Amplification Status Research Articles

The Expression and Amplification of HER2 Has a Significant Impact on the Prognosis of Endometrial Carcinoma in Korean Patients.

Objective: The purpose of this study was to analyze the protein overexpression and gene amplification of HER2 in endometrial carcinoma (EC) and to evaluate its role as a prognostic factor in Korean women. Methods: A tissue microarray (TMA) was constructed from samples from 191 patients with diverse histologic types of EC. HER2 protein expression and gene amplification status were analyzed using immunohistochemistry (IHC) and silver in situ hybridization (SISH), respectively. All patients were treated and followed up at a single tertiary medical center in Seoul, Korea, between July 2009 and October 2020. Results: In terms of histological type, among the 191 EC patients, 157 had endometrioid carcinoma, nine had uterine serous papillary carcinoma (USPC), one had clear cell carcinoma, one had squamous cell carcinoma, eight had mixed carcinoma, and 15 had uterine carcinosarcoma (UC). HER2 protein overexpression was observed in eight of the 191 (4.2%) EC patients; of these patients, five had IHC scores of 2+, and three had IHC scores of 3+. The HER2 overexpression rates of USPC, UC, and endometrioid carcinomas were 33.3%, 26.6%, and 0.6%, respectively. HER2 protein overexpression was significant in USPC and UC tissues (p < 0.000) and was associated with poor overall survival (OS) (p < 0.001). HER2 gene amplification was confirmed in seven of 184 patients (3.8%), including three patients with USPC and four patients with UC. OS was significantly shorter in patients who had HER2 amplification (p < 0.001). On multivariate analysis, HER2 expression and HER2 amplification were statistically significantly associated with worse OS (p = 0.006). However, HER2 expression without amplification was not statistically associated with OS (p = 0.993). Conclusions: HER2 protein overexpression and gene amplification are significantly correlated with shorter OS in Korean women. HER2 can be considered an important predictor of survival outcomes in EC patients.

Abstract 562: Frequent copy number gain of MCL1 is a therapeutic target for osteosarcoma

Abstract Osteosarcoma (OS) is the most common primary malignant bone tumor that predominantly occurs in children, adolescents, and young adults. The treatment for OS that combines surgery with chemotherapy, which consists of a four-drug combination of adriamycin (DOX), cisplatin (CDDP), high-dose methotrexate (MTX), and ifosfamide, was established in 1970s, and it is still used as a standard therapy. Oncogenic driver mutations and fusion genes common to OS have not been identified, which is one of the reasons for the lack of success in drug development for OS. Herein, to explore the characteristic vulnerability in OS, molecular targeted drugs were screened against OS cell lines and patient-derived cells; obatoclax, a pan-BH3 mimetic, and a concomitant drug that enhances obatoclax-induced apoptosis, OSI906, a dual inhibitor of IGF1R and IR, were found. Fluorescence in situ hybridization (FISH) analysis revealed that copy number gains of MCL1, an antiapoptotic Bcl-2 family protein, were observed in 46.3% of formalin-fixed paraffin-embedded (FFPE) specimens from patients with OS (N = 41) and in 45.5% of OS cell lines (N = 11), thereby causing vulnerability to BH3 mimetics. IHC staining also revealed high expression of Mcl-1 protein in specimens with MCL1-amplification in FISH analysis. Pharmacological or genetic inhibition of Mcl-1 induced potent apoptosis in MCL1-amplified OS cells, which was enhanced by the co-inhibition with Bcl-xL. Moreover, chromosome 1q21.2-3, where MCL1 is located, contains several IGF1R/PI3K pathway-related genes, including PIP5K1A, TARS2, OUTD7B, and ENSA, whose copy numbers were also increased in MCL1-amplified OS cells, suggesting that 1q21.2-3-amplified OS cells readily activate downstream pathways via IGF1R. IGF signaling activation in 1q21.2-3-amplified OS cells negated the obatoclax-induced apoptosis, which was overcome by OSI906 treatment. Combined obatoclax and OSI906 administration remarkably suppressed MCL1-amplified OS tumor growth in the xenograft mouse model and resulted in tumor regression; however, none of the treatments reduced tumor growth of OS without MCL1 amplification. These results suggest that combining obatoclax with OSI906 could be a potential therapeutic intervention for 1q21.2-3-amplified OS, and that prior stratification of OS based on the 1q21.2-3 amplification status would be important for the success of this combination therapy. Thus, we elucidated the mechanism of action of drugs and their potential as a novel therapeutic strategy for approximately 50% of patients with OS. Moreover, a FISH analysis that can detect copy number gains of MCL1 in FFPE specimens from patients with OS was established to stratify patients eligible for this therapy. Citation Format: Satoshi Takagi, Ryohei Katayama. Frequent copy number gain of MCL1 is a therapeutic target for osteosarcoma [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 562.

