALK tyrosine kinase inhibitors). In addition to diagnostic tumor-derived biomarkers, significant effort is being directed toward identification of markers to predict response to chemotherapy and immunotherapies. With the increasing use of GD2-containing immunotherapy regimens, efforts are aimed at identifying host or tumor microenvironment immune correlatives that can serve as predictive biomarkers. Understanding the potential role of liquid biopsies as biomarkers during and following treatment, including sequential circulating tumor DNA or tumor-specific mRNA transcripts, is expected to enhance the ability to predict recurrences and also inform understanding of tumor evolution and therapy resistance. These and other emerging biomarkers will lead to refinement and optimization of future neuroblastoma risk classification systems.

IKZF3 amplification predicts worse prognosis especially in intestinal-type gastric cancer

PurposeIKAROS family zinc finger 3 (IKZF3) is an oncogene involved in different malignancies, particularly in the development and malignant progression of lymphocytes. However, IKZF3 amplification and clinical significance in gastric cancers (GCs) remain unexplored.MethodsWe examined IKZF3 amplification status in 404 GCs with HER2 amplification status using tissue microarray (TMA) and fluorescence in situ hybridization (FISH) assays.ResultsIKZF3 amplification was detected in 6.9% (28/404) of all GC patients, with higher rates in intestinal-type gastric cancer (IGC) (11.22%, 22/196) compared to other types (2.88%, 6/208). HER2 amplification was identified in 16.09% (65/404) of all GC patients, with higher rates in IGC (20.92%, 41/196) compared to other types (11.54%, 24/208). Co-amplification of IKZF3 and HER2 was detected in 8.16% (16/196) of IGC patients and in 2.40% (5/208) of other types. IKZF3 amplification showed significant correlation with IGC (P = 0.001) and HER2 amplification (P = 0.0001). IKZF3 amplification exhibited significantly worse disease-free survival (DFS) (P = 0.014) and overall survival (OS) (P = 0.018) in GC patients, particularly in IGC (DFS: P < 0.001; OS: P < 0.001), rather than other types. Cox regression analysis demonstrate IKZF3 amplification as an independent poor prognostic factor in all GCs (P = 0.006, P = 0.004 respectively) and in IGC patients, regardless of stages I-II or III-IV (P = 0.007, P = 0.004 respectively). On the other hand, HER2 amplification was significantly associated with worse DFS (P = 0.008) and OS (P = 0.01) in IGC patients, but not in all GCs and in multivariate analysis. Within the subset of patients with HER2 amplification, those also exhibiting IKZF3 amplification displayed potential poorer prognosis (P = 0.08, P = 0.11 respectively).ConclusionIKZF3 amplification was detected in minority of GC patients, especially in IGC, and was an independent indicator of poor prognosis. Our study, for the first time, found the prognostic value of IKZF3 was superior to HER2 for GC patients.

Application of the FISH method and high-density SNP arrays to assess genetic changes in neuroblastoma-research by one institute.

Neuroblastoma is the most common extracranial solid tumor in children. Amplification of the MYCN gene has been observed in approximately 20%-30% of tumors. It is strongly correlated with advanced-stage disease, rapid tumor progression, resistance to chemotherapy and poor outcomes independent of patient age and stage of advanced disease. MYCN amplification identifies high-risk patients. To assess neuroblastoma tumors with MYCN amplification we used paraffin-embedded tissue sections in 57 patients and intraoperative tumor imprints in 10 patients by fluorescence in situ hybridization (FISH). Positive results for MYCN amplification have been observed in twelve patients' paraffin-embedded tissue sections and in three patients' intraoperative tumor imprints, which represents 22.4% of all patients tested in the analysis. Fluorescence in situ hybridization is a highly sensitive and useful technique for detecting MYCN amplification on paraffin-embedded tissue sections of neuroblastoma tumors and intraoperative tumor imprints thus facilitating therapeutic decisions based on the presence or absence of this important biologic marker. The presence of structural changes, regardless of MYCN gene amplification status, influences the clinical behavior of neuroblastoma. High-Density SNP Arrays have emerged as the perfect tools for detecting these changes due to their exceptional accuracy, sensitivity and ability to analyze copy number and allele information. Consequently, they are proven to be highly valuable in the genomic diagnosis of immature neuroectodermal tumors.

