1
|
Tabaei S, Haghshenas MR, Webster TJ, Ghaderi A. Proteomics strategies for urothelial bladder cancer diagnosis, prognosis and treatment: Trends for tumor biomarker sources. Anal Biochem 2023; 666:115074. [PMID: 36738874 DOI: 10.1016/j.ab.2023.115074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Urothelial bladder cancer (UBC) is a heterogeneous multifactorial malignancy with a high recurrence rate. Current procedures for UBC diagnosis suffering from the lack of clinical sensitivity and specificity screening tests. Therefore, biomarkers have promising values to predict pathological conditions and can be considered as effective targets for early diagnosis, prognosis and antitumor immunotherapy. Recently, researchers have been interested for tumor proteins as biomarkers for different diseases. At present, proteomics methods have rapidly progressive that has potential identified biomarkers of UBC. Specifically, there has been several studies on the potential application of proteomics for the identification, quantification, and profiling of proteins for UBC in different sources. Based on these studies, using the panel of biomarkers as proteomic patterns may achieve higher sensitivity and specificity than single proteins in the diagnosis of UBC. In the present review, we evaluate recent literature related to the UBC proteome focusing especially on new proteomics techniques. Moreover, we classify UBC tumor biomarkers as diagnostic, prognostic, and therapeutic targets based on their sources (urine, serum/plasm, cell line, and tumor tissue) and we also discuss the advantages and limitations of each source. In this manner, this review article provides a critical assessment presentation of the advances in proteomics for all aspects of UBC diagnosis, prognosis, and treatment based on sources.
Collapse
Affiliation(s)
- Samira Tabaei
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Haghshenas
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Thomas J Webster
- School of Biomedical Engineering and Health Sciences, Hebei University of Technology, Tianjin, China
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
2
|
Hypoxia-Inducible Factor-2-Altered Urothelial Carcinoma: Clinical and Genomic Features. Curr Oncol 2022; 29:8638-8649. [PMID: 36421334 PMCID: PMC9689673 DOI: 10.3390/curroncol29110681] [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: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Hypoxia is recognized as a key feature of cancer growth and is involved in various cellular processes, including proliferation, angiogenesis, and immune surveillance. Besides hypoxia-inducible factor 1-alpha (HIF-1α), which is the main mediator of hypoxia effects and can also be activated under normoxic conditions, little is known about its counterpart, HIF-2. This study focused on investigating the clinical and molecular landscape of HIF-2-altered urothelial carcinoma (UC). Methods: Publicly available next-generation sequencing (NGS) data from muscle-invasive UC cell lines and patient tumor samples from the MSK/TCGA 2020 cohort (n = 476) were interrogated for the level of expression (mRNA, protein) and presence of mutations, copy number variations, structural variants in the EPAS1 gene encoding HIF-2, and findings among various clinical (stage, grade, progression-free and overall survival) and molecular (tumor mutational burden, enriched gene expression) parameters were compared between altered and unaltered tumors. Results: 19% (7/37) of UC cell lines and 7% (27/380) of patients with muscle-invasive UC display high EPAS1 mRNA and protein expression or/and EPAS1 alterations. EPAS1-altered tumors are associated with higher stage, grade, and lymph node metastasis as well as with shorter PFS (14 vs. 51 months, q = 0.01) and OS (15 vs. 55 months, q = 0.01). EPAS1 mRNA expression is directly correlated with that of its target-genes, including VEGF, FLT1, KDR, DLL4, CDH5, ANGPT1 (q < 0.001). While there is a slightly higher tumor mutational burden in EPAS1-altered tumors (9.9 vs. 4.9 mut/Mb), they are enriched in and associated with genes promoting immune evasion, including ARID5B, SPINT1, AAK1, CLIC3, SORT1, SASH1, and FGFR3, respectively (q < 0.001). Conclusions: HIF-2-altered UC has an aggressive clinical and a distinct genomic and immunogenomic profile enriched in angiogenesis- and immune evasion-promoting genes.
Collapse
|
3
|
Integrative analysis of differentially expressed mRNAs and proteins induced by PGC-1β in breast cancer cells. Biochem Biophys Res Commun 2022; 637:73-82. [DOI: 10.1016/j.bbrc.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
|
4
|
Zhou Q, Yang C, Mou Z, Wu S, Dai X, Chen X, Ou Y, Zhang L, Sha J, Jiang H. Identification and validation of a poor clinical outcome subtype of primary prostate cancer with Midkine abundance. Cancer Sci 2022; 113:3698-3709. [PMID: 36018546 PMCID: PMC9633304 DOI: 10.1111/cas.15546] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022] Open
Abstract
Recent studies identified Midkine (MDK) as playing a key role in immune regulation. In this study, we aimed to discover the clinical significance and translational relevance in prostate cancer (PCa). We retrospectively analyzed 759 PCa patients who underwent radical prostatectomy from Huashan Hospital, Fudan University (training cohort, n = 369) and Chinese Prostate Cancer Consortium (validation cohort, n = 390). A total of 325 PCa patients from The Cancer Genome Atlas (TCGA) database (external cohort) were analyzed for exploration. Immune landscape and antitumor immunity were assessed through immunohistochemistry and flow cytometry. Patient‐derived explant culture system was applied for evaluating the targeting potential of MDK. We found that intratumoral MDK expression correlated with PCa progression, which indicated an unfavorable biochemical recurrence (BCR)‐free survival for postoperative PCa patients. Addition of MDK expression to the postoperative risk assessment tool CAPRA‐S could improve its prognostic value. Tumors with MDK abundance characterized the tumor‐infiltrating CD8+ T cells with less cytotoxicity production and increased immune checkpoint expression, which were accompanied by enriched immunosuppressive contexture. Moreover, MDK inhibition could reactivate CD8+ T cell antitumor immunity. MDK mRNA expression negatively correlated with androgen receptor activity signature and positively associated with radiotherapy‐related signature. In conclusion, intratumoral MDK expression could serve as an independent prognosticator for BCR in postoperative PCa patients. MDK expression impaired the antitumor function of CD8+ T cells through orchestrating an immunoevasive microenvironment, which could be reversed by MDK inhibition. Moreover, tumors with MDK enrichment possessed potential sensitivity to postoperative radiotherapy while resistance to adjuvant hormonal therapy of PCa. MDK could be considered as a potential therapeutic target for PCa.
Collapse
Affiliation(s)
- Quan Zhou
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chen Yang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Fudan University, Shanghai, China
| | - Zezhong Mou
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Siqi Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiyu Dai
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinan Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxi Ou
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Limin Zhang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianjun Sha
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China.,National Clinical Research Center for Aging and Medicine, Fudan University, Shanghai, China
| |
Collapse
|
5
|
Zhang Y, Lin Y, Lv D, Wu X, Li W, Wang X, Jiang D. Identification and validation of a novel signature for prediction the prognosis and immunotherapy benefit in bladder cancer. PeerJ 2022; 10:e12843. [PMID: 35127296 PMCID: PMC8796709 DOI: 10.7717/peerj.12843] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Bladder cancer (BC) is a common urinary tract system tumor with high recurrence rate and different populations show distinct response to immunotherapy. Novel biomarkers that can accurately predict prognosis and therapeutic responses are urgently needed. Here, we aim to identify a novel prognostic and therapeutic responses immune-related gene signature of BC through a comprehensive bioinformatics analysis. METHODS The robust rank aggregation was conducted to integrate differently expressed genes (DEGs) in datasets of the Cancer Genome Atlas (TCGA) and the gene expression omnibus (GEO). Lasso and Cox regression analyses were performed to formulate a novel mRNA signature that could predict prognosis of BC patients. Subsequently, the prognostic value and predictive value of the signature was validated with two independent cohorts GSE13507 and IMvigor210. Finally, quantitative Real-time PCR (qRT-PCR) analysis was conducted to determine the expression of mRNAs in BC cell lines (UM-UC-3, EJ-1, SW780 and T24). RESULTS We built a signature comprised the eight mRNAs: CNKSR1, COPZ2, CXorf57, FASN, PCOLCE2, RGS1, SPINT1 and TPST1. Our prognostic signature could be used to stratify BC population into two risk groups with distinct immune profile and responsiveness to immunotherapy. The results of qRT-PCR demonstrated that the eight mRNAs exhibited different expression levels in BC cell lines. CONCLUSION Our study constructed a convenient and reliable 8-mRNA gene signature, which might provide prognostic prediction and aid treatment decision making of BC patients in clinical practice.
