Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy
Clinical misdiagnosis between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans. We report a tissue sampling approach with molecular biopsy using electroporation. This method, coined electroporation-based biopsy (e-biopsy), enables nondestructive nonther...
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Elsevier
2024-11-01
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| Series: | JID Innovations |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667026724000511 |
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| author | Edward Vitkin Julia Wise Ariel Berl Ofir Shir-az Batel Gabay Amrita Singh Vladimir Kravtsov Zohar Yakhini Avshalom Shalom Alexander Golberg |
| author_facet | Edward Vitkin Julia Wise Ariel Berl Ofir Shir-az Batel Gabay Amrita Singh Vladimir Kravtsov Zohar Yakhini Avshalom Shalom Alexander Golberg |
| author_sort | Edward Vitkin |
| collection | DOAJ |
| description | Clinical misdiagnosis between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans. We report a tissue sampling approach with molecular biopsy using electroporation. This method, coined electroporation-based biopsy (e-biopsy), enables nondestructive nonthermal permeabilization of cells in the skin for vacuum-assisted extraction of biomolecules. We used e-biopsy for ex vivo proteome extraction from 3 locations per patient in 21 cSCC, 20 BCC, and 7 actinic keratosis human skin samples. Using liquid chromatography with tandem mass spectrometry, we identified 5966 proteins observed with nonzero intensity in at least 1 sample. The intrapatient Pearson correlation of 0.888 ± 0.065 for patients with BCC, 0.858 ± 0.077 for patients with cSCC, and 0.876 ± 0.116 for those with solar actinic keratosis indicates high consistency of the e-biopsy sampling. The mass spectra presented significantly different proteome profiles for cSCC, BCC, and solar actinic keratosis, with several hundreds of proteins differentially expressed. Notably, our study showed that proteomes sampled with e-biopsy from cSCC and BCC lesions are different and that proteins of CRNN, SULT1E1, and ITPK1 genes are significantly overexpressed in BCC in comparison with those in cSCC. Our results provide evidence that the e-biopsy approach could potentially be used as a tool to support cutaneous lesions classification with molecular pathology. |
| format | Article |
| id | doaj-art-83f79ac46db54585a183d657582ec882 |
| institution | Kabale University |
| issn | 2667-0267 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | JID Innovations |
| spelling | doaj-art-83f79ac46db54585a183d657582ec8822024-11-16T05:12:04ZengElsevierJID Innovations2667-02672024-11-0146100304Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based BiopsyEdward Vitkin0Julia Wise1Ariel Berl2Ofir Shir-az3Batel Gabay4Amrita Singh5Vladimir Kravtsov6Zohar Yakhini7Avshalom Shalom8Alexander Golberg9Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel; Efi Arazi School of Computer Science, Reichman University, Herzliya, IsraelPorter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, IsraelDepartment of Plastic Surgery, Meir Medical Center, Kfar Sava, IsraelDepartment of Plastic Surgery, Meir Medical Center, Kfar Sava, IsraelPorter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, IsraelPorter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, IsraelDepartment of Pathology, Meir Medical Center, Kfar Sava, IsraelEfi Arazi School of Computer Science, Reichman University, Herzliya, Israel; Department of Computer Science, Technion - Israel Institute of Technology, Haifa, IsraelDepartment of Plastic Surgery, Meir Medical Center, Kfar Sava, IsraelPorter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel; Correspondence: Alexander Golberg, Center for Engineering in Medicine & Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, 51 Blossom, Boston, Massachusetts 02114, USA.Clinical misdiagnosis between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans. We report a tissue sampling approach with molecular biopsy using electroporation. This method, coined electroporation-based biopsy (e-biopsy), enables nondestructive nonthermal permeabilization of cells in the skin for vacuum-assisted extraction of biomolecules. We used e-biopsy for ex vivo proteome extraction from 3 locations per patient in 21 cSCC, 20 BCC, and 7 actinic keratosis human skin samples. Using liquid chromatography with tandem mass spectrometry, we identified 5966 proteins observed with nonzero intensity in at least 1 sample. The intrapatient Pearson correlation of 0.888 ± 0.065 for patients with BCC, 0.858 ± 0.077 for patients with cSCC, and 0.876 ± 0.116 for those with solar actinic keratosis indicates high consistency of the e-biopsy sampling. The mass spectra presented significantly different proteome profiles for cSCC, BCC, and solar actinic keratosis, with several hundreds of proteins differentially expressed. Notably, our study showed that proteomes sampled with e-biopsy from cSCC and BCC lesions are different and that proteins of CRNN, SULT1E1, and ITPK1 genes are significantly overexpressed in BCC in comparison with those in cSCC. Our results provide evidence that the e-biopsy approach could potentially be used as a tool to support cutaneous lesions classification with molecular pathology.http://www.sciencedirect.com/science/article/pii/S2667026724000511DiagnosticsFinite elements modelingMachine learningMolecular pathologyProtein–protein interactionSkin cancer |
| spellingShingle | Edward Vitkin Julia Wise Ariel Berl Ofir Shir-az Batel Gabay Amrita Singh Vladimir Kravtsov Zohar Yakhini Avshalom Shalom Alexander Golberg Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy JID Innovations Diagnostics Finite elements modeling Machine learning Molecular pathology Protein–protein interaction Skin cancer |
| title | Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy |
| title_full | Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy |
| title_fullStr | Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy |
| title_full_unstemmed | Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy |
| title_short | Differential Expression Analysis of Cutaneous Squamous Cell Carcinoma and Basal Cell Carcinoma Proteomic Profiles Sampled with Electroporation-Based Biopsy |
| title_sort | differential expression analysis of cutaneous squamous cell carcinoma and basal cell carcinoma proteomic profiles sampled with electroporation based biopsy |
| topic | Diagnostics Finite elements modeling Machine learning Molecular pathology Protein–protein interaction Skin cancer |
| url | http://www.sciencedirect.com/science/article/pii/S2667026724000511 |
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