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Chang Q, Chen Y, Yin J, Wang T, Dai Y, Wu Z, Guo Y, Wang L, Zhao Y, Yuan H, Song D, Zhang L. Comprehensive Urinary Proteome Profiling Analysis Identifies Diagnosis and Relapse Surveillance Biomarkers for Bladder Cancer. J Proteome Res 2024. [PMID: 38787199 DOI: 10.1021/acs.jproteome.4c00199] [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: 05/25/2024]
Abstract
Bladder cancer (BCa) is the predominant malignancy of the urinary system. Herein, a comprehensive urine proteomic feature was initially established for the noninvasive diagnosis and recurrence monitoring of bladder cancer. 279 cases (63 primary BCa, 87 nontumor controls (NT), 73 relapsed BCa (BCR), and 56 nonrelapsed BCa (BCNR)) were collected to screen urinary protein biomarkers. 4761 and 3668 proteins were qualified and quantified by DDA and sequential window acquisition of all theoretical mass spectra (SWATH-MS) analysis in two discovery sets, respectively. Upregulated proteins were validated by multiple reaction monitoring (MRM) in two independent combined sets. Using the multi-support vector machine-recursive feature elimination (mSVM-RFE) algorithm, a model comprising 13 proteins exhibited good performance between BCa and NT with an AUC of 0.821 (95% CI: 0.675-0.967), 90.9% sensitivity (95% CI: 72.7-100%), and 73.3% specificity (95% CI: 53.3-93.3%) in the diagnosis test set. Meanwhile, an 11-marker classifier significantly distinguished BCR from BCNR with 75.0% sensitivity (95% CI: 50.0-100%), 81.8% specificity (95% CI: 54.5-100%), and an AUC of 0.784 (95% CI: 0.609-0.959) in the test cohort for relapse surveillance. Notably, six proteins (SPR, AK1, CD2AP, ADGRF1, GMPS, and C8A) of 24 markers were newly reported. This paper reveals novel urinary protein biomarkers for BCa and offers new theoretical insights into the pathogenesis of bladder cancer (data identifier PXD044896).
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Affiliation(s)
- Qi Chang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongqiang Chen
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Jianjian Yin
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yuanheng Dai
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zixin Wu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yufeng Guo
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lingang Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Yufen Zhao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Hang Yuan
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Dongkui Song
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou 450001, China
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Pfeffer T, Krug SM, Kracke T, Schürfeld R, Colbatzky F, Kirschner P, Medert R, Freichel M, Schumacher D, Bartosova M, Zarogiannis SG, Muckenthaler MU, Altamura S, Pezer S, Volk N, Schwab C, Duensing S, Fleming T, Heidenreich E, Zschocke J, Hell R, Poschet G, Schmitt CP, Peters V. Knock-out of dipeptidase CN2 in human proximal tubular cells disrupts dipeptide and amino acid homeostasis and para- and transcellular solute transport. Acta Physiol (Oxf) 2024; 240:e14126. [PMID: 38517248 DOI: 10.1111/apha.14126] [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: 08/24/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024]
Abstract
AIM Although of potential biomedical relevance, dipeptide metabolism has hardly been studied. We found the dipeptidase carnosinase-2 (CN2) to be abundant in human proximal tubules, which regulate water and solute homeostasis. We therefore hypothesized, that CN2 has a key metabolic role, impacting proximal tubular transport function. METHODS A knockout of the CN2 gene (CNDP2-KO) was generated in human proximal tubule cells and characterized by metabolomics, RNA-seq analysis, paracellular permeability analysis and ion transport. RESULTS CNDP2-KO in human proximal tubule cells resulted in the accumulation of cellular dipeptides, reduction of amino acids and imbalance of related metabolic pathways, and of energy supply. RNA-seq analyses indicated altered protein metabolism and ion transport. Detailed functional studies demonstrated lower CNDP2-KO cell viability and proliferation, and altered ion and macromolecule transport via trans- and paracellular pathways. Regulatory and transport protein abundance was disturbed, either as a consequence of the metabolic imbalance or the resulting functional disequilibrium. CONCLUSION CN2 function has a major impact on intracellular amino acid and dipeptide metabolism and is essential for key metabolic and regulatory functions of proximal tubular cells. These findings deserve in vivo analysis of the relevance of CN2 for nephron function and regulation of body homeostasis.
