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Hu H, Feng Z, Lin H, Cheng J, Lyu J, Zhang Y, Zhao J, Xu F, Lin T, Zhao Q, Shuai J. Gene function and cell surface protein association analysis based on single-cell multiomics data. Comput Biol Med 2023; 157:106733. [PMID: 36924730 DOI: 10.1016/j.compbiomed.2023.106733] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Single-cell transcriptomics provides researchers with a powerful tool to resolve the transcriptome heterogeneity of individual cells. However, this method falls short in revealing cellular heterogeneity at the protein level. Previous single-cell multiomics studies have focused on data integration rather than exploiting the full potential of multiomics data. Here we introduce a new analysis framework, gene function and protein association (GFPA), that mines reliable associations between gene function and cell surface protein from single-cell multimodal data. Applying GFPA to human peripheral blood mononuclear cells (PBMCs), we observe an association of epithelial mesenchymal transition (EMT) with the CD99 protein in CD4 T cells, which is consistent with previous findings. Our results show that GFPA is reliable across multiple cell subtypes and PBMC samples. The GFPA python packages and detailed tutorials are freely available at https://github.com/studentiz/GFPA.
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Itakura Y, Sasaki N, Toyoda M. Glycan characteristics of human heart constituent cells maintaining organ function: relatively stable glycan profiles in cellular senescence. Biogerontology 2021; 22:623-37. [PMID: 34637040 DOI: 10.1007/s10522-021-09940-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/07/2021] [Indexed: 11/22/2022]
Abstract
Cell surface glycoproteins, which are good indicators of cellular types and biological function; are suited for cell evaluation. Tissue remodeling using various cells is a key feature of regenerative therapy. For artificial heart remodeling, a mixture of heart constituent cells has been investigated for organ assembly, however, the cellular characteristics remain unclear. In this study, the glycan profiles of human cardiomyocytes (HCMs), human cardiac fibroblasts (HCFs), and human vascular endothelial cells (ECs) were analyzed using evanescent-field lectin microarray analysis, a tool of glycan profiling, to clarify the required cellular characteristics. We found that ECs had more “α1-2fucose” and “core α1-6fucose” residues than other cells, and that “α2-6sialic acid” residue was more abundant in ECs and HCMs than in HCFs. HCFs showed higher abundance of “β-galactose” and “β-N-acetylgalactosamine” residues on N-glycan and O-glycan, respectively, compared to other cells. Interestingly, cardiac glycan profiles were insignificantly changed with cellular senescence. The residues identified in this study may participate in organ maintenance by contributing to the preservation of glycan components. Therefore, future studies should investigate the roles of glycans in optimal tissue remodeling since identifying cellular characteristics is important for the development of regenerative therapies.
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Brignole C, Bensa V, Fonseca NA, Del Zotto G, Bruno S, Cruz AF, Malaguti F, Carlini B, Morandi F, Calarco E, Perri P, Moura V, Emionite L, Cilli M, De Leonardis F, Tondo A, Amoroso L, Conte M, Garaventa A, Sementa AR, Corrias MV, Ponzoni M, Moreira JN, Pastorino F. Cell surface Nucleolin represents a novel cellular target for neuroblastoma therapy. J Exp Clin Cancer Res 2021; 40:180. [PMID: 34078433 PMCID: PMC8170797 DOI: 10.1186/s13046-021-01993-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/24/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) represents the most frequent and aggressive form of extracranial solid tumor of infants. Nucleolin (NCL) is a protein overexpressed and partially localized on the cell surface of tumor cells of adult cancers. Little is known about NCL and pediatric tumors and nothing is reported about cell surface NCL and NB. METHODS NB cell lines, Schwannian stroma-poor NB tumors and bone marrow (BM)-infiltrating NB cells were evaluated for the expression of cell surface NCL by Flow Cytometry, Imaging Flow Cytometry and Immunohistochemistry analyses. The cytotoxic activity of doxorubicin (DXR)-loaded nanocarriers decorated with the NCL-recognizing F3 peptide (T-DXR) was evaluated in terms of inhibition of NB cell proliferation and induction of cell death in vitro, whereas metastatic and orthotopic animal models of NB were used to examine their in vivo anti-tumor potential. RESULTS NB cell lines, NB tumor cells (including patient-derived and Patient-Derived Xenografts-PDX) and 70% of BM-infiltrating NB cells show cell surface NCL expression. NCL staining was evident on both tumor and endothelial tumor cells in NB xenografts. F3 peptide-targeted nanoparticles, co-localizing with cell surface NCL, strongly associates with NB cells showing selective tumor cell internalization. T-DXR result significantly more effective, in terms of inhibition of cell proliferation and reduction of cell viability in vitro, and in terms of delay of tumor growth in all NB animal model tested, when compared to both control mice and those treated with the untargeted formulation. CONCLUSIONS Our findings demonstrate that NCL could represent an innovative therapeutic cellular target for NB.