Evaluating Twitter’s algorithmic amplification of low-credibility content: an observational study

Artificial intelligence (AI)-powered recommender systems play a crucial role in determining the content that users are exposed to on social media platforms. However, the behavioural patterns of these systems are often opaque, complicating the evaluation of their impact on the dissemination and consumption of disinformation and misinformation. To begin addressing this evidence gap, this study presents a measurement approach that uses observed digital traces to infer the status of algorithmic amplification of low-credibility content on Twitter over a 14-day period in January 2023. Using an original dataset of ≈ 2.7 million posts on COVID-19 and climate change published on the platform, this study identifies tweets sharing information from low-credibility domains, and uses a bootstrapping model with two stratifications, a tweet’s engagement level and a user’s followers level, to compare any differences in impressions generated between low-credibility and high-credibility samples. Additional stratification variables of toxicity, political bias, and verified status are also examined. This analysis provides valuable observational evidence on whether the Twitter algorithm favours the visibility of low-credibility content, with results indicating that, on aggregate, tweets containing low-credibility URL domains perform better than tweets that do not across both datasets. However, this effect is largely attributable to a difference in high-engagement, high-followers tweets, which are very impactful in terms of impressions generation, and are more likely receive amplified visibility when containing low-credibility content. Furthermore, high toxicity tweets and those with right-leaning bias see heightened amplification, as do low-credibility tweets from verified accounts. Ultimately, this suggests that Twitter’s recommender system may have facilitated the diffusion of false content by amplifying the visibility of low-credibility content with high-engagement generated by very influential users.

Abstract B004: Clinico-genomic characteristics of breast cancer brain metastasis: A multi-institutional analysis from AACR Project GENIE BPC

Abstract Purpose: The presence of Her2 amplification is associated with an increased risk of developing brain metastases. Brain metastases in breast cancer can be particularly challenging and have significant implications for prognosis and treatment. Common Her2-targeted therapies and small tyrosine kinase inhibitors have demonstrated the ability to penetrate the blood brain barrier and be effective in treating brain metastases. We investigated the clinico-genomic characteristics and the prognosis of brain metastasis in patients with breast cancer. Experimental design: Patients with breast cancer whose tumors underwent targeted sequencing from 2013-2018 at age 56 years old or younger at three institutions from the American Association of Cancer Research Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (AACR Project GENIE BPC) registry were selected for data curation. The PRISSMM data model was used for real world outcomes including overall survival. We analyzed clinical and genomic characteristics, treatment, and clinical outcome data among patients with and without brain metastases, stratified by Her2 amplification and hormone-receptor status (Her2+ vs. Her2-/HR+ vs. triple-negative breast cancer (TNBC)). We explored the top 20 most frequently altered genes that were included on at least 20% of sequencing panels. Results: A total of 1019 patients with breast cancer along with their receptor subtype information were included in the study (110 patients were excluded due to either post- mortem sequencing or unknown receptor subtype). Among them, 336 (33%) patients were identified to have developed brain metastasis (n=87 with Her2+; n=181 with Her2-/HR+; and n=68 with TNBC). At time of advanced disease, the brain was the first and only distant site of disease in 41/336 (12%) and detected with extracranial sites of disease in 22/336 (7%) patients. For patients presenting with stage I-III breast cancer, the cumulative incidence of brain metastasis at 5 years from breast cancer diagnosis was higher in those with TNBC (35%; 95% CI: 25, 50) as compared to 24% (95% CI: 16, 37) and 21% (95% CI: 15, 29) for those with Her2+ and Her2-/HR+ subtypes, respectively. Median overall survival from brain metastasis was significantly longer (log-rank p&amp;lt;0.001) for those with Her2+ disease (19m, 95% CI: 13, 36) compared to those with Her2-/HR+ (8.9m, 95% CI: 6.3, 15) or TNBC (7.4m, 95% CI: 4.6, 11). Among patients who ever developed brain metastases, IKZF3 alterations occurred in 71% (20/28) of Her2+ patients but did not occur in either Her2- subtype. Additionally, frequencies of CDK12, MYC, and PTEN alterations differed across subtypes. Conclusions: Brain involvement at metastatic presentation conferred a higher risk of death than brain-sparing metastases. Triple negative and Her2+ histologies were associated with higher risk of brain involvement at metastasis presentation. Further exploration by treatment received across receptor subtypes and genomic alterations will be presented. Citation Format: Samantha Brown, Hannah E. Fuchs, Jessica A. Lavery, Katherine S. Panageas, Nelson S. Moss. Clinico-genomic characteristics of breast cancer brain metastasis: A multi-institutional analysis from AACR Project GENIE BPC [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr B004.

