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Chen Z, Jiang H, Qin Q, Li Q, Hong L. DNA methylation signatures provide novel diagnostic biomarkers and predict responses of immune therapy for breast cancer. Front Genet 2024; 15:1403907. [PMID: 38911294 PMCID: PMC11190699 DOI: 10.3389/fgene.2024.1403907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Breast cancer (BRCA) is one of the most common malignant tumors affecting women worldwide. DNA methylation modifications can influence oncogenic pathways and provide potential diagnostic and therapeutic targets for precision oncology. In this study, we used non-parametric permutation tests to identify differentially methylated positions (DMPs) between paired tumor and normal BRCA tissue samples from the Cancer Genome Atlas (TCGA) database. Then, we applied non-negative matrix factorization (NMF) to the DMPs to derive eight distinct DNA methylation signatures. Among them, signatures Hyper-S3 and Hypo-S4 signatures were associated with later tumor stages, while Hyper-S1 and Hypo-S3 exhibited higher methylation levels in earlier stages. Signature Hyper-S3 displayed an effect on overall survival. We further validated the four stage-associated signatures using an independent BRCA DNA methylation dataset from peripheral blood samples. Results demonstrated that 24 commonly hypomethylated sites in Hypo-S4 showed lower methylation in BRCA patients compared to healthy individuals, suggesting its potential as an early diagnostic biomarker. Furthermore, we found that methylation of 23 probes from four stage-related signatures exhibited predictive power for immune therapy response. Notably, methylation levels of all three probes from the Hypo-S4 and activity of the Hypo-S4 demonstrated highly positive relevance to PD-L1 gene expression, implying their significant predictive values for immunotherapy outcomes. GO and KEGG pathway enrichment analysis revealed that genes with these 23 immunotherapy-related methylation probes are mainly involved in glycan degradation or protein deglycosylation. These methylation signatures and probes may serve as novel epigenetic biomarkers for predicting tumor immunotherapy response. Our findings provide new insights into precision oncology approaches for BRCA.
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Affiliation(s)
- Zhishan Chen
- Department of Breast and Thyroid Surgery, Nan’an Hospital, Quanzhou, China
| | - Han Jiang
- Department of General Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Qingqing Qin
- School of Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- School of Medicine, Xiamen University, Xiamen, China
| | - Liqing Hong
- Department of Breast and Thyroid Surgery, Nan’an Hospital, Quanzhou, China
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Wang H, Zheng J, Ma Q, Zhang J, Li Y. GLT8D2 is a prognostic biomarker and regulator of immune cell infiltration in gastric cancer. Front Immunol 2024; 15:1370367. [PMID: 38840920 PMCID: PMC11150579 DOI: 10.3389/fimmu.2024.1370367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Because of the considerable tumor heterogeneity in gastric cancer (GC), only a limited group of patients experiences positive outcomes from immunotherapy. Herein, we aim to develop predictive models related to glycosylation genes to provide a more comprehensive understanding of immunotherapy for GC. RNA sequencing (RNA-seq) data and corresponding clinical outcomes were obtained from GEO and TCGA databases, and glycosylation-related genes were obtained from GlycoGene DataBase. We identified 48 differentially expressed glycosylation-related genes and established a prognostic model (seven prognosis genes including GLT8D2, GALNT6, ST3GAL6, GALNT15, GBGT1, FUT2, GXYLT2) based on these glycosylation-related genes using the results from Cox regression analysis. We found that these glycosylation-related genes revealed a robust correlation with the abundance of Tumor Infiltrating Lymphocytes (TILs), especially the GLT8D2 which is associated with many TILs. Finally, we employed immunohistochemistry and Multiplex Immunohistochemical to discover that GLT8D2 serves as a valuable prognostic biomarker in GC and is closely associated with macrophage-related markers. Collectively, we established a prognostic model based on glycosylation-related genes to provide a more comprehensive understanding of prediction for GC prognosis, and identified that GLT8D2 is closely correlated with adverse prognosis and may underscore its role in regulating immune cell infiltration in GC patients.
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Affiliation(s)
- Han Wang
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jiabin Zheng
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qingyang Ma
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Junchang Zhang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Yong Li
- Department of Gastrointestinal Surgery, Department of General Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y. Spatial imaging of glycoRNA in single cells with ARPLA. Nat Biotechnol 2024; 42:608-616. [PMID: 37217750 PMCID: PMC10663388 DOI: 10.1038/s41587-023-01801-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.
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Affiliation(s)
- Yuan Ma
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Weijie Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Quanbing Mou
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xiangli Shao
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Mingkuan Lyu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Valeria Garcia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Linggen Kong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Whitney Lewis
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Carson Ward
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhenglin Yang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xingxin Pan
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - S Stephen Yi
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA.
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Rostami Abookheili A, Asadi J, Khosravi A, Gorji A. Fucosyltransferase 3 and 8 promote the metastatic capacity of cancer stem-like cells via CD15s and E-cadherin in esophageal cancer. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:985-995. [PMID: 38911244 PMCID: PMC11193496 DOI: 10.22038/ijbms.2024.74726.16228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/30/2023] [Indexed: 06/25/2024]
Abstract
Objectives Esophageal cancer stem cells (ECSCs) have been identified as the subset of cells within esophageal squamous cell carcinoma that possess tumorigenic, invasive, and metastatic properties. One important aspect of cancer metastasis is the binding of sialyl-Lewis X (CD15s) with E- or P-selectin, which facilitates the adhesion and migration of cancer cells to distant sites. This study was conducted to investigate the impact of fucosylation processes on the metastatic behavior of ECSCs. Materials and Methods The esophageal cancer cell line (KYSE-30) was cultured and divided into control and 2F-peracetyl fucose (2F-PerAcFuc) treated groups. Spheres were harvested from these cultures. Cell invasion assay and qPCR were conducted to examine migration and marker expression in both groups. Cancer cell line-derived xenografts were established in nude mice to validate findings in vivo. Results Our results initially indicated that the addition of 2F-PerAcFuc, an inhibitor of fucosylation, resulted in the down-regulation of the Fut3/CD15s pathway in both cancer stem-like cells and the xenograft model. Measurements of subcutaneous xenograft tumor volume revealed a significant decrease in tumor size among nude mice after treatment with 2F-PerAcFuc. Additionally, a reduction in Fut8/E-cadherin levels was observed in the xenograft model of nude mice. Furthermore, the administration of 2F-PerAcFuc lowered the levels of fucosylated glycoconjugates in nude mice. Conclusion Our data suggest that inhibition of fucosyltransferase 3 and 8 can reduce the metastatic capacity of cancer stem-like cells by down-regulating CD15s and E-cadherin in a mouse model of esophageal cancer.
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Affiliation(s)
- Aliakbar Rostami Abookheili
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
- Shefa Neuroscience Research Center, Khatam Al-anbia Hospital, Tehran, Iran
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ayyoob Khosravi
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Gorji
- Shefa Neuroscience Research Center, Khatam Al-anbia Hospital, Tehran, Iran
- Epilepsy Research Center, Westfälische Wilhelms-Universität Münster, Münster, Germany
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Wang D. Targeting the stage-specific embryonic antigen (SSEA)-0 tumor neoantigen. CURRENT TRENDS IN IMMUNOLOGY 2023; 24:1-7. [PMID: 38699667 PMCID: PMC11064955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Recognition of abnormal glycosylation in virtually any cancer type has raised a great interest in the glycan-based tumor biomarkers. Our team explored carbohydrate microarrays as a broad-spectrum immunoassay to probe the immunologically potent tumor glycan targets. This effort has led to the identification of a blood group precursor antigen SSEA-0 as a conserved breast cancer (BCA) marker. Since this immunogenic O-core glycan is normally hidden as a cryptic antigen but becomes overexpressed and surface-exposed by metastatic breast cancer cells (MBCA), its potential as a novel immunological target for precision immunotherapy against tumor metastasis warrants a focused investigation.
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Affiliation(s)
- Denong Wang
- Tumor Glycomics Laboratory, SRI International Biosciences Division, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
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Enzymatic Digestion of Cell-surface Heparan Sulfate Alters the Radiation Response in Triple-negative Breast Cancer Cells. Arch Med Res 2022; 53:826-839. [PMID: 36411172 DOI: 10.1016/j.arcmed.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND AIM Radiation resistance represents a major challenge in the treatment of breast cancer. As heparan sulfate (HS) chains are known to contribute to tumorigenesis, we aimed to investigate the interplay between HS degradation and radiation response in triple-negative breast cancer (TNBC) cells. METHODS HS chains were degraded in vitro as TNBC cells MDA-MB-231 and HCC1806 were treated with heparinase I and III. Subsequently, radioresistance was determined via colony formation assay after doses of 2, 4 and 6 Gy. Cell cycle profile, stem cell characteristics, expression of HS, activation of beta integrins, and apoptosis were determined by flow cytometry. Additionally, cell motility was analyzed via wound-healing assays, and expression and activation of FAK, CDK-6, Src, and Erk1/2 were quantified by western blot pre- and post-irradiation. Finally, the expression of cytokines was analyzed using a cytokine array. RESULTS Radiation promoted cell cycle changes, while heparinase treatment induced apoptosis in both cell lines. Colony formation assays showed significantly increased radio-resistance for both cell lines after degradation of HS. Cell migration was similarly upregulated after degradation of HS compared to controls. This effect was even more prominent after irradiation. Interestingly, FAK, a marker of radioresistance, was significantly activated in the heparinase-treated group. Additionally, we found Src to be dysregulated in MDA-MB-231 cells. Finally, we observed differential secretion of GRO, CXCL1, IGFBP1, IL8, Angiogenin, and Osteoprotegerin after HS degradation and radiotherapy. CONCLUSION Our results suggest an influence of HS chains on the development of radioresistance in TNBC.
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Rujchanarong D, Scott D, Park Y, Brown S, Mehta AS, Drake R, Sandusky GE, Nakshatri H, Angel PM. Metabolic Links to Socioeconomic Stresses Uniquely Affecting Ancestry in Normal Breast Tissue at Risk for Breast Cancer. Front Oncol 2022; 12:876651. [PMID: 35832545 PMCID: PMC9273232 DOI: 10.3389/fonc.2022.876651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
A primary difference between black women (BW) and white women (WW) diagnosed with breast cancer is aggressiveness of the tumor. Black women have higher mortalities with similar incidence of breast cancer compared to other race/ethnicities, and they are diagnosed at a younger age with more advanced tumors with double the rate of lethal, triple negative breast cancers. One hypothesis is that chronic social and economic stressors result in ancestry-dependent molecular responses that create a tumor permissive tissue microenvironment in normal breast tissue. Altered regulation of N-glycosylation of proteins, a glucose metabolism-linked post-translational modification attached to an asparagine (N) residue, has been associated with two strong independent risk factors for breast cancer: increased breast density and body mass index (BMI). Interestingly, high body mass index (BMI) levels have been reported to associate with increases of cancer-associated N-glycan signatures. In this study, we used matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) to investigate molecular pattern changes of N-glycosylation in ancestry defined normal breast tissue from BW and WW with significant 5-year risk of breast cancer by Gail score. N-glycosylation was tested against social stressors including marital status, single, education, economic status (income), personal reproductive history, the risk factors BMI and age. Normal breast tissue microarrays from the Susan G. Komen tissue bank (BW=43; WW= 43) were used to evaluate glycosylation against socioeconomic stress and risk factors. One specific N-glycan (2158 m/z) appeared dependent on ancestry with high sensitivity and specificity (AUC 0.77, Brown/Wilson p-value<0.0001). Application of a linear regression model with ancestry as group variable and socioeconomic covariates as predictors identified a specific N-glycan signature associated with different socioeconomic stresses. For WW, household income was strongly associated to certain N-glycans, while for BW, marital status (married and single) was strongly associated with the same N-glycan signature. Current work focuses on understanding if combined N-glycan biosignatures can further help understand normal breast tissue at risk. This study lays the foundation for understanding the complexities linking socioeconomic stresses and molecular factors to their role in ancestry dependent breast cancer risk.
