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Kollerits B, Gruber S, Steinbrenner I, Schwaiger JP, Weissensteiner H, Schönherr S, Forer L, Kotsis F, Schultheiss UT, Meiselbach H, Wanner C, Eckardt KU, Kronenberg F. Apolipoprotein A-IV concentrations and cancer in a large cohort of chronic kidney disease patients: results from the GCKD study. BMC Cancer 2024; 24:320. [PMID: 38454416 PMCID: PMC10921727 DOI: 10.1186/s12885-024-12053-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is highly connected to inflammation and oxidative stress. Both favour the development of cancer in CKD patients. Serum apolipoprotein A-IV (apoA-IV) concentrations are influenced by kidney function and are an early marker of kidney impairment. Besides others, it has antioxidant and anti-inflammatory properties. Proteomic studies and small case-control studies identified low apoA-IV as a biomarker for various forms of cancer; however, prospective studies are lacking. We therefore investigated whether serum apoA-IV is associated with cancer in the German Chronic Kidney Disease (GCKD) study. METHODS These analyses include 5039 Caucasian patients from the prospective GCKD cohort study followed for 6.5 years. Main inclusion criteria were an eGFR of 30-60 mL/min/1.73m2 or an eGFR > 60 mL/min/1.73m2 in the presence of overt proteinuria. RESULTS Mean apoA-IV concentrations of the entire cohort were 28.9 ± 9.8 mg/dL (median 27.6 mg/dL). 615 patients had a history of cancer before the enrolment into the study. ApoA-IV concentrations above the median were associated with a lower odds for a history of cancer (OR = 0.79, p = 0.02 when adjusted age, sex, smoking, diabetes, BMI, albuminuria, statin intake, and eGFRcreatinine). During follow-up 368 patients developed an incident cancer event and those with apoA-IV above the median had a lower risk (HR = 0.72, 95%CI 0.57-0.90, P = 0.004). Finally, 62 patients died from such an incident cancer event and each 10 mg/dL higher apoA-IV concentrations were associated with a lower risk for fatal cancer (HR = 0.62, 95%CI 0.44-0.88, P = 0.007). CONCLUSIONS Our data indicate an association of high apoA-IV concentrations with reduced frequencies of a history of cancer as well as incident fatal and non-fatal cancer events in a large cohort of patients with CKD.
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Affiliation(s)
- Barbara Kollerits
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria
| | - Simon Gruber
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Johannes P Schwaiger
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Medicine IV - Nephrology and Primary Care, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- German Chronic Kidney Disease Study, Erlangen, Germany
| | - Christoph Wanner
- Division of Nephrology, Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- German Chronic Kidney Disease Study, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Austria.
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2
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Yang S, Zhu G, He R, Fang D, Feng J. Advances in transcriptomics and proteomics in differentiated thyroid cancer: An updated perspective (Review). Oncol Lett 2023; 26:396. [PMID: 37600346 PMCID: PMC10433702 DOI: 10.3892/ol.2023.13982] [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: 02/14/2023] [Accepted: 05/25/2023] [Indexed: 08/22/2023] Open
Abstract
Thyroid cancer (TC) is a broad classification of neoplasms that includes differentiated thyroid cancer (DTC) as a common histological subtype. DTC is characterized by an increased mortality rate in advanced stages, which contributes to the overall high mortality rate of DTC. This progression is mainly attributed to alterations in molecular driver genes, resulting in changes in phenotypes such as invasion, metastasis and dedifferentiation. Clinical management of DTC is challenging due to insufficient diagnostic and therapeutic options. The advent of-omics technology has presented a promising avenue for the diagnosis and treatment of DTC. Identifying molecular markers that can predict the early progression of DTC to a late adverse outcome is essential for precise diagnosis and treatment. The present review aimed to enhance our understanding of DTC by integrating big data with biological systems through-omics technology, specifically transcriptomics and proteomics, which can shed light on the molecular mechanisms underlying carcinogenesis.
