1
|
Küffer S, Müller D, Marx A, Ströbel P. Non-Mutational Key Features in the Biology of Thymomas. Cancers (Basel) 2024; 16:942. [PMID: 38473304 DOI: 10.3390/cancers16050942] [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: 02/08/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Thymomas (THs) are a unique group of heterogeneous tumors of the thymic epithelium. In particular, the subtypes B2 and B3 tend to be aggressive and metastatic. Radical tumor resection remains the only curative option for localized tumors, while more advanced THs require multimodal treatment. Deep sequencing analyses have failed to identify known oncogenic driver mutations in TH, with the notable exception of the GTF2I mutation, which occurs predominantly in type A and AB THs. However, there are multiple alternative non-mutational mechanisms (e.g., perturbed thymic developmental programs, metabolism, non-coding RNA networks) that control cellular behavior and tumorigenesis through the deregulation of critical molecular pathways. Here, we attempted to show how the results of studies investigating such alternative mechanisms could be integrated into a current model of TH biology. This model could be used to focus ongoing research and therapeutic strategies.
Collapse
Affiliation(s)
- Stefan Küffer
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Denise Müller
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Alexander Marx
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, 37075 Göttingen, Germany
| |
Collapse
|
2
|
Li J, Qi G, Liu Y. Proteomics analysis of serum from thymoma patients. Sci Rep 2023; 13:5117. [PMID: 36991043 PMCID: PMC10060243 DOI: 10.1038/s41598-023-32339-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/26/2023] [Indexed: 03/31/2023] Open
Abstract
Thymoma is the most common malignant tumor in thymic epithelial tumors (TETS). This study aimed to identify the changes in serum proteomics in patients with thymoma. Proteins were extracted from twenty patients with thymoma serum and nine healthy controls and prepared for mass spectrometry (MS) analysis. Data independent acquisition (DIA) quantitative proteomics technique was used to examine the serum proteome. Differential proteins of abundance changes in the serum were identified. Bioinformatics was used to examine the differential proteins. Functional tagging and enrichment analysis were conducted using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The string database was used to assess the interaction of different proteins. In all, 486 proteins were found in all samples. There were differences in 58 serum proteins between patients and healthy blood donors, 35 up-regulated and 23 down-regulated. These proteins are primarily exocrine and serum membrane proteins involved in controlling immunological responses and antigen binding, according to GO functional annotation. KEGG functional annotation showed that these proteins play a significant role in the complement and coagulation cascade and the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signal pathway. Notably, the KEGG pathway (complement and coagulation cascade) is enriched, and three key activators were up-regulated: von willebrand factor (VWF), coagulation factor v (F5) and vitamin k-dependent protein c (PC). Protein-protein interaction (PPI) analysis showed that six proteins ((VWF, F5, thrombin reactive protein 1 (THBS1), mannose-binding lectin-associated serine protease 2 (MASP2), apolipoprotein B (APOB), and apolipoprotein (a) (LPA)) were up-regulated and two proteins (Metalloproteinase inhibitor 1(TIMP1), ferritin light chain (FTL)) were down-regulated. The results of this study showed that several proteins involved in complement and coagulation cascades were up-regulated in the serum of patients.
Collapse
Affiliation(s)
- Jiaduo Li
- People's Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, Hebei, China
| | - Guoyan Qi
- People's Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Yaling Liu
- People's Hospital of Shijiazhuang Affiliated to Hebei Medical University, Shijiazhuang, Hebei, China
| |
Collapse
|
3
|
Zhou Z, Lu Y, Gu Z, Sun Q, Fang W, Yan W, Ku X, Liang Z, Hu G. HNRNPA2B1 as a potential therapeutic target for thymic epithelial tumor recurrence: An integrative network analysis. Comput Biol Med 2023; 155:106665. [PMID: 36791552 DOI: 10.1016/j.compbiomed.2023.106665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023]
Abstract
Thymic epithelial tumors (TETs) are rare malignant tumors, and the molecular mechanisms of both primary and recurrent TETs are poorly understood. Here we established comprehensive proteomic signatures of 15 tumors (5 recurrent and 10 non-recurrent) and 15 pair wised tumor adjacent normal tissues. We then proposed an integrative network approach for studying the proteomics data by constructing protein-protein interaction networks based on differentially expressed proteins and a machine learning-based score, followed by network modular analysis, functional enrichment annotation and shortest path inference analysis. Network modular analysis revealed that primary and recurrent TETs shared certain common molecular mechanisms, including a spliceosome module consisting of RNA splicing and RNA processing, but the recurrent TET was specifically related to the ribosome pathway. Applying the shortest path inference to the collected seed gene module identified that the ribonucleoprotein hnRNPA2B1 probably serves as a potential target for recurrent TET therapy. The drug repositioning combined molecular dynamics simulations suggested that the compound ergotamine could potentially act as a repurposing drug to treat recurrent TETs by targeting hnRNPA2B1. Our study demonstrates the value of integrative network analysis to understand proteotype robustness and its relationships with genotype, and provides hits for further research on cancer therapeutics.
