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Di Meo F, Kale B, Koomen JM, Perna F. Mapping the cancer surface proteome in search of target antigens for immunotherapy. Mol Ther 2024; 32:2892-2904. [PMID: 39068512 PMCID: PMC11403220 DOI: 10.1016/j.ymthe.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/26/2024] [Accepted: 07/25/2024] [Indexed: 07/30/2024] Open
Abstract
Immune-based therapeutic interventions recognizing proteins localized on the cell surface of cancer cells are emerging as a promising cancer treatment. Antibody-based therapies and engineered T cells are now approved by the Food and Drug Administration to treat some malignancies. These therapies utilize a few cell surface proteins highly expressed on cancer cells to release the negative regulation of immune activation that limits antitumor responses (e.g., PD-1, PD-L1, CTLA4) or to redirect the T cell specificity toward blood cancer cells (e.g., CD19 and B cell maturation antigen). One limitation preventing broader application of these novel therapeutic strategies to all cancer types is the lack of suitable target antigens for all indications owing in part to the challenges in identifying such targets. Ideal target antigens are cell surface proteins highly expressed on malignant cells and absent in healthy tissues. Technological advances in mass spectrometry, enrichment protocols, and computational tools for cell surface protein isolation and annotation have recently enabled comprehensive analyses of the cancer cell surface proteome, from which novel immunotherapeutic target antigens may emerge. Here, we review the most recent progress in this field.
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Affiliation(s)
- Francesco Di Meo
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - Brandon Kale
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Fabiana Perna
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Tampa, FL, USA.
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2
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Cheng D, Chu F, Liang F, Zhang N, Wang J, Yue W. Downregulation of circ-RAPGEF5 inhibits colorectal cancer progression by reducing the expression of polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). ENVIRONMENTAL TOXICOLOGY 2024; 39:4249-4260. [PMID: 38775215 DOI: 10.1002/tox.24278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/11/2024] [Accepted: 03/31/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Circular RNA (circRNA) plays a crucial role in the pathogenesis and progression of colorectal cancer (CRC). However, the current understanding of the emerging function and mechanism of circ-RAPGEF5 in CRC remains poorly understood. METHODS We first evaluated the expression level of circ-RAPGEF5 in CRC tissues and cells by quantitative real-time polymerase chain reaction (qRT-PCR). Then, we analyzed cell proliferation (EdU and colony formation assay), migration (cell wound healing assay), invasion (transwell assay), and apoptosis (flow cytometry assay). To further elucidate the mechanism of circ-RAPGEF5 in CRC, bioinformatics tools, Dual-luciferase reporter assay, Ago2 RNA immunoprecipitation assay, and RNA pull-down assay were employed. Moreover, we established a CRC transplantation tumor model to evaluate the effect of circ-RAPGEF5 on tumor growth in vivo. RESULTS circ-RAPGEF5 was significantly upregulated in CRC tissues and CRC cells. Furthermore, the downregulation of circ-RAPGEF5 restrained CRC cell proliferation, migration, and invasion, and promoted cell apoptosis in vitro. Mechanistically, circ-RAPGEF5 accelerated the malignant behaviors of CRC cells by sponging miR-545-5p, which targeted polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). In addition, we revealed that circ-RAPGEF5 silence curbed tumor growth in vivo. CONCLUSION These findings revealed that circ-RAPGEF5 played an oncogenic role through the miR-545-5p/GALNT3 axis in CRC progression, providing potential therapeutic targets for the treatment of CRC.
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Affiliation(s)
- Duo Cheng
- Department of Oncology and Rehabilitation, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou City, Henan, China
| | - Feifei Chu
- Department of Digestive Diseases, Zhengzhou Central Hospital Affiliated to Zhengzhou University of Zhengzhou, Zhengzhou City, Henan, China
| | - Fang Liang
- Department of Oncology and Rehabilitation, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou City, Henan, China
| | - Nan Zhang
- Department of Oncology and Rehabilitation, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou City, Henan, China
| | - Jingjing Wang
- Department of Oncology and Rehabilitation, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou City, Henan, China
| | - Wenli Yue
- Department of Oncology and Rehabilitation, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou City, Henan, China
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3
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Ali MY, Bar-Peled L. Chemical proteomics to study metabolism, a reductionist approach applied at the systems level. Cell Chem Biol 2024; 31:446-451. [PMID: 38518745 DOI: 10.1016/j.chembiol.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 02/28/2024] [Indexed: 03/24/2024]
Abstract
Cellular metabolism encompasses a complex array of interconnected biochemical pathways that are required for cellular homeostasis. When dysregulated, metabolism underlies multiple human pathologies. At the heart of metabolic networks are enzymes that have been historically studied through a reductionist lens, and more recently, using high throughput approaches including genomics and proteomics. Merging these two divergent viewpoints are chemical proteomic technologies, including activity-based protein profiling, which combines chemical probes specific to distinct enzyme families or amino acid residues with proteomic analysis. This enables the study of metabolism at the network level with the precision of powerful biochemical approaches. Herein, we provide a primer on how chemical proteomic technologies custom-built for studying metabolism have unearthed fundamental principles in metabolic control. In parallel, these technologies have leap-frogged drug discovery through identification of novel targets and drug specificity. Collectively, chemical proteomics technologies appear to do the impossible: uniting systematic analysis with a reductionist approach.
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Affiliation(s)
- Md Yousuf Ali
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Liron Bar-Peled
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02114, USA.
