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Lin B, Wang K, Yuan Y, Wang Y, Liu Q, Wang Y, Sun J, Wang W, Wang H, Zhou S, Jin K, Zhang M, Lai Y. A novel approach to the analysis of Overall Survival (OS) as response with Progression-Free Interval (PFI) as condition based on the RNA-seq expression data in The Cancer Genome Atlas (TCGA). BMC Bioinformatics 2024; 25:300. [PMID: 39271985 PMCID: PMC11395968 DOI: 10.1186/s12859-024-05897-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/09/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Overall Survival (OS) and Progression-Free Interval (PFI) as survival times have been collected in The Cancer Genome Atlas (TCGA). It is of biomedical interest to consider their dependence in pathway detection and survival prediction. We intend to develop novel methods for integrating PFI as condition based on parametric survival models for identifying pathways associated with OS and predicting OS. RESULTS Based on the framework of conditional probability, we developed a family of frailty-based parametric-models for this purpose, with exponential or Weibull distribution as baseline. We also considered two classes of existing methods with PFI as a covariate. We evaluated the performance of three approaches by analyzing RNA-seq expression data from TCGA for lung squamous cell carcinoma and lung adenocarcinoma (LUNG), brain lower grade glioma and glioblastoma multiforme (GBMLGG), as well as skin cutaneous melanoma (SKCM). Our focus was on fourteen general cancer-related pathways. The 10-fold cross-validation was employed for the evaluation of predictive accuracy. For LUNG, p53 signaling and cell cycle pathways were detected by all approaches. Furthermore, three approaches with the consideration of PFI demonstrated significantly better predictive performance compared to the approaches without the consideration of PFI. For GBMLGG, ten pathways (e.g., Wnt signaling, JAK-STAT signaling, ECM-receptor interaction, etc.) were detected by all approaches. Furthermore, three approaches with the consideration of PFI demonstrated better predictive performance compared to the approaches without the consideration of PFI. For SKCM, p53 signaling pathway was detected only by our Weibull-baseline-based model. And three approaches with the consideration of PFI demonstrated significantly better predictive performance compared to the approaches without the consideration of PFI. CONCLUSIONS Based on our study, it is necessary to incorporate PFI into the survival analysis of OS. Furthermore, PFI is a survival-type time, and improved results can be achieved by our conditional-probability-based approach.
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Affiliation(s)
- Bo Lin
- School of Mathematical Sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Kaipeng Wang
- School of Mathematics and Statistics, Nanjing University of Science and Technology, Nanjing, 210094, Jiangsu, China
| | - Yuan Yuan
- Graduate School of Bengbu Medical College, Bengbu, Anhui, China
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yueguo Wang
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Qingyuan Liu
- School of Mathematics and Physics, Anhui Jianzhu University, Hefei, 230009, Anhui, China
| | - Yulan Wang
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Jian Sun
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Wenwen Wang
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Huanli Wang
- Department of Information Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Shusheng Zhou
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Kui Jin
- Department of Emergency Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Mengping Zhang
- School of Mathematical Sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Yinglei Lai
- School of Mathematical Sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China.
- Department of Statistics, The George Washington University, Washington, DC, USA.