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Affiliation(s)
- Denys Rujchanarong
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Danielle Scott
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Yeonhee Park
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sean Brown
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Anand S. Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - Richard Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
| | - George E. Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Peggi M. Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence, Clinical Glycomics, Medical University of South Carolina, Charleston, SC, United States
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Xu S, Liu Y, Ma H, Fang S, Wei S, Li X, Lu Z, Zheng Y, Liu T, Zhu X, Xu D, Pan Y. A Novel Signature Integrated of Immunoglobulin, Glycosylation and Anti-Viral Genes to Predict Prognosis for Breast Cancer. Front Genet 2022; 13:834731. [PMID: 35432482 PMCID: PMC9011196 DOI: 10.3389/fgene.2022.834731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/14/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Aberrant glycosylation is significantly related to the occurrence, progression, metastasis, and drug resistance of tumors. It is essential to identify glycosylation and related genes with prognostic value for breast cancer. Objective: We aimed to construct and validate a prognostic model based on glycosylation and related genes, and further investigate its prognosis values in validation set and external independent cohorts. Materials and Methods: The transcriptome and clinical data of breast cancer patients were downloaded from The Cancer Genome Atlas (TCGA, n = 1072), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC, n = 1451), and GSE2741 (n = 120). Glycosylation-related genes were downloaded from the Genecards website. Differentially expressed glycosylation-related geneswere identified by comparing the tumor tissues with the adjacent tissues. The TCGA data were randomly divided into training set and validation set in a 1:1 ratio for further analysis. The glycosylation risk-scoring prognosis model was constructed by univariate and multivariate Cox regression analysis, followed by confirmation in TCGA validation, METABRIC, and GEO datasets. Gene set enrichment analysis (GSEA) and Gene ontology analysis for identifying the affected pathways in the high- and low-risk groups were performed. Results: We attained 1072 breast cancer samples from the TCGA database and 786 glycosylation genes from the Genecards website. A signature contains immunoglobulin, glycosylation and anti-viral related genes was constructed to separate BRCA patients into two risk groups. Low-risk patients had better overall survival than high-risk patients (p < 0.001). A nomogram was constructed with risk scores and clinical characteristics. The area under time-dependent ROC curve reached 0.764 at 1 year, 0.744 at 3 years, and 0.765 at 5 years in the training set. Subgroup analysis showed differences in OS between the high- and low-risk patients in different subgroups. Moreover, the risk score was confirmed as an independent prognostic indicator of BRCA patients and was potentially correlated with immunotherapy response and drug sensitivity. Conclusion: We identified a novel signature integrated of immunoglobulin (IGHA2), glycosylation-related (SLC35A2) and anti-viral gene (BST2) that was an independent prognostic indicator for BRCA patients. The risk-scoring model could be used for predicting prognosis and immunotherapy in BRCA, thus providing a powerful instrument for combating BRCA.
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Affiliation(s)
- Shengshan Xu
- Department of Thoracic Surgery, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yuchen Liu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yuchen Liu, ; Dongming Xu, ; Yihang Pan,
| | - Hansu Ma
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shuo Fang
- Department of Oncology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Shoupeng Wei
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiaoping Li
- Department of Breast, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
| | - Zhuming Lu
- Department of Thoracic Surgery, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
| | - Youbin Zheng
- Department of Radiology, Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen, China
| | - Tong Liu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, China
| | - Xiaojian Zhu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Dongming Xu
- Department of Neurosurgery, The Country Hospital of Qianguo, Songyuan, China
- *Correspondence: Yuchen Liu, ; Dongming Xu, ; Yihang Pan,
| | - Yihang Pan
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yuchen Liu, ; Dongming Xu, ; Yihang Pan,
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Glycomic and Glycoproteomic Techniques in Neurodegenerative Disorders and Neurotrauma: Towards Personalized Markers. Cells 2022; 11:cells11030581. [PMID: 35159390 PMCID: PMC8834236 DOI: 10.3390/cells11030581] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The proteome represents all the proteins expressed by a genome, a cell, a tissue, or an organism at any given time under defined physiological or pathological circumstances. Proteomic analysis has provided unparalleled opportunities for the discovery of expression patterns of proteins in a biological system, yielding precise and inclusive data about the system. Advances in the proteomics field opened the door to wider knowledge of the mechanisms underlying various post-translational modifications (PTMs) of proteins, including glycosylation. As of yet, the role of most of these PTMs remains unidentified. In this state-of-the-art review, we present a synopsis of glycosylation processes and the pathophysiological conditions that might ensue secondary to glycosylation shortcomings. The dynamics of protein glycosylation, a crucial mechanism that allows gene and pathway regulation, is described. We also explain how-at a biomolecular level-mutations in glycosylation-related genes may lead to neuropsychiatric manifestations and neurodegenerative disorders. We then analyze the shortcomings of glycoproteomic studies, putting into perspective their downfalls and the different advanced enrichment techniques that emanated to overcome some of these challenges. Furthermore, we summarize studies tackling the association between glycosylation and neuropsychiatric disorders and explore glycoproteomic changes in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington disease, multiple sclerosis, and amyotrophic lateral sclerosis. We finally conclude with the role of glycomics in the area of traumatic brain injury (TBI) and provide perspectives on the clinical application of glycoproteomics as potential diagnostic tools and their application in personalized medicine.
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Bertok T, Pinkova Gajdosova V, Bertokova A, Svecova N, Kasak P, Tkac J. Breast cancer glycan biomarkers: their link to tumour cell metabolism and their perspectives in clinical practice. Expert Rev Proteomics 2021; 18:881-910. [PMID: 34711108 DOI: 10.1080/14789450.2021.1996231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Breast cancer (BCa) is the most common cancer type diagnosed in women and 5th most common cause of deaths among all cancer deaths despite the fact that screening program is at place. This is why novel diagnostics approaches are needed in order to decrease number of BCa cases and disease mortality. AREAS COVERED In this review paper, we aim to cover some basic aspects regarding cellular metabolism and signalling in BCa behind altered glycosylation. We also discuss novel exciting discoveries regarding glycan-based analysis, which can provide useful information for better understanding of the disease. The final part deals with clinical usefulness of glycan-based biomarkers and the clinical performance of such biomarkers is compared to already approved BCa biomarkers and diagnostic tools based on imaging. EXPERT OPINION Recent discoveries suggest that glycan-based biomarkers offer high accuracy for possible BCa diagnostics in blood, but also for better monitoring and management of BCa patients. The review article was written using Web of Science search engine to include articles published between 2019 and 2021.
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Affiliation(s)
- Tomas Bertok
- Glycanostics Ltd., Bratislava, Slovak Republic.,Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Veronika Pinkova Gajdosova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | | | - Natalia Svecova
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kasak
- Center for Advanced Materials, Qatar University, Doha, Qatar
| | - Jan Tkac
- Glycanostics Ltd., Bratislava, Slovak Republic.,Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
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Polypeptide-GalNAc-Transferase-13 Shows Prognostic Impact in Breast Cancer. Cancers (Basel) 2021; 13:cancers13225616. [PMID: 34830771 PMCID: PMC8616257 DOI: 10.3390/cancers13225616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Breast cancer is a public health concern and is currently the fifth cause of mortality worldwide. Identification of different biological subtypes is essential for clinical management; therefore, the role of pathologists is essential and useful tools for immunohistochemistry diagnosis are needed. Polypeptide-GalNAc-transferases are emerging novel biomarkers related to cancer behavior and GalNAc-T13, correlated with aggressiveness in some tumors, is an interesting candidate. Few monoclonal antibodies reacting with native proteins, and not affected by fixation and paraffin embedding, have been reported. The aim of this work was to develop a useful monoclonal antibody anti-GalNAc-T13 and to assess its potential significance in breast cancer diagnosis. We evaluated 6 human breast cancer cell lines, 338 primary breast tumors and 48 metastatic lymph nodes and looked for clinical significance correlating GalNAc-T13 expression with patients' clinical features and survival. We found high GalNAc-T13 expression in 43.8% of the cases and observed a significant higher expression in metastatic lymph nodes, correlating with worse overall survival. We hypothesized several possible molecular mechanisms and their implications. We conclude that GalNAc-T13 may be a novel biomarker in breast cancer, useful for routine pathological diagnosis. Elucidation of molecular mechanisms related to aggressiveness should contribute to understand the role of GalNAc-T13 in breast cancer biology.
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Huang YF, Mizumoto S, Fujita M. Novel Insight Into Glycosaminoglycan Biosynthesis Based on Gene Expression Profiles. Front Cell Dev Biol 2021; 9:709018. [PMID: 34552927 PMCID: PMC8450405 DOI: 10.3389/fcell.2021.709018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/18/2021] [Indexed: 01/11/2023] Open
Abstract
Glycosaminoglycans (GAGs) including chondroitin sulfate, dermatan sulfate, heparan sulfate, and keratan sulfate, except for hyaluronan that is a free polysaccharide, are covalently attached to core proteins to form proteoglycans. More than 50 gene products are involved in the biosynthesis of GAGs. We recently developed a comprehensive glycosylation mapping tool, GlycoMaple, for visualization and estimation of glycan structures based on gene expression profiles. Using this tool, the expression levels of GAG biosynthetic genes were analyzed in various human tissues as well as tumor tissues. In brain and pancreatic tumors, the pathways for biosynthesis of chondroitin and dermatan sulfate were predicted to be upregulated. In breast cancerous tissues, the pathways for biosynthesis of chondroitin and dermatan sulfate were predicted to be up- and down-regulated, respectively, which are consistent with biochemical findings published in the literature. In addition, the expression levels of the chondroitin sulfate-proteoglycan versican and the dermatan sulfate-proteoglycan decorin were up- and down-regulated, respectively. These findings may provide new insight into GAG profiles in various human diseases including cancerous tumors as well as neurodegenerative disease using GlycoMaple analysis.
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Affiliation(s)
- Yi-Fan Huang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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13
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Fores-Martos J, Cervera-Vidal R, Sierra-Roca J, Lozano-Asencio C, Fedele V, Cornelissen S, Edvarsen H, Tadeo-Cervera I, Eroles P, Lluch A, Tabares-Seisdedos R, Falcó A, Van't Veer LJ, Schmidt M, Quigley DA, Børresen-Dale AL, Kristensen VN, Balmain A, Climent J. Circadian PERformance in breast cancer: a germline and somatic genetic study of PER3 VNTR polymorphisms and gene co-expression. NPJ Breast Cancer 2021; 7:118. [PMID: 34508103 PMCID: PMC8433453 DOI: 10.1038/s41523-021-00329-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/16/2021] [Indexed: 11/30/2022] Open
Abstract
Polymorphisms in the PER3 gene have been associated with several human disease phenotypes, including sleep disorders and cancer. In particular, the long allele of a variable number of tandem repeat (VNTR) polymorphism has been previously linked to an increased risk of breast cancer. Here we carried out a combined germline and somatic genetic analysis of the role of the PER3VNRT polymorphism in breast cancer. The combined data from 8284 individuals showed a non-significant trend towards increased breast cancer risk in the 5-repeat allele homozygous carriers (OR = 1.17, 95% CI: 0.97–1.42). We observed allelic imbalance at the PER3 locus in matched blood and tumor DNA samples, showing a significant retention of the long variant (risk) allele in tumor samples, and a preferential loss of the short repetition allele (p = 0.0005). Gene co-expression analysis in healthy and tumoral breast tissue samples uncovered significant associations between PER3 expression levels with those from genes which belong to several cancer-associated pathways. Finally, relapse-free survival (RFS) analysis showed that low expression levels of PER3 were linked to a significant lower RSF in luminal A (p = 3 × 10−12) but not in the rest of breast cancer subtypes.