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Affiliation(s)
- Tilman Pfeffer
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
- Tissue Bank of the German Center for Infection Research (DZIF), Partner Site Heidelberg, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Susanne M Krug
- Clinical Physiology/Nutritional Medicine, Charité-Universitätsmedizin Berlin, CBF, Berlin, Germany
| | - Tamara Kracke
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Robin Schürfeld
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Florian Colbatzky
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Philip Kirschner
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Dagmar Schumacher
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Maria Bartosova
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Sotiris G Zarogiannis
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Martina U Muckenthaler
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center (KiTZ), University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), EMBL and University of Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Sandro Altamura
- Department of Pediatric Oncology, Hematology and Immunology and Hopp Children Cancer Center (KiTZ), University Hospital Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), EMBL and University of Heidelberg, Heidelberg, Germany
| | - Silvia Pezer
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Volk
- Tissue Bank of the National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Constantin Schwab
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan Duensing
- Department of Urology, University Hospital Heidelberg and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Fleming
- Internal Medicine I and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Elena Heidenreich
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Claus P Schmitt
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
| | - Verena Peters
- Medical Faculty Heidelberg, Center for Pediatric and Adolescent Medicine, Department I, Division of Pediatric Neurology and Metabolic Medicine, Heidelberg University, Heidelberg, Germany
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Pan Y, Wong CYP, Ma H, Tse RTH, Cheng CKL, Tan M, Chiu PKF, Teoh JYC, Wang X, Ng CF, Zhang L. Quantitative comparison of the renal pelvic urine and bladder urine to examine modifications of the urine proteome by the lower urinary tract. Proteomics Clin Appl 2024; 18:e2300004. [PMID: 37574260 DOI: 10.1002/prca.202300004] [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: 01/13/2023] [Revised: 06/21/2023] [Accepted: 08/04/2023] [Indexed: 08/15/2023]
Abstract
PURPOSE Urine proteome is a valuable reservoir of biomarkers for disease diagnosis and monitoring. Following formation as the plasma filtrate in the kidney, urine is progressively modified by the active reabsorption and secretion of the urinary tract. However, little is known about how the urine proteome changes as it passes along the urinary tract. EXPERIMENTAL DESIGN To investigate this, we compared the proteome composition of the renal pelvis urine (RPU) and individually self-voided bladder urine (BU) collected from seven unilateral urinary tract obstruction male patients by LC-MS/MS screening. To our knowledge, this is the first proteomic comparison of RPU and BU samples from the same individual. RESULTS Overall, RPU and BU proteomes did not exhibit proteins that were exclusively present in all samples of one urine type while in none of the other type. Nonetheless, BU had more overrepresented proteins that were observed at a higher frequency than RPU. Label-free quantitative analyses revealed BU-RPU differential proteins that are enriched in exosomes and extracellular proteins. However, the differences were not significant after corrections for multiple testing. Interestingly, we observed a significant increase of collagen peptides with hydroxyproline modifications in the BU samples, suggesting differences in protein modifications. CONCLUSIONS AND CLINICAL RELEVANCE Our study revealed no substantial differences at the protein level between the BU and RPU samples. Future investigations with expanded cohorts would provide more insights about the urothelial-urinary interactions.
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Affiliation(s)
- Yilin Pan
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
| | - Christine Yim-Ping Wong
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Haiying Ma
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ryan Tsz-Hei Tse
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Carol Ka-Lo Cheng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Miaomiao Tan
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Peter Ka-Fung Chiu
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Jeremy Yuen-Chun Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- Department of Biomedical Sciences, and Tung Biomedical Sciences Center, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
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Götz L, Rueckschloss U, Balk G, Pfeiffer V, Ergün S, Kleefeldt F. The role of carcinoembryonic antigen-related cell adhesion molecule 1 in cancer. Front Immunol 2023; 14:1295232. [PMID: 38077351 PMCID: PMC10704240 DOI: 10.3389/fimmu.2023.1295232] [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: 09/15/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
The Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), also known as CD66a, is a member of the immunoglobulin superfamily. CEACAM1 was shown to be a prognostic marker in patients suffering from cancer. In this review, we summarize pre-clinical and clinical evidence linking CEACAM1 to tumorigenicity and cancer progression. Furthermore, we discuss potential CEACAM1-based mechanisms that may affect cancer biology.
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Affiliation(s)
- Lisa Götz
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Uwe Rueckschloss
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Gözde Balk
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Verena Pfeiffer
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
| | - Florian Kleefeldt
- Institute of Anatomy and Cell Biology, Julius‐Maximilians‐University Würzburg, Würzburg, Germany
- Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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Liu X, Zhang M, Shao C, Sun H, Zhang B, Guo Z, Sun J, Qi F, Zhang Y, Niu H, Sun W. Blood- and Urine-Based Liquid Biopsy for Early-Stage Cancer Investigation: Taken Clear Renal Cell Carcinoma as a Model. Mol Cell Proteomics 2023; 22:100603. [PMID: 37348606 PMCID: PMC10416070 DOI: 10.1016/j.mcpro.2023.100603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/12/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023] Open
Abstract
Liquid biopsy is a noninvasive technique that can provide valuable information for disease characterization by using biofluids as a source of biomarkers. Proteins found in biofluids can offer a wealth of information for understanding pathological processes. In this study, we used early-stage clear cell renal cell carcinoma (ccRCC) as a model to explore the proteomic relationships among tissue, plasma, and urine. We analyzed samples of tumor tissue, plasma, and urine from a cohort of 27 ccRCC patients with T1-2 stage and 27 matched healthy controls, using liquid chromatography-mass spectrometry (LC-MS) for proteomic analysis. We integrated the differential proteins found in the three types of samples to explore ccRCC-associated molecular changes. Our results showed that both plasma and urine proteomes could reflect functional changes in tumor tissue. In plasma, cytoskeletal proteins and metabolic enzymes were differentially expressed, while in urine, adhesion molecules and defense proteins showed differential levels. The differential proteins found in plasma and urine both reflect the binding and catalytic activity of tumor tissue. Additionally, proteins only changed in biofluids could reflect body immune response changes, with plasma proteins involved in actin cytoskeleton and oxidative stress, and urine proteins involved in granulocyte adhesion and leukocyte extravasation signaling. Plasma and urine proteins could effectively distinguish RCC from control, with good performances (plasma/urine: 92.6%/92.6% specificity, 96.3%/92.6% sensitivity, and an area under the curve of 0.981/0.97). In conclusion, biofluids could not only reflect functional changes in tumor tissue but also reflect changes in the body's immune response. These findings will benefit the understanding of body biomarkers in tumors and the discovery of potential disease biomarkers.
