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Nitusca D, Socaciu C, Socaciu AI, Sirbu IO, Bardan R, Cumpanas AA, Seclaman E, Marian C. Potential Diagnostic Biomarker Detection for Prostate Cancer Using Untargeted and Targeted Metabolomic Profiling. Curr Issues Mol Biol 2023; 45:5036-5051. [PMID: 37367069 DOI: 10.3390/cimb45060320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/27/2023] [Accepted: 06/03/2023] [Indexed: 06/28/2023] Open
Abstract
Prostate cancer (PCa) remains one of the leading causes of cancer mortality in men worldwide, currently lacking specific, early detection and staging biomarkers. In this regard, modern research focuses efforts on the discovery of novel molecules that could represent potential future non-invasive biomarkers for the diagnosis of PCa, as well as therapeutic targets. Mounting evidence shows that cancer cells express an altered metabolism in their early stages, making metabolomics a promising tool for the discovery of altered pathways and potential biomarker molecules. In this study, we first performed untargeted metabolomic profiling on 48 PCa plasma samples and 23 healthy controls using ultra-high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-[ESI+]-MS) for the discovery of metabolites with altered profiles. Secondly, we selected five molecules (L-proline, L-tryptophan, acetylcarnitine, lysophosphatidylcholine C18:2 and spermine) for the downstream targeted metabolomics and found out that all the molecules, regardless of the PCa stage, were decreased in the PCa plasma samples when compared to the controls, making them potential biomarkers for PCa detection. Moreover, spermine, acetylcarnitine and L-tryptophan had very high diagnostic accuracy, with AUC values of 0.992, 0.923 and 0.981, respectively. Consistent with other literature findings, these altered metabolites could represent future specific and non-invasive candidate biomarkers for PCa detection, which opens novel horizons in the field of metabolomics.
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Affiliation(s)
- Diana Nitusca
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Carmen Socaciu
- BIODIATECH, Research Center for Applied Biotechnology in Diagnosis and Molecular Therapy, 400478 Cluj-Napoca, Romania
| | - Andreea Iulia Socaciu
- Department of Occupational Health, Iuliu Hateganu University of Medicine and Pharmacy, Str. Victor Babes Nr. 8, 400347 Cluj-Napoca, Romania
| | - Ioan Ovidiu Sirbu
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Razvan Bardan
- Department of Urology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Urology Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania
| | - Alin Adrian Cumpanas
- Department of Urology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Urology Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania
| | - Edward Seclaman
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
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Meng S, Wang YU, Wang S, Qian W, Shao Q, Dou M, Zhao S, Wang J, Li M, An Y, He L, Zhang C. Establishment and characterization of an immortalized bovine intestinal epithelial cell line. J Anim Sci 2023; 101:skad215. [PMID: 37351870 PMCID: PMC10347977 DOI: 10.1093/jas/skad215] [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: 03/30/2023] [Accepted: 06/22/2023] [Indexed: 06/24/2023] Open
Abstract
Primary bovine intestinal epithelial cells (PBIECs) are an important model for studying the molecular and pathogenic mechanisms of diseases affecting the bovine intestine. It is difficult to obtain and grow PBIECs stably, and their short lifespan greatly limits their application. Therefore, the purpose of this study was to create a cell line for exploring the mechanisms of pathogen infection in bovine intestinal epithelial cells in vitro. We isolated and cultured PBIECs and established an immortalized BIEC line by transfecting PBIECs with the pCI-neo-hTERT (human telomerase reverse transcriptase) recombinant plasmid. The immortalized cell line (BIECs-21) retained structure and function similar to that of the PBIECs. The marker proteins characteristic of epithelial cells, cytokeratin 18, occludin, zonula occludens protein 1 (ZO-1), E-cadherin and enterokinase, were all positive in the immortalized cell line, and the cell structure, growth rate, karyotype, serum dependence and contact inhibition were normal. The hTERT gene was successfully transferred into BIECs-21 where it remained stable and was highly expressed. The transport of short-chain fatty acids and glucose uptake by the BIECs-21 was consistent with PBIECs, and we showed that they could be infected with the intestinal parasite, Neospora caninum. The immortalized BIECs-21, which have exceeded 80 passages, were structurally and functionally similar to the primary BIECs and thus provide a valuable research tool for investigating the mechanism of pathogen infection of the bovine intestinal epithelium in vitro.
