Proteome sampling with e-biopsy enables differentiation between cutaneous squamous cell carcinoma and basal cell carcinoma

Abstract

Clinical misclassification between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans and carries risks of potential for recurrence, metastases morbidity and mortality. We report the development of a novel tissue sampling approach with molecular biopsy using electroporation. The methods, coined e-biopsy, enables non-thermal permeabilization of cells in the skin for efficient vacuum-assistant extraction of informative biomolecules for rapid diagnosis. We used e-biopsy for ex vivo proteome extraction from 3 locations per patient in 21 cSCC and 21 BCC pathologically validated human tissue samples. The total 126 extracted proteomes were profiled using LC/MS/MS. The obtained mass spectra presented significantly different proteome profiles for cSCC and BCC with several hundreds of proteins significantly differentially expressed in each tumor in comparison to the other. Notably, 17 proteins were uniquely expressed in BCC and 7 were uniquely expressed in cSCC patients. Statistical analysis of differentially expressed proteins found 31 cellular processes, 23 cellular functions and 10 cellular components significantly different between cSCC and BCC. Machine Learning classification models constructed on the sampled proteomes enabled the separation of cSCC patients from BCC with average cross-validation accuracy of 81%, cSCC prediction positive predictive value (PPV) of 78.7% and sensitivity of 92.3%, which is comparable to initial diagnostics in a clinical setup. Finally, the protein-protein interaction analysis of the 11 most informative proteins, derived from Machine Learning framework, enabled detection of a novel protein-protein interaction network valuable for further understanding of skin tumors. Our results provide evidence that the e-biopsy approach could potentially be used as a tool to support cutaneous tumors classification with rapid molecular profiling.

High‐throughput lipidomic profiles sampled with electroporation‐based biopsy differentiate healthy skin, cutaneous squamous cell carcinoma, and basal cell carcinoma

“…E-biopsy was performed with a custom-made high-voltage pulsed electric field generator under conditions previously described for protein extraction from cSCC and BCC. 16 The liquids sampled were immediately transferred to 1.5 mL tubes with 100 µL double distilled water and stored at −20 • C until shipped to Beijing Genomics Institute for analysis.…”

“…We have entered the era of personalized medicine where biological profiling provides useful information in cancer research and treatment 13–15 . Previously, high‐throughput analyses of genes, proteins, and metabolites have been reported for cSCC and BCC 16–20 . Lipids profiles, however, have mostly been reported for BCC 21–23 using low‐throughput methods and serum samples with the exception of one high‐throughput cSCC study that included 70 lipids among metabolites 24 .…”

“…Here we perform a comparative analysis of the first high‐throughput lipidomic profiling of cSCC, BCC, and healthy skin tissue using e‐biopsy. These profiles were collected with the e‐biopsy approach, thus adding to previous e‐biopsy enabled profiling in transcriptomics, proteomics, and metabolomics 16,25–27 …”

“… 13 , 14 , 15 Previously, high‐throughput analyses of genes, proteins, and metabolites have been reported for cSCC and BCC. 16 , 17 , 18 , 19 , 20 Lipids profiles, however, have mostly been reported for BCC 21 , 22 , 23 using low‐throughput methods and serum samples with the exception of one high‐throughput cSCC study that included 70 lipids among metabolites. 24 Beyond medicine, molecular profiling plays an important role in other aspects of life such use in agriculture food and safety, forensic science, and environmental monitoring.…”

Comparison of lipidomic profiles sampled with electroporation-based biopsy from healthy skin, squamous cell carcinoma, and basal cell carcinoma

“…Here we perform a comparative analysis of the first high-throughput lipidomic profiling of cSCC, BCC, and healthy skin tissue using e-biopsy. These profiles were collected with the e-biopsy approach, thus adding to previous e-biopsy enabled profiling in transcriptomics, proteomics, and metabolomics [16,[25][26][27].…”