MDB-102. CDK8 IS A DEPENDENCY IN GROUP 3 MEDULLOBLASTOMA AND COMBINES WITH BET BROMODOMAIN INHIBITION

Abstract Medulloblastoma (MB) is the most common pediatric CNS malignancy with varying prognoses depending on subgroup diagnosis. Group 3 MB displays the poorest overall prognosis, specifically in cases characterized by MYC hyperactivation. Current standard treatment can cause lifelong debilitating side effects, therefore the identification of targeted therapeutic agents will be critical in enhancing patient survival and bypassing therapy-induced aftereffects. We utilized the Pediatric Cancer Dependency Map to identify CDK8 as the most striking dependency in MB compared to all other pediatric malignancies. Further analysis revealed dependencies on its cognate cyclin, Cyclin C, and other members of the CDK8 kinase module (CKM). The CKM functions as a transcriptional regulator, phosphorylating RNAPol2 and other transcription factors. Interestingly, CDK8 dependency correlates with MYC amplification status in cell lines suggesting it to be a strong dependency in G3 MB. CDK8 expression, both RNA and protein, is highest in G3 tumors. We depleted CDK8 both genetically and pharmacologically and demonstrated downregulation of MYC expression in tumor cells and decreased cell survival. We next tested the efficacy of a CDK8 kinase inhibitor currently in clinical trials. Treatment with SEL-120 reduced cell proliferation and viability in vitro and inhibited tumor growth in vivo. This effect was limited to G3 models, as SEL120 showed little efficacy in SHH MB. Analysis of gene expression revealed that targeting CDK8 did not affect MYC-dependent gene expression but led to de-repression of differentiation genes regulated by PRC2. We further observed a global de-repression of H3K27me3 in cells treated with CDK8i. Finally, we tested the first ever blood-brain barrier penetrant CDK8i which mimics the activity of SEL-120 and potently synergizes with BETi, which antagonizes MYC signaling. In summary, we have identified and validated CDK8 as a novel target in G3 MB and identified a possible synergistic combination to move forward in clinical trials.

Expression and Clinical Significance of Ki-67, CD10, BCL6, MUM1, c-MYC, and EBV in Diffuse Large B Cell Lymphoma Patients.

Diffuse large B cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma (NHL) in adults. Although studies regarding the association between the expression of Ki-67, CD10, BCL6, and MUM1 proteins, as well as c-MYC amplification and EBV status with clinicopathologic characteristics have rapidly progressed, their co-expression and prognostic role remain unsatisfactory. Therefore, this study aimed to investigate the association between the expression of all markers and clinicopathologic features and their prognostic value in DLBCL. Also, the co-expression of markers was investigated. The protein expression levels and prognostic significance of Ki-67, CD10, BCL6, and MUM1 were investigated with clinical follow-up in a total of 53 DLBCL specimens (including germinal center B [GCB] and activated B cell [ABC] subtypes) as well as adjacent normal samples using immunohistochemistry (IHC). Besides, the clinical significance and prognostic value of c-MYC and EBV status were also evaluated through chromogenic in situ hybridization (CISH), and their correlation with other markers was also assessed. The results demonstrated a positive correlation between CD10 and BCL6 expression, with both markers being associated with the GCB subtype ( P< 0.001 and P =0.001, respectively). Besides, we observe a statistically significant association between MUM1 protein expression and clinicopathologic type ( P< 0.005) as well as a positive association between c-MYC and recurrence ( P =0.028). Our survival analysis showed that patients who had responded to R-CHOP treatment had better overall survival (OS) and progression-free survival (PFS) than those who did not. Collectively, this study's results add these markers' value to the existing clinical understanding of DLBCL. However, further investigations are needed to explore markers' prognostic and biological roles in DLBCL patients.

