{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T01:37:56Z","timestamp":1790213876166,"version":"4.1.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T00:00:00Z","timestamp":1718928000000},"content-version":"vor","delay-in-days":172,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hengenix Biotech, Inc"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Bispecific antibodies (bsAbs) that bind to two distinct surface antigens on cancer cells are emerging as an appealing therapeutic strategy in cancer immunotherapy. However, considering the vast number of surface proteins, experimental identification of potential antigen pairs that are selectively expressed in cancer cells and not in normal cells is both costly and time-consuming. Recent studies have utilized large bulk RNA-seq databases to propose bispecific targets for various cancers. However, co-expressed pairs derived from bulk RNA-seq do not necessarily indicate true co-expression of both markers in malignant cells. Single-cell RNA-seq (scRNA-seq) can circumvent this issue but the issues in low coverage of transcripts impede the large-scale characterization of co-expressed pairs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a computational pipeline for bsAbs target identification which combines the advantages of bulk and scRNA-seq while minimizing the issues associated with using these approaches separately. We select hepatocellular carcinoma (HCC) as a case study to demonstrate the utility of the approach. First, using the bulk RNA-seq samples in the OCTAD database, we identified target pairs that most distinctly differentiate tumor cases from healthy controls. Next, we confirmed our findings on the scRNA-seq database comprising 39 361 healthy cells from vital organs and 18 000 cells from HCC tumors. The top pair was GPC3\u2013MUC13, where both genes are co-expressed on the surface of over 30% of malignant hepatocytes and have very low expression in other cells. Finally, we leveraged the emerging spatial transcriptomic to validate the co-expressed pair in situ.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>A standalone R package (https:\/\/github.com\/Bin-Chen-Lab\/bsAbsFinder).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbae096","type":"journal-article","created":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T03:20:28Z","timestamp":1718940028000},"source":"Crossref","is-referenced-by-count":3,"title":["Computational discovery of co-expressed antigens as dual targeting candidates for cancer therapy through bulk, single-cell, and spatial transcriptomics"],"prefix":"10.1093","volume":"4","author":[{"given":"Evgenii","family":"Chekalin","sequence":"first","affiliation":[{"name":"Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9247-7847","authenticated-orcid":false,"given":"Shreya","family":"Paithankar","sequence":"additional","affiliation":[{"name":"Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rama","family":"Shankar","sequence":"additional","affiliation":[{"name":"Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4726-8525","authenticated-orcid":false,"given":"Jing","family":"Xing","sequence":"additional","affiliation":[{"name":"Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenfeng","family":"Xu","sequence":"additional","affiliation":[{"name":"Hengenix Biotech, Inc. , Milpitas, CA 95035, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8858-874X","authenticated-orcid":false,"given":"Bin","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, MI 49503, United States"},{"name":"Department of Pharmacology and Toxicology, Michigan State University , East Lansing, MI 48824, United States"},{"name":"Department of Computer Science and Engineering, Michigan State University , East Lansing, MI 48824, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,6,20]]},"reference":[{"key":"2024070500263065300_vbae096-B1","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41586-019-1373-2","article-title":"A human liver cell atlas reveals heterogeneity and epithelial progenitors","volume":"572","author":"Aizarani","year":"2019","journal-title":"Nature"},{"key":"2024070500263065300_vbae096-B2","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/s13059-019-1862-5","article-title":"scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data","volume":"20","author":"Alquicira-Hernandez","year":"2019","journal-title":"Genome Biol"},{"key":"2024070500263065300_vbae096-B3","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat Immunol"},{"key":"2024070500263065300_vbae096-B4","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1186\/s12864-020-06832-3","article-title":"Seamless integration of image and molecular analysis for spatial transcriptomics workflows","volume":"21","author":"Bergenstr\u00e5hle","year":"2020","journal-title":"BMC Genomics"},{"key":"2024070500263065300_vbae096-B5","doi-asserted-by":"crossref","first-page":"bau012","DOI":"10.1093\/database\/bau012","article-title":"COMPARTMENTS: unification and visualization of protein subcellular localization evidence","volume":"2014","author":"Binder","year":"2014","journal-title":"Database (Oxford)"},{"key":"2024070500263065300_vbae096-B6","author":"Broadinstitute\/infercnv","year":"2023"},{"key":"2024070500263065300_vbae096-B7","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/j.ajpath.2017.10.016","article-title":"Overexpression of MUC13, a poor prognostic predictor, promotes cell growth by activating WNT signaling in hepatocellular carcinoma","volume":"188","author":"Dai","year":"2018","journal-title":"Am J