Collapse
Affiliation(s)
- Yichi Zhang
- Department of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Nanshan School, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yifeng Lin
- Department of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China,Department of Urology, Meizhou Hospital of Traditional Chinese Medicine, Meizhou, China
| | - Daojun Lv
- Department of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiangkun Wu
- Department of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenjie Li
- Department of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xueqing Wang
- Department of Ultrasound, Shantou Central Hospital, Shantou, Guangdong, China
| | - Dongmei Jiang
- Department of Pathology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangzhou, China
| |
Collapse
|
6
|
Humayun-Zakaria N, Ward DG, Arnold R, Bryan RT. Trends in urine biomarker discovery for urothelial bladder cancer: DNA, RNA, or protein? Transl Androl Urol 2021; 10:2787-2808. [PMID: 34295762 PMCID: PMC8261432 DOI: 10.21037/tau-20-1327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/23/2021] [Indexed: 02/01/2023] Open
Abstract
Urothelial bladder cancer is a complex disease displaying a landscape of heterogenous molecular subtypes, mutation profiles and clinical presentations. Diagnosis and surveillance rely on flexible cystoscopy which has high accuracy, albeit accompanied by a high-cost burden for healthcare providers and discomfort for patients. Advances in "omic" technologies and computational biology have provided insights into the molecular pathogenesis of bladder cancer and provided powerful tools to identify markers for disease detection, risk stratification, and predicting responses to therapy. To date, numerous attempts have been made to discover and validate diagnostic biomarkers that could be deployed as an adjunct to the cystoscopic diagnosis and long-term surveillance of bladder cancer. We report a comprehensive literature analysis using PubMed to assess the changing trends in investigating DNA, RNA, or proteins as diagnostic urinary biomarkers over a period of 5 decades: 1970-2020. A gradual shift has been observed in research away from protein biomarkers to nucleic acids including different classes of RNA, and DNA methylation and mutation markers. Until 2000, publications involving protein biomarker discovery constituted 87% of the total number of research articles with DNA comprising 6% and RNA 7%. Since 2000 the proportion of protein biomarker articles has fallen to 40%, and DNA and RNA studies increased to 32% and 28%, respectively. Clearly research focus, perhaps driven by technological innovation, has shifted from proteins to nucleic acids. We optimistically hypothesise that, following thorough validation, a clinically useful detection test for bladder cancer based on a panel of DNA or RNA markers could become reality within 5-10 years.
Collapse
Affiliation(s)
- Nada Humayun-Zakaria
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
7
|
Charpentier M, Gutierrez C, Guillaudeux T, Verhoest G, Pedeux R. Noninvasive Urine-Based Tests to Diagnose or Detect Recurrence of Bladder Cancer. Cancers (Basel) 2021; 13:cancers13071650. [PMID: 33916038 PMCID: PMC8036846 DOI: 10.3390/cancers13071650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/10/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022] Open
Abstract
Liquid biopsies are increasingly used for the diagnosis and follow-up of cancer patients. Urine is a body fluid that can be used to detect cancers and others diseases. It is noninvasive and easy to collect. To detect Bladder Cancer (BC), cytology is the first assay used. It is an effective way to detect high grade BC but has a high rate of equivocal results, especially for low grade BC. Furthermore, cystoscopy is used to confirm cytology results and to determine cancer status. Cystoscopy is also effective but highly invasive, and not well accepted by patients, especially for BC follow-up. In this review we survey the numerous assays recently developed in order to diagnose BC at an early stage, and to facilitate the follow-up of patients. We discuss their effectiveness, ease of use, and applications. Finally, we discuss assays that, in the future, could improve the diagnosis and management of BC patients.
Collapse
Affiliation(s)
- Marine Charpentier
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
| | - Charly Gutierrez
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
| | - Thierry Guillaudeux
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
| | - Grégory Verhoest
- Department of Urology, CHU RENNES, Rue Henri le Guilloux, 35033 Rennes, France;
| | - Rémy Pedeux
- COSS (Chemistry Oncogenesis Stress Signaling)—UMR_S 1242, University of Rennes, INSERM, CLCC Eugène Marquis, F-35000 Rennes, France; (M.C.); (C.G.); (T.G.)
- Correspondence: ; Tel.: +33-223-234-702
| |
Collapse
|
8
|
Chen CJ, Chou CY, Shu KH, Chen HC, Wang MC, Chang CC, Hsu BG, Wu MS, Yang YL, Liao WL, Yang C, Hsiao YT, Huang CC. Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Urothelial Cancer Using iTRAQ Proteomics. J Proteome Res 2021; 20:2953-2963. [PMID: 33780252 DOI: 10.1021/acs.jproteome.1c00164] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Urothelial carcinoma (UC) is the ninth most prevalent malignancy worldwide. Noninvasive and efficient biomarkers with high accuracy are imperative for the surveillance and diagnosis of UC. CKD patients were enrolled as a control group in this study for the discovery of highly specific urinary protein markers of UC. An iTRAQ-labeled quantitative proteomic approach was used to discover novel potential markers. These markers were further validated with 501 samples by ELISA assay, and their diagnostic accuracies were compared to those of other reported UC markers. BRDT, CYBP, GARS, and HDGF were identified as novel urinary UC biomarkers with a high discrimination ability in a population comprising CKD and healthy subjects. The diagnostic values of the four novel UC markers were better than that of a panel of well-known or FDA-approved urinary protein markers CYFR21.1, Midkine, and NUMA1. Three of our discovered markers (BRDT, HDGF, GARS) and one well-known marker (CYFR21.1) were finally selected and combined as a marker panel having AUC values of 0.962 (95% CI, 0.94-0.98) and 0.860 (95% CI, 0.83-0.89) for the discrimination between UC and normal groups and UC and control (healthy + CKD) groups, respectively.
Collapse
Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 404333, Taiwan.,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung 404332, Taiwan
| | - Che-Yi Chou
- Department of Internal Medicine, Asia University Hospital, Taichung 41354, Taiwan.,Department of Post-baccalaureate Veterinary Medicine, Asia University, Taichung, Taiwan.,Division of Nephrology, China Medical University Hospital, Taichung 404332, Taiwan
| | - Kuo-Hsiung Shu
- Division of Nephrology, Lin Shin Hospital, Taichung 40867, Taiwan
| | - Hung-Chun Chen
- Division of Nephrology, Kaohsiung Medical University and Hospitals, Kaohsiung 80708, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Cheng Kung University Hospital, Tainan 70403, Taiwan
| | - Chia-Chu Chang
- Department of Internal Medicine, Kuang Tien General Hospital, Taichung 43303, Taiwan
| | - Bang-Gee Hsu
- Division of Nephrology, Buddhist Tzu Chi General Hospital, Hualien 43303, Taiwan
| | - Mai-Szu Wu
- Division of Nephrology, Taipei Medical University and Hospitals, Taipei 110, Taiwan
| | - Yuan-Lung Yang
- Division of Urology, St. Mary's Hospital, Yilan 26546, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 404333, Taiwan.,Center for Personalized Medicine, China Medical University Hospital, Taichung 404332, Taiwan
| | - Chieh Yang
- Division of Nephrology and the Kidney Institute, Department of Internal Medicine, China Medical University and Hospitals, Taichung 404332, Taiwan
| | - Yu-Tien Hsiao
- Division of Nephrology and the Kidney Institute, Department of Internal Medicine, China Medical University and Hospitals, Taichung 404332, Taiwan
| | - Chiu-Ching Huang
- Division of Nephrology and the Kidney Institute, Department of Internal Medicine, China Medical University and Hospitals, Taichung 404332, Taiwan
| |
Collapse
|
9
|
Midkine (MDK) growth factor: a key player in cancer progression and a promising therapeutic target. Oncogene 2019; 39:2040-2054. [PMID: 31801970 DOI: 10.1038/s41388-019-1124-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022]
Abstract
Midkine is a heparin-binding growth factor, originally reported as the product of a retinoic acid-responsive gene during embryogenesis, but currently viewed as a multifaceted factor contributing to both normal tissue homeostasis and disease development. Midkine is abnormally expressed at high levels in various human malignancies and acts as a mediator for the acquisition of critical hallmarks of cancer, including cell growth, survival, metastasis, migration, and angiogenesis. Several studies have investigated the role of midkine as a cancer biomarker for the detection, prognosis, and management of cancer, as well as for monitoring the response to cancer treatment. Moreover, several efforts are also being made to elucidate its underlying mechanisms in therapeutic resistance and immunomodulation within the tumor microenvironment. We hereby summarize the current knowledge on midkine expression and function in cancer development and progression, and highlight its promising potential as a cancer biomarker and as a future therapeutic target in personalized cancer medicine.