Abstract B073: A spatially resolved single-cell tumor microenvironment of clinicomolecular subtypes of high-grade serous ovarian cancer

Abstract Background &amp; objective: High grade serous ovarian cancer (HGSC) is the most lethal type of ovarian cancer malignancies. Around 50% of HGSCs are DNA-repair homologous recombination deficient (HRD) and 15% have CCNE1 gene amplification. Previous results have shown that tumor microenvironment (TME) can impact clinical prognosis in HGSC. In this study our objective was to characterize the interplay of the TME with HRD and CCNE1 amplification in HGSC and its association with clinical outcomes. Materials and methods: We collected TME spatial protein expression, genomics, and clinical data from 250 HGSC patients. We determined BRCA1/2 germline and somatic mutation status using targeted sequencing and promoter hyper-methylation. For the tumors without BRCA1/2 mutations, we performed shallow whole genome sequencing, and estimated the CCNE1 amplification and HRD status using shallowHRD and BRCAness copy number profiles. Immune cell infiltration was assessed also using IHC for CD8, CD20, CD68, and CD103. The single-cell spatial landscapes were analyzed for 1000 tumor cores from the tumor center and tumor periphery using cyclic immunofluorescence (tCycIF) imaging for 34 different protein markers. We categorized and spatially analyzed the single cells from the TME to distinct cellular subpopulations using the TRIBUS and scimap software. Results: In our study of the TME using highly multiplexed tissue imaging we identified a total of 4.8 million single cells of them 1.6 million were immune cells belonging to eight biological subpopulations. The immune cell proportion detected in each sample showed high concordance with the IHC estimation by a pathologist. Interestingly, the CD8+, CD20+, CD11c+, and CD15+ high immune cell infiltrations were higher in BRCA1/2 mutated as compared to the CCNE1 amplified tumors. High immune infiltration was associated with prolonged overall survival only in samples debulked before chemotherapy but not in samples debulked after chemotherapy. Using consensus clustering for cell protein expression and cell morphology, we identified five distinct tumoral and stromal cell clusters which showed significant heterogeneity among the tumor genotypes and association with clinical outcomes. Then, after clustering of the spatial single-cell proximity data, we identified 13 distinct recurrent cellular neighborhoods (RCNs). The two RCNs related to the tumor-stroma and tumor-immune interfaces exhibited the highest differences between HRD and CCNE1 samples. Finally, by using random forest machine learning classifiers of the cells and its neighborhoods, and using an approach to minimize overfitting, we were able to detect the features more representative in HRD samples, for example, MHC-I expression in cancer cells and in stromal cells. Conclusion: The integration of multi-omics data revealed distinct TMEs associated with HRD and clinical outcomes; this has the potential to be used to discover biomarkers for precision oncology in HGSCs. Citation Format: Fernando Perez-Villatoro, Lilian van Wagensveld, Aleksandra Shabanova, Siamak Hajizadeh, Julia Casado, Ella Anttila, Maaike A. van der Aa, Roy F.P.M. Kruitwagen, Gabe S. Sonke, Koen K. Van de Vijver, Peter K. Sorger, Hugo M. Horlings, Anniina Färkkilä. A spatially resolved single-cell tumor microenvironment of clinicomolecular subtypes of high-grade serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B073.

Image-defined risk factors associated with MYCN oncogene amplification in neuroblastoma and their association with overall survival.

The MYCN oncogene is a critical factor in the development and progression of neuroblastoma, and image-defined risk factors (IDRFs) are radiological findings used for the preoperative staging of neuroblastoma. This study aimed to investigate the specific categories of IDRFs associated with MYCN amplification in neuroblastoma and their association with overall survival. A retrospective analysis was conducted on a cohort of 280 pediatric patients diagnosed with neuroblastoma, utilizing a combination of clinical and radiological data. MYCN amplification status was ascertained through molecular testing, and the assessment of IDRFs was conducted using either contrast-enhanced computed tomography or magnetic resonance imaging. The specific categories of IDRFs associated with MYCN amplification and their association with overall survival were analyzed. MYCN amplification was identified in 19.6% (55/280) of patients, with the majority of primary lesions located in the abdomen (53/55, 96.4%). Lesions accompanied by MYCN amplification exhibited significantly larger tumor volume and a greater number of IDRFs compared with those without MYCN amplification (P < 0.001). Both univariate and multivariate analyses revealed that coeliac axis/superior mesenteric artery encasement and infiltration of adjacent organs/structures were independently associated with MYCN amplification in abdominal neuroblastoma (P < 0.05). Patients presenting with more than four IDRFs experienced a worse prognosis (P = 0.017), and infiltration of adjacent organs/structures independently correlated with overall survival in abdominal neuroblastoma (P = 0.009). The IDRFs are closely correlated with the MYCN amplification status and overall survival in neuroblastoma.