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Affiliation(s)
- Shici Yang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Gaohong Zhu
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Rui He
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Dong Fang
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Jiaojiao Feng
- Department of Nuclear Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
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3
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Ye G, Zhang X, Li M, Lin Z, Xu Y, Dong H, Zhou J, Zhang J, Wang S, Zhu Y, Yu X, Qian X. Integrated analysis of circulating and tissue proteomes reveals that fibronectin 1 is a potential biomarker in papillary thyroid cancer. BMC Cancer 2023; 23:412. [PMID: 37158852 PMCID: PMC10165821 DOI: 10.1186/s12885-023-10839-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Papillary thyroid cancer (PTC) is the most frequent subtype of thyroid cancer, but 20% of cases are indeterminate (i.e., cannot be accurately diagnosed) based on preoperative cytology, which might lead to surgical removal of a normal thyroid gland. To address this concern, we performed an in-depth analysis of the serum proteomes of 26 PTC patients and 23 healthy controls using antibody microarrays and data-independent acquisition mass spectrometry (DIA-MS). We identified a total of 1091 serum proteins spanning 10-12 orders of magnitude. 166 differentially expressed proteins were identified that participate in complement activation, coagulation cascades, and platelet degranulation pathways. Furthermore, the analysis of serum proteomes before and after surgery indicated that the expression of proteins such as lactate dehydrogenase A and olfactory receptor family 52 subfamily B member 4, which participate in fibrin clot formation and extracellular matrix-receptor interaction pathways, were changed. Further analysis of the proteomes of PTC and neighboring tissues revealed integrin-mediated pathways with possible crosstalk between the tissue and circulating compartments. Among these cross-talk proteins, circulating fibronectin 1 (FN1), gelsolin (GSN) and UDP-glucose 4-epimerase (GALE) were indicated as promising biomarkers for PTC identification and validated in an independent cohort. In differentiating between patients with benign nodules or PTC, FN1 produced the best ELISA result (sensitivity = 96.89%, specificity = 91.67%). Overall, our results present proteomic landscapes of PTC before and after surgery as well as the crosstalk between tissue and the circulatory system, which is valuable to understand PTC pathology and improve PTC diagnostics in the future.
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Affiliation(s)
- Guochao Ye
- Department of General Surgery, Huzhou Central Hospital, Huzhou, 313000, P. R. China
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Mansheng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Zixiang Lin
- School of Basic Medical Sciences, Peking University, Beijing, 100191, P. R. China
| | - Yongcan Xu
- Department of General Surgery, Huzhou Central Hospital, Huzhou, 313000, P. R. China
| | - Haoru Dong
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), The Chinese Academy of Sciences, Hangzhou, 310022, P. R. China
| | - Jie Zhou
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), The Chinese Academy of Sciences, Hangzhou, 310022, P. R. China
| | - Jiaqi Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, P. R. China
| | - Sheng Wang
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), The Chinese Academy of Sciences, Hangzhou, 310022, P. R. China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, P. R. China.
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, P. R. China.
| | - Xu Qian
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), The Chinese Academy of Sciences, Hangzhou, 310022, P. R. China.
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4
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Li WH, Zhang L, Li YY, Wang XY, Li JL, Zhao SN, Ni MQ, Li Q, Sun H. Apolipoprotein A-IV Has Bi-Functional Actions in Alcoholic Hepatitis by Regulating Hepatocyte Injury and Immune Cell Infiltration. Int J Mol Sci 2022; 24:ijms24010670. [PMID: 36614113 PMCID: PMC9820766 DOI: 10.3390/ijms24010670] [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: 10/04/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
Alcohol abuse can lead to alcoholic hepatitis (AH), a worldwide public health issue with high morbidity and mortality. Here, we identified apolipoprotein A-IV (APOA4) as a biomarker and potential therapeutic target for AH. APOA4 expression was detected by Gene Expression Omnibus (GEO) databases, Immunohistochemistry, and qRT-PCR in AH. Bioinformatics Methods (protein-protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Set Enrichment Analysis (GSEA) were used to show down-stream gene and pathways of APOA4 in AH. AML-12 cells were used to evaluate the biological function of APOA4 using an ELISA kit (AST, ALT, and IL-1β) and flow cytometry (ROS activity). Both in vivo and in vitro, APOA4 expression was significantly elevated in the AH model induced by alcohol (ETOH). AML-12 cell damage was specifically repaired by APOA4 deficiency, while AST, ALT, and IL-1β activity that was increased by ETOH (200 µmol, 12 h) were suppressed. APOA4 inhibition increased intracellular ROS induced by ETOH, which was detected by flow cytometry. Functional and PPI network analyses showed Fcgamma receptor (FCGR) and platelet activation signaling were potential downstream pathways. We identified CIDEC as a downstream gene of APOA4. The CIDEC AUC values for the ROC curves were 0.861. At the same time, APOA4 silencing downregulated the expression of CIDEC, whereas the knockdown of CIDEC did not influence the expression of APOA4 in AML-12 cells. Collectively, APOA4 regulates CIDEC expression and immune cell infiltration and may hold great potential as a biomarker and therapeutic target for AH.
