Nault and MSU Superfund Team Publish Exciting Developments in Single-Cell RNA Sequencing

September 10, 2020

Postdoctoral researcher and EITS alumnus, Rance Nault, in collaboration with a team of MSU Superfund scientists including Kelly Fader, Sudin Bhattacharya and Timothy Zacharewski, recently published exciting research on single-cell RNA sequencing. The paper, “Single nuclei RNA sequencing assessment of the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin,” was published in August 2020 in the journal, Cellular and Molecular Gastroenterology and Hepatology.

The liver is composed of several different cell types working together to maintain normal function. Exposure to chemicals, drugs, and supplements can modulate these normal processes, and in some cases even lead to toxicity and disease. Traditionally, evaluation of how foreign compounds modify gene expression is achieved by averaging their levels in a tissue sample and as a result some cell type specific responses can be lost. As innovative technologies are emerging to allow the measurement of gene expression levels in a single cell or nucleus, the objective of the study by Nault was to demonstrate its application for characterizing the cell-specific effects of the persistent environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, aka dioxin). Nault and his team showed that single-nuclei RNA sequencing can be used to demonstrate shifts in cell populations.

Single-cell RNA sequencing is most commonly performed on freshly collected tissues. In typical toxicology study designs multiple doses are used to establish safety of chemicals, drugs, and supplements. The number of samples, coupled with the severe effects observed at higher doses, present a significant hurdle in the use of this technology. The work by Nault shows that by using nuclei isolated from frozen livers, it is possible to identify known responses caused by dioxin exposure, as well as gain novel insight into how specific cell populations respond.

Demonstration of the feasibility and value of a single-nuclei RNA sequencing approach was a first critical step for investigating more complex study designs. Future efforts by Nault and the team of MSU Superfund researchers will explore the use of this technology to characterize the cell-specific sensitivity upon exposure to liver toxicants in order to better understand the development and progression of non-alcoholic fatty liver disease.

Nault’s research was generated under Project 3, “TCDD-Elicited Steatosis: The Role of Aryl Hydrocarbon Receptor Regulation in Lipid Uptake, Metabolism, and Transport,” and Core A, “Computational Modeling of Mammalian Biomolecular Responses,” of the MSU Superfund Project. Led by Dr. Zacharewski, Project 3 explores the adverse effects of dioxin and related compounds, commonly found Superfund contaminants, on liver metabolism and function. By using innovative technologies such as single-nuclei RNA sequencing, this MSU Superfund team is able to gain further insight on the role of aryl hydrocarbon receptor (AhR)-mediated changes in lipid metabolism which leads to the accumulation of fat, inflammation, and scarring of liver tissue.