Collapse
|
10
|
Chen YT, Tsai CH, Chen CL, Yu JS, Chang YH. Development of biomarkers of genitourinary cancer using mass spectrometry-based clinical proteomics. J Food Drug Anal 2019; 27:387-403. [PMID: 30987711 PMCID: PMC9296213 DOI: 10.1016/j.jfda.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 12/23/2022] Open
Abstract
Prostate, bladder and kidney cancer are the three most common types of genitourinary cancer in the world. Of these, prostate and bladder cancers are within the top 10 most common cancers in men. Notably, kidney cancer causes no obvious symptoms in the early stages. To satisfy clinical-management requirements, researchers have developed numerous biomarkers by applying proteomic approaches using clinical serum, urine and tissue specimens, as well as cell and animal models. Through application of biomarker pipeline protocols, including discovery, verification and validation phases, and mass-spectrometric based proteomic platforms coupled with multiplexed quantification assays, these studies have led to recent rapid progress in this area. With improvements in mass-spectrometric based proteomic techniques, numerous promising biomarker candidates and marker panels for various clinical purposes have been proposed. Verification of novel protein biomarker candidates is very resource demanding (e.g. on the clinical and laboratory sides). With the support of national consortia, it is now possible to investigate the future clinical use of such biomarker strategies and assess their cost-effectiveness in personalized medicine.
Collapse
Affiliation(s)
- Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taiwan University, Taoyuan,
Taiwan
- Corresponding author. Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Han Tsai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Chien-Lun Chen
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou,
Taiwan
| | - Ying-Hsu Chang
- Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Corresponding author. Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan, Taiwan. E-mail addresses: (Y.-T. Chen), (Y.-H. Chang)
| |
Collapse
|
11
|
Anjo SI, Manadas B. A translational view of cells' secretome analysis - from untargeted proteomics to potential circulating biomarkers. Biochimie 2018; 155:37-49. [DOI: 10.1016/j.biochi.2018.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023]
|
12
|
Novel protein signatures suggest progression to muscular invasiveness in bladder cancer. PLoS One 2018; 13:e0206475. [PMID: 30419021 PMCID: PMC6231613 DOI: 10.1371/journal.pone.0206475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Patients with bladder cancer need frequent controls over long follow-up time due to high recurrence rate and risk of conversion to muscle invasive cancer with poor prognosis. We identified cancer-related molecular signatures in apparently healthy bladder in patients with subsequent muscular invasiveness during follow-up. Global proteomics of the normal tissue biopsies revealed specific proteome fingerprints in these patients prior to subsequent muscular invasiveness. In these presumed normal samples, we detected modulations of proteins previously associated with different cancer types. This study indicates that analyzing apparently healthy tissue of a cancer-invaded organ may suggest disease progression.
Collapse
|
13
|
Snell KIE, Ward DG, Gordon NS, Goldsmith JC, Sutton AJ, Patel P, James ND, Zeegers MP, Cheng KK, Bryan RT. Exploring the roles of urinary HAI-1, EpCAM & EGFR in bladder cancer prognosis & risk stratification. Oncotarget 2018; 9:25244-25253. [PMID: 29861867 PMCID: PMC5982738 DOI: 10.18632/oncotarget.25397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/28/2018] [Indexed: 11/25/2022] Open
Abstract
Objectives To investigate whether elevated urinary HAI-1, EpCAM and EGFR are independent prognostic biomarkers within non-muscle-invasive bladder cancer (NMIBC) patients, and have utility for risk stratification to facilitate treatment decisions. Results After accounting for EAU risk group in NMIBC patients, the risk of BC-specific death was 2.14 times higher (95% CI: 1.08 to 4.24) if HAI-1 was elevated and 2.04 times higher (95% CI: 1.02 to 4.07) if EpCAM was elevated. The majority of events occurred in the high-risk NMIBC group and this is where the biggest difference is seen in the survival curves when plotted for EAU risk groups separately. In MIBC patients, being elevated for any of the three biomarkers was significantly associated with BC-specific mortality after accounting for other risk factors, HR = 4.30 (95% CI: 1.85 to 10.03). Patients and Methods Urinary levels of HAI-1, EpCAM and EGFR were measured by ELISA in 683 and 175 patients with newly-diagnosed NMIBC and MIBC, respectively, recruited to the Bladder Cancer Prognosis Programme. Associations between biomarkers and progression, BC-specific mortality and all-cause mortality were evaluated using univariable and multivariable Cox regression models, adjusted for European Association of Urology (EAU) NMIBC risk groups. The upper 25% of values for each biomarker within NMIBC patients were considered as elevated. Exploratory analyses in urine from MIBC patients were also undertaken. Conclusion Urinary HAI-1 and EpCAM are prognostic biomarkers for NMIBC patients. These biomarkers have potential to guide treatment decisions for high-risk NMIBC patients. Further analyses are required to define the roles of HAI-1, EpCAM and EGFR in MIBC patients.
Collapse
Affiliation(s)
- Kym I E Snell
- Centre for Prognosis Research, Research Institute for Primary Care and Health Science, Keele University, Newcastle-under-Lyme, ST5 5BG, UK
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Naheema S Gordon
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - James C Goldsmith
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew J Sutton
- Leeds Institute of Health Sciences, University of Leeds and The Diagnostic Evidence Cooperative, Leeds LS2 9JT, UK
| | - Prashant Patel
- Institute of Cancer and Genomic Sciences, University of Birmingham and University Hospitals Birmingham NHS Foundation Trust, Birmingham B15 2TH, UK
| | - Nicholas D James
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Maurice P Zeegers
- NUTRIM School for Nutrition and Translational Research in Metabolism and CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht 6200 MD, The Netherlands
| | - K K Cheng
- Institute of Applied Health Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard T Bryan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
14
|
Liu CL, Yang PS, Chien MN, Chang YC, Lin CH, Cheng SP. Expression of serine peptidase inhibitor Kunitz type 1 in differentiated thyroid cancer. Histochem Cell Biol 2018. [PMID: 29532159 DOI: 10.1007/s00418-018-1660-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
SPINT1, also known as HAI-1, is a Kunitz-type serine protease inhibitor that inhibits multiple proteases including hepatocyte growth factor (HGF) activator and matriptase. SPINT1 has been shown to modulate HGF/MET activation in certain cancer types. In the present study, we analyzed microarray datasets and found that SPINT1 was consistently upregulated in differentiated thyroid cancer. SPINT1 protein expression was investigated using tissue microarrays and independent samples of our 143 patients. Strong SPINT1 expression was observed in 61-68% of papillary thyroid cancer and 41-50% of follicular thyroid cancer. The overexpression diminished in anaplastic thyroid cancer. The SPINT1 expression in normal thyroid tissues and benign thyroid lesions was low. Furthermore, we noted that the SPINT1 expression was associated with extrathyroidal invasion, lymphovascular invasion, lymph node metastasis, advanced TNM stage, and a higher risk of recurrence in differentiated thyroid cancer. The results were in accordance with our analysis of The Cancer Genome Atlas data. In conclusion, an overexpression of SPINT1 appears to be associated with an invasive phenotype in differentiated thyroid cancer.
