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Rong L, Wang J, Wang Q, Zhu Y, Ren W. Exploration of immunocytochemical biomarkers related to central lymph node metastasis in papillary thyroid microcarcinoma. Cytojournal 2025; 22:18. [PMID: 40134573 PMCID: PMC11932946 DOI: 10.25259/cytojournal_162_2024] [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: 08/19/2024] [Accepted: 12/13/2024] [Indexed: 03/27/2025] Open
Abstract
Objective The presence of central lymph node metastasis (CLNM) represents a critical determinant in ascertaining the necessity for surgical intervention in patients with papillary thyroid microcarcinoma (PTMC). However, the predominant current methodologies for confirming the central lymph node status in clinical practice are hampered by the low predictive accuracy of preoperative ultrasound examination and the high risk of preoperative fine needle aspiration (FNA). Consequently, the objective of this study is to investigate and identify specific immunocytochemical biomarkers for predicting CLNM in PTMC patients based on preoperative thyroid FNA samples. Material and Methods In this study, the messenger ribonucleic acid sequencing data of pathological tumor stage 1 (pT1) papillary thyroid carcinoma (PTC) accompanied by pathological node stage information were initially retrieved from The Cancer Genome Atlas database. The differential expression genes (DEGs) between the pT1N1-PTC group and the pT1N0-PTC group were ascertained through bioinformatics methodology. Subsequently, these DEGs were imported into Cytoscape software to identify hub genes. Ultimately, immunohistochemical and immunocytochemical staining were employed to validate whether the biomarkers corresponding to the main hub genes demonstrated statistical significance in predicting CLNM within propensity score-matched PTMC samples. Results In this study, a total of 292 DEGs and 10 hub genes were successfully identified. Subsequently, immunohistochemical and immunocytochemical staining were conducted on 208 PTMC cases selected through propensity score matching. Among these 208 cases, the biomarkers (Cytokeratin 5/6 [CK5/6], Chromogranin A [CgA], and Pair box gene 2 [Pax-2]) corresponding to the main hub genes (Cytokeratin 5 [KRT5], Cytokeratin 6 [KRT6A], Chromogranin A [CHGA], and PAX2) were subjected to immunohistochemical staining in postoperative thyroidectomy specimens, the immunohistochemical staining results revealed a statistically significant difference in CK5/6 expression between PTMCs with and without CLNM (P = 0.002). Subsequently, CK5/6 immunocytochemical staining performed on preoperative thyroid FNA liquid-based samples further corroborated that CK5/6 expression was more prone to being positive in PTMCs with CLNM (P = 0.010). Conclusion CK5/6 is a valuable immunocytochemical biomarker capable of predicting the occurrence of CLNM in PTMC patients prior to surgery.
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Affiliation(s)
- Lulu Rong
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jie Wang
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Qian Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yanli Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Wenhao Ren
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, China
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Peng L, Zhang Z, Du W, Zhu J, Duan W. Proteomic and Phosphoproteomic analysis of thyroid papillary carcinoma: Identification of potential biomarkers for metastasis. J Proteomics 2024; 306:105260. [PMID: 39029786 DOI: 10.1016/j.jprot.2024.105260] [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: 11/23/2023] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Thyroid cancer has emerged as the most rapidly proliferating solid neoplasm. In this study, we included a cohort of patients who underwent sonographic assessment and surgical intervention at the Sir Run Run Shaw Hospital, associated with the School of Medicine at Zhejiang University, spanning from January 2019 to June 2020. Stratification of cases was based on a combination of preoperative ultrasonographic evaluations and postoperative histopathological diagnoses, resulting in three distinct groups: high-risk papillary thyroid carcinoma (PTC) labeled as C1, low-risk PTC designated as C2, and a control group (N) composed of benign thyroid tissue adjacent to the carcinoma. Proteomic and phosphoproteomic analyses were conducted on PTC specimens. The comparative assessment revealed that proteins up-regulated in the C1/N and C2/N groups were predominantly involved in functions such as amino acid binding, binding of phosphorylated compounds, and serine protease activity. Notably, proteins like NADH dehydrogenase, ATP synthase, oxidoreductases, and iron ion channels were significantly elevated in the C1 versus C2 comparative group. Through meticulous analysis of differential expression multiples, statistical significance, and involvement in metabolic pathways, this study identified eight potential biomarkers pertinent to PTC metastasis diagnostics, encompassing phosphorylated myosin 10, phosphorylated proline-directed protein kinase, leucine tRNA synthetase, 2-oxo-isovalerate dehydrogenase, succinic semialdehyde