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4
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Tardif G, Paré F, Gotti C, Roux-Dalvai F, Droit A, Zhai G, Sun G, Fahmi H, Pelletier JP, Martel-Pelletier J. Mass spectrometry-based proteomics identify novel serum osteoarthritis biomarkers. Arthritis Res Ther 2022; 24:120. [PMID: 35606786 PMCID: PMC9125906 DOI: 10.1186/s13075-022-02801-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Osteoarthritis (OA) is a slowly developing and debilitating disease, and there are no validated specific biomarkers for its early detection. To improve therapeutic approaches, identification of specific molecules/biomarkers enabling early determination of this disease is needed. This study aimed at identifying, with the use of proteomics/mass spectrometry, novel OA-specific serum biomarkers. As obesity is a major risk factor for OA, we discriminated obesity-regulated proteins to target only OA-specific proteins as biomarkers. Methods Serum from the Osteoarthritis Initiative cohort was used and divided into 3 groups: controls (n=8), OA-obese (n=10) and OA-non-obese (n=10). Proteins were identified and quantified from the liquid chromatography–tandem mass spectrometry analyses using MaxQuant software. Statistical analysis used the Limma test followed by the Benjamini-Hochberg method. To compare the proteomic profiles, the multivariate unsupervised principal component analysis (PCA) followed by the pairwise comparison was used. To select the most predictive/discriminative features, the supervised linear classification model sparse partial least squares regression discriminant analysis (sPLS-DA) was employed. Validation of three differential proteins was performed with protein-specific assays using plasma from a cohort derived from the Newfoundland Osteoarthritis. Results In total, 509 proteins were identified, and 279 proteins were quantified. PCA-pairwise differential comparisons between the 3 groups revealed that 8 proteins were differentially regulated between the OA-obese and/or OA-non-obese with controls. Further experiments using the sPLS-DA revealed two components discriminating OA from controls (component 1, 9 proteins), and OA-obese from OA-non-obese (component 2, 23 proteins). Proteins from component 2 were considered related to obesity. In component 1, compared to controls, 7 proteins were significantly upregulated by both OA groups and 2 by the OA-obese. Among upregulated proteins from both OA groups, some of them alone would not be a suitable choice as specific OA biomarkers due to their rather non-specific role or their strong link to other pathological conditions. Altogether, data revealed that the protein CRTAC1 appears to be a strong OA biomarker candidate. Other potential new biomarker candidates are the proteins FBN1, VDBP, and possibly SERPINF1. Validation experiments revealed statistical differences between controls and OA for FBN1 (p=0.044) and VDPB (p=0.022), and a trend for SERPINF1 (p=0.064). Conclusion Our study suggests that 4 proteins, CRTAC1, FBN1, VDBP, and possibly SERPINF1, warrant further investigation as potential new biomarker candidates for the whole OA population. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-022-02801-1.
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Affiliation(s)
- Ginette Tardif
- Osteoarthritis Research Unit, University of Montreal Hospital Research Centre (CRCHUM), 900 Saint-Denis, Suite R11.412B, Montreal, QC, H2X 0A9, Canada
| | - Frédéric Paré
- Osteoarthritis Research Unit, University of Montreal Hospital Research Centre (CRCHUM), 900 Saint-Denis, Suite R11.412B, Montreal, QC, H2X 0A9, Canada
| | - Clarisse Gotti
- CHU de Québec Research Center, Laval University, Quebec, QC, G1V 4G2, Canada
| | | | - Arnaud Droit
- CHU de Québec Research Center, Laval University, Quebec, QC, G1V 4G2, Canada
| | - Guangju Zhai
- Division of Biomedical Sciences (Genetics), Memorial University of Newfoundland, St. John's, NL, A1B 3V6, Canada
| | - Guang Sun
- Discipline of Medicine, Memorial University of Newfoundland, St. John's, NL, A1B 3V6, Canada
| | - Hassan Fahmi
- Osteoarthritis Research Unit, University of Montreal Hospital Research Centre (CRCHUM), 900 Saint-Denis, Suite R11.412B, Montreal, QC, H2X 0A9, Canada
| | - Jean-Pierre Pelletier
- Osteoarthritis Research Unit, University of Montreal Hospital Research Centre (CRCHUM), 900 Saint-Denis, Suite R11.412B, Montreal, QC, H2X 0A9, Canada
| | - Johanne Martel-Pelletier
- Osteoarthritis Research Unit, University of Montreal Hospital Research Centre (CRCHUM), 900 Saint-Denis, Suite R11.412B, Montreal, QC, H2X 0A9, Canada.
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5
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Xu Z, Jin H, Duan X, Liu H, Zhao X, Fan S, Wang Y, Yao T. LncRNA PSMA3-AS1 promotes cell proliferation, migration, and invasion in ovarian cancer by activating the PI3K/Akt pathway via the miR-378a-3p/GALNT3 axis. ENVIRONMENTAL TOXICOLOGY 2021; 36:2562-2577. [PMID: 34520102 DOI: 10.1002/tox.23370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
The crucial roles of the long noncoding RNAs (lncRNAs) in the development of ovarian cancer (OC) have been extensively studied. According to the prediction result from the Kaplan-Meier Plotter database, high expression of lncRNA proteasome subunit α type-3 antisense RNA1 (PSMA3-AS1) is associated with the poor prognosis in patients with OC. Thus, the study aimed to investigate the role of lncRNA PSMA3-AS1 in OC. Reverse transcription quantitative polymerase chain reaction analysis revealed that PSMA3-AS1 expression was significantly upregulated in OC cells and tissues. PSMA3-AS1 silencing inhibited OC cell proliferation, migration, and invasion, as shown by results of cell counting kit-8, colony formation, wound healing, and Transwell assays, respectively. Additionally, PSMA3-AS1 deficiency suppressed tumor growth in vivo. Mechanistically, luciferase reporter and RNA pulldown assays implied that PSMA3-AS1 served as a competing endogenous RNA for miR-378a-3p to upregulate the expression of polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). GALNT3 was a target gene of miR-378a-3p in OC. Moreover, PSMA3-AS1 activated the PI3K/Akt pathway by upregulating GALNT3 expression. Overall, PSMA3-AS1 promotes OC cell proliferation, migration, invasion, and xenograft tumor growth by activating the PI3K/Akt pathway via the miR-378a-3p/GALNT3 axis.