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Ai F, Wang W, Liu S, Zhang D, Yang Z, Liu F. Integrative Proteo-Genomic Analysis for Recurrent Survival Prognosis in Colon Adenocarcinoma. Front Oncol 2022; 12:871568. [PMID: 35847888 PMCID: PMC9281446 DOI: 10.3389/fonc.2022.871568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/09/2022] [Indexed: 12/09/2022] Open
Abstract
Background The survival prognosis is the hallmark of cancer progression. Here, we aimed to develop a recurrence-related gene signature to predict the prognosis of colon adenocarcinoma (COAD). Methods The proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and genomic data from the cancer genomic maps [The Cancer Genome Atlas (TCGA)] dataset were analyzed to identify co-differentially expressed genes (cDEGs) between recurrence samples and non-recurrence samples in COAD using limma package. Functional enrichment analysis, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was conducted. Univariate and multivariate Cox regressions were applied to identify the independent prognostic feature cDEGs and establish the signature whose performance was evaluated by Kaplan–Meier curve, receiver operating characteristic (ROC), Harrell’s concordance index (C-index), and calibration curve. The area under the receiver operating characteristic (ROC) curve (AUROC) and a nomogram were calculated to assess the predictive accuracy. GSE17538 and GSE39582 were used for external validation. Quantitative real-time PCR and Western blot analysis were carried out to validate our findings. Results We identified 86 cDEGs in recurrence samples compared with non-recurrence samples. These genes were primarily enriched in the regulation of carbon metabolic process, fructose and mannose metabolism, and extracellular exosome. Then, an eight-gene-based signature (CA12, HBB, NCF1, KBTBD11, MMAA, DMBT1, AHNAK2, and FBLN2) was developed to separate patients into high- and low-risk groups. Patients in the low-risk group had significantly better prognosis than those in the high-risk group. Four prognostic clinical features, including pathological M, N, T, and RS model status, were screened for building the nomogram survival model. The PCR and Western blot analysis results suggested that CA12 and AHNAK2 were significantly upregulated, while MMAA and DMBT1 were downregulated in the tumor sample compared with adjacent tissues, and in non-recurrent samples compared with non-recurrent samples in COAD. Conclusion These identified recurrence-related gene signatures might provide an effective prognostic predictor and promising therapeutic targets for COAD patients.
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Affiliation(s)
- FeiYan Ai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wenhao Wang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of University of South China, Hengyang, China
| | - Shaojun Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Decai Zhang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhenyu Yang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Fen Liu
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory of Non-Resolving Inflammation and Cancer The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Fen Liu,
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The Prediction of a 3-Protein-Based Model on the Prognosis of Head and Neck Squamous Cell Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2161122. [PMID: 35756403 PMCID: PMC9232309 DOI: 10.1155/2022/2161122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is one of the commonest malignant tumors. Using high-throughput genomic methods, RNA-based diagnostic and prognostic models for HNSCC with potential clinical value have been developed. However, the clinical utility and reproducibility of these models are uncertain. Because the complex regulatory processes occurring after mRNA is transcribed, the abundance of proteins in a cell can never be fully predicted or explained by their corresponding mRNA expression. We aimed to assume and verify a novel protein signature for checking the HNSCC patients' prognosis. Methods The functional proteomic data of 332 HNSCC cases were collected from The Cancer Proteome Atlas (TCPA), and the related follow-up and clinical data were acquired from The Cancer Genome Atlas (TCGA). This study adopted multivariate and univariate Cox regression analysis, Akaike Information Criterion, receiver operating characteristic (ROC) analysis, and Kaplan-Meier method. Results Patients' clinical features in both sets were comparable (all, P > 0.05). The area under the ROC curve (AUC) for the 3-protein signature (X4EBP1_pT37T46, HER3_pY1289, and NF2) in the test set was 0.655 and in the combined cohort (all 332 patients combined) was 0.699. In addition, the 3-protein signature exhibited better predictive value for the survival of HNSCC patients as in comparison with conventional clinical factors like age, gender, tumor stage, and smoking history (TNM stage). Conclusion The 3-protein signature developed in this study exhibits good performance in predicting the overall survival of with HNSCC patients. The 3-protein signature exhibited better predictive value for survival than conventional clinical factors just like gender, TNM stage, smoking history, and age.