TM4SF19 controls GABP-dependent YAP transcription in head and neck cancer under oxidative stress conditions

Tobacco and alcohol are risk factors for human papillomavirus-negative head and neck squamous cell carcinoma (HPV- HNSCC), which arises from the mucosal epithelium of the upper aerodigestive tract. Notably, despite the mutagenic potential of smoking, HPV- HNSCC exhibits a low mutational load directly attributed to smoking, which implies an undefined role of smoking in HPV- HNSCC. Elevated YAP (Yes-associated protein) mRNA is prevalent in HPV- HNSCC, irrespective of the YAP gene amplification status, and the mechanism behind this upregulation remains elusive. Here, we report that oxidative stress, induced by major risk factors for HPV- HNSCC such as tobacco and alcohol, promotes YAP transcription via TM4SF19 (transmembrane 4 L six family member 19). TM4SF19 modulates YAP transcription by interacting with the GABP (Guanine and adenine-binding protein) transcription factor complex. Mechanistically, oxidative stress induces TM4SF19 dimerization and topology inversion in the endoplasmic reticulum membrane, which in turn protects the GABPβ1 subunit from proteasomal degradation. Conversely, depletion of TM4SF19 impairs the survival, proliferation, and migration of HPV- HNSCC cells, highlighting the potential therapeutic relevance of targeting TM4SF19. Our findings reveal the roles of the key risk factors of HPV- HNSCC in tumor development via oxidative stress, offering implications for upcoming therapeutic approaches in HPV- HNSCC.

Automated Quantification of HER2 Amplification Levels Using Deep Learning.

HER2 assessment is necessary for patient selection in anti-HER2 targeted treatment. However, manual assessment of HER2 amplification is time-costly, labor-intensive, highly subjective and error-prone. Challenges in HER2 analysis in fluorescence in situ hybridization (FISH) and dual in situ hybridization (DISH) images include unclear and blurry cell boundaries, large variations in cell shapes and signals, overlapping and clustered cells and sparse label issues with manual annotations only on cells with high confidences, producing subjective assessment scores according to the individual choices on cell selection. To address the above-mentioned issues, we have developed a soft-sampling cascade deep learning model and a signal detection model in quantifying CEN17 and HER2 of cells to assist assessment of HER2 amplification status for patient selection of HER2 targeting therapy to breast cancer. In evaluation with two different kinds of clinical datasets, including a FISH data set and a DISH data set, the proposed method achieves high accuracy, recall and F1-score for both datasets in instance segmentation of HER2 related cells that must contain both CEN17 and HER2 signals. Moreover, the proposed method is demonstrated to significantly outperform seven state of the art recently published deep learning methods, including contour proposal network (CPN), soft label-based FCN (SL-FCN), modified fully convolutional network (M-FCN), bilayer convolutional network (BCNet), SOLOv2, Cascade R-CNN and DeepLabv3+ with three different backbones (p ≤ 0.01). Clinically, anti-HER2 therapy can also be applied to gastric cancer patients. We applied the developed model to assist in HER2 DISH amplification assessment for gastric cancer patients, and it also showed promising predictive results (accuracy 97.67 ±1.46%, precision 96.15 ±5.82%, respectively).

Pan-cancer analysis portrays NVL2 as a novel diagnostic and prognostic biomarker

Nuclear VCP Like 2 or NVL2, an ATPases Associated with diverse cellular Activities (AAA+) family protein, has recently been linked with various cancers. By systematic bioinformatics analyses, here we predict the prospect of NVL2 as a cancer biomarker. Our pan-cancer analyses reveal that NVL2 is overexpressed in cancers [GEPIA2, OncoDB, and UALCAN (TCGA) databases] and the top five cancers with elevated expression (more than two fold) of NVL2 are Breast Invasive Carcinoma, Testicular Germ Cell Tumors, Cholangiocarcinoma, Diffuse large B cell lymphoma, and Thymoma. NVL2 is also highly expressed in all stages of most cancers. Additionally, this high expression was found to be associated with the reduced survival rate of cancer patients (Kaplan-Meier Plotter, GEPIA2, and OncoDB databases). Since genetic alteration is one of the major causes of cancer, we investigated the mutation and copy number amplification status (cBioPortal and COSMIC databases) of NVL2 across the cancers. Many potential mutation sites were predicted (cBioPortal and COSMIC databases) and most strikingly, a total of fourteen mutation sites were observed at the ATPase domain of NVL2. This signifies that these are the mutations that might have a role in carcinogenesis. The copy number amplification study also revealed the high amplification percentage of NVL2 across different cancers. We further focused on the functional characteristics of the protein NVL2 across the cancers. The protein-protein interaction analyses found the proteins like SKIV2L2, WDR12, WDR74, UTP18, NAT10, TERT, DKC1, GTPBP4, BOP1, TEP1 directly interact with NVL2. The top canonical pathways indicated that NVL2 has crucial functions in oncogenesis (DAVID). We, therefore, surmise that NVL2 could be considered as a potential prognostic and diagnostic biomarker and a promising target for multiple cancers.