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Affiliation(s)
- Zhihong Xu
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hui Jin
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaoyang Duan
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Hong Liu
- Department of Gynecology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiwa Zhao
- Department of Gynecology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shaoshuang Fan
- Department of Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yan Wang
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Tiezhu Yao
- Department of Cardiology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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6
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Shannon NB, Tan LLY, Tan QX, Tan JWS, Hendrikson J, Ng WH, Ng G, Liu Y, Ong XYS, Nadarajah R, Wong JSM, Tan GHC, Soo KC, Teo MCC, Chia CS, Ong CAJ. A machine learning approach to identify predictive molecular markers for cisplatin chemosensitivity following surgical resection in ovarian cancer. Sci Rep 2021; 11:16829. [PMID: 34413360 PMCID: PMC8377048 DOI: 10.1038/s41598-021-96072-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/31/2021] [Indexed: 12/27/2022] Open
Abstract
Ovarian cancer is associated with poor prognosis. Platinum resistance contributes significantly to the high rate of tumour recurrence. We aimed to identify a set of molecular markers for predicting platinum sensitivity. A signature predicting cisplatin sensitivity was generated using the Genomics of Drug Sensitivity in Cancer and The Cancer Genome Atlas databases. Four potential biomarkers (CYTH3, GALNT3, S100A14, and ERI1) were identified and optimized for immunohistochemistry (IHC). Validation was performed on a cohort of patients (n = 50) treated with surgical resection followed by adjuvant carboplatin. Predictive models were established to predict chemosensitivity. The four biomarkers were also assessed for their ability to prognosticate overall survival in three ovarian cancer microarray expression datasets from The Gene Expression Omnibus. The extreme gradient boosting (XGBoost) algorithm was selected for the final model to validate the accuracy in an independent validation dataset (n = 10). CYTH3 and S100A14, followed by nodal stage, were the features with the greatest importance. The four gene signature had comparable prognostication as clinical information for two-year survival. Assessment of tumour biology by means of gene expression can serve as an adjunct for prediction of chemosensitivity and prognostication. Potentially, the assessment of molecular markers alongside clinical information offers a chance to further optimise therapeutic decision making.
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Affiliation(s)
- Nicholas Brian Shannon
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Laura Ling Ying Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Qiu Xuan Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Joey Wee-Shan Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Josephine Hendrikson
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Wai Har Ng
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Gillian Ng
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Ying Liu
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Xing-Yi Sarah Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Ravichandran Nadarajah
- Department of Obstetrics and Gynaecology, Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Jolene Si Min Wong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Grace Hwei Ching Tan
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore
| | - Khee Chee Soo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Melissa Ching Ching Teo
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Claramae Shulyn Chia
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore.,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Chin-Ann Johnny Ong
- Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore. .,Department of Sarcoma, Peritoneal and Rare Tumours (SPRinT), Division of Surgery and Surgical Oncology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore. .,Laboratory of Applied Human Genetics, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore. .,SingHealth Duke-NUS Oncology Academic Clinical Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Institute of Molecular and Cell Biology, A*STAR Research Entities, 61 Biopolis Drive, Singapore, 138673, Singapore.
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7
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Cell membrane-camouflaged liposomes for tumor cell-selective glycans engineering and imaging in vivo. Proc Natl Acad Sci U S A 2021; 118:2022769118. [PMID: 34301864 DOI: 10.1073/pnas.2022769118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The dynamic change of cell-surface glycans is involved in diverse biological and pathological events such as oncogenesis and metastasis. Despite tremendous efforts, it remains a great challenge to selectively distinguish and label glycans of different cancer cells or cancer subtypes. Inspired by biomimetic cell membrane-coating technology, herein, we construct pH-responsive azidosugar liposomes camouflaged with natural cancer-cell membrane for tumor cell-selective glycan engineering. With cancer cell-membrane camouflage, the biomimetic liposomes can prevent protein corona formation and evade phagocytosis of macrophages, facilitating metabolic glycans labeling in vivo. More importantly, due to multiple membrane receptors, the biomimetic liposomes have prominent cell selectivity to homotypic cancer cells, showing higher glycan-labeling efficacy than a single-ligand targeting strategy. Further in vitro and in vivo experiments indicate that cancer cell membrane-camouflaged azidosugar liposomes not only realize cell-selective glycan imaging of different cancer cells and triple-negative breast cancer subtypes but also do well in labeling metastatic tumors. Meanwhile, the strategy is also applicable to the use of tumor tissue-derived cell membranes, which shows the prospect for individual diagnosis and treatment. This work may pave a way for efficient cancer cell-selective engineering and visualization of glycans in vivo.
