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Liu L, Zhang M, Cui N, Liu W, Di G, Wang Y, Xi X, Li H, Shen Z, Gu M, Wang Z, Jiang S, Liu B. Integration of single-cell RNA-seq and bulk RNA-seq to construct liver hepatocellular carcinoma stem cell signatures to explore their impact on patient prognosis and treatment. PLoS One 2024; 19:e0298004. [PMID: 38635528 PMCID: PMC11025768 DOI: 10.1371/journal.pone.0298004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/11/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Liver hepatocellular carcinoma (LIHC) is a prevalent form of primary liver cancer. Research has demonstrated the contribution of tumor stem cells in facilitating tumor recurrence, metastasis, and treatment resistance. Despite this, there remains a lack of established cancer stem cells (CSCs)-associated genes signatures for effectively predicting the prognosis and guiding the treatment strategies for patients diagnosed with LIHC. METHODS The single-cell RNA sequencing (scRNA-seq) and bulk RNA transcriptome data were obtained based on public datasets and computerized firstly using CytoTRACE package and One Class Linear Regression (OCLR) algorithm to evaluate stemness level, respectively. Then, we explored the association of stemness indicators (CytoTRACE score and stemness index, mRNAsi) with survival outcomes and clinical characteristics by combining clinical information and survival analyses. Subsequently, weighted co-expression network analysis (WGCNA) and Cox were applied to assess mRNAsi-related genes in bulk LIHC data and construct a prognostic model for LIHC patients. Single-sample gene-set enrichment analysis (ssGSEA), Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and Tumor Immune Estimation Resource (TIMER) analysis were employed for immune infiltration assessment. Finally, the potential immunotherapeutic response was predicted by the Tumor Immune Dysfunction and Exclusion (TIDE), and the tumor mutation burden (TMB). Additionally, pRRophetic package was applied to evaluate the sensitivity of high and low-risk groups to common chemotherapeutic drugs. RESULTS A total of four genes (including STIP1, H2AFZ, BRIX1, and TUBB) associated with stemness score (CytoTRACE score and mRNAsi) were identified and constructed a risk model that could predict prognosis in LIHC patients. It was observed that high stemness cells occurred predominantly in the late stages of LIHC and that poor overall survival in LIHC patients was also associated with high mRNAsi scores. In addition, pathway analysis confirmed the biological uniqueness of the two risk groups. Personalized treatment predictions suggest that patients with a low risk benefited more from immunotherapy, while those with a high risk group may be conducive to chemotherapeutic drugs. CONCLUSION The current study developed a novel prognostic risk signature with genes related to CSCs, which provides novel ideas for the diagnosis, prognosis and treatment of LIHC.
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Affiliation(s)
- Lixia Liu
- Department of Ultrasound and Hebei Key Laboratory of Precise Imaging of Inflammation Related Tumors, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Meng Zhang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Naipeng Cui
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Wenwen Liu
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Guixin Di
- Department of Ultrasound, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Yanan Wang
- Department of Pathology, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Xin Xi
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Hao Li
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Zhou Shen
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Miaomiao Gu
- Department of Ultrasound, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Zichao Wang
- Department of Ultrasound, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Shan Jiang
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071052, China
| | - Bin Liu
- Central Laboratory, Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, Affiliated Hospital of Hebei University, Baoding, 071052, China
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Varzaru VB, Eftenoiu AE, Vlad DC, Vlad CS, Moatar AE, Popescu R, Cobec IM. The Influence of Tumor-Specific Markers in Breast Cancer on Other Blood Parameters. Life (Basel) 2024; 14:458. [PMID: 38672729 PMCID: PMC11051489 DOI: 10.3390/life14040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/17/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Breast cancer is the most frequently diagnosed cancer among women, responsible for the highest number of cancer-related deaths worldwide. There is limited data available related to serum tumor markers in breast cancer and other blood parameters or other glandular laboratory parameters. This study aims to evaluate the correlation of tumor-specific markers for breast cancer with other blood parameters and how these correlations could impact clinical management. MATERIAL AND METHOD This retrospective study represents a data analysis from 1 January 2020 to 31 May 2023, in the County Hospital of Timisoara, Romania. We reviewed all the cases where, in the laboratory analyses, the serum tumor specific biomarkers for breast cancer were analyzed. RESULTS A statistical analysis was performed in order to identify a possible relationship between CA 15-3 and the various biomarkers and blood parameters included in the present study. Values were classified according to reference ranges. The tests revealed no statistically significant associations between CA 15-3 values and the levels of CA125 (χ2(1) = 1.852, p = 0.174), CEA (χ2(1) = 1.139, p = 0.286), AFP (Fisher's exact test, p = 0.341), fT4 (Fisher's exact test, p = 0.310), TSH (Fisher's exact test, p = 0.177), or PTH (Fisher's exact test, p = 0.650). CONCLUSION The findings indicate a lack of strong correlation between CA 15-3 and CA125, CEA, AFP, thyroid function markers, or PTH within this cohort.