dehydrogenase, ADP/ATPtranslocase, pyruvate carboxylase, and fibrinogen. Therapeutic assays employing metformin, an AMP-activated protein kinase (AMPK) activator, alongside the phosphorylation-specific inhibitor ML-7 targeting Myosin10, demonstrated attenuated cellular proliferation, migration, and invasion capabilities in thyroid cancer cells, accompanied by a reduction in amino acid pools. Cellular colocalization and interaction studies elucidated that AMPK activation imposes an inhibitory influence on Myosin10 levels. The findings of this research corroborate the utility of proteomic and phosphoproteomic platforms in the identification of metastatic markers for PTC and suggest that modulation of AMPK activity, coupled with the inhibition of Myosin10 phosphorylation, may forge novel therapeutic avenues in the management of thyroid carcinoma. SIGNIFICANCE: The significance of our research lies in its potential to transform the current understanding and management of thyroid papillary carcinoma (PTC), particularly in its metastatic form. By integrating both proteomic and phosphoproteomic analyses, our study not only sheds light on the molecular alterations associated with PTC but also identifies eight novel biomarkers that could serve as indicators of metastatic potential.
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Affiliation(s)
- Lingyao Peng
- Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310007, China
| | - Zhenxian Zhang
- Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou 310007, China
| | - Wei Du
- Hangzhou Institute of Standardization, Hangzhou 310000, China
| | - Jiang Zhu
- Women's Hospital School of Medicine Zhejiang University, 310006 Hangzhou, China.
| | - Wenkai Duan
- Hangzhou Vocational and Technical College, Hangzhou 310018, China.
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Provine NM, Al-Diwani A, Agarwal D, Dooley K, Heslington A, Murchison AG, Garner LC, Sheerin F, Klenerman P, Irani SR. Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming. Eur J Immunol 2024; 54:e2350872. [PMID: 38388988 DOI: 10.1002/eji.202350872] [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: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies in this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone-fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.
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Affiliation(s)
- Nicholas M Provine
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Al-Diwani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Devika Agarwal
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kyla Dooley
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amelia Heslington
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew G Murchison
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fintan Sheerin
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Wang Z, Wang H, Zhou Y, Li L, Lyu M, Wu C, He T, Tan L, Zhu Y, Guo T, Wu H, Zhang H, Sun Y. An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma. Nat Commun 2024; 15:3560. [PMID: 38671151 PMCID: PMC11053152 DOI: 10.1038/s41467-024-47926-w] [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: 06/02/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Pediatric papillary thyroid carcinomas (PPTCs) exhibit high inter-tumor heterogeneity and currently lack widely adopted recurrence risk stratification criteria. Hence, we propose a machine learning-based objective method to individually predict their recurrence risk. We retrospectively collect and evaluate the clinical factors and proteomes of 83 pediatric benign (PB), 85 pediatric malignant (PM) and 66 adult malignant (AM) nodules, and quantify 10,426 proteins by mass spectrometry. We find 243 and 121 significantly dysregulated proteins from PM vs. PB and PM vs. AM, respectively. Function and pathway analyses show the enhanced activation of the inflammatory and immune system in PM patients compared with the others. Nineteen proteins are selected to predict recurrence using a machine learning model with an accuracy of 88.24%. Our study generates a protein-based personalized prognostic prediction model that can stratify PPTC patients into high- or low-recurrence risk groups, providing a reference for clinical decision-making and individualized treatment.
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Affiliation(s)
- Zhihong Wang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - He Wang
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Yan Zhou
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Lu Li
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Mengge Lyu
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Chunlong Wu
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Tianen He
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Lingling Tan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Yi Zhu
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Tiannan Guo
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, China
| | - Hongkun Wu
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China.
| | - Yaoting Sun
- School of Medicine, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Research Center for Industries of the Future, Westlake University, Hangzhou, China.
