Overview of  TRAIN

This training network  was brought together  in the context of the medical need to tackle the clinical consequences of obesity-related diseases more holistically. Dysregulation of common molecular pathways that govern the physiological functioning of adipocytes, immune cells and prostate epithelial cells have been reported in immuno-metabolic disease (e.g. obesity) and several cancers. The projects described in this project will investigate regulators of these pathways, focusing on tribbles (TRIB) proteins, a recently described family of pseudokinases, that have a key role in controlling immunity, metabolism and cancer, and which here will serve as prototypical examples for integrative metabolocentric cancer research. Specifically, TRIBs are envisaged to contribute directly to the development and progression of prostate cancer (PCa), the prognosis of which is substantially worsened in individuals with immuno-metabolic disease

The overall objective of this multidisciplinary research-training programme will be to uncover cell-specific aspects of TRIB-mediated control of immuno-metabolism and their impact on PCa progression. We will approach this by integrating cell biology and sophisticated in vivo models of both immuno-metabolic disease and PCa, complemented by specialist human disease biobank materials, cutting-edge genomics approaches, plus a drug discovery pipeline. This will be carried out by an alliance of leading academic research groups and specialist SMEs with complementary backgrounds in inflammation, adipose tissue (AT) biology, tumourigenesis, genomics, translational models of human disease, medicinal chemistry and drug discovery.

Research Objectives

TRAIN was conceived around five main research objectives as follows:

  1. Characterise the roles of TRIB1 and -n 3 expressed by resident cells (e.g. macrophages, regulatory T Cells (Tregs), iNKT) of adipose tissue in regulating the inflammatory status of individual adipose tissue deposits, including peri-prostatic adipose tissue
  2. Determine the roles of adipocyte-specific TRIB1 and -3 expression in regulating adipocyte differentiation, immune cell content and activities of metabolic and peri-prostatic AT plus the systemic changes arising from altered AT compositions and functions, including the impact of diet-induced obesity
  3. Define isoform-specific effects of prostatic epithelial cell TRIB expression on Tribbles-mediated functions and activities, as well as the effects of TRIB1 and -3 on prostate cancer progression, via local and systemic alterations in immuno-metabolism
  4. Analyse/define the mechanisms regulating cell- & isoform-specific TRIB1 &-3-mediated effects on immuno-metabolic profiles in health & disease (e.g. human tissues, mouse models) by genomics and systems biology strategies
  5. Characterise the immuno-metabolic outcomes of altering TRIB activity via cell- and isoform-specific Trib knockout and transgenic mice models, miRNA-mediated regulation of TRIB levels in vitro and by developing inhibitors of TRIB3 degradation

Research Methodology

TRAIN draws on the expertise and commitment  of leading researchers from six European Universities, three European Research Centres, three Hospitals/Biobanks, five SMEs, plus a world-class Advisory Board  to study obesity-related diseases at a holistic or “systems” level. The scientific programme contains four work packages ( 2, 3, 4 & 5 ) that are designed to gain clinical/mechanistic insights into the cell-specific metabolic and signalling pathways that both regulate and contribute to cell proliferation/ differentiation decisions made in AT depots, as well as prostatic epithelial cells . A further scientific work package (WP6) deals with the development and testing of Intervention Strategies for early translation studies. Each WP is led by an Investigator with long-standing expertise and contacts in the required specialities  and the crosscutting WPs (5, 6) benefit hugely from the commitment, expertise and infrastructure provided by TRAIN’s non-academic Beneficiaries.

 

train-wp-diagram

       Overview of TRAIN’s workpackage structure

Each of the scientific Work Packages is described briefly below:

 Work Package 1: Management.

Lead: University of Sheffield

TRAIN’s joint governing structure comprises a Supervisory Board (SB), an Advisory Board, plus individual domain Coordinators for: Management (i.e. Programme Coordinator, Programme Manager), Science, Training, Knowledge Transfer, Exploitation, Dissemination and Ethics. To increase their training in transferable skills, ESRs will contribute to TRAIN’s management and governance structures.

Work Package 2: Adipose Tissue Resident Immune Cells

Lead: University Medical Centre Utrecht and University of Nantes

Full-body Trib1 deficiency decreases adiposity and increases macrophage-driven inflammation. By contrast, full-body, Trib3-deficient mice (our unpublished data) are obese and have impaired glucose handling. These mice also display augmented macrophage responses in acute inflammatory models. Work in this WP will define contributions of TRIB1/3 in regulating iNKT, Tregs and macrophage numbers and activities in distinct AT depots (e.g. subcutaneous, intra-abdominal, peri-prostatic), and how the inflammatory states of these depots are affected by a HFD. The interaction between adipocytes and immune cells and between three different immune cell types will be investigated and their overall physiological impact on local and distant tissues assessed. Complementary transcriptomic and metabolome analyses contributing to the four envisaged major scientific outputs from this WP are outlined in WP5