Collapse
Affiliation(s)
- Chien-Liang Liu
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, 92, Section 2, Chung-Shan North Road, Taipei, 10449, Taiwan.,Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Po-Sheng Yang
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, 92, Section 2, Chung-Shan North Road, Taipei, 10449, Taiwan
| | - Ming-Nan Chien
- Division of Endocrinology and Metabolism, Department of Internal Medicine, MacKay Memorial Hospital and Mackay Medical College, Taipei, Taiwan
| | - Yuan-Ching Chang
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, 92, Section 2, Chung-Shan North Road, Taipei, 10449, Taiwan
| | - Chi-Hsin Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan.,Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan, Taiwan
| | - Shih-Ping Cheng
- Department of Surgery, MacKay Memorial Hospital and Mackay Medical College, 92, Section 2, Chung-Shan North Road, Taipei, 10449, Taiwan. .,Department of Pharmacology, Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
15
|
Zhang L, Song X, Shao Y, Wu C, Jiang J. Prognostic value of Midkine expression in patients with solid tumors: a systematic review and meta-analysis. Oncotarget 2018; 9:24821-24829. [PMID: 29872508 PMCID: PMC5973861 DOI: 10.18632/oncotarget.23892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/13/2017] [Indexed: 12/23/2022] Open
Abstract
Background Accumulated studies have shown the important role of Midkine (MDK) protein in various solid tumors and indicated its correlation with patients' survival. This meta-analysis was performed to further explore the prognostic value of MDK expression in solid tumors. Materials and Methods We collected the literatures through searching PubMed, Embase and the Cochrane Library (last up to April 10, 2017) to assess the effect of MDK on survival in solid tumor patients. The STATA 12.0 software was used for the meta-analysis. Fixed-effects models or random-effects models were used to estimate the pooled hazard ratios (HRs) for overall survival (OS). Results A total of 2097 patients from 17 observational studies were summarized. High expression of MDK was notably associated with worse OS in solid tumor patients. (pooled HR = 1.96; 95% CI = 1.67-2.31). The subgroup analysis of tumor type demonstrated negative impact of elevated MDK on OS in most solid tumor patients (P < 0.05), while MDK had no relevance with OS in the patients with OSCC (pooled HR = 1.68; 95% CI = 0.84-3.36; P = 0.145) or HNSCC (pooled HR = 1.56; 95% CI = 0.96-2.51; P = 0.075). Conclusions The present meta-analysis clarifies that MDK is a potential prognostic biomarker in solid tumor patients. Future large-scale prospective clinical trials are needed to determine the prognostic value of MDK in solid tumor patients.
Collapse
Affiliation(s)
- Luo Zhang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Xing Song
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Yingjie Shao
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Changping Wu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| | - Jingting Jiang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu Province, China
| |
Collapse
|
16
|
Sigdel TK, Nicora CD, Qian WJ, Sarwal MM. Optimization for Peptide Sample Preparation for Urine Peptidomics. Methods Mol Biol 2018; 1788:63-72. [PMID: 29623538 DOI: 10.1007/7651_2017_90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of native or endogenous peptides in biofluids can provide valuable insight into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for noninvasive monitoring of human diseases. The noninvasive nature of urine collection and the abundance of peptides in the urine make analysis by high-throughput "peptidomics" methods an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regard to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements, in that it hampers both the identification of peptides and the depth of the peptidomics read when utilizing LC-MS-based peptidome analysis. We report on a novel adaptation of the standard solid-phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS-based peptidomics, in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. The mSPE method provides significantly improved efficiencies for the preparation of samples from urine. The mSPE method is found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis, due to optimized sample cleanup that provides improved experimental inference from confidently identified peptides.
Collapse
Affiliation(s)
- Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Minnie M Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
17
|
Zhang H, Fan Y, Xia L, Gao C, Tong X, Wang H, Sun L, Ji T, Jin M, Gu B, Fan B. The impact of advanced proteomics in the search for markers and therapeutic targets of bladder cancer. Tumour Biol 2017; 39:1010428317691183. [PMID: 28345451 DOI: 10.1177/1010428317691183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bladder cancer is the most common cancer of the urinary tract and can be avoided through proper surveillance and monitoring. Several genetic factors are known to contribute to the progression of bladder cancer, many of which produce molecules that serve as cancer biomarkers. Blood, urine, and tissue are commonly analyzed for the presence of biomarkers, which can be derived from either the nucleus or the mitochondria. Recent advances in proteomics have facilitated the high-throughput profiling of data generated from bladder cancer-related proteins or peptides in parallel with high sensitivity and specificity, providing a wealth of information for biomarker discovery and validation. However, the transmission of screening results from one laboratory to another remains the main disadvantage of these methods, a fact that emphasizes the need for consistent and standardized procedures as suggested by the Human Proteome Organization. This review summarizes the latest discoveries and progress of biomarker identification for the early diagnosis, projected prognosis, and therapeutic response of bladder cancer, informs the readers of the current status of proteomic-based biomarker findings, and suggests avenues for future work.
Collapse
Affiliation(s)
- Hongshuo Zhang
- 1 Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, P.R. China
| | - Yue Fan
- 2 Department of Propaganda, Jinzhou Medical University, Jinzhou, P.R. China
| | - Lingling Xia
- 3 Graduate School, Guangzhou Medical University, Guangzhou, P.R. China.,4 Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, P.R. China
| | - Chunhui Gao
- 5 Department of Gastrointestinal Surgery, The Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Xin Tong
- 6 Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P.R. China
| | - Hanfu Wang
- 7 Medical Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P.R. China
| | - Lili Sun
- 8 Department of Ophthalmology, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, P.R. China
| | - Tuo Ji
- 9 Department of Hospital Management, Jinzhou Medical University, Jinzhou, P.R. China
| | - Mingyu Jin
- 10 Graduate School, Dalian Medical University, Dalian, P.R. China
| | - Bing Gu
- 11 Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, P.R. China
| | - Bo Fan
- 12 Department of Urology, Second Affiliated Hospital, Dalian Medical University, Dalian, P.R. China
| |
Collapse
|
18
|
Abstract
Research efforts targeting the identification of bladder cancer biomarkers have been extensive during the past decade. Investigations have been performed at the genome, transcriptome, proteome, and metabolome levels and outputs have started appearing including the sketching of disease molecular subtypes. Proteins are directly linked to cell phenotype hence they accumulate special interest as both biomarkers and therapeutic targets. Multiple technical challenges exist, of the main, being the protein concentration vast dynamic range and presence of proteins in modified forms. The scope of this review is to summarize the contribution of proteomics research in this quest of bladder cancer biomarkers. To obtain an unbiased and comprehensive overview, the scientific literature was searched for manuscripts describing proteomic studies on urothelial cancer from the last ten years and those including independent verification studies in urine, tissue and blood are briefly presented. General observations include: a) in most cases, suboptimal experimental design including healthy controls in biomarker discovery and frequently biomarker verification, is followed; b) variability in protein findings between studies can be observed, to some extent reflecting complexity of experimental approaches and proteome itself; c) consistently reported biomarkers include mainly plasma proteins and d) compilation of protein markers into diagnostic panels appears the most promising way forward. Two main avenues of research can now be foreseen: targeting integration of the existing disparate data with proteomic findings being placed in the context of existing knowledge on bladder cancer subtypes and in parallel, accumulation of clinical samples to support proper validation studies of promising marker combinations.
