Ryan, E. M. | Search bioRxiv

bioRxiv2026

Loss of Acid Ceramidase in Myeloid Cells Protects from Chronic Colitis in IL10-Deficent Mice

Background & AimsPatients with inflammatory bowel disease (IBD) exhibit elevated expression of acid ceramidase (AC), a sphingolipid metabolism enzyme. Recent studies have shown that myeloid cells contribute to the elevated expression of AC, such that the conditional loss of AC is protective in IBD. MethodsBone marrow derived macrophages (BMDMs) and neutrophils (BMDNs) were utilized to assess the role of AC in immune cell mediated inflammation. We then crossed conditional ASAH1 LyzMCRE knockout mice with IL10 knockout mice to determine the role of AC in a model of spontaneous colitis. Colon tissues were analyzed for lipids, mRNA, and protein. We performed flow cytometry to determine the role of myeloid AC in recruiting effector T cells in disease. ResultsIn this study, we found that loss of AC impaired secretory and migratory functions in BMDMs, but not BMDNs. Further, the conditional loss of AC protected from spontaneous, chronic colitis. Loss of AC reduced inflammatory markers, increased colon ceramides, and reduced the inflammatory metabolite sphingosine-1-phosphate (S1P). Recruitment of immune cells into intestinal tissue was significantly impaired, namely neutrophils and effector Th1/Th17 T cells. ConclusionsLoss of AC reduced inflammation and impaired immune cell recruitment in chronic colitis. Targeting AC may serve as a promising therapeutic potential for patients with IBD by modulating immune cell sphingolipid metabolism. WHAT YOU NEED TO KNOWO_ST_ABSBACKGROUND AND CONTEXTC_ST_ABSAcid ceramidase expression is increased in immune cells in patients with inflammatory bowel disease, specifically in macrophages. NEW FINDINGSWe determined that loss of acid ceramidase (AC) in macrophages, but not neutrophils, impairs inflammatory functions in vitro, and that loss of AC in myeloid cells partially protects from spontaneous colitis in vivo by reducing immune cell recruitment into intestinal tissue. LIMITATIONSThe IL10 knockout model of colitis exhibits highly variable onset and severity of disease, which may be challenging to distinguish the extent of protection. CLINICAL RESEARCH RELEVENCEThis study identifies AC as a promising therapeutic target for treating inflammatory bowel disease. BASIC RESEARCH RELEVENCEThis study contributes to our understanding of the role that AC plays in inflammation within immune cells, specifically myeloid cells. Additionally, this study underscores the role of immune cell sphingolipid metabolism in inflammatory bowel disease. LAY SUMMARYLoss of acid ceramidase in myeloid cells protects from chronic colitis by decreasing inflammation, altering immune cell function, and impairing the recruitment of effector immune cells to the colon.

physiology↗

bioRxiv2017

An Oxidative Pathway of Deoxyribose Catabolism

Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-D-ribose and 2-deoxy-D-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl-CoA and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro. In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either non-specific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism.\n\nImportanceDeoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not encode any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of human metabolism and is present in urine. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.

microbiology↗