Strategic Research

Mechanisms of cancer and cell differentiation

The main focus of our research is the characterization of the molecular mechanisms underlying cancer cell programs and the identification of molecular markers with clinical applications. The specific topics we are currently developing in our lab include:

  • Chromatin architecture in cell differentiation and cancer. We are investigating the organization of chromatin in normal and cancer cells. We are especially interested in the characterization of the mechanisms determining long range interactions and genome compartmentalization.
  • The role of repeat elements in genome structure and function. About half of the human genome is composed by repeat sequences. We are analyzing the epigenetics of some of these elements in normal and cancer cells and trying to determine their contribution to regulate the structure of the chromatin and gene expression.
  • Clinically oriented research on the epigenetic changes involved in human cancer. Initiation and progression of cancer disease is accompanied by multiple molecular changes, including epigenetic alterations. We search for epigenetic markers appearing early in the disease to facilitate cancer detection and intervention. Our group also devotes a large effort to develop or adapt molecular techniques to clinical settings with the aim of translating science progress in a better management of patients. Most of our studies are focused on colorectal cancer.
  • Epigenetic mechanisms during muscle lineage-commitment, cell activation and terminal differentiation. Muscle development and regeneration is driven by myogenic factors and epigenetic changes. We investigate the mechanisms and crosstalk of the different elements involved in these processes in physiological and pathological models.

Moreover, our lab aims to contribute to the advance of Genomic Medicine by developing new technologies and bioinformatic tools. Our group has also created Aniling, a spin-off company of the IGTP focused on the improvement of next generation genomic technologies to integrate molecular data into biologically and clinically meaningful information.


Main projects

  • 1.

    GEUS: Unified analysis of genome and epigenome with high fidelity

    The general objective of the project is the development and validation of a sequencing technology for the unified analysis of genome and epigenome. The new technology should improve the performance of current next generation sequencing platforms and offer high quality genomic and epigenomic information in a cost-effective manner. This project is a partnership between Aniling, the IGTP and the Institut Català d’Oncologia (ICO). Funding: RTC-2015-3867-1

  • 2.

    Functional anatomy of cancer epigenomic architecture

    The general objective of this project is to characterize epigenetic phenotypes revealing the functional organization of human cancer cell’s genome and to identify the underlying mechanisms. Specific objectives: 1. To characterize the epigenetic modularity of the cancer cell genome by deconstruction of DNA methylation covariation. 2. To determine the role of Alu retrotransposons in the epigenomic architecture of cancer cells. 3. Insights into the association between DNA methylation and chromatin organization and its role on gene expression regulation in human cancer cells. Three particular instances. 4. To identify and to characterize the functionality of odd-CpG sites. Funding: SAF 2015-64521-R



Bioinformatics expertise:

Group Leader:

Miguel Angel Peinado

Bioinformatics services offered

  • We have developed several web tools for genomic data analysis and visualization. These tools are free, open source and may be accessed at

  • Wanderer

    A gene centered viewer of gene expression and DNA methylation profiles obtained from the The Cancer Genome Atlas (TCGA) database.

  • Methylation plotter

    A simple interface to represent DNA methylation data.

  • Chainy

    A flexible and user-friendly tool for qPCR references validation and relative quantification.