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Affiliation(s)
- Vlad Bogdan Varzaru
- Doctoral School, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- ANAPATMOL Research Center, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Anca-Elena Eftenoiu
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy Bucharest, 050474 Bucharest, Romania
| | - Daliborca Cristina Vlad
- Department of Pharmacology, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Emergency County Clinical Hospital Pius Brinzeu Timisoara, 300723 Timisoara, Romania
| | - Cristian Sebastian Vlad
- Department of Pharmacology, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
| | - Aurica Elisabeta Moatar
- ANAPATMOL Research Center, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Clinic of Internal Medicine-Cardiology, Klinikum Freudenstadt, 72250 Freudenstadt, Germany
| | - Roxana Popescu
- ANAPATMOL Research Center, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Emergency County Clinical Hospital Pius Brinzeu Timisoara, 300723 Timisoara, Romania
| | - Ionut Marcel Cobec
- ANAPATMOL Research Center, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy Timisoara, 300041 Timisoara, Romania
- Clinic of Obstetrics and Gynecology, Klinikum Freudenstadt, 72250 Freudenstadt, Germany
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Cancer proteomics: Application of case studies in diverse cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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4
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Weaver C, Bin Satter K, Richardson KP, Tran LKH, Tran PMH, Purohit S. Diagnostic and Prognostic Biomarkers in Renal Clear Cell Carcinoma. Biomedicines 2022; 10:biomedicines10112953. [PMID: 36428521 PMCID: PMC9687861 DOI: 10.3390/biomedicines10112953] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Renal clear cell carcinoma (ccRCC) comprises over 75% of all renal tumors and arises in the epithelial cells of the proximal convoluted tubule. Molecularly ccRCC is characterized by copy number alterations (CNAs) such as the loss of chromosome 3p and VHL inactivation. Additional driver mutations (SETD2, PBRM1, BAP1, and others) promote genomic instability and tumor cell metastasis through the dysregulation of various metabolic and immune-response pathways. Many researchers identified mutation, gene expression, and proteomic signatures for early diagnosis and prognostics for ccRCC. Despite a tremendous influx of data regarding DNA alterations, gene expression, and protein expression, the incorporation of these analyses for diagnosis and prognosis of RCC into the clinical application has not been implemented yet. In this review, we focused on the molecular changes associated with ccRCC development, along with gene expression and protein signatures, to emphasize the utilization of these molecular profiles in clinical practice. These findings, in the context of machine learning and precision medicine, may help to overcome some of the barriers encountered for implementing molecular profiles of tumors into the diagnosis and treatment of ccRCC.
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Affiliation(s)
- Chaston Weaver
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
| | - Khaled Bin Satter
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
| | - Katherine P. Richardson
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Interdisciplinary Health Science, College of Allied Health Sciences, Augusta University, 1120 15th St., Augusta, GA 30912, USA
| | - Lynn K. H. Tran
- Department of Urology, Baylor College of Medicine, Houston, TX 76798, USA
| | - Paul M. H. Tran
- Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Sharad Purohit
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Interdisciplinary Health Science, College of Allied Health Sciences, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Undergraduate Health Professionals, College of Allied Health Sciences, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Department of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, 1120 15th St., Augusta, GA 30912, USA
- Correspondence:
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Alhammad R. Bioinformatics Identification of TUBB as Potential Prognostic Biomarker for Worse Prognosis in ERα-Positive and Better Prognosis in ERα-Negative Breast Cancer. Diagnostics (Basel) 2022; 12:diagnostics12092067. [PMID: 36140469 PMCID: PMC9498198 DOI: 10.3390/diagnostics12092067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Tubulin β class I gene (TUBB) is highly expressed in various cancers and plays several roles in carcinogenesis. However, the prognostic value of TUBB in breast cancer remains to be investigated. GEPIA and Breast Cancer Gene-Expression Miner were used to explore TUBB expression in breast cancer patients. Kaplan–Meier Plotter was used to assess the relationship between TUBB expression and several prognostic indicators including overall, distant metastasis-free, and relapse-free survival in ERα-positive and ERα-negative breast cancer. The genes that correlate with TUBB in ERα-positive and ERα-negative breast cancer were explored and the pathways were investigated using GSCA. The correlation between TUBB and several gene markers of immune cells was explored using GEPIA. ERα-positive breast cancer patients with increased TUBB showed worse prognosis, possibly through the activation of the TSC/mTOR pathway, whereas ERα-negative breast cancer patients with increased TUBB mRNA showed better prognosis. Significant positive correlations were observed between TUBB and gene markers of immune cells in ERα-positive breast cancer patients, whereas significant negative correlations were observed in ERα-negative breast cancer patients. The analysis revealed that TUBB might be considered as a predictive biomarker for worse prognosis in ERα-positive and better prognosis in ERα-negative breast cancer.
