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Cheng G, Zhou Z, Li S, Ye Z, Wang Y, Wen J, Ren C. Integration of proteomics and transcriptomics to construct a prognostic signature of renal clear cell carcinoma. Int J Med Sci 2024; 21:2215-2232. [PMID: 39239554 PMCID: PMC11373548 DOI: 10.7150/ijms.99992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 08/06/2024] [Indexed: 09/07/2024] Open
Abstract
Background: Protein information is often replaced by RNA data in studies to understand cancer-related biological processes or molecular functions, and proteins of prognostic significance in Kidney clear cell carcinoma (KIRC) remain to be mined. Methods: The cancer genome atlas program (TCGA) data was utilized to screen for proteins that are prognostically significant in KIRC. Machine learning algorithms were employed to develop protein prognostic models. Additionally, immune infiltration abundance, somatic mutation differences, and immunotherapeutic responses were analyzed in various protein risk subgroups. Ultimately, the validation of protein-coding genes was confirmed by utilizing an online database and implementing quantitative real-time PCR (qRT-PCR). Results: The patients were divided into two risk categories based on prognostic proteins, and notable disparities in both overall survival (OS) and progression free interval (PFI) were observed between the two groups. The OS was more unfavorable in the high-risk group, and there was a noteworthy disparity in the level of immune infiltration observed between the two groups. In addition, the nomogram showed high accuracy in predicting survival in KIRC patients. Conclusion: In this research, we elucidated the core proteins associated with prognosis in terms of survival prediction, immunotherapeutic response, somatic mutation, and immune microenvironment. Additionally, we have developed a reliable prognostic model with excellent predictive capabilities.
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Affiliation(s)
- Guangyang Cheng
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
| | - Zhaokai Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
- Henan Joint International Pediatric Urodynamic Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
- Bladder Structure and Function Reconstruction Henan Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
| | - Shiqi Li
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
| | - Zhuo Ye
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
| | - Yan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
| | - Jianguo Wen
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
- Henan Joint International Pediatric Urodynamic Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
- Bladder Structure and Function Reconstruction Henan Engineering Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
| | - Chuanchuan Ren
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450052, China
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Manukonda R, Jakati S, Attem J, Mishra DK, Mocherla TR, Reddy MM, Gulati K, Poluri KM, Vemuganti GK, Kaliki S. Identifying Treatment Resistance Related Pathways by Analyzing Serum Extracellular Vesicles of Patients With Resistant Versus Regressed Retinoblastoma. Invest Ophthalmol Vis Sci 2023; 64:26. [PMID: 37603355 PMCID: PMC10445180 DOI: 10.1167/iovs.64.11.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/30/2023] [Indexed: 08/22/2023] Open
Abstract
Purpose To identify the genes and pathways responsible for treatment resistance (TR) in retinoblastoma (RB) by analyzing serum small extracellular vesicles (sEVs) of patients with TR active RB (TR-RB) and completely regressed RB (CR-RB). Methods Serum-derived sEVs were characterized by transmission electron microscopy and nanoparticle tracking analysis. sEV transcriptome profiles of two TR-RB and one CR-RB with good response (>20 years tumor free) were compared to their age-matched controls (n = 3). Gene expression data were analyzed by the R Bioconductor package. The CD9 protein and mRNA expression of CD9, CD63, and CD81 were studied in five RB tumors and two control retinae by immunohistochemistry and quantitative reverse transcription-polymerase chain reaction. Results The isolated serum sEVs were round shaped and within the expected size (30-150 nm), and they had zeta potentials ranging from -10.8 to 15.9 mV. The mean ± SD concentrations of sEVs for two adults and four children were 1.1 × 1012 ± 0.1 and 5.8 × 1011 ± 1.7 particles/mL. Based on log2 fold change of ±2 and P < 0.05 criteria, there were 492 dysregulated genes in TR-RB and 184 in CR-RB. KAT2B, VWA1, CX3CL1, MLYCD, NR2F2, USP46-AS1, miR6724-4, and LINC01257 genes were specifically dysregulated in TR-RB. Negative regulation of apoptotic signaling, cell growth, and proton transport genes were greater than fivefold expressed only in TR-RB. CD9, CD63, and CD81 mRNA levels were high in RB tumors versus control retina, with increased and variable CD9 immunoreactivity in the invasive areas of the tumor. Conclusions Serum sEVs could serve as a potential liquid biopsy source for understanding TR mechanisms in RB.