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Jiang F, Mao Y, Lu B, Zhou G, Wang J. A hypoxia risk signature for the tumor immune microenvironment evaluation and prognosis prediction in acute myeloid leukemia. Sci Rep 2021; 11:14657. [PMID: 34282207 PMCID: PMC8289869 DOI: 10.1038/s41598-021-94128-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is the most prevalent form of acute leukemia. Patients with AML often have poor clinical prognoses. Hypoxia can activate a series of immunosuppressive processes in tumors, resulting in diseases and poor clinical prognoses. However, how to evaluate the severity of hypoxia in tumor immune microenvironment remains unknown. In this study, we downloaded the profiles of RNA sequence and clinicopathological data of pediatric AML patients from Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, as well as those of AML patients from Gene Expression Omnibus (GEO). In order to explore the immune microenvironment in AML, we established a risk signature to predict clinical prognosis. Our data showed that patients with high hypoxia risk score had shorter overall survival, indicating that higher hypoxia risk scores was significantly linked to immunosuppressive microenvironment in AML. Further analysis showed that the hypoxia could be used to serve as an independent prognostic indicator for AML patients. Moreover, we found gene sets enriched in high-risk AML group participated in the carcinogenesis. In summary, the established hypoxia-related risk model could act as an independent predictor for the clinical prognosis of AML, and also reflect the response intensity of the immune microenvironment in AML.
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Affiliation(s)
- Feng Jiang
- grid.8547.e0000 0001 0125 2443Department of Neonatology, Obstetrics and Gynecology Hospital, Fudan University, No. 419, Fangxie Road, Shanghai, 200011 China
| | - Yan Mao
- grid.412676.00000 0004 1799 0784Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 China
| | - Binbin Lu
- grid.412676.00000 0004 1799 0784Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 China
| | - Guoping Zhou
- grid.412676.00000 0004 1799 0784Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 China
| | - Jimei Wang
- grid.8547.e0000 0001 0125 2443Department of Neonatology, Obstetrics and Gynecology Hospital, Fudan University, No. 419, Fangxie Road, Shanghai, 200011 China
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5
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Khella CA, Mehta GA, Mehta RN, Gatza ML. Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer. J Pers Med 2021; 11:149. [PMID: 33669749 PMCID: PMC7922242 DOI: 10.3390/jpm11020149] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
The underlying molecular heterogeneity of cancer is responsible for the dynamic clinical landscape of this disease. The combination of genomic and proteomic alterations, including both inherited and acquired mutations, promotes tumor diversity and accounts for variable disease progression, therapeutic response, and clinical outcome. Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the prediction of drug sensitivity and disease progression; and have contributed to the development of novel and more effective treatment strategies. In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal forms of cancer for women, and discuss the molecular similarities of these diseases, the impact of these findings on our understanding of tumor biology as well as the clinical applicability of these discoveries.
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Affiliation(s)
- Christen A Khella
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Gaurav A Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Rushabh N Mehta
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Michael L Gatza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
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6
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Thomas SN, Friedrich B, Schnaubelt M, Chan DW, Zhang H, Aebersold R. Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes. iScience 2020; 23:101079. [PMID: 32534439 PMCID: PMC7298555 DOI: 10.1016/j.isci.2020.101079] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/19/2019] [Accepted: 04/14/2020] [Indexed: 12/15/2022] Open
Abstract
The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) established a harmonized method for large-scale clinical proteomic studies. SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, is an alternate proteomic approach. In this study, we used SWATH-MS to analyze remnant peptides from the original retrospective TCGA samples generated for the CPTAC ovarian cancer proteogenomic study. The SWATH-MS results recapitulated the confident identification of differentially expressed proteins in enriched pathways associated with the robust Mesenchymal high-grade serous ovarian cancer subtype and the homologous recombination deficient tumors. Hence, SWATH/DIA-MS presents a promising complementary or orthogonal alternative to the CPTAC proteomic workflow, with the advantages of simpler and faster workflows and lower sample consumption, albeit with shallower proteome coverage. In summary, both analytical methods are suitable to characterize clinical samples, providing proteomic workflow alternatives for cancer researchers depending on the context-specific goals of the studies. SWATH-MS and iTRAQ-DDA are used to classify 103 high-grade serous ovarian cancer SWATH-MS re-capitulates differentially expressed proteins in ovarian cancer subtypes SWATH-MS is a robust proteomic approach for large-scale clinical proteomic studies
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Affiliation(s)
- Stefani N Thomas
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Betty Friedrich
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Michael Schnaubelt
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel W Chan
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hui Zhang
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland.
