Research Interest:

The Environmental Epigenetics group is broadly interested in the epigenetic control of metabolism within and across generations, and within this topic, we have a historical interest in circulating RNAs. Circulating, cell-free nucleic acids (both DNA and RNA) are actively secreted from peripheral tissues under physiological and pathological conditions and are promising biomarker candidates for early detection of pathophysiological alterations. Circulating cell-free RNAs in particular have been directly implicated in the development of several pathologies including cancer and obesity and are intensively studied as disease biomarkers. Their function in physiological and developmental settings as well as in mediating cell-cell communication remains still largely elusive. The main challenge to fully address this question lays on the need to track circulating RNAs from their transcriptional source to their functional sink in an unbiased and cell-type specific manner. To this goal, we recently developed iTAG-RNA [1], a method for the unbiased tagging of RNA transcripts in mice in vivo. Using iTAG-RNA we have been able to isolate cell-type specific transcriptional responses to a dietary challenge in vivo and 
identify a novel RNA-based endocrine axis where hepatocyte-secreted smallRNAs – in response to High Fat Diet feeding – buffer transcriptional response to the dietary challenge in muscle and adipose tissue to maintain glucose and lipid homeostasis. iTAG-RNA combines the expression of the human Cyp3A4 enzyme with a HepDirect modified 5-ethynyl-2'-deoxyuridine (5EU), which is converted by the Cyp3A4 enzyme into 5EU and incorporated into transcribing RNA polymerase.  

Project Title:

Circulating RNAs as sensors and effectors of metabolic homeostasis

Project Description:

The aim of this project is to dynamically track circulating RNAs from transcriptional source to functional sink in mouse models pre- and overt diabetes, by using iTAG-RNA with conditional hCyp3A4 over expressing mice coupled to metabolic phenotyping and state-of-the art transcriptomics. Here, we plan to upgrade iTAG-RNA by generating a conditional hCyp3A4 transgenic, where the expression of the transgene is dependent on the tissue-specific activity of a Cre Recombinase. With this model at hand, we will draw the first catalog of circulating RNAs tracked from their transcriptional source at muscle and adipose tissue to their functional target tissues in a mouse model of pre- and overt diabetes. We will then consider relative smallRNA abundance in the circulation, site of action and target genes to build a ranking score from the most to the least likely smallRNA to have human translational relevance and validate – by TaqMan based qPCR – the ten top-scoring in human pre-diabetes and diabetes in collaboration with the German Diabetes Center and the Alberta Diabetes Institute (ADI). 
Ideally, one or two final candidates will be tested for their physiological relevance using different in vivo approaches to interfere with their expression/function and metabolic phenotyping methods. 

Selected Publications:

1. J. Darr et al., iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental 
Stimuli and Identifies an RNA-Based Endocrine Axis. Cell Rep 30, 3183-3194 e3184 (2020).