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8
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Stewart TJ, Takahashi K, Xu N, Prakash A, Brown R, Raska M, Renfrow MB, Novak J. Quantitative assessment of successive carbohydrate additions to the clustered O-glycosylation sites of IgA1 by glycosyltransferases. Glycobiology 2020; 31:540-556. [PMID: 33295603 DOI: 10.1093/glycob/cwaa111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/12/2022] Open
Abstract
Mucin-type O-glycosylation occurs on many proteins that transit the Golgi apparatus. These glycans impact structure and function of many proteins and have important roles in cellular biosynthetic processes, signaling and differentiation. Although recent technological advances have enhanced our ability to profile glycosylation of glycoproteins, limitations in the understanding of the biosynthesis of these glycan structures remain. Some of these limitations stem from the difficulty to track the biosynthetic process of mucin-type O-glycosylation, especially when glycans occur in dense clusters in repeat regions of proteins, such as the mucins or immunoglobulin A1 (IgA1). Here, we describe a series of nano-liquid chromatography (LC)-mass spectrometry (MS) analyses that demonstrate the range of glycosyltransferase enzymatic activities involved in the biosynthesis of clustered O-glycans on IgA1. By utilizing nano-LC-MS relative quantitation of in vitro reaction products, our results provide unique insights into the biosynthesis of clustered IgA1 O-glycans. We have developed a workflow to determine glycoform-specific apparent rates of a human UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltrasnfersase (GalNAc-T EC 2.4.1.41) and demonstrated how pre-existing glycans affect subsequent activity of glycosyltransferases, such as core 1 galactosyltransferase and α2,3- and α2,6-specific sialyltransferases, in successive additions in the biosynthesis of clustered O-glycans. In the context of IgA1, these results have potential to provide insight into the molecular mechanisms implicated in the pathogenesis of IgA nephropathy, an autoimmune renal disease involving aberrant IgA1 O-glycosylation. In a broader sense, these methods and workflows are applicable to the studies of the concerted and competing functions of other glycosyltransferases that initiate and extend mucin-type core 1 clustered O-glycosylation.
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Affiliation(s)
- Tyler J Stewart
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, KAUL 524, Birmingham, AL 35294, USA
| | - Kazuo Takahashi
- Department of Biomedical Molecular Sciences, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake, Aichi, Toyoake 470-1192, Japan.,Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA
| | - Nuo Xu
- Department of Management, Information Systems & Quantitative Methods, 710 13th Street South, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Amol Prakash
- Optys Tech Corporation, Shrewsbury, MA 01545, USA
| | - Rhubell Brown
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA
| | - Milan Raska
- Department of Immunology, Palacky University and University Hospital, Hnevotinska 3, Olomouc 775 15, Czech Republic
| | - Matthew B Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, KAUL 524, Birmingham, AL 35294, USA
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, 845 19th Street South, BBRB 761A, Birmingham, AL 35294, USA
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9
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Investigating the Product Profiles and Structural Relationships of New Levansucrases with Conventional and Non-Conventional Substrates. Int J Mol Sci 2020; 21:ijms21155402. [PMID: 32751348 PMCID: PMC7432509 DOI: 10.3390/ijms21155402] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 12/25/2022] Open
Abstract
The synthesis of complex oligosaccharides is desired for their potential as prebiotics, and their role in the pharmaceutical and food industry. Levansucrase (LS, EC 2.4.1.10), a fructosyl-transferase, can catalyze the synthesis of these compounds. LS acquires a fructosyl residue from a donor molecule and performs a non-Lenoir transfer to an acceptor molecule, via β-(2→6)-glycosidic linkages. Genome mining was used to uncover new LS enzymes with increased transfructosylating activity and wider acceptor promiscuity, with an initial screening revealing five LS enzymes. The product profiles and activities of these enzymes were examined after their incubation with sucrose. Alternate acceptor molecules were also incubated with the enzymes to study their consumption. LSs from Gluconobacter oxydans and Novosphingobium aromaticivorans synthesized fructooligosaccharides (FOSs) with up to 13 units in length. Alignment of their amino acid sequences and substrate docking with homology models identified structural elements causing differences in their product spectra. Raffinose, over sucrose, was the preferred donor molecule for the LS from Vibrio natriegens, N. aromaticivorans, and Paraburkolderia graminis. The LSs examined were found to have wide acceptor promiscuity, utilizing monosaccharides, disaccharides, and two alcohols to a high degree.
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Xu Z, Ku X, Tomioka A, Xie W, Liang T, Zou X, Cui Y, Sato T, Kaji H, Narimatsu H, Yan W, Zhang Y. O-linked N-acetylgalactosamine modification is present on the tumor suppressor p53. Biochim Biophys Acta Gen Subj 2020; 1864:129635. [PMID: 32417172 DOI: 10.1016/j.bbagen.2020.129635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Mucin-type O-glycosylation (referred to as O-GalNAc glycosylation) is the most abundant O-glycosylation on membrane and secretory proteins. Recently several evidences suggest that nuclear or cytoplasmic proteins might also have O-GalNAc glycosylation. However, what nucleocytoplasmic proteins are O-GalNAc glycosylated and what the biological function of this modification in cells are still poorly understood. Previously, we reported the tumor suppressor p53 could be O-GalNAc glycosylated in vitro. To investigate the existence and function of O-GalNAc glycosylation on nucleocytoplasmic proteins in cell, p53 as a representative nucleocytoplasmic protein was studied. METHODS Using lectin blotting with GalNAc specific lectins, enzymatic treatments with O-GlcNAcase, core 1 β1, 3-galactosyltransferase and O-glycosidase, and metabolic labeling with un-O-acetylated GalNAz in UDP-Gal/UDP-GalNAc 4-epimerase (GALE) knockout cells, we validated the O-GalNAc glycosylation on p53. Using mass spectrometry analysis and site-directed mutagenesis, we identified the glycosylated sites and studied the functions of O-GalNAc glycosylation on p53. RESULTS The p53 was O-GalNAc glycosylated in cells. Ser121 residue was one of the glycosylated sites on p53. The O-GalNAc glycosylation at Ser121 was associated with the stability and activity of p53. CONCLUSIONS These results revealed that the O-GalNAc glycosylation was a novel modification on p53. GENERAL SIGNIFICANCE Our study provided a pilot evidence that the O-GalNAc glycosylation existed on nucleocytoplasmic protein.
