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Öztürk M, Salih B, Eroğlu AE, Boyaci E. Development and functionalization of electrospun fiber coated thin film microextraction devices for rapid mass spectrometric determination of biologically important polar molecules. J Pharm Biomed Anal 2024; 243:116074. [PMID: 38437785 DOI: 10.1016/j.jpba.2024.116074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 03/06/2024]
Abstract
Rapid diagnosis of diseases is one of the challenging areas in clinical research. From the analytical chemist's perspective, the main challenges are isolating the compounds from the bio-specimen and lengthy analysis times. In this regard, solid phase microextraction offers a platform to address the abovementioned challenges. Moreover, its sharp tip-thin film geometry, known as coated blade spray (CBS), can enhance the extraction and act as an ionization source in direct mass spectrometric analysis. In this study, a new CBS device specifically designed for polar analytes was prepared and optimized to determine urinary metabolites. For this purpose, polyacrylonitrile (PAN) was selected as a base polymer as it can be electrospun to form a nanofibrous structure, and it can be modified with weak ion exchange moieties to interact with polar analytes. Following the electrospinning of PAN, hydrolysis was optimized, and conditions leading to sufficient extraction enhancement without dissolving the polymer were obtained when probes were treated with 5.0 M of NaOH for 2.5 h. Using the coated blades prepared as explained, the evaluation of various extraction conditions showed that 5 min is sufficient for equilibrium extraction. In addition, the solution's ionic strength and pH significantly affect the extraction. Optimum sorption was obtained at no salt added and pH 7.0 conditions. The CBS-MS optimization showed that 10.0 µL of ACN/MeOH/H2O (40:40:20, v/v/v) with formic acid kept for 15 seconds on the blade before voltage application leads to the highest signal. The limits of quantification of the analytes are between 50 and 100 ng/mL.
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Affiliation(s)
- Merve Öztürk
- Department of Chemistry, Middle East Technical University, Ankara 06800, Türkiye
| | - Bekir Salih
- Department of Chemistry, Hacettepe University, Ankara 06800, Türkiye
| | - Ahmet E Eroğlu
- Department of Chemistry, İzmir Institute of Technology Urla, İzmir 35430, Türkiye
| | - Ezel Boyaci
- Department of Chemistry, Middle East Technical University, Ankara 06800, Türkiye.
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Li F, Wang P, Ye J, Xie G, Yang J, Liu W. Serum EZH2 is a novel biomarker for bladder cancer diagnosis and prognosis. Front Oncol 2024; 14:1303918. [PMID: 38476362 PMCID: PMC10927824 DOI: 10.3389/fonc.2024.1303918] [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: 09/29/2023] [Accepted: 01/19/2024] [Indexed: 03/14/2024] Open
Abstract
Objective The primary objective of this study was to examine the levels of serum EZH2 in patients diagnosed with bladder cancer, and subsequently evaluate its potential as a biomarker for both the diagnosis and prognosis of bladder cancer. Methods Blood samples were obtained from 115 bladder cancer patients and 115 healthy persons. We measured the EZH2 concentrations in the serum of these subjects via enzyme-linked immunosorbent assay (ELISA). To assess the diagnostic performance of serum EZH2 in detecting bladder cancer, we plotted receiver operating characteristic (ROC) curves and calculated their corresponding area under the curve (AUC). We also used the Cox regression model and log-rank test to investigate the correlation between EZH2 levels and clinicopathological characteristics, and survival rates of bladder cancer patients. Results Serum EZH2 levels were significantly higher in bladder cancer patients when compared to those in healthy persons. Serum EZH2 levels exhibited a significant correlation with TNM stage, lymph node metastasis, muscle invasion, and tumor size. At a cutoff value of 8.23 ng/mL, EZH2 was able to differentiate bladder cancer patients from healthy persons, with an AUC of 0.87, a sensitivity of 81.31%, and a specificity of 78.42%. High EZH2 levels correlated with poor overall survival rates and progression-free survival rates of bladder cancer patients. Conclusions Serum EZH2 levels were elevated in bladder cancer patients, and patients with higher serum EZH2 levels exhibited a poorer prognosis. This indicates that serum EZH2 could be a novel biomarker for bladder cancer diagnosis and prognosis. Such findings could improve the prognosis of bladder cancer patients by facilitating early detection and continuous monitoring.