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Affiliation(s)
- Jaume Fores-Martos
- ESI International Chair at CEU-UCH, CEU Universities, Valencia, Spain.,Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain
| | | | | | - Carlos Lozano-Asencio
- INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Vita Fedele
- Digestive Molecular Clinical Oncology Research Unit, Section of Medical Oncology, Department of Medicine, University of Verona, Verona, Italy
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Hege Edvarsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Irene Tadeo-Cervera
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos. Facultad de Veterinaria, Universidad CEU Cardenal Herrera. CEU Universities, Valencia, Spain
| | - Pilar Eroles
- INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Ana Lluch
- INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Rafa Tabares-Seisdedos
- Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Medicine, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Antonio Falcó
- ESI International Chair at CEU-UCH, CEU Universities, Valencia, Spain.,Departamento de Matemáticas, Física y Ciencias Tecnológicas, Escuela Superior de Enseñanzas Técnicas, Universidad CEU Cardenal Herrera, CEU Universities, Valencia, Spain
| | - Laura J Van't Veer
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Marjanka Schmidt
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos. Facultad de Veterinaria, Universidad CEU Cardenal Herrera. CEU Universities, Valencia, Spain
| | - David A Quigley
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Departments of Urology and Epidemiology & Biostatistics, University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Joan Climent
- ESI International Chair at CEU-UCH, CEU Universities, Valencia, Spain. .,INCLIVA Research Institute. Hospital Clínico Universitario de Valencia, Valencia, Spain. .,Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos. Facultad de Veterinaria, Universidad CEU Cardenal Herrera. CEU Universities, Valencia, Spain.
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14
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Mohamed Abd-El-Halim Y, El Kaoutari A, Silvy F, Rubis M, Bigonnet M, Roques J, Cros J, Nicolle R, Iovanna J, Dusetti N, Mas E. A glycosyltransferase gene signature to detect pancreatic ductal adenocarcinoma patients with poor prognosis. EBioMedicine 2021; 71:103541. [PMID: 34425307 PMCID: PMC8379629 DOI: 10.1016/j.ebiom.2021.103541] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
Background Pancreatic ductal adenocarcinoma (PDAC) is characterized by an important heterogeneity, reflected by different clinical outcomes and chemoresistance. During carcinogenesis, tumor cells display aberrant glycosylated structures, synthetized by deregulated glycosyltransferases, supporting the tumor progression. In this study, we aimed to determine whether PDAC could be stratified through their glycosyltransferase expression profiles better than the current binary classification (basal-like and classical) in order to improve detection of patients with poor prognosis. Methods Bioinformatic analysis of 169 glycosyltransferase RNA sequencing data were performed for 74 patient-derived xenografts (PDX) of resected and unresectable tumors. The Australian cohort of International Cancer Genome Consortium and the microarray dataset from Puleo patient's cohort were used as independent validation datasets. Findings New PDAC stratification based on glycosyltransferase expression profile allowed to distinguish different groups of patients with distinct clinical outcome (p-value = 0.007). A combination of 19 glycosyltransferases differentially expressed in PDX defined a glyco-signature, whose prognostic value was validated on datasets including resected whole tumor tissues. The glyco-signature was able to discriminate three clusters of PDAC patients on the validation cohorts, two clusters displaying a short overall survival compared to one cluster having a better prognosis. Both poor prognostic clusters having different glyco-profiles in Puleo patient's cohort were correlated with stroma activated or desmoplastic subtypes corresponding to distinct microenvironment features (p-value < 0.0001). Besides, differential expression and enrichment analyses revealed deregulated functional pathways specific to different clusters. Interpretation This study identifies a glyco-signature relevant for a prognostic use, potentially applicable to resected and unresectable PDAC. Furthermore, it provides new potential therapeutic targets. Funding This work was supported by INCa (Grants number 2018-078 and 2018-079), Fondation ARC (Grant number ARCPJA32020070002326), Cancéropôle PACA, DGOS (labelization SIRIC, Grant number 6038), Amidex Foundation and Ligue Nationale Contre le Cancer and by institutional fundings from INSERM and the Aix-Marseille Université.
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Affiliation(s)
- Yousra Mohamed Abd-El-Halim
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Abdessamad El Kaoutari
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Françoise Silvy
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Marion Rubis
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Martin Bigonnet
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Julie Roques
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Jérôme Cros
- Department of Pathology, Beaujon Hospital, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France
| | - Juan Iovanna
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Nelson Dusetti
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.
| | - Eric Mas
- Cancer Research Center of Marseille, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille, France.
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15
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Glycosylation Modulates Plasma Membrane Trafficking of CD24 in Breast Cancer Cells. Int J Mol Sci 2021; 22:ijms22158165. [PMID: 34360932 PMCID: PMC8347636 DOI: 10.3390/ijms22158165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022] Open
Abstract
In breast cancer, expression of Cluster of Differentiation 24 (CD24), a small GPI-anchored glycoprotein at the cell periphery, is associated with metastasis and immune escape, while its absence is associated with tumor-initiating capacity. Since the mechanism of CD24 sorting is unknown, we investigated the role of glycosylation in the subcellular localization of CD24. Expression and localization of wild type N36- and/or N52-mutated CD24 were analyzed using immunofluorescence in luminal (MCF-7) and basal B (MDA-MB-231 and Hs578T) breast cancer cells lines, as well as HEK293T cells. Endogenous and exogenously expressed wild type and mutated CD24 were found localized at the plasma membrane and the cytoplasm, but not the nucleoplasm. The cell lines showed different kinetics for the sorting of CD24 through the secretory/endocytic pathway. N-glycosylation, especially at N52, and its processing in the Golgi were critical for the sorting and expression of CD24 at the plasma membrane of HEK293T and basal B type cells, but not of MCF-7 cells. In conclusion, our study highlights the contribution of N-glycosylation for the subcellular localization of CD24. Aberrant N-glycosylation at N52 of CD24 could account for the lack of CD24 expression at the cell surface of basal B breast cancer cells.
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16
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Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer. Cancers (Basel) 2021; 13:cancers13133330. [PMID: 34283051 PMCID: PMC8268693 DOI: 10.3390/cancers13133330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast cancer with limited treatment options. Glycosylation has been implicated in cancer development, but TNBC-specific glycosylation pathways have not been examined. Here, we applied bioinformatic analyses on public datasets to discover TNBC-specific glycogenes and pathways, as well as their upstream regulatory mechanisms. Unsupervised clustering of 345 glycogene expressions in breast cancer datasets revealed a relative homogenous expression pattern in basal-like TNBC subtype. Differential expression analyses of the 345 glycogenes between basal-like TNBC (hereafter termed TNBC) and other BC subtypes, or normal controls, revealed 84 differential glycogenes in TNBC. Pathway enrichment showed two common TNBC-enriched pathways across all three datasets, cell cycle and lacto-/neolacto- glycosphingolipid (GSL) biosynthesis, while a total of four glycosylation-related pathways were significantly enriched in TNBC. We applied a selection criterion of the top 50% differential anabolic/catabolic glycogenes in the enriched pathways to define 34 TNBC-specific glycogenes. The lacto-/neolacto- GSL biosynthesis pathway was the most highly enriched, with seven glycogenes all up-regulated in TNBC. This data led us to investigate the hypothesis that a common upstream mechanism in TNBC up-regulates the lacto-/neolacto-GSL biosynthesis pathway. Using public multi-omic datasets, we excluded the involvement of copy-number alteration and DNA methylation, but identified three transcription factors (AR, GATA3 and ZNG622) that each target three candidate genes in the lacto-/neolacto- GSL biosynthesis pathway. Interestingly, a subset of TNBC has been reported to express AR and GATA3, and AR antagonists are being trialed for TNBC. Our findings suggest that AR and GATA3 may contribute to TNBC via GSL regulation, and provide a list of candidate glycogenes for further investigation.
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17
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Ciummo SL, D’Antonio L, Sorrentino C, Fieni C, Lanuti P, Stassi G, Todaro M, Di Carlo E. The C-X-C Motif Chemokine Ligand 1 Sustains Breast Cancer Stem Cell Self-Renewal and Promotes Tumor Progression and Immune Escape Programs. Front Cell Dev Biol 2021; 9:689286. [PMID: 34195201 PMCID: PMC8237942 DOI: 10.3389/fcell.2021.689286] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 01/01/2023] Open
Abstract
Breast cancer (BC) mortality is mainly due to metastatic disease, which is primarily driven by cancer stem cells (CSC). The chemokine C-X-C motif ligand-1 (CXCL1) is involved in BC metastasis, but the question of whether it regulates breast cancer stem cell (BCSC) behavior is yet to be explored. Here, we demonstrate that BCSCs express CXCR2 and produce CXCL1, which stimulates their proliferation and self-renewal, and that CXCL1 blockade inhibits both BCSC proliferation and mammosphere formation efficiency. CXCL1 amplifies its own production and remarkably induces both tumor-promoting and immunosuppressive factors, including SPP1/OPN, ACKR3/CXCR7, TLR4, TNFSF10/TRAIL and CCL18 and, to a lesser extent, immunostimulatory cytokines, including IL15, while it downregulates CCL2, CCL28, and CXCR4. CXCL1 downregulates TWIST2 and SNAI2, while it boosts TWIST1 expression in association with the loss of E-Cadherin, ultimately promoting BCSC epithelial-mesenchymal transition. Bioinformatic analyses of transcriptional data obtained from BC samples of 1,084 patients, reveals that CXCL1 expressing BCs mostly belong to the Triple-Negative (TN) subtype, and that BC expression of CXCL1 strongly correlates with that of pro-angiogenic and cancer promoting genes, such as CXCL2-3-5-6, FGFBP1, BCL11A, PI3, B3GNT5, BBOX1, and PTX3, suggesting that the CXCL1 signaling cascade is part of a broader tumor-promoting signaling network. Our findings reveal that CXCL1 functions as an autocrine growth factor for BCSCs and elicits primarily tumor progression and immune escape programs. Targeting the CXCL1/CXCR2 axis could restrain the BCSC compartment and improve the treatment of aggressive BC.
