Lymphoma Genomics

bertoni-group2013

Members

Afua Mensah, PhD
Alberto Arribas Carmena, PhD
Cesare Rech, MS Student
Chiara Tarantelli, PhD
Elisabetta Curti, stage
Eugenio Gaudio, PhD
Filippo Spriano, PhD student
Francesco Bertoni, MD Group Leader
Giulia Pontali MS student
Giulio Sartori, Visting research fellow
Ivo Kwee, PhD
Luca Aresu, DVM
Luciano Cascione, PhD
Murodzhon Akhmedov
Sara Napoli, PhD
Valdemar Priebe, PhD student

Overview

We apply genomics techniques followed by functional studies to elucidate the lesions underlying lymphomas and to identify new gene and new potential therapeutic targets. Since the ultimate goal of our research is the improvement of patients outcome, we work in strict collaboration with pharmaceuticals companies in testing potentially active compounds. The strict connection with the lymphoma team of the Oncology Institute of Southern Switzerland (IOSI) running clinical trials dedicated to lymphoma patients allows the development of new drugs from pre-clinical to clinical settings. We also perform molecular follow-up studies within national lymphoma clinical trials (SAKK) and analyse the immunoglobulin heavy chain mutational status in patients with chronic lymphocytic leukemia.

Our group has two main areas of interest, which are interconnected. The first is the application of genome-wide technologies to better characterise lymphoma subtypes, to understand the biology of the disease and to identify lesions or patterns of lesions with an impact on the outcome. The second is the evaluation of new compounds for their possible anti-lymphoma effect. Since the ultimate goal of our research is the improvement of patients outcome, we work in strict collaboration with pharmaceuticals companies in testing potentially active compounds. The strict connection with the lymphoma team of the IOSI Oncology Institute of Southern Switzerland running clinical trials dedicated to lymphoma patients allows the development of new drugs from pre-clinical to clinical settings.

Among the instruments, we have an Illumina HiScanSQ and an Illumina MiSeq, which we can be used for different types of microarrays and NGS applications. We have set up the technology to obtain cancer genome wide DNA profiling with array-based comparative genomic hybridization (arrayCGH): the genomic profiles of almost 2,000 human lymphoid tumors have been obtained so far. All the samples have been processed and hybridized in our laboratory on an Affymetrix platform, and, more recently, on an Illumina system. We are now also performing genome-wide methylations studies, and both DNA and RNA profiling also on formalin-fixed paraffin-embedded (FFPE) material, and Next-Generation Sequencing (NGS) studies. Moreover, we have moved the genomic profiling to the context of prospective trials.

With support of the Bioinformatics Core Unit, we also perform computational and statistical studies. We develop innovative data analysis tools, and visualization software and database resources for genomics research in collaboration with the Dalle Molle Institute of Artificial Intelligence (IDSIA), and the SIB Swiss Institute of Bioinformatics.

Current projects

  • Genetic and epigenetic landscape of marginal zone lymphomas,
  • Functional characterization of ETS1 and FLI1 in diffuse large B-cell lymphomas,
  • Characterization of new anti-lymphoma compounds and identification of biomarkers.