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Affiliation(s)
- Feng Li
- Department of Urology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Pengqiao Wang
- Department of Medical Administration, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Jun Ye
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guizhou Medical University, Kaili, China
| | - Guoping Xie
- Department of Urology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Jinfeng Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Wei Liu
- Department of Oncology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
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Guan X, Lu D, Chen Z, Wang Z, Zhou G, Fan Y. Non-invasive detection of bladder cancer via microfluidic immunoassay of the protein biomarker NMP22. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023. [PMID: 37377044 DOI: 10.1039/d3ay00664f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Bladder cancer (BC) is a malignant tumor that occurs in the bladder mucosa and has a high morbidity and mortality rate. Early diagnosis means that cystoscopy-aided imaging is invasive and pricey. Microfluidic immunoassay enables noninvasive detection of early BC. However, its clinical applications are limited due to the poor internal design and hydrophobic surface of polydimethylsiloxane (PDMS) chip. This study aims to design a PDMS chip with right-moon capture arrays and prepare a hydrophilic surface by APTES with different concentrations (PDMS-three-step: O2 plasma-5-98% APTES), which facilitates early detection of BC with enhanced sensitivity. Simulations showed that the right-moon arrays in the capture chamber reduced the flow velocity and shear stress of the target molecule NMP22, improving the capture performance of the chip. PDMS-three-step surface was measured by X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), contact angle, and antibody immobilization. The results displayed that the contact angle of PDMS-three-step remained in the range of 40° to 50° even after 30 days of exposure to air, leading to a more stable hydrophilic surface. The effectiveness of the PDMS chip was assessed via the quantitative immunoassay of the protein marker NMP22 and its sensitivity analysis to urine. After the assessment, the LOD of NMP22 was 2.57 ng mL-1, and the sensitivity was 86.67%, which proved that the PDMS chip was effective. Thus, this study provided a novel design and modification method of the microfluidic chip for the early detection of BC.
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Affiliation(s)
- Xiali Guan
- School of Biological Science and Medical Engineering, Beihang University, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing 100083, China.
| | - Da Lu
- School of Biological Science and Medical Engineering, Beihang University, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing 100083, China.
| | - Zhigang Chen
- School of Biological Science and Medical Engineering, Beihang University, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing 100083, China.
| | - Zhuya Wang
- School of Biological Science and Medical Engineering, Beihang University, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing 100083, China.
| | - Gang Zhou
- School of Biological Science and Medical Engineering, Beihang University, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing 100083, China.
- Shenzhen Research Institute, Beihang University, Shenzhen, 518057, China
| | - Yubo Fan
- School of Biological Science and Medical Engineering, Beihang University, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing 100083, China.