MDM2 FISH testing criteria in adipose tissue tumors with mature adipocytic morphology – A resection case-based study

The current criteria for utilizing MDM2 Fluorescence In Situ Hybridization (FISH) in adipose-derived tumors were first introduced in 2015 and have been widely adopted. However, these criteria may fail to identify some atypical lipomatous tumors / well-differentiated liposarcoma (ALT/WDL) with mature adipocytic morphology in clinical practice, possibly due to the fact that the existing criteria are primarily based on biopsy cases. Hence, a criterion based on resection cases is needed. In this study, we included 87 adipose tissue tumors with mature adipocytic morphology which were first resected, as well as 9 consultation cases and 25 recurrent resection cases. The final diagnosis was based on MDM2 amplification status. Among the 87 first-time resection cohort, MDM2 FISH amplification was observed in only 2 (5%) of the 39 superficial cases. Marginal infiltration was significantly different in both the MDM2 FISH negative and positive groups (p < 0.05). Of the 37 intramuscular tumors, 17 (46%) showed MDM2 FISH amplification. The MDM2 amplification positive group had a larger tumor size than MDM2 amplification negative group (p = 0.042). Tumors of larger size (≥11 cm) were highly correlated with MDM2 amplification (p = 0.003), but still, 35.3% of the MDM2 amplification-positive cases had tumor sizes less than 11 cm. Eight (66.7%) out of twelve retroperitoneal/ pelvic cases were MDM2 FISH positive. Among the 25 recurrent cases, twenty (80%) of them had MDM2 FISH amplification. In conclusion, we recommend MDM2 FISH for: 1. superficial cases with marginal infiltration based on adequate margin sampling; 2. all intramuscular tumors, retroperitoneal/pelvic tumors and recurrent tumors, both in resection cases and biopsy cases.

Abstract C014: Pan-cancer analysis portrays NVL as a diagnostic and prognostic biomarker

Abstract NVL (also known as NVL2), an AAA+ ATPase, has recently been linked with various cancers. By systematic bioinformatics analyses, here we predict the prospect of NVL as a cancer biomarker. Our pan-cancer analyses reveal that NVL is overexpressed in cancers [GEPIA and UALCAN (TCGA) databases] and the top five cancers with elevated expression (more than twofold) of NVL are Breast Invasive Carcinoma, Testicular Germ Cell Tumors, Cholangiocarcinoma, Diffuse large B cell lymphoma, and Thymoma. NVL is also highly expressed in all stages of most cancers. Additionally, this high expression was found to be correlated to the poor survival of cancer patients (Kaplan-Meier Plotter and OncoDB databases). Since, genetic alteration is one of the major cause of cancer, we investigated mutation and copy number amplification status (cBioPortal and COSMIC databases) of NVL across the cancers. Many potential mutation sites were predicted (cBioPortal and COSMIC databases) and most strikingly, four mutation sites at the ATPase domain of NVL. This signifies that these are the mutations that might have role in carcinogenesis. The copy number amplification study also revealed the high amplification percentage of NVL across different cancers. We further focused on the functional characteristics of the protein NVL across cancers. The protein-protein interaction analyses found the proteins like SKIV2L2, WDR12, WDR74, UTP18, NAT10, TERT, DKC1, GTPBP4, BOP1, TEP1 directly interact with NVL. The top canonical pathways of NVL also indicate that NVL has crucial functions in cancer cell proliferation (DAVID). We, therefore, surmise that NVL could be considered as a potential diagnostic and prognostic marker for multiple cancers and a very promising biomarker and target for cancer. Citation Format: Mousumi Datta, Dr. Aditi Nayak. Pan-cancer analysis portrays NVL as a diagnostic and prognostic biomarker [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C014.

Decreased HER2 expression in endometrial cancer following anti-HER2 therapy.

Trastuzumab has demonstrated clinical efficacy in the treatment of HER2-positive serous endometrial cancer (EC), which led to its incorporation into standard-of-care management of this aggressive disease. Acquired resistance remains an important challenge, however, and its underlying mechanisms in EC are unknown. To define the molecular changes that occur in response to anti-HER2 therapy in EC, targeted next-generation sequencing (NGS), HER2 immunohistochemistry (IHC), and fluorescence in situ hybridization (FISH) were performed on pre- and post-treatment tumour samples from 14 patients with EC treated with trastuzumab or trastuzumab emtansine. Recurrent tumours after anti-HER2 therapy acquired additional genetic alterations compared with matched pre-treatment ECs and frequently showed decreased HER2 protein expression by IHC (7/14, 50%). Complete/near-complete absence of HER2 protein expression (score 0/1+) observed post-treatment (4/14, 29%) was associated with retained HER2 gene amplification (n = 3) or copy number neutral status (n = 1). Whole-exome sequencing performed on primary and recurrent tumours from the latter case, which exhibited genetic heterogeneity of HER2 amplification in the primary tumour, revealed selection of an early HER2-non-amplified clone following therapy. Our findings demonstrate that loss of target expression, by selection of HER2-non-amplified clones or, more commonly, by downregulation of expression, may constitute a mechanism of resistance to anti-HER2 therapy in HER2-positive EC. © 2023 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