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Affiliation(s)
- Zhijue Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xin Ku
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Azusa Tomioka
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Wenxian Xie
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tao Liang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yalu Cui
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Takashi Sato
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Hiroyuki Kaji
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan; SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai, China
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai, China.
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11
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LY75 Ablation Mediates Mesenchymal-Epithelial Transition (MET) in Epithelial Ovarian Cancer (EOC) Cells Associated with DNA Methylation Alterations and Suppression of the Wnt/β-Catenin Pathway. Int J Mol Sci 2020; 21:ijms21051848. [PMID: 32156068 PMCID: PMC7084525 DOI: 10.3390/ijms21051848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 02/07/2023] Open
Abstract
Growing evidence demonstrates that epithelial-mesenchymal transition (EMT) plays an important role in epithelial ovarian cancer (EOC) progression and spreading; however, its molecular mechanisms remain poorly defined. We have previously shown that the antigen receptor LY75 can modulate EOC cell phenotype and metastatic potential, as LY75 depletion directed mesenchymal-epithelial transition (MET) in EOC cell lines with mesenchymal phenotype. We used the LY75-mediated modulation of EMT as a model to investigate for DNA methylation changes during EMT in EOC cells, by applying the reduced representation bisulfite sequencing (RRBS) methodology. Numerous genes have displayed EMT-related DNA methylation patterns alterations in their promoter/exon regions. Ten selected genes, whose DNA methylation alterations were further confirmed by alternative methods, were further identified, some of which could represent new EOC biomarkers/therapeutic targets. Moreover, our methylation data were strongly indicative for the predominant implication of the Wnt/β-catenin pathway in the EMT-induced DNA methylation variations in EOC cells. Consecutive experiments, including alterations in the Wnt/β-catenin pathway activity in EOC cells with a specific inhibitor and the identification of LY75-interacting partners by a proteomic approach, were strongly indicative for the direct implication of the LY75 receptor in modulating the Wnt/β-catenin signaling in EOC cells.
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12
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Sheta R, Bachvarova M, Macdonald E, Gobeil S, Vanderhyden B, Bachvarov D. The polypeptide GALNT6 Displays Redundant Functions upon Suppression of its Closest Homolog GALNT3 in Mediating Aberrant O-Glycosylation, Associated with Ovarian Cancer Progression. Int J Mol Sci 2019; 20:E2264. [PMID: 31071912 PMCID: PMC6539655 DOI: 10.3390/ijms20092264] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 11/17/2022] Open
Abstract
Epithelial ovarian cancer (EOC) represents the most lethal gynecologic malignancy; a better understanding of the molecular mechanisms associated with EOC etiology could substantially improve EOC management. Aberrant O-glycosylation in cancer is attributed to alteration of N-acetylgalactosaminyltransferases (GalNAc-Ts). Reports suggest a genetic and functional redundancy between GalNAc-Ts, and our previous data are indicative of an induction of GALNT6 expression upon GALNT3 suppression in EOC cells. We performed single GALNT3 and double GALNT3/T6 suppression in EOC cells, using a combination of the CRISPR-Cas9 system and shRNA-mediated gene silencing. The effect of single GALNT3 and double GALNT3/T6 inhibition was monitored both in vitro (on EOC cells roliferation, migration, and invasion) and in vivo (on tumor formation and survival of experimental animals). We confirmed that GALNT3 gene ablation leads to strong and rather compensatory GALNT6 upregulation in EOC cells. Moreover, double GALNT3/T6 suppression was significantly associated with stronger inhibitory effects on EOC cell proliferation, migration, and invasion, and accordingly displayed a significant increase in animal survival rates compared with GALNT3-ablated and control (Ctrl) EOC cells. Our data suggest a possible functional redundancy of GalNAc-Ts (GALNT3 and T6) in EOC, with the perspective of using both these enzymes as novel EOC biomarkers and/or therapeutic targets.
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Affiliation(s)
- Razan Sheta
- Department of Molecular Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
- CHU de Québec Research Center, Oncology axis Québec, Québec, QC G1V 4G2, Canada.
| | - Magdalena Bachvarova
- CHU de Québec Research Center, Oncology axis Québec, Québec, QC G1V 4G2, Canada.
| | - Elizabeth Macdonald
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Stephane Gobeil
- Department of Molecular Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
- CHU de Québec Research Center, Endocrinology and Nephrology axis Québec, Québec, QC G1V 4G2, Canada.
| | - Barbara Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Dimcho Bachvarov
- Department of Molecular Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
- CHU de Québec Research Center, Oncology axis Québec, Québec, QC G1V 4G2, Canada.