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Affiliation(s)
- Rashed Alhammad
- Department of Pharmacology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
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The Role of Circulating Biomarkers in the Oncological Management of Metastatic Renal Cell Carcinoma: Where Do We Stand Now? Biomedicines 2021; 10:biomedicines10010090. [PMID: 35052770 PMCID: PMC8773056 DOI: 10.3390/biomedicines10010090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/25/2021] [Accepted: 12/29/2021] [Indexed: 01/08/2023] Open
Abstract
Renal cell carcinoma (RCC) is an increasingly common malignancy that can progress to metastatic renal cell carcinoma (mRCC) in approximately one-third of RCC patients. The 5-year survival rate for mRCC is abysmally low, and, at the present time, there are sparingly few if any effective treatments. Current surgical and pharmacological treatments can have a long-lasting impact on renal function, as well. Thus, there is a compelling unmet need to discover novel biomarkers and surveillance methods to improve patient outcomes with more targeted therapies earlier in the course of the disease. Circulating biomarkers, such as circulating tumor DNA, noncoding RNA, proteins, extracellular vesicles, or cancer cells themselves potentially represent a minimally invasive tool to fill this gap and accelerate both diagnosis and treatment. Here, we discuss the clinical relevance of different circulating biomarkers in metastatic renal cell carcinoma by clarifying their potential role as novel biomarkers of response or resistance to treatments but also by guiding clinicians in novel therapeutic approaches.
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Lakshminarayanan H, Rutishauser D, Schraml P, Moch H, Bolck HA. Liquid Biopsies in Renal Cell Carcinoma-Recent Advances and Promising New Technologies for the Early Detection of Metastatic Disease. Front Oncol 2020; 10:582843. [PMID: 33194717 PMCID: PMC7656014 DOI: 10.3389/fonc.2020.582843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) displays a highly varying clinical progression, from slow growing localized tumors to very aggressive metastatic disease (mRCC). Almost a third of all patients with ccRCC show metastatic dissemination at presentation while another third develop metastasis during the course of the disease. Survival rates of mRCC patients remain low despite the development of novel targeted treatment regimens. Biomarkers indicating disease progression could help to define its aggressive potential and thus guide patient management. However, molecular markers that can reliably assess metastatic dissemination and disease recurrence in ccRCC have not been recommended for clinical practice to date. Liquid biopsies could provide an attractive and non-invasive method to determine the risk of recurrence or metastatic dissemination during follow-up and thus assist the search for surveillance biomarkers in ccRCC tumors. A wide spectrum of circulating molecules have already shown considerable potential for ccRCC diagnosis and prognostication. In this review, we outline state of the art of the key circulating analytes such as cfDNA, cfRNA, proteins, and exosomes that may serve as biomarkers for the longitudinal monitoring of ccRCC progression to metastasis. Moreover, we address some of the prevailing limitations in the past approaches and present promising adoptable technologies that could help to pursue the implementation of liquid biopsies as a prognostic tool for mRCC.
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Affiliation(s)
| | | | | | - Holger Moch
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Hella A. Bolck
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
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Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer. Cancers (Basel) 2020; 12:cancers12092428. [PMID: 32867043 PMCID: PMC7564506 DOI: 10.3390/cancers12092428] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The traditional approach in identifying cancer related protein biomarkers has focused on evaluation of a single peptide/protein in tissue or circulation. At best, this approach has had limited success for clinical applications, since multiple pathological tumor pathways may be involved during initiation or progression of cancer which diminishes the significance of a single candidate protein/peptide. Emerging sensitive proteomic based technologies like liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics can provide a platform for evaluating serial serum or plasma samples to interrogate secreted products of tumor–host interactions, thereby revealing a more “complete” repertoire of biological variables encompassing heterogeneous tumor biology. However, several challenges need to be met for successful application of serum/plasma based proteomics. These include uniform pre-analyte processing of specimens, sensitive and specific proteomic analytical platforms and adequate attention to study design during discovery phase followed by validation of discovery-level signatures for prognostic, predictive, and diagnostic cancer biomarker applications. Abstract Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
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Clark DJ, Zhang H. Proteomic approaches for characterizing renal cell carcinoma. Clin Proteomics 2020; 17:28. [PMID: 32742246 PMCID: PMC7391522 DOI: 10.1186/s12014-020-09291-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 12/24/2022] Open
Abstract
Renal cell carcinoma is among the top 15 most commonly diagnosed cancers worldwide, comprising multiple sub-histologies with distinct genomic, proteomic, and clinicopathological features. Proteomic methodologies enable the detection and quantitation of protein profiles associated with the disease state and have been explored to delineate the dysregulated cellular processes associated with renal cell carcinoma. In this review we highlight the reports that employed proteomic technologies to characterize tissue, blood, and urine samples obtained from renal cell carcinoma patients. We describe the proteomic approaches utilized and relate the results of studies in the larger context of renal cell carcinoma biology. Moreover, we discuss some unmet clinical needs and how emerging proteomic approaches can seek to address them. There has been significant progress to characterize the molecular features of renal cell carcinoma; however, despite the large-scale studies that have characterized the genomic and transcriptomic profiles, curative treatments are still elusive. Proteomics facilitates a direct evaluation of the functional modules that drive pathobiology, and the resulting protein profiles would have applications in diagnostics, patient stratification, and identification of novel therapeutic interventions.