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7
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Yang F, Fu Z, Yang M, Sun C, Li Y, Chu J, Zhang Y, Li W, Huang X, Li J, Wu H, Ding X, Yin Y. Expression pattern of microRNAs related with response to trastuzumab in breast cancer. J Cell Physiol 2019; 234:16102-16113. [PMID: 30770556 DOI: 10.1002/jcp.28268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Although an immense effort has been made to develop a novel biomarker for response to trastuzumab, no reliable biomarkers are available to guide management, expect for HER2. The aim of this study was to examine the relationship between microRNA (miRNA) expression and resistance to trastuzumab. METHODS Differentially expressed miRNAs between trastuzumab-resistant and trastuzumab-sensitive cell lines were analyzed using microarrays. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to determine the functions of differentially expressed miRNA and their targeted genes. Furthermore, the protein-protein interactions (PPI) network was analyzed. Serum samples were collected from patients with HER2-positive breast cancer who were treated with trastuzumab. We validated the miRNAs expression levels by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in these serums. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the predictive performance of the miRNA. RESULTS Using miRNA microarrays, 151 miRNAs that significant differentially expressed between the trastuzumab-resistant and sensitive cells were identified, including 46 upregulated and 105 downregulated miRNAs. Results of real-time PCR confirmed seven miRNAs in cell lines. PI3K-Akt signaling pathway was involved in regulating biological function according to KEGG analysis. Compared with the serums of trastuzumab-sensitive patients, three miRNAs, namely miR-200b, miR-135b, and miR-29a, were identified to be upregulated, and miR-224 was downregulated in the trastuzumab-resistant serums. ROC analysis showed that four miRNAs were correlated with trastuzumab resistance. Furthermore, three subnetwork modules of PPI network were obtained. CONCLUSION The results indicated that miRNAs were reliable predictive biomarkers for response to trastuzumab.
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Affiliation(s)
- Fan Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Nanjing Maternal and Child Health Institute, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Mengzhu Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Chunxiao Sun
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Yongfei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Jiahui Chu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Yanhong Zhang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiang Huang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaorong Ding
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,The First Clinical College of Nanjing Medical University, Nanjing, China
| | - Yongmei Yin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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8
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Xie H, Xu H, Hou Y, Cai Y, Rong Z, Song W, Wang W, Li K. Integrative prognostic subtype discovery in high-grade serous ovarian cancer. J Cell Biochem 2019; 120:18659-18666. [PMID: 31347734 DOI: 10.1002/jcb.29049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/30/2019] [Indexed: 01/19/2023]
Abstract
OBJECTIVE We sought to identify novel molecular subtypes of high-grade serous ovarian cancer (HGSC) by the integration of gene expression and proteomics data and to find the underlying biological characteristics of ovarian cancer to improve the clinical outcome. METHODS The iCluster method was utilized to analysis 131 common HGSC samples between TCGA and Clinical Proteomic Tumor Analysis Consortium databases. Kaplan-Meier survival curves were used to estimate the overall survival of patients, and the differences in survival curves were assessed using the log-rank test. RESULTS Two novel ovarian cancer subtypes with different overall survival (P = .00114) and different platinum status (P = .0061) were identified. Eighteen messenger RNAs and 38 proteins were selected as differential molecules between subtypes. Pathway analysis demonstrated arrhythmogenic right ventricular cardiomyopathy pathway played a critical role in the discrimination of these two subtypes and desmosomal cadherin DSG2, DSP, JUP, and PKP2 in this pathway were overexpression in subtype I compared with subtype II. CONCLUSION Our study extended the underlying prognosis-related biological characteristics of high-grade serous ovarian cancer. Enrichment of desmosomal cadherin increased the risk for HGSC prognosis among platinum-sensitive patients, the results guided the revision of the treatment options for platinum-sensitive ovarian cancer patients to improve outcomes.
