Rare Esophageal Cancer Subtype Reveals Diagnostic and Therapeutic Signatures Through Multi-Omics Profiling

Esophageal basaloid squamous cell carcinoma, one of the rarest and most aggressive forms of esophageal cancer, has long evaded detailed molecular study. Now, an integrated analysis of its proteins, metabolites, and lipids has delivered the first comprehensive multi-omics portrait of this elusive tumor, revealing molecular signatures that could sharpen diagnosis and point toward new treatments. The findings are particularly significant because this subtype, which accounts for between 0.068 and 11.0 percent of all esophageal malignancies, has no standardized management guidelines and is frequently confused with the far more common conventional esophageal squamous cell carcinoma under the microscope.

The stakes are high. Esophageal cancer is the sixth leading cause of cancer-related death worldwide, with a five-year survival rate of only 15 to 20 percent. The two major subtypes are esophageal squamous cell carcinoma and adenocarcinoma, but basaloid squamous cell carcinoma stands apart as a poorly differentiated variant characterized by both basaloid and squamous features. It is thought to arise from totipotent basal cells of the esophageal epithelium and occurs predominantly in males. Because of its low incidence, clinicians have lacked subtype-specific molecular profiles that could differentiate it from conventional squamous cell carcinoma, restricting both mechanistic insight and therapeutic innovation.

To close this gap, researchers at Anyang Cancer Hospital performed integrated proteomic, metabolomic, and lipidomic profiling on 12 histopathologically confirmed basaloid squamous cell carcinoma tumors and paired adjacent normal tissues. The retrospective cohort was drawn from a database of 9,000 esophageal squamous or basaloid squamous carcinoma cases reviewed between 2010 and 2020, of which only 155, or 1.7 percent, were basaloid squamous cell carcinoma. From these, 12 cases with intact paired tumor and adjacent normal tissues were selected for analysis, including three female and nine male patients with a mean age of 65.5 years, ranging from 57 to 76. All patient data were pseudonymized, and the study was conducted in accordance with STROBE reporting guidelines.

The analytical strategy combined three complementary mass spectrometry platforms. For metabolites, the team applied targeted quantification covering 300 metabolites from diverse chemical classes, including bile acids, amino acids, fatty acids, carboxylic acids, and indoles, using ultra-performance liquid chromatography coupled to a triple quadrupole mass spectrometer in multiple reaction monitoring mode. Targeted metabolomics offers superior accuracy for endogenous metabolite quantification relative to untargeted approaches. For lipids, untargeted profiling on a Q Exactive system annotated and quantified 1,048 lipid species, including 866 glycerophospholipids, 107 sphingolipids, and 68 glycerolipids. For proteins, data-independent acquisition on a Q Exactive HF system reliably quantified 9,020 proteins at a false discovery rate below one percent. To identify protein alterations specific to the basaloid subtype, the researchers incorporated proteomic data from 46 conventional squamous cell carcinoma tumor samples processed with an identical analytical pipeline.

The proteomic results revealed clear separation between tumors and adjacent tissues in principal component analysis. Gene set enrichment analysis showed that proteins involved in bile acid metabolism, estrogen metabolism, fatty acid metabolism, and xenobiotic metabolism were down-regulated in the tumors, a pattern consistent with basal-like breast cancers, which lack estrogen and progesterone receptors. Conversely, proteins associated with DNA repair, E2F targets, the G2M checkpoint, and MYC targets were up-regulated. The high expression of MYC targets aligns with previous observations linking MYC activity to poor prognostic factors in basal-like carcinomas, suggesting that these targets are more specific to basal-like tumors than to conventional esophageal cancer.

Perhaps the most diagnostically valuable finding concerns the epidermal growth factor receptor family. Compared with adjacent tissues, basaloid tumors exhibited higher expression of EGFR and lower expression of HER2/ERBB2. In conventional squamous cell carcinoma, by contrast, there was no significant difference in EGFR expression between tumor and adjacent samples. These observations imply that patients with the basaloid subtype may derive greater benefit from EGFR-targeted therapies. The team also identified a panel of esophageal tissue-specific proteins, including DSC3, SERPINB5, ERO1A, GLTP, IL18, and LAD1, that were markedly lower in basaloid tumors than in conventional squamous cell carcinoma. Since DSC3, SERPINB5, IL18, and LAD1 are preferentially expressed in squamous cell carcinoma, these proteins constitute conventional-squamous-enriched signatures that could serve as markers for differential diagnosis.

