LMO3 is a suppressor of the basal-like/squamous PDAC subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism

Abstract

Pancreatic ductal adenocarcinoma (PDAC) encompasses diverse molecular subtypes, including the classical/progenitor and basal-like/squamous subtypes, each exhibiting distinct characteristics, with the latter known for its aggressiveness. We employed an integrative approach combining transcriptomic and metabolomic analyses to pinpoint potential genes contributing to the basal-like/squamous subtype differentiation. Applying this approach to our NCI-UMD-German and a validation cohort, we identified LIM Domain Only 3 (LMO3), a transcription co-factor, as a candidate suppressor of the basal-like/squamous subtype. Reduced LMO3 expression was significantly associated with higher pathological grade, advanced disease stage, induction of the basal-like/squamous subtype, and decreased survival among PDAC patients.In vitroexperiments demonstrated thatLMO3transgene expression inhibited PDAC cell proliferation and migration/invasion, concurrently downregulating the basal-like/squamous gene signature. Metabolomic analysis of patient tumors and PDAC cells revealed a metabolic program linked to elevated LMO3 expression and the classical/progenitor subtype, characterized by enhanced lipogenesis and suppressed amino acid metabolism. Notably, glycerol 3-phosphate (G3P) levels positively correlated with LMO3 expression and associated with improved patient survival. Furthermore, glycerol-3-phosphate dehydrogenase 1 (GPD1), a crucial enzyme in G3P synthesis, showed upregulation in LMO3-high and classical/progenitor PDAC, suggesting its potential role in mitigating disease aggressiveness. Collectively, our findings suggest that heightened LMO3 expression reduces transcriptomic and metabolomic characteristics indicative of basal-like/squamous tumors with decreased disease aggressiveness in PDAC patients. The observations describe LMO3 as a candidate for diagnostic and therapeutic targeting in PDAC.Graphical abstractHighlightsLMO3 is downregulated in basal-like/squamous PDAC while its expression is maintained in the classical/progenitor PDAC subtypeUpregulated LMO3 expression correlates with improved PDAC survival and reduced proliferation and migration/invasion in PDAC cellsUpregulated LMO3 suppresses basal-like/squamous differentiation and induces a unique metabolic signature characterized by elevated lipogenesis and diminished amino acid metabolism, resembling the classical/progenitor PDAC subtypeEnhanced LMO3 expression associates with elevated glycerol 3-phosphate levels in PDAC, correlating with improved patient survival in PDAC

ADRA2A promotes the classical/progenitor subtype and reduces disease aggressiveness of pancreatic cancer

“…Applying pathway enrichment analysis using MetaboAnalyst 5.0 (25), we noticed that ADRA2A-overexpressing Panc 10.05 cells exhibited diminished amino acid metabolism (Figure 4D). Our findings corroborate earlier research conducted by our group, indicating that the basallike/squamous subtype fosters amino acid metabolism, whereas the classical/progenitor subtype suppresses it (17,23,24). Additionally, ADRA2A-high tumors and ADRA2A-overexpressing Panc 10.05 cells showed the downregulation of carnitine/acylcarnitines.…”

“…Recognizing the biological similarity, we grouped unclassified and classical/progenitor subtypes into a unified group termed "unified classical/progenitor subtype" (23). LIM Domain Only 3 (LMO3) downregulated both basal-like genes and classical genes developed by Moffitt et al (4) to induce the unified classical/progenitor subtype (23). However, the current study revealed that ADRA2A upregulates the classical genes while downregulating the basal-like genes to promote classical/progenitor subtype differentiation.…”

“…The basal-like/squamous subtype upregulated amino acid and carnitine/acylcarnitine metabolism compared to the classical/progenitor subtype, while unclassified subtype upregulated lipogenesis. Recognizing the biological similarity, we grouped unclassified and classical/progenitor subtypes into a unified group termed "unified classical/progenitor subtype" (23). LIM Domain Only 3 (LMO3) downregulated both basal-like genes and classical genes developed by Moffitt et al (4) to induce the unified classical/progenitor subtype (23).…”

“…Metabolon's untargeted metabolic platform employs two separate ultra-high performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) injections and one gas chromatography/mass spectrometry injection for each sample, enabling the measurement of all metabolites. The resulting dataset from the NCI-UMD-German cohort (n = 50) was normalized across samples before delivery (23,24), following Metabolon's established protocol. The normalized relative abundance levels for each metabolite were collated and utilized for subsequent data analysis.…”

“…Expanding our investigation to include metabolome analysis, we employed transcriptome and metabolome analyses on a cohort of 50 patients from our NCI-UMD-German cohort (23). We identified 7 significantly upregulated and 76 downregulated metabolites in ADRA2A-high tumors when compared to ADRA2A-low tumors (Figure 4A).…”