Scientific Objectives

The main objective of the iDIFFER network is to generate a working framework for comprehensive and multidisciplinary research aimed to understand how the balance between cell proliferation and differentiation is controlled in mammalian cells and tissues, and how deregulation of this balance may influence human disease.

iDIFFER team members have made relevant contributions in the past to different areas of the various processes that regulate cell proliferation and differentiation in mammals, mostly using mouse or human-derived models

Scientific objetives

As indicated above, the iDIFFER network is scientifically and technically supported by multiple projects under development in the different participating laboratories.

In general, most of these projects are aimed at understanding the molecular mechanisms behind the transitions that occur between progenitor cells, differentiated, functionally mature cells in different tissues, and malfunctioning cells that ultimately cause disease.

In general, most of these projects are aimed at understanding the molecular mechanisms behind the transitions that occur between progenitor cells, differentiated, functionally mature cells in different tissues, and malfunctioning cells that ultimately cause disease.

Main scientific objectives within the iDIFFER network:

Including DNA replication, chromatin structure and epigenetics, mitosis, and the control of transcription and translation, either by proteins or non-coding RNAs. [Carnero, Huarte, Luders, Malumbres, Mendez, Nebreda, Ortega, Zubiaga]

Special emphasis will be made on the decision of cells on whether entering a new cell cycle or exiting cell proliferation by inactivating the cell cycle machinery in favor of cell differentiation. These decisions are at the base of the onset of differentiation but also of the decision of stem cells to remain quiescent. [Carnero, Fariñas, Huarte, Luders, Malumbres, Nebreda, Zubiaga]

We are especially interested in the balance between these two types of cell division typical of progenitor cells. The basic mechanisms regulating this balance are critical in most tissues but we will focus to the neural system, one of the few systems in which this balance has been studied more in detail with important contributions from iDIFFER members. [Fariñas, Luders, Malumbres]

It is well established that major repressors of cell proliferation (e.g. retinoblastoma protein) trigger in parallel cell differentiation and the diverse forms of this mechanism shape major cellular decisions during development or homeostasis in every tissue. Every group in the network is interested in investigating these regulatory mechanisms either during development or regeneration or in specific diseases [Carnero, Djouder, Fariñas, Huarte, Luders, Malumbres, Mendez, Nebreda, Ortega, Zubiaga]

Emerging data suggest that cell cycle regulators influence the fate of daughter cells after division. Centrosome and spindle regulators, in addition to mitotic kinases, are among the involved molecules and several groups in the network will investigate the links between basic cell cycle mechanisms and cell fate after division, and its consequences in development and regeneration. [Djouder, Fariñas, Luders, Malumbres, Ortega]

As important as the core machinery that executes many cellular processes are the pathways that monitor possible cellular stresses (either exogenous or endogenous) and modulate the function of the core machinery. Not surprisingly, many stress-regulated molecules are malfunctioning in human disease (e.g. many tumor-suppressor genes in cancer). [Djouder, Huarte, Méndez, Nebreda, Zubiaga]

Cellular and systemic metabolism is tightly controlled by major proliferation/differentiation networks and several groups in the network are interested in establishing the reciprocal controls between the cell cycle and metabolism, connections between cell proliferation and the AKT/mTOR pathway, effect of diet and environmental stresses, etc. [Djouder, Luders, Malumbres, Méndez, Nebreda, Zubiaga]

Data from our groups and others in the last years suggest that development of the neural system is a perfect model for studying the balance between proliferation and differentiation and its consequences in adult tissues. Some of the models already generated in our labs are critical for investigating neural stem cells, their niches, their connection with the cell cycle machinery and its relevance in developmental diseases such as microcephaly [Fariñas, Luders, Malumbres, Méndez]

Arguably, cancer is tightly linked to defects in cell proliferation and differentiation and most groups in the network are studying tumor development and therapy, and therefore interested in the balance between cell proliferation and differentiation. Although the spectrum of neoplasias is wide, special collaborative focus on breast, liver and lung cancer will emerge from the network. [Carnero, Djouder, Malumbres, Mendez, Nebreda, Ortega]

Schematic summary of major scientific fields of interest within the network indicating the participation of the different labs. Blue, red and purple headings indicate normal physiological, pathological or therapeutic areas, respectively.

Main technical objectives within the iDIFFER network:

It is obvious that networking provides additional technical advantages in addition to the scientific collaboration between participating groups

Our network has identified some models or techniques of common interest that will strongly benefit from sharing setup protocols, equipment, platforms and data generated.

Many laboratories in the network have used a variety of mouse models to study the balance between proliferation and differentiation in vivo. In particular, one of the laboratories (Ortega) has generated more than 100 models in the last 10 years in collaboration with laboratories of more than 10 institutions in Spain or other European countries. Her laboratory has recently setup the use of CRISPR techniques in mouse embryos and ES cells for faster generation of new models and for genome wide genetic screenings. This experience will be shared to accelerate similar developments in other groups within the consortium.

Many of the participating groups are interested in incorporating to their projects single-cell technologies. Some of the participating institutions (CNIO, FIMA, IRB, Univ. Valencia) have recently acquired and setup new equipment (10X Genomics, NextSeq, C1 Fluidigm, CyTOF) to run this technology in-house. The possibility of sharing these technologies and using them in collaborative projects will be a critical point for discussion, especially given the possibility of sharing data or using common controls in the tissues of interest.

To better understand long-range signaling networks and modeling of molecular and cellular processes implicated in proliferation and differentiation in vitro and in silico, a special effort will be put to develop new technical advances with the particular use of organoid culture. This can be combined with the quantitative assessment and analysis of single cell RNA sequencing. Mammary gland, pancreatic and colon organoids have already been generated in participating labs and further efforts will be made to setup brain and lung organoids.

The Advanced Digital Microscopy Imaging Facility of the IRB-Barcelona and the CNIO provide imaging platforms that will be particularly useful for imaging of cells in the tissue and organ context including in embryos and organoids. Available advanced technologies include live cell spinning disk microscopy, high content/screening live cell multi-well scanning microscopy, light sheet microscopy for imaging in tissue/thick specimen, and super resolution microscopy for sub-diffraction imaging of structures that are relevant to this network such as kinetochores, centrosomes or cilia and other subcellular structures. These technologies will allow the analysis of proliferation, differentiation, and other fates such as senescence or death of cells in their native environment and provide high resolution information on the relevant cellular structures involved in these cell fate decisions.

Given the experience of the iDIFFER teams in different areas, the different technical platforms available in the participating entities and the protocols (including scientific collaboration, institutions agreements, etc.) necessary for the use of these techniques by the members of the network will be discussed. Of particular interest are those technologies helping in the use of animal models (histopathology, genomics, proteomics, cytomics) and bioinformatics pipelines for their analysis.