Beyond receptor profiling, the analysis uncovered ten proteins up-regulated specifically in the basaloid subtype compared with both adjacent and conventional tumor tissues, including GNG10, GRB7, LZTS1, MOXD1, MTA2, NOP2, TAF9B, TFAP2A, TFAP4, and WDR36. These elevated basal and stem-like markers contrasted with the reduced expression of squamous differentiation markers such as ERO1A, GLTP, IL18, LGALS7, IL1RN, SERPINB3, FABP5, S100A9, and SERPINB1. Among 283 basal-like cell specific proteins, 79 were quantified in the basaloid tissue samples. This combination of accumulated stem-like features and lost differentiation markers provides a molecular explanation for the poorly differentiated morphology that defines this subtype and offers a set of unreported molecules highly accumulated in the tumor.

The metabolomic and lipidomic layers revealed profound metabolic reprogramming during tumor progression. Targeted quantification measured 157 metabolites, and supervised modeling showed distinct separation between tumors and adjacent tissues. Twenty-six metabolites were up-regulated and 19 down-regulated, with the up-regulated molecules predominantly amino acids and the down-regulated molecules including carnitines and organic acids. Five metabolic pathways were significantly enriched, including D-glutamine and D-glutamate metabolism, alanine, aspartate and glutamate metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, glycine, serine and threonine metabolism, and ubiquinone and other terpenoid-quinone biosynthesis. Lipid profiling identified 132 up-regulated and 99 down-regulated lipid species, with most up-regulated lipids belonging to the glycerophosphocholine, glycerophosphoglycerol, and glycerophosphoinositol classes, while most down-regulated lipids belonged to the glycerophosphoserine class. These glycerophospholipid alterations are closely associated with cell membrane integrity, signal transduction, and malignant progression, and may contribute to the rapid proliferation and aggressive phenotype of the tumor.

Integrating the three omics layers through KEGG pathway enrichment exposed a coordinated disruption of glutamine-glutamate metabolism that ran through the proteome, metabolome, and lipidome. The abundance of glutamine was lower in the tumors, accompanied by down-regulation of GLUL, the enzyme that catalyzes the conversion of glutamate to glutamine. Simultaneously, up-regulation of PPAT, GFPT2, and CAD enhanced glutamine consumption toward 5-phosphoribosylamine, D-glucosamine 6-phosphate, and carbamoyl phosphate, respectively. These changes led to increased glutamate levels, which could be further metabolized into alpha-ketoglutarate and pyrroline-5-carboxylate to support tumor growth through the tricarboxylic acid cycle and proline synthesis. Up-regulation of PYCR2, which catalyzes the conversion of glutamate to proline, resulted in elevated proline abundance, potentially promoting tumor progression. This glutamine-addiction phenomenon, in which tumor cells depend on glutamine for survival and proliferation, represents a subtype-specific molecular feature linked to basaloid carcinoma progression and nominates several enzymes as candidate therapeutic targets.

The authors are careful to frame these findings as predictive rather than proven. No in vitro or in vivo functional assays were performed to validate the proposed mechanisms, and the quantification of key enzymes involved in glutamine conversion, such as GLU1 and GLU2, was not achieved, limiting full mechanistic interpretation. The sample size was small, a constraint imposed by the rarity of the disease, and most tissues were formalin-fixed paraffin-embedded rather than fresh-frozen, which may have affected the accuracy of metabolomic and lipidomic quantification. Future studies with larger cohorts and functional experiments in cellular or animal models are needed to validate the molecular mechanisms and therapeutic potential of the identified targets. Even so, this first comprehensive multi-omics investigation of the basaloid subtype provides quantitative data on more than 9,000 proteins, 157 metabolites, and 1,048 lipid species, advancing understanding of a highly aggressive cancer that has remained in the molecular shadows for decades.

Subject of Research: Multi-omics profiling of esophagus basaloid squamous cell carcinoma reveals potential signatures for diagnosis and therapeutics

Article Title: Multi-omics profiling of esophagus basaloid squamous cell carcinoma reveals potential signatures for diagnosis and therapeutics

Article References: Li, J., Xu, H., Tan, Y., Yang, H., Dai, N., Xu, Y., Miao, L., Lei, R., Yuan, Y., Hou, G., Liu, S., & Zhou, F. (2026). Multi-omics profiling of esophagus basaloid squamous cell carcinoma reveals potential signatures for diagnosis and therapeutics. Heliyon, 12(16), Article e45584. https://doi.org/10.1016/j.heliyon.2026.e45584

Image Credits: AI Generated

DOI: 10.1016/j.heliyon.2026.e45584

Keywords: Multi-omics, profiling, esophagus, basaloid, squamous, cell, carcinoma, reveals, potential, signatures, diagnosis, therapeutics