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Wang Z, Ji X, Zhang H, Sun W. Clinical and molecular features of progressive papillary thyroid microcarcinoma. Int J Surg 2024; 110:2313-2322. [PMID: 38241301 PMCID: PMC11019976 DOI: 10.1097/js9.0000000000001117] [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: 08/22/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
In recent decades, the prevalence of thyroid cancer has risen substantially, with papillary thyroid microcarcinoma (PTMC) constituting over 50% of cases. Although most PTMCs exhibit indolent growth and a favorable prognosis, some present an increased risk of recurrence and an unfavorable prognosis due to high-risk characteristics such as lymph node metastasis, extrathyroidal extension, and distant metastasis. The early identification of clinically progressing PTMC remains elusive. In this review, the authors summarize findings from PTMC progression-related literature, highlighting that factors such as larger tumor size, cervical lymph node metastasis, extrathyroidal extension, younger age, higher preoperative serum thyroid-stimulating hormone levels, family history, and obesity positively correlate with PTMC progression. The role of multifocality in promoting PTMC progression; however, remains contentious. Furthermore, recent studies have shed light on the impact of mutations, such as BRAF and TERT mutations, on PTMC progression. Researchers have identified several mRNAs, noncoding RNAs, and proteins associated with various features of PTMC progression. Some studies propose that peripheral and tumor tissue-infiltrating immune cells could serve as biomarkers for the clinical progression of PTMC. Collectively, these clinical and molecular features offer a rationale for the early detection and the development of precision theranostic strategies of clinically progressive PTMC.
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Affiliation(s)
| | | | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, People’s Republic of China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province, People’s Republic of China
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6
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Matovinovic F, Novak R, Hrkac S, Salai G, Mocibob M, Pranjic M, Košec A, Bedekovic V, Grgurevic L. In search of new stratification strategies: tissue proteomic profiling of papillary thyroid microcarcinoma in patients with localized disease and lateral neck metastases. J Cancer Res Clin Oncol 2023; 149:17405-17417. [PMID: 37861757 DOI: 10.1007/s00432-023-05452-0] [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: 07/14/2023] [Accepted: 09/30/2023] [Indexed: 10/21/2023]
Abstract
INTRODUCTION Papillary thyroid carcinomas (PTC) are the most common thyroid malignancies that are often diagnosed as microcarcinomas when the tumor is less than one centimetre in diameter. Currently, there are no valid stratification strategies that would reliably assess the risk of lateral neck metastases and optimize surgical treatment. MATERIALS AND METHODS Aiming to find potential tissue biomarkers of metastatic potential, we conducted a cross-sectional proteomic pilot study on formalin-fixed paraffin-embedded tissues of metastatic (N = 10) and non-metastatic (N = 10) papillary thyroid microcarcinoma patients. Samples were analysed individually using liquid chromatography/mass spectrometry, and the differentially expressed proteins (DEP) were functionally annotated. RESULTS We identified five overexpressed DEPs in the metastatic group (EPB41L2, CSE1L, GLIPR2, FGA and FGG) with a known association to tumour biology. Using bioinformatic-based tools, we found markedly different profiles of significantly enriched biological processes between the two groups. CONCLUSIONS The identified DEPs might have a role as potential tissue biomarkers for PTC metastases. However, further prospective research is needed to confirm our findings.
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Affiliation(s)
- Filip Matovinovic
- Department of Otorhinolaryngology and Head and Neck Surgery, Sestre Milosrdnice University Hospital Center, 10000, Zagreb, Croatia
| | - Rudjer Novak
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Stela Hrkac
- Department of Clinical Immunology, Allergology and Rheumatology, University Hospital Dubrava, 10000, Zagreb, Croatia
| | - Grgur Salai
- Department of Pulmonology, University Hospital Dubrava, 10000, Zagreb, Croatia
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Marija Pranjic
- Department of Chemistry, Faculty of Science, University of Zagreb, 10000, Zagreb, Croatia
| | - Andro Košec
- Department of Otorhinolaryngology and Head and Neck Surgery, Sestre Milosrdnice University Hospital Center, 10000, Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000, Zagreb, Croatia
| | - Vladimir Bedekovic
- Department of Otorhinolaryngology and Head and Neck Surgery, Sestre Milosrdnice University Hospital Center, 10000, Zagreb, Croatia
| | - Lovorka Grgurevic
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000, Zagreb, Croatia.
- Department of Anatomy, "Drago Perovic", School of Medicine, University of Zagreb, 10000, Zagreb, Croatia.
