High-Throughput Metabolomic Profiling of Skin Lesions: Comparative Study of Cutaneous Squamous Cell Carcinoma, Basal Cell Carcinoma, and Normal Skin Via e-Biopsy Sampling

Abstract

Purpose: Rising rates of cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) make standard histopathology diagnostic methods a bottleneck. Using tissue molecular information for diagnostics offers a promising alternative. Faster specimen collection and high-throughput molecular identification can improve the processing of the increasing number of tumors. This study aims (i) to confirm the ability of e-biopsy technique to harvest metabolites, (ii) to obtain high-resolution metabolomic profiles of cSCC, BCC, and healthy skin tissues, and (iii) to perform a comparative analysis of the collected profiles.

Methods: Tumor specimens were collected with electroporation-based biopsy (e-biopsy), a minimally invasive sampling collection tool, from 13 tissue samples (cSCC, BCC, and healthy skin) from 12 patients. Ultra performance liquid chromatography and tandem mass spectrometry (UPLC-MS-MS) was used for molecular identification and quantification of resulting metabolomic profiles.

Results: Here we report measurements of 2325 small metabolites identified (301 with high confidence) in 13 tissue samples from 12 patients. Comparative analysis identified 34 significantly (p < 0.05) differentially expressed high-confidence metabolites. Generally, we observed a greater number of metabolites with higher expression, in cSCC and in BCC compared to healthy tissues, belonging to the subclass amino acids, peptides, and analogues.

Conclusions: These findings confirm the ability of e-biopsy technique to obtain high-resolution metabolomic profiles suitable to downstream bioinformatics analysis. This highlights the potential of e-biopsy coupled with UPLC-MS-MS for rapid, high-throughput metabolomic profiling in skin cancers and supports its utility as a promising diagnostic alternative to standard histopathology.

Supplementary information: The online version contains supplementary material available at 10.1007/s12195-025-00846-1.

Keywords: Basal cell carcinoma; Cutaneous squamous cell carcinoma; E-Biopsy; Electroporation-based biopsy; High-throughput metabolomics; Metabolomic profiles.

Fig. 1.

Study workflow: A pulsed electric field (PEF) is delivered to a tissue sample for extraction of water-soluble molecules and sample extracts are stored in 1.5 mL tubes until ready for UPLC-MS-MS analysis. Data from UPLC-MS-MS is used for differential expression analysis

Fig. 2.

a–l Overabundance plots comparing the distribution of metabolites differential expression (both over- and under-expression) p-values between control (normal skin tissue), cSCC, BCC tumor samples. Results from 2 chromatography column types and mode is shown by the background color. A total of 13 samples, and 301 metabolites extracted by e-biopsy were analyzed. a–d cSCC vs. Healthy, e–h BCC vs. healthy and i–l cSCC vs. BCC

Fig. 3.

a–l Volcano plots showing the fold-change difference of metabolite intensities. a–d cSCC vs. Healthy. b BCC vs. Healthy. c cSCC vs. BCC. Numbered datapoints correspond to metabolite names found in the table below the plots. Fold-change and p-value data for the metabolites identified in the table can be found in Tables 2, S5–S7. High-resolution plots can be found in Figs. S1–S12