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Affiliation(s)
- Xiaoyan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chen Shao
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China; Bioinformatics Department, DeepKinase Biotechnologies, Ltd, Beijing, China
| | - Haidan Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Binbin Zhang
- Department of Pharmacy, No.79 Army Group Hospital of People's Liberation Army Ground Force, Liaoyang, China
| | - Zhengguang Guo
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jiameng Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Feng Qi
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yushi Zhang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Haitao Niu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Xu N, Yu Y, Duan C, Wei J, Sun W, Jiang C, Jian B, Cao W, Jia L, Ma X. Quantitative proteomics identifies and validates urinary biomarkers of rhabdomyosarcoma in children. Clin Proteomics 2023; 20:10. [PMID: 36918772 PMCID: PMC10012572 DOI: 10.1186/s12014-023-09401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma with poor prognosis in children. The 5-year survival rate for early RMS has improved, whereas it remains unsatisfactory for advanced patients. Urine can rapidly reflect changes in the body and identify low-abundance proteins. Early screening of tumor markers through urine in RMS allows for earlier treatment, which is associated with better outcomes. METHODS RMS patients under 18 years old, including those newly diagnosed and after surgery, were enrolled. Urine samples were collected at the time points of admission and after four cycles of chemotherapy during follow-up. Then, a two-stage workflow was established. (1) In the discovery stage, differential proteins (DPs) were initially identified in 43 RMS patients and 12 healthy controls (HCs) using a data-independent acquisition method. (2) In the verification stage, DPs were further verified as biomarkers in 54 RMS patients and 25 HCs using parallel reaction monitoring analysis. Furthermore, a receiver operating characteristic (ROC) curve was used to construct the protein panels for the diagnosis of RMS. Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software were used to perform bioinformatics analysis. RESULTS A total of 251 proteins were significantly altered in the discovery stage, most of which were enriched in the head, neck and urogenital tract, consistent with the most common sites of RMS. The most overrepresented biological processes from GO analysis included immunity, inflammation, tumor invasion and neuronal damage. Pathways engaging the identified proteins revealed 33 common pathways, including WNT/β-catenin signaling and PI3K/AKT signaling. Finally, 39 proteins were confirmed as urinary biomarkers for RMS, and a diagnostic panel composed of 5 candidate proteins (EPS8L2, SPARC, HLA-DRB1, ACAN, and CILP) was constructed for the early screening of RMS (AUC: 0.79, 95%CI = 0.66 ~ 0.92). CONCLUSIONS These findings provide novel biomarkers in urine that are easy to translate into clinical diagnosis of RMS and illustrate the value of global and targeted urine proteomics to identify and qualify candidate biomarkers for noninvasive molecular diagnosis.
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Affiliation(s)
- Na Xu
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.,Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yuncui Yu
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Chao Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Jing Wei
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Wei Sun
- Proteomics Research Center, Core Facility of Instruments, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chiyi Jiang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Binglin Jian
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China
| | - Wang Cao
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Lulu Jia
- Clinical Research Center, Department of Pharmacy, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, No. 56 Nanlishi Road, Beijing, 100045, China.
| | - Xiaoli Ma
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, No. 56 Nalishi Road, Beijing, 100045, China.
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Li M, Li L, Zheng J, Li Z, Li S, Wang K, Chen X. Liquid biopsy at the frontier in renal cell carcinoma: recent analysis of techniques and clinical application. Mol Cancer 2023; 22:37. [PMID: 36810071 PMCID: PMC9942319 DOI: 10.1186/s12943-023-01745-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/11/2023] [Indexed: 02/23/2023] Open
Abstract
Renal cell carcinoma (RCC) is a major pathological type of kidney cancer and is one of the most common malignancies worldwide. The unremarkable symptoms of early stages, proneness to postoperative metastasis or recurrence, and low sensitivity to radiotherapy and chemotherapy pose a challenge for the diagnosis and treatment of RCC. Liquid biopsy is an emerging test that measures patient biomarkers, including circulating tumor cells, cell-free DNA/cell-free tumor DNA, cell-free RNA, exosomes, and tumor-derived metabolites and proteins. Owing to its non-invasiveness, liquid biopsy enables continuous and real-time collection of patient information for diagnosis, prognostic assessment, treatment monitoring, and response evaluation. Therefore, the selection of appropriate biomarkers for liquid biopsy is crucial for identifying high-risk patients, developing personalized therapeutic plans, and practicing precision medicine. In recent years, owing to the rapid development and iteration of extraction and analysis technologies, liquid biopsy has emerged as a low cost, high efficiency, and high accuracy clinical detection method. Here, we comprehensively review liquid biopsy components and their clinical applications over the past 5 years. Additionally, we discuss its limitations and predict its future prospects.
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Affiliation(s)
- Mingyang Li
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning Shenyang, 110004 People’s Republic of China
| | - Lei Li
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning Shenyang, 110004 People’s Republic of China
| | - Jianyi Zheng
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning Shenyang, 110004 People’s Republic of China
| | - Zeyu Li
- grid.412467.20000 0004 1806 3501Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning Shenyang, 110004 People’s Republic of China
| | - Shijie Li
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Liaoning, Shenyang, 110004, People's Republic of China.