Development of red blood cell-derived extracellular particles as a biocompatible nanocarrier of microRNA-204 (REP-204) to harness anti-neuroblastoma effect

Neuroblastoma (NB) is the most common extracranial solid tumor in the pediatric population with a high degree of heterogeneity in clinical outcomes. Upregulation of the tumor suppressor miR-204 in neuroblastoma is associated with good prognosis. Although miR-204 has been recognized as a potential therapeutic candidate, its delivery is unavailable. We hypothesized that REP-204, the red blood cell-derived extracellular particles (REP) with miR-204 loading, can suppress neuroblastoma cells in vitro. After miR-204 loading by electroporation, REP-204, but not REP carriers, inhibited the viability, migration, and 3D spheroid growth of neuroblastoma cells regardless of MYCN amplification status. SWATH-proteomics revealed that REP-204 treatment may trigger a negative regulation of mRNA splicing by the spliceosome, suppression of amino acid metabolism and protein production, and prevent SLIT/ROBO signaling-mediated cell migration, to halt neuroblastoma tumor growth and metastasis. The therapeutic efficacy of REP-204 should be further investigated in preclinical models and clinical studies.

Genetic Prognostic Factors in Adult Diffuse Gliomas: A 10-Year Experience at a Single Institution.

Gliomas are primary brain lesions involving cerebral structures without well-defined boundaries and constitute the most prevalent central nervous system (CNS) neoplasms. Among gliomas, glioblastoma (GB) is a glioma of the highest grade and is associated with a grim prognosis. We examined how clinical variables and molecular profiles may have affected overall survival (OS) over the past ten years. A retrospective study was conducted at Sina Hospital in Tehran, Iran and examined patients with confirmed glioma diagnoses between 2012 and 2020. We evaluated the correlation between OS in GB patients and sociodemographic as well as clinical factors and molecular profiling based on IDH1, O-6-Methylguanine-DNA Methyltransferase (MGMT), TERTp, and epidermal growth factor receptor (EGFR) amplification (EGFR-amp) status. Kaplan-Meier and multivariate Cox regression models were used to assess patient survival. A total of 178 patients were enrolled in the study. The median OS was 20 months, with a 2-year survival rate of 61.0%. Among the 127 patients with available IDH measurements, 100 (78.7%) exhibited mutated IDH1 (IDH1-mut) tumors. Of the 127 patients with assessed MGMT promoter methylation (MGMTp-met), 89 (70.1%) had MGMT methylated tumors. Mutant TERTp (TERTp-mut) was detected in 20 out of 127 cases (15.7%), while wildtype TERTp (wildtype TERTp-wt) was observed in 107 cases (84.3%). Analyses using multivariable models revealed that age at histological grade (p < 0.0001), adjuvant radiotherapy (p < 0.018), IDH1 status (p < 0.043), and TERT-p status (p < 0.014) were independently associated with OS. Our study demonstrates that patients with higher tumor histological grades who had received adjuvant radiotherapy exhibited IDH1-mut or presented with TERTp-wt experienced improved OS. Besides, an interesting finding showed an association between methylation of MGMTp and TERTp status with tumor location.

MRI compared to 123I-MIBG scan for detection of central nervous system relapse in neuroblastoma.

