Cancer Genomics and Bioinformatics

Our group studies cancer genomics using large-scale sequencing data to identify and characterize the molecular mechanisms driving cancer onset and progression. Through the use of mathematical and statistical models our research aims to disentangle the complexity of genomic data to provide a personalized medicine able to be incorporated into clinical practice. The group's activity focuses on identifying somatic alterations, recontructing the clonal evolution of tumors, and identifying novel molecular mechanisms that are favourable clinical intervention points. Particular interest is devoted to the study of splicing factors and their role in the onset and progression of cancer.

Innovative features
With the growth of large-scale sequencing projects, modern biology is facing new bottlenecks caused by the massive production of genomic data. One of the new challenges is to extract relevant information from these genomic Big Data taking into account their inherent heterogeneity. Our unit addresses a wide range of biological problems resulting from the analysis of genomic, transcriptomic and epigenetic experiments of large scale. In our activity we apply the most recent bioinformatic, statistical and mathematical approaches to disentangle the complexity of these high-volume genomic data and identify the biological processes associated to a phenotype. Our goal is to develop new tools and paradigms to compare large sets of genomic data and characterize new molecular models responsible for the disease.

Head of Unit
Matteo Cereda, M.Eng., Ph.D. – Junior Group Leader
Tel. +39 011 6706498

Selected Publications
1. Foster JC, Arkell R, Del Giudice M, Anene C, Lauria A, Kelly J, Lemoine R, Oliviero S, Cereda M*, Rajan P*. Dysregulation of splicing-related proteins in prostate cancer is controlled by FOXA1. bioRxiv. 2018.
2. Mourikis T, Benedetti L, Foxall E, J Perner J, Cereda M, Lagergren J, Howell M, Yau C, Fitzgerald R, Scaffidi P, Ciccarelli FD. Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma. bioRxiv. 2018.
3. Cereda M, Gambardella G, Benedetti L, Iannelli F, Patel D, Basso G, Guerra RF, Mourikis TP, Puccio I, Sinha S, Laghi L, Spencer J, Rodriguez-Justo M, Ciccarelli FD. Patients with genetically heterogeneous synchronous colorectal cancer carry rare damaging germline mutations in immune-related genes. Nat Commun. 2016
4. Cereda M, Mourikis TP, Ciccarelli FD. Genetic Redundancy, Functional Compensation, and Cancer Vulnerability. Trends in Cancer. 2016
5. Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J. RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol. 2014

Group Members
• Marco Del Giudice, Ph.D., post-doc (IIGM)
• Serena Peirone, Ph.D. student (IIGM, INFN)

On-going projects

1. Pan-cancer assessment of tumour heterogeneity and clonal evolution

2. Deciphering alternative splicing dysregulation in cancer to identify new therapeutic targets

3. Characterization of new molecular mechanisms responsible for the onset and progression of cancer

Link to Projects

Inter-Units Projects

Functional genomics applied to pediatric neoplasms: from mutations, to function, to therapy Link