Discovering mechanisms of metabolic dysfunction-associated steatotic liver disease in cell-type and cellular subtypes of multiple metabolic tissues

About This Grant

Subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT), and the liver are the key metabolic tissues involved in maintaining homeostasis and cardiometabolic health. In individuals with metabolic dysfunction- associated steatotic liver disease (MASLD), the liver is inundated with fat and unable to perform optimally. MASLD may further progress to its pro-inflammatory stage, metabolic dysfunction-associated steatohepatitis (MASH), which is often coupled with cardiovascular disease (CVD), including coronary artery disease (CAD). Both MASLD/MASH and CAD are associated with obesity and related cardiometabolic disease (CMD) and CVD traits. In line with this, recent studies have identified two types of MASLD: one that manifests into more severe liver disease (“liver MASLD”) and another that is primarily associated with CVD (“systemic MASLD”). This suggests that there are multiple distinct mechanisms and pathways in the pathogenesis of MASLD, making prevention and treatment of MASLD challenging. This is of clinical significance because MASLD is growing globally, and CVD is the leading cause of death in individuals with MASLD. Therefore, it is important to improve understanding of the multisystem mechanisms underlying MASLD. Single nucleus RNA-sequencing (snRNA- seq) provides a granular view of gene expression by cell-type and cellular subtypes. Coupled with genotype data it allows the investigation of genetic regulation of cell-type and cellular subtype level gene expression and how that relates to MASLD susceptibility. We hypothesize that there are cell-type and cellular subtype level regulomes and susceptibility genes associated with development of MASLD and its two types. Leveraging cohorts with matched tissue samples, we will 1) discover master transcription factors (TFs) trans regulating cell-type or cellular subtype level expression of genes associated with MASLD and 2) elucidate cis variants regulating cell- type or cellular subtype level gene expression of genes differentially expressed (DE) by MASLD across the SAT, VAT, and the liver. In Specific Aim 1, we will use co-expression network methods to find the TFs regulating gene expression in cell-type level networks that we hypothesize to reflect cellular subtypes. We will then assess the DE genes by MASLD regulated by TFs in the networks and functionally validate TF target genes with existing functional data and knockdown experiments to improve understanding of complex cell-type and subtype level trans regulation of tightly coordinated co-expressed genes involved in MASLD in SAT, VAT, and the liver. In Specific Aim 2, we will first identify cell-type and cellular subtype level cis-expression quantitative trait locus (eQTL) variants and genes DE by MASLD in the three key metabolic tissue. Following this, we will colocalize these cis regulatory variants with GWAS variants of the two MASLD types to discover cell-type and cellular subtype level genes involved in the two types of MASLD, “liver MASLD” versus “systemic MASLD”. Accomplishing Specific aims 1-2 will improve understanding of 1) cell-type level key trans regulators of MASLD genes and 2) cis regulatory variants and their genes underlying the two types of MASLD.