Collapse
Affiliation(s)
- Ziyun Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou, 215123, China
| | - Yu Lu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Zhitao Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qiangling Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China; Thoracic Cancer Institute, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Ku
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou, 215123, China; Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou, 215123, China.
| |
Collapse
|
4
|
Ozaki S, Umakoshi A, Yano H, Ohsumi S, Sumida Y, Hayase E, Usa E, Islam A, Choudhury ME, Nishi Y, Yamashita D, Ohtsuka Y, Nishikawa M, Inoue A, Suehiro S, Kuwabara J, Watanabe H, Takada Y, Watanabe Y, Nakano I, Kunieda T, Tanaka J. Chloride intracellular channel protein 2 is secreted and inhibits MMP14 activity, while preventing tumor cell invasion and metastasis. Neoplasia 2021; 23:754-765. [PMID: 34229297 PMCID: PMC8260957 DOI: 10.1016/j.neo.2021.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 12/20/2022] Open
Abstract
CLIC2 is highly expressed in benign, less invasive and less metastatic tumors. Forced expression of CLIC2 prevents metastasis and invasion in animal tumor models. CLIC2 is associated with decreased vascular permeability in tumor masses. CLIC2, a secretable soluble protein, can bind to and inhibit MMP14. Extracellular CLIC2 can suppress malignant cell invasion.
The abilities to invade surrounding tissues and metastasize to distant organs are the most outstanding features that distinguish malignant from benign tumors. However, the mechanisms preventing the invasion and metastasis of benign tumor cells remain unclear. By using our own rat distant metastasis model, gene expression of cells in primary tumors was compared with that in metastasized tumors. Among many distinct gene expressions, we have focused on chloride intracellular channel protein 2 (CLIC2), an ion channel protein of as-yet unknown function, which was predominantly expressed in the primary tumors. We created CLIC2 overexpressing rat glioma cell line and utilized benign human meningioma cells with naturally high CLIC2 expression. CLIC2 was expressed at higher levels in benign human brain tumors than in their malignant counterparts. Moreover, its high expression was associated with prolonged survival in the rat metastasis and brain tumor models as well as with progression-free survival in patients with brain tumors. CLIC2 was also correlated with the decreased blood vessel permeability likely by increased contents of cell adhesion molecules. We found that CLIC2 was secreted extracellularly, and bound to matrix metalloproteinase (MMP) 14. Furthermore, CLIC2 prevented the localization of MMP14 in the plasma membrane, and inhibited its enzymatic activity. Indeed, overexpressing CLIC2 and recombinant CLIC2 protein effectively suppressed malignant cell invasion, whereas CLIC2 knockdown reversed these effects. Thus, CLIC2 suppress invasion and metastasis of benign tumors at least partly by inhibiting MMP14 activity.
Collapse
Affiliation(s)
- Saya Ozaki
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Akihiro Umakoshi
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Hajime Yano
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Shota Ohsumi
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Yutaro Sumida
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Erika Hayase
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Eika Usa
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Afsana Islam
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Mohammed E Choudhury
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan
| | - Yusuke Nishi
- Department of Hepato-biliary Pancreatic Surgery and Breast Surgery, Graduate School of Medicine, Ehime University, Japan
| | - Daisuke Yamashita
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Yoshihiro Ohtsuka
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Masahiro Nishikawa
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Akihiro Inoue
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Satoshi Suehiro
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Jun Kuwabara
- Department of Gastrointestinal Surgery and Surgical Oncology, Graduate School of Medicine, Ehime University, Japan
| | - Hideaki Watanabe
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Yasutsugu Takada
- Department of Hepato-biliary Pancreatic Surgery and Breast Surgery, Graduate School of Medicine, Ehime University, Japan
| | - Yuji Watanabe
- Department of Gastrointestinal Surgery and Surgical Oncology, Graduate School of Medicine, Ehime University, Japan
| | - Ichiro Nakano
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takeharu Kunieda
- Department of Neurosurgery, Graduate School of Medicine, Ehime University, Japan
| | - Junya Tanaka
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Ehime University, Japan.