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Affiliation(s)
- Wan-Hong Li
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Li Zhang
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Yue-Ying Li
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Xin-Yue Wang
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Jin-Liang Li
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Shu-Ning Zhao
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Ming-Qi Ni
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Qian Li
- Pharmaceutical Analysis and Analytical Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
- Correspondence: (Q.L.); (H.S.); Tel./Fax: +86-451-86699347 (Q.L.)
| | - Hui Sun
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin 150081, China
- Correspondence: (Q.L.); (H.S.); Tel./Fax: +86-451-86699347 (Q.L.)
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5
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Li J, Mi L, Ran B, Sui C, Zhou L, Li F, Dionigi G, Sun H, Liang N. Identification of potential diagnostic and prognostic biomarkers for papillary thyroid microcarcinoma (PTMC) based on TMT-labeled LC-MS/MS and machine learning. J Endocrinol Invest 2022; 46:1131-1143. [PMID: 36418670 DOI: 10.1007/s40618-022-01960-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To explore the molecular mechanisms underlying aggressive progression of papillary thyroid microcarcinoma and identify potential biomarkers. METHODS Samples were collected and sequenced using tandem mass tag-labeled liquid chromatography-tandem mass spectrometry. Differentially expressed proteins (DEPs) were identified and further analyzed using Mfuzz and protein-protein interaction analysis (PPI). Parallel reaction monitoring (PRM) and immunohistochemistry (IHC) were performed to validate the DEPs. RESULTS Five thousand, two hundred and three DEPs were identified and quantified from the tumor/normal comparison group or the N1/N0 comparison group. Mfuzz analysis showed that clusters of DEPs were enriched according to progressive status, followed by normal tissue, tumors without lymphatic metastases, and tumors with lymphatic metastases. Analysis of PPI revealed that DEPs interacted with and were enriched in the following metabolic pathways: apoptosis, tricarboxylic acid cycle, PI3K-Akt pathway, cholesterol metabolism, pyruvate metabolism, and thyroid hormone synthesis. In addition, 18 of the 20 target proteins were successfully validated with PRM and IHC in another 20 paired validation samples. Based on machine learning, the five proteins that showed the best performance in discriminating between tumor and normal nodules were PDLIM4, ANXA1, PKM, NPC2, and LMNA. FN1 performed well in discriminating between patients with lymph node metastases (N1) and N0 with an AUC of 0.690. Finally, five validated DEPs showed a potential prognostic role after examining The Cancer Genome Atlas database: FN1, IDH2, VDAC1, FABP4, and TG. Accordingly, a nomogram was constructed whose concordance index was 0.685 (confidence interval: 0.645-0.726). CONCLUSIONS PDLIM4, ANXA1, PKM, NPC2, LMNA, and FN1 are potential diagnostic biomarkers. The five-protein nomogram could be a prognostic biomarker.
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Affiliation(s)
- J Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - L Mi
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - B Ran
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - C Sui
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - L Zhou
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - F Li
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China
| | - G Dionigi
- Division of General and Endocrine Surgery, Department of Medical Biotechnology and Translational Medicine, Istituto Auxologico Italiano IRCCS, University of Milan, Milan, Italy
| | - H Sun
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China.
| | - N Liang
- Division of Thyroid Surgery, Jilin Provincial Key Laboratory of Surgical Translational Medicine, Jilin Provincial Precision Medicine Laboratory of Molecular Biology and Translational Medicine on Differentiated Thyroid Carcinoma, China-Japan Union Hospital of Jilin University, 126 Xiantai Street, Changchun, 130033, Jilin, China.