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Affiliation(s)
- Stefania Livia Ciummo
- Department of Medicine and Sciences of Aging, “G. d’Annunzio” University, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
| | - Luigi D’Antonio
- Department of Medicine and Sciences of Aging, “G. d’Annunzio” University, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
| | - Carlo Sorrentino
- Department of Medicine and Sciences of Aging, “G. d’Annunzio” University, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
| | - Cristiano Fieni
- Department of Medicine and Sciences of Aging, “G. d’Annunzio” University, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
| | - Paola Lanuti
- Department of Medicine and Sciences of Aging, “G. d’Annunzio” University, Chieti, Italy
| | - Giorgio Stassi
- Department of Surgical, Oncological and Stomatological Sciences (DICHIRONS), University of Palermo, Palermo, Italy
| | - Matilde Todaro
- Department of Health Promotion Sciences, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Emma Di Carlo
- Department of Medicine and Sciences of Aging, “G. d’Annunzio” University, Chieti, Italy
- Anatomic Pathology and Immuno-Oncology Unit, Center for Advanced Studies and Technology (CAST), “G. d’Annunzio” University, Chieti, Italy
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18
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Cao L, Zhou Y, Li X, Lin S, Tan Z, Guan F. Integrating transcriptomics, proteomics, glycomics and glycoproteomics to characterize paclitaxel resistance in breast cancer cells. J Proteomics 2021; 243:104266. [PMID: 34000456 DOI: 10.1016/j.jprot.2021.104266] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/24/2021] [Accepted: 05/07/2021] [Indexed: 12/24/2022]
Abstract
Chemoresistance is a major factor driving breast cancer (BC) relapse and the high rates of cancer-related deaths. Aberrant levels of glycans are closely correlated with chemoresistance. The essential functions of glycans in chemoresistance is not systematically studied. In this study, an integrated strategy with a combination of transcriptomics, proteomics, glycomics and glycoproteomics was applied to explore the dysregulation of glycogenes, glycan structures and glycoproteins in chemoresistance of breast cancer cells. In paclitaxel (PTX) resistant MCF7 cells, 19 differentially expressed N-glycan-related proteins were identified, of which MGAT4A was the most significantly down-regulated, consistent with decrease in MGAT4A expression at mRNA level in PTX treated BC cells. Glycomic analysis consistently revealed suppressed levels of multi-antennary branching structures using MALDI-TOF/TOF-MS and lectin microarray. Several target glycoproteins bearing suppressed levels of multi-antennary branching structures were identified, and ERK signaling pathway was strongly suppressed in PTX resistant MCF7 cells. Our findings demonstrated the aberrant levels of multi-antennary branching structures and their target glycoproteins on PTX resistance. Systematically integrative multi-omic analysis is expected to facilitate the discovery of the aberrant glycosyltransferases, N-glycosylation and glycoproteins in tumor progression and chemoresistance. SIGNIFICANCE: An integrated strategy with a combination of transcriptomics, proteomics, glycomics and glycoproteomics is crucial to understand the association between glycans and chemoresistance in BC. In this multi-omic analysis, we identified unique glycan-related protein, glycan and glycoprotein signatures defining PTX chemoresistance in BC. This study might provide valuable information to understand molecular mechanisms underlying chemoresistance in BC.
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Affiliation(s)
- Lin Cao
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China
| | - Yue Zhou
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China; The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiang Li
- Institute of Hematology, School of Medicine, Northwest University, Xi'an 710069, PR China
| | - Shuai Lin
- Department of Oncology, The second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, China
| | - Zengqi Tan
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China
| | - Feng Guan
- International Research Laboratory of Glycobiology and Medicinal Chemistry, College of Life Science, Northwest University, Xi'an 710069, PR China.
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19
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Li Z, Zhang L, Liu D, Wang C. Ceramide glycosylation and related enzymes in cancer signaling and therapy. Biomed Pharmacother 2021; 139:111565. [PMID: 33887691 DOI: 10.1016/j.biopha.2021.111565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 02/09/2023] Open
Abstract
Ceramides, the core of the sphingolipid metabolism, draw wide attention as tumor suppressor, and act directly on mitochondria to trigger apoptotic cell death. Ceramide-based therapies are being developed by using promote ceramide generating agents. The ceramide metabolism balance is regulated by multifaceted factors in cancer development. Ceramide metabolic enzymes can increase the elimination of ceramide and counteract the anti-tumor effects of ceramide. However, recent research showed that these metabolic enzymes were highly expressed in several cancers. Especially ceramide glycosyltransferases, they catalyze ceramide glycosylation and synthesis the skeleton of glycosphingolipids (GSLs), play an important role in regulating tumor progression and have a significant correlation with the poor prognosis of cancer patients. To further understand the biological characteristics of ceramide metabolism in tumor, this review focuses on the role of ceramide glycosylation and related enzymes in cancer signaling and therapy. Besides, the research on multidrug resistance and potential inhibitors of ceramide glycosyltransferases are also discussed. Advance study on the structure of ceramide glycosyltransferases and ceramide glycosylation signaling pathway will open the path to new therapies and treatments.
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Affiliation(s)
- Zibo Li
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Lin Zhang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Dan Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Caiyan Wang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China.
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20
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Jongsma MLM, de Waard AA, Raaben M, Zhang T, Cabukusta B, Platzer R, Blomen VA, Xagara A, Verkerk T, Bliss S, Kong X, Gerke C, Janssen L, Stickel E, Holst S, Plomp R, Mulder A, Ferrone S, Claas FHJ, Heemskerk MHM, Griffioen M, Halenius A, Overkleeft H, Huppa JB, Wuhrer M, Brummelkamp TR, Neefjes J, Spaapen RM. The SPPL3-Defined Glycosphingolipid Repertoire Orchestrates HLA Class I-Mediated Immune Responses. Immunity 2021; 54:132-150.e9. [PMID: 33271119 PMCID: PMC8722104 DOI: 10.1016/j.immuni.2020.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/25/2020] [Accepted: 11/06/2020] [Indexed: 12/26/2022]
Abstract
HLA class I (HLA-I) glycoproteins drive immune responses by presenting antigens to cognate CD8+ T cells. This process is often hijacked by tumors and pathogens for immune evasion. Because options for restoring HLA-I antigen presentation are limited, we aimed to identify druggable HLA-I pathway targets. Using iterative genome-wide screens, we uncovered that the cell surface glycosphingolipid (GSL) repertoire determines effective HLA-I antigen presentation. We show that absence of the protease SPPL3 augmented B3GNT5 enzyme activity, resulting in upregulation of surface neolacto-series GSLs. These GSLs sterically impeded antibody and receptor interactions with HLA-I and diminished CD8+ T cell activation. Furthermore, a disturbed SPPL3-B3GNT5 pathway in glioma correlated with decreased patient survival. We show that the immunomodulatory effect could be reversed through GSL synthesis inhibition using clinically approved drugs. Overall, our study identifies a GSL signature that inhibits immune recognition and represents a potential therapeutic target in cancer, infection, and autoimmunity.
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Affiliation(s)
- Marlieke L M Jongsma
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands; Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Antonius A de Waard
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Matthijs Raaben
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tao Zhang
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Birol Cabukusta
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - René Platzer
- Institut für Hygiene und Angewandte Immunologie, Vienna, Austria
| | - Vincent A Blomen
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Anastasia Xagara
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Tamara Verkerk
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Sophie Bliss
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Xiangrui Kong
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Carolin Gerke
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Lennert Janssen
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Elmer Stickel
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Stephanie Holst
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Rosina Plomp
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Arend Mulder
- Department of Immunology, LUMC, Leiden, the Netherlands
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hermen Overkleeft
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Johannes B Huppa
- Institut für Hygiene und Angewandte Immunologie, Vienna, Austria
| | - Manfred Wuhrer
- Center for Proteomics and Metabolics, LUMC, Leiden, the Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Cancer Genomics Center, Amsterdam, the Netherlands
| | - Jacques Neefjes
- Oncode Institute and Department of Cell and Chemical Biology, LUMC, Leiden, the Netherlands
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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21
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Malavia N, Kuche K, Ghadi R, Jain S. A bird's eye view of the advanced approaches and strategies for overshadowing triple negative breast cancer. J Control Release 2020; 330:72-100. [PMID: 33321156 DOI: 10.1016/j.jconrel.2020.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022]
Abstract
Triple negative breast cancer (TNBC) is one of the most aggressive form of breast cancer. It is characterized by the absence of estrogen, progesterone and human epidermal growth factor receptors. The main issue with TNBC is that it exhibits poor prognosis, high risk of relapse, short progression-free survival and low overall survival in patients. This is because the conventional therapy used for managing TNBC has issues pertaining to poor bioavailability, lower cellular uptake, increased off-target effects and development of resistance. To overcome such pitfalls, several other approaches are explored. In this context, the present manuscript showcases three of the most widely used approaches which are (i) nanotechnology-based approach; (ii) gene therapy approach and (iii) Phytochemical-based approach. The ultimate focus is to present and explain the insightful reports based on these approaches. Further, the review also expounds on the identified molecular targets and novel targeting ligands which are explored for managing TNBC effectively. Thus, in a nutshell, the review tries to highlight these existing treatment approaches which might inspire for future development of novel therapies with a potential of overshadowing TNBC.
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Affiliation(s)
- Nilesh Malavia
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Mohali, Punjab, India
| | - Kaushik Kuche
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Mohali, Punjab, India
| | - Rohan Ghadi
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Mohali, Punjab, India
| | - Sanyog Jain
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Mohali, Punjab, India.
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22
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Guo Z, Sun Q, Liao Y, Liu C, Zhao W, Li X, Liu H, Dong M, Shang Y, Sui L, Kong Y. MiR-30a-5p inhibits proliferation and metastasis of hydatidiform mole by regulating B3GNT5 through ERK/AKT pathways. J Cell Mol Med 2020; 24:8350-8362. [PMID: 32575164 PMCID: PMC7412694 DOI: 10.1111/jcmm.15247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/15/2020] [Accepted: 02/15/2020] [Indexed: 12/20/2022] Open
Abstract
Hydatidiform moles are gestational trophoblastic disease. They are abnormal proliferations of trophoblast cells that have the potential to become cancerous. miR-miR30a-5p is a tumour suppressor that participates in the development of numerous diseases. However, the role of miR-30a in hydatidiform moles and the mechanisms underlying its effects are presently unclear. This study explored the levels of miR-30a and B3GNT5 expression in human hydatidiform mole tissue. The results showed that miR-30a and B3GNT5 were differentially expressed in normal placenta and hydatidiform mole, and miR-30a decreased cell proliferation, invasion and migration in trophoblast cell lines. Upon further examination, it was confirmed that miR-30a directly targeted the 3'untranslated region of B3GNT5 using a dual-luciferase assay. The results of the present study also revealed that miR-30a reduced the proliferation, invasion and migration ability in JAR and BeWo cells by regulating B3GNT5, which may inactivate the ERK and AKT signalling pathways. This study demonstrated that miR-30a was a novel target B3GNT5 that serves an important role in the development of hydatidiform moles, suggesting that miR-30a may serve as a novel potential biomarker or useful diagnostic and therapeutic tool for hydatidiform moles in clinical settings.