Collapse
Affiliation(s)
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens , Biotechnology Division, Athens, Greece
| |
Collapse
|
19
|
Kawahara R, Meirelles GV, Heberle H, Domingues RR, Granato DC, Yokoo S, Canevarolo RR, Winck FV, Ribeiro ACP, Brandão TB, Filgueiras PR, Cruz KSP, Barbuto JA, Poppi RJ, Minghim R, Telles GP, Fonseca FP, Fox JW, Santos-Silva AR, Coletta RD, Sherman NE, Paes Leme AF. Integrative analysis to select cancer candidate biomarkers to targeted validation. Oncotarget 2016; 6:43635-52. [PMID: 26540631 PMCID: PMC4791256 DOI: 10.18632/oncotarget.6018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/17/2015] [Indexed: 01/15/2023] Open
Abstract
Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS.
Collapse
Affiliation(s)
- Rebeca Kawahara
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Gabriela V Meirelles
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Henry Heberle
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil
| | - Romênia R Domingues
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Daniela C Granato
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Sami Yokoo
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Rafael R Canevarolo
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil.,Centro Infantil Boldrini, Campinas, Brazil
| | - Flavia V Winck
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| | - Ana Carolina P Ribeiro
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Thaís Bianca Brandão
- Instituto do Câncer do Estado de São Paulo, Octavio Frias de Oliveira, São Paulo, Brazil
| | - Paulo R Filgueiras
- Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Karen S P Cruz
- Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - José Alexandre Barbuto
- Instituto de Ciências Biomédicas, Departamento de Imunologia, Universidade de São Paulo, USP, São Paulo, Brazil
| | - Ronei J Poppi
- Instituto de Química, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Rosane Minghim
- Instituto de Ciências Matemáticas e de Computação, Universidade de São Paulo, USP, São Carlos, Brazil
| | - Guilherme P Telles
- Instituto de Computação, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil
| | - Felipe Paiva Fonseca
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Jay W Fox
- W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA
| | - Alan R Santos-Silva
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Ricardo D Coletta
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas, UNICAMP, Piracicaba, Brazil
| | - Nicholas E Sherman
- W. M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, Virginia, USA
| | - Adriana F Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, CNPEM, Campinas, Brazil
| |
Collapse
|
20
|
Proteome Profiling of Urinary Exosomes Identifies Alpha 1-Antitrypsin and H2B1K as Diagnostic and Prognostic Biomarkers for Urothelial Carcinoma. Sci Rep 2016; 6:34446. [PMID: 27686150 PMCID: PMC5043375 DOI: 10.1038/srep34446] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/14/2016] [Indexed: 11/09/2022] Open
Abstract
MALDI-TOF spectrometry has not been used for urinary exosome analysis. We used it for determining UC biomarkers. From 2012 to 2015, we enrolled 129 consecutive patients with UC and 62 participants without UC. Exosomes from their urine were isolated, and analyzed through MALDI-TOF spectrometry. Immunohistochemical (IHC) analysis of another 122 UC and 26 non-UC tissues was conducted to verify the discovered biomarkers. Two peaks at m/z 5593 (fragmented peptide of alpha-1-antitrypsin; sensitivity, 50.4%; specificity, 96.9%) and m/z 5947 (fragmented peptide of histone H2B1K sensitivity, 62.0%; specificity, 92.3%) were identified as UC diagnosis exosome biomarkers. UC patients with detectable histone H2B1K showed 2.29- and 3.11-fold increased risks of recurrence and progression, respectively, compared with those with nondetectable histone H2B1K. Verification results of IHC staining revealed significantly higher expression of alpha 1-antitrypsin (p = 0.038) and H2B1K (p = 0.005) in UC tissues than in normal tissues. The expression of alpha 1-antitrypsin and H2B1K in UC tissues was significantly correlated with UC grades (p < 0.05). Urinary exosome proteins alpha 1-antitrypsin and histone H2B1K, which are identified through MALDI-TOF analysis, could facilitate rapid diagnosis and prognosis of UC.
Collapse
|
21
|
Kumar D, Bansal G, Narang A, Basak T, Abbas T, Dash D. Integrating transcriptome and proteome profiling: Strategies and applications. Proteomics 2016; 16:2533-2544. [PMID: 27343053 DOI: 10.1002/pmic.201600140] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/12/2016] [Accepted: 06/23/2016] [Indexed: 12/17/2022]
Abstract
Discovering the gene expression signature associated with a cellular state is one of the basic quests in majority of biological studies. For most of the clinical and cellular manifestations, these molecular differences may be exhibited across multiple layers of gene regulation like genomic variations, gene expression, protein translation and post-translational modifications. These system wide variations are dynamic in nature and their crosstalk is overwhelmingly complex, thus analyzing them separately may not be very informative. This necessitates the integrative analysis of such multiple layers of information to understand the interplay of the individual components of the biological system. Recent developments in high throughput RNA sequencing and mass spectrometric (MS) technologies to probe transcripts and proteins made these as preferred methods for understanding global gene regulation. Subsequently, improvements in "big-data" analysis techniques enable novel conclusions to be drawn from integrative transcriptomic-proteomic analysis. The unified analyses of both these data types have been rewarding for several biological objectives like improving genome annotation, predicting RNA-protein quantities, deciphering gene regulations, discovering disease markers and drug targets. There are different ways in which transcriptomics and proteomics data can be integrated; each aiming for different research objectives. Here, we review various studies, approaches and computational tools targeted for integrative analysis of these two high-throughput omics methods.
Collapse
Affiliation(s)
- Dhirendra Kumar
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA
| | - Gourja Bansal
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA
| | - Ankita Narang
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA
| | - Trayambak Basak
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India
| | - Tahseen Abbas
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India
| | - Debasis Dash
- G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, New Delhi, INDIA. , .,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, New Delhi, India. ,
| |
Collapse
|
22
|
Vu Van D, Heberling U, Wirth MP, Fuessel S. Validation of the diagnostic utility of urinary midkine for the detection of bladder cancer. Oncol Lett 2016; 12:3143-3152. [PMID: 27899974 PMCID: PMC5103912 DOI: 10.3892/ol.2016.5040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 07/12/2016] [Indexed: 01/06/2023] Open
Abstract
As it has been demonstrated previously that midkine (also known as neurite growth-promoting factor 2) protein levels in urine of bladder cancer (BCa) patients are increased compared to healthy controls, the present study validated the diagnostic utility of midkine in an independent patient cohort and compared the observed values with voided urine cytology (VUC), which is the current reference standard for non-invasive diagnosis of BCa. Voided urine samples were prospectively collected from 92 BCa patients and 70 control subjects. Protein levels of midkine were assessed using a commercially available enzyme-linked immunosorbent assay and normalized to urinary creatinine. The diagnostic performance of urinary midkine was evaluated by receiver operating characteristic curves. The best combinations of sensitivities and specificities were determined by Youden's Index. Midkine concentrations were significantly elevated in urine samples from BCa patients compared to controls (P<0.001; Mann-Whitney U Test). The level of midkine was associated with disease progression, with the highest concentrations in urine specimens of patients with pT1 and ≥pT2a, as well as high-grade tumors (P<0.001; Mann-Whitney U test). Sensitivities of urinary midkine and VUC were 69.7 and 87.6%, respectively. The corresponding specificities for midkine and VUC were 77.9 and 87.7%, respectively. The combined use of VUC and midkine improved the sensitivity to 93.3%, but reduced the specificity to 66.2%. Despite its reduced discriminatory power for low-grade and low-stage BCa, urinary midkine can be utilized for the identification of high-grade pT1 and ≥pT2a tumors. This means that midkine may potentially be suitable for the identification of patients with high risk BCa.