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Zhang W, Liu W, Yang Y, Xiao C, Xiao Y, Tan X, Pang Q, Wu H, Hua M, Shi X. Integrative analysis of transcriptomic landscape and urinary signature reveals prognostic biomarkers for clear cell renal cell carcinoma. Front Oncol 2023; 13:1102623. [PMID: 37035174 PMCID: PMC10079990 DOI: 10.3389/fonc.2023.1102623] [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: 11/19/2022] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) patients with venous tumor thrombus (VTT) have poor prognosis. We aimed to reveal features of ccRCC with VTT and develop a urine-based prognostic classifier to predict ccRCC prognosis through integrative analyses of transcriptomic landscape and urinary signature. Methods RNA sequencing was performed in five patients with ccRCC thrombus-tumor-normal tissue triples, while mass spectrometry was performed for urine samples from 12 ccRCC and 11 healthy controls. A urine-based classifier consisting of three proteins was developed to predict patients' survival and validated in an independent cohort. Results Transcriptomic analysis identified 856 invasion-associated differentially expressed genes (DEGs). Furthermore, proteomic analysis showed 133 differentially expressed proteins (DEPs). Integration of transcriptomic landscape and urinary signature reveals 6 urinary detectable proteins (VSIG4, C3, GAL3ST1, TGFBI, AKR1C3, P4HB) displaying abundance changes consistent with corresponding genes in transcriptomic profiling. According to TCGA database, VSIG4, TGFBI, and P4HB were significantly overexpressed in patients with shorter survival and might be independent prognostic factors for ccRCC (all p<0.05). A prognostic classifier consisting of the three DEPs highly associated with survival performed satisfactorily in predicting overall survival (HR=2.0, p<0.01) and disease-free survival (HR=1.6, p<0.001) of ccRCC patients. The ELISA analysis of urine samples from an independent cohort confirmed the satisfied predictive power of the classifier for pathological grade (AUC=0.795, p<0.001) and stage (AUC=0.894, p<0.001). Conclusion Based on integrative analyses of transcriptomic landscape and urinary signature, the urine-based prognostic classifier consisting of VSIG4, TGFBI, and P4HB has satisfied predictive power of ccRCC prognosis and may facilitate ccRCC molecular subtyping and treatment.
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Affiliation(s)
- Wei Zhang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Wenqiang Liu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yiren Yang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Chengwu Xiao
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yutian Xiao
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaojie Tan
- Department of Epidemiology, Naval Medical University, Shanghai, China
| | - Qingyang Pang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Han Wu
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Meimian Hua
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Xiaolei Shi, ; Meimian Hua,
| | - Xiaolei Shi
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
- *Correspondence: Xiaolei Shi, ; Meimian Hua,
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9
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Urine Molecular Biomarkers for Detection and Follow-Up of Small Renal Masses. Int J Mol Sci 2022; 23:ijms232416110. [PMID: 36555747 PMCID: PMC9785854 DOI: 10.3390/ijms232416110] [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: 11/15/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Active surveillance (AS) is the best strategy for small renal masses (SRMs) management; however, reliable methods for early detection and disease aggressiveness prediction are urgently needed. The aim of the present study was to validate DNA methylation biomarkers for non-invasive SRM detection and prognosis. The levels of methylated genes TFAP2B, TAC1, PCDH8, ZNF677, FLRT2, and FBN2 were evaluated in 165 serial urine samples prospectively collected from 39 patients diagnosed with SRM, specifically renal cell carcinoma (RCC), before and during the AS via quantitative methylation-specific polymerase chain reaction. Voided urine samples from 92 asymptomatic volunteers were used as the control. Significantly higher methylated TFAP2B, TAC1, PCDH8, ZNF677, and FLRT2 levels and/or frequencies were detected in SRM patients' urine samples as compared to the control. The highest diagnostic power (AUC = 0.74) was observed for the four biomarkers panel with 92% sensitivity and 52% specificity. Methylated PCDH8 level positively correlated with SRM size at diagnosis, while TFAP2B had the opposite effect and was related to SRM progression. To sum up, SRMs contribute significantly to the amount of methylated DNA detectable in urine, which might be used for very early RCC detection. Moreover, PCDH8 and TFAP2B methylation have the potential to be prognostic biomarkers for SRMs.
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10
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Shlyapnikov YM, Malakhova EA, Potoldykova NV, Svetocheva YA, Vinarov AZ, Zinchenko DV, Zernii EY, Zamyatnin AA, Shlyapnikova EA. Non-Invasive Diagnostics of Renal Cell Carcinoma Using Ultrasensitive Immunodetection of Cancer-Retina Antigens. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:658-666. [PMID: 36154884 DOI: 10.1134/s0006297922070070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/15/2022] [Indexed: 06/16/2023]
Abstract
Renal cell carcinoma (RCC) is the most common urological malignancy with a high mortality and low detection rate. One of the approaches to improving its diagnostics may be the search for new non-invasive biomarkers in liquid biopsy and development of more sensitive methods for their detection. Cancer-retina antigens, which are known to be aberrantly expressed in malignant tumors, are present in liquid biopsy at extremely low concentrations. Using the developed multiplex immunoassay with a detection limit of 0.1 pg/ml, urine and serum samples of 89 patients with RCC and 50 non-cancer patients were examined for the presence of cancer-retina antigens (arrestin, recoverin, rhodopsin kinase, and transducin); the difference between the RCC and control groups was evaluated with the χ2 test. The results showed high diagnostic efficiency of a combination of arrestin and recoverin: at a threshold of 0.1 pg/ml, the sensitivity was 96%, specificity 92%, and AUC = 0.96 (95% confidence interval, 0.93-0.99). Seven days after nephrectomy, the concentration of the antigens returned to the level characteristic of the control group. Therefore, arrestin in a combination with recoverin can serve as a diagnostic non-invasive urinary biomarker of RCC.