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Affiliation(s)
- David J. Clark
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University, Baltimore, MD 21231 USA
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Yin XH, Yu LP, Zhao XH, Li QM, Liu XP, He L. Development and validation of a 4-gene combination for the prognostication in lung adenocarcinoma patients. J Cancer 2020; 11:1940-1948. [PMID: 32194805 PMCID: PMC7052877 DOI: 10.7150/jca.37003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023] Open
Abstract
Objective: To identify a multi-gene prognostic factor in patients with lung adenocarcinoma (LUAD). Materials and methods Prognosis-related genes were screened in the TCGA-LUAD cohort. Then, patients in this cohort were randomly separated into training set and test set. Least absolute shrinkage and selection operator (LASSO) regression was performed to the penalized the Cox proportional hazards regression (CPH) model on the training set, and a prognostication combination based on the result of LASSO analysis was developed. By performing Kaplan-Meier curve analysis, univariate and multivariable CPH model on the overall survival (OS) as well as recurrence free survival (RFS), the prognostication performance of the multigene combination were evaluated. Moreover, we constructed a nomogram and performed decision curve analysis to evaluate the clinical application of the multigene combination. Results We obtained 99 prognosis-related genes and screened out a 4-gene combination (including CIDEC, ZFP3, DKK1, and USP4) according to the LASSO analysis. The results of survival analyses suggested that patients in the 4-gene combination low-risk group had better OS and RFS than those in the 4-gene combination high-risk group. The 4-gene mentioned was demonstrated to be independent prognostic factor of patients with LUAD in the training set(OS, HR=11.962, P<0.001; RFS, HR=9.281, P<0.001) and test set (OS, HR=5.377, P=0.003; RFS, HR=2.949, P=0.104). More importantly, its prognosis performance was well in the validation set (OS, HR=0.955, P=0.002; RFS, HR=1.042, P<0.001). Conclusions We introduced a 4-gene combination which could predict the survival of LUAD patients and might be an independent prognostic factor in LUAD.
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Affiliation(s)
- Xiao-Hong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei province, China.,Wuhan University School of Health Sciences, Wuhan, Hubei province, China
| | - Li-Ping Yu
- Wuhan University School of Health Sciences, Wuhan, Hubei province, China
| | - Xiao-Hong Zhao
- Wuhan University School of Health Sciences, Wuhan, Hubei province, China
| | - Qin-Mei Li
- Department of Epidemiology, Department of Epidemiology, School of Health Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei province, China
| | - Li He
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei province, China
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Kandil NS, Ghazala RA, El Sharkawy RM, Youssif TA, Noha Abouseda N. Evaluation of Protein Profiling in a Cohort of Egyptian Population with Renal Cell Carcinoma and Benign Kidney Neoplasms. Asian Pac J Cancer Prev 2019; 20:2145-2152. [PMID: 31350978 PMCID: PMC6745217 DOI: 10.31557/apjcp.2019.20.7.2145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Indexed: 12/27/2022] Open
Abstract
Section Title Abdominal imaging leads to the detection of a large number of renal tumors without the ability to distinguish the type of tumor detected. It is necessary to find a precise way to know the type of tumor to determine the appropriate treatment. The use of urine samples for detecting new biomarkers especially proteins has a great potential. In this work we assessed the proteomic profiling difference in a cohort of Egyptian population with renal neoplasms. Methods: This cohort study was conducted on 85 subjects. They were classified as 40 RCC, 15 benign kidney patients, and 30 healthy controls. Morning urine samples were used for peptidome separation using magnetic beads. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) was applied Using FlexControlTM software. Results: Benign tumors were differentiated from controls by 5 integrated peaks, 12 significant and 2 integrated significant peaks, 17:3,418.8 and 25:4,173.41. While RCC were differentiated from benign by 5 integrated, 28 significant and one integrated significant peak. The RCC group was discriminated from the controls by 5 peaks which were integrated from which 1 was integrated and significant (with mass to charge ratio of 12:3,408.97). The three groups showed protein profiles ranging from 1 to 10 kDa. The external validation was performed for the RCC group versus the control reveled sensitivity of 88.7% and specificity of 73.2% by genetic algorithm. Conclusion: Proteomic approach can be used as a sensitive urinary marker differentiating renal masses in an early diagnostic approach.