Pathol"},{"key":"2024070500263065300_vbae096-B8","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.cels.2020.08.002","article-title":"Discriminatory power of combinatorial antigen recognition in cancer T cell therapies","volume":"11","author":"Dannenfelser","year":"2020","journal-title":"Cell Syst"},{"key":"2024070500263065300_vbae096-B9","doi-asserted-by":"crossref","first-page":"e147703","DOI":"10.1172\/jci.insight.147703","article-title":"Integration of spatial and single-cell transcriptomics localizes epithelial cell\u2013immune cross-talk in kidney injury","volume":"6","author":"Ferreira","year":"2021","journal-title":"JCI Insight"},{"key":"2024070500263065300_vbae096-B10","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1002\/hep.30326","article-title":"Glypican-3 specific antibody drug conjugates targeting hepatocellular carcinoma (HEP-10-1020)","volume":"70","author":"Fu","year":"2019","journal-title":"Hepatology"},{"key":"2024070500263065300_vbae096-B11","doi-asserted-by":"crossref","first-page":"bbaa127","DOI":"10.1093\/bib\/bbaa127","article-title":"scCancer: a package for automated processing of single-cell RNA-seq data in cancer","volume":"22","author":"Guo","year":"2021","journal-title":"Brief Bioinform"},{"key":"2024070500263065300_vbae096-B12","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1038\/nmeth.4407","article-title":"Massively parallel single-nucleus RNA-seq with DroNc-seq","volume":"14","author":"Habib","year":"2017","journal-title":"Nat Methods"},{"key":"2024070500263065300_vbae096-B13","doi-asserted-by":"crossref","first-page":"D1425","DOI":"10.1093\/nar\/gkac959","article-title":"TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment","volume":"51","author":"Han","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024070500263065300_vbae096-B14","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1038\/s43018-021-00244-2","article-title":"Dual-targeting CAR-T cells with optimal co-stimulation and metabolic fitness enhance antitumor activity and prevent escape in solid tumors","volume":"2","author":"Hirabayashi","year":"2021","journal-title":"Nat Cancer"},{"key":"2024070500263065300_vbae096-B15","doi-asserted-by":"crossref","first-page":"3111","DOI":"10.1007\/s00432-020-03404-6","article-title":"Bispecific antibodies targeting dual tumor-associated antigens in cancer therapy","volume":"146","author":"Huang","year":"2020","journal-title":"J Cancer Res Clin Oncol"},{"key":"2024070500263065300_vbae096-B16","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/s41573-024-00896-6","article-title":"The present and future of bispecific antibodies for cancer therapy","volume":"23","author":"Klein","year":"2024","journal-title":"Nat Rev Drug Discov"},{"key":"2024070500263065300_vbae096-B17","doi-asserted-by":"crossref","first-page":"959","DOI":"10.2147\/JHC.S376210","article-title":"Impaired autophagy response in hepatocellular carcinomas enriches glypican-3 in exosomes, not in the microvesicles","volume":"9","author":"Koksal","year":"2022","journal-title":"J Hepatocell Carcinoma"},{"key":"2024070500263065300_vbae096-B18","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2024070500263065300_vbae096-B19","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41573-019-0028-1","article-title":"Bispecific antibodies: a mechanistic review of the pipeline","volume":"18","author":"Labrijn","year":"2019","journal-title":"Nat Rev Drug Discov"},{"key":"2024070500263065300_vbae096-B20","doi-asserted-by":"crossref","first-page":"32607","DOI":"10.18632\/oncotarget.8927","article-title":"Potential diagnostic and prognostic marker dimethylglycine dehydrogenase (DMGDH) suppresses hepatocellular carcinoma metastasis in vitro and in vivo","volume":"7","author":"Liu","year":"2016","journal-title":"Oncotarget"},{"key":"2024070500263065300_vbae096-B21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-022-32283-3","article-title":"A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma","volume":"13","author":"Lu","year":"2022","journal-title":"Nat Commun"},{"key":"2024070500263065300_vbae096-B22","author":"Ludvigla","year":"2019"},{"key":"2024070500263065300_vbae096-B23","doi-asserted-by":"crossref","first-page":"7533","DOI":"10.1038\/s41467-022-35291-5","article-title":"Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer","volume":"13","author":"Ma","year":"2022","journal-title":"Nat Commun"},{"key":"2024070500263065300_vbae096-B24","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1016\/j.jhep.2021.06.028","article-title":"Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma","volume":"75","author":"Ma","year":"2021","journal-title":"J Hepatol"},{"key":"2024070500263065300_vbae096-B25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1124\/molpharm.121.000331","article-title":"Ibrutinib blocks YAP1 activation and reverses BRAF inhibitor resistance in melanoma cells","volume":"101","author":"Misek","year":"2022","journal-title":"Mol Pharmacol"},{"key":"2024070500263065300_vbae096-B2500","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.1126\/science.132.3441.1770","article-title":"Properties of the major component of a peptic digest of rabbit antibody","volume":"132","year":"1960","journal-title":"Science"},{"key":"2024070500263065300_vbae096-B26","first-page":"e27041","article-title":"Human Cell Atlas Meeting Participants. The Human Cell Atlas","volume":"6","year":"2017","journal-title":"eLife"},{"key":"2024070500263065300_vbae096-B27","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/nature23306","article-title":"Integrative clinical genomics of metastatic cancer","volume":"548","author":"Robinson","year":"2017","journal-title":"Nature"},{"key":"2024070500263065300_vbae096-B28","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2024070500263065300_vbae096-B29","doi-asserted-by":"crossref","first-page":"25106","DOI":"10.1074\/jbc.M116.753491","article-title":"Balancing selectivity and efficacy of bispecific epidermal growth factor receptor (EGFR) \u00d7 c-MET antibodies and antibody\u2013drug conjugates","volume":"291","author":"Sellmann","year":"2016","journal-title":"J Biol Chem"},{"key":"2024070500263065300_vbae096-B30","author":"Single-cell Atlas in Liver Cancer","year":"."