10040 Background: Neuroblastoma (NB) relapsing in the central nervous system (CNS), though uncommon, is historically incurable. However, a multimodality approach has improved long term survival (1). Timely detection of CNS relapse may reduce or prevent morbidity and mortality. In most centers, surveillance for NB includes whole-body MIBG scans but does not require dedicated anatomical brain imaging. At Memorial Sloan Kettering Cancer Center (MSK), head MRI at regular intervals is standard. The objective of this retrospective study was to determine the optimal imaging modality for detecting CNS relapse in NB. Methods: After MSK IRB approval, records of patients with CNS NB seen at MSK from 2004-2023 were evaluated. In most cases, relapse was diagnosed at other institutions before referral to MSK. Analyzed data included symptoms and findings on brain CT/MRI and MIBG scans. Results: Of 206 patients with MIBG-avid CNS NB, 7 were excluded because they had CNS disease at diagnosis. For the remaining 199 patients, median time to CNS relapse from diagnosis was 18 months. 132 (66%) patients had CNS relapse at a median of 9.8 months after achieving complete remission. In 67 patients with prior systemic progression, median time to CNS relapse was 10.9 months from the last relapse. Relapse was isolated to CNS in 130/199 (65%) patients. 118 (59%) patients had neurological symptoms at time of CNS disease; 81(41%) were asymptomatic, relapse being detected on surveillance scans. Multiple (&gt;1) parenchymal lesions were noted in 74 (37%), diffuse leptomeningeal disease without parenchymal involvement in 15 (7%) and solitary lesions in 110 (55%) patients. Median diameter of the largest lesion was 2.7 (range &lt;0.5-6.8) cm. Anatomical imaging was performed with MRI (65%), CT (14%) or both (34%). Of those undergoing both scans, CNS relapse was missed on CT in 4/67 (6%) patients. 137 patients had MIBG scans before resection of CNS relapse. All sites of CNS disease noted on MRI/CT were positive by MIBG in 46 (33%) patients. However, MIBG scan was either totally or partly negative in 69 (50%) and 22 (16%) patients, respectively. Even for lesions ≥2cm in diameter, MIBG was completely negative in 27/57 (47%). MIBG positivity did not correlate with age, size &gt;2cm, MYCN amplification or ALK mutation status (p&gt;0.05 for each). Lesions &lt;1cm and infratentorially located were more likely to be negative on MIBG scan (p&lt;0.05). Lesions in symptomatic patients, dural lesions and hemorrhagic lesions were more likely to be positive on MIBG scan (p&lt; 0.05). Conclusions: CNS relapse is isolated to the brain in most patients. MIBG scan has poor sensitivity for the detection of CNS NB, regardless of size or location. Although CT or MRI are both effective in detecting CNS relapse, the former can miss some lesions. We recommend brain MRI for surveillance of high-risk NB for ≥2 years after initial diagnosis or last systemic relapse. 1. J. Neurooncology 97:409, 2010.

Endometrial cancer (EC) by ERBB2 amplification (ERBB2amp) status: Differences in molecular subtypes, ancestry, and real-world outcomes.

Endometrial cancer (EC) by ERBB2 amplification (ERBB2amp) status: Differences in molecular subtypes, ancestry, and real-world outcomes.

RAS/RAF mutations and microsatellite instability status in primary colorectal cancers according to HER2 amplification.

HER2 amplification-associated molecular alterations and clinicopathologic features in colorectal cancers (CRCs) have not been well established. In this study, we assessed the prevalence of HER2 amplification and microsatellite instability (MSI) status of 992 patients with primary CRC. In addition, molecular alterations of HER2 amplified and unamplified CRCs were examined and compared by next-generation sequencing. HER2 amplifications were found in 41 (4.1%) of 992 primary CRCs. HER2 amplification was identified in 1.0% of the right colonic tumors, 5.1% of the left colonic tumors, and 4.8% of the rectal tumors. Approximately 95% of HER2 amplification was observed in the left colon and rectum. Seven (87.5%) of eight metastatic tumors showed HER2 amplification. Most clinicopathologic features were unrelated to HER2 amplification except tumor size and MSI status. All 41 HER2 amplified CRCs were microsatellite stable. In a molecular analysis of frequently identified somatic mutations in CRCs, HER2 amplified CRCs showed a lower rate of KRAS mutations (24.4%) but a higher rate of TP53 mutations (83%) than unamplified CRCs. No BRAF and NRAS mutations were identified in HER2 amplified CRCs. Our study suggests that HER2 amplified CRCs are mutually exclusive of MSI and harbor less frequent KRAS/NRAS/BRAF mutations but frequent T53 mutations.

EGFR, HER2, and MET gene amplification and protein expression profiles in biliary tract cancer and their prognostic significance.