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Affiliation(s)
- Noha Said Kandil
- Department of Chemical Pathology, Medical Research Institute, Faculty of Medicine, Alexandria University, Egypt.
| | | | - Rania Mohamed El Sharkawy
- Department of Chemical Pathology, Medical Research Institute, Faculty of Medicine, Alexandria University, Egypt.
| | - Tamer Abou Youssif
- Department of Urology, Faculty of Medicine, Alexandria University, Egypt
| | - Noha Noha Abouseda
- Department of Microbiology, Faculty of Medicine, Alexandria University, Egypt
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12
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Identification of salivary peptidomic biomarkers in chronic kidney disease patients undergoing haemodialysis. Clin Chim Acta 2019; 489:154-161. [DOI: 10.1016/j.cca.2018.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/20/2018] [Accepted: 12/06/2018] [Indexed: 11/24/2022]
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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Shi F, Wu H, Qu K, Sun Q, Li F, Shi C, Li Y, Xiong X, Qin Q, Yu T, Jin X, Cheng L, Wei Q, Li Y, She J. Identification of serum proteins AHSG, FGA and APOA-I as diagnostic biomarkers for gastric cancer. Clin Proteomics 2018; 15:18. [PMID: 29719494 PMCID: PMC5925839 DOI: 10.1186/s12014-018-9194-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/18/2018] [Indexed: 12/15/2022] Open
Abstract
Background The development of clinically accessible biomarkers is critical for the early diagnosis of gastric cancer (GC) in patients. High-throughput proteomics techniques could not only effectively generate a serum peptide profile but also provide a new approach to identify potentially diagnostic and prognostic biomarkers for cancer patients. Methods In this study, we aim to identify potentially discriminating serum biomarkers for GC. In the discovery cohort, we screened potential biomarkers using magnetic-bead-based purification and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in 64 samples from 32 GC patients that were taken both pre- and post-operatively and 30 healthy volunteers that served as controls. In the validation cohort, the expression patterns and diagnostic values of serum FGA, AHSG and APOA-I were further confirmed by ELISA in 42 paired GC patients (pre- and post-operative samples from 16 patients with pathologic stage I/II and 26 with stage III/IV), 30 colorectal cancer patients, 30 hepatocellular carcinoma patients, and 28 healthy volunteers. Results ClinProTools software was used and annotated 107 peptides, 12 of which were differentially expressed among three groups (P < 0.0001, fold > 1.5). These 12 peptide peaks were further identified as FGA, AHSG, APOA-I, HBB, TXNRD1, GSPT2 and CAKP5. ELISA data suggested that the serum levels of FGA, AHSG and APOA-I in GC patients were significantly different compared with healthy controls and had favorable diagnostic values for GC patients. Moreover, we found that the serum levels of these three proteins were associated with TNM stages and could reflect tumor burden. Conclusion Our findings suggested that FGA, AHSG and APOA-I might be potential serum biomarkers for GC diagnosis.
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Affiliation(s)
- Feiyu Shi
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Hong Wu
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Kai Qu
- 2Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Qi Sun
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Fanni Li
- 3Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Chengxin Shi
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Yaguang Li
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Xiaofan Xiong
- 4Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiao Tong University Health Science Center, 76 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Qian Qin
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Tianyu Yu
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Xin Jin
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Liang Cheng
- 2Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Qingxia Wei
- 5Department of Developmental and Stem Cell Biology, Hospital for Sick Children, University of Toronto, Toronto, ON M5G0A4 Canada
| | - Yingchao Li
- 6Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
| | - Junjun She
- 1Department of General Surgery, The First Affiliated Hospital of Xi'an Jiao Tong University, 277 Yanta West Road, Xi'an, 710061 Shaanxi China
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15
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MALDI-TOF-MS analysis in discovery and identification of serum proteomic patterns of ovarian cancer. BMC Cancer 2017; 17:472. [PMID: 28683725 PMCID: PMC5501370 DOI: 10.1186/s12885-017-3467-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/30/2017] [Indexed: 12/11/2022] Open
Abstract
Background Due to high mortality and lack of efficient screening, new tools for ovarian cancer (OC) diagnosis are urgently needed. To broaden the knowledge on the pathological processes that occur during ovarian cancer tumorigenesis, protein-peptide profiling was proposed. Methods Serum proteomic patterns in samples from OC patients were obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Eighty nine serum samples (44 ovarian cancer and 45 healthy controls) were pretreated using solid-phase extraction method. Next, a classification model with the most discriminative factors was identified using chemometric algorithms. Finally, the results were verified by external validation on an independent test set of samples. Results Main outcome of this study was an identification of potential OC biomarkers by applying liquid chromatography coupled with tandem mass spectrometry. Application of this novel strategy enabled the identification of four potential OC serum biomarkers (complement C3, kininogen-1, inter-alpha-trypsin inhibitor heavy chain H4, and transthyretin). The role of these proteins was discussed in relation to OC pathomechanism. Conclusions The study results may contribute to the development of clinically useful multi-component diagnostic tools in OC. In addition, identifying a novel panel of discriminative proteins could provide a new insight into complex signaling and functional networks associated with this multifactorial disease. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3467-2) contains supplementary material, which is available to authorized users.