Collapse
Affiliation(s)
- Dana Vu Van
- Department of Urology, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Ulrike Heberling
- Department of Urology, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Manfred P Wirth
- Department of Urology, Technische Universität Dresden, D-01307 Dresden, Germany
| | - Susanne Fuessel
- Department of Urology, Technische Universität Dresden, D-01307 Dresden, Germany
| |
Collapse
|
23
|
Site-specific characterization of N-linked glycosylation in human urinary glycoproteins and endogenous glycopeptides. Glycoconj J 2016; 33:937-951. [PMID: 27234710 DOI: 10.1007/s10719-016-9677-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 12/19/2022]
Abstract
Glycosylation is a very important post-translational modification involved in various cellular processes, such as cell adhesion, signal transduction and immune response. Urine is a rich source of glycoproteins and attractive biological fluid for biomarker discovery, owing to its availability, ease of collection, and correlation with pathophysiology of diseases. Although the urinary proteomics have been explored previously, the urinary glycoproteome characterization remains challenging requiring the development and optimization of analytical and bioinformatics methods for protein glycoprofiling. This study describes the high confident identification of 472 unique N-glycosylation sites covering 256 urinary glycoproteins. Besides, 202 unique N-glycosylation sites were identified in low molecular weight endogenous glycopeptides, which belong to 90 glycoproteins. Global site-specific characterization of the N-linked glycan heterogeneity was achieved by intact glycopeptide analysis, revealing 303 unique glycopeptides most of them displaying complex/hybrid glycans composed by sialic acid and fucose. These datasets consist in a valuable resource of glycoproteins and N-glycosylation sites found in healthy human urine that can be further explored in different disorders, in which the N-linked glycosylation may be aberrant.
Collapse
|
24
|
Ishige T, Nishimura M, Satoh M, Fujimoto M, Fukuyo M, Semba T, Kado S, Tsuchida S, Sawai S, Matsushita K, Togawa A, Matsubara H, Kaneda A, Nomura F. Combined Secretomics and Transcriptomics Revealed Cancer-Derived GDF15 is Involved in Diffuse-Type Gastric Cancer Progression and Fibroblast Activation. Sci Rep 2016; 6:21681. [PMID: 26892343 PMCID: PMC4759594 DOI: 10.1038/srep21681] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/27/2016] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer is classified into two subtypes, diffuse and intestinal. The diffuse-type gastric cancer (DGC) has poorer prognosis, and the molecular pathology is not yet fully understood. The purpose of this study was to identify functional secreted molecules involved in DGC progression. We integrated the secretomics of six gastric cancer cell lines and gene expression analysis of gastric cancer tissues with publicly available microarray data. Hierarchical clustering revealed characteristic gene expression differences between diffuse- and intestinal-types. GDF15 was selected as a functional secreted molecule owing to high expression only in fetal tissues. Protein expression of GDF15 was higher in DGC cell lines and tissues. Serum levels of GDF15 were significant higher in DGC patients as compared with healthy individuals and chronic gastritis patients, and positively correlated with wall invasion and lymph node metastasis. In addition, the stimulation of GDF15 on NIH3T3 fibroblast enhanced proliferation and up-regulated expression of extracellular matrix genes, which were similar to TGF-β stimulation. These results indicate that GDF15 contributes to fibroblast activation. In conclusion, this study revealed that GDF15 may be a novel functional secreted molecule for DGC progression, possibly having important roles for cancer progression via the affecting fibroblast function, as well as TGF-β.
Collapse
Affiliation(s)
- Takayuki Ishige
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoi Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Mamoru Satoh
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Mai Fujimoto
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshihisa Semba
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Sayaka Kado
- Center for Analytical Instrumentation, Chiba University, Chiba, Japan
| | - Sachio Tsuchida
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Setsu Sawai
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Kazuyuki Matsushita
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| | - Akira Togawa
- Department of Surgery, Toyo Municipal Hospital, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumio Nomura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Clinical Proteomics Research Center, Chiba University Hospital, Chiba, Japan
| |
Collapse
|
25
|
Bryan RT. Cell adhesion and urothelial bladder cancer: the role of cadherin switching and related phenomena. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140042. [PMID: 25533099 DOI: 10.1098/rstb.2014.0042] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cadherins are mediators of cell-cell adhesion in epithelial tissues. E-cadherin is a known tumour suppressor and plays a central role in suppressing the invasive phenotype of cancer cells. However, the abnormal expression of N- and P-cadherin ('cadherin switching', CS) has been shown to promote a more invasive and m̀alignant phenotype of cancer, with P-cadherin possibly acting as a key mediator of invasion and metastasis in bladder cancer. Cadherins are also implicated in numerous signalling events related to embryonic development, tissue morphogenesis and homeostasis. It is these wide ranging effects and the serious implications of CS that make the cadherin cell adhesion molecules and their related pathways strong candidate targets for the inhibition of cancer progression, including bladder cancer. This review focuses on CS in the context of bladder cancer and in particular the switch to P-cadherin expression, and discusses other related molecules and phenomena, including EpCAM and the development of the cancer stem cell phenotype.
Collapse
Affiliation(s)
- Richard T Bryan
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
26
|
Tilki D, Zlotta AR. Utility of urine biomarkers. Bladder Cancer 2015. [DOI: 10.1002/9781118674826.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
27
|
Bergman N, Bergquist J. Recent developments in proteomic methods and disease biomarkers. Analyst 2015; 139:3836-51. [PMID: 24975697 DOI: 10.1039/c4an00627e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic methodologies for identification and analysis of biomarkers have gained more attention during recent years and have evolved rapidly. Identification and detection of disease biomarkers are important to foresee outbreaks of certain diseases thereby avoiding surgery and other invasive and expensive medical treatments for patients. Thus, more research into discovering new biomarkers and new methods for faster and more accurate detection is needed. It is often difficult to detect and measure biomarkers because of their low concentrations and the complexity of their respective matrices. Therefore it is hard to find and validate methods for accurate screening methods suitable for clinical use. The most recent developments during the last three years and also some historical considerations of proteomic methodologies for identification and validation of disease biomarkers are presented in this review.
Collapse
Affiliation(s)
- Nina Bergman
- Analytical Chemistry, BMC, Department of Chemistry, Uppsala University, Sweden.
| | | |
Collapse
|
28
|
Arul AB, Byambadorj M, Han NY, Park JM, Lee H. Development of an Automated, High-throughput Sample Preparation Protocol for Proteomics Analysis. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10338] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Albert-Baskar Arul
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
| | | | - Na-Young Han
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
| | - Jong Moon Park
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
| | - Hookeun Lee
- Lee Gil Ya Cancer and Diabetes Institute; Gachon University; Incheon Republic of Korea
- Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy; Gachon University; Incheon 406-799 Republic of Korea
- Gachon Medical Research Institute; Gil Medical Center; Incheon 405-760 Republic of Korea
| |
Collapse
|
29
|
Chen CL, Chung T, Wu CC, Ng KF, Yu JS, Tsai CH, Chang YS, Liang Y, Tsui KH, Chen YT. Comparative Tissue Proteomics of Microdissected Specimens Reveals Novel Candidate Biomarkers of Bladder Cancer. Mol Cell Proteomics 2015; 14:2466-78. [PMID: 26081836 DOI: 10.1074/mcp.m115.051524] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Indexed: 12/22/2022] Open
Abstract
More than 380,000 new cases of bladder cancer are diagnosed worldwide, accounting for ∼150,200 deaths each year. To discover potential biomarkers of bladder cancer, we employed a strategy combining laser microdissection, isobaric tags for relative and absolute quantitation labeling, and liquid chromatography-tandem MS (LC-MS/MS) analysis to profile proteomic changes in fresh-frozen bladder tumor specimens. Cellular proteins from four pairs of surgically resected primary bladder cancer tumor and adjacent nontumorous tissue were extracted for use in two batches of isobaric tags for relative and absolute quantitation experiments, which identified a total of 3220 proteins. A DAVID (database for annotation, visualization and integrated discovery) analysis of dysregulated proteins revealed that the three top-ranking biological processes were extracellular matrix organization, extracellular structure organization, and oxidation-reduction. Biological processes including response to organic substances, response to metal ions, and response to inorganic substances were highlighted by up-expressed proteins in bladder cancer. Seven differentially expressed proteins were selected as potential bladder cancer biomarkers for further verification. Immunohistochemical analyses showed significantly elevated levels of three proteins-SLC3A2, STMN1, and TAGLN2-in tumor cells compared with noncancerous bladder epithelial cells, and suggested that TAGLN2 could be a useful tumor tissue marker for diagnosis (AUC = 0.999) and evaluating lymph node metastasis in bladder cancer patients. ELISA results revealed significantly increased urinary levels of both STMN1 and TAGLN2 in bladder cancer subgroups compared with control groups. In comparisons with age-matched hernia urine specimens, urinary TAGLN2 in bladder cancer samples showed the largest fold change (7.13-fold), with an area-under-the-curve value of 0.70 (p < 0.001, n = 205). Overall, TAGLN2 showed the most significant overexpression in individual bladder cancer tissues and urine specimens, and thus represents a potential biomarker for noninvasive screening for bladder cancer. Our findings highlight the value of bladder tissue proteome in providing valuable information for future validation studies of potential biomarkers in urothelial carcinoma.