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Lu H, Pan Y, Ruan Y, Zhu C, Hassan HM, Gao J, Gao J, Fan L, Liang X, Wang H, Ying S, Chen Q. Biomarker Discovery for Early Diagnosis of Papillary Thyroid Carcinoma Using High-Throughput Enhanced Quantitative Plasma Proteomics. J Proteome Res 2023; 22:3200-3212. [PMID: 37624590 DOI: 10.1021/acs.jproteome.3c00187] [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: 08/26/2023]
Abstract
The incidence of thyroid cancer (TC) has been increasing over the last 50 years worldwide. A higher rate of overdiagnosis in indolent thyroid lesions has resulted in unnecessary treatment. An accurate detection of TC at an early stage is highly demanded. We aim to develop an enhanced isobaric labeling-based high-throughput plasma quantitative proteomics to identify biomarkers in a discovery cohort. Selected candidates were tested by enzyme-linked immunosorbent assay (ELISA) in the training cohort and validation cohort. In total, 1063 proteins were quantified, and 129 proteins were differentially expressed between patients and healthy subjects. Serum levels of ISG15 and PLXNB2 were significantly elevated in patients with papillary thyroid cancer (PTC) or thyroid adenoma, compared to healthy subjects (p < 0.001) and patients with nodular goiter (p < 0.001). Receiver operating characteristic (ROC) analysis of combined markers (ISG15 and PLXNB2) significantly distinguished PTC from healthy control (HC) subjects. Similar differentiations were also found between thyroid adenoma and HC subjects. Notably, this combined marker could distinguish stage-I PTC from HC subjects (area under the curve (AUC) = 0.872). Our results revealed that ISG15 and PLXNB2 are independent diagnostic biomarkers for PTC and thyroid adenoma, showing a promising value for the early detection of PTC.
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Affiliation(s)
- Hongsheng Lu
- Department of Pathology, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Yin Pan
- Surgical Oncology, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Yanyun Ruan
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Chumeng Zhu
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Hozeifa M Hassan
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Junshun Gao
- Hangzhou Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, 198 Qidi Road, Xiaoshan District, Hangzhou 311202, Zhejiang, P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, 198 Qidi Road, Xiaoshan District, Hangzhou 311202, Zhejiang, P. R. China
| | - Junli Gao
- Hangzhou Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, 198 Qidi Road, Xiaoshan District, Hangzhou 311202, Zhejiang, P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, 198 Qidi Road, Xiaoshan District, Hangzhou 311202, Zhejiang, P. R. China
| | - Lilong Fan
- Department of Pathology, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Xi Liang
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Hong Wang
- Hangzhou Cosmos Wisdom Mass Spectrometry Center of Zhejiang University Medical School, 198 Qidi Road, Xiaoshan District, Hangzhou 311202, Zhejiang, P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, 198 Qidi Road, Xiaoshan District, Hangzhou 311202, Zhejiang, P. R. China
| | - Shenpeng Ying
- Department of Radiotherapy, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
| | - Qi Chen
- Precision Medicine Center, Taizhou Central Hospital (Taizhou University Hospital), 999 Donghai Avenue, Taizhou 318000, Zhejiang, P. R. China
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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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Piga I, L'Imperio V, Capitoli G, Denti V, Smith A, Magni F, Pagni F. Paving the path toward multi-omics approaches in the diagnostic challenges faced in thyroid pathology. Expert Rev Proteomics 2023; 20:419-437. [PMID: 38000782 DOI: 10.1080/14789450.2023.2288222] [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: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023]
Abstract
INTRODUCTION Despite advancements in diagnostic methods, the classification of indeterminate thyroid nodules still poses diagnostic challenges not only in pre-surgical evaluation but even after histological evaluation of surgical specimens. Proteomics, aided by mass spectrometry and integrated with artificial intelligence and machine learning algorithms, shows great promise in identifying diagnostic markers for thyroid lesions. AREAS COVERED This review provides in-depth exploration of how proteomics has contributed to the understanding of thyroid pathology. It discusses the technical advancements related to immunohistochemistry, genetic and proteomic techniques, such as mass spectrometry, which have greatly improved sensitivity and spatial resolution up to single-cell level. These improvements allowed the identification of specific protein signatures associated with different types of thyroid lesions. EXPERT COMMENTARY Among all the proteomics approaches, spatial proteomics stands out due to its unique ability to capture the spatial context of proteins in both cytological and tissue thyroid samples. The integration of multi-layers of molecular information combining spatial proteomics, genomics, immunohistochemistry or metabolomics and the implementation of artificial intelligence and machine learning approaches, represent hugely promising steps forward toward the possibility to uncover intricate relationships and interactions among various molecular components, providing a complete picture of the biological landscape whilst fostering thyroid nodule diagnosis.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
