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Multi-Omics and Translational Genomics in Cancer Research

IRCCS National Cancer Institute Regina Elena

The Dr. Fanciulli Laboratory’s Next-Generation Sequencing Facility supports advanced genomic, transcriptomic, and epigenomic research through cutting-edge sequencing technologies and integrated bioinformatic analysis. The facility develops and applies next-generation sequencing methods to uncover mechanisms driving tumor heterogeneity, progression, and therapeutic response.

Combining exome, RNA, and epigenetic profiling, researchers identify gene expression alterations, fusion transcripts, immune signatures, and chromatin accessibility changes that shape cancer biology. Studies on non-coding RNAs—including miRNAs, eRNAs, and lncRNAs—focus on discovering novel tumor-specific biomarkers and regulatory pathways.

Equipped with Illumina, Oxford Nanopore, NanoString, and 10x Genomics systems, the facility enables high-throughput, single-cell, and spatial analyses. Current research includes identifying epigenetic biomarkers in multiple myeloma, studying ferroptosis regulation in lung cancer, and investigating transcriptional cofactor AATF in glioma. Through multi-omic integration, the NGS Facility advances translational oncology and precision medicine.

Main Areas of Interest

1. Integrated Multi-Omic Profiling in Cancer

The facility focuses on combining genomic, transcriptomic, and epigenomic analyses to enable comprehensive molecular characterization of tumors. By integrating exome sequencing, RNA-seq, and ATAC-seq data, researchers identify tumor-specific neoantigens, fusion proteins, and chromatin accessibility patterns that drive neoplastic transformation. These approaches support translational applications in biomarker discovery and precision oncology.

2. Transcriptomic and Non-Coding RNA Signatures in Tumor Biology

Through RNA sequencing, the group investigates transcriptional dysregulation, gene fusions, and immune cell infiltration profiles in diverse tumor types. Particular emphasis is placed on the role of non-coding RNAs—miRNAs, enhancer RNAs (eRNAs), and long non-coding RNAs (lncRNAs)—as potential tumor-specific biomarkers and regulators of oncogenic signaling.

3. Epigenetic Regulation and Chromatin Dynamics in Cancer Progression

The team explores how epigenetic modifications and chromatin remodeling contribute to oncogenesis, disease progression, and treatment response. Studies on multiple myeloma, lung cancer, and glioma aim to uncover how changes in chromatin conformation and DNA accessibility influence transcription factor binding, ferroptosis regulation, and tumor transformation.

4. Advanced Sequencing Platforms and Computational Bioinformatics

The facility provides access to a broad spectrum of sequencing technologies—including Illumina, Oxford Nanopore, NanoString, and 10x Genomics platforms—enabling high-throughput and single-cell analyses. Dedicated bioinformatics teams support data processing, integration, and interpretation to ensure accuracy, reproducibility, and scalability across multi-dimensional omic datasets.

Specialties

Molecular Biology

Techniques You Will Learn

NGS Techniques (Exome sequencing, RNA-seq, ATAC-seq, etc.)
Immunohistochemistry, RT-qPCR, ChIP-qPCR.
2D and 3D cell culture using human and murine tumor cells.
Immunoblotting, co-immunoprecipitation
Gene silencing strategy via ASO, siRNA and CRISPR/Cas-9.
Gene overexpression via trasfections and infections.
Cell viability assays
Cell metabolism assays
Fluorescence and confocal microscope

Curriculum

Foundations & Core Methods

Orientation & Background
· Overview of next-generation sequencing (NGS) and its applications in cancer genomics.
· Introduction to transcriptomic and epigenomic profiling (RNA-seq, ATAC-seq, methylome).
· Concepts of gene regulation, chromatin dynamics, and biomarker discovery.

Molecular Biology & Genomic Techniques

NGS and Molecular Profiling
· Hands-on training in exome sequencing, RNA-seq, and ATAC-seq workflows.
· Quality control and library preparation using Illumina and Nanopore platforms.
· Data interpretation and bioinformatics-assisted analysis.

Gene Expression & Regulation
· RT-qPCR and ChIP-qPCR for transcript and chromatin-level validation.
· Gene silencing via ASO, siRNA, and CRISPR/Cas9; overexpression through transfection/infection.

Cellular & Functional Assays

Tumor Cell Biology
· 2D and 3D culture of human and murine tumor cells.
· Cell viability and metabolism assays to assess drug or genetic perturbations.
· Immunoblotting and co-immunoprecipitation for pathway analysis.

Imaging & Visualization
· Fluorescence and confocal microscopy for protein localization and expression studies.

Applied Research & Integration

· Data integration across genomic, transcriptomic, and epigenetic layers.
· Translational applications: linking molecular findings to cancer diagnostics and therapy.
· Presentation of experimental results and mentor-led evaluation.

Accommodation

Try airbnb.com

Fees and Program Logistics

This program has the following durations available:

Duration	Fee
2 weeks	$1,094.00
6 weeks	$1,875.00
12 weeks	$3,438.00

This program allows Merit Applications. This program allows merit-based applications for virtual and onsite clinical and research programs. If you are successfully awarded under this category, Trialect or the host mentor will cover the tuition fee only. All applications will be evaluated based on merit. Due to the high level of competition, the chances of being selected under the merit category are quite limited.

Who Can Apply

All are eligible.

Host Details

Host Name: Dr. Maurizio Fanciulli

Affiliation: IRCCS National Cancer Institute Regina Elena

Address: Via Elio Chianesi 53, 00144 Rome, Italy

Website URL: https://trovamedico.ifo.it/listing/fanciulli-maurizio/

Disclaimer:It is mandatory that all applicants carry workplace liability insurance, e.g., https://www.protrip-world-liability.com (Erasmus students use this package and typically costs around 5 € per month - please check) in addition to health insurance when you join any of the onsite Trialect partnered fellowships.

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