Collapse
Affiliation(s)
- Chien-Lun Chen
- From the ‡Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; §School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ting Chung
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‖Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kwai-Fong Ng
- **Department of Pathology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jau-Song Yu
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Han Tsai
- ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ying Liang
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Ke-Hung Tsui
- From the ‡Department of Urology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; §School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ting Chen
- ¶Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; ‡‡Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; §§Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
30
|
Frantzi M, Latosinska A, Flühe L, Hupe MC, Critselis E, Kramer MW, Merseburger AS, Mischak H, Vlahou A. Developing proteomic biomarkers for bladder cancer: towards clinical application. Nat Rev Urol 2015; 12:317-30. [PMID: 26032553 DOI: 10.1038/nrurol.2015.100] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Clinical use of proteomic biomarkers has the potential to substantially improve the outcomes of patients with bladder cancer. An unmet clinical need evidently exists for noninvasive biomarkers, which might enable improvements in both the diagnosis and prognosis of patients with bladder cancer, as well as improved monitoring of patients for the presence of recurrence. Urine is considered the optimal noninvasive source of proteomic biomarkers in patients with bladder cancer. Currently, a number of single-protein biomarkers have been detected in urine and tissue using a variety of proteomic techniques, each having specific conceptual considerations and technical implications. Promising preclinical data are available for several of these proteins; however, the combination of single urinary proteins into multimarker panels might better encompass the molecular heterogeneity of bladder cancer within this patient population, and prove more effective in clinical use.
Collapse
Affiliation(s)
- Maria Frantzi
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece
| | - Leif Flühe
- Mosaiques Diagnostics GmbH, Rotenburger Strasse 20, 30659 Hannover, Germany
| | - Marie C Hupe
- Department of Urology and Urological Oncology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Elena Critselis
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece
| | - Mario W Kramer
- Department of Urology and Urological Oncology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Axel S Merseburger
- Department of Urology and Urological Oncology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Harald Mischak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Avenue, Glasgow G12 8TA, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, 4 Soranou Ephessiou Street, 115 27 Athens, Greece
| |
Collapse
|
31
|
Kageyama S, Isono T, Iwaki H, Hanada E, Tomita K, Yoshida T, Yoshiki T, Kawauchi A. Proteome research in urothelial carcinoma. Int J Urol 2015; 22:621-8. [DOI: 10.1111/iju.12793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/01/2015] [Accepted: 03/18/2015] [Indexed: 01/10/2023]
Affiliation(s)
| | - Takahiro Isono
- Central Research Laboratory; Shiga University of Medical Science; Otsu Shiga
| | - Hideaki Iwaki
- Department of Urology; Shiga University of Medical Science
| | - Eiki Hanada
- Department of Urology; Shiga University of Medical Science
| | - Keiji Tomita
- Department of Urology; Shiga University of Medical Science
| | | | - Tatsuhiro Yoshiki
- Department of Clinical Oncology; Kyoto Pharmaceutical University; Kyoto Japan
| | | |
Collapse
|
32
|
Soukup V, Kalousová M, Capoun O, Sobotka R, Breyl Z, Pešl M, Zima T, Hanuš T. Panel of Urinary Diagnostic Markers for Non-Invasive Detection of Primary and Recurrent Urothelial Urinary Bladder Carcinoma. Urol Int 2015; 95:56-64. [PMID: 25662337 DOI: 10.1159/000368166] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/04/2014] [Indexed: 11/19/2022]
Abstract
OBJECTIVES To determine the combination of urinary protein markers for noninvasive detection of primary and recurrent urothelial bladder carcinomas. METHODS Urinary concentrations of 27 biomarkers (NSE, ATT, AFABP, Resistin, Midkine, Clusterin, Uromodulin, ZAG2, HSP27, HSP 60, NCAM1/CD56, Angiogenin, Calreticulin, Chromogranin A, CEACAM1, CXCL1, IL13Ra2, Progranulin, VEGFA, CarbAnhydIX, Annexin-V, TIM4, Galectin1, Cystatin B, Synuclein G, ApoA1 and ApoA2) were assessed by enzyme-linked immunosorbent assay or by electrochemiluminiscence immunoassay. RESULTS During the primary diagnostics, a group of 70 patients with primary occurrence of bladder cancer and 49 healthy control subjects were compared. For this clinical situation, the most accurate combination proved to be the combination of cytology with markers Midkine and Synuclein G (sensitivity 91.8%, specificity 97.5%). During the monitoring of patients with non-muscle invasive bladder cancer (NMIBC), a group of 44 patients with cancer recurrence was compared with the group of 61 patients with a history of NMIBC without current disease. For this clinical situation, the most accurate combination proved to be the combination of cytology and erythrocytes count in urine sediment with markers Midkine, ZAG2, CEACAM1, and Synuclein G (sensitivity 92.68%, specificity 90.16%). A lower accuracy of the diagnostic panel and the necessity to use more markers in the case of recurrence was connected with a different structure of patients. CONCLUSIONS Multi-marker test can significantly improve the bladder cancer detection both during the primary diagnostics and monitoring of patients with NMIBC. This outcome should result in other, larger studies.
Collapse
Affiliation(s)
- Viktor Soukup
- Department of Urology, General University Hospital and The First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Yu Y, Suh MJ, Sikorski P, Kwon K, Nelson KE, Pieper R. Urine sample preparation in 96-well filter plates for quantitative clinical proteomics. Anal Chem 2014; 86:5470-7. [PMID: 24797144 PMCID: PMC4045327 DOI: 10.1021/ac5008317] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/05/2014] [Indexed: 01/03/2023]
Abstract
Urine is an important, noninvasively collected body fluid source for the diagnosis and prognosis of human diseases. Liquid chromatography mass spectrometry (LC-MS) based shotgun proteomics has evolved as a sensitive and informative technique to discover candidate disease biomarkers from urine specimens. Filter-aided sample preparation (FASP) generates peptide samples from protein mixtures of cell lysate or body fluid origin. Here, we describe a FASP method adapted to 96-well filter plates, named 96FASP. Soluble urine concentrates containing ~10 μg of total protein were processed by 96FASP and LC-MS resulting in 700-900 protein identifications at a 1% false discovery rate (FDR). The experimental repeatability, as assessed by label-free quantification and Pearson correlation analysis for shared proteins among replicates, was high (R ≥ 0.97). Application to urinary pellet lysates which is of particular interest in the context of urinary tract infection analysis was also demonstrated. On average, 1700 proteins (±398) were identified in five experiments. In a pilot study using 96FASP for analysis of eight soluble urine samples, we demonstrated that protein profiles of technical replicates invariably clustered; the protein profiles for distinct urine donors were very different from each other. Robust, highly parallel methods to generate peptide mixtures from urine and other body fluids are critical to increase cost-effectiveness in clinical proteomics projects. This 96FASP method has potential to become a gold standard for high-throughput quantitative clinical proteomics.