| | - Giulia Capitoli
- Department of Medicine and Surgery, Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milan - Bicocca (UNIMIB), Monza, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
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Yuan Y, Qin H, Li H, Shi W, Bao L, Xu S, Yin J, Zheng L. The Functional Roles of ISG15/ISGylation in Cancer. Molecules 2023; 28:1337. [PMID: 36771004 PMCID: PMC9918931 DOI: 10.3390/molecules28031337] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/11/2023] [Accepted: 01/28/2023] [Indexed: 02/01/2023] Open
Abstract
The protein ISG15 encoded by interferon-stimulated gene (ISG) 15 is the first identified member of the ubiquitin-like protein family and exists in the form of monomers and conjugated complexes. Like ubiquitin, ISG15 can mediate an ubiquitin-like modification by covalently modifying other proteins, known as ISGylation. There is growing evidence showing that both the free and conjugated ISG15 are involved in multiple key cellular processes, including autophagy, exosome secretion, DNA repair, immune regulation, and cancer occurrence and progression. In this review, we aim to further clarify the function of ISG15 and ISGylation in cancer, demonstrate the important relationship between ISG15/ISGylation and cancer, and emphasize new insights into the different roles of ISG15/ISGylation in cancer progression. This review may contribute to therapeutic intervention in cancer. However, due to the limitations of current research, the regulation of ISG15/ISGylation on cancer progression is not completely clear, thus further comprehensive and sufficient correlation studies are still needed.
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Affiliation(s)
- Yin Yuan
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Medicinal Chemistry, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Hai Qin
- Department of Clinical Laboratory, Guizhou Provincial Orthopedic Hospital, No. 206, Sixian Street, Baiyun District, Guiyang 550002, China
| | - Huilong Li
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Medicinal Chemistry, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Wanjin Shi
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Medicinal Chemistry, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Lichen Bao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 210029, China
| | - Shengtao Xu
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Medicinal Chemistry, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Jun Yin
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Medicinal Chemistry, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
| | - Lufeng Zheng
- Jiangsu Key Laboratory of Carcinogenesis and Intervention, Department of Medicinal Chemistry, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Road, Nanjing 211198, China
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11
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Cao Z, Zhang Z, Tang X, Liu R, Wu M, Wu J, Liu Z. Comprehensive analysis of tissue proteomics in patients with papillary thyroid microcarcinoma uncovers the underlying mechanism of lymph node metastasis and its significant sex disparities. Front Oncol 2022; 12:887977. [PMID: 36106120 PMCID: PMC9465038 DOI: 10.3389/fonc.2022.887977] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Background Lymph node metastasis (LNM) in papillary thyroid microcarcinoma (PTMC) is associated with an increased risk of recurrence and poor prognosis. Sex has been regarded as a critical risk factor for LNM. The present study aimed to investigate the molecular mechanisms underlying LNM and its significant sex disparities in PTMC development. Methods A direct data-independent acquisition (DIA) proteomics approach was used to identify differentially expressed proteins (DEPs) in PTMC tumorous tissues with or without LNM and from male and female patients with LNM. The functional annotation of DEPs was performed using bioinformatics methods. Furthermore, The Cancer Genome Atlas Thyroid Carcinoma (TCGA-THCA) dataset and immunohistochemistry (IHC) were used to validate selected DEPs. Results The proteomics profile in PTMC with LNM differed from that of PTMC without LNM. The metastasis-related DEPs were primarily enriched in categories associated with mitochondrial dysfunction and may promote tumor progression by activating oxidative phosphorylation and PI3K/AKT signaling pathways. Comparative analyses of these DEPs revealed downregulated expression of specific proteins with well-established links to tumor metastasis, such as SLC25A15, DIRAS2, PLA2R1, and MTARC1. Additionally, the proteomics profiles of male and female PTMC patients with LNM were dramatically distinguishable. An elevated level of ECM-associated proteins might be related to more LNM in male PTMC than in female PTMC patients. The upregulated expression levels of MMRN2 and NID2 correlated with sex disparities and showed a positive relationship with unfavorable variables, such as LNMs and poor prognosis. Conclusions The proteomics profiles of PTMC show significant differences associated with LNM and its sex disparities, which further expands our understanding of the functional networks and signaling pathways related to PTMC with LNM.