90MO Panitumumab (PAN) vs bevacizumab (BEV) in metastatic colorectal cancer (mCRC) by microsatellite stable (MSS), RAS/BRAF, and HER2 amplification (HER2amp) status: Phase III PARADIGM biomarker study

90MO Panitumumab (PAN) vs bevacizumab (BEV) in metastatic colorectal cancer (mCRC) by microsatellite stable (MSS), RAS/BRAF, and HER2 amplification (HER2amp) status: Phase III PARADIGM biomarker study

Liquid biopsy based HER2 amplification status in gastric cancer patients indicates clinical response

Gastric carcinomas are among the most common cancers in Germany, with approximately 18,000 new cases per year.About 10 years ago, based on results of the Trastuzumab for gastric cancer (ToGA) trial, the addition of the monoclonal antibody trastuzumab to a platinum-fluoropyrimidine chemotherapy backbone became the standard-of-care 1st-line therapy for human epidermal growth factor receptor 2 (HER2)-positive gastric cancers. Only patients with primary HER2 gene amplification benefit from this therapy. Thus, accurate HER2 gene amplification detection is predictive and critical for therapy selection. As a gold standard the HER2 status is currently determined in tumor tissue specimens using immune histochemistry and fluorescent in situ hybridisation. However, HER2 amplification is detectable in only about 20 % of gastric carcinomas. The recent approval of an antibody-drug conjugate Trastuzumab deruxtecan (T-DXd) and the establishment of a new subgroup of HER2-low tumors due to the bystander effect associated with T-DXd increases the relevance of precise HER2 diagnostics.Aim of this analysis was to determine the HER2 amplification status from circulating DNA fragments in blood using a HER2 Copy Number Variation assay to establish a minimal invasive approach.For the present study, a digital droplet PCR-based method was validated relative to established tissue-based methods. Furthermore and most importantly, the changes of HER2 status during therapy were investigated in seven patients indicating that the changes of HER2 status and number of HER2 copies detected in blood can reflect on therapy efficiency and uncover treatment resistance.

Posttreatment complications in pediatric cervical neuroblastoma: A retrospective case series at a tertiary cancer center.

Neuroblastomas rarely occur as primary tumors in the cervical region. Therefore, very little has been reported regarding treatment strategies, complications, and outcomes of these cervical neuroblastomas. The goal of this study is to review the presentation, management, and outcomes of all primary cervical pediatric neuroblastoma cases at a single tertiary care center. A retrospective cohort review of all neuroblastoma patients treated at a single center were performed. All patients with primary cervical neuroblastoma were reviewed for demographic information, tumor characteristics, treatment, and outcomes. Thirty (1.8%) patients were found to have undergone treatment for cervical neuroblastoma tumors diagnosed on average at 2.1 years old. Most presented with a swollen neck/palpable mass ± Horner's syndrome. Based on features including tumor staging, N-myc proto-oncogene protein (MYCN) amplification status, histology, most were deemed intermediate or high risk. Treatment strategies centered around chemotherapeutic regimens with surgery when possible as well as various adjuvant treatments including radiation therapy, immunotherapy, bone marrow transplant, and a neuroblastoma vaccine. Ten (33.3%) of patients experienced treatment-related complications and four (13.3%) died as a result of their disease progression. All four patients were high-risk patients, two of which had MYCN amplification. Cervical neuroblastomas generally have favorable outcomes. These tumors can be treated effectively with chemotherapy and surgical intervention with various adjuvant therapies. MYCN amplification and higher stage disease presentation contribute to worse outcomes.