Collapse
Affiliation(s)
- Yanbao Yu
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Moo-Jin Suh
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Patricia Sikorski
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Keehwan Kwon
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Karen E. Nelson
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Rembert Pieper
- The J.
Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, United States
| |
Collapse
|
34
|
Chen CD, Wang CL, Yu CJ, Chien KY, Chen YT, Chen MC, Chang YS, Wu CC, Yu JS. Targeted proteomics pipeline reveals potential biomarkers for the diagnosis of metastatic lung cancer in pleural effusion. J Proteome Res 2014; 13:2818-29. [PMID: 24787432 DOI: 10.1021/pr4012377] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability to discriminate lung cancer malignant pleural effusion (LC-MPE) from benign pleural effusion has profound implications for the therapy and prognosis of lung cancer. Here, we established a pipeline to verify potential biomarkers for this purpose. In the discovery phase, label-free quantification was performed for the proteome profiling of exudative pleural effusion in order to select 34 candidate biomarkers with significantly elevated levels in LC-MPE. In the verification phase, signature peptides for 34 candidates were first confirmed by accurate inclusion mass screening (AIMS). To quantify the candidates in PEs, multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope-labeled standards (SIS) peptides was performed for the 34 candidate biomarkers using the QconCAT approach for the generation of the SIS peptides. The results of the MRM assay were used to prioritize candidates based on their discriminatory power in 82 exudative PE samples. The five potential biomarkers (ALCAM, CDH1, MUC1, SPINT1, and THBS4; AUC > 0.7) and one three-marker panel (SPINT1/SVEP1/THBS4; AUC = 0.95) were able to effectively differentiate LC-MPE from benign PE. Collectively, these results demonstrate that our pipeline is a feasible platform for verifying potential biomarkers for human diseases.
Collapse
Affiliation(s)
- Chi-De Chen
- Graduate Institute of Biomedical Sciences, ‡Department of Cell and Molecular Biology, §Department of Biomedical Sciences, ∥Department of Public Health and Biostatistics Consulting Center, and ⊥Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University , Taoyuan 33302, Taiwan
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Frantzi M, Bhat A, Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 2014; 3:7. [PMID: 24679154 PMCID: PMC3994249 DOI: 10.1186/2001-1326-3-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/06/2014] [Indexed: 12/11/2022] Open
Abstract
Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
Collapse
Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
36
|
Sigdel TK, Nicora CD, Hsieh SC, Dai H, Qian WJ, Camp DG, Sarwal MM. Optimization for peptide sample preparation for urine peptidomics. Clin Proteomics 2014; 11:7. [PMID: 24568099 PMCID: PMC3944950 DOI: 10.1186/1559-0275-11-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 12/10/2013] [Indexed: 11/10/2022] Open
Abstract
Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput ‘peptidomics’ methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regards to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements that it hampers both the identification of peptides and the depth of the peptidomics read when utilizing LC-MS based peptidome analysis. We report on a novel adaptation of the standard solid phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. Expense and time requirements were comparable for both SPE and mSPE, but more interfering contaminants from the urine matrix were evident in the SPE preparations (e.g., clogging of the LC-MS columns, yellowish background coloration of prepared samples due to retained urobilin, lower peptide yields) when compared to the mSPE method. When we compared data from technical replicates of 4 runs, the mSPE method provided significantly improved efficiencies for the preparation of samples from urine (e.g., mSPE peptide identification 82% versus 18% with SPE; p = 8.92E-05). Additionally, peptide identifications, when applying the mSPE method, highlighted the biology of differential activation of urine peptidases during acute renal transplant rejection with distinct laddering of specific peptides, which was obscured for most proteins when utilizing the conventional SPE method. In conclusion, the mSPE method was found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis due to the optimized sample clean up that provided improved experimental inference from the confidently identified peptides.
Collapse
Affiliation(s)
| | | | | | | | | | - David G Camp
- California Pacific Medical Center Research Institute, 475 Brannan St,, Ste 220, San Francisco, CA 9410, USA.
| | | |
Collapse
|
37
|
Bryan RT, Shimwell NJ, Wei W, Devall AJ, Pirrie SJ, James ND, Zeegers MP, Cheng KK, Martin A, Ward DG. Urinary EpCAM in urothelial bladder cancer patients: characterisation and evaluation of biomarker potential. Br J Cancer 2013; 110:679-85. [PMID: 24292452 PMCID: PMC3915119 DOI: 10.1038/bjc.2013.744] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/11/2013] [Accepted: 11/05/2013] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Epithelial cell adhesion molecule is overexpressed in bladder tumours and released from bladder cancer cells in vitro. We test the hypotheses that urinary EpCAM could act as a biomarker for primary bladder cancer detection and risk stratification. METHODS Epithelial cell adhesion molecule was measured by ELISA in urine from 607 patients with primary bladder tumours and in urine from 53 non-cancer controls. Mann-Whitney tests and ROC analyses were used to determine statistical significance and discrimination between non-cancer controls and different stages and grades of disease. Multivariable modelling and Kaplan-Meier analyses were used to determine prognostic significance. The structure of urinary EpCAM was investigated by western blotting and mass spectrometry. RESULTS Urinary EpCAM levels increase with stage and grade of bladder cancer. Alongside grade and stage, elevated urinary EpCAM is an independent indicator of poor prognosis with a hazard ratio of 1.76 for bladder cancer-specific mortality. The soluble form of EpCAM in urine is the extracellular domain generated by cleavage between ala243 and gly244. Further studies are required to define the influence of other urinary tract malignancies and benign urological conditions on urinary EpCAM. CONCLUSION The extracellular domain of EpCAM is shed into urine by bladder tumours. Urinary EpCAM is a strong indicator of bladder cancer-specific survival, and may be useful within a multi-marker panel for disease detection or as a stand-alone marker to prioritise the investigation and treatment of patients. The mechanisms and effects of EpCAM cleavage in bladder cancer are worthy of further investigation, and may identify novel therapeutic targets.
Collapse
Affiliation(s)
- R T Bryan
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - N J Shimwell
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - W Wei
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - A J Devall
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - S J Pirrie
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - N D James
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - M P Zeegers
- 1] School of Health and Population Sciences, University of Birmingham, Birmingham B15 2TT, UK [2] Department of Complex Genetics, Cluster of Genetics and Cell Biology, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - K K Cheng
- School of Health and Population Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - A Martin
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - D G Ward
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| |
Collapse
|
38
|
Eissa S, Matboli M. Integrated technologies in the post-genomic era for discovery of bladder cancer urinary markers. World J Clin Urol 2013; 2:20-31. [DOI: 10.5410/wjcu.v2.i3.20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/10/2013] [Accepted: 11/21/2013] [Indexed: 02/06/2023] Open
Abstract
The incidence of bladder cancer (BC) continues to rise with high recurrence and mortality rate, especially in the past three decades. The development of accurate and successful BC treatment relies mainly on early diagnosis. BC is a heterogeneous disease reflected by the presence of many potential biomarkers associated with different disease phenotypes. Nowadays, cystoscopy and urinary cytology are considered the gold standard diagnostic tools for BC. There are many limitations to cystoscopy including being invasive, labor-intensive and carcinoma in situ of the bladder may easily be missed. Urinary cytology is still a noninvasive technique with high accuracy in high-grade BC with a median sensitivity of 35%. Furthermore, the need for a sensitive, specific, non invasive, easily accessible BC biomarker is a major clinical need. The field of urinary BC biomarkers discovery is still a rapidly evolving discipline in which more recent technologies are evaluated and often optimized if they are not clinically significant to the urologists. Most of the current strategies for BC urinary biomarker detection depend on integration of information gleaned from the fields of genomics, transcriptomics, proteomics, epigenetics, metabolomics and bionanotechnology. Effort is currently being made to identify the most potentially beneficial urinary biomarkers. The purpose of this review is to summarize and explore the efficacy of gathering the information revealed from the cooperation of different omic strategies that paves the way towards various urinary markers discovery for screening, diagnosis and prognosis of human BC.
Collapse
|