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6
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Maciejewski A, Lacka K. Vitamin D-Related Genes and Thyroid Cancer-A Systematic Review. Int J Mol Sci 2022; 23:13661. [PMID: 36362448 PMCID: PMC9658610 DOI: 10.3390/ijms232113661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 10/29/2023] Open
Abstract
Vitamin D, formerly known for its role in calcium-phosphorus homeostasis, was shown to exert a broad influence on immunity and on differentiation and proliferation processes in the last few years. In the field of endocrinology, there is proof of the potential role of vitamin D and vitamin D-related genes in the pathogenesis of thyroid cancer-the most prevalent endocrine malignancy. Therefore, the study aimed to systematically review the publications on the association between vitamin D-related gene variants (polymorphisms, mutations, etc.) and thyroid cancer. PubMed, EMBASE, Scopus, and Web of Science electronic databases were searched for relevant studies. A total of ten studies were found that met the inclusion criteria. Six vitamin D-related genes were analyzed (VDR-vitamin D receptor, CYP2R1-cytochrome P450 family 2 subfamily R member 1, CYP24A1-cytochrome P450 family 24 subfamily A member 1, CYP27B1-cytochrome P450 family 27 subfamily B member 1, DHCR7-7-dehydrocholesterol reductase and CUBN-cubilin). Moreover, a meta-analysis was conducted to summarize the data from the studies on VDR polymorphisms (rs2228570/FokI, rs1544410/BsmI, rs7975232/ApaI and rs731236/TaqI). Some associations between thyroid cancer risk (VDR, CYP24A1, DHCR7) or the clinical course of the disease (VDR) and vitamin D-related gene polymorphisms were described in the literature. However, these results seem inconclusive and need validation. A meta-analysis of the five studies of common VDR polymorphisms did not confirm their association with increased susceptibility to differentiated thyroid cancer. Further efforts are necessary to improve our understanding of thyroid cancer pathogenesis and implement targeted therapies for refractory cases.
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Affiliation(s)
| | - Katarzyna Lacka
- Department of Endocrinology, Metabolism and Internal Diseases, Poznan University of Medical Sciences, 60355 Poznan, Poland
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7
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Naryzhny S, Ronzhina N, Zorina E, Kabachenko F, Klopov N, Zgoda V. Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers. Int J Mol Sci 2022; 23:ijms231911113. [PMID: 36232415 PMCID: PMC9569744 DOI: 10.3390/ijms231911113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
The use of tumor markers aids in the early detection of cancer recurrence and prognosis. There is a hope that they might also be useful in screening tests for the early detection of cancer. Here, the question of finding ideal tumor markers, which should be sensitive, specific, and reliable, is an acute issue. Human plasma is one of the most popular samples as it is commonly collected in the clinic and provides noninvasive, rapid analysis for any type of disease including cancer. Many efforts have been applied in searching for “ideal” tumor markers, digging very deep into plasma proteomes. The situation in this area can be improved in two ways—by attempting to find an ideal single tumor marker or by generating panels of different markers. In both cases, proteomics certainly plays a major role. There is a line of evidence that the most abundant, so-called “classical plasma proteins”, may be used to generate a tumor biomarker profile. To be comprehensive these profiles should have information not only about protein levels but also proteoform distribution for each protein. Initially, the profile of these proteins in norm should be generated. In our work, we collected bibliographic information about the connection of cancers with levels of “classical plasma proteins”. Additionally, we presented the proteoform profiles (2DE patterns) of these proteins in norm generated by two-dimensional electrophoresis with mass spectrometry and immunodetection. As a next step, similar profiles representing protein perturbations in plasma produced in the case of different cancers will be generated. Additionally, based on this information, different test systems can be developed.
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Affiliation(s)
- Stanislav Naryzhny
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
- Correspondence: ; Tel.: +7-911-176-4453
| | - Natalia Ronzhina
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
| | - Elena Zorina
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
| | - Fedor Kabachenko
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Nikolay Klopov
- Petersburg Institute of Nuclear Physics (PNPI) of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya, 10, 119121 Moscow, Russia
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8
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Sun Y, Selvarajan S, Zang Z, Liu W, Zhu Y, Zhang H, Chen W, Chen H, Li L, Cai X, Gao H, Wu Z, Zhao Y, Chen L, Teng X, Mantoo S, Lim TKH, Hariraman B, Yeow S, Alkaff SMF, Lee SS, Ruan G, Zhang Q, Zhu T, Hu Y, Dong Z, Ge W, Xiao Q, Wang W, Wang G, Xiao J, He Y, Wang Z, Sun W, Qin Y, Zhu J, Zheng X, Wang L, Zheng X, Xu K, Shao Y, Zheng S, Liu K, Aebersold R, Guan H, Wu X, Luo D, Tian W, Li SZ, Kon OL, Iyer NG, Guo T. Artificial intelligence defines protein-based classification of thyroid nodules. Cell Discov 2022; 8:85. [PMID: 36068205 PMCID: PMC9448820 DOI: 10.1038/s41421-022-00442-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 06/28/2022] [Indexed: 01/21/2023] Open
Abstract
Determination of malignancy in thyroid nodules remains a major diagnostic challenge. Here we report the feasibility and clinical utility of developing an AI-defined protein-based biomarker panel for diagnostic classification of thyroid nodules: based initially on formalin-fixed paraffin-embedded (FFPE), and further refined for fine-needle aspiration (FNA) tissue specimens of minute amounts which pose technical challenges for other methods. We first developed a neural network model of 19 protein biomarkers based on the proteomes of 1724 FFPE thyroid tissue samples from a retrospective cohort. This classifier achieved over 91% accuracy in the discovery set for classifying malignant thyroid nodules. The classifier was externally validated by blinded analyses in a retrospective cohort of 288 nodules (89% accuracy; FFPE) and a prospective cohort of 294 FNA biopsies (85% accuracy) from twelve independent clinical centers. This study shows that integrating high-throughput proteomics and AI technology in multi-center retrospective and prospective clinical cohorts facilitates precise disease diagnosis which is otherwise difficult to achieve by other methods.