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Affiliation(s)
- Sudan Meng
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
- Innovative Research Team of Livestock Intelligent Breeding and Equipment, Longmen Laboratory, Luoyang 471023, China
| | - Y uexin Wang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Shuai Wang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Weifeng Qian
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Qi Shao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Mengying Dou
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Shujuan Zhao
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Jianguo Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Mengyun Li
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Yongsheng An
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Lei He
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
| | - Cai Zhang
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Research Center of Livestock and Poultry Eerging Disease Detection and Control, Luoyang 471023, China
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Feng Y, Sun C, Zhang L, Wan H, Zhou H, Chen Y, Zhu L, Xia G, Mi Y. Upregulation of COPB2 Promotes Prostate Cancer Proliferation and Invasion Through the MAPK/TGF-β Signaling Pathway. Front Oncol 2022; 12:865317. [PMID: 35600351 PMCID: PMC9120942 DOI: 10.3389/fonc.2022.865317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/11/2022] [Indexed: 12/29/2022] Open
Abstract
There is increasing evidence that coatomer protein complex subunit beta 2 (COPB2) plays an important role in various cancer types. This study explored the role and the downstream mediators of COPB2 in prostate cancer (PCa). The expression of COPB2 was determined by the Cancer Genome Atlas database and enzyme-linked immunosorbent assay. COPB2 expression was upregulated in PCa tissues and correlated with Gleason score, biochemical recurrence, and poor prognosis. The functional roles of COPB2 in PCa were verified through a series of experiments. Knocking down COPB2 expression inhibited the growth and clonogenesis of PCa cells, promoted cell apoptosis, and inhibited the ability of scratch repair, invasion of PCa cells, and tumor growth in Nude mice. To analyze downstream signaling pathways, ingenuity pathway analysis, GSEA, and whole-genome expression spectrum GeneChip analysis were used. Western blot revealed that COPB2 expression promoted the proliferation and invasion of PCa cells by regulating the MAPK/TGF-β signaling pathway. The interacting protein (nuclear protein 1, NUPR1) was identified via Co-IP, real-time PCR, Western blot, and TCGA database in sampled tissues. The expressions of the interaction proteins NUPR1 and COPB2 were negatively regulated by each other. COPB2 could be a new biomarker for PCa diagnosis and monitoring and to provide a theoretical basis for identifying effective drug intervention targets through in-depth mechanistic studies.
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Affiliation(s)
- Yanyan Feng
- Wuxi Medical College, Jiangnan University, Wuxi, China
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Chuanyu Sun
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lifeng Zhang
- Department of Urology, Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, China
| | - Hongyuan Wan
- Wuxi Medical College, Jiangnan University, Wuxi, China
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Hangsheng Zhou
- Wuxi Medical College, Jiangnan University, Wuxi, China
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Yongquan Chen
- Wuxi Medical College, Jiangnan University, Wuxi, China
| | - Lijie Zhu
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Guowei Xia
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
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Intasqui P, Bertolla RP, Sadi MV. Prostate cancer proteomics: clinically useful protein biomarkers and future perspectives. Expert Rev Proteomics 2017; 15:65-79. [PMID: 29251021 DOI: 10.1080/14789450.2018.1417846] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Although prostate cancer constitutes one of the most important, death-related diseases in the male population, there is still a need for identification of sensitive biomarkers that could precociously detect the disease and differentiate aggressive from indolent cancers, in order to decrease overtreatment. Proteomics research has improved understanding on mechanisms underlying tumorigenesis, cancer cells migration and invasion potential, and castration resistance. This review has focused on proteomic studies of prostate cancer published in the recent years, with a special emphasis on determination of biomarkers for cancer progression and diagnosis. Areas covered: Shotgun and targeted-proteomic studies of prostate cancer in different matrices are reviewed, i.e., prostate tissue, prostate cell lines, blood (serum and plasma), urine, seminal plasma, and exosomes. The most important biomarkers for cancer diagnosis and aggressiveness characterization are highlighted. Expert commentary: In general, results demonstrate alteration in cell cycle control, DNA repair, proteasomal degradation, and metabolic activity. However, these studies suffer from low reproducibility due to heterogeneity of the cancer itself, as well as to techniques utilized for protein identification/quantification. Downstream confirmatory studies in separate cohorts are warranted in order to demonstrate accuracy of these results.