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Affiliation(s)
- Zhenzhen Guo
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Qiannan Sun
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Yangyou Liao
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Chao Liu
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Wenjie Zhao
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Xiaoxue Li
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Huan Liu
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Ming Dong
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Yuhong Shang
- Department of GynecologyFirst Affiliated HospitalDalian Med UniversityDalianChina
| | - Linlin Sui
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
| | - Ying Kong
- Core Lab Glycobiol & GlycoengnCollege of Basic Medical SciencesDalian Medical UniversityDalianChina
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23
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Abstract
Background Gene fusions have been studied extensively, as frequent drivers of tumorigenesis as well as potential therapeutic targets. In many well-known cases, breakpoints occur at two intragenic positions, leading to in-frame gene-gene fusions that generate chimeric mRNAs. However, fusions often occur with intergenic breakpoints, and the role of such fusions has not been carefully examined. Results We analyze whole-genome sequencing data from 268 patients to catalog gene-intergenic and intergenic-intergenic fusions and characterize their impact. First, we discover that, in contrast to the common assumption, chimeric oncogenic transcripts—such as those involving ETV4, ERG, RSPO3, and PIK3CA—can be generated by gene-intergenic fusions through splicing of the intervening region. Second, we find that over-expression of an upstream or downstream gene by a fusion-mediated repositioning of a regulatory sequence is much more common than previously suspected, with enhancers sometimes located megabases away. We detect a number of recurrent fusions, such as those involving ANO3, RGS9, FUT5, CHI3L1, OR1D4, and LIPG in breast; IGF2 in colon; ETV1 in prostate; and IGF2BP3 and SIX2 in thyroid cancers. Conclusion Our findings elucidate the potential oncogenic function of intergenic fusions and highlight the wide-ranging consequences of structural rearrangements in cancer genomes.
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24
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Chierici M, Bussola N, Marcolini A, Francescatto M, Zandonà A, Trastulla L, Agostinelli C, Jurman G, Furlanello C. Integrative Network Fusion: A Multi-Omics Approach in Molecular Profiling. Front Oncol 2020; 10:1065. [PMID: 32714870 PMCID: PMC7340129 DOI: 10.3389/fonc.2020.01065] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Recent technological advances and international efforts, such as The Cancer Genome Atlas (TCGA), have made available several pan-cancer datasets encompassing multiple omics layers with detailed clinical information in large collection of samples. The need has thus arisen for the development of computational methods aimed at improving cancer subtyping and biomarker identification from multi-modal data. Here we apply the Integrative Network Fusion (INF) pipeline, which combines multiple omics layers exploiting Similarity Network Fusion (SNF) within a machine learning predictive framework. INF includes a feature ranking scheme (rSNF) on SNF-integrated features, used by a classifier over juxtaposed multi-omics features (juXT). In particular, we show instances of INF implementing Random Forest (RF) and linear Support Vector Machine (LSVM) as the classifier, and two baseline RF and LSVM models are also trained on juXT. A compact RF model, called rSNFi, trained on the intersection of top-ranked biomarkers from the two approaches juXT and rSNF is finally derived. All the classifiers are run in a 10x5-fold cross-validation schema to warrant reproducibility, following the guidelines for an unbiased Data Analysis Plan by the US FDA-led initiatives MAQC/SEQC. INF is demonstrated on four classification tasks on three multi-modal TCGA oncogenomics datasets. Gene expression, protein expression and copy number variants are used to predict estrogen receptor status (BRCA-ER, N = 381) and breast invasive carcinoma subtypes (BRCA-subtypes, N = 305), while gene expression, miRNA expression and methylation data is used as predictor layers for acute myeloid leukemia and renal clear cell carcinoma survival (AML-OS, N = 157; KIRC-OS, N = 181). In test, INF achieved similar Matthews Correlation Coefficient (MCC) values and 97% to 83% smaller feature sizes (FS), compared with juXT for BRCA-ER (MCC: 0.83 vs. 0.80; FS: 56 vs. 1801) and BRCA-subtypes (0.84 vs. 0.80; 302 vs. 1801), improving KIRC-OS performance (0.38 vs. 0.31; 111 vs. 2319). INF predictions are generally more accurate in test than one-dimensional omics models, with smaller signatures too, where transcriptomics consistently play the leading role. Overall, the INF framework effectively integrates multiple data levels in oncogenomics classification tasks, improving over the performance of single layers alone and naive juxtaposition, and provides compact signature sizes.
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Affiliation(s)
| | - Nicole Bussola
- Fondazione Bruno Kessler, Trento, Italy
- University of Trento, Trento, Italy
| | | | - Margherita Francescatto
- Fondazione Bruno Kessler, Trento, Italy
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
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25
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Hu X, Tang F, Liu P, Zhong T, Yuan F, He Q, von Itzstein M, Li H, Weng L, Yu X. Structural and Functional Insight Into the Glycosylation Impact Upon the HGF/c-Met Signaling Pathway. Front Cell Dev Biol 2020; 8:490. [PMID: 32626713 PMCID: PMC7314907 DOI: 10.3389/fcell.2020.00490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/25/2020] [Indexed: 12/31/2022] Open
Abstract
Upon interactions with its specific ligand hepatocyte growth factor (HGF), the c-Met signal is relayed to series of downstream pathways, exerting essential biological roles. Dysregulation of the HGF-c-Met signaling pathway has been implicated in the onset, progression and metastasis of various cancers, making the HGF-c-Met axis a promising therapeutic target. Both c-Met and HGF undergo glycosylation, which appears to be biologically relevant to their function and structural integrity. Different types of glycoconjugates in the local cellular environment can also regulate HGF/c-Met signaling by distinct mechanisms. However, detailed knowledge pertaining to the glycosylation machinery of the HGF-c-Met axis as well as its potential applications in oncology research is yet to be established. This mini review highlights the significance of the HGF-c-Met signaling pathway in physiological and pathological context, and discusses the molecular mechanisms by which affect the glycosylation of the HGF-c-Met axis. Owing to the crucial role played by glycosylation in the regulation of HGF/c-Met activity, better understanding of this less exploited field may contribute to the development of novel therapeutics targeting glycoepitopes.
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Affiliation(s)
- Xinyue Hu
- College of Medicine, Hunan Normal University, Changsha, China
| | - Feiyu Tang
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Peilin Liu
- College of Medicine, Hunan Normal University, Changsha, China
| | - Taowei Zhong
- College of Medicine, Hunan Normal University, Changsha, China
| | - Fengyan Yuan
- College of Medicine, Hunan Normal University, Changsha, China
| | - Quanyuan He
- College of Medicine, Hunan Normal University, Changsha, China.,Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, Hunan Normal University, Changsha, China
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Hao Li
- Biliary Tract Surgery Laboratory, Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China.,Hunan Research Center of Biliary Disease, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Liang Weng
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Molecular Radiation Oncology in Hunan Province, Central South University, Changsha, China
| | - Xing Yu
- College of Medicine, Hunan Normal University, Changsha, China.,Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
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26
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Song J, Liu W, Wang J, Hao J, Wang Y, You X, Du X, Zhou Y, Ben J, Zhang X, Ye M, Wang Q. GALNT6 promotes invasion and metastasis of human lung adenocarcinoma cells through O-glycosylating chaperone protein GRP78. Cell Death Dis 2020; 11:352. [PMID: 32393740 PMCID: PMC7214460 DOI: 10.1038/s41419-020-2537-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022]
Abstract
Lung adenocarcinoma remains a threat to human health due to its high rate of recurrence and distant metastasis. However, the molecular mechanism underlying lung adenocarcinoma metastasis remains yet incompletely understood. Here, we show that upregulated expression of polypeptide N-acetylgalactosaminyltransferase6 (GALNT6) in lung adenocarcinoma is associated with lymph node metastasis and poor prognosis. In lung adenocarcinoma cells, GALNT6 over-expression promoted epithelial-mesenchymal transition (EMT), wound healing, and invasion which could be significantly reversed by GALNT6 silencing. GALNT6 silencing also mitigated the metastasis of lung adenocarcinoma and prolonged the survival of xenograft tumor-bearing mice. Furthermore, GALNT6 directly interacted with, and O-glycosylated chaperone protein GRP78, which promoted EMT by enhancing the MEK1/2/ERK1/2 signaling in lung cancer cells. Therefore, GALNT6 is emerging as novel positive regulator for the malignancy of human lung adenocarcinoma. Targeting GALNT6-GRP78-MEK1/2/ERK1/2 may thus represent a new avenue to develop therapeutics against lung cancer metastasis.
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Affiliation(s)
- Jing Song
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Wenwen Liu
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Jianzhen Wang
- Department of Respiratory and Critical Care Medicine, The First Hospital, Shanxi Medical University, No. 85Jiefang South Road, Taiyuan, Shanxi, 030001, China
| | - Junxia Hao
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Yingyan Wang
- Laboratory Center for Diagnostics, Dalian Medical University, No. 9 West Section Lvshun South Road, Dalian, Liaoning, 116044, China
| | - Xin You
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, No. 457 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Xiaohui Du
- Department of Scientific Research Center, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Yang Zhou
- Department of Scientific Research Center, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Jing Ben
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China
| | - Xinri Zhang
- Department of Respiratory and Critical Care Medicine, The First Hospital, Shanxi Medical University, No. 85Jiefang South Road, Taiyuan, Shanxi, 030001, China.
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, No. 457 Zhongshan Road, Dalian, Liaoning, 116023, China.
| | - Qi Wang
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, No. 467 Zhongshan Road, Dalian, Liaoning, 116023, China.
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27
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Takayama H, Ohta M, Iwashita Y, Uchida H, Shitomi Y, Yada K, Inomata M. Altered glycosylation associated with dedifferentiation of hepatocellular carcinoma: a lectin microarray-based study. BMC Cancer 2020; 20:192. [PMID: 32143591 PMCID: PMC7060603 DOI: 10.1186/s12885-020-6699-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
Background Altered glycosylation associated with hepatocellular carcinoma (HCC) is well documented. However, few reports have investigated the association between dedifferentiation and glycosylation. Therefore, the aim of this study was to analyze glycosylation associated with dedifferentiation of HCC within the same nodule and to investigate glycosyltransferase related to the glycosylation. Methods We analyzed resected HCC specimens (n = 50) using lectin microarray to comprehensively and sensitively analyze glycan profiles, and identify changes to glycosylation between well- and moderately-differentiated components within the same nodule. Moreover, we performed immunohistochemical staining of mannosyl(α-1,3-)-glycoprotein β-1,2-N-acetylglucosaminyltransferase (MGAT1), which is an essential glycosyltransferase that converts high-mannose glycans to complex- or hybrid-type N-glycans. Results Four lectins from Narcissus pseudonarcissus agglutinin (NPA), Concanavalin A, Galanthus nivalis agglutinin, and Calystegia sepium agglutinin were significantly elevated in moderately-differentiated components of HCC compared with well-differentiated components, and all lectins showed binding specificity to high-mannose glycans. Therefore, these structures were represented to a greater extent in moderately-differentiated components than in well-differentiated ones. Immunohistochemical staining revealed significantly increased NPA expression and decreased MGAT1 expression in moderately-differentiated components. Low MGAT1 expression in moderately-differentiated components of tumors was associated with intrahepatic metastasis and had tendency for poor prognosis. Conclusion Dedifferentiation of well-differentiated HCC is associated with an increase in high-mannose glycans. MGAT1 may play a role in the dedifferentiation of HCC.