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Affiliation(s)
- Yuri M Shlyapnikov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Ekaterina A Malakhova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Natalia V Potoldykova
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Yana A Svetocheva
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Andrei Z Vinarov
- Institute for Urology and Reproductive Health, Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Dmitry V Zinchenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 117997, Russia.
| | - Evgeni Yu Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Andrey A Zamyatnin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, 354340, Russia
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK
| | - Elena A Shlyapnikova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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11
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Transcriptome profiling and proteomic validation reveals targets of the androgen receptor signaling in the BT-474 breast cancer cell line. Clin Proteomics 2022; 19:14. [PMID: 35568821 PMCID: PMC9107748 DOI: 10.1186/s12014-022-09352-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accumulating evidence suggests that the androgen receptor (AR) and its endogenous ligands influence disease progression in breast cancer (BCa). However, AR-mediated changes in BCa differ among the various BCa subtypes according to their hormone receptor profile [i.e., presence/absence of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2, (HER2)]. Thus, we explored the androgen-regulated transcriptomic changes in the ER+PR+HER2+ BCa cell line, BT-474, and compared them with PR-mediated changes. METHODS We performed RNA sequencing analysis in treated BT-474 cells with dihydrotestosterone (DHT) and progesterone. Validation of the top ten differentially androgen-regulated genes and a number of other genes found in enriched signaling pathways was performed by qRT-PCR in BT-474 and other BCa cell lines. In addition, a parallel reaction monitoring targeted proteomic approach was developed to verify selected transcripts at the protein level. RESULTS In total 19,450 transcripts were detected, of which 224 were differentially regulated after DHT treatment. The increased expression of two well-known androgen-regulated genes, KLK2 (p < 0.05) and KLK3 (p < 0.001), confirmed the successful androgen stimulation in BT-474 cells. The transcription factor, ZBTB16, was the most highly upregulated gene, with ~ 1000-fold change (p < 0.001). Pathway enrichment analysis revealed downregulation of the DNA replication processes (p < 0.05) and upregulation of the androgen signaling and fatty acid metabolism pathways (p < 0.05). Changes related to progesterone treatment showed opposite effects in gene expression than DHT treatment. Similar expression profiles were observed among other BCa cell lines expressing high levels of AR (ZR75.1 and MBA-MB-453). The parallel reaction monitoring targeted proteomic analysis further confirmed that altered protein expression (KLK3, ALOX15B) in the supernatant and cell lysate of DHT-treated BT-474 cells, compared to control cells. DISCUSSION Our findings suggest that AR modulates the metabolism of BT-474 cells by affecting the expression of a large number of genes and proteins. Based on further pathway analysis, we suggest that androgen receptor acts as a tumor suppressor in the BT-474 cells.
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12
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Belousov PV. The Autoantibodies against Tumor-Associated Antigens as Potential Blood-Based Biomarkers in Thyroid Neoplasia: Rationales, Opportunities and Challenges. Biomedicines 2022; 10:biomedicines10020468. [PMID: 35203677 PMCID: PMC8962333 DOI: 10.3390/biomedicines10020468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022] Open
Abstract
The Autoantibodies targeting Tumor-Associated Antigens (TAA-AAbs) emerge as a result of a variety of tumor-related immunogenic stimuli and may be regarded as the eyewitnesses to the anti-tumor immune response. TAA-AAbs may be readily detected in peripheral blood to unveil the presence of a particular TAA-expressing tumor, and a fair number of TAAs eliciting the tumor-associated autoantibody response have been identified. The potential of TAA-AAbs as tumor biomarkers has been extensively studied in many human malignancies with a major influence on public health; however, tumors of the endocrine system, and, in particular, the well-differentiated follicular cell-derived thyroid neoplasms, remain understudied in this context. This review provides a detailed perspective on and legitimate rationales for the potential use of TAA-AAbs in thyroid neoplasia, with particular reference to the already established diagnostic implications of the TAA-AAbs in human cancer, to the windows for improvement and diagnostic niches in the current workup strategies in nodular thyroid disease and differentiated thyroid cancer that TAA-AAbs may successfully occupy, as well as to the proof-of-concept studies demonstrating the usefulness of TAA-AAbs in thyroid oncology, particularly for the pre-surgical discrimination between tumors of different malignant potential in the context of the indeterminate results of the fine-needle aspiration cytology.