There are limited conventional chemotherapy options for biliary tract cancers (BTCs), a heterogenous group of lethal, rare malignancies. The receptor tyrosine kinase (RTK) is closely associated with the progression of human malignancies through the regulation of cell cycle. Overexpression or amplification of RTKs has been investigated as a potential biomarker and therapeutic target in BTC; herein, we investigate the value of such interventions. Overexpression of RTK proteins was examined by immunohistochemistry in 193 BTC samples, of which 137 were gallbladder carcinoma, 29 were perihilar cholangiocarcinoma, and 27 were intrahepatic cholangiocarcinoma. Silver in situ hybridization of MET and HER2 was performed to assess gene amplification. In the entire cancer group, gallbladder, perihilar, and intrahepatic, MET amplification rates were 15.7%, 19.0%, 3.4%, and 14.8%, respectively, and of HER2 amplification rates were 22.4%, 27.2%, 17.2%, and 3.7%, respectively. MET and HER2 protein expressions were significantly correlated with their gene amplification status. RTKs were significantly associated with adverse clinicopathologic features such as advanced pT category and lymph node metastasis. Overall survival was significantly shorter in MET-amplified (P = .024) and EGFR-overexpressed cases (P = .045). Recurrence-free survival was significantly correlated with HER2-amplified (P = .038) and EGFR-overexpressed cases (P = .046) in all patient groups. Overall and recurrence-free survival were significantly shorter in patients who were double positive for HER2 and EGFR. Our data suggested that MET, HER2, and EGFR might be potential therapeutic targets and that their co-expression is a strong prognostic factor for BTCs.

Abstract PO4-15-08: Comprehensive genomic profiling of HER2-low advanced breast cancers

Abstract Background: With the recent approval of the HER2-targeted antibody-drug conjugate (ADC) trastuzumab deruxtecan (T-Dxd) for the treatment of HER2-low advanced breast cancers (aBC), [defined as HER2 immunohistochemistry (IHC) 1+, or 2+ with negative in-situ hybridization (ISH)], there is interest to understand whether this population represents a distinct molecular entity and if there are additional biomarkers that can improve patient selection for these therapies. Here, we examined 2086 aBC cases profiled with comprehensive genomic profiling (CGP) stratified by HER2 status (negative, low, and positive) and hormone receptor (HR) status (positive and negative). Methods: Hybrid-capture CGP targeting 324 genes was performed on advanced BC samples (FoundationOne®CDx). HER2 IHC status was abstracted from pathology reports while HER2 amplification status was abstracted from CGP. Results: We examined 2086 samples of aBC patients distributed as HER2-negative (n=657; IHC 0), HER2-low (n=1012, IHC 1+, 2+ ISH non-amplified), and HER2-positive (n=417; HER2 IHC 3+). HER2-low patients were significantly older than HER2-negative patients (median 60 v 57 years, p=0.0006). HER2-low cases were more common in HR-positive than in HR-negative disease (67% vs 46%, respectively). Overall, characteristics were generally similar for genetic ancestry and TMB-H frequency across all HER2-statuses. MSI-H was rare across all HER2-statuses groups. HER2-low cases were more likely to have alterations in GATA3 (12.6% v 6.5%), ESR1 (12.4% v 7.8%), FGFR2 (4.0% v 1.8%), AR (1.1% v 0.2%), and CDH1 (15.3% v 11.6%) and less likely to harbor alterations in TP53 (44.0% v 62.4%), RB1 (6.8% v 12%), NF1 (5.5% v 9.3%), and BRCA1 (3.0% v 5.2%) when compared to HER2-negative. Some genes showed a consistent pattern of decreased frequency as HER2-IHC expression decreased from HER2-positive to HER2-low and to HER2-negative (e.g. AR alterations seen in 2.6%, 1.1% and 0.2%, respectively) while others had a increasing frequency pattern (e.g. RB1 alterations observed in 2.4%, 6.8% and 12.0%; BRCA1 seen in 1.7%, 3% and 5.2%, respectively). However, some genomic characteristics were unique to the HER2-low population (e.g. TP53 seen in 69.5% of HER2-positive and 62.4% of HER2-negative, but at a lower frequency of 44% in HER2-low cases) [Table 1]. Within the HR-positive subgroup, a lower frequency of NF1 (4.4% v 10.4%), TP53 (30.6% v 41.1%), and RB1 (4.4% v 8.0%) and a higher frequency of AR (1.0% v 0.0%) and GATA3 (16.2% v 10.9%) were observed in HER2-low vs HER2-negative cases, while within the HR-negative subgroup there was a higher frequency of GATA3 (1.2% v 0.7%) and AR (1.2% v 0.4%) and trending lower frequency of TP53 (85.7% v 90.8%) and RB1 (14.3% v 17.4%) in the HER2-low vs. HER2-negative cases. Mutations in homologous recombination repair genes (BRCA1, BRCA2, PALB2) were less frequent in HER2-low cases vs. HER2-negative cases overall (8.4% v 10.7%) and in the HR-positive (3.6% v 5.6%) and HR-negative subgroups (10.6% v 17.4%). Consistent with this, the rate of scar-based HRD signature (HRDsig) was lower in the HER2-low vs. HER2-negative subgroup (15.9% v 20.4%, p=0.02). Conclusions: These data suggest the HER2-low aBC has distinct genomic alterations before and after stratification by HR-status when compared to HER2-negative and HER2-positive aBC cases. Higher prevalence of some potentially actionable alterations in HER2-low cases, including FGFR2, AR, and ESR1, may aid in patient selection and drug development considering new combination approaches. Table 1 Summary of comprehensive genomic profiling alterations observed in HER2-low aBC compared to HER2-positive and HER2-negative cases Citation Format: Adriana Kahn, Ethan Sokol, Jeffrey Ross, Maureen Pelletier, Neal Fischbach, Lajos Pusztai, Maryam Lustberg. Comprehensive genomic profiling of HER2-low advanced breast cancers [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-15-08.