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Affiliation(s)
- Zhen Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - 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
| | - Xiaoyue Tang
- 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
| | - Rui Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mengwei Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - 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
- *Correspondence: Jianqiang Wu, ; Ziwen Liu,
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Jianqiang Wu, ; Ziwen Liu,
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12
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Comparative Proteomic Profiling of Ectosomes Derived from Thyroid Carcinoma and Normal Thyroid Cells Uncovers Multiple Proteins with Functional Implications in Cancer. Cells 2022; 11:cells11071184. [PMID: 35406748 PMCID: PMC8997476 DOI: 10.3390/cells11071184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023] Open
Abstract
Proteins carried by tumor-derived ectosomes play an important role in cancer progression, and are considered promising diagnostic markers. In the present study, a shotgun nanoLC–MS/MS proteomic approach was applied to profile and compare the protein content of ectosomes released in vitro by normal human thyroid follicular epithelial Nthy-ori 3-1 cells and human anaplastic thyroid carcinoma (TC) 8305C cells. Additionally, the pro-migratory and pro-proliferative effects of Nthy-ori 3-1- and 8305C-derived ectosomes exerted on the recipient cells were assessed in wound closure and Alamar Blue assays. A total of 919 proteins were identified in all replicates of 8305C-derived ectosomes, while Nthy-ori 3-1-derived ectosomes contained a significantly lower number of 420 identified proteins. Qualitative analysis revealed 568 proteins present uniquely in 8305C-derived ectosomes, suggesting their applicability in TC diagnosis and management. In addition, 8305C-derived ectosomes were able to increase the proliferation and motility rates of the recipient cells, likely due to the ectosomal transfer of the identified cancer-promoting molecules. Our description of ectosome protein content and its related functions provides the first insight into the role of ectosomes in TC development and progression. The results also indicate the applicability of some of these ectosomal proteins for further investigation regarding their potential as circulating TC biomarkers.
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13
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Yan C, He X, Chen Z, Wang Y. Central Compartment Lymph Nodes Have Distinct Metastatic Patterns in Different Age Groups. Front Endocrinol (Lausanne) 2022; 13:807431. [PMID: 35250865 PMCID: PMC8892199 DOI: 10.3389/fendo.2022.807431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND AND PURPOSE Central compartment lymph node metastasis (CLNM) is a manifestation of tumor aggressiveness and an indicator of tumor prognosis. The purpose of this study was to construct a nomogram for evaluating CLNM patterns in papillary thyroid carcinoma (PTC) in different age groups. METHOD A total of 907 patients diagnosed with PTC from August 2014 to December 2018 were enrolled. A nomogram illustrating CLNM was generated using the results of multivariate logistic regression analysis. RESULTS According to the best Youden index, we set the cut-off age at 45 years. Multivariate logistic regression analysis showed that in patients aged <45 years, large tumor size (P<0.05), extra-thyroid extension (P<0.05) and thyroglobulin level >40 ng/ml (OR=2.985, 95% CI 1.379-6.462; P<0.05) were independent risk factors; meanwhile, Hashimoto's thyroiditis (OR=0.532, 95% CI 0.324-0.874; P<0.05) was a protective factor of CLNM. In the subgroup with age ≥45 years, large tumor size (P<0.05), extra-thyroid extension (P<0.05), unclear margin (OR=1.604, 95% CI 1.065-2.416; P<0.05), male gender (OR=2.009, 95% CI 1.257-3.212; P<0.05) were independent risk factors for CLNM. In the subgroup with age <45 years, an area under the curve (AUC) of 0.729 (95% CI 0.680-0.777); P<0.05) was obtained. In the ≥45 years subgroup, the AUC was 0.668 (95% CI 0.619-0.716; P<0.05). CONCLUSION CLNM of PTC in different age groups may have distinct patterns. Based on the potential risk factors for CLNM in patients with different age stratification, a user-friendly predictive model was established.