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16
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Li B, Li B, Guo T, Sun Z, Li X, Li X, Wang H, Chen W, Chen P, Qiao M, Xia L, Mao Y. Application Value of Mass Spectrometry in the Differentiation of Benign and Malignant Liver Tumors. Med Sci Monit 2017; 23:1636-1644. [PMID: 28376075 PMCID: PMC5388305 DOI: 10.12659/msm.901064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Differentiation of malignant from benign liver tumors remains a challenging problem. In recent years, mass spectrometry (MS) technique has emerged as a promising strategy to diagnose a wide range of malignant tumors. The purpose of this study was to establish classification models to distinguish benign and malignant liver tumors and identify the liver cancer-specific peptides by mass spectrometry. Material/Methods In our study, serum samples from 43 patients with malignant liver tumors and 52 patients with benign liver tumors were treated with weak cation-exchange chromatography Magnetic Beads (MB-WCX) kits and analyzed by the Matrix-Assisted Laser Desorption Time of Flight Mass Spectrometry (MALDI-TOF-MS). Then we established genetic algorithm (GA), supervised neural networks (SNN), and quick classifier (QC) models to distinguish malignant from benign liver tumors. To confirm the clinical applicability of the established models, the blinded validation test was performed in 50 clinical serum samples. Discriminatory peaks associated with malignant liver tumors were subsequently identified by a qTOF Synapt G2-S system. Results A total of 27 discriminant peaks (p<0.05) in mass spectra of serum samples were found by ClinPro Tools software. Recognition capabilities of the established models were 100% (GA), 89.38% (SNN), and 80.84% (QC); cross-validation rates were 81.67% (GA), 81.11% (SNN), and 86.11% (QC). The accuracy rates of the blinded validation test were 78% (GA), 84% (SNN), and 84% (QC). From the 27 discriminatory peptide peaks analyzed, 3 peaks of m/z 2860.34, 2881.54, and 3155.67 were identified as a fragment of fibrinogen alpha chain, fibrinogen beta chain, and inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4), respectively. Conclusions Our results demonstrated that MS technique can be helpful in differentiation of benign and malignant liver tumors. Fibrinogen and ITIH4 might be used as biomarkers for the diagnosis of malignant liver tumors.
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Affiliation(s)
- Bo Li
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Boan Li
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Tongsheng Guo
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Zhiqiang Sun
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Xiaohan Li
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland).,Graduate Student Team, Medical University of PLA, Beijing, China (mainland)
| | - Xiaoxi Li
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Han Wang
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Weijiao Chen
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Peng Chen
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Mengran Qiao
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Lifang Xia
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland)
| | - Yuanli Mao
- Center for Clinical Laboratory, 302 Hospital of PLA, Beijing, China (mainland).,Graduate Student Team, Medical University of PLA, Beijing, China (mainland)
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17
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Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS. Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures. Mol Cell Proteomics 2017; 16:386-406. [PMID: 28062796 DOI: 10.1074/mcp.m116.063511] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 12/19/2016] [Indexed: 12/11/2022] Open
Abstract
Approximately 800,000 leukemia and lymphoma cases are diagnosed worldwide each year. Burkitt's lymphoma (BL) and chronic lymphocytic leukemia (CLL) are examples of contrasting B-cell cancers; BL is a highly aggressive lymphoid tumor, frequently affecting children, whereas CLL typically presents as an indolent, slow-progressing leukemia affecting the elderly. The B-cell-specific overexpression of the myc and TCL1 oncogenes in mice induce spontaneous malignancies modeling BL and CLL, respectively. Quantitative mass spectrometry proteomics and isobaric labeling were employed to examine the biology underpinning contrasting Eμ-myc and Eμ-TCL1 B-cell tumors. Additionally, the plasma proteome was evaluated using subproteome enrichment to interrogate biomarker emergence and the systemic effects of tumor burden. Over 10,000 proteins were identified (q<0.01) of which 8270 cellular and 2095 plasma proteins were quantitatively profiled. A common B-cell tumor signature of 695 overexpressed proteins highlighted ribosome biogenesis, cell-cycle promotion and chromosome segregation. Eμ-myc tumors overexpressed several methylating enzymes and underexpressed many cytoskeletal components. Eμ-TCL1 tumors specifically overexpressed ER stress response proteins and signaling components in addition to both subunits of the interleukin-5 (IL5) receptor. IL5 treatment promoted Eμ-TCL1 tumor proliferation, suggesting an amplification of IL5-induced AKT signaling by TCL1. Tumor plasma contained a substantial tumor lysis signature, most prominent in Eμ-myc plasma, whereas Eμ-TCL1 plasma contained signatures of immune-response, inflammation and microenvironment interactions, with putative biomarkers in early-stage cancer. These findings provide a detailed characterization of contrasting B-cell tumor models, identifying common and specific tumor mechanisms. Integrated plasma proteomics allowed the dissection of a systemic response and a tumor lysis signature present in early- and late-stage cancers, respectively. Overall, this study suggests common B-cell cancer signatures exist and illustrates the potential of the further evaluation of B-cell cancer subtypes by integrative proteomics.