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13
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Duan J, Chen L, Gao H, Zhen T, Li H, Liang J, Zhang F, Shi H, Han A. GALNT6 suppresses progression of colorectal cancer. Am J Cancer Res 2018; 8:2419-2435. [PMID: 30662801 PMCID: PMC6325480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/14/2018] [Indexed: 06/09/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors in the world. Invasion and metastasis are the main cause of mortality in most CRC patients. Polypeptide N-acetylgalactosaminyltransferase 6 (GALNT6) regulated glycosylation, which is frequently altered in cancers, and play an important role in cancer development. However, the role of GALNT6 in CRC remains unknown. To investigate the role of GALNT6 in CRC, first we studied correlation of GALNT6 expression levels with outcomes of CRC patients and found CRC patients with higher expression of GALNT6 had a better overall survival than those with lower expression. In addition, GALNT6 expression were significantly associated with tumor size, histological differentiation and lymph node metastasis. In vitro, GALNT6 overexpression dramatically inhibited cellular colony formation, migration, and invasion, and promoted the apoptosis of CRC cells. In vivo, CRC with GALNT6 overexpression showed reduced pulmonary metastasis in recipient mice compared with the controls. GALNT6 expression was significantly increased in SW480 and SW1116 cells cultured in hypoxic condition, and decreased in HT29 and LOVO cells with oxidative stress. Affimetrix microarray analysis showed that GALNT6 overexpression induced 279 genes up-regulated and 215 genes down-regulated in CRC. GALNT6 overexpression dramatically suppressed AKT and activated CD28 signaling pathway in CRC. AKT rescue experiment found that AKT was involved in GALNT6-induced CRC cell migration and invasion. In conclusion, our results first suggest that GALNT6 plays an important role in development and progression of CRC as a tumor suppressor gene.
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Affiliation(s)
- Jing Duan
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Lin Chen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Huabin Gao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Tiantian Zhen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Hui Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Jiangtao Liang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Fenfen Zhang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Huijuan Shi
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
| | - Anjia Han
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University Guangzhou, China
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14
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Sahasrabudhe NM, Lenos K, van der Horst JC, Rodríguez E, van Vliet SJ. Oncogenic BRAFV600E drives expression of MGL ligands in the colorectal cancer cell line HT29 through N-acetylgalactosamine-transferase 3. Biol Chem 2018; 399:649-659. [PMID: 29894293 DOI: 10.1515/hsz-2018-0120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/12/2018] [Indexed: 01/06/2023]
Abstract
Colorectal cancer is the third most common cancer type worldwide. It is characterized by a high expression of aberrantly glycosylated ligands, such as the Tn antigen (GalNAcα1-Ser/Thr), which is a major ligand for the C-type lectin macrophage galactose-type lectin (MGL). We have previously determined that a high level of MGL ligands in colorectal tumors is associated with lower disease-free survival in patients with late stage disease, which we could attribute to the presence of oncogenic BRAFV600E mutations. Here we aimed to elucidate the downstream pathway of BRAFV600E governing high MGL ligand and Tn antigen expression. We focused on glycosylation-related enzymes involved in the synthesis or elongation of Tn antigen, N-acetylgalactosamine-transferases (GALNTs) and C1GalT1/COSMC, respectively. Both the activity and expression of C1GalT1 and COSMC were unrelated to the BRAF mutational status. In contrast, GALNT3, GALNT7 and GALNT12 were increased in colorectal cancer cells harboring the BRAFV600E mutation. Through CRISPR-Cas9 gene knockouts we could establish that GALNT3 increased MGL ligand synthesis in the HT29 cell line, while GALNT7 and GALNT12 appeared to have redundant roles. Together our results highlight a novel mechanistic pathway connecting BRAFV600E to aberrant glycosylation in colorectal cancer through GALNT3.
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Affiliation(s)
- Neha M Sahasrabudhe
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Kristiaan Lenos
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Joost C van der Horst
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Ernesto Rodríguez
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - Sandra J van Vliet
- Department of Molecular Cell Biology and Immunology, Cancer Center Amsterdam, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
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15
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Kailemia MJ, Xu G, Wong M, Li Q, Goonatilleke E, Leon F, Lebrilla CB. Recent Advances in the Mass Spectrometry Methods for Glycomics and Cancer. Anal Chem 2018; 90:208-224. [PMID: 29049885 PMCID: PMC6200424 DOI: 10.1021/acs.analchem.7b04202] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Muchena J. Kailemia
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- These authors contributed equally to this work
| | - Maurice Wong
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Frank Leon
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
- Foods for Health Institute, University of California, Davis, CA 95616, USA
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16
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Sheta R, Bachvarova M, Plante M, Gregoire J, Renaud MC, Sebastianelli A, Popa I, Bachvarov D. Altered expression of different GalNAc‑transferases is associated with disease progression and poor prognosis in women with high-grade serous ovarian cancer. Int J Oncol 2017; 51:1887-1897. [PMID: 29039611 DOI: 10.3892/ijo.2017.4147] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/25/2017] [Indexed: 11/06/2022] Open
Abstract
Protein glycosylation perturbations are implicated in a variety of diseases, including cancer. Aberrant glycosylation in cancer is frequently attributed to altered expression of polypeptide GalNAc transferases (GalNAc‑Ts) - enzymes initiating mucin-type O-glycosylation. A previous study from our group demonstrated that one member of this family (GALNT3) is overexpressed in epithelial ovarian cancer (EOC), and GALNT3 expression correlated with shorter progression-free survival (PFS) in EOC patients with advanced disease. As considerable degree of redundancy between members of the GalNAc‑Ts gene family has been frequently observed, we decided to investigate whether other members of this family are essential in EOC progression. In silico analysis based on publically available data was indicative for altered expression of five GalNAc‑Ts (GALNT2, T4, T6, T9 and T14) in ovarian high-grade serous carcinoma (HGSC) samples compared to non-tumoral (control) ovarian tissue. We analyzed protein expression of these GalNAc‑Ts in EOC cells and tumors by western blotting, followed by immunohistochemical (IHC) evaluation of their expression in EOC tumor and control samples using tissue microarrays (TMAs). Western blot analyses were indicative for low expression of GALNT2 and strong expression of GALNT6, T9 and T14 in both EOC cells and tumors. These observations were confirmed by IHC. GALNT2 displayed significantly lower expression, while GALNT6, GALNT9 and GALNT14 showed significantly higher expression in HGSC tumors compared to control tissue. Importantly, GALNT6 and GALNT14 expression correlated with poor prognosis of serous EOC patients. Moreover, our results suggest for overlapping functions of some GalNAc‑Ts, more specifically GALNT3 and GALNT6, in directing EOC progression. Our results are indicative for a possible implication of different members of the GalNAc‑T gene family in modulating EOC progression, and the potential use of GALNT6 and GALNT14 as novel prognostic EOC biomarkers. These data warrant future studies on the role of members of the GalNAc‑Ts gene family in ovarian tumorigenesis.
