Excision tissue biopsy, while central to cancer treatment and precision medicine, presents risks to the patient and does not provide a sufficiently broad and faithful representation of the heterogeneity of solid tumors. Here we introduce e-biopsy—a novel concept for molecular profiling of solid tumors using molecular sampling with electroporation. As e-biopsy provides access to the molecular composition of a solid tumor by permeabilization of the cell membrane, it facilitates tumor diagnostics without tissue resection. Furthermore, thanks to its non tissue destructive characteristics, e-biopsy enables probing the solid tumor multiple times in several distinct locations in the same procedure, thereby enabling the spatial profiling of tumor molecular heterogeneity.We demonstrate e-biopsy in vivo, using the 4T1 breast cancer model in mice to assess its performance, as well as the inferred spatial differential protein expression. In particular, we show that proteomic profiles obtained via e-biopsy in vivo distinguish the tumors from healthy breast tissue and reflect spatial tumor differential protein expression. E-biopsy provides a completely new molecular sampling modality for solid tumors molecular cartography, providing information that potentially enables more rapid and sensitive detection at lesser risk, as well as more precise personalized medicine.

A major concern in tissue biopsies with a needle is missing the most lethal clone of a tumor, leading to a false negative result. This concern is well justified, since needle-based biopsies gather tissue information limited to needle size. In this work, we show that molecular harvesting with electroporation, e-biopsy, could increase the sampled tissue volume in comparison to tissue sampling by a needle alone. Suggested by numerical models of electric fields distribution, the increased sampled volume is achieved by electroporation-driven permeabilization of cellular membranes in the tissue around the sampling needle. We show that proteomic profiles, sampled by e-biopsy from the brain tissue, ex vivo, at 0.5mm distance outside the visible margins of mice brain melanoma metastasis, have protein patterns similar to melanoma tumor center and different from the healthy brain tissue. In addition, we show that e-biopsy probed proteome signature differentiates between melanoma tumor center and healthy brain in mice. This study suggests that e-biopsy could provide a novel tool for a minimally invasive sampling of molecules in tissue in larger volumes than achieved with traditional needle biopsies.

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.

No abstract

Background. Excision tissue biopsy, while central to cancer treatment and precision medicine, presents risks to the patient and does not provide a sufficiently broad and faithful representation of the heterogeneity of sampled solid tumors. Methods. Here we introduce e-biopsy – a novel concept for molecular profiling of solid tumors using molecular extraction with electroporation. As e-biopsy provides access to the molecular composition of a solid tumor, it potentially facilitates tumor diagnostics without tissue resection. Furthermore, thanks to its less invasive characteristics, e-biopsy enables probing the solid tumor multiple times in several distinct locations in the same procedure, thereby enabling the spatial profiling of tumor molecular heterogeneity.Results. We demonstrate e-biopsy in vivo, using the 4T1 breast cancer model in mice to assess its performance, as well as the inferred spatial differential protein expression. In particular, we show that proteomic profiles obtained via e-biopsy in vivo distinguish the tumors from healthy tissue and reflect spatial tumor differential protein expression.Conclusions. E-biopsy provides a completely new molecular cartography modality for solid tumors, providing information that potentially enables more sensitive detection, at lesser risk, as well as more precise personalized medicine.