SERPINB3 induces the basal-like/squamous subtype and enhances disease progression in pancreatic cancer

Abstract

Pancreatic cancer is a heterogeneous disease with distinct subtypes. Here, we investigated candidate driver genes of the highly aggressive basal-like/squamous molecular subtype of pancreatic ductal adenocarcinoma (PDAC). Integrative transcriptomic analyses identified the upregulated serine/cysteine protease inhibitor, SERPINB3 (squamous cell carcinoma antigen 1, SCCA1) in basal-like/squamous PDAC using discovery and validation approaches. Upregulation of SERPINB3 associated with decreased patient survival and a transcriptome profile indicative of the basal-like/squamous subtype. In human PDAC cell lines, SERPINB3 transgene expression enhanced their invasion capability. Moreover, upregulated expression of SERPINB3 in AsPC-1 cells resulted in enhanced lung metastasis in an orthotopic xenograft model. Molecular analysis of the primary tumor xenografts indicated activation of pathways related to metastasis, increased oxidative damage, and angiogenesis when SERPINB3 was upregulated. Furthermore, metabolomic analysis, using patient cohorts and PDAC cell lines showed a distinct metabolic pattern closely associated with both SERPINB3 and the basal-like/squamous subtype, which included upregulation of carnitine/acylcarnitine, amino acid, glutathione, and purine metabolic pathways, and glycolysis. Further RNA-seq and metabolomic analyses indicated that SERPINB3 may potentially induce the basal-like/squamous subtype and metabolic reprogramming through MYC activation. Taken together, our findings identified SERPINB3 as a candidate marker gene for the basal-like/squamous subtype, which may contribute to the disease aggressiveness in this subtype of PDAC.

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

“…Applying pathway enrichment analysis using MetaboAnalyst 5.0, we found that LMO3-overexpressing Panc 10.05 cells exhibited heightened lipogenesis and diminished amino acid metabolism (Figure 4E and 4F). Our findings align with previous research from our group, which showed that the basal-like/squamous subtype promotes amino acid metabolism whereas classical/progenitor tumors favor increased lipogenesis 17,23 . Notably, we observed analogous metabolic adaptation patterns in basal-like/squamous PDAC and LMO3-low PDAC cells, potentially contributing to disease progression.…”

“…Comparative analysis between the basal-like/squamous and classical/progenitor subtypes was performed using Partek Genomics Suite 7.0 (Partek Inc., Chesterfield, MO). For the integrated transcriptomic and metabolomic investigations, we utilized RNA sequencing data from patient PDAC tumors within the NCI-UMD-German cohort (GSE224564) 17 .…”

“…Signal amplification was achieved using the Dako envision+ system-HRP labeled polymer anti-rabbit antibody (Agilent Technologies, Santa Clara, CA), followed by color development with 3,3'-diaminobenzidine (DAB, Agilent Technologies). Immunohistochemistry (IHC) was assessed by assigning intensity and prevalence scores 17,22 .…”

“…We next investigated whether LMO3 expression would mitigate the characteristics associated with the basal-like/squamous subtype, thereby reducing disease aggressiveness. In a prior study, we characterized the molecular subtypes of 175 patients in our NCI-UMD-German cohort (unclassified; n = 32, classical/progenitor; n = 95, basal-like/squamous; n = 48) 17 . We showed that pathways related to cellular movement exhibited heightened activity in the basallike/squamous subtype compared to the classical/progenitor subtype.…”

“…However, the intricate relationship between metabolic adaptations and gene expression profiles in PDAC remains insufficiently explored, often constrained by small sample sizes. Building on our previous identification of SERPINB3 as an oncogenic driver of the basal-like/squamous subtype 17 , this study investigated the interplay between gene expression and metabolic reprogramming in the development of the classical/progenitor subtype in PDAC. Our results highlight the role of LIM Domain Only 3 (LMO3) upregulation in shaping the metabolic landscape of the classical/progenitor subtype in PDAC.…”