- Shenzhen Research Institute, Beihang University, Shenzhen, 518057, China
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Giribaldi G, Filippini C, Viberti C, Khadjavi A, Finesso N, Ulliers D, Turini S, Bressan BE, Pecoraro F, Prato M, Allione A, Bellis MD, Montefusco G, Bonomessi G, Allasia M, Matullo G, Soria F, Gontero P. Combination of urinary fibrinogen β-chain and tyrosine-phosphorylated proteins for the detection of bladder cancer. Future Sci OA 2021; 7:FSO758. [PMID: 34737890 PMCID: PMC8558871 DOI: 10.2144/fsoa-2021-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022] Open
Abstract
Aim: To evaluate the performance of urinary fibrinogen β-chain (FBC) – either alone or associated with urinary tyrosine-phosphorylated proteins (UPY) – as bladder cancer (BCa) diagnostic biomarker. Materials & methods: 164 subjects were tested. Results: Significantly different FBC and UPY levels were found between BCa patients and controls, as well as between low-grade and high-grade cancers. The diagnostic accuracy was 0.84 for FBC and 0.87 for UPY. The combination of FBC and UPY improved the accuracy to 0.91. The addition of clinical variables (age, gender, and smoking habit) to FBC and UPY into a model for BCa prediction significantly improved the accuracy to 0.99. The combination of FBC and UPY adjusted for clinical variables associates with the highest sensitivity and good specificity. Conclusion: Urinary FBC and UPY could be used as biomarkers for BCa diagnosis. This research has developed and validated a highly accurate predictive model for BCa diagnosis based on the combination of two urinary biomarkers, fibrinogen β-chain (FBC), and urinary tyrosine-phosphorylated proteins (UPY), and some clinical variables (age, gender and smoking habit). If the preliminary promising results will be confirmed by external validations and prospective trials in selected clinical scenarios, our model could be transferred to clinical practice for screening of high-risk population.
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Affiliation(s)
| | | | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Amina Khadjavi
- Department of Oncology, University of Turin, Turin, Italy
| | - Nicole Finesso
- Department of Oncology, University of Turin, Turin, Italy
| | | | - Stefano Turini
- Department of Neurosciences, University of Turin, Turin, Italy
| | | | | | - Mauro Prato
- Department of Neurosciences, University of Turin, Turin, Italy
| | | | - Matteo De Bellis
- Division of Urology, Department of Surgical Sciences, AOU Città della Salute e della Scienza, Torino School of Medicine, Turin, Italy
| | - Gabriele Montefusco
- Division of Urology, Department of Surgical Sciences, AOU Città della Salute e della Scienza, Torino School of Medicine, Turin, Italy
| | - Giulia Bonomessi
- Division of Urology, Department of Surgical Sciences, AOU Città della Salute e della Scienza, Torino School of Medicine, Turin, Italy
| | - Marco Allasia
- Division of Urology, Department of Surgical Sciences, AOU Città della Salute e della Scienza, Torino School of Medicine, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy.,SC Medical Genetics, AOU Città della Salute e della Scienza, Turin, Italy
| | - Francesco Soria
- Division of Urology, Department of Surgical Sciences, AOU Città della Salute e della Scienza, Torino School of Medicine, Turin, Italy
| | - Paolo Gontero
- Division of Urology, Department of Surgical Sciences, AOU Città della Salute e della Scienza, Torino School of Medicine, Turin, Italy
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Mason J, Hasnain Z, Miranda G, Gill K, Djaladat H, Desai M, Newton PK, Gill IS, Kuhn P. Prediction of Metastatic Patterns in Bladder Cancer: Spatiotemporal Progression and Development of a Novel, Web-based Platform for Clinical Utility. EUR UROL SUPPL 2021; 32:8-18. [PMID: 34667954 PMCID: PMC8505202 DOI: 10.1016/j.euros.2021.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
Background Bladder cancer (BCa), the sixth commonest cancer in the USA, is highly lethal when metastatic. Spatial and temporal patterns of patient-specific metastatic spread are deemed random and unpredictable. Whether BCa metastatic patterns can be quantified and predicted more accurately is unknown. Objective To develop a web-based calculator for forecasting metastatic progression in individual BCa patients. Design setting and participants We used a prospectively collected longitudinal dataset of 3503 BCa patients who underwent a radical cystectomy following diagnosis and were enrolled continuously. We subdivided patients by their pathologic subgroup stages of organ confined (OC), extravesical (EV), and node positive (N+). We illustrated metastatic pathway progression using color-coded, circular, tree ring diagrams. We created a dynamical, data-visualization, web-based platform that displays temporal, spatial, and Markov modeling figures with predictive capability. Outcome measurements and statistical analysis Patients underwent history and physical examination, serum studies, and liver function tests. Surveillance follow-up included computed tomography scans, chest x-rays, and