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Affiliation(s)
- Chiara Brignole
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Veronica Bensa
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nuno A Fonseca
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- TREAT U, SA - Parque Industrial de Taveiro, Lote 44, 3045-508, Coimbra, Portugal
| | - Genny Del Zotto
- Department of Research and Diagnostics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Silvia Bruno
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Ana F Cruz
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- UC - University of Coimbra, CIBB, Faculty of Pharmacy, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
| | - Fabiana Malaguti
- Department of Pathology, Istituto Giannina Gaslini, Genoa, Italy
| | - Barbara Carlini
- Department of Pathology, Istituto Giannina Gaslini, Genoa, Italy
| | - Fabio Morandi
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Enzo Calarco
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Patrizia Perri
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Vera Moura
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- TREAT U, SA - Parque Industrial de Taveiro, Lote 44, 3045-508, Coimbra, Portugal
| | - Laura Emionite
- Animal Facility, IRCSS Ospedale Policlinico San Martino, Genoa, Italy
| | - Michele Cilli
- Animal Facility, IRCSS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Annalisa Tondo
- UOC Oncologia Pediatrica, Ospedale Meyer, Florence, Italy
| | | | | | | | - Angela R Sementa
- Department of Pathology, Istituto Giannina Gaslini, Genoa, Italy
| | - Maria V Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
| | - Joao N Moreira
- CNC - Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- UC - University of Coimbra, CIBB, Faculty of Pharmacy, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548, Coimbra, Portugal
| | - Fabio Pastorino
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
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Bailey DK, Kosman DJ. Is brain iron trafficking part of the physiology of the amyloid precursor protein? J Biol Inorg Chem 2019; 24:1171-7. [PMID: 31578640 DOI: 10.1007/s00775-019-01684-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
Abstract
The amyloid precursor protein is so named, because a proteolytic fragment of it was found associated with a neuropathic disorder now known as Alzheimer's disease. This fragment, Aβ, along with tau makes up the plaques and tangles that are the hallmark of AD. Iron (and other first-row transition metals) is found associated with these proteinaceous deposits. Much research has focused on the relationship of the plaques and iron to the etiology of the disease. This commentary asks another question, one only more recently addressed namely, what is the physiologic function of the amyloid precursor protein (APP) and of its secretase-generated soluble species? Overall, the data make clear that APP and its products have neurotrophic functions and some data indicate one of these may be to modulate the trafficking of iron in the brain.
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Omoteyama K, Sato T, Arito M, Sato M, Suematsu N, Kurokawa MS, Kato T. Effects of salazosulfapyridine on the profile of cell surface proteins, revealed by biotinylation of cell surface proteins and 2-dimentional electrophoresis. Biochim Biophys Acta Proteins Proteom 2018; 1867:47-56. [PMID: 29753087 DOI: 10.1016/j.bbapap.2018.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/18/2018] [Accepted: 05/08/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVE We investigated effects of salazosulfapyridine (SASP) on the protein profile of cell surface (CS)-proteins of SW982, a human synovial sarcoma cell line, using biotinylation of CS-proteins and 2-dimensional fluorescence difference gel electrophoresis (2D-DIGE). METHODS SW982 cells were treated with SASP and its metabolites, sulfapyridine (SP) and 5-aminosalicylic acid (5ASA). Then the cells were treated with a membrane-impermeable biotinylating reagent. Biotinylated CS-proteins were isolated using NeutrAvidin-bound beads. CS-proteins affected by the drugs were detected by 2D-DIGE and subjected to mass spectrometry. RESULTS By the 2D-DIGE analysis, in total 576 spots were detected, 29 out of which showed more than ±1.5-fold different intensity in the SASP-, SP-, and 5ASA-treated cells, compared to non-treated cells (p < 0.05). Interestingly, 7 out of the 29 spots changed their intensity only by SASP and 17 spots changed their intensity only by SP. We identified 9 protein from 15 out of the 29 spots, most of which were evidenced to exist on the cell surface by flow cytometry. CONCLUSION We found novel effects of SASP and its metabolites on SW982 cells by the combination of biotinylation of cell surface proteins and 2D-DIGE analysis. These data would help understanding of anti-rheumatic actions of SASP. Furthermore, the combination would be a useful method for the analysis of CS-proteins in various conditions.
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Affiliation(s)
- Kazuki Omoteyama
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine.
| | - Toshiyuki Sato
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine
| | - Mitsumi Arito
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine
| | - Masaaki Sato
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine
| | - Naoya Suematsu
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine
| | - Manae S Kurokawa
- Disease Biomarker Analysis and Molecular Regulation, St. Marianna University Graduate School of Medicine
| | - Tomohiro Kato
- Clinical Proteomics and Molecular Medicine, St. Marianna University Graduate School of Medicine
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Abstract
High affinity binders targeting specific cell surface proteins are vital for development of basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acid aptamers have potential as binding molecules for cell surface proteins, because they form distinct structures that have high affinity and specificity for a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX). Among advantages of this method, purified and complex heterogeneous targets, such as bacteria, viruses, and whole-living cells, can be used for selection of aptamers. Moreover, SELEX allows generation of cell-surface-specific aptamers without prior knowledge of expression profiles in target cells. Therefore, the technology has been widely used as a valid and feasible method to generate aptamers binding to cell surface proteins with intact structure. Herein, this review summarizes and updates iconic SELEX technologies that target membrane proteins.
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Affiliation(s)
- Masaki Takahashi
- Division of RNA Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, Japan.
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