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Affiliation(s)
- Yaoting Sun
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Sathiyamoorthy Selvarajan
- Department of Anatomical Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Zelin Zang
- School of Engineering, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Wei Liu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Hao Zhang
- Department of Thyroid Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wanyuan Chen
- Cancer Center, Department of Pathology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Hao Chen
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou, Zhejiang, China
| | - Lu Li
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Xue Cai
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Huanhuan Gao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Zhicheng Wu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Yongfu Zhao
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Lirong Chen
- Department of Pathology, The Second Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaodong Teng
- Department of Pathology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sangeeta Mantoo
- Department of Anatomical Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tony Kiat-Hon Lim
- Department of Anatomical Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Bhuvaneswari Hariraman
- Department of Head and Neck Surgery, National Cancer Center Singapore, Singapore, Singapore
| | - Serene Yeow
- Division of Medical Sciences, National Cancer Center Singapore, Singapore, Singapore
| | - Syed Muhammad Fahmy Alkaff
- Department of Anatomical Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Sze Sing Lee
- Division of Medical Sciences, National Cancer Center Singapore, Singapore, Singapore
| | - Guan Ruan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou, Zhejiang, China
| | - Qiushi Zhang
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou, Zhejiang, China
| | - Tiansheng Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Yifan Hu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou, Zhejiang, China
| | - Zhen Dong
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., No.1 Yunmeng Road, Hangzhou, Zhejiang, China
| | - Qi Xiao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Weibin Wang
- Department of Surgical Oncology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Guangzhi Wang
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Junhong Xiao
- Department of General Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yi He
- Department of Urology, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Zhihong Wang
- Department of Thyroid Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wei Sun
- Department of Thyroid Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuan Qin
- Department of Thyroid Surgery, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jiang Zhu
- Department of Ultrasound, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xu Zheng
- Liaoning Laboratory of Cancer Genetics and Epigenetics and Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning, China
| | - Linyan Wang
- Department of Ophthalmology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xi Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kailun Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yingkuan Shao
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kexin Liu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Haixia Guan
- Department of Endocrinology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaohong Wu
- Department of Endocrinology, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou, Zhejiang, China
| | - Dingcun Luo
- Department of Surgical Oncology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wen Tian
- Department of General Surgery, PLA General Hospital, Beijing, China
| | - Stan Ziqing Li
- School of Engineering, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang, China.
| | - Oi Lian Kon
- Division of Medical Sciences, National Cancer Center Singapore, Singapore, Singapore.
| | - Narayanan Gopalakrishna Iyer
- Department of Head and Neck Surgery, National Cancer Center Singapore, Singapore, Singapore. .,Division of Medical Sciences, National Cancer Center Singapore, Singapore, Singapore.
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. .,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. .,Research Center for Industries of the Future, Westlake University, No.18 Shilongshan Road, Hangzhou, Zhejiang, China.
