Abstract
Nicotinamide adenine dinucleotide (NAD) is synthesized through both amidated salvage and deamidated pathways. Although NAD-producing enzymes are often overexpressed in cancer cells to meet the high metabolic demands of rapid proliferation and are considered oncogenic, we report that physiological levels of nicotinic acid phosphoribosyl transferase (NAPRT), the first enzyme in the Preiss-Handler arm of the deamidated pathways, suppress tumorigenesis. We show that NAPRT is enriched in gut epithelial cells, where it sustains the NAD pool for an efficient response to stress-induced acute NAD depletion. Consequently, NAPRT deficiency impairs the activity of poly-(ADP-ribose) polymerases and DNA repair, sensitizes mice to chemical-induced colitis and tumorigenesis, as well as to age-associated spontaneous tumor development. Moreover, low NAPRT expression correlates with poor prognosis in several human cancer types. Thus, homeostatic levels of deamidated NAD biosynthesis contribute to tumor suppression, and boosting this pathway may offer a strategy for cancer prevention.
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Data availability
The RNA-seq and scRNA-seq datasets of this study have been deposited to Gene Expression Omnibus under the following accession numbers: RNA-seq dataset of the AOM experiment: GSE271834 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE271834]RNA-seq dataset of the DSS-colitis experiment: GSE271250 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE271250]. scRNA-seq datasets of colon tissues: GSE271836 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE271836]
scRNA-seq datasets of small intestinal tissues: GSE261216 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= GSE261216], Metabolomics data of this study have been deposited to massive.ucsd.edu with the accession number MSV000100103, https://doi.org/10.25345/C56M33H4M. The detailed data of 277 identified or annotated metabolites are provided in Supplementary Data 1. LC-MS data for targeted measurement of mouse tissue NAD metabolites have been deposited to massive.ucsd.edu with the accession number MSV000100196, https://doi.org/10.25345/C5639KJ8W. The representative spectral peaks are provided in Supplementary Data 8. LC-MS parameters and representative spectral peaks from targeted measurement of NUA in mouse kidney are provided in Supplementary Data 9. The LC-MS raw data files for NAD metabolites in mouse plasma have been uploaded to metabolomicsworkbench.org under tracking ID 6868 (NA and NAM) and 6875 (NAR), https://doi.org/10.21228/M8BN9Z. The LC-MS data and representative spectral peaks are provided in Supplementary Data 10. Public datasets used in this study are: GSE111889. GSE201348. HTAN VUMC [https://cellxgene.cziscience.com/collections/a48f5033-3438-4550-8574-cdff3263fdfd]. TCGA PanCancer datasets: https://www.cbioportal.org/. Source data containing the exact p-values for all statistical tests are provided with this paper.
Code availability
Scripts used for scRNA-seq analyses in this study are available with no restriction at github: https:github.com/JohnXu24/NAPRTKO_scRNA. Published software packages and pipelines are used for RNA-seq and scRNA-seq analyses. Detailed description of these data analyses is included in Methods.
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Acknowledgements
We thank NIEHS Comparative Medicine Branch for support to animal experiments; NIEHS Fluorescence Microscopy and Imaging Center for help with immunofluorescent analyses; NIEHS Epigenomics Core for bulk and single cell RNA sequencing; NIEHS Histology Core for tissue processing and staining; NIEHS Pathology Core laboratory for histopathological evaluation of DSS-colitis and AOM/DSS-induced CRC; NIEHS Flow Cytometry Center for assistance with FACS analysis; and the University of South Alabama Mass Spectrometry Core Facility for measurement of NUA. This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH) to Xiaoling Li (Z01 ES102205). X. W. was supported in part by the NIH Office of Dietary Supplements (ODS) Scholars Award (TAS # 075-24-0846). Xiaojing Liu was supported by the National Institutes of Health Grant (GM150985). Joshua Hartsell (J. H.) was partially supported by a National Science Foundation STEM training grant (1643814). The contributions of the NIH authors were made as part of their official duties as NIH federal employees, are in compliance with agency policy requirements, and are considered Works of the United States Government. However, the findings and conclusions presented in this paper are those of the authors and do not necessarily reflect the views of the NIH or the U.S. Department of Health and Human Services.
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X. W. designed and performed experiments, analyzed data and wrote the manuscript. J. G. W performed LC-MS analysis of NAD metabolites in tissues. A. G. generated NAPRT KO mice. H. L., and Xiaojiang Xu analyzed bulk and single cell RNAseq data. J. H., J. S., and X. Liu performed LC-MS analysis of NAD metabolites in mouse plasma using LC-MS. R. M., C. D., M. J., and P. P. assisted with experiments. Y. F. generated the targeting plasmid for NAPRT inactivation in CRC119 cells. Xin Xu performed scRNAseq sequencing. Z. Z. and H. Y. assisted with organoid culture experiments. H. W. and A. K. J. performed metabolomic analysis. A. R. P. performed pathological evaluation of tumors in aged mice. M. E. M performed LC-MS analysis of NUA. J.-L. L. coordinated data analysis of scRNA-seq and RNA-seq and analyzed the expression of NAD metabolic enzymes in DC TCGA datasets and polyps datasets. I. S. designed and performed experiments, guided, designed, and coordinated the study, analyzed data and wrote the manuscript. X. Li guided, designed, and coordinated the study, analyzed data, and wrote the manuscript. All authors critically reviewed the manuscript.
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Wu, X., Williams, J.G., Liang, H. et al. NAPRT-mediated deamidated NAD biosynthesis enhances colon tissue resiliency and suppresses tumorigenesis. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68998-w
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DOI: https://doi.org/10.1038/s41467-026-68998-w