| |
Collapse
|
5
|
Chen D, Hu G, Zhang S, Zhang H, Teng X. Ammonia-triggered apoptosis via immune function and metabolic process in the thymuses of chickens by proteomics analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110619. [PMID: 32344265 DOI: 10.1016/j.ecoenv.2020.110619] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Ammonia (NH3), an environmental pollutant with a pungent odor, is not only an important volatile in fertilizer production and ranching, but also main basic component of haze. In present study, we found that ultrastructural changes and 3167 differentially expressed proteins (DEPs) using proteomics analysis in the thymuses of chickens exposed to NH3 on day 42. Obtained DEPs were enriched using GO and KEGG; and 66 DEPs took part in immune function, metabolic process, and apoptosis in the thymuses of chickens treated with NH3. 9 genes of DEPs were validated using qRT-PCR, and mRNA expression of 2 immune-related genes (CTSG and NFATC2), 3 metabolic process-related genes (APOA1, GOT1, and GOLGA3), and 4 apoptosis-related genes (PIK3CD, CTSS, CAMP, and NSD2) were consistent with DEPs in chicken thymuses. Our results indicated that excess NH3 led to immunosuppression, metabolic disorder, and apoptosis in chicken thymuses. Present study gives a novel insight into the mechanism of NH3 toxicity and demonstrated that immune response, metabolism process, and apoptosis were important in the mechanism of NH3 toxicity of chicken exposure to high concentration of NH3.
Collapse
Affiliation(s)
- Dechun Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China; College of Life Science and Technology, Southwest University for Nationalities, Chengdu, 610041, China
| | - Guanghui Hu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Shuai Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xiaohua Teng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
6
|
Peric J, Samaradzic N, Skodric Trifunovic V, Tosic N, Stojsic J, Pavlovic S, Jovanovic D. Genomic profiling of thymoma using a targeted high-throughput approach. Arch Med Sci 2020; 20:909-917. [PMID: 39050176 PMCID: PMC11264071 DOI: 10.5114/aoms.2020.96537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/21/2019] [Indexed: 07/27/2024] Open
Abstract
Introduction Thymomas and thymic carcinoma (TC) are the most common neoplasms localised in the thymus. These diseases are poorly understood, but progress made in next-generation sequencing (NGS) technology has provided novel data on their molecular pathology. Material and methods Genomic DNA was isolated from formalin-fixed paraffin-embedded tumour tissue. We investigated somatic variants in 35 thymoma patients using amplicon-based TruSeq Amplicon Cancer Panel (TSACP) that covers 48 cancer related genes. We also analysed three samples from healthy individuals by TSACP platform and 32 healthy controls using exome sequencing. Results The total number of detected variants was 4447, out of which 2906 were in the coding region (median per patient 83, range: 2-300) and 1541 were in the non-coding area (median per patient 44, range: 0-172). We identified four genes, APC, ATM, ERBB4, and SMAD4, having more than 100 protein-changing variants. Additionally, more than 70% of the analysed cases harboured protein-changing variants in SMAD4, APC, ATM, PTEN, KDR, and TP53. Moreover, this study revealed 168 recurrent variants, out of which 15 were shown to be pathogenic. Comparison to controls revealed that the variants we reported in this study were somatic thymoma-specific variants. Additionally, we found that the presence of variants in SMAD4 gene predicted shorter overall survival in thymoma patients. Conclusions The most frequently mutated genes in thymoma samples analysed in this study belong to the EGFR, ATM, and TP53 signalling pathways, regulating cell cycle check points, gene expression, and apoptosis. The results of our study complement the knowledge of thymoma molecular pathogenesis.
Collapse
Affiliation(s)
- Jelena Peric
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Natalija Samaradzic
- University Hospital of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
| | - Vesna Skodric Trifunovic
- University Hospital of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Natasa Tosic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Centre of Serbia, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Dragana Jovanovic
- University Hospital of Pulmonology, Clinical Centre of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
7
|
Gururaja Rao S, Patel NJ, Singh H. Intracellular Chloride Channels: Novel Biomarkers in Diseases. Front Physiol 2020; 11:96. [PMID: 32116799 PMCID: PMC7034325 DOI: 10.3389/fphys.2020.00096] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Ion channels are integral membrane proteins present on the plasma membrane as well as intracellular membranes. In the human genome, there are more than 400 known genes encoding ion channel proteins. Ion channels are known to regulate several cellular, organellar, and physiological processes. Any mutation or disruption in their function can result in pathological disorders, both common or rare. Ion channels present on the plasma membrane are widely acknowledged for their role in various biological processes, but in recent years, several studies have pointed out the importance of ion channels located in intracellular organelles. However, ion channels located in intracellular organelles are not well-understood in the context of physiological conditions, such as the generation of cellular excitability and ionic homeostasis. Due to the lack of information regarding their molecular identity and technical limitations of studying them, intracellular organelle ion channels have thus far been overlooked as potential therapeutic targets. In this review, we focus on a novel class of intracellular organelle ion channels, Chloride Intracellular Ion Channels (CLICs), mainly documented for their role in cardiovascular, neurophysiology, and tumor biology. CLICs have a single transmembrane domain, and in cells, they exist in cytosolic as well as membranous forms. They are predominantly present in intracellular organelles and have recently been shown to be localized to cardiomyocyte mitochondria as well as exosomes. In fact, a member of this family, CLIC5, is the first mitochondrial chloride channel to be identified on the molecular level in the inner mitochondrial membrane, while another member, CLIC4, is located predominantly in the outer mitochondrial membrane. In this review, we discuss this unique class of intracellular chloride channels, their role in pathologies, such as cardiovascular, cancer, and neurodegenerative diseases, and the recent developments concerning their usage as theraputic targets.
