Transcriptional mechanisms of chronic inflammation in genetically diverse tissue macrophages

Cincinnati Children's Hospital Medical Center received a $441,375 Project Grant from the National Institute of Allergy and Infectious Diseases (NIAID) under the Allergy and Infectious Diseases Research program (CFDA 93.855), awarded August 12, 2025, with a completion date of July 31, 2027. This grant supports investigator-initiated biomedical research examining the transcriptional mechanisms of chronic inflammation in genetically diverse tissue macrophages, specifically focusing on Kupffer cells—the predominant liver resident macrophages—and their role in metabolic dysfunction-associated steatotic liver disease (MASLD) progression.

The research project will deliver scientific knowledge and methodological advances addressing how genetic variation controls transcriptional regulatory mechanisms in Kupffer cells across different genetic backgrounds. By studying tissue macrophages in genetically diverse model systems rather than single inbred strains, the research aims to identify novel transcription factors and signaling pathways linked to disease-associated genetic variants, thereby unveiling insights into inflammation and MASLD mechanisms relevant to human disease. This work addresses a significant gap in current understanding of MASLD, where most preclinical studies assess macrophage biology in limited genetic contexts despite the existence of disparate disease phenotypes observed in the genetically diverse human population and varied outcomes across different mouse strains.

Abstract

Metabolic dysfunction-associated steatotic liver disease (masld) is an inflammatory liver disease associated with progressive fibrosis, cirrhosis, hepatocellular carcinoma, and death from cardiovascular disease. Despite knowledge of masld risk loci identified in genome wide association studies (gwas), IT is not yet possible to predict masld using DNA sequences alone, justifying an urgent requirement for additional research on genetic mechanisms of masld. One cell type that is instrumental to sensing and responding to tissue changes during masld are kupffer cells, the predominant liver resident macrophage. Kupffer cells contribute to masld progression by promoting local and systemic inflammation, immune cell infiltration, hepatocellular damage, and fibrosis. Additional research on the function and recruitment of kupffer cells is important for understanding masld because blocking macrophage infiltration or globally ablating macrophages protects against severe disease in experimental models. A major shortcoming in our understanding of masld and associated inflammation is that most preclinical studies assessing kupffer cell biology occur in a single genetic background. This shortcoming is significant because disparate phenotypes exist in masld models between inbred mouse strains, similar to the varied outcomes in the genetically diverse human population. Importantly, more than 90% percent of trait linked genetic variants are found in noncoding regulatory regions that control gene expression in cell type- and context-restricted manners. Therefore, studies defining roles for genetic variation in controlling transcriptional regulatory mechanisms in kupffer cells may unveil novel insights into inflammation and masld relevant to human disease. In our recent publication, we predicted the identities of many transcription factors and pathways linked to allele-specific regulation of kupffer cell gene expression in response to acute inflammation. However, we still do not understand with cell type resolution how genetic variation contributes to masld. For this proposal, the central hypothesis is that genetic variation controls the environmental signals sensed by kupffer cells and that knowledge on regulatory mechanisms will identify new pathways relevant to masld in human patients. In specific aim 1, we will define genetic mechanisms controlling kupffer cell transcription during experimental masld. In specific aim 2, we will assess the feasibility of gene editing for defining strain-specific functions of in vivo liver macrophages using an innovative combination of crispr/CAS9 and bone marrow transplantation. These results will support feasibility for expanded functional studies assessing roles for genetic variation in kupffer cells during disease and be extendable to tissue macrophages from other organs and disease contexts. This research may define novel pathways and mechanisms controlling macrophage participation in masld pathogenesis, which may be required for the development of novel therapeutics.