Copy-number-gain of telomerase reverse transcriptase (hTERT) is associated with an unfavorable prognosis in esophageal adenocarcinoma

Esophageal adenocarcinoma exhibits one of the highest mortality rates among all cancer entities. Multimodal therapy strategies have improved patients’ survival significantly. However, patients in early stages are currently limited to receiving only local therapies, even though some patients within this group showcase short survival periods. Until now, there has been no widely established clinically used biomarker to detect these high-risk patients. Telomerase reverse transcriptase (TERT), a gene encoding a crucial subunit of the telomerase enzyme, plays a significant role in establishing cancer cell immortality and is under suspicion for its potential contribution to tumor progression. Therefore, we aimed to evaluate the clinical relevance of the TERT amplification status. We included 643 patients with esophageal adenocarcinoma, who underwent Ivor-Lewis esophagectomy at the University Hospital of Cologne. The TERT amplification status was characterized using fluorescence in situ hybridization. Clinicopathological values and patients’ overall survival were compared between patients with and without TERT amplification. Further sub-cohort analyses were conducted for patients with pT1N0-3 tumor stage. Eighty-One patients (12.6%) exhibited TERT amplification. Patients with amplified TERT showed significantly worse overall survival (median OS: 22.6 vs. 36.8 months, p = 0.009). Interestingly, TERT amplification could be characterized as an independent risk factor for worse overall survival in multivariate analysis in patients with pT1N0-3 tumor stage (HR = 2.440, 95% CI 1.095–5.440, p = 0.029). In this study, we describe the TERT amplification status as an independent risk factor for worse survival in patients diagnosed with esophageal adenocarcinoma at pT1N0-3 tumor stage, encompassing cases involving tumor infiltration of the lamina propria, muscularis mucosae, and/or submucosa. Based on our findings, we put forth the proposition that evaluating the TERT amplification status may serve as a valuable tool in identifying a specific subgroup of patients, namely those with TERT amplification and pT1N0-3 tumor-stage esophageal adenocarcinoma. The patients of this subgroup could potentially benefit from enhanced follow-up protocols, more aggressive treatment approaches, or possible targeted TERT inhibition therapies, all aimed at improving their overall clinical outcomes.

Clinico-Genomics Model to Predict Survival in Non-Metastatic Breast Cancer: Comparing the Performance of Machine Learning Models

Breast cancer is a heterogenous spectrum of disease with variable outcome. This heterogeneity of outcome could be driven by underlying heterogeneity in the genotypes. There remains an unmet need of defining prognosis based on underlying genetic heterogeneity. The primary objective of this study was to build a combined clinic-genomics model to predict overall survival (OS) in patients with non-metastatic breast cancer. The Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) database is a combined Canada-UK Project which contains information on 31 demographic, clinical and treatment characteristics in addition to m-RNA level z-score for 331 genes for 1904 breast cancer patients. We excluded patients with metaplastic breast cancer (n = 1) or unknown histologic subtype (n = 13), and those with missing information on breast surgery (n = 22) and cellularity (n = 54). Demographic characteristics included age of the patient and menopausal status while clinical characteristics included tumor stage, number of positive lymph nodes, pathologic grade, cellularity, receptor status for estrogen and progesterone receptors, and HER2neu gene amplification status. Treatment included type of breast cancer surgery, chemotherapy, hormone therapy, and radiation therapy. The data was split randomly at an 80:20 ratio into training and testing dataset. Subsequently, two cross-validated supervised machine learning algorithms were applied to build the prognostic model - elastic net logistic regression and random forest classifier. We compared the performance of the models in the testing dataset using area under receiver operating curve (AUC). All analysis were done using sparklyr - an R interface to Apache SparkTM. Overall, 1814 patients were included in the analysis. The AUC for elastic net logistic regression model and random forest classifier was 0.74, and 0.73, respectively. The sensitivity and specificity of the elastic net logistic regression model was 0.84 and 0.45, respectively while those for the random forest classifier was 0.83 and 0.51, respectively. STAT5A, CASP8, HSD17b11, and CDKN2c were common to the list of important genes predicting OS in both models while age, lymph node count, Nottingham Prognostic Index (NPI), and type of breast surgery were common to the list of clinical factors predicting OS in both models. This study shows that a multivariable prognostic model with combination of clinical and demographic parameters with Z-score expression data can predict for overall survival.

A novel clinical tool and risk stratification system for predicting the event-free survival of neuroblastoma patients: A TARGET-based study.

Neuroblastoma (NB), considered the most common non-intracranial solid tumor in children, accounts for nearly 8% of pediatric malignancies. This study aimed to develop a simple and practical nomogram to predict event-free survival (EFS) in NB patients and establish a new risk stratification system. In this study, 763 patients primarily diagnosed with NB in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database were included and randomly assigned to a training set (70%) and a validation set (30%) in a 7:3 ratio. First, the independent prognostic factors of EFS for NB patients were identified through univariate and multivariate Cox regression analyses. Second, a nomogram was created based on these factors and was validated for calibration capability, discriminative, and clinical significance by C-curves, receiver operating characteristic (ROC) curves, and decision curve analysis. Finally, a new risk stratification system was established for NB patients based on the nomogram. The univariate Cox analysis demonstrated that NB patients with age at diagnosis >318 days, International Neuroblastoma Staging System (INSS) stage 4, DNA diploidy, MYCN amplification status, and children oncology group (COG) high-risk group had a relatively poor prognosis. However, according to the multivariate Cox regression analysis, only age, INSS stage, and DNA ploidy were independent predictive factors in NB patients regarding EFS, and a nomogram was created based on these factors. The area under the curve (AUC) values of the ROC curves for the 3-, 5-, and 10-year EFS of this nomogram were 0.681, 0.706, and 0.720, respectively. Additionally, the AUC values of individual independent prognostic factors of EFS were lower than those of the nomogram, suggesting that the developed nomogram had a higher predictive reliability for prognosis. In addition, a new risk stratification system was developed to better stratify NB patients and provide clinical practitioners with a better reference for clinical decision-making. NB patients' EFS could be predicted more accurately and easily through the constructed nomogram and event-occurrence risk stratification system, allowing clinicians to better differentiate NB patients and establish individualized treatment plans to maximize patient benefits.