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Affiliation(s)
- Caigu Yan
- Department of General Surgery, The People’s Hospital of Liuyang, Changsha, China
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zuoyu Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, China
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14
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de Lima-Souza RA, Scarini JF, Lavareze L, Emerick C, dos Santos ES, Leme AFP, Egal ESA, Altemani A, Mariano FV. Protein markers of primary Salivary Gland Tumors: A systematic review of proteomic profiling studies. Arch Oral Biol 2022; 136:105373. [DOI: 10.1016/j.archoralbio.2022.105373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/06/2022] [Accepted: 02/08/2022] [Indexed: 11/02/2022]
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15
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Song F, Zhang Y, Pan Z, Hu X, Yi Y, Zheng X, Wei H, Huang P. Identification of novel key genes associated with the metastasis of prostate cancer based on bioinformatics prediction and validation. Cancer Cell Int 2021; 21:559. [PMID: 34696780 PMCID: PMC8547030 DOI: 10.1186/s12935-021-02258-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Abstract
Background Metastatic prostate cancer (PCa) is a lethal tumor. However, the molecular mechanisms underlying PCa progression have not been fully elucidated. Methods Transcriptome expression profiling and clinical information on primary and metastatic PCa samples were obtained from TCGA. R software was used to screen the DEGs, and LASSO logistical regression method was utilized to identify the pivotal PCa metastasis-related DEGs. The transcriptional expression levels of the key genes were analyzed using the UALCAN database, and the corresponding protein expression were validated by Immunohistochemistry (IHC). Survival analysis of the key genes was performed using the GEPIA database. Wound healing assay and Transwell assay were conducted to determine whether knockdown of the key genes influence the migration and invasion abilities of PCa cells (22Rv1 and PC3). GSEA was performed to predict key genes-mediated signaling pathways for the development of PCa. Western blotting was used to evaluate the expression changes of E-cadherin, Twist1, and Vimentin in PCa cells with the key genes silencing. An in vivo mouse metastatic model for PCa was also generated to verify the important role of ISG15 and CST2 in PCa metastasis. Results A comparison between primary and metastatic PCa tissues was conducted, and 19 DEGs were screened. Among these, three key genes were identified that might be closely associated with PCa progression according to the LASSO logistical analysis, namely ISG15, DNAH8, and CST2. Further functional experiments revealed that knockdown of ISG15 and CST2 suppressed wound healing, migration, and invasion of PCa cells. To explore the molecular mechanism of ISG15 and CST2 in the development of PCa, GSEA was performed, and it was found that both genes play crucial roles in cell adhesion molecules, extracellular matrix-receptor interaction, and focal adhesion. Western blotting results exhibited that inhibiting ISG15 and CST2 led to increase the expression of E-cadherin and decrease the expression of Twist1 and Vimentin. Additionally, the metastatic in vivo study demonstrated that both PC3 and 22Rv1 cells expressing with luciferase-shISG15 and luciferase-shCST2 had significantly lower detectable bioluminescence than that in the control PCa cells. Conclusion ISG15 and CST2 may participate in PCa metastasis by regulating the epithelial-mesenchymal transition (EMT) signaling pathway. These findings may help to better understand the pathogenetic mechanisms governing PCa and provide promising therapeutic targets for metastatic PCa therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02258-3.
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Affiliation(s)
- Feifeng Song
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.,Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, Zhejiang, China
| | - Yiwen Zhang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.,Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, Zhejiang, China
| | - Zongfu Pan
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.,Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, Zhejiang, China
| | - Xiaoping Hu
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yaodong Yi
- Laboratory of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaochun Zheng
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Haibin Wei
- Department of Urology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Ping Huang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China. .,Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou, 310014, Zhejiang, China.
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16
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Su M, Zhang Z, Zhou L, Han C, Huang C, Nice EC. Proteomics, Personalized Medicine and Cancer. Cancers (Basel) 2021; 13:2512. [PMID: 34063807 PMCID: PMC8196570 DOI: 10.3390/cancers13112512] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.
