A5070851027- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- Genetic factors in colorectal cancer
- Renal cell carcinoma treatment
- Molecular Biology Techniques and Applications
- Cancer Cells and Metastasis
- Prostate Cancer Treatment and Research
- Ovarian cancer diagnosis and treatment
- RNA modifications and cancer
- PARP inhibition in cancer therapy
- PI3K/AKT/mTOR signaling in cancer
- Estrogen and related hormone effects
- Cancer Treatment and Pharmacology
- Advanced Breast Cancer Therapies
- Cancer-related molecular mechanisms research
- Prostate Cancer Diagnosis and Treatment
- HER2/EGFR in Cancer Research
- Ferroptosis and cancer prognosis
- Lung Cancer Treatments and Mutations
- Fibroblast Growth Factor Research
- BRCA gene mutations in cancer
- FOXO transcription factor regulation
- Genomics and Phylogenetic Studies
- Ear and Head Tumors
- Plant Disease Resistance and Genetics
Erasmus MC Cancer Institute
2016-2025
Erasmus MC
2010-2024
University of Catania
2017
Cancer Genomics Centre
2017
Meertens Institute
2010
Epithelial ovarian cancer is a highly heterogeneous disease and remains the most lethal gynaecological malignancy in Western world. Therapeutic approaches need to account for inter-patient intra-tumoural heterogeneity detailed characterization of vitro models representing different histological molecular subtypes critical enable reliable preclinical testing. There are approximately 100 publicly available cell lines but their cellular characteristics largely undescribed. We have characterized...
Abstract Introduction Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression analysis cohort molecularly well-characterized human breast cell lines to identify associated with most common subtypes frequent genetic aberrations. Methods Using microarray carrying LNA™ modified oligonucleotide capture probes), levels 725 were measured 51 lines. Differential was explored by unsupervised...
Circulating tumor DNA (ctDNA) has emerged as a potential new biomarker with diagnostic, predictive, and prognostic applications for various solid types. Before beginning large prospective clinical trials to prove the added value of utilizing ctDNA in practice, it is essential investigate effects preanalytical conditions on quality cell-free (cfDNA) general particular order optimize standardize these conditions. Whole blood samples were collected from patients metastatic cancer bearing known...
Abstract Assessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in minimally‐invasive way. In group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, each patient cell‐free (cfDNA), the primary tumor, tissue, normal tumor‐adjacent colon or and whole blood were obtained. Investigated was feasibility targeted NGS approach identify ctDNA. This also compared with preceded by mutant allele enrichment...
The emerging interest in circulating tumor DNA (ctDNA) analyses for clinical trials has necessitated the development of a high-throughput method fast, reproducible, and efficient isolation ctDNA. Currently, majority ctDNA studies use manual QIAamp (QA) platform to isolate from blood. purpose this study was compare two competing automated platforms [Maxwell (MX) QIAsymphony (QS)] current 'gold standard' QA facilitate processing samples prospective trials. We obtained blood healthy donors...
Cell-free circulating tumor DNA (ctDNA) has emerged as a promising biomarker for response evaluation in metastatic castration-resistant prostate cancer (mCRPC). The current study evaluated the modified fast aneuploidy screening test-sequencing system (mFast-SeqS), quick, tumor-agnostic and affordable ctDNA assay that requires small input of DNA, to generate genome-wide (GWA) score mCRPC patients, correlated this matched biopsies. In prospective multicenter study, GWA scores were from blood...
The aim was to identify mutations in serum cell-free DNA (cfDNA) associated with disease progression on tamoxifen treatment metastatic breast cancer (MBC). Sera available at start of therapy, during therapy and were selected from 10 estrogen receptor (ER)-positive patients. primary tumor normal tissue cfDNA minute amounts sera analyzed by targeted next generation sequencing (NGS) 45 genes (1,242 exons). At progression, stop-gain single nucleotide variants (SNVs) for CREBBP (1 patient) SMAD4...
The aim of this study was to determine an optimal workflow detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients define whether are suitable as biomarker for disease. investigated tissue archived 20 HGSOC by a next-generation sequencing (NGS) alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels customized dPCR assays were used cfDNAs, Oncomine panel molecular barcoding cfDNAs. missense...
Abstract Here, we describe a novel approach for rapid discovery of set tumor-specific genomic structural variants (SVs), based on combination low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples high-grade ovarian prostate patients validated average ten somatic SVs per patient breakpoint-spanning PCR mini-amplicons. These could be quantified in ctDNA metastatic digital assay. The results suggest that...