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Affiliation(s)
- Hiroomi Takayama
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan.
| | - Masayuki Ohta
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan.,Global Oita Medical Advanced Research Center for Health, Oita University, Oita, Japan
| | - Yukio Iwashita
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Hiroki Uchida
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Yuki Shitomi
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Kazuhiro Yada
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
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Sulfated Glycoaminoglycans and Proteoglycan Syndecan-4 Are Involved in Membrane Fixation of LL-37 and Its Pro-Migratory Effect in Breast Cancer Cells. Biomolecules 2019; 9:biom9090481. [PMID: 31547381 PMCID: PMC6769752 DOI: 10.3390/biom9090481] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
Initially characterized by its antimicrobial activities, LL-37 has also been shown to significantly contribute to tumor development. On breast cancer cell lines, LL-37 increases intracellular calcium via the TRPV2 channel and their migration via the activation of PI3K/AKT signaling. Its all-d enantiomer d-LL-37 induces similar effects, which excludes a protein-protein interaction of LL-37 in a classic ligand-receptor manner. Its net charge of +6 gave rise to the hypothesis that the peptide uses the negative charges of sulfoglycans or sialic acids to facilitate its attachment to the cell membrane and to induce its activities. Whereas several vegetal lectins, specifically attaching to sialylated or sulfated structures, blocked the activities of LL-37 on both calcium increase and cell migration, several sialidases had no effect. However, the competitive use of free sulfated glycoaminoglycans (GAGs) as chrondroitin and heparin, or treatment of the cell surface with chondroitinase and heparinase resulted in an activity loss of 50–100% for LL-37. Concordant results were obtained by blocking the synthesis of GAGs with 4-Methylumbelliferyl-β-d-xyloside, and by suppression of glycan sulfatation by sodium chlorate. Using a candidate approach by suppressing proteoglycan synthesis using RNA interference, syndecan-4 was shown to be required for the activities of LL-37 and its binding to the cell surface. This leads to the conclusion that syndecan-4, by means of sulfated GAGs, could act as a receptor for LL-37.
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29
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Gangliosides profiling in serum of breast cancer patient: GM3 as a potential diagnostic biomarker. Glycoconj J 2019; 36:419-428. [PMID: 31297734 DOI: 10.1007/s10719-019-09885-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 02/08/2023]
Abstract
Gangliosides altered during the pathological conditions and particularly in cancers. Here, we aimed to profile the gangliosides in breast cancer serum and propose potential biomarkers. LC-FTMS method was first used to identify all the ganglioside species in serum, then LC-MS/MS-MRM method was employed to quantitate the levels of gangliosides in serum from healthy volunteers and patients with benign breast tumor or breast cancer. 49 ganglioside species were determined, including GM1, GM2, GM3, GD1, GD3 and GT1 species. Compared to healthy volunteers, the levels of GM1, GM2, GM3, GD1 and GD3 displayed a rising trend in breast cancer patients. In particular, as the major glycosphingolipid component, GM3 showed excellent diagnostic accuracy in cancer serum (AUC > 0.9). PCA profile of the GM3 species showed clear distinction between normal and cancer serum. What's more, ROC curve proved great diagnostic accuracy of GM3 between cancer and benign serum. In addition, GM3 was discovered as a diagnostic marker to differentiate luminal B subtype from other subtypes. Furthermore, a positive correlation between GM3 and Ki-67 status of patients was identified. In conclusion, our results introduced the alteration patterns of serum gangliosides in breast cancer and suggested serum GM3 as a potential diagnostic biomarker in breast cancer diagnosis and luminal B subtype distinction.
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30
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Wang S, Jeong HH, Sohn KA. ClearF: a supervised feature scoring method to find biomarkers using class-wise embedding and reconstruction. BMC Med Genomics 2019; 12:95. [PMID: 31296201 PMCID: PMC6624178 DOI: 10.1186/s12920-019-0512-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Feature selection or scoring methods for the detection of biomarkers are essential in bioinformatics. Various feature selection methods have been developed for the detection of biomarkers, and several studies have employed information-theoretic approaches. However, most of these methods generally require a long processing time. In addition, information-theoretic methods discretize continuous features, which is a drawback that can lead to the loss of information. RESULTS In this paper, a novel supervised feature scoring method named ClearF is proposed. The proposed method is suitable for continuous-valued data, which is similar to the principle of feature selection using mutual information, with the added advantage of a reduced computation time. The proposed score calculation is motivated by the association between the reconstruction error and the information-theoretic measurement. Our method is based on class-wise low-dimensional embedding and the resulting reconstruction error. Given multi-class datasets such as a case-control study dataset, low-dimensional embedding is first applied to each class to obtain a compressed representation of the class, and also for the entire dataset. Reconstruction is then performed to calculate the error of each feature and the final score for each feature is defined in terms of the reconstruction errors. The correlation between the information theoretic measurement and the proposed method is demonstrated using a simulation. For performance validation, we compared the classification performance of the proposed method with those of various algorithms on benchmark datasets. CONCLUSIONS The proposed method showed higher accuracy and lower execution time than the other established methods. Moreover, an experiment was conducted on the TCGA breast cancer dataset, and it was confirmed that the genes with the highest scores were highly associated with subtypes of breast cancer.
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Affiliation(s)
- Sehee Wang
- Department of Computer Engineering, Ajou University, Suwon, 16499 South Korea
| | - Hyun-Hwan Jeong
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Kyung-Ah Sohn
- Department of Computer Engineering, Ajou University, Suwon, 16499 South Korea
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31
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Albuquerque APB, Balmaña M, Mereiter S, Pinto F, Reis CA, Beltrão EIC. Hypoxia and serum deprivation induces glycan alterations in triple negative breast cancer cells. Biol Chem 2019; 399:661-672. [PMID: 29894296 DOI: 10.1515/hsz-2018-0121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/27/2018] [Indexed: 12/26/2022]
Abstract
Triple negative breast cancer (TNBC) is a major global public health problem. The lack of targeted therapy and the elevated mortality evidence the need for better knowledge of the tumor biology. Hypoxia and aberrant glycosylation are associated with advanced stages of malignancy, tumor progression and treatment resistance. Importantly, serum deprivation regulates the invasive phenotype and favors TNBC cell survival. However, in TNBC, the role of hypoxia and serum deprivation in the regulation of glycosylation remains largely unknown. The effects of hypoxia and serum deprivation on the expression of glycosyltransferases and glycan profile were evaluated in the MDA-MB-231 cell line. We showed that the overexpression of HIF-1α was accompanied by acquisition of epithelial-mesenchimal transition features. Significant upregulation of fucosyl- and sialyltransferases involved in the synthesis of tumor-associated carbohydrate antigens was observed together with changes in fucosylation and sialylation detected by Aleuria aurantia lectin and Sambucus nigra agglutinin lectin blots. Bioinformatic analysis further indicated a mechanism by which HIF-1α can regulate ST3GAL6 expression and the relationship within the intrinsic characteristics of TNBC tumors. In conclusion, our results showed the involvement of hypoxia and serum deprivation in glycosylation profile regulation of TNBC cells triggering breast cancer aggressive features and suggesting glycosylation as a potential diagnostic and therapeutic target.
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Affiliation(s)
- Amanda P B Albuquerque
- Biomarkers in Cancer Research Group (BmC) - Federal University of Pernambuco (UFPE), 50670-901 Recife, Pernambuco, Brazil.,Department of Biochemistry, Federal University of Pernambuco (UFPE), 50670-901 Recife, Pernambuco, Brazil
| | - Meritxell Balmaña
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Stefan Mereiter
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Filipe Pinto
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Celso A Reis
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal.,Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Eduardo I C Beltrão
- Biomarkers in Cancer Research Group (BmC) - Federal University of Pernambuco (UFPE), 50670-901 Recife, Pernambuco, Brazil.,Department of Biochemistry, Federal University of Pernambuco (UFPE), 50670-901 Recife, Pernambuco, Brazil
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32
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Peng W, Zhao J, Dong X, Banazadeh A, Huang Y, Hussien A, Mechref Y. Clinical application of quantitative glycomics. Expert Rev Proteomics 2018; 15:1007-1031. [PMID: 30380947 PMCID: PMC6647030 DOI: 10.1080/14789450.2018.1543594] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Aberrant glycosylation has been associated with many diseases. Decades of research activities have reported many reliable glycan biomarkers of different diseases which enable effective disease diagnostics and prognostics. However, none of the glycan markers have been approved for clinical diagnosis. Thus, a review of these studies is needed to guide the successful clinical translation. Area covered: In this review, we describe and discuss advances in analytical methods enabling clinical glycan biomarker discovery, focusing only on studies of released glycans. This review also summarizes the different glycobiomarkers identified for cancers, Alzheimer's disease, diabetes, hepatitis B and C, and other diseases. Expert commentary: Along with the development of techniques in quantitative glycomics, more glycans or glycan patterns have been reported as better potential biomarkers of different diseases and proved to have greater diagnostic/diagnostic sensitivity and specificity than existing markers. However, to successfully apply glycan markers in clinical diagnosis, more studies and verifications on large biological cohorts need to be performed. In addition, faster and more efficient glycomic strategies need to be developed to shorten the turnaround time. Thus, glycan biomarkers have an immense chance to be used in clinical prognosis and diagnosis of many diseases in the near future.
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Affiliation(s)
- Wenjing Peng
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA
| | - Jingfu Zhao
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA
| | - Xue Dong
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA
| | - Alireza Banazadeh
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA
| | - Yifan Huang
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA
| | - Ahmed Hussien
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA.,b Department of Biotechnology , Institute of Graduate Studies and Research, University of Alexandria , Alexandria , Egypt
| | - Yehia Mechref
- a Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , TX , USA
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Deng B, Tarhan YE, Ueda K, Ren L, Katagiri T, Park JH, Nakamura Y. Critical Role of Estrogen Receptor Alpha O-Glycosylation by N-Acetylgalactosaminyltransferase 6 (GALNT6) in Its Nuclear Localization in Breast Cancer Cells. Neoplasia 2018; 20:1038-1044. [PMID: 30208353 PMCID: PMC6138801 DOI: 10.1016/j.neo.2018.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/12/2018] [Accepted: 08/20/2018] [Indexed: 12/28/2022]
Abstract
Alteration of protein O-glycosylation in various human cancers including breast cancer is well known, but molecular roles of their aberrant glycosylations on cancer have not been fully understood. We previously reported critical roles of polypeptide N-acetylgalactosaminyltransferase 6 (GALNT6 or GalNAc-T6) that was upregulated in a great majority of breast cancer tissues. Here we further report O-glycosylation of estrogen receptor alpha (ER-α) by GALNT6 and the significant role of its nuclear localization in breast cancer cells. Knockdown of GALNT6 expression in two breast cancer cell lines, T47D and MCF7, in which both ER-α and GALNT6 were highly expressed, by small interfering RNA could significantly attenuate expression of ER-α. Immunocytochemical analysis clearly demonstrated the drastic decrease of ER-α protein in the nucleus of these cancer cells. Accordingly, the downstream genes of the ER-α pathway such as MYC, CCND1, and CTSD were significantly downregulated. We confirmed GALNT6-dependent ER-α O-glycosylation and identified O-glycosylation of S573 in an F domain of ER-α by GALNT6 through LC-MS/MS analysis. We also obtained evidences showing that the glycosylation of ER-α at S573 by GALNT6 is essential for protein stability and nuclear localization of ER-α in breast cancer cells. Furthermore, we designed cell membrane-permeable peptides including the O-glycosylation site and found a significant decrease of the cell viability of breast cancer cells by treatment of these peptides in a GALNT6 expression-dependent manner. Our study suggests that targeting the GALNT6 enzymatic activity as well as the GALNT6/ER-α interaction could be a promising therapeutic approach to ER-α-positive breast cancer patients.
