Biology subjects

Helms, J. B.

Publications and source records attributed to Helms, J. B..

4 recordsLinked to original sources

bioRxiv2026

MASH-in-a-dish reveals fatty acid-driven itaconate crosstalk between Kupffer cells and hepatocytes

Metabolic dysfunction-associated steatohepatitis (MASH) is characterized by lipid-driven sterile inflammation and fibrosis that leads to liver failure and liver cancer. Metabolites are increasingly recognized as signaling molecules and regulate disease progression through cell-cell crosstalk. To overcome the challenges of studying metabolite crosstalk between different cell types in MASH livers, we developed a novel in vitro MASH model, "MASH-in-a-dish", a Transwell co-culture system of mouse hepatocyte-derived organoids (HepOrgs), Kupffer cells (KCs), and hepatic stellate cells (HSCs) in a chemically defined liver co-culture medium. MASH-in-a-dish models key clinical features of clinical MASH, including steatosis, hepatocyte ballooning, inflammation and fibrosis. MASH-in-a-dish allowed for rapid and specific separation of co-cultured HepOrgs, KCs and HSCs, enabling cell type-specific metabolomics and stable-isotope fluxomics analysis. Using MASH-in-a-dish, we identified 19 MASH-associated, cell interaction-responsive metabolites and demonstrated that fatty acids, via the carnitine shuttle, drive KC itaconate production, which aggravated oxidative stress, steatosis, and cell damage in lipid-stressed HepOrgs. Inhibiting itaconate production by KC-specific Acod1 knockout in the MASH-in-a-dish system mitigated hepatocyte damage. Our results show that MASH-in-a-dish is a powerful in vitro platform to study cell-cell interactions in MASH pathogenesis and identify itaconate crosstalk between Kupffer cells and hepatocytes as a novel pathogenic mechanism and a potential therapeutic target in MASH.

biochemistry↗

bioRxiv2026

Hepatic stellate cells drive hypoxia-inducible factor (HIF)-dependent metabolic rewiring and proliferation in hepatocellular carcinoma cells

Hepatocellular carcinoma (HCC) is the most prevalent primary liver cancer in adults and represents the third most common cause of cancer-related deaths worldwide. With limited treatment options, HCC remains a major global health problem. The majority of HCC develops in a cirrhotic liver, where the tumor microenvironment (TME) is enriched in fibroblasts derived from activated hepatic stellate cells (HSCs). Cell-cell interactions in TME play an important role in metabolic reprogramming, which is increasingly recognized as a crucial driver in HCC proliferation. The tumor-promoting and metabolic effects of HSCs on HCC cells however remain incompletely characterized. Understanding how HSC-HCC interaction regulates HCC proliferation can lead to identification of novel therapeutic targets. Here, we established a Transwell co-culture model of HSCs and HCC cells to investigate how HSC-HCC interactions regulate HCC metabolism and proliferation. Using isotope tracing metabolomics, we show that co-culture with HSCs increases proliferation of HCC cells by rewiring glucose metabolism to increase glycolysis and de novo synthesis of nucleotides. Transcriptomic and immunofluorescence staining analyses revealed that HSCs upregulate hypoxia-inducible factor (HIF) signaling in HCC cells, which contributes to metabolic rewiring and HCC proliferation. We further identified H2O2 as a candidate crosstalk signal that could mediate HSC-dependent activation of HIF signaling in HCC cells. Together, these findings reveal a previously overlooked modulatory role of HSC-HCC interaction in metabolism-driven HCC progression. Targeting these pathways may represent a promising strategy to improve HCC treatment.

cancer biology↗

bioRxiv2019

Lecithin:Retinol Acyl Transferase (LRAT) inducesthe formation of lipid droplets

Lipid droplets are unique and nearly ubiquitous organelles that store neutral lipids in a hydrophobic core, surrounded by a monolayer of phospholipids. The primary neutral lipids are triacylglycerols and steryl esters. It is not known whether other classes of neutral lipids can form lipid droplets by themselves. Here we show that production of retinyl esters by lecithin:retinol acyl transferase (LRAT) in yeast cells, incapable of producing triacylglycerols and steryl esters, causes the formation of lipid droplets. By electron microscopy, these lipid droplets are morphologically indistinguishable from those in wild-type cells. In silico and in vitro experiments confirmed the propensity of retinyl esters to segregate from membranes and to form lipid droplets. The hydrophobic N-terminus of LRAT displays preferential interactions with retinyl esters in membranes and promotes the formation of large retinyl ester-containing lipid droplets in mammalian cells. Our combined data indicate that the molecular design of LRAT is optimally suited to allow the formation of characteristic large lipid droplets in retinyl ester-storing cells.

biochemistry↗

bioRxiv2018

LION/web: a web-based ontology enrichment tool for lipidomic data analysis

A major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the involvement of lipids in biological systems. We built a new lipid ontology (LION) that associates over 50,000 lipid species to biophysical, chemical and cell biological features. By making use of enrichment algorithms, we used LION to develop a web-based interface (LION/web, www.lipidontology.com) that allows identification of lipid-associated terms in lipidomes. LION/web was validated by analyzing a lipidomic dataset derived from well-characterized sub-cellular fractions of RAW 264.7 macrophages. Comparison of isolated plasma membranes with the microsomal fraction showed a significant enrichment of relevant LION-terms including plasma membrane, headgroup with negative charge, glycerophosphoserines, above average bilayer thickness, and below average lateral diffusion. A second validation was performed by analyzing the membrane fluidity of CHO cells incubated with arachidonic acid. An increase in membrane fluidity was observed both experimentally by using pyrene decanoic acid and by using LION/web, showing significant enrichment of terms associated with high membrane fluidity ('above average, 'very high and 'high lateral diffusion, and 'below average transition temperature). The results demonstrate the functionality of LION/web, which is freely accessible in a platform-independent way.

biochemistry↗