radiographic evaluation of the reservoir and upper tracts, with bone scans performed only if clinically indicated. Outcomes were measured by time to clinical recurrence and overall or progression-free survival. Results and limitations Metastases developed in 29% of patients (n = 812; median follow-up 15.3 yr), with 5-yr overall survival of 20.2%, compared with 78.6% in those without metastases (n = 1983; median follow-up 10.9 yr). The three commonest sites of spread at the time of first progression were bone (n = 214; 26.4%), pelvis (n = 194; 23.9%), and lung (n = 194; 23.9%). The order and frequency of these sites vary when divided by pathologic subgroup stages of OC (lung [n = 65; 25.1%], urethra [n = 45; 17.4%], and bone [n = 29; 11.2%]), EV (pelvis [n = 63; 33.0%], bone [n = 45; 23.6%], and lung [n = 29; 15.2%]), and N+ (bone [n = 111; 30.7%], retroperitoneum [n = 70; 19.3%], and pelvis [n = 60; 16.6%]). Markov chain modeling indicated a higher probability of spread from bladder to bone (15.5%), pelvis (14.7%), and lung (14.2%). Conclusions Our web-based calculator allows real-time analyses in the clinic based on individual patient-specific demographic and cancer data elements. For contrasting subgroups, the models indicated differences in Markov transition probabilities. Spatiotemporal patterns of BCa metastasis and sites of spread indicated underlying organotropic mechanisms in the prediction of response. This recognition opens the possibility of organ site-specific therapeutic targeting in the oligometastatic BCa setting. In the precision medicine era, visualization of complex, time-resolved clinical data will enhance management of postoperative metastatic BCa patients. Patient summary We developed a web-based calculator to forecast metastatic progression for individual bladder cancer (BCa) patients, based on the clinical and demographic information obtained at diagnosis. This can help in predicting disease status and survival, and improving management in postoperative metastatic BCa patients. Take Home Message Future pathways of metastatic progression for individual bladder cancer patients can be determined based on currently available clinical and demographic information obtained at diagnosis. In focused subgroups of patients, these metastatic spread patterns can also portend disease status and survival.
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Affiliation(s)
- Jeremy Mason
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zaki Hasnain
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Gus Miranda
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Karanvir Gill
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Hooman Djaladat
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mihir Desai
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Paul K Newton
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Mathematics, University of Southern California, Los Angeles, CA, USA
| | - Inderbir S Gill
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peter Kuhn
- USC Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.,Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Mathematics, University of Southern California, Los Angeles, CA, USA.,Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
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Chao Y, Ou Q, Shang J. Expression and prognostic value of SULT1A2 in bladder cancer. Exp Ther Med 2021; 22:779. [PMID: 34055078 PMCID: PMC8145616 DOI: 10.3892/etm.2021.10211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/02/2021] [Indexed: 12/31/2022] Open
Abstract
Sulfotransferase Family 1A Member 2 (SULT1A2) is a protein coding gene. Several studies have reported that SULT1A2 may have a chemical carcinogenic effect if expressed as a functional protein. The present study aimed to investigate the expression and potential role of SULT1A2 in bladder cancer (BC). Data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases were used to analyze SULT1A2 expression in BC. In addition, reverse transcription-quantitative PCR and western blot analyses were performed to detect SULT1A2 expression in BC cells and tissues. Immunohistochemistry analysis was performed on 100 formalin-fixed, paraffin-embedded BC tissues and corresponding adjacent normal bladder tissues (ANBTs) to verify SULT1A2 expression and determine the clinical significance of SULT1A2 in BC. Gene set enrichment analysis (GSEA) was performed to determine the potential biological processes and internal molecular mechanisms. The results demonstrated that SULT1A2 was highly expressed in BC tissues compared with ANBTs. Furthermore, high SULT1A2 expression was significantly associated with the staging of BC. Analyses of TCGA datasets and BC tissue microarray indicated that high SULT1A2 expression was significantly associated with a favorable overall survival in patients with BC. In addition, GSEA revealed pathways, diseases and biological processes associated with SULT1A2. Taken together, the results of the present study suggest that SULT1A2 acts as an oncogene in BC, and thus may serve as a biomarker for tumor staging and prognosis in patients with BC.