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Affiliation(s)
- Radhika Manukonda
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Brien Holden Eye Research Center, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Saumya Jakati
- Ophthalmic Pathology Laboratory, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Prof. Krothapalli Ravindranath Ophthalmic Research Biorepository, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Jyothi Attem
- School of Medical Sciences, Science Complex, University of Hyderabad, Hyderabad, Telangana, India
| | - Dilip K. Mishra
- Ophthalmic Pathology Laboratory, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Tirupathi Rao Mocherla
- Prof. Krothapalli Ravindranath Ophthalmic Research Biorepository, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Mamatha M. Reddy
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Bhubaneswar, Odisha, India
| | - Khushboo Gulati
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Hyderabad, Telangana, India
- Brien Holden Eye Research Center, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Geeta K. Vemuganti
- School of Medical Sciences, Science Complex, University of Hyderabad, Hyderabad, Telangana, India
| | - Swathi Kaliki
- The Operation Eyesight Universal Institute for Eye Cancer, L V Prasad Eye Institute, Hyderabad, Telangana, India
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Kakkassery V, Gemoll T, Kraemer MM, Sauer T, Tura A, Ranjbar M, Grisanti S, Joachim SC, Mergler S, Reinhard J. Protein Profiling of WERI-RB1 and Etoposide-Resistant WERI-ETOR Reveals New Insights into Topoisomerase Inhibitor Resistance in Retinoblastoma. Int J Mol Sci 2022; 23:4058. [PMID: 35409416 PMCID: PMC9000009 DOI: 10.3390/ijms23074058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/23/2022] [Accepted: 04/02/2022] [Indexed: 12/16/2022] Open
Abstract
Chemotherapy resistance is one of the reasons for eye loss in patients with retinoblastoma (RB). RB chemotherapy resistance has been studied in different cell culture models, such as WERI-RB1. In addition, chemotherapy-resistant RB subclones, such as the etoposide-resistant WERI-ETOR cell line have been established to improve the understanding of chemotherapy resistance in RB. The objective of this study was to characterize cell line models of an etoposide-sensitive WERI-RB1 and its etoposide-resistant subclone, WERI-ETOR, by proteomic analysis. Subsequently, quantitative proteomics data served for correlation analysis with known drug perturbation profiles. Methodically, WERI-RB1 and WERI-ETOR were cultured, and prepared for quantitative mass spectrometry (MS). This was carried out in a data-independent acquisition (DIA) mode. The raw SWATH (sequential window acquisition of all theoretical mass spectra) files were processed using neural networks in a library-free mode along with machine-learning algorithms. Pathway-enrichment analysis was performed using the REACTOME-pathway resource, and correlated to the molecular signature database (MSigDB) hallmark gene set collections for functional annotation. Furthermore, a drug-connectivity analysis using the L1000 database was carried out to associate the mechanism of action (MOA) for different anticancer reagents to WERI-RB1/WERI-ETOR signatures. A total of 4756 proteins were identified across all samples, showing a distinct clustering between the groups. Of these proteins, 64 were significantly altered (q < 0.05 & log2FC |>2|, 22 higher in WERI-ETOR). Pathway analysis revealed the “retinoid metabolism and transport” pathway as an enriched metabolic pathway in WERI-ETOR cells, while the “sphingolipid de novo biosynthesis” pathway was identified in the WERI-RB1 cell line. In addition, this study revealed similar protein signatures of topoisomerase inhibitors in WERI-ETOR cells as well as ATPase inhibitors, acetylcholine receptor antagonists, and vascular endothelial growth factor receptor (VEGFR) inhibitors in the WERI-RB1 cell line. In this study, WERI-RB1 and WERI-ETOR were analyzed as a cell line model for chemotherapy resistance in RB using data-independent MS. Analysis of the global proteome identified activation of “sphingolipid de novo biosynthesis” in WERI-RB1, and revealed future potential treatment options for etoposide resistance in RB.
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Affiliation(s)
- Vinodh Kakkassery
- Department of Ophthalmology, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (A.T.); (M.R.); (S.G.)
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Luebeck and University Hospital Clinic Schleswig-Holstein, Ratzeburger Allee 160, 23538 Luebeck, Germany; (T.G.); (T.S.)
| | - Miriam M. Kraemer
- Department of Cell Morphology and Molecular Neurobiology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitaetsstraße 150, 44780 Bochum, Germany;
| | - Thorben Sauer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Luebeck and University Hospital Clinic Schleswig-Holstein, Ratzeburger Allee 160, 23538 Luebeck, Germany; (T.G.); (T.S.)
| | - Aysegül Tura
- Department of Ophthalmology, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (A.T.); (M.R.); (S.G.)
| | - Mahdy Ranjbar
- Department of Ophthalmology, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (A.T.); (M.R.); (S.G.)
| | - Salvatore Grisanti
- Department of Ophthalmology, University of Luebeck, Ratzeburger Allee 160, 23538 Luebeck, Germany; (A.T.); (M.R.); (S.G.)
| | - Stephanie C. Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany;
| | - Stefan Mergler
- Department of Ophthalmology, Charité-Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, Augustenberger Platz 1, 13353 Berlin, Germany;
| | - Jacqueline Reinhard
- Department of Cell Morphology and Molecular Neurobiology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitaetsstraße 150, 44780 Bochum, Germany;
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