Abstract PO5-01-04: HER2 Amplification Level and Focal/Broad Region Size as Predictors of Treatment Response in Neoadjuvant Chemotherapy and Anti-HER2 Therapy for HER2-Positive Breast Cancer

Abstract Background: Neoadjuvant chemotherapy combined with anti-HER2 therapy has become the standard treatment approach for HER2-positive breast cancer. However, not all HER2-positive patients can achieve pathological complete response after neoadjuvant therapy. This raises the question of which subset of HER2+ patients derive the greatest benefit from pre-operative HER2-targeted treatment. Therefore, this study aims to determine whether the level and amplification region size of HER2 amplification are associated with the efficacy of neoadjuvant chemotherapy combined with anti-HER2 therapy. Methods: A total of 523 breast cancer samples were collected from 2017 to 2018, among which 202 cases were HER2-positive patients. Among these, 55 HER2-positive patients received neoadjuvant chemotherapy combined with anti-HER2 targeted therapy. The amplification status of HER2 was assessed using immunohistochemistry/fluorescence in situ hybridization (IHC/FISH) and next-generation sequencing (NGS). The HER2/CEP17 ratio, determined by FISH, was used to represent the amplification level of HER2. The size of the amplification region was calculated using NGS and neighboring genes located in chr17q. Amplification regions smaller than 1 Mb were classified as focal amplification, while those larger than 1 Mb were classified as broad amplification. Results: We compared the HER2/ERBB2 status of 523 breast cancer patients using different detection methods and found a high concordance between ERBB2 amplification detected by NGS and HER2-positivity detected by IHC and FISH, with a sensitivity of 96.0%, specificity of 97.8%, and overall concordance of 97.1%. Based on the HER2/CEP17 ratio determined by FISH, we observed that using a threshold of 6 for classification, the high amplification group had a significantly higher pCR rate compared to the low amplification group (86.7% vs. 41.7%; p=0.037, odds ratio [OR]=0.121, 95% confidence interval [CI]: 0.009-0.919). Moreover, the focal amplification group showed a higher pCR rate compared to the broad amplification group (65.9% vs. 30.8%, p=0.051, OR=0.237, 95% CI: 0.045-1.035). Additionally, within the low amplification group (HER2/CEP17 &amp;lt; 6), the pCR rate was 66.7% for focal amplification and 20% for broad amplification, suggesting that focal amplification of ERBB2 may further guide clinical benefit in the low HER2/CEP17 ratio group. Conclusion: This study demonstrates a high concordance between ERBB2 amplification determined by NGS and HER2-positivity determined by IHC/FISH. High HER2/CEP17 ratio and focal amplification of ERBB2 are associated with a higher pCR rate in neoadjuvant chemotherapy combined with anti-HER2 targeted therapy. Citation Format: Ning Liao, Guochun Zhang, Xinze Lv, Kai Li, Ting Hou, Zhou Zhang. HER2 Amplification Level and Focal/Broad Region Size as Predictors of Treatment Response in Neoadjuvant Chemotherapy and Anti-HER2 Therapy for HER2-Positive Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-01-04.