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Affiliation(s)
- Miao Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Chao Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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17
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Kostas JC, Greguš M, Schejbal J, Ray S, Ivanov AR. Simple and Efficient Microsolid-Phase Extraction Tip-Based Sample Preparation Workflow to Enable Sensitive Proteomic Profiling of Limited Samples (200 to 10,000 Cells). J Proteome Res 2021; 20:1676-1688. [PMID: 33625864 PMCID: PMC7954648 DOI: 10.1021/acs.jproteome.0c00890] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In-depth LC-MS-based proteomic profiling of limited biological and clinical samples, such as rare cells or tissue sections from laser capture microdissection or microneedle biopsies, has been problematic due, in large, to the inefficiency of sample preparation and attendant sample losses. To address this issue, we developed on-microsolid-phase extraction tip (OmSET)-based sample preparation for limited biological samples. OmSET is simple, efficient, reproducible, and scalable and is a widely accessible method for processing ∼200 to 10,000 cells. The developed method benefits from minimal sample processing volumes (1-3 μL) and conducting all sample processing steps on-membrane within a single microreactor. We first assessed the feasibility of using micro-SPE tips for nanogram-level amounts of tryptic peptides, minimized the number of required sample handling steps, and reduced the hands-on time. We then evaluated the capability of OmSET for quantitative analysis of low numbers of human monocytes. Reliable and reproducible label-free quantitation results were obtained with excellent correlations between protein abundances and the amounts of starting material (R2 = 0.93) and pairwise correlations between sample processing replicates (R2 = 0.95) along with the identification of approximately 300, 1800, and 2000 protein groups from injected ∼10, 100, and 500 cell equivalents, resulting from processing approximately 200, 2000, and 10,000 cells, respectively.
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Affiliation(s)
- James C Kostas
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Michal Greguš
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jan Schejbal
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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Cell and Molecular Biology of Thyroid Disorders 2.0. Int J Mol Sci 2021; 22:ijms22041990. [PMID: 33671462 PMCID: PMC7922009 DOI: 10.3390/ijms22041990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/09/2022] Open
Abstract
This issue is the second volume of the previous Special Issue, "Cell and Molecular Biology of Thyroid Disorders" [...].
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Proteomics in thyroid cancer and other thyroid-related diseases: A review of the literature. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140510. [DOI: 10.1016/j.bbapap.2020.140510] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/26/2020] [Accepted: 07/19/2020] [Indexed: 12/21/2022]
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20
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Duan J, Dong W, Xie L, Fan S, Xu Y, Li Y. Integrative proteomics-metabolomics strategy reveals the mechanism of hepatotoxicity induced by Fructus Psoraleae. J Proteomics 2020; 221:103767. [DOI: 10.1016/j.jprot.2020.103767] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/11/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
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21
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Wang Y, Xu F, Zhong JY, Lin X, Shan SK, Guo B, Zheng MH, Yuan LQ. Exosomes as Mediators of Cell-to-Cell Communication in Thyroid Disease. Int J Endocrinol 2020; 2020:4378345. [PMID: 32411222 PMCID: PMC7204309 DOI: 10.1155/2020/4378345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/21/2020] [Accepted: 02/28/2020] [Indexed: 02/07/2023] Open
Abstract
Exosomes are a type of extracellular vehicle, formed by budding cell membranes, containing proteins, DNA, and RNA. Concentrated cargoes from parent cells are enveloped in exosomes, which are cell specific and may have functions in the recipient cell, reflecting a novel physiological and pathological mechanism in disease development. As a transmitter, exosomes shuttle to different cells or tissues and mediate communications among these organelles. To date, several studies have demonstrated that exosomes play crucial roles in disease pathogenesis and development, such as breast and prostate cancer. However, studies investigating connections between exosomes and thyroid disease are limited. In this review, recent research advances on exosomes in thyroid cancer and Graves' disease are reviewed. These studies suggest that exosomes are involved in thyroid disease and appear as impressive potentials in thyroid therapeutic areas.
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Affiliation(s)
- Yi Wang
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Feng Xu
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Jia-Yu Zhong
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Xiao Lin
- Department of Radiology, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Su-Kang Shan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Bei Guo
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Ming-Hui Zheng
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
| | - Ling-Qing Yuan
- Department of Metabolism and Endocrinology, National Clinical Research Center for Metabolic Diseases, Hunan Provincial Key Laboratory of Metabolic Bone Diseases, The Second Xiang-Ya Hospital, Central South University, Changsha, Hunan, China
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