Joint PhD project the University of Birmingham, UK and Maastricht University

This joint PhD project performed by NUTRIM PhD Amadeo Muñoz García is guided by Prof. dr. Chris Evelo (UM), Prof. dr. Martin Hewison (UoB) and dr. Susan Steinbusch-Coort (UM). At the moment Amadeo is performing novel experiments on the immunometabolic effect of vitamin D in order to confirm and mechanistically understand the effect seen in pathway analysis.

With this research Amadeo Muñoz Garcíaobtains expertise on laboratory technologies and he will combine it with his bioinformatics knowledge, demonstrating the strength of his PhD project.

Amadeo Muñoz García and colleagues at the University of Birmingham, UK and Maastricht University, NL recently published "Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D" in Journal of Molecular Endocrinology (J Mol Endocrinol (2018) 60, 95-108 doi: 10.1530/JME-17-0186). We interviewed Amadeo about their recent research article, the transcriptomics approach that it used and the close collaboration between the University of Birmingham and Maastricht University.

Please give a brief introduction of yourself and the aim of the joint PhD project.

This project is a collaborative work between Maastricht University and University of Birmingham that brings together wet and dry laboratory tools to give new insights into the role of vitamin D in immune function by bringing. To date studies of immune regulation by vitamin D have relied on analysis of specific cell types and specific genes. We applied state of the art bioinformatic tools developed at Maastricht University to analyse multiple genomic datasets from previous studies of the effects of vitamin D on immune cells. In particular, we have used bioinformatics tools that allow analysis of known biological pathways that may be affected by vitamin D. The overall result is a much broader, and unbiased, view of the immunomodulatory effects of vitamin D. Using this approach, we were able to show that the predominant effects of vitamin D on monocytic and macrophage cells from the innate immune system are not, as anticipated, immune-related but instead involve regulation of cell metabolism.

Recently you published the first collaborative paper on the immunometabolic effects of vitamin D. Could you outline your analysis and the motivation behind it?

The first approach of our project was to compile all gene expression raw datasets from works that studied vitamin D in human myeloid cells. Our objective was to give a biological context to the gene expression modulation of vitamin D in different myeloid cells models and highlight which metabolic/signaling processes were altered. This analysis revealed that metabolic pathways related to the energy uptake of the cell were highly up-regulated in different immune cell types, indicating that vitamin D have an important role in metabolism in myeloid cells. Currently we are working in the University of Birmingham with a tolerogenic dendritic cell models and we are studying the effects of vitamin D in different bioenergetic pathways of this cell types.

In the research, transcriptomics data from three experiments was reanalysed. These were transcriptomes of three models of different types of white blood cells in response to active vitamin D, what does your work add to these initial pieces of research?

The original studies reported the effects of vitamin D on gene expression in different types of monocytic/macrophage-like cells. Although these studies were unbiased in their approach, in most cases the outcome was to analyse effects of vitamin D on specific genes ‘cherry-picked’ from this unbiased analysis. In our study we have shown how to incorporate multiple datasets and all the analysed genes to provide a more complete picture of what happens when a cell type is treated with a particular factor. In this case we included every single gene analysed by each study to give a more complete overview of the modulation of biological pathways by vitamin D. This analysis is done using PathVisio, a software that is able to highlight biological pathways that are significantly altered by taking into account the entire collection of genes measured.

What is the significance of the 230 genes that show differential regulation in response to vitamin D in all three cell types?

After the analysis of the whole transcriptome data of the three datasets at the pathway level, we decided to identify which genes were commonly and significantly altered (p value < 0.05). The result was a list of 230 genes that was used as a gene list input in ClueGO (a tool from Cytoscape). This tool performs a gene ontology analysis which clusters the genes in groups based on their biological function. The result is a biological network which interconnects the groups based on the similarity of their associated genes. This approach revealed that in the three datasets, vitamin D commonly affects the expression of genes that are related to bioenergetic pathways, immune function and apoptotic processes. We used this approach as a different, but complementary, approach to the pathway analysis we carried out using PathVisio.

It's interesting that much of the differential expression in response to vitamin D was related to metabolism – do you have any theories on why this might be the case?

Previously, Ferreira et al. reported that glycolysis is crucial for the development of the tolerogenic phenotype of dendritic cells but it remains unclear what the molecular implications of vitamin D in metabolic pathways of dendritic cells and how these processes modulates the immune function. Our hypothesis is that a metabolic reprogramming occurs in tolerogenic dendritic cells that implicates changes in glycolysis activity, TCA pathways related and oxygen consumption rates. Overall, we think that vitamin D has a great impact mitochondria metabolic pathways and their modulation may have implications in their immune function.

How do you experience the close collaboration between the two universities? What makes it unique or challenging and what are the benefits of such a collaboration?

I consider myself a very lucky PhD student working in this joint project between the Maastricht University and the University of Birmingham. It gives me good experiences in professional ways (working in different departments, learning state of the art techniques, collaborations with several groups) and in the personal aspect (discover new places, new cultures and meeting great people). Finally, it terms of research, the promotion of collaborations with Universities that bring together different tools/techniques results in more complete and productive work.

Amadeo Muñoz García

Special thanks to Dr. Susan Steinbusch-Coort for the interview