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Affiliation(s)
- Harvey E Johnston
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton SO16 6YD, UK.,§Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Matthew J Carter
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton SO16 6YD, UK
| | - Kerry L Cox
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton SO16 6YD, UK
| | - Melanie Dunscombe
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton SO16 6YD, UK
| | - Antigoni Manousopoulou
- §Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK.,¶Clinical and Experimental Sciences Unit, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Paul A Townsend
- ‖Molecular and Clinical Cancer Sciences, Paterson Building, Manchester Cancer Research Centre, Manchester Academic Health Science Centre, University of Manchester, Manchester, M20 4BX
| | - Spiros D Garbis
- §Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK.,¶Clinical and Experimental Sciences Unit, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Mark S Cragg
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton SO16 6YD, UK;
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18
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Chinello C, L'imperio V, Stella M, Smith AJ, Bovo G, Grasso A, Grasso M, Raimondo F, Pitto M, Pagni F, Magni F. The proteomic landscape of renal tumors. Expert Rev Proteomics 2016; 13:1103-1120. [PMID: 27748142 DOI: 10.1080/14789450.2016.1248415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids. Expert commentary: Currently, no reliable biomarkers or targets for RCC have been translated into the clinical setting. Moreover, despite the efforts of proteomics and other -omics disciplines, only a small number of them have been observed as shared targets between the different analytical platforms and biological specimens. The difficulty to define a specific molecular pattern for RCC and its subtypes highlights a peculiar profile and a heterogeneity that must be taken into account in future studies.
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Affiliation(s)
- Clizia Chinello
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Vincenzo L'imperio
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Martina Stella
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Andrew James Smith
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Giorgio Bovo
- b Pathology unit , San Gerardo Hospital , Monza , Italy
| | - Angelica Grasso
- c Department of Specialistic Surgical Sciences, Urology unit , Ospedale Maggiore Policlinico Foundation , Milano , Italy
| | - Marco Grasso
- d Department of Urology , San Gerardo Hospital , Monza , Italy
| | - Francesca Raimondo
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Marina Pitto
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Fabio Pagni
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Fulvio Magni
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
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19
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Chen SJ, Lin JH, Yao XD, Peng B, Xu YF, Liu M, Zheng JH. Nrdp1-mediated degradation of BRUCE decreases cell viability and induces apoptosis in human 786-O renal cell carcinoma cells. Exp Ther Med 2016; 12:597-602. [PMID: 27446249 PMCID: PMC4950747 DOI: 10.3892/etm.2016.3356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/30/2016] [Indexed: 12/20/2022] Open
Abstract
Neuregulin receptor degradation protein-1 (Nrdp1) is involved in a plethora of cellular processes and plays an essential role in the development and progression of human cancers. However, its role in renal cell carcinoma (RCC) remains unclear. Therefore, the present study aimed to explore the biological significance of Nrdp1 in RCC. Western blot analyses of tissue samples from 24 patients with primary RCC revealed lower Nrdp1 and higher baculovirus inhibitor of apoptosis repeat-containing ubiquitin-conjugating enzyme (BRUCE) protein levels in RCC tissues compared with adjacent normal tissues. In addition, MTT and apoptosis assays demonstrated that Nrdp1 overexpression resulted in decreased cell viability and enhanced apoptosis in RCC 786-O cells; conversely, Nrdp1 knockdown increased 786-O cell viability and inhibited apoptosis. Further analysis showed that BRUCE downregulation partially attenuated the effects of Nrdp1 knockdown on RCC cell viability and apoptosis. Moreover, an inverse association was obtained between BRUCE and Nrdp1 protein levels. These findings suggest that Nrdp1-mediated degradation of BRUCE decreases cell viability and induces apoptosis in RCC cells, highlighting Nrdp1 as a potential target for RCC treatment.