Abstract PO1-27-06: HER2 Amplification Level and Focal/Broad Region Size as Predictors of Treatment Response in Neoadjuvant Chemotherapy and Anti-HER2 Therapy for HER2-Positive Breast Cancer

Abstract Background: Neoadjuvant chemotherapy combined with anti-HER2 therapy has become the standard treatment approach for HER2-positive breast cancer. However, not all HER2-positive patients can achieve pathological complete response after neoadjuvant therapy. This raises the question of which subset of HER2+ patients derive the greatest benefit from pre-operative HER2-targeted treatment. Therefore, this study aims to determine whether the level and amplification region size of HER2 amplification are associated with the efficacy of neoadjuvant chemotherapy combined with anti-HER2 therapy. Methods: A total of 523 breast cancer samples were collected from 2017 to 2018, among which 202 cases were HER2-positive patients. Among these, 55 HER2-positive patients received neoadjuvant chemotherapy combined with anti-HER2 targeted therapy. The amplification status of HER2 was assessed using immunohistochemistry/fluorescence in situ hybridization (IHC/FISH) and next-generation sequencing (NGS). The HER2/CEP17 ratio, determined by FISH, was used to represent the amplification level of HER2. The size of the amplification region was calculated using NGS and neighboring genes located in chr17q. Amplification regions smaller than 1 Mb were classified as focal amplification, while those larger than 1 Mb were classified as broad amplification.&amp;gt; Results: We compared the HER2/ERBB2 status of 523 breast cancer patients using different detection methods and found a high concordance between ERBB2 amplification detected by NGS and HER2-positivity detected by IHC and FISH, with a sensitivity of 96.0%, specificity of 97.8%, and overall concordance of 97.1%. Based on the HER2/CEP17 ratio determined by FISH, we observed that using a threshold of 6 for classification, the high amplification group had a significantly higher pCR rate compared to the low amplification group (86.7% vs. 41.7%; p=0.037, odds ratio [OR]=0.121, 95% confidence interval [CI]: 0.009-0.919). Moreover, the focal amplification group showed a higher pCR rate compared to the broad amplification group (65.9% vs. 30.8%, p=0.051, OR=0.237, 95% CI: 0.045-1.035). Additionally, within the low amplification group (HER2/CEP17 &amp;lt; 6), the pCR rate was 66.7% for focal amplification and 20% for broad amplification, suggesting that focal amplification of ERBB2 may further guide clinical benefit in the low HER2/CEP17 ratio group. Conclusion: This study demonstrates a high concordance between ERBB2 amplification determined by NGS and HER2-positivity determined by IHC/FISH. High HER2/CEP17 ratio and focal amplification of ERBB2 are associated with a higher pCR rate in neoadjuvant chemotherapy combined with anti-HER2 targeted therapy. Citation Format: Ning Liao, Guochun Zhang, Xinze Lv, Kai Li, Ting Hou, Zhou Zhang. HER2 Amplification Level and Focal/Broad Region Size as Predictors of Treatment Response in Neoadjuvant Chemotherapy and Anti-HER2 Therapy for HER2-Positive Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-27-06.

Ensemble learning prediction framework for EGFR amplification status of glioma based on terahertz spectral features

Epidermal growth factor receptor (EGFR) plays a pivotal role in the initiation and progression of gliomas. In particular, in glioblastoma, EGFR amplification emerges as a catalyst for invasion, proliferation, and resistance to radiotherapy and chemotherapy. Current approaches are not capable of providing rapid diagnostic results of molecular pathology. In this study, we propose a terahertz spectroscopic approach for predicting the EGFR amplification status of gliomas for the first time. A machine learning model was constructed using the terahertz response of the measured glioma tissues, including the absorption coefficient, refractive index, and dielectric loss tangent. The novelty of our model is the integration of three classical base classifiers, i.e., support vector machine, random forest, and extreme gradient boosting. The ensemble learning method combines the advantages of various base classifiers, this model has more generalization ability. The effectiveness of the proposed method was validated by applying an individual test set. The optimal performance of the integrated algorithm was verified with an area under the curve (AUC) maximum of 85.8 %. This signifies a significant stride toward more effective and rapid diagnostic tools for guiding postoperative therapy in gliomas.