Understanding multi-organ consequences of dysregulated macrophage TGF-β activity to guide targeted interventions

Background

Transforming growth factor-β (TGF- β) is a multi-functional growth factor and modulator of immune function that is involved in tissue development, homeostasis, remodeling and repair across many organs in the body. Macrophages, resident immune cells that occupy most organs, are key producers of TGF-β. Dysregulation of TGF-β activity (both over- and under-activity) is associated with several chronic neurological, fibrotic, autoimmune diseases and cancers. Targeting the TGF-β pathway may offer therapeutic potential yet is challenging because of the body-wide actions of TGF-β. Understanding the comparative regulation of macrophage TGF-β activity between and within organs is crucial to guide design of more precise therapeutics so that patients can be stratified to disease/compartment-optimized interventions. TGF-β activity is regulated at multiple levels, including by molecules (LTBPs and LRRCs) that enable conversion of the inactive TGF-β precursor to its bioactive form. Macrophages located in different tissues and sub-tissue compartments appear to express a variety of these LTBPs and LRRCs. We recently described mutations in one of these, LRRC33 (also known as NRROS) as the cause of an early-onset fatal neurodegenerative disease, likely because of abnormal TGF-β function in microglia (the macrophages of the brain). Ongoing work in our labs suggests that LRRC33/TGF-β expression and function is sub-tissue compartment restricted in the brain and that this pattern extends to selected systemic organs, suggesting; (1) that LRRC33 may have important physiological roles in macrophages outside the CNS, and (2) that LRRC33 could be a more selective target for modulating TGF-β activity in certain diseases.

Aims

The overall project goal is to develop a multi-organ understanding of how dysregulated TGF-β activation, through LRRC33 loss-of-function, affects macrophages and health outcomes. 

Specific aims, as follows, are complementary but independent of one another and intended to address the overall goal from different perspectives. 

1. Compare effects of LRRC33 deficiency on macrophage transcriptome profiles in different organs and sub-organ niches using preclinical model datasets and tissues. Working with macrophage single-cell RNA sequencing (scRNAseq) datasets from multiple organs generated previously in our labs, the student will use established computational workflows to conduct dataset integration and identify organ-specific/common macrophage phenotypes. Signatures will be mapped to a human macrophage expression atlas and key marker genes examined in situ for spatial validation. 

2. Determine if effects of LRRC33 deficiency and disruption to other components of the TGF-β pathway phenocopy in macrophages within and across organs. Our recent findings suggest similar, but not identical, clinical neurological signs resulting from disruption to LRRC33 and other components involved in TGF-β signaling. The comparative effects on microglia are unknown. Analysis of altered microglial states using integrated scRNAseq datasets from knockout of differing TGF-β pathway components will be conducted to understand how modulating LRRC33 compares to more broadly-acting TGF-β interventions. This approach may extend to other organs as new datasets are generated within our labs (funded separately). 

3. Assess if LRRC33 gene variants associate with adverse health outcomes related to TGF-β function in a large population cohort. LRRC33 variants will be identified from exome sequencing data in UK Biobank, annotated and filtered to focus on high-confidence loss-of-function or deleterious missense mutations. Associations between heterozygous variant carriage with outcomes relating to TGF-β function, both for disease (including fibrotic diseases, autoimmune disease, cancer, cardiovascular remodeling disease, neurodegenerative disease) and quantitative biomarkers, will be determined.

Training outcomes

The project will equip the student with a range of knowledge and skills, and offer a breadth of training opportunities. 

Knowledge - The student will gain knowledge and understanding of tissue macrophage and TGF-β biology, immune-mediated mechanisms of chronic disease, genomics, transcriptomics and molecular epidemiology, and how to apply integrative data-driven - omics and population health data science approaches to tackle questions on disease mechanisms and targets. A key outcome will be information to guide more refined targeting of TGF-β activity tailored for diseases affecting different organ systems. 

Skills – the student will gain skills in a full package of methods in selection, curation, QC, pre-processing, integration, data analysis/visualization and interpretation of multi-omics datasets. Opportunities to acquire selected lab skills in techniques important for in situ validation of -omics profiles will be available. Further quantitative and statistical skills will be gained in curating and analysing genetic and population health data (from UK Biobank and related population health resources). Gaining transferable skills in experimental design, written and oral presentation of data, network building and collaboration will be a central part of the student’s training.