Collapse
Affiliation(s)
- Shubha Gururaja Rao
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Neel J Patel
- Department of Cardiology, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| |
Collapse
|
8
|
Ku X, Sun Q, Zhu L, Gu Z, Han Y, Xu N, Meng C, Yang X, Yan W, Fang W. Deciphering tissue-based proteome signatures revealed novel subtyping and prognostic markers for thymic epithelial tumors. Mol Oncol 2020; 14:721-741. [PMID: 31967407 PMCID: PMC7138395 DOI: 10.1002/1878-0261.12642] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/18/2019] [Accepted: 01/17/2020] [Indexed: 11/21/2022] Open
Abstract
Thymic epithelial tumors (TETs) belong to a group of tumors that rarely occur, but have unresolved mechanisms and heterogeneous clinical behaviors. Current care of TET patients demands biomarkers of high sensitivity and specificity for accurate histological classification and prognosis management. In this study, 134 fresh‐frozen tissue samples (84 tumor, 40 tumor adjacent, and 10 normal thymus) were recruited to generate a quantitative and systematic view of proteomic landscape of TETs. Among them, 90 samples were analyzed by data‐independent acquisition mass spectrometry (DIA‐MS) leading to discovery of novel classifying molecules among different TET subtypes. The correlation between clinical outcome and the identified molecules was probed, and the prioritized proteins of interest were further validated on the remaining samples (n = 44) via parallel reaction monitoring (PRM) as well as immunohistochemical and confocal imaging analysis. In particular, two proteins, the cellular mRNA deadenylase CCR4 (carbon catabolite repressor 4)‐NOT (negative on TATA) complex subunit 2/9 (CNOT2/9) and the serine hydroxymethyltransferase that catalyzes the reversible interconversions of serine and glycine (SHMT1), were found at dramatic low levels in the thymic epithelia of more malignant subtype, thymic squamous cell carcinoma (TSCC). Interestingly, the mRNA levels of these two genes were shown to be closely correlated with prognosis of the TET patients. These results extended the existing human tissue proteome atlas and allowed us to identify several new protein classifiers for TET subtyping. Newly identified subtyping and prognosis markers, CNOT2/9 and SHMT1, will expand current diagnostic arsenal in terms of higher specificity and prognostic insights for TET diagnosis and management.
Collapse
Affiliation(s)
- Xin Ku
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, China
| | - Qiangling Sun
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, China.,Thoracic Cancer Institute, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - Zhitao Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - Ning Xu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, Freising, Germany
| | - Xiaohua Yang
- Central Lab, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| | - Wei Yan
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, China
| | - Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, China
| |
Collapse
|
9
|
A practical approach to enrich intact tryptic N-glycopeptides through size exclusion chromatography and hydrophilicity (SELIC) using an acrylamide-agarose composite gel system. Anal Chim Acta 2019; 1058:107-116. [PMID: 30851844 DOI: 10.1016/j.aca.2019.01.044] [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: 11/06/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 12/18/2022]
Abstract
Increasing researches proved that abnormal glycosylation is strongly correlated with many diseases. Specially, site-specific glycosylation and its associated heterogeneity are closely related to the function and activity of the glycoprotein. However, intact N-glycopeptide analysis still faces great challenges because the presence of highly abundant non-glycosylated peptides would suppress the ionization of lowly abundant glycopeptides. In the present study, we developed a practical intact tryptic N-glycopeptide enrichment method using acrylamide-agarose composite gel that combined the size exclusion chromatography and hydrophilic (named SELIC) effects, aimed to remove the detergent rapidly and effectively, as well as enrich intact N-glycopeptides while extracting peptides. This is a useful tool to facilitate the intact N-glycopeptides analysis of complex protein mixtures, particularly for samples that extracted from formalin-fixed and paraffin-embedded (FFPE) tissues by SDS. Using this method, we successfully identified 700 site-specific intact tryptic N-glycopeptides corresponding to 261 glycosylation sites on 191 glycoproteins from FFPE thymoma tissues.
Collapse
|