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9
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Mass Spectrometry and Mass Spectrometry Imaging-based Thyroid Cancer Analysis. JOURNAL OF ANALYSIS AND TESTING 2022. [DOI: 10.1007/s41664-022-00218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Salivary Proteome, Inflammatory, and NETosis Biomarkers in Older Adult Practitioners and Nonpractitioners of Physical Exercise. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3725056. [PMID: 35502212 PMCID: PMC9056209 DOI: 10.1155/2022/3725056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/22/2022] [Indexed: 11/18/2022]
Abstract
Since aging has been associated with increased production of inflammatory biomarkers, the ability to monitor older adults repeatedly is highly desirable, and saliva is an interesting biofluid for the search of biomarkers, as it is easily accessible in a noninvasive manner. However, given the incipient knowledge of salivary biomarkers in aging and its relationship to physical exercise, the present study is aimed at evaluating the protein expression and the levels of inflammatory and NETosis biomarkers in the saliva of practitioners (PE) and nonpractitioners (NPE) of physical exercise older adults. Six (6) practitioner and 4 nonpractitioner older adults were enrolled in this study. Unstimulated whole saliva was collected for analysis of the proteome by label-free mass spectrometry, as well as of the inflammatory status by evaluation of C-reactive protein (CRP), vascular endothelial growth factor (VEGF), and cytokines (TNF-α, interleukin- (IL-) 1β, and IL-8), while NETosis was assessed by myeloperoxidase (MPO) and neutrophil elastase. Regarding oral health, the decayed, missing, and filled teeth (DMF-T) index, bleeding on probing, suppuration, and probing depth measurement (mm) were evaluated. In addition, functional capacity was investigated using the General Physical Fitness Index (GPFI). In relation to the proteome analysis, 93 and 143 proteins were found exclusively in the PE and NPE groups, respectively; 224 proteins were common to both groups. Among these proteins, 10 proteins showed statistical difference (
) between the groups: alpha-2-macroglobulin, component 3 of the complement, serotransferrin, and protein soluble in brain acid 1 were less expressed, while lactotransferrin, alpha-amylase 1, S100-A8, S100-A9, lactoperoxidase, and galectin-3 binding protein were more expressed in the PE group. No differences between groups were observed in the analysis of inflammatory and NETosis biomarkers. This study shows the potential utility of saliva for detecting protein biomarkers in a noninvasive biological sample of the elderly population.
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Hosseinkhani S, Arjmand B, Bandarian F, Aazami H, Hadizadeh N, Najjar N, Pasalar P, Razi F. Omics experiments in Iran, a review in endocrine and metabolism disorders studies. J Diabetes Metab Disord 2021. [DOI: 10.1007/s40200-021-00727-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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12
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Zhang Z, Reiding KR, Wu J, Li Z, Xu X. Distinguishing Benign and Malignant Thyroid Nodules and Identifying Lymph Node Metastasis in Papillary Thyroid Cancer by Plasma N-Glycomics. Front Endocrinol (Lausanne) 2021; 12:692910. [PMID: 34248851 PMCID: PMC8267918 DOI: 10.3389/fendo.2021.692910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/04/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Biomarkers are needed for patient stratification between benign thyroid nodules (BTN) and thyroid cancer (TC) and identifying metastasis in TC. Though plasma N-glycome profiling has shown potential in the discovery of biomarkers and can provide new insight into the mechanisms involved, little is known about it in TC and BTN. Besides, several studies have indicated associations between abnormal glycosylation and TC. Here, we aimed to explore plasma protein N-glycome of a TC cohort with regard to their applicability to serve as biomarkers. METHODS Plasma protein N-glycomes of TC, BTN, and matched healthy controls (HC) were obtained using a robust quantitative strategy based on MALDI-TOF MS and included linkage-specific sialylation information. RESULTS Plasma N-glycans were found to differ between BTN, TC, and HC in main glycosylation features, namely complexity, galactosylation, fucosylation, and sialylation. Four altered glycan traits, which were consecutively decreased in BTN and TC, and classification models based on them showed high potential as biomarkers for discrimination between BTN and TC ("moderately accurate" to "accurate"). Additionally, strong associations were found between plasma N-glycans and lymph node metastasis in TC, which added the accuracy of predicting metastasis before surgery to the existing method. CONCLUSIONS We comprehensively evaluated the plasma N-glycomic changes in patients with TC or BTN for the first time. We determined several N-glycan biomarkers, some of them have potential in the differential diagnosis of TC, and the others can help to stratify TC patients to low or high risk of lymph node metastasis. The findings enhanced the understanding of TC.
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Affiliation(s)
- Zejian Zhang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Karli R. Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
- Netherlands Proteomics Center, Utrecht, Netherlands
| | - Jianqiang Wu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zepeng Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiequn Xu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Xiequn Xu,
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