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Affiliation(s)
- Yinghui Chao
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Qifeng Ou
- Laboratory of Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Jin Shang
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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Tran PHL, Xiang D, Nguyen TNG, Tran TTD, Chen Q, Yin W, Zhang Y, Kong L, Duan A, Chen K, Sun M, Li Y, Hou Y, Zhu Y, Ma Y, Jiang G, Duan W. Aptamer-guided extracellular vesicle theranostics in oncology. Theranostics 2020; 10:3849-3866. [PMID: 32226524 PMCID: PMC7086349 DOI: 10.7150/thno.39706] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022] Open
Abstract
In the past decade, the study of exosomes, nanosized vesicles (50-150 nm) released into the extracellular space via the fusion of multivesicular bodies with the plasma membrane, has burgeoned with impressive achievements in theranostics applications. These nanosized vesicles have emerged as key players in homeostasis and in the pathogenesis of diseases owing to the variety of the cargos they can carry, the nature of the molecules packaged inside the vesicles, and the robust interactions between exosomes and target cells or tissues. Accordingly, the development of exosome-based liquid biopsy techniques for early disease detection and for monitoring disease progression marks a new era of precision medicine in the 21st century. Moreover, exosomes possess intrinsic properties - a nanosized structure and unique "homing effects" - that make them outstanding drug delivery vehicles. In addition, targeted exosome-based drug delivery systems can be further optimized using active targeting ligands such as nucleic acid aptamers. Indeed, the aptamers themselves can function as therapeutic and/or diagnostic tools based on their attributes of unique target-binding and non-immunogenicity. This review aims to provide readers with a current picture of the research on exosomes and aptamers and their applications in cancer theranostics, highlighting recent advances in their transition from the bench to the clinic.
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Affiliation(s)
- Phuong H-L Tran
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Dongxi Xiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, 77 Avenue Louise Pasteur, Boston, MA 02115, USA
| | - Tuong N-G Nguyen
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Thao T-D Tran
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Qian Chen
- Translational Medical Center, The Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing, China, 100853
| | - Wang Yin
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Yumei Zhang
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Lingxue Kong
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Andrew Duan
- School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, 27 Rainforest Walk, Clayton VIC 3800, Australia
| | - Kuisheng Chen
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, He'nan Key Laboratory of Tumor Pathology, Zhengzhou 450052, China
| | - Miomio Sun
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, He'nan Key Laboratory of Tumor Pathology, Zhengzhou 450052, China
| | - Yong Li
- Cancer Care Centre, St George Hospital, Kogarah, and St George and Sutherland Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Yingchun Hou
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, Shaanxi 710119, China
| | - Yimin Zhu
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yongchao Ma
- Clinical School, Luohe Medical College, 148, Daxue Road, Luohe City, Henan Province, 462000, China
| | - Guoqin Jiang
- Department of General Surgery, Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, P.R. China, 215004
| | - Wei Duan
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
- GenePharma-Deakin Joint Laboratory of Aptamer Medicine, Suzhou 215123, China and Waurn Ponds, Victoria 3216, Australia
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Molecular subtyping of cancer and nomination of kinase candidates for inhibition with phosphoproteomics: Reanalysis of CPTAC ovarian cancer. EBioMedicine 2018; 40:305-317. [PMID: 30594550 PMCID: PMC6412074 DOI: 10.1016/j.ebiom.2018.12.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 11/27/2022] Open
Abstract
Background Molecular subtyping of cancer aimed to predict patient overall survival (OS) and nominate drug targets for patient treatments is central to precision oncology. Owing to the rapid development of phosphoproteomics, we can now measure thousands of phosphoproteins in human cancer tissues. However, limited studies report how to analyse the complex phosphoproteomic data for cancer subtyping and to nominate druggable kinase candidates. Findings In this work, we reanalysed the phosphoproteomic data of high-grade serous ovarian cancer (HGSOC) from the Clinical Proteomic Tumour Analysis Consortium (CPTAC). Our analysis classified HGSOC into 5 major subtypes that were associated with different OS and appeared to be more accurate than that achieved with protein profiling. We provided a workflow to identify 29 kinases whose increased activities in tumours are associated with poor survival. The altered kinase signalling landscape of HGSOC included the PI3K/AKT/mTOR, cell cycle and MAP kinase signalling pathways. We also developed a “patient-specific” hierarchy of clinically actionable kinases and selected kinase inhibitors by considering kinase activation and kinase inhibitor selectivity. Interpretation Our study offered a global phosphoproteomics data analysis workflow to aid in cancer molecular subtyping, determining phosphorylation-based cancer hallmarks and facilitating nomination of kinase inhibition in cancer.