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Affiliation(s)
- Pavel V. Belousov
- National Center for Personalized Medicine of Endocrine Diseases, National Medical Research Center for Endocrinology, Ministry of Health of the Russian Federation, 117036 Moscow, Russia; or
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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13
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Ma G, Wang Z, Liu J, Fu S, Zhang L, Zheng D, Shang P, Yue Z. Quantitative proteomic analysis reveals sophisticated metabolic alteration and identifies FMNL1 as a prognostic marker in clear cell renal cell carcinoma. J Cancer 2021; 12:6563-6575. [PMID: 34659547 PMCID: PMC8489142 DOI: 10.7150/jca.62309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/22/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose: In this study, we have undertaken the whole proteomic analysis and got a better understanding of biological processes involved in the development and progression of ccRCC. We hope promising biomarkers can be uncovered to facilitate early diagnosis, predict the prognosis and progression, more importantly, to be applied as potential therapeutic targets. Experimental design: Fresh frozen tissue samples were surgically resected from patients with local or locally advanced ccRCC. Trypsin digested proteins were analyzed using TMT-based LC-MS/MS proteomic approach, followed by bioinformatic analysis. A potential prognostic marker FMNL1 was chosen to be validated in TCGA_KIRC datasets (n=525 and 72), further validation sets (n=10 and 10) and expanded validation sets (n=81 and 16). The effects of FMNL1 on proliferation, migration and invasion were determined by colony formation, wound healing, and transwell assays in 786-O and Caki-1 cells in vitro study. Results: A total of 657 differentially expressed proteins were identified and quantified between ccRCC and adjacent normal tissues (p-value<0.05, FC>2 or<1/2), of which 186 proteins were up-regulated and 471 proteins were down-regulated. Bioinformatic analysis showed enriched metabolic biological processes and pathways. Univariate and multivariate analysis defined FMNL1 as an independent negative prognostic marker in the TCGA datasets. High expression of FMNL1 correlated significantly with tumor stage and distant metastasis (P<0.05) both in the TCGA-KIRC datasets and expanded validation sets. Kaplan-Meier survival curve illustrated that the patients with high FMNL1 protein level had shorter OS time in the expanded validation sets (p=0.0273). In vitro experiments presented the functional effects of FMNL1 knockdown on the inhibition of proliferation, migration and invasion in cancer cell lines. Conclusion and clinical relevance: The proteomic results uncovered sophisticated metabolic reprogramming of ccRCC and indicated that the upregulation of rate-limiting enzymes in glycolysis and mitochondrial impairment may be the cause of metabolic reprogramming in ccRCC. Moreover, FMNL1 has been identified as a promising prognostic marker, and knockdown of FMNL1 could inhibit ccRCC cell proliferation, migration and invasion, which might be used as a new effective therapeutic strategy to inhibit the progression of ccRCC.
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Affiliation(s)
- Gui Ma
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China
| | - Zirui Wang
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China
| | - Junyao Liu
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China
| | - Shengjun Fu
- Key Laboratory of Urological Diseases in Gansu Province, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
| | - Lili Zhang
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China
| | - Duo Zheng
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China
| | - Panfeng Shang
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China.,Department of Urology, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
| | - Zhongjin Yue
- The Second Clinical College, Lanzhou University, Lanzhou 730030, Gansu, China.,Department of Urology, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, China
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14
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Flitcroft JG, Verheyen J, Vemulkar T, Welbourne EN, Rossi SH, Welsh SJ, Cowburn RP, Stewart GD. Early detection of kidney cancer using urinary proteins: a truly non-invasive strategy. BJU Int 2021; 129:290-303. [PMID: 34570419 DOI: 10.1111/bju.15601] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES To review urinary protein biomarkers as potential non-invasive, easily obtainable, early diagnostic tools in renal cell carcinoma (RCC). METHODS A PubMed database search was performed up to the year 2020 to identify primary studies reporting potential urinary protein biomarkers for RCC. Separate searches were conducted to identify studies describing appropriate methods of developing cancer screening programmes and detection of cancer biomarkers. RESULTS Several urinary protein biomarkers are under validation for RCC diagnostics, e.g. aquaporin-1, perilipin-2, carbonic anhydrase-9, Raf-kinase inhibitory protein, nuclear matrix protein-22, 14-3-3 Protein β/α and neutrophil gelatinase-associated lipocalin. However, none has yet been validated or approved for clinical use due to low sensitivity or specificity, inconsistencies in appropriate study design, or lack of external validation. CONCLUSIONS Evaluation of biomarkers' feasibility, sample preparation and storage, biomarker validation, and the application of novel technologies may provide a solution that maximises the potential for a truly non-invasive biomarker in early RCC diagnostics.
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Affiliation(s)
- Jordan G Flitcroft
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Jeroen Verheyen
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Tarun Vemulkar
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Emma N Welbourne
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Sabrina H Rossi
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Sarah J Welsh
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
| | - Russell P Cowburn
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
| | - Grant D Stewart
- Department of Surgery, Addenbrookes Hospital, University of Cambridge, Cambridge, UK
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15
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Patel SH, Singla N, Pierorazio PM. Decision-making in active surveillance in kidney cancer: current trends and future urine and tissue markers. World J Urol 2021; 39:2869-2874. [PMID: 34370079 DOI: 10.1007/s00345-021-03786-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Surveillance for small renal masses is a growing choice of management amongst physicians and patients. These decisions, however, can be difficult as patient factors and tumor factors may blur the line between continued surveillance and intervention. Currently, there are no biomarkers that are readily available to aid in the decision making for patients with known renal cell carcinoma; however, many show promise. We herein review the literature of the adjunct tools that are currently available for decision making in small renal masses, but also new potential biomarkers that can potentially be of use.
