RNA (de)regulation in disease contexts

The advent of next-generation sequencing (NGS) impacted our ability to characterize genomes, epigenomes and transcriptomes. In particular, RNA-Seq allows the investigation of disease transcriptomes to be expanded from measuring the expression of protein-coding genes to the analysis of alternative splicing, non-coding RNAs, etc. The evidence for the involvement of splicing regulation in cellular programs altered in oncogenesis, for example, motivates the NMorais Lab to use NGS to find disease-specific transcriptomic signatures beyond gene expression.
The Lab's experience in the analysis of different types of high-throughput transcriptomic data and in the definition of molecular signature scomplements that of oncologists, immunologists and molecular biologists at the iMM, enabling the experimental validation and the functional and clinical exploration of promising targets. Moreover, the IMM benefits from a specimen-rich biobank and the prospective collection of clinically annotated samples.

These are some of the projects being developed in the Lab:
- Transcriptomic profiling of colorectal cancer: novel biomarkers for early metastatic disease
- Brain metastases’ transcriptomes: organ tropism and the search for therapeutic targets
- Alternative splicing as a therapeutic target in Parkinson’s disease
- Human aging transcriptomics: regulation and functional consequences in longevity and disease
- Mechanisms of centrosome amplification and their therapeutic value in cancer
- Intron retention as a mechanism for dynamic regulation of gene expression

Splicing Bioinformatics

We are also developing bioinformatic tools for the analysis of alternative splicing from large RNA-Seq datasets. We are dealing with issues such as isoform annotation, statistics of differential splicing, data variance or the integration with clinical information. These tools are assisting in elucidating mechanisms of alternative splicing regulation (and deregulation in disease contexts).
We have just released psichomics, an interactive R package for the analysis of alternative splicing.


Collaborators

Anna Sablina (VIB, Belgium)
David Elliot (Newcastle University, UK)
George Garinis (FORTH, Greece)
Jesus Gil (Imperial College London, UK)
Julian Koenig (IMB Mainz, Germany)
Yogesh Kulathu (University of Dundee, UK)

Henrique Veiga-Fernandes (Champalimaud, Portugal)
Mónica Bettencourt Dias (IGC, Portugal)
Rui Martinho (U. Algarve, Portugal)
Susana Vinga (CSI-IDMEC-IST, Portugal) & Alexandra Carvalho (IT-IST, Portugal) (PERSEIDS)

Cláudia Faria (Hospital de Santa Maria / JBarata Lab, Instituto de Medicina Molecular, Portugal)
Gonçalo Bernardes (Instituto de Medicina Molecular, Portugal)
Leonor Saúde (Instituto de Medicina Molecular, Portugal)
Luis Costa (Instituto de Medicina Molecular, Portugal)
Luisa Figueiredo (Instituto de Medicina Molecular, Portugal)
Sérgio de Almeida (Instituto de Medicina Molecular, Portugal)



Funding