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Affiliation(s)
- Boya Deng
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Yunus Emre Tarhan
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Research Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Lili Ren
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan
| | - Jae-Hyun Park
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Yusuke Nakamura
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
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Segaert P, Lopes MB, Casimiro S, Vinga S, Rousseeuw PJ. Robust identification of target genes and outliers in triple-negative breast cancer data. Stat Methods Med Res 2018; 28:3042-3056. [PMID: 30146936 PMCID: PMC6745616 DOI: 10.1177/0962280218794722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Correct classification of breast cancer subtypes is of high importance as it directly affects the therapeutic options. We focus on triple-negative breast cancer which has the worst prognosis among breast cancer types. Using cutting edge methods from the field of robust statistics, we analyze Breast Invasive Carcinoma transcriptomic data publicly available from The Cancer Genome Atlas data portal. Our analysis identifies statistical outliers that may correspond to misdiagnosed patients. Furthermore, it is illustrated that classical statistical methods may fail to identify outliers due to their heavy influence, prompting the need for robust statistics. Using robust sparse logistic regression we obtain 36 relevant genes, of which ca. 60% have been previously reported as biologically relevant to triple-negative breast cancer, reinforcing the validity of the method. The remaining 14 genes identified are new potential biomarkers for triple-negative breast cancer. Out of these, JAM3, SFT2D2, and PAPSS1 were previously associated to breast tumors or other types of cancer. The relevance of these genes is confirmed by the new DetectDeviatingCells outlier detection technique. A comparison of gene networks on the selected genes showed significant differences between triple-negative breast cancer and non-triple-negative breast cancer data. The individual role of FOXA1 in triple-negative breast cancer and non-triple-negative breast cancer, and the strong FOXA1-AGR2 connection in triple-negative breast cancer stand out. The goal of our paper is to contribute to the breast cancer/triple-negative breast cancer understanding and management. At the same time it demonstrates that robust regression and outlier detection constitute key strategies to cope with high-dimensional clinical data such as omics data.
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Affiliation(s)
| | - Marta B Lopes
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra Casimiro
- Luís Costa Lab, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Susana Vinga
- IDMEC, Instituto de Engenharia Mecânica, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,INESC-ID, Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento, Lisboa, Portugal
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35
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ICAM1 expression is induced by proinflammatory cytokines and associated with TLS formation in aggressive breast cancer subtypes. Sci Rep 2018; 8:11720. [PMID: 30082828 PMCID: PMC6079003 DOI: 10.1038/s41598-018-29604-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022] Open
Abstract
Intratumoral formation of tertiary lymphoid structures (TLS) within the tumor microenvironment is considered to be a consequence of antigen challenge during anti-tumor responses. Intracellular adhesion molecule 1 (ICAM1) has been implicated in a variety of immune and inflammatory responses, in addition to associate with triple negative breast cancer (TNBC). In this study, we detected TLS in the aggressive tumor phenotypes TNBC, HER2+ and luminal B, whereas the TLS negative group contained solely tumors of the luminal A subtype. We show that ICAM1 is exclusively expressed in TNBC and HER2 enriched subtypes known to be associated with inflammation and the formation of TLS. Furthermore, cell from normal mammary epithelium and breast cancer cell lines expressed ICAM1 upon stimulation with the proinflammatory cytokines TNFα, IL1β and IFNγ. ICAM1 overexpression was induced in MCF7, MDA-MB-468 and SK-BR-3 cells regardless of hormone receptor status. Taken together, our findings show that ICAM1 is expressed in aggressive subtypes of breast cancer and its expression is inducible by well-known proinflammatory cytokines. ICAM1 may be an attractive molecular target for TNBC, but further investigations elucidating the role of ICAM1 in targeted therapies have to take into consideration selective subtypes of breast cancer.
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36
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Kennedy BM, Harris RE. Cyclooxygenase and lipoxygenase gene expression in the inflammogenesis of breast cancer. Inflammopharmacology 2018; 26:10.1007/s10787-018-0489-6. [PMID: 29736687 DOI: 10.1007/s10787-018-0489-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023]
Abstract
We examined the expression of major inflammatory genes, cyclooxygenase-1 and 2 (COX1, COX2) and arachidonate 5-lipoxygenase (ALOX5) in 1090 tumor samples of invasive breast cancer from The Cancer Genome Atlas (TCGA). Mean cyclooxygenase expression (COX1 + COX2) ranked in the upper 99th percentile of all 20,531 genes and surprisingly, the mean expression of COX1 was more than tenfold higher than COX2. Highly significant correlations were observed between COX2 with eight tumor-promoting genes (EGR2, IL6, RGS2, B3GNT5, SGK1, SLC2A3, SFRP1 and ETS2) and between ALOX5 and ten tumor promoter genes (CD33, MYOF1, NLRP1, GAB3, CD4, IFR8, CYTH4, BTK, FGR, CD37). Expression of CYP19A1 (aromatase) was significantly correlated with COX2, but only in tumors positive for ER, PR and HER2. Tumor-promoting genes correlated with the expression of COX1, COX2, and ALOX5 are known to effectively increase mitogenesis, mutagenesis, angiogenesis, cell survival, immunosuppression and metastasis in the pathogenesis of breast cancer.
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Affiliation(s)
- Brian M Kennedy
- Colleges of Public Health and Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, 1841 Neil Avenue (306 Cunz Hall), Columbus, OH, 43210-1351, USA
| | - Randall E Harris
- Colleges of Public Health and Medicine, The Ohio State University Comprehensive Cancer Center, The Ohio State University, 1841 Neil Avenue (306 Cunz Hall), Columbus, OH, 43210-1351, USA.
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37
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Vecchio G, Parascandolo A, Allocca C, Ugolini C, Basolo F, Moracci M, Strazzulli A, Cobucci-Ponzano B, Laukkanen MO, Castellone MD, Tsuchida N. Human a-L-fucosidase-1 attenuates the invasive properties of thyroid cancer. Oncotarget 2018; 8:27075-27092. [PMID: 28404918 PMCID: PMC5432319 DOI: 10.18632/oncotarget.15635] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Glycans containing α-L-fucose participate in diverse interactions between cells and extracellular matrix. High glycan expression on cell surface is often associated with neoplastic progression. The lysosomal exoenzyme, α-L-fucosidase-1 (FUCA-1) removes fucose residues from glycans. The FUCA-1 gene is down-regulated in highly aggressive and metastatic human tumors. However, the role of FUCA-1 in tumor progression remains unclear. It is speculated that its inactivation perturbs glycosylation of proteins involved in cell adhesion and promotes cancer. FUCA-1 expression of various thyroid normal and cancer tissues assayed by immunohistochemical (IHC) staining was high in normal thyroids and papillary thyroid carcinomas (PTC), whereas it progressively decreased in poorly differentiated, metastatic and anaplastic thyroid carcinomas (ATC). FUCA-1 mRNA expression from tissue samples and cell lines and protein expression levels and enzyme activity in thyroid cancer cell lines paralleled those of IHC staining. Furthermore, ATC-derived 8505C cells adhesion to human E-selectin and HUVEC cells was inhibited by bovine α-L-fucosidase or Lewis antigens, thus pointing to an essential role of fucose residues in the adhesive phenotype of this cancer cell line. Finally, 8505C cells transfected with a FUCA-1 containing plasmid displayed a less invasive phenotype versus the parental 8505C. These results demonstrate that FUCA-1 is down-regulated in ATC compared to PTC and normal thyroid tissues and cell lines. As shown for other human cancers, the down-regulation of FUCA-1 correlates with increased aggressiveness of the cancer type. This is the first report indicating that the down-regulation of FUCA-1 is related to the increased aggressiveness of thyroid cancer.
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Affiliation(s)
- Giancarlo Vecchio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini, 5, Naples, Italy.,Istituto Superiore di Oncologia, Via Sergio Pansini, 5, Naples and Via Balbi 5, Genoa, Italy
| | | | - Chiara Allocca
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Sergio Pansini, 5, Naples, Italy
| | - Clara Ugolini
- Dipartimento di Medicina di Laboratorio, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Fulvio Basolo
- Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell'Area Critica, University of Pisa, Italy
| | - Marco Moracci
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Via P. Castellino, 111, Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Andrea Strazzulli
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Via P. Castellino, 111, Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and Bioresources (IBBR), National Research Council of Italy (CNR), Via P. Castellino, 111, Naples, Italy
| | | | | | - Nobuo Tsuchida
- Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University, Tokyo, Japan
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38
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Bonin S, Parascandolo A, Aversa C, Barbazza R, Tsuchida N, Castellone MD, Stanta G, Vecchio G. Reduced expression of α-L-Fucosidase-1 (FUCA-1) predicts recurrence and shorter cancer specific survival in luminal B LN+ breast cancer patients. Oncotarget 2018; 9:15228-15238. [PMID: 29632639 PMCID: PMC5880599 DOI: 10.18632/oncotarget.24445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/01/2018] [Indexed: 01/11/2023] Open
Abstract
Background The lysosomal enzyme α-L-Fucosidase-1 (FUCA-1) catalyzes the hydrolytic cleavage of terminal fucose residues. FUCA-1 gene is down-regulated in highly aggressive and metastatic human tumors as its inactivation perturbs the fucosylation of proteins involved in cell adhesion, migration and metastases. Results Negativity to FUCA-1 was significantly related to the development of later recurrences in breast cancer patients with lymph node involvement at diagnosis. Cancer specific survival of luminal B LN+ patients was influenced by FUCA-1 expression as luminal B LN+ patients with positive expression had a longer cancer specific survival. FUCA-1 mRNA expression was inversely related to cancer stage and lymph node involvement. WB and qPCR analysis of FUCA-1 expression in breast cancer-derived cell lines confirmed an inverse relationship with tumor aggressiveness. Conclusions This study shows that, within LN+ breast cancer patients, FUCA-1 is able to identify a sub-set of non recurrent patients characterized by the positive expression of FUCA-1 and that, within luminal B LN+ patients, the expression of FUCA-1 predicts longer cancer specific survival. Methods We have analyzed FUCA-1 in 305 breast cancer patients by Immunohistochemistry (IHC), and by qPCR in breast cancer patients and in breast cancer cell lines.
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Affiliation(s)
- Serena Bonin
- Dipartimento di Scienze Mediche, Università di Trieste-Cattinara, Trieste, Italy
| | | | - Cinzia Aversa
- Dipartimento di Scienze Mediche, Università di Trieste-Cattinara, Trieste, Italy
| | - Renzo Barbazza
- Dipartimento di Scienze Mediche, Università di Trieste-Cattinara, Trieste, Italy
| | - Nobuo Tsuchida
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Giorgio Stanta
- Dipartimento di Scienze Mediche, Università di Trieste-Cattinara, Trieste, Italy
| | - Giancarlo Vecchio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy.,Istituto Superiore di Oncologia, Naples, Italy.,Istituto Superiore di Oncologia, Genoa, Italy
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39
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Mueller C, Haymond A, Davis JB, Williams A, Espina V. Protein biomarkers for subtyping breast cancer and implications for future research. Expert Rev Proteomics 2018; 15:131-152. [PMID: 29271260 PMCID: PMC6104835 DOI: 10.1080/14789450.2018.1421071] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure. Areas covered: This review provides a summary of immunohistochemistry, reverse phase protein array, mass spectrometry, and integrative studies that are revealing differences in biological functions within and between breast cancer subtypes. We conclude with a discussion of rigor and reproducibility for proteomic-based biomarker discovery. Expert commentary: Innovations in proteomics, including implementation of assay guidelines and standards, are facilitating refinement of breast cancer subtypes. Proteomic and phosphoproteomic information distinguish biologically functional subtypes, are predictive of recurrence, and indicate likelihood of drug resistance. Actionable, activated signal transduction pathways can now be quantified and characterized. Proteomic biomarker validation in large, well-designed studies should become a public health priority to capitalize on the wealth of information gleaned from the proteome.