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Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018; 20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra-many of which likely harbour PTMs-through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
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Affiliation(s)
- Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Chitra Joseph
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
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10
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Chen Y, Liu L, Guo Z, Wang Y, Yang Y, Liu X. Lost expression of cell adhesion molecule 1 is associated with bladder cancer progression and recurrence and its overexpression inhibited tumor cell malignant behaviors. Oncol Lett 2018; 17:2047-2056. [PMID: 30719104 PMCID: PMC6350208 DOI: 10.3892/ol.2018.9845] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 03/17/2017] [Indexed: 02/06/2023] Open
Abstract
Cell adhesion molecule 1 (CADM1) regulates cell-cell adhesion and an altered expression level is associated with tumorigenesis and progression. The present study assessed CADM1 expression level in 84 bladder tissues to investigate the association with clinicopathological parameters from bladder cancer patients and then investigated the effects of CADM1 overexpression on T24 bladder cancer cells in vitro. The results demonstrated that expression level of CADM1 protein was significantly reduced in bladder cancer tissues (0.26±0.14) compared with in normal bladder mucosa (0.69±0.092; P<0.01), and methylation of CADM1 promoter was responsible for silencing of CADM1 protein expression and significantly associated with tumor size, recurrence, pathology classification and clinical stage (P<0.05). Overexpression of CADM1 protein inhibited tumor cell proliferation, reduced tumor cell invasion capacity and induced tumor cell apoptosis in vitro. At the gene level, CADM1 expression level upregulated caspase-3 activity and expression of Bax and p27 protein and downregulated levels of B cell lymphoma-2, cyclinD1, cyclinE1 and cyclin dependent kinase 2 proteins. Furthermore, overexpression of CADM1 regulated the expression level of epithelial to mesenchymal transition markers, including increased expression level of E-cadherin and β-catenin, whereas it decreased the levels of Vimentin. The present study demonstrated that lost expression of CADM1 protein may exert an essential role in the development and progression of bladder cancer and suggested that CADM1 may be a novel molecular target for the control of this disease in clinical practice.
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Affiliation(s)
- Yegang Chen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China.,Tianjin Institute of Urology, Tianjin 300211, P.R. China
| | - Li Liu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China.,Tianjin Institute of Urology, Tianjin 300211, P.R. China
| | - Zhanjun Guo
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China.,Tianjin Institute of Urology, Tianjin 300211, P.R. China
| | - Yi Wang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China.,Tianjin Institute of Urology, Tianjin 300211, P.R. China
| | - Yongjiao Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China.,Tianjin Institute of Urology, Tianjin 300211, P.R. China
| | - Xiaoqiang Liu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China.,Tianjin Institute of Urology, Tianjin 300211, P.R. China
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11
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Chemometrics-aided Metabolic Fingerprint Method Applied in Bladder Cancer Stages Differentiating. DIGITAL CHINESE MEDICINE 2018. [DOI: 10.1016/s2589-3777(19)30028-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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