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Affiliation(s)
- Sunil H Patel
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nirmish Singla
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Phillip M Pierorazio
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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16
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Wu Q, Fenton RA. Urinary proteomics for kidney dysfunction: insights and trends. Expert Rev Proteomics 2021; 18:437-452. [PMID: 34187288 DOI: 10.1080/14789450.2021.1950535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introduction: Kidney dysfunction poses a high burden on patients and health care systems. Early detection and accurate prediction of kidney disease progression remains a major challenge. Compared to existing clinical parameters, urinary proteomics has the potential to reveal molecular alterations within the kidney that may alter its function before the onset of clinical symptoms. Thus, urinary proteomics has greater prognostic potential for assessment of kidney dysfunction progression.Areas covered: Advances in urinary proteomics for major causes of kidney dysfunction are discussed. The application of urinary extracellular vesicles for studying kidney dysfunction are discussed. Technological advances in urinary proteomics are discussed. The literature was identified using a database search for titles containing 'proteom*' and 'urin*' and published within the past 5 years. Retrieved literature was manually filtered to retain kidney dysfunctions-related studies.Expert opinion: Despite major advances, diagnosis by urinary proteomics has not been fully applied in any clinical settings. This could be attributed to the complex nature of kidney diseases, in addition to the constraints on study power and feasibility of incorporating mass spectrometry techniques in daily routine analysis. Nevertheless, we are confident that advances in urinary proteomics will soon provide superior insights into kidney disease beyond existing clinical parameters.
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Affiliation(s)
- Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
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17
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Sun H, Wang Y, Jing HY, Yang XY, Shi XX, Zhang JH, Yu YX, Gao L, Wang XY, Li WH, Yu L. Chaperonin-Containing TCP1 Subunit 6A Is a Prognostic Potential Biomarker That Correlates With the Presence of Immune Infiltrates in Colorectal Cancer. Front Genet 2021; 12:629856. [PMID: 34017352 PMCID: PMC8129517 DOI: 10.3389/fgene.2021.629856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/23/2021] [Indexed: 01/17/2023] Open
Abstract
Aims Chaperonin-containing TCP1 subunit (CCT) 6A is an oncogenic 6th subunit of the CCT family. Nevertheless, not much is documented regarding its function in colorectal cancer (COAD). This investigation seeks to explore the role of CCT6A in the prognosis of COAD. Main Methods Sequencing data from the Gene Expression Omnibus (GEO) and Cancer Genome Atlas database (TCGA) were employed to analyze the expression of CCT6A and its involvement in various regulatory networks behind COAD. Oncomine and Gene Expression Profiling Interactive Analysis (GEPIA) analyzed Levels of expression and survival rates, while GEPIA was used to uncover further the functional networks that involved CCT6A. Database for Annotation, Visualization, and Integrated Discovery (DAVID) tools were used to interpret Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. Evaluation of the expression levels of CCT6A in COAD samples was also verified via immunohistochemistry. Key Findings We found that the expression of CCT6A is up-regulated in COAD. CCT6A correlated with poor prognosis and decreased immune infiltrates such as CD4+ T cells, B cells, and dendritic cells. CCT6A is increased in COAD patients. CCT6A is associated with several gene networks related to the DDX family and mismatch repair pathways. Significance Our data showed that data mining was able to uncover data regarding levels of CCT6A and its involvement in genetic regulating pathways in COAD.
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Affiliation(s)
- Hui Sun
- College of Pharmacy, Harbin Medical University, Harbin, China.,Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yan Wang
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Hao-Yu Jing
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xin-Yu Yang
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Xin-Xiu Shi
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Jia-Hui Zhang
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Yuan-Xiu Yu
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Li Gao
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xin-Yue Wang
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Wan-Hong Li
- College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lei Yu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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18
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Jiang J, Liu C, Xu G, Liang T, Yu C, Liao S, Zhang Z, Lu Z, Wang Z, Chen J, Chen T, Li H, Zhan X. CCT6A, a novel prognostic biomarker for Ewing sarcoma. Medicine (Baltimore) 2021; 100:e24484. [PMID: 33530265 PMCID: PMC7850773 DOI: 10.1097/md.0000000000024484] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/30/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Ewing sarcoma (ES), the second most prevalent bone malignant tumor has no widely known prognostic biomarker. Earlier studies have suggested that chaperonin containing TCP1 complex 6A (CCT6A), which encodes a molecular protein chaperone, is involved in the pathogenesis of many cancers. However, there are no known reports providing clear evidence of its role in ES pathogenesis. METHODS We performed a bioinformatic analysis of 32 ES specimens from the GSE17618 dataset concentrating on the differences in gene expression, OS, event-free survival (EFS) in the different subgroups. Immunohistochemical studies were also performed to identify the expression levels of selected genes in ES and immediate paracancerous tissues. RESULTS After 3 screenings, CCT6A was identified to be highly correlated with ES prognosis. Our survival analysis revealed a low overall survival (OS) for high CCT6A expression (P-value = .024). Our Cox regression analysis identified CCT6A expression, lEFS, and age were strongly associated with prognosis of ES. Our multivariate Cox regression analysis shows that CCT6A (P-value = .015), age (P-value = .026), and EFS (P-value = .002) were independent poor prognostic biomarkers. Our immunohistochemical analysis showed that the expression levels of CCT6A were significantly higher in ES tissues compared to the paracancerous tissues. CONCLUSION From the results of our study, we identified the expression levels of CCT6A to be strongly associated with prognosis of ES. Thus, the expression levels of the CCT6A gene could serve as a biomarker for the prediction of ES prognosis.