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Affiliation(s)
- Razan Sheta
- Department of Molecular Medicine, Laval University, Quebec, Quebec G1V 0A6, Canada
| | | | - Marie Plante
- CHU de Québec Research Center, Hotel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Jean Gregoire
- CHU de Québec Research Center, Hotel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | - Marie-Claude Renaud
- CHU de Québec Research Center, Hotel-Dieu de Québec, Quebec, QC G1R 3S3, Canada
| | | | - Ion Popa
- Molecular Biology, Medical Biochemistry, and Pathology, Laval University, QC G1V 0A6, Canada
| | - Dimcho Bachvarov
- Department of Molecular Medicine, Laval University, Quebec, Quebec G1V 0A6, Canada
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17
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Xu Z, Li X, Zhou S, Xie W, Wang J, Cheng L, Wang S, Guo S, Xu Z, Cao X, Zhang M, Yu B, Narimatsu H, Tao SC, Zhang Y. Systematic identification of the protein substrates of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T1/T2/T3 using a human proteome microarray. Proteomics 2017; 17. [PMID: 28394504 DOI: 10.1002/pmic.201600485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/31/2017] [Accepted: 04/07/2017] [Indexed: 12/12/2022]
Abstract
O-GalNAc glycosylation is the initial step of the mucin-type O-glycosylation. In humans, it is catalyzed by a family of 20 homologous UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts). So far, there is very limited information on their protein substrate specificities. In this study, we developed an on-chip ppGalNAc-Ts assay that could rapidly and systematically identify the protein substrates of each ppGalNAc-T. In detail, we utilized a human proteome microarray as the protein substrates and UDP-GalNAz as the nucleotide sugar donor for click chemistry detection. From a total of 16 368 human proteins, we identified 570 potential substrates of ppGalNAc-T1, T2, and T3. Among them, 128 substrates were overlapped, while the rest were isoform specific. Further cluster analysis of these substrates showed that the substrates of ppGalNAc-T1 had a closer phylogenetic relationship with that of ppGalNAc-T3 compared with ppGalNAc-T2, which was consistent with the topology of the phylogenetic tree of these ppGalNAc-Ts. Taken together, our microarray-based enzymatic assay comprehensively reveals the substrate profile of the ppGalNAc-T1, T2, and T3, which not only provides a plausible explanation for their partial functional redundancy as reported, but clearly implies some specialized roles of each enzyme in different biological processes.
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Affiliation(s)
- Zhijue Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xing Li
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shumin Zhou
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenxian Xie
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Jing Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Microbial metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Li Cheng
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, P. R. China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Sheng Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Shujuan Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Zhaowei Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xin Cao
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Menghui Zhang
- State Key Laboratory of Microbial metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Biao Yu
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Hisashi Narimatsu
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- SCSB (China) - AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, P. R. China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine (SCSB), Shanghai Jiao Tong University, Shanghai, P. R. China
- State Key Laboratory of Microbial metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
- SCSB (China) - AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai Jiao Tong University, Shanghai, P. R. China
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Tremblay RR, Bourassa S, Nehmé B, Calvo EL. Daylily protein constituents of the pollen and stigma a proteomics approach. JOURNAL OF PLANT PHYSIOLOGY 2017; 212:1-12. [PMID: 28242413 DOI: 10.1016/j.jplph.2017.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 01/18/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
This study was aimed at the identification and quantification of the protein components of the pollen grains in parallel with the distal stigmatic tissue of tetraploid cultivars. Proteomes were analyzed using iTRAQ 4plex labeling, peptides separation by online RP-nano-LC and analysis by ESI-MS/MS. Protein identification and quantification were made using the Asparagales database as a reference. A total of 524,037 MS/MS spectra were produced from pollen and stigma samples. From these, a total of 8368 peptides wereidentified corresponding to 994 unique peptides and 432 protein groups. Among them, 128 differentially expressed proteins were retained for further analysis. In absence of the daylily genome availability, we exploited numerous databases and bioinformatics resources to exploring the putative biological functions of these proteins. The profile of differentially expressed proteins suggests an important representation of functions associated to the signalling and response against endogenous and environmental stresses, including several enzymes implicated in the biosynthesis of antibiotics. The abundance in stigma of several structural proteins of the ribosomal sub-units as well as of the core histones suggest that the translation processes and the regulation of gene expression in stigma is a more active mechanism than in pollen. In addition, pollen prioritizes the synthesis of fructose and glucose as opposed to sucrose in stigma as a source of energy. Finally, the modulated proteins in Hemerocallis point to several pathways that give potential clues concerning the molecular mechanisms underlying the functions of the pollen and the stigmatic fluid in daylily reproduction.