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Affiliation(s)
- Shao-Jun Chen
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Jian-Hai Lin
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Xu-Dong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Yun-Fei Xu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Min Liu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
| | - Jun-Hua Zheng
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, P.R. China
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20
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Yang J, Xiong X, Liu S, Zhu J, Luo M, Liu L, Zhao L, Qin Y, Song T, Huang C. Identification of novel serum peptides biomarkers for female breast cancer patients in Western China. Proteomics 2016; 16:925-34. [PMID: 26705257 DOI: 10.1002/pmic.201500321] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/19/2015] [Accepted: 12/18/2015] [Indexed: 11/09/2022]
Abstract
This study aimed to identify novel serum peptides biomarkers for female breast cancer (BC) patients. We analyzed the serum proteomic profiling of 247 serum samples from 96 BC patients, 48 additional paired pre- and postoperative BC patients, 39 fibroadenoma patients as benign disease controls, and 64 healthy controls, using magnetic-bead-based separation followed by MALDI-TOF MS. ClinProTools software identified 78 m/z peaks that differed among all analyzed groups, ten peaks were significantly different (P < 0.0001), with Peaks 1-6 upregulated and Peaks 7-10 downregulated in BC. Moreover, three peaks of ten (Peak 1, m/z: 2660.11; Peak 2, m/z: 1061.09; Peak 10, m/z: 1041.25) showed a tendency to return to healthy control values after surgery. And these three peptide biomarkers were identified as FGA605-629, ITIH4 347-356, and APOA2 43-52. Methods used in this study could generate serum peptidome profiles of BC, and provide a new approach to identify potential biomarkers for diagnosis as well as prognosis of this malignancy.
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Affiliation(s)
- Juan Yang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Xiaofan Xiong
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Siyuan Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Jiang Zhu
- Department of Mastopathy, Shaanxi Provincial Tumor Hospital, Xi'an, P. R. China
| | - Mai Luo
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Liying Liu
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Lingyu Zhao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Yannan Qin
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Tusheng Song
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
| | - Chen Huang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Health Science Center, Xi'an, P. R. China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an, P. R. China
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21
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Zhao Y, Liu YN, Li Y, Tian L, Ye X, Cui H, Chang XH. Identification of biomarkers for endometriosis using clinical proteomics. Chin Med J (Engl) 2015; 128:520-7. [PMID: 25673457 PMCID: PMC4836258 DOI: 10.4103/0366-6999.151108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Background: We investigated possible biomarkers for endometriosis (EM) using the ClinProt technique and proteomics methods. Methods: We enrolled 50 patients with EM, 34 with benign ovarian neoplasms and 40 healthy volunteers in this study. Serum proteomic spectra were generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS) combined with weak cationic exchange (WCX) magnetic beads. Possible biomarkers were analyzed by a random and repeat pattern model-validation method that we designed, and ClinProtools software, results were refined using online liquid chromatography-tandem MS. Results: We found a cluster of 5 peptides (4210, 5264, 2660, 5635, and 5904 Da), using 3 peptides (4210, 5904, 2660 Da) to discriminate EM patients from healthy volunteers, with 96.67% sensitivity and 100% specificity. We selected 4210 and 5904 m/z, which differed most between patients with EM and controls, and identified them as fragments of ATP1B4, and the fibrinogen alpha (FGA) isoform 1/2 of the FGA chain precursor, respectively. Conclusions: ClinProt can identify EM biomarkers, which – most notably – distinguish even early-stage or minimal disease. We found 5 stable peaks at 4210, 5264, 2660, 5635, and 5904 Da as potential EM biomarkers, the strongest of which were associated with ATP1B4 (4210 Da) and FGA (5904 Da); this indicates that ATP1B4 and FGA are associated with EM pathogenesis.
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Affiliation(s)
| | | | | | | | | | | | - Xiao-Hong Chang
- Gynecology Oncology Center, Peking University People's Hospital, Beijing 100044, China
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22
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Majer W, Kluzek K, Bluyssen H, Wesoły J. Potential Approaches and Recent Advances in Biomarker Discovery in Clear-Cell Renal Cell Carcinoma. J Cancer 2015; 6:1105-13. [PMID: 26516358 PMCID: PMC4615346 DOI: 10.7150/jca.12145] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/12/2015] [Indexed: 02/06/2023] Open
Abstract
The early diagnosis and monitoring of clear-cell Renal Cell Carcinoma (ccRCC), which is the most common renal malignancy, remains challenging. The late diagnosis and lack of tools that can be used to assess the progression of the disease and metastasis significantly influence the chance of survival of ccRCC patients. Molecular biomarkers have been shown to aid the diagnosis and disease monitoring for other cancers, but such markers are not currently available for ccRCC. Recently, plasma and serum circulating nucleic acids, nucleic acids present in urine, and plasma and urine proteins gained interest in the field of cancer biomarker discovery. Here, we describe the applicability of plasma and urine nucleic acids as cancer biomarkers with a particular focus on DNA, small RNA, and protein markers for ccRCC.
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Affiliation(s)
- Weronika Majer
- 1. Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 61-614 Poznan, Poland, Tel. +4861 829 5832, Fax. +4861 829 5949
| | - Katarzyna Kluzek
- 2. Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 64-614 Poznan, Tel. +4861 829 5832
| | - Hans Bluyssen
- 2. Department of Human Molecular Genetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 64-614 Poznan, Tel. +4861 829 5832
| | - Joanna Wesoły
- 1. Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, University of Adam Mickiewicz, Umultowska 89, 61-614 Poznan, Poland, Tel. +4861 829 5832, Fax. +4861 829 5949
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