{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:51:12Z","timestamp":1785408672226,"version":"3.56.0"},"reference-count":100,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T00:00:00Z","timestamp":1781222400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund","award":["K146314"],"award-info":[{"award-number":["K146314"]}]},{"name":"Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund","award":["K142904"],"award-info":[{"award-number":["K142904"]}]},{"name":"Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund","award":["C1793861"],"award-info":[{"award-number":["C1793861"]}]},{"award":["K146314"],"award-info":[{"award-number":["K146314"]}],"id":[{"id":"https:\/\/ror.org\/03vhmm238","id-type":"ROR","asserted-by":"publisher"}]},{"award":["K142904"],"award-info":[{"award-number":["K142904"]}],"id":[{"id":"https:\/\/ror.org\/03vhmm238","id-type":"ROR","asserted-by":"publisher"}]},{"award":["C1793861"],"award-info":[{"award-number":["C1793861"]}],"id":[{"id":"https:\/\/ror.org\/03vhmm238","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Colorectal cancer (CRC) is the third most common malignancy worldwide. Detailed characterization of cell surface proteins (CSPs) is essential for the identification of prognostic biomarkers and the development of novel therapeutic strategies. Cancer progression and epithelial cell polarity influence the expression levels and subcellular localization of these proteins. However, quantitative information on the distribution of CSPs between the apical and basolateral membranes remains limited, particularly in CRC cells. Here, we developed a rapid, high-throughput method based on the enrichment of biotinylated peptides and proteins from the apical and basolateral surfaces of polarized CRC epithelial cells (HT29 and HCT116), followed by LC-MS\/MS analysis. This approach enables the simultaneous identification of the side-specific distribution of ~1200 CSPs. In addition, almost 500 potential N-glycosylation sites with the canonical consensus sequence of these proteins were identified, which may serve as targets for future site-specific glycosylation analyses. To evaluate the sensitivity of the method, we altered the surface proteome by generating TKS4-knockout cells and identified several surface markers whose expression levels differed significantly from those of wild-type cells. Overall, our findings provide new insights into the role of CSPs in CRC cells and gene-edited models, particularly in the context of TKS4-dependent epithelial-to-mesenchymal transition (EMT)-like phenotypes that model cancer metastasis.<\/jats:p>","DOI":"10.3390\/biom16060865","type":"journal-article","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:49:42Z","timestamp":1781743782000},"page":"865","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Decoding the Apical\u2013Basal Surfaceome of Colon Epithelial Cells via Side-Selective Biotinylation"],"prefix":"10.3390","volume":"16","author":[{"given":"Katalin","family":"Kuffa","sequence":"first","affiliation":[{"name":"Doctoral School of Biology, Institute of Biology, ELTE E\u00f6tv\u00f6s Lor\u00e1nd University, P\u00e1zm\u00e1ny P. stny. 1\/C, H-1117 Budapest, Hungary"},{"name":"Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar Tud\u00f3sok krt 2, H-1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6948-3721","authenticated-orcid":false,"given":"Tam\u00e1s","family":"Lang\u00f3","sequence":"additional","affiliation":[{"name":"Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar Tud\u00f3sok krt 2, H-1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e1s","family":"Czir\u00f3k","sequence":"additional","affiliation":[{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd University, P\u00e1zm\u00e1ny P. stny. 1\/A, H-1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00falia","family":"T\u00e1rnoki-Z\u00e1ch","sequence":"additional","affiliation":[{"name":"Department of Biological Physics, E\u00f6tv\u00f6s Lor\u00e1nd University, P\u00e1zm\u00e1ny P. stny. 1\/A, H-1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Szilvia","family":"B\u0151sze","sequence":"additional","affiliation":[{"name":"HUN-REN-ELTE Research Group of Peptide Chemistry, Hungarian Research Network, E\u00f6tv\u00f6s Lor\u00e1nd University, P\u00e1zm\u00e1ny P. stny. 1\/A, H-1117 Budapest, Hungary"},{"name":"Department of Genetics, Cell- and Immunobiology, Faculty of Science, Semmelweis University, Nagyv\u00e1rad t\u00e9r 4, H-1089 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0367-4900","authenticated-orcid":false,"given":"Loretta","family":"L\u00e1szl\u00f3","sequence":"additional","affiliation":[{"name":"Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar Tud\u00f3sok krt 2, H-1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7249-6816","authenticated-orcid":false,"given":"Vir\u00e1g","family":"Vas","sequence":"additional","affiliation":[{"name":"Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar Tud\u00f3sok krt 2, H-1117 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8278-8038","authenticated-orcid":false,"given":"Zolt\u00e1n","family":"Szab\u00f3","sequence":"additional","affiliation":[{"name":"Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar Tud\u00f3sok krt 2, H-1117 Budapest, Hungary"},{"name":"Department of Medical Chemistry, Albert Szent-Gy\u00f6rgyi Medical School, University of Szeged, H-6725 Szeged, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8105-0285","authenticated-orcid":false,"given":"G\u00e1bor E.","family":"Tusn\u00e1dy","sequence":"additional","affiliation":[{"name":"Institute of Molecular Life Sciences, Research Centre for Natural Sciences, HUN-REN, Magyar Tud\u00f3sok krt 2, H-1117 Budapest, Hungary"},{"name":"Department of Bioinformatics, Semmelweis University, T\u0171zolt\u00f3 u. 7, H-1094 Budapest, Hungary"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Roshandel, G., Ghasemi-Kebria, F., and Malekzadeh, R. 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