Work Package 3: Adipocyte Cell Biology

Lead:  Helmholtz Zentrum Muenchen

In many senses, adipose tissue (AT) is an endocrine organ communicating with distant tissues through secreted factors (e.g. adipokines), and consequently may impinge on many aspects of energy storage/utilization and development/progression of obesity-related cancers. This WP will define adipocyte-specific, TRIB-mediated functions and their isoform-specific contribution to the accrual of VAT, subcutaneous and per-prostatic fat depots and the impact of altered adipocyte-TRIB activity on adipocyte differentiation, its endocrine functions and in turn on serum adipokine activity & metabolome and AT-tumour cross-talk pathways. As such, the studies in this WP contribute to many of the envisaged major scientific outputs from WP4 and 5

Work Package 4: Obesity Regulated Disease – Prostate Cancer

Lead: Universidad Complutense de Madrid (IdISSC-UCM) plus CIC Biogune and University of Beira Interior

This WP aims to unravel the complex (remote and local) signals that dictate the aggressiveness of cancerous lesions, with a focus on understanding the cell-specific functions of TRIB1 and 3 in this process(es). At the cellular level, TRAIN’s research groups showed that loss of TRIB3 enhances tumourigenesis in several genetic contexts, including in the presence of activating mutations of Ras and heterozygous PTEN deletion. Further, our database interrogation studies revealed that TRIB1 is over-expressed in PCa but whether this represents an adaptive response to the metabolic demands of tumourigenesis, increased recruitment, proliferation and/or retention of Tregs and/or macrophages in a PCa lesion’s local environment, are just a few of the questions that will be answered in TRAIN, with obvious therapeutic implications as a result of increased understanding of the processes promoting PCa.

Work Package 5: Genomics & Systems Biology; Analysis of Cell-specific signalling, Inter-tissue communication and Effects of a HFD

Lead: Queen Mary’s London and SeqOmics

The purpose of this WP is to holistically define the transcriptional and cellular pathways perturbed by cell-and isoform-specific Trib deficiency but in a targeted cell- and disease-orientated manner to make sure that this knowledge is effectively translated/integrated with the data produced in WPs 2, 3, 4 and 6; and that we maximize the ‘meaning’ of the data produced in the more tissue- and systemic-based approaches used in each of these WPs. SO provides considerable added value to this package, not only by reducing the associated costs of transcriptome analysis, but by providing access to powerful computers for statistical and bioinformatic analyses of large datasets. This WP also benefits from two proposed (targeted) proteomic analyses, transcription factor (TF) assays and complementary analyses of human tissue samples.

Work Package 6: Intervention and Inhibitor Development

Lead: University of Sheffield and Intelligent Pharma

This WP will explore a range of mechanisms by which cellular levels of TRIB (and, by inference, activity) could be controlled, with the long-term goal of exploiting these for therapeutic interventions. These experiments, combined with data from Trib-/- mice (WP2-5) will provide critical information on the action of TRIB1 and -3 in AT physiology, their contribution to the pathogenesis of dysfunctional AT syndromes and validating them as critical regulators of cell proliferation in the context of cancer. In addition, our work will reveal novel, TRIB-dependent “druggable” avenues for future therapeutic development in tackling these diseases. Crucially, for validating drugs in murine & human systems, the amino sequence of Trib1 as well as Trib3 are highly conserved (>95% identical) between mouse and human, and the atomic structure of TRIB is now resolved. Thus, knowledge/results obtained in either system will be readily transferrable, thus aiding the development of TRIB-dependent intervention strategies.

Work Package 7: Communication, Dissemination and Exploitation

Lead: CIC Biogune with University of Beira Interior and University Medical Center Utrecht

TRAIN’s communication and dissemination activities will be coordinated widely. The Supervisory Board will oversee all aspects of Communication and Dissemination; these will be jointly organised by the Programme Manager and appropriate Coordinators, whose tasks will include organising ETN e-Newsletters, Open days, Public Talks and coordinating TRAIN’s Website, Facebook and Twitter content. Other objectives will be delivered via focussed task groups, such as the IP Management Group, as appropriate. As part of our emphasis on transferrable skills training, ESRs will also contribute to these activities, when they would promote such training.

 

ESR Projects

The TRAIN network has been built around 15 individual ESR projects, all of which are interlinked, complementary and synergistic  and benefit from multi-disciplinary and -sectorial expertise

Each individual ESR project  is designed to include data from  a range of  study disciplines, which we believe is a pre-requisite for the proper holistic dissection/understanding of disease. Thus, students with a diverse range of backgrounds (e.g. cell biology, genetics, mathematics) will undertake a secondment that increases their individual skill-base, as well as produce a complementary dataset for their individual research project.  For example, ESR1 (biochemistry graduate) will acquire cell-sorting expertise in their secondment; ESR2 (largely immunology-based project (WP2)) will undertake a secondment at SO to become proficient in both the production and analysis of transcriptomic data (WP5); ESR4 (a molecular biology graduate) will complement their gene expression studies with a (protein-based) Tandem Spectrometry secondment. ESR10 with a bioinformatics/mathematics degree will gain hands-on molecular biology skills. Similarly, ESR15 (theoretical chemist, based at IP) will acquire cell-based in vitro assays skills in their secondment.