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Affiliation(s)
- Jie Jiang
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Chong Liu
- Department of Spine and Osteopathic Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Guoyong Xu
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Tuo Liang
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Chaojie Yu
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Shian Liao
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Zide Zhang
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Zhaojun Lu
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Zequn Wang
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Jiarui Chen
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Tianyou Chen
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Hao Li
- Guangxi Medical University, Department First School of Clinical Medicine
| | - Xinli Zhan
- Department of Spine and Osteopathic Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
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19
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Clark DJ, Zhang H. Proteomic approaches for characterizing renal cell carcinoma. Clin Proteomics 2020; 17:28. [PMID: 32742246 PMCID: PMC7391522 DOI: 10.1186/s12014-020-09291-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 12/24/2022] Open
Abstract
Renal cell carcinoma is among the top 15 most commonly diagnosed cancers worldwide, comprising multiple sub-histologies with distinct genomic, proteomic, and clinicopathological features. Proteomic methodologies enable the detection and quantitation of protein profiles associated with the disease state and have been explored to delineate the dysregulated cellular processes associated with renal cell carcinoma. In this review we highlight the reports that employed proteomic technologies to characterize tissue, blood, and urine samples obtained from renal cell carcinoma patients. We describe the proteomic approaches utilized and relate the results of studies in the larger context of renal cell carcinoma biology. Moreover, we discuss some unmet clinical needs and how emerging proteomic approaches can seek to address them. There has been significant progress to characterize the molecular features of renal cell carcinoma; however, despite the large-scale studies that have characterized the genomic and transcriptomic profiles, curative treatments are still elusive. Proteomics facilitates a direct evaluation of the functional modules that drive pathobiology, and the resulting protein profiles would have applications in diagnostics, patient stratification, and identification of novel therapeutic interventions.
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Affiliation(s)
- David J. Clark
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA
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20
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Raimondo F, Pitto M. Prognostic significance of proteomics and multi-omics studies in renal carcinoma. Expert Rev Proteomics 2020; 17:323-334. [PMID: 32428425 DOI: 10.1080/14789450.2020.1772058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Renal carcinoma, and in particular its most common variant, the clear cell subtype, is often diagnosed incidentally through abdominal imaging and frequently, the tumor is discovered at an early stage. However, 20% to 40% of patients undergoing nephrectomy for clinically localized renal cancer, even after accurate histological and clinical classification, will develop metastasis or recurrence, justifying the associated mortality rate. Therefore, even if renal carcinoma is not among the most frequent nor deadly cancers, a better prognostication is needed. AREAS COVERED Recently proteomics or other omics combinations have been applied to both cancer tissues, on the neoplasia itself and surrounding microenvironment, cultured cells, and biological fluids (so-called liquid biopsy) generating a list of prognostic molecular tools that will be reviewed in the present paper. EXPERT OPINION Although promising, none of the approaches listed above has been yet translated in clinics. This is likely due to the peculiar genetic and phenotypic heterogeneity of this cancer, which makes nearly each tumor different from all the others. Attempts to overcome this issue will be also revised. In particular, we will discuss how the application of omics-integrated approaches could provide the determinants of response to the different targeted drugs.
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Affiliation(s)
- Francesca Raimondo
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano - Bicocca , Vedano al Lambro, Italy
| | - Marina Pitto
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano - Bicocca , Vedano al Lambro, Italy
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Macklin A, Khan S, Kislinger T. Recent advances in mass spectrometry based clinical proteomics: applications to cancer research. Clin Proteomics 2020; 17:17. [PMID: 32489335 PMCID: PMC7247207 DOI: 10.1186/s12014-020-09283-w] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer biomarkers have transformed current practices in the oncology clinic. Continued discovery and validation are crucial for improving early diagnosis, risk stratification, and monitoring patient response to treatment. Profiling of the tumour genome and transcriptome are now established tools for the discovery of novel biomarkers, but alterations in proteome expression are more likely to reflect changes in tumour pathophysiology. In the past, clinical diagnostics have strongly relied on antibody-based detection strategies, but these methods carry certain limitations. Mass spectrometry (MS) is a powerful method that enables increasingly comprehensive insights into changes of the proteome to advance personalized medicine. In this review, recent improvements in MS-based clinical proteomics are highlighted with a focus on oncology. We will provide a detailed overview of clinically relevant samples types, as well as, consideration for sample preparation methods, protein quantitation strategies, MS configurations, and data analysis pipelines currently available to researchers. Critical consideration of each step is necessary to address the pressing clinical questions that advance cancer patient diagnosis and prognosis. While the majority of studies focus on the discovery of clinically-relevant biomarkers, there is a growing demand for rigorous biomarker validation. These studies focus on high-throughput targeted MS assays and multi-centre studies with standardized protocols. Additionally, improvements in MS sensitivity are opening the door to new classes of tumour-specific proteoforms including post-translational modifications and variants originating from genomic aberrations. Overlaying proteomic data to complement genomic and transcriptomic datasets forges the growing field of proteogenomics, which shows great potential to improve our understanding of cancer biology. Overall, these advancements not only solidify MS-based clinical proteomics' integral position in cancer research, but also accelerate the shift towards becoming a regular component of routine analysis and clinical practice.
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Affiliation(s)
- Andrew Macklin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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