Integrated spatial transcriptomics and lipidomics of precursor lesions of pancreatic cancer identifies enrichment of long chain sulfatide biosynthesis as an early metabolic alteration

Sans, M.; Chen, Y.; Thege, F. I.; Dou, R.; Min, J.; Yip-Schneider, M.; Zhang, J.; Wu, R.; Irajizad, E.; Makino, Y.; Rajapakshe, K. I.; Hurd, M. W.; Leon, R. A.; Vykoukal, J.; Dennison, J. B.; Do, K.-a.; Wolff, R. A.; Guerrero, P. A.; Kim, M. P.; Schmidt, C. M.; Maitra, A.; Hanash, S.; Fahrmann, J. F.

doi:10.1101/2023.08.14.553002

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bioRxiv · 10.1101/2023.08.14.553002

Integrated spatial transcriptomics and lipidomics of precursor lesions of pancreatic cancer identifies enrichment of long chain sulfatide biosynthesis as an early metabolic alteration

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Abstract

BackgroundThe development of diverse spatial profiling technologies has provided an unprecedented insight into molecular mechanisms driving cancer pathogenesis. Here, we conducted the first integrated cross-species assessment of spatial transcriptomics and spatial metabolomics alterations associated with progression of intraductal papillary mucinous neoplasms (IPMN), bona fide cystic precursors of pancreatic ductal adenocarcinoma (PDAC). MethodsMatrix Assisted Laster Desorption/Ionization (MALDI) mass spectrometry (MS)-based spatial imaging and Visium spatial transcriptomics (ST) (10X Genomics) was performed on human resected IPMN tissues (N= 23) as well as pancreata from a mutant Kras;Gnas mouse model of IPMN. Findings were further compared with lipidomic analyses of cystic fluid from 89 patients with histologically confirmed IPMNs, as well as single-cell and bulk transcriptomic data of PDAC and normal tissues. ResultsMALDI-MS analyses of IPMN tissues revealed long-chain hydroxylated sulfatides, particularly the C24:0(OH) and C24:1(OH) species, to be selectively enriched in the IPMN and PDAC neoplastic epithelium. Integrated ST analyses confirmed that the cognate transcripts engaged in sulfatide biosynthesis, including UGT8, Gal3St1, and FA2H, were co-localized with areas of sulfatide enrichment. Lipidomic analyses of cystic fluid identified several sulfatide species, including the C24:0(OH) and C24:1(OH) species, to be significantly elevated in patients with IPMN/PDAC compared to those with low-grade IPMN. Targeting of sulfatide metabolism via the selective galactosylceramide synthase inhibitor, UGT8-IN-1, resulted in ceramide-induced lethal mitophagy and subsequent cancer cell death in vitro, and attenuated tumor growth of mutant Kras;Gnas allografts. Transcript levels of UGT8 and FA2H were also selectively enriched in PDAC transcriptomic datasets compared to non-cancerous areas, and elevated tumoral UGT8 was prognostic for poor overall survival. ConclusionEnhanced sulfatide metabolism is an early metabolic alteration in cystic pre-cancerous lesions of the pancreas that persists through invasive neoplasia. Targeting sulfatide biosynthesis might represent an actionable vulnerability for cancer interception.

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Sans, M., Chen, Y., Thege, F. I., Dou, R., Min, J., Yip-Schneider, M., Zhang, J., Wu, R., Irajizad, E., Makino, Y., Rajapakshe, K. I., Hurd, M. W., Leon, R. A., Vykoukal, J., Dennison, J. B., Do, K.-a., Wolff, R. A., Guerrero, P. A., Kim, M. P., Schmidt, C. M., Maitra, A., Hanash, S., Fahrmann, J. F.. 2023-08-15. Integrated spatial transcriptomics and lipidomics of precursor lesions of pancreatic cancer identifies enrichment of long chain sulfatide biosynthesis as an early metabolic alteration. https://doi.org/10.1101/2023.08.14.553002

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