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Affiliation(s)
- Claudius Mueller
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Amanda Haymond
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin B Davis
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Alexa Williams
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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40
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Munkley J, Elliott DJ. Hallmarks of glycosylation in cancer. Oncotarget 2018; 7:35478-89. [PMID: 27007155 PMCID: PMC5085245 DOI: 10.18632/oncotarget.8155] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/02/2016] [Indexed: 12/12/2022] Open
Abstract
Aberrant glycosylation plays a fundamental role in key pathological steps of tumour development and progression. Glycans have roles in cancer cell signalling, tumour cell dissociation and invasion, cell-matrix interactions, angiogenesis, metastasis and immune modulation. Aberrant glycosylation is often cited as a ‘hallmark of cancer’ but is notably absent from both the original hallmarks of cancer and from the next generation of emerging hallmarks. This review discusses how glycosylation is clearly an enabling characteristic that is causally associated with the acquisition of all the hallmark capabilities. Rather than aberrant glycosylation being itself a hallmark of cancer, another perspective is that glycans play a role in every recognised cancer hallmark.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, NE1 3BZ, UK
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41
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Lavrsen K, Dabelsteen S, Vakhrushev SY, Levann AMR, Haue AD, Dylander A, Mandel U, Hansen L, Frödin M, Bennett EP, Wandall HH. De novo expression of human polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6) in colon adenocarcinoma inhibits the differentiation of colonic epithelium. J Biol Chem 2017; 293:1298-1314. [PMID: 29187600 DOI: 10.1074/jbc.m117.812826] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
Aberrant expression of O-glycans is a hallmark of epithelial cancers. Mucin-type O-glycosylation is initiated by a large family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) that target different proteins and are differentially expressed in cells and organs. Here, we investigated the expression patterns of all of the GalNAc-Ts in colon cancer by analyzing transcriptomic data. We found that GalNAc-T6 was highly up-regulated in colon adenocarcinomas but absent in normal-appearing adjacent colon tissue. These results were verified by immunohistochemistry, suggesting that GalNAc-T6 plays a role in colon carcinogenesis. To investigate the function of GalNAc-T6 in colon cancer, we used precise gene targeting to produce isogenic colon cancer cell lines with a knockout/rescue system for GALNT6 GalNAc-T6 expression was associated with a cancer-like, dysplastic growth pattern, whereas GALNT6 knockout cells showed a more normal differentiation pattern, reduced proliferation, normalized cell-cell adhesion, and formation of crypts in tissue cultures. O-Glycoproteomic analysis of the engineered cell lines identified a small set of GalNAc-T6-specific targets, suggesting that this isoform has unique cellular functions. In support of this notion, the genetically and functionally closely related GalNAc-T3 homolog did not show compensatory functionality for effects observed for GalNAc-T6. Taken together, these data strongly suggest that aberrant GalNAc-T6 expression and site-specific glycosylation is involved in oncogenic transformation.
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Affiliation(s)
- Kirstine Lavrsen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Sally Dabelsteen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Sergey Y Vakhrushev
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Asha M R Levann
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Amalie Dahl Haue
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - August Dylander
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Ulla Mandel
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Lars Hansen
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK 2200, Copenhagen N, Denmark
| | - Eric P Bennett
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
| | - Hans H Wandall
- From the Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, and
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Kirby MK, Ramaker RC, Gertz J, Davis NS, Johnston BE, Oliver PG, Sexton KC, Greeno EW, Christein JD, Heslin MJ, Posey JA, Grizzle WE, Vickers SM, Buchsbaum DJ, Cooper SJ, Myers RM. RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4. Mol Oncol 2016; 10:1169-82. [PMID: 27282075 PMCID: PMC5423196 DOI: 10.1016/j.molonc.2016.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/25/2016] [Accepted: 05/17/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma patients have low survival rates due to late-stage diagnosis and high rates of cancer recurrence even after surgical resection. It is important to understand the molecular characteristics associated with survival differences in pancreatic adenocarcinoma tumors that may inform patient care. RESULTS RNA sequencing was performed for 51 patient tumor tissues extracted from patients undergoing surgical resection, and expression was associated with overall survival time from diagnosis. Our analysis uncovered 323 transcripts whose expression correlates with survival time in our pancreatic patient cohort. This genomic signature was validated in an independent RNA-seq dataset of 68 additional patients from the International Cancer Genome Consortium. We demonstrate that this transcriptional profile is largely independent of markers of cellular division and present a 19-transcript predictive model built from a subset of the 323 transcripts that can distinguish patients with differing survival times across both the training and validation patient cohorts. We present evidence that a subset of the survival-associated transcripts is associated with resistance to gemcitabine treatment in vitro, and reveal that reduced expression of one of the survival-associated transcripts, Angiopoietin-like 4, impairs growth of a gemcitabine-resistant pancreatic cancer cell line. CONCLUSIONS Gene expression patterns in pancreatic adenocarcinoma tumors can distinguish patients with differing survival outcomes after undergoing surgical resection, and the survival difference could be associated with the intrinsic gemcitabine sensitivity of primary patient tumors. Thus, these transcriptional differences may impact patient care by distinguishing patients who would benefit from a non-gemcitabine based therapy.
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Affiliation(s)
- Marie K Kirby
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jason Gertz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Patsy G Oliver
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - James A Posey
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
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Greville G, McCann A, Rudd PM, Saldova R. Epigenetic regulation of glycosylation and the impact on chemo-resistance in breast and ovarian cancer. Epigenetics 2016; 11:845-857. [PMID: 27689695 DOI: 10.1080/15592294.2016.1241932] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glycosylation is one of the most fundamental posttranslational modifications in cellular biology and has been shown to be epigenetically regulated. Understanding this process is important as epigenetic therapies such as those using DNA methyltransferase inhibitors are undergoing clinical trials for the treatment of ovarian and breast cancer. Previous work has demonstrated that altered glycosylation patterns are associated with aggressive disease in women presenting with breast and ovarian cancer. Moreover, the tumor microenvironment of hypoxia results in globally altered DNA methylation and is associated with aggressive cancer phenotypes and chemo-resistance, a feature integral to many cancers. There is sparse knowledge on the impact of these therapies on glycosylation. Moreover, little is known about the efficacy of DNA methyltransferase inhibitors in hypoxic tumors. In this review, we interrogate the impact that hypoxia and epigenetic regulation has on cancer cell glycosylation in relation to resultant tumor cell aggressiveness and chemo-resistance.
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Affiliation(s)
- Gordon Greville
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| | - Amanda McCann
- b UCD School of Medicine, College of Health and Agricultural Science, University College Dublin , UCD, Belfield, Dublin , Ireland.,c UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , UCD, Belfield, Dublin , Ireland
| | - Pauline M Rudd
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
| | - Radka Saldova
- a NIBRT GlycoScience Group , The National Institute for Bioprocessing Research and Training , Mount Merrion, Blackrock, Dublin , Ireland
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Haakensen VD, Steinfeld I, Saldova R, Shehni AA, Kifer I, Naume B, Rudd PM, Børresen-Dale AL, Yakhini Z. Serum N-glycan analysis in breast cancer patients--Relation to tumour biology and clinical outcome. Mol Oncol 2015; 10:59-72. [PMID: 26321095 DOI: 10.1016/j.molonc.2015.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/02/2015] [Accepted: 08/03/2015] [Indexed: 12/13/2022] Open
Abstract
Glycosylation and related processes play important roles in cancer development and progression, including metastasis. Several studies have shown that N-glycans have potential diagnostic value as cancer serum biomarkers. We have explored the significance of the abundance of particular serum N-glycan structures as important features of breast tumour biology by studying the serum glycome and tumour transcriptome (mRNA and miRNA) of 104 breast cancer patients. Integration of these types of molecular data allows us to study the relationship between serum glycans and transcripts representing functional pathways, such as metabolic pathways or DNA damage response. We identified tri antennary trigalactosylated trisialylated glycans in serum as being associated with lower levels of tumour transcripts involved in focal adhesion and integrin-mediated cell adhesion. These glycan structures were also linked to poor prognosis in patients with ER negative tumours. High abundance of simple monoantennary glycan structures were associated with increased survival, particularly in the basal-like subgroup. The presence of circulating tumour cells was found to be significantly associated with several serum glycome structures like bi and triantennary, di- and trigalactosylated, di- and trisialylated. The link between tumour miRNA expression levels and N-glycan production is also examined.
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Affiliation(s)
- Vilde D Haakensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Israel Steinfeld
- Department of Computer Science, Technion, Haifa, Israel; Agilent Laboratories, Agilent Technologies, Tel-Aviv, Israel
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Akram Asadi Shehni
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Ilona Kifer
- Agilent Laboratories, Agilent Technologies, Tel-Aviv, Israel
| | - Bjørn Naume
- Department of Oncology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Pauline M Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin 4, Ireland
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Zohar Yakhini
- Department of Computer Science, Technion, Haifa, Israel; Agilent Laboratories, Agilent Technologies, Tel-Aviv, Israel.
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Potapenko IO, Lüders T, Russnes HG, Helland Å, Sørlie T, Kristensen VN, Nord S, Lingjærde OC, Børresen-Dale AL, Haakensen VD. Glycan-related gene expression signatures in breast cancer subtypes; relation to survival. Mol Oncol 2015; 9:861-76. [PMID: 25655580 DOI: 10.1016/j.molonc.2014.12.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/27/2014] [Indexed: 01/23/2023] Open
Abstract
Alterations in glycan structures are early signs of malignancy and have recently been proposed to be in part a driving force behind malignant transformation. Here, we explore whether differences in expression of genes related to the process of glycosylation exist between breast carcinoma subtypes - and look for their association to clinical parameters. Five expression datasets of 454 invasive breast carcinomas, 31 ductal carcinomas in situ (DCIS), and 79 non-malignant breast tissue samples were analysed. Results were validated in 1960 breast carcinomas. 419 genes encoding glycosylation-related proteins were selected. The DCIS samples appeared expression-wise similar to carcinomas, showing altered gene expression related to glycosaminoglycans (GAGs) and N-glycans when compared to non-malignant samples. In-situ lesions with different aggressiveness potentials demonstrated changes in glycosaminoglycan sulfation and adhesion proteins. Subtype-specific expression patterns revealed down-regulation of genes encoding glycan-binding proteins in the luminal A and B subtypes. Clustering basal-like samples using a consensus list of genes differentially expressed across discovery datasets produced two clusters with significantly differing prognosis in the validation dataset. Finally, our analyses suggest that glycolipids may play an important role in carcinogenesis of breast tumors - as demonstrated by association of B3GNT5 and UGCG genes to patient survival. In conclusion, most glycan-specific changes occur early in the carcinogenic process. We have identified glycan-related alterations specific to breast cancer subtypes including a prognostic signature for two basal-like subgroups. Future research in this area may potentially lead to markers for better prognostication and treatment stratification of breast cancer patients.
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Affiliation(s)
- Ivan O Potapenko
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Torben Lüders
- Department of Clinical Epidemiology and Molecular Biology (Epi-Gen), Akershus University Hospital, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Hege G Russnes
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Åslaug Helland
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Oncology, Oslo University Hospital Radiumhospitalet, Norway
| | - Therese Sørlie
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Clinical Epidemiology and Molecular Biology (Epi-Gen), Akershus University Hospital, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Ole C Lingjærde
- Institute for Informatics, Faculty of Natural Sciences and Mathematics, University of Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Vilde D Haakensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
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