Background PIK3CA is the most frequent somatic mutated oncogene in estrogen receptor (ER) positive breast cancer. We previously observed an association between genotype and aromatase inhibitors (AI) treatment outcome. This study now evaluates whether expression of mRNAs miRs are linked to independently related AI therapy response order define potential expressed biomarkers for Materials methods The miR mRNA levels were evaluated their relationship with two tumor datasets, i.e. 286 luminal...
Circulating tumor cells (CTCs) or circulating DNA (ctDNA) may be used for diagnostic prognostic purposes in patients with hepatocellular carcinoma (HCC). We aim to determine whether CTCs ctDNA are suitable oncogenic mutations HCC patients. Twenty-six mostly advanced were enrolled. 30 mL peripheral blood from each patient was obtained. CellSearch system CTC detection. A sequencing panel covering 14 cancer-relevant genes identify mutations. TERT promoter C228T and C250T determined by droplet...
Background: Patients with advanced-stage epithelial ovarian cancer (EOC) receive treatment a poly-ADP ribose-polymerase (PARP) inhibitor (PARPi) as maintenance therapy after surgery and chemotherapy. Unfortunately, many patients experience disease progression because of acquired resistance. This study aims to characterize epigenetic genomic changes in cell-free DNA (cfDNA) associated PARPi Materials Methods: Blood was taken from 31 EOC receiving before at during/after treatment. Resistance...
Abstract: Circulating tumor DNA (ctDNA) analysis is a promising non-invasive technique for active surveillance after chemoradiotherapy locally advanced resectable esophageal carcinoma. In other malignancies false-positive results in ctDNA have been reported due to clonal hematopoiesis. this case, we present 66-year-old male who had adenocarcinoma of the gastroesophageal junction which he received neoadjuvant and underwent transhiatal esophagectomy. Postoperatively our patient follow-up with...
Metastatic castration-resistant prostate cancer (mCRPC) patients with positive AR-V7 expression in their circulating tumour cells (CTCs) rarely derive benefit from abiraterone and enzalutamide.We performed a prospective, multicenter, single arm phase II clinical trial (CABA-V7) mCRPC previously treated docetaxel androgen deprivation therapy.In this trial, we investigated whether cabazitaxel treatment resulted clinically meaningful PSA response rates CTC-based collected liquid biopsies for...
Abstract The use of blood-circulating cell-free DNA (cfDNA) as ‘liquid-biopsy’ is explored worldwide, with hopes for its potential in providing prognostic or predictive information cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. this study, we aimed to detect tumor-specific mutations only minute amounts serum-derived cfDNA by using a targeted next generation...
Abstract Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of circulating tumor DNA (ctDNA) in liquid biopsies. However, affordable fast identification such SV is challenging, which hinders routine use the clinic. Here, we developed a novel approach - termed SHARC rapid discovery somatic SVs as biomarkers. combines low coverage cancer genome sketching by using Oxford Nanopore sequencing with random forest classification...
Abstract Introduction: Treatment failure to multiple treatment lines in hormone receptor positive (HR+) patients brings cross-resistance into the stage. The study aimed determine if tamoxifen resistance genes cause commonly employed metastatic breast cancer (combination) treatments. Materials & Methods: Parental and resistant MCF7A models (BCAR3, BCAR4, EGFR, AKT1 AKT2) were cultured for 10 days with different concentrations of fulvestrant (endocrine therapy), ribo-, abema-, palbociclib...
Abstract Background and objective: CDK4/6 inhibitors (CDK4/6i) improve the outcome of patients with ER+/HER2- advanced breast cancer when added to endocrine therapy in first line or second treatment. The recently reported SONIA trial shows no difference progression free survival after two lines treatment (PFS2), overall (OS) quality life benefit CDK4/6i first-line compared second-line, while adverse events are substantially higher is first-line. However, a subgroup early on mono-treatment...
Advances in therapeutic approaches for melanoma urge the need biomarkers that can identify patients at risk recurrence and to guide treatment. The potential use of liquid biopsies identifying is increasingly being recognized. Here, we present a head‐to‐head comparison several techniques analyze circulating tumor cells (CTCs) cell‐free DNA (cfDNA) 20 with metastatic melanoma. In this study, investigated whether diagnostic leukapheresis (DLA) combined multimarker flow cytometry (FCM) increased...
Activating mutations in the phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) gene have been detected often solid tumors. Targeted therapy for mutant PIK3CA is now available clinic, making molecular diagnostics pivotal. Our aim was to design a multiplex digital PCR (dPCR) assay evaluate 4 most common hotspot simultaneously characterize and quantify these liquid biopsies.