},{"key":"2024070500263065300_vbae096-B31","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1038\/s41591-021-01436-0","article-title":"CAR T cells with dual targeting of CD19 and CD22 in adult patients with recurrent or refractory B cell malignancies: a phase 1 trial","volume":"27","author":"Spiegel","year":"2021","journal-title":"Nat Med"},{"key":"2024070500263065300_vbae096-B32","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2024070500263065300_vbae096-B33","doi-asserted-by":"crossref","first-page":"D1420","DOI":"10.1093\/nar\/gkaa1020","article-title":"TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment","volume":"49","author":"Sun","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024070500263065300_vbae096-B34","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1038\/s41591-019-0468-5","article-title":"A cellular census of human lungs identifies novel cell states in health and in asthma","volume":"25","author":"Vieira Braga","year":"2019","journal-title":"Nat Med"},{"key":"2024070500263065300_vbae096-B35","author":"Visualizing Large-scale Copy Number Variation in Single-Cell RNA-Seq Expression Data","year":"."},{"key":"2024070500263065300_vbae096-B36","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/s41556-019-0446-7","article-title":"Single-cell reconstruction of the adult human heart during heart failure and recovery reveals the cellular landscape underlying cardiac function","volume":"22","author":"Wang","year":"2020","journal-title":"Nat Cell Biol"},{"key":"2024070500263065300_vbae096-B37","doi-asserted-by":"crossref","first-page":"eabg3750","DOI":"10.1126\/sciadv.abg3750","article-title":"Comprehensive analysis of spatial architecture in primary liver cancer","volume":"7","author":"Wu","year":"2021","journal-title":"Sci Adv"},{"key":"2024070500263065300_vbae096-B38","doi-asserted-by":"crossref","first-page":"109393","DOI":"10.1016\/j.intimp.2022.109393","article-title":"Construction and evaluation of GPC3-targeted immunotoxins as a novel therapeutic modality for hepatocellular carcinoma","volume":"113","author":"Wu","year":"2022","journal-title":"Int Immunopharmacol"},{"key":"2024070500263065300_vbae096-B39","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1080\/15384047.2020.1743158","article-title":"A novel targeted GPC3\/CD3 bispecific antibody for the treatment hepatocellular carcinoma","volume":"21","author":"Yu","year":"2020","journal-title":"Cancer Biol Ther"},{"key":"2024070500263065300_vbae096-B40","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/s41596-020-00430-z","article-title":"OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features","volume":"16","author":"Zeng","year":"2021","journal-title":"Nat Protoc"},{"key":"2024070500263065300_vbae096-B41","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s12920-018-0463-6","article-title":"Selecting precise reference normal tissue samples for cancer research using a deep learning approach","volume":"12","author":"Zeng","year":"2019","journal-title":"BMC Med Genomics"},{"key":"2024070500263065300_vbae096-B42","doi-asserted-by":"crossref","first-page":"231","DOI":"10.3892\/ol.2020.12094","article-title":"Identification of diagnostic and prognostic biomarkers, and candidate targeted agents for hepatitis B virus-associated early stage hepatocellular carcinoma based on RNA-sequencing data","volume":"20","author":"Zeng","year":"2020","journal-title":"Oncol Lett"},{"key":"2024070500263065300_vbae096-B43","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/s40478-022-01463-z","article-title":"Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma","volume":"10","author":"Zhao","year":"2022","journal-title":"Acta Neuropathol Commun"},{"key":"2024070500263065300_vbae096-B44","doi-asserted-by":"crossref","first-page":"824208","DOI":"10.3389\/fonc.2022.824208","article-title":"Glypican-3: a novel and promising target for the treatment of hepatocellular carcinoma","volume":"12","author":"Zheng","year":"2022","journal-title":"Front Oncol"}],"container-title":["Bioinformatics Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/advance-article-pdf\/doi\/10.1093\/bioadv\/vbae096\/58292568\/vbae096.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/4\/1\/vbae096\/58444813\/vbae096.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article-pdf\/4\/1\/vbae096\/58444813\/vbae096.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,4]],"date-time":"2024-07-04T20:27:21Z","timestamp":1720124841000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformaticsadvances\/article\/doi\/10.1093\/bioadv\/vbae096\/7696853"}},"subtitle":[],"editor":[{"given":"Franca","family":"Fraternali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024]]},"references-count":45,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioadv\/vbae096","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.10.17.562711","asserted-by":"object"}]},"ISSN":["2635-0041"],"issn-type":[{"value":"2635-0041","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024]]},"published":{"date-parts":[[2024]]},"article-number":"vbae096"}}