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Affiliation(s)
- Roland R Tremblay
- CHUL Research Center in Reproduction, Centre de Recherche du CHU de Québec,2705 Boulevard Laurier, Suite T3-67, Quebec City, QC, G1 V 4G2, Canada.
| | - Sylvie Bourassa
- Proteomics Platform Quebec Genomics Center, CRCHUL, Centre de Recherche du CHU de Quebec, Canada.
| | - Benjamin Nehmé
- Proteomics Platform Quebec Genomics Center, CRCHUL, Centre de Recherche du CHU de Quebec, Canada.
| | - Ezequiel L Calvo
- Scientific Consultant in Genomics, 701 Leonard, Quebec City, QC, G1X 4C9, Canada.
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Hernandez-Unzueta I, Benedicto A, Olaso E, Sanz E, Viera C, Arteta B, Márquez J. Ocoxin oral solution ® as a complement to irinotecan chemotherapy in the metastatic progression of colorectal cancer to the liver. Oncol Lett 2017; 13:4002-4012. [PMID: 28599406 PMCID: PMC5453048 DOI: 10.3892/ol.2017.6016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/07/2017] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is an aggressive disease in which patients usually die due to its metastatic progression to the liver. Up to date, irinotecan is one of the most used chemotherapeutic agents to treat CRC metastasis with demonstrated efficacy. However, the severity of the side effects constitute the main limitation to its use in the treatment. Consequently, new complementary therapies are being developed to avoid these adverse effects while maintaining the efficacy of the antitumoral drugs. Ocoxin oral solution (OOS®) is a nutritional mixture containing biologically active compounds with demonstrated antitumoral and immunomodulatory effects. Thus, we aimed to analyze the effect of OOS® as a suitable complement to irinotecan therapy in the treatment of CRC metastasis to the liver. First, the effect of OOS®, irinotecan and the combination of both on the viability of C26 cells was tested in vitro and in vivo. Second, the expression of caspase-3, Ki67 and the macrophage infiltration by F4/80 marker was quantified in liver tissue sections by immunohistochemistry. Finally, mRNA microarray study was carried out on tumor cells isolated from tumor-bearing livers collected from mice subjected to the above treatments. Our results show that OOS® administered as a complementary therapy to irinotecan reduced tumor cell viability in vitro. Moreover, irinotecan administered either alone or in combination with 100 µl OOS® from the 7th day after tumor cell inoculation decreased the metastatic growth in the liver. Besides, several genes with binding and catalytic activities showed to be deregulated by RNA microarray analysis. In conclusion, OOS®, when administered as a complement to irinotecan, reduced the metastatic development of colorectal cancer to the liver. Additionally, the overall health state of the animals improved. These results point out OOS® as a potential supplement to the anti-tumoral treatments used in clinical settings in patients suffering from disseminated colorectal cancer.
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Affiliation(s)
- Iera Hernandez-Unzueta
- Department Cell Biology and Histology, School of Medicine and Dentistry, Basque Country University, Leioa, E-48940 Bizkaia, Spain
| | - Aitor Benedicto
- Department Cell Biology and Histology, School of Medicine and Dentistry, Basque Country University, Leioa, E-48940 Bizkaia, Spain
| | - Elvira Olaso
- Department Cell Biology and Histology, School of Medicine and Dentistry, Basque Country University, Leioa, E-48940 Bizkaia, Spain
| | | | - Cristina Viera
- Department Cell Biology and Histology, School of Medicine and Dentistry, Basque Country University, Leioa, E-48940 Bizkaia, Spain
| | - Beatriz Arteta
- Department Cell Biology and Histology, School of Medicine and Dentistry, Basque Country University, Leioa, E-48940 Bizkaia, Spain
| | - Joana Márquez
- Department Cell Biology and Histology, School of Medicine and Dentistry, Basque Country University, Leioa, E-48940 Bizkaia, Spain
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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Proteomic dataset for altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells. Data Brief 2016; 8:342-9. [PMID: 27331112 PMCID: PMC4908283 DOI: 10.1016/j.dib.2016.05.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/12/2016] [Accepted: 05/24/2016] [Indexed: 01/20/2023] Open
Abstract
This article contains raw and processed data related to research published in "Role of the polypeptide N-acetylgalactosaminyltransferase 3 in ovarian cancer progression: possible implications in abnormal mucin O-glycosylation" [1]. The data presented here was obtained with the application of a bioorthogonal chemical reporter strategy analyzing differential glycoprotein expression following the knock-down (KD) of the GALNT3 gene in the epithelial ovarian cancer (EOC) cell line A2780s. LC-MS/MS mass spectrometry analysis was then performed and the processed data related to the identified glycoproteins show that several hundred proteins are differentially expressed between control and GALNT3 KD A2780s cells. The obtained data also uncover numerous novel glycoproteins; some of which could represent new potential EOC biomarkers and/or therapeutic targets.
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