High-Throughput Metabolomic Profiling of Skin Lesions: Comparative Study of Cutaneous Squamous Cell Carcinoma, Basal Cell Carcinoma, and Normal Skin via E-Biopsy Sampling
Academic Background
Cutaneous Squamous Cell Carcinoma (CSCC) and Basal Cell Carcinoma (BCC) are among the most common types of skin cancer globally. Although the mortality rates of these cancers are relatively low, their incidence has been increasing year by year, significantly impacting patients’ quality of life and potentially leading to premature death. Traditional diagnostic methods rely on histopathological examination following tissue excision, which is not only time-consuming but may also cause additional complications due to surgical removal and subsequent treatments such as electrodesiccation and cautery. With the rising number of cases, existing diagnostic methods have become a bottleneck, necessitating faster and less invasive diagnostic approaches.
In recent years, advancements in molecular diagnostics have provided new possibilities for cancer diagnosis. Metabolomics, in particular, as a high-throughput molecular analysis method, can reveal the molecular characteristics of cancer by detecting small molecule metabolites in tissues. However, traditional metabolomic analysis often requires complex sample processing workflows, limiting its clinical application. Therefore, developing a rapid and efficient method for metabolite sampling and analysis has become a key focus of current research.
Source of the Paper
This paper was co-authored by Leetal Louie, Julia Wise, Ariel Berl, and others, with the research team hailing from multiple institutions, including the School of Mechanical Engineering at Tel Aviv University, the School of Computer Science at Reichman University, and the Department of Plastic Surgery at Meir Medical Center in Israel. The paper was published in 2025 in the journal Cellular and Molecular Bioengineering, titled “High-throughput metabolomic profiling of skin lesions: comparative study of cutaneous squamous cell carcinoma, basal cell carcinoma, and normal skin via e-biopsy sampling.”
Research Process
1. Sample Collection and e-Biopsy Technology
The research team developed a minimally invasive sampling technique based on electroporation, termed e-biopsy. This technology uses a pulsed electric field (PEF) to permeabilize cell membranes, thereby releasing intracellular metabolites, which are then collected into a syringe via vacuum suction. The e-biopsy technique not only reduces tissue damage but also enables rapid sample acquisition, making it suitable for clinical settings.
A total of 13 tissue samples, including CSCC, BCC, and healthy skin, were collected from 12 patients. Samples were extracted using the e-biopsy technique within 10–20 minutes after surgical excision and then frozen for subsequent analysis at the Beijing Genomics Institute.
2. High-Throughput Metabolomic Analysis
Metabolomic analysis was performed using Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS-MS). The study employed two types of chromatography columns (C18 and amide columns) and two modes (positive and negative ion modes) for separation and detection, resulting in a total of four analyses. Through this technology, the research team successfully identified 2,325 small molecule metabolites, 301 of which were identified with high confidence.
3. Statistical Data Analysis
The research team conducted power analysis using Python’s statistical library to calculate the effect size for each tissue type. Subsequently, differential expression of metabolites was screened using t-tests and fold change analysis. Overabundance analysis and volcano plot analysis were also performed to validate the differential expression of metabolites.
Key Findings
1. Comparison of CSCC and Healthy Skin
The study identified 22 metabolites with significant differential expression (p < 0.05) between CSCC and healthy skin, of which 14 were upregulated and 7 were downregulated in CSCC. For example, L-proline and creatine were significantly upregulated in CSCC, while L-arginine was significantly downregulated.
2. Comparison of BCC and Healthy Skin
In the comparison between BCC and healthy skin, 19 metabolites were identified with significant differential expression (p < 0.05), of which 8 were upregulated and 8 were downregulated in BCC. For instance, L-glutamine and uric acid were significantly upregulated in BCC, while 4-oxoproline was significantly downregulated.
3. Comparison of CSCC and BCC
In the comparison between CSCC and BCC, 4 metabolites were identified with significant differential expression (p < 0.05), of which 3 were upregulated in CSCC, including DL-arginine and xanthine.
Conclusion
This study is the first to conduct high-throughput metabolomic analysis of CSCC, BCC, and healthy skin using the e-biopsy technique, successfully identifying 34 significantly differentially expressed metabolites. The results indicate that the metabolomic profiles of CSCC and BCC differ significantly from healthy skin, particularly in the subclass of amino acids, peptides, and analogues, where metabolite expression levels are generally upregulated. These findings provide new possibilities for the molecular diagnosis of skin cancer and demonstrate the potential of e-biopsy technology in high-throughput metabolomic analysis.
Research Highlights
- Innovative Sampling Technology: The e-biopsy technique, as a minimally invasive sampling method, enables rapid tissue sample acquisition, significantly improving the efficiency of metabolomic analysis.
- High-Throughput Metabolomic Analysis: Using UPLC-MS-MS technology, the research team successfully identified a large number of metabolites, revealing the molecular characteristics of CSCC and BCC.
- Discovery of Differential Metabolites: The study identified multiple metabolites with significant differential expression in CSCC and BCC, providing new biomarkers for the diagnosis and treatment of skin cancer.
- Potential for Clinical Application: The combination of e-biopsy technology and high-throughput metabolomic analysis holds promise as an alternative diagnostic method for skin cancer, reducing reliance on traditional histopathological examination.
Additional Valuable Information
The research team plans to further validate the reliability of these differentially expressed metabolites in future studies and explore their application in tumor spatial heterogeneity. Additionally, the e-biopsy technique can be applied to other cancer types, such as breast and pancreatic cancers, offering new tools for molecular diagnosis and treatment.