Efficacy of neoadjuvant therapy on HER2-positive breast cancer: a clinicopathological analysis

Objective: To investigate the efficacy of neoadjuvant therapy (NAT) on HER2-positive breast cancer and to analyze their clinicopathological features. Methods: A total of 480 cases of HER2-positive breast cancer who received neoadjuvant therapy (NAT), diagnosed at the Department of Pathology of Fudan University Shanghai Cancer Center from 2015 to 2020, were retrospectively identified. Clinicopathological parameters such as age, tumor size, molecular subtype, type of targeted therapy, Ki-67 proliferation index, ER and HER2 immunohistochemical expression, and HER2 amplification status were analyzed to correlate with the efficacy of NAT. Results: Among 480 patients with HER2-positive breast cancer, 209 achieved pathology complete response (pCR) after NAT, with a pCR rate of 43.5%. Of all the cases,457 patients received chemotherapy plus trastuzumab and 23 patients received chemotherapy with trastuzumab and pertuzumab. A total of 198 cases (43.3%) achieved pCR in patients with chemotherapy plus trastuzumab, and 11 cases (47.8%) achieved pCR in patients with chemotherapy plus trastuzumab and pertuzumab. The pCR rate in the latter group was higher, but there was no statistical significance. The results showed that the pCR rate of IHC-HER2 3+patients (49%) was significantly higher than that of IHC-HER2 2+patients (26.1%, P<0.001). The higher the mean HER2 copy number in the FISH assay, the higher the pCR rate was achieved. The expression level of ER was inversely correlated with the efficacy of NAT, and the pCR rate in the ER-positive group (28.2%) was significantly lower than that in the ER-negative group (55.8%, P<0.001). The pCR rate (29.1%) of patients with luminal B type was lower than that of HER2 overexpression type (55.8%, P<0.001). In addition, higher Ki-67 proliferation index was associated with higher pCR rate (P<0.001). The pCR rate was the highest in the tumor ≤2 cm group (57.7%), while the pCR rate in the tumor >5 cm group was the lowest (31.1%). The difference between the groups was significant (P=0.005). Conclusions: HER2 copy numbers, HER2 immunohistochemical expression level, molecular subtype, ER expression level and Ki-67 proliferation index are significantly associated with pCR after NAT. In addition, fluorescence in situ hybridization results, HER2/CEP17 ratio and tumor size could also significantly affect the efficacy of NAT.

Dynamic contrast-enhanced MRI radiomics model predicts epidermal growth factor receptor amplification in glioblastoma, IDH-wildtype.

To develop and validate a dynamic contrast-enhanced (DCE) MRI-based radiomics model to predict epidermal growth factor receptor (EGFR) amplification in patients with glioblastoma, isocitrate dehydrogenase (IDH) wildtype. Patients with pathologically confirmed glioblastoma, IDH wildtype, from January 2015 to December 2020, with an EGFR amplification status, were included. Patients who did not undergo DCE or conventional brain MRI were excluded. Patients were categorized into training and test sets by a ratio of 7:3. DCE MRI data were used to generate volume transfer constant (Ktrans) and extracellular volume fraction (Ve) maps. Ktrans, Ve, and conventional MRI were then used to extract the radiomics features, from which the prediction models for EGFR amplification status were developed and validated. A total of 190 patients (mean age, 59.9; male, 55.3%), divided into training (n = 133) and test (n = 57) sets, were enrolled. In the test set, the radiomics model using the Ktrans map exhibited the highest area under the receiver operating characteristic curve (AUROC), 0.80 (95% confidence interval [CI], 0.65-0.95). The AUROC for the Ve map-based and conventional MRI-based models were 0.74 (95% CI, 0.58-0.90) and 0.76 (95% CI, 0.61-0.91). The DCE MRI-based radiomics model that predicts EGFR amplification in glioblastoma, IDH wildtype, was developed and validated. The MRI-based radiomics model using the Ktrans map has higher AUROC than conventional MRI.