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Affiliation(s)
- Hongyu Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Huan Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yan Hou
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yuqing Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Zhiwei Rong
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Wei Song
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Wenjie Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Kang Li
- Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
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Jablonska J, Pietrowska M, Ludwig S, Lang S, Thakur BK. Challenges in the Isolation and Proteomic Analysis of Cancer Exosomes-Implications for Translational Research. Proteomes 2019; 7:proteomes7020022. [PMID: 31096692 PMCID: PMC6631388 DOI: 10.3390/proteomes7020022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/21/2022] Open
Abstract
Exosomes belong to the group of extracellular vesicles (EVs) that derive from various cell populations and mediate intercellular communication in health and disease. Like hormones or cytokines, exosomes released by cells can play a potent role in the communication between the cell of origin and distant cells in the body to maintain homeostatic or pathological processes, including tumorigenesis. The nucleic acids, and lipid and protein cargo present in the exosomes are involved in a myriad of carcinogenic processes, including cell proliferation, tumor angiogenesis, immunomodulation, and metastasis formation. The ability of exosomal proteins to mediate direct functions by interaction with other cells qualifies them as tumor-specific biomarkers and targeted therapeutic approaches. However, the heterogeneity of plasma-derived exosomes consistent of (a) exosomes derived from all kinds of body cells, including cancer cells and (b) contamination of exosome preparation with other extracellular vesicles, such as apoptotic bodies, makes it challenging to obtain solid proteomics data for downstream clinical application. In this manuscript, we review these challenges beginning with the choice of different isolation methods, through the evaluation of obtained exosomes and limitations in the process of proteome analysis of cancer-derived exosomes to identify novel protein targets with functional impact in the context of translational oncology.
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Affiliation(s)
- Jadwiga Jablonska
- Translational Oncology, Department of Otorhinolaryngology, University Hospital Essen, 45147 Essen, Germany.
| | - Monika Pietrowska
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute⁻Oncology Center, Gliwice Branch, 44-100 Gliwice, Poland.
| | - Sonja Ludwig
- Translational Oncology, Department of Otorhinolaryngology, University Hospital Essen, 45147 Essen, Germany.
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, 45147 Essen, Germany.
| | - Stephan Lang
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Essen, 45147 Essen, Germany.
| | - Basant Kumar Thakur
- Cancer Exosome Research Lab, Department of Pediatric Hematology and Oncology, University Hospital Essen, 45147 Essen, Germany.
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10
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Gomig THB, Cavalli IJ, Souza RLRD, Vieira E, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, de Andrade Urban C, Cavalli LR, Ribeiro EMDSF. Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer. J Proteomics 2019; 199:1-14. [PMID: 30772490 DOI: 10.1016/j.jprot.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/27/2019] [Accepted: 02/11/2019] [Indexed: 02/08/2023]
Abstract
Proteins play an essential role in the biological processes associated with cancer. Their altered expression levels can deregulate critical cellular pathways and interactive networks. In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) and axillary metastatic lymph node (LN) and corresponding non-tumor tissues contralateral (NCT) and adjacent (ANT) from patients diagnosed with invasive ductal carcinoma. A total of 462 proteins was observed as differentially expressed (DEPs) among the groups analyzed. A high level of similarity was observed in the proteome profile of both non-tumor breast tissues and DEPs (n = 12) were mainly predicted in the RNA metabolism. The DEPs among the malignant and non-tumor breast tissues [n = 396 (PTxNCT) and n = 410 (LNxNCT)] were related to pathways of the LXR/RXR, NO, eNOS, eIF2 and sirtuins, tumor-related functions, fatty acid metabolism and oxidative stress. Remarkable similarity was observed between both malignant tissues, which the DEPs were related to metastatic capabilities. Altogether, our findings revealed differential proteomic profiles that affected cancer associated and interconnected signaling processes. Validation studies are recommended to demonstrate the potential of individual proteins and/or pathways as biological markers in breast cancer. SIGNIFICANCE: The proteomic analysis of this study revealed high similarity in the proteomic profile of the contralateral and adjacent non-tumor breast tissues. Significant differences were identified among the proteome of the malignant and non-tumor tissue groups of the same patients, providing relevant insights into the hallmarks, signaling pathways, biological functions, and interactive protein networks that act during tumorigenesis and breast cancer progression. These proteins are suggested as targets of relevant interest to be explored as potential biological markers related to tumor development and metastatic progression in the breast cancer disease.
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Affiliation(s)
| | | | | | - Evelyn Vieira
- Genetics Department, Federal University of Parana, Curitiba, Brazil
| | | | - Michel Batista
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility - RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | | | - Fabricio Klerynton Marchini
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility - RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | | | | | | | - Luciane Regina Cavalli
- Research Institute Pele Pequeno Principe, Curitiba, Brazil; Lombardi Comprehensive Cancer Center, Georgetown University, USA
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Patil V, Mahalingam K. A four-protein expression prognostic signature predicts clinical outcome of lower-grade glioma. Gene 2018; 679:57-64. [DOI: 10.1016/j.gene.2018.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/01/2018] [Indexed: 01/07/2023]
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12
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Clifford C, Vitkin N, Nersesian S, Reid-Schachter G, Francis JA, Koti M. Multi-omics in high-grade serous ovarian cancer: Biomarkers from genome to the immunome. Am J Reprod Immunol 2018; 80:e12975. [DOI: 10.1111/aji.12975] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Cole Clifford
- Department of Biomedical and Molecular Sciences; Queen's University; Kingston ON Canada
| | - Natasha Vitkin
- Department of Biomedical and Molecular Sciences; Queen's University; Kingston ON Canada
- Cancer Biology and Genetics; Queen's Cancer Research Institute; Queen's University; Kingston ON Canada
| | - Sarah Nersesian
- Department of Biomedical and Molecular Sciences; Queen's University; Kingston ON Canada
- Cancer Biology and Genetics; Queen's Cancer Research Institute; Queen's University; Kingston ON Canada
| | | | - Julie-Ann Francis
- Department of Obstetrics and Gynecology; Kingston Health Sciences Center; Queen's University; Kingston ON Canada
| | - Madhuri Koti
- Department of Biomedical and Molecular Sciences; Queen's University; Kingston ON Canada
- Cancer Biology and Genetics; Queen's Cancer Research Institute; Queen's University; Kingston ON Canada
- Department of Obstetrics and Gynecology; Kingston Health Sciences Center; Queen's University; Kingston ON Canada
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Zhang Y, Fang L, Zang Y, Xu Z. Identification of Core Genes and Key Pathways via Integrated Analysis of Gene Expression and DNA Methylation Profiles in Bladder Cancer. Med Sci Monit 2018; 24:3024-3033. [PMID: 29739919 PMCID: PMC5968840 DOI: 10.12659/msm.909514] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Bladder cancer (BC) is the most common urological malignant tumor. In BC, aberrant DNA methylation is believed to be associated with carcinogenesis. Therefore, the identification of key genes and pathways could help determine the potential molecular mechanisms of BC development. Material/Methods Microarray data on gene expression and gene methylation were downloaded from the Gene Expression Omnibus (GEO) database. Abnormal methylated/expressed genes were analyzed by GEO2R and statistical software R. Gene Ontology term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID database and KOBAS 3.0. STRING and Cytoscape software were used to construct protein–protein interaction (PPI) networks and analyze modules of the PPI network. Results A total of 71 hypomethylated/upregulated genes were significantly enriched in cell–cell adhesion and blood vessel development. KEGG pathway analysis highlighted p53 signaling and metabolic pathways. Five core genes in the PPI network were determined: CDH1, DDOST, CASP8, DHX15, and PTPRF. Additionally, 89 hypermethylated/downregulated genes were found. These genes were enriched mostly in cell adhesion and signal transduction. KEGG pathway analysis revealed enrichment in focal adhesion. The top 5 core genes in the PPI network were GNG4, ADCY9, NPY, ADRA2B, and PENK. We found most of the core genes were also significantly altered in the Cancer Genome Atlas database. Conclusions Abnormal methylated/expressed genes and key signaling pathways involved in BC were identified through integrated bioinformatics analysis. In the future, these genes may serve as biomarkers for diagnosis and therapeutic targets in BC.
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Affiliation(s)
- Yongzhen Zhang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Liang Fang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yuanwei Zang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Zhonghua Xu
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China (mainland)
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