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Affiliation(s)
- Paula Intasqui
- a Department of Surgery, Division of Urology, Human Reproduction Section , Universidade Federal de São Paulo (UNIFESP) - Sao Paulo Hospital , Sao Paulo , Brazil
| | - Ricardo P Bertolla
- a Department of Surgery, Division of Urology, Human Reproduction Section , Universidade Federal de São Paulo (UNIFESP) - Sao Paulo Hospital , Sao Paulo , Brazil
| | - Marcus Vinicius Sadi
- a Department of Surgery, Division of Urology, Human Reproduction Section , Universidade Federal de São Paulo (UNIFESP) - Sao Paulo Hospital , Sao Paulo , Brazil
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Dereziński P, Klupczynska A, Sawicki W, Pałka JA, Kokot ZJ. Amino Acid Profiles of Serum and Urine in Search for Prostate Cancer Biomarkers: a Pilot Study. Int J Med Sci 2017; 14:1-12. [PMID: 28138303 PMCID: PMC5278653 DOI: 10.7150/ijms.15783] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 10/24/2016] [Indexed: 12/17/2022] Open
Abstract
There is a great interest in searching for diagnostic biomarkers in prostate cancer patients. The aim of the pilot study was to evaluate free amino acid profiles in their serum and urine. The presented paper shows the first comprehensive analysis of a wide panel of amino acids in two different physiological fluids obtained from the same groups of prostate cancer patients (n = 49) and healthy men (n = 40). The potential of free amino acids, both proteinogenic and non-proteinogenic, as prostate cancer biomarkers and their utility in classification of study participants have been assessed. Several metabolites, which deserve special attention in the further metabolomic investigations on searching for prostate cancer markers, were indicated. Moreover, free amino acid profiles enabled to classify samples to one of the studied groups with high sensitivity and specificity. The presented research provides a strong evidence that ethanolamine, arginine and branched-chain amino acids metabolic pathways can be a valuable source of markers for prostate cancer. The altered concentrations of the above-mentioned metabolites suggest their role in pathogenesis of prostate cancer and they should be further evaluated as clinically useful markers of prostate cancer.
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Affiliation(s)
- Paweł Dereziński
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland
| | - Agnieszka Klupczynska
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland
| | - Wojciech Sawicki
- Ward of Urology, The Holy Family Hospital, 18 Jarochowskiego Street, 60-235 Poznań, Poland
| | - Jerzy A. Pałka
- Department of Medicinal Chemistry, Medical University of Bialystok, 2d Mickiewicza Street, 15-222 Białystok, Poland
| | - Zenon J. Kokot
- Department of Inorganic and Analytical Chemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznań, Poland
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Zheng CL, Ratnakar V, Gil Y, McWeeney SK. Use of semantic workflows to enhance transparency and reproducibility in clinical omics. Genome Med 2015; 7:73. [PMID: 26289940 PMCID: PMC4545705 DOI: 10.1186/s13073-015-0202-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 07/14/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Recent highly publicized cases of premature patient assignment into clinical trials, resulting from non-reproducible omics analyses, have prompted many to call for a more thorough examination of translational omics and highlighted the critical need for transparency and reproducibility to ensure patient safety. The use of workflow platforms such as Galaxy and Taverna have greatly enhanced the use, transparency and reproducibility of omics analysis pipelines in the research domain and would be an invaluable tool in a clinical setting. However, the use of these workflow platforms requires deep domain expertise that, particularly within the multi-disciplinary fields of translational and clinical omics, may not always be present in a clinical setting. This lack of domain expertise may put patient safety at risk and make these workflow platforms difficult to operationalize in a clinical setting. In contrast, semantic workflows are a different class of workflow platform where resultant workflow runs are transparent, reproducible, and semantically validated. Through semantic enforcement of all datasets, analyses and user-defined rules/constraints, users are guided through each workflow run, enhancing analytical validity and patient safety. METHODS To evaluate the effectiveness of semantic workflows within translational and clinical omics, we have implemented a clinical omics pipeline for annotating DNA sequence variants identified through next generation sequencing using the Workflow Instance Generation and Specialization (WINGS) semantic workflow platform. RESULTS We found that the implementation and execution of our clinical omics pipeline in a semantic workflow helped us to meet the requirements for enhanced transparency, reproducibility and analytical validity recommended for clinical omics. We further found that many features of the WINGS platform were particularly primed to help support the critical needs of clinical omics analyses. CONCLUSIONS This is the first implementation and execution of a clinical omics pipeline using semantic workflows. Evaluation of this implementation provides guidance for their use in both translational and clinical settings.
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Affiliation(s)
- Christina L Zheng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Varun Ratnakar
- Information Sciences Institute, University of Southern California, Los Angeles, CA, USA.
| | - Yolanda Gil
- Information Sciences Institute, University of Southern California, Los Angeles, CA, USA.
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA.
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Biostatistics, Department of Public Health and Preventative Medicine, Oregon Health & Science University, Portland, OR, USA.
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Abstract
Exosomes and other microvesicles are emerging as rich reservoirs of tumor-specific proteins and biomarkers for cancer detection and progression. For prostate cancer, exosomes secreted by the prostate can be isolated from prostatic secretions, seminal fluid, tissue, urine or blood for further proteomic analysis. Structurally, prostate-derived exosomes are distinct in size, membrane composition and specific prostate protein content, potentially providing a novel and easily isolatable source of biomarkers from clinical biofluids. The key to these isolation strategies will be the targeting of specific prostatic proteins expressed in these exosomes, thus requiring detailed proteomic characterizations. A summary of ongoing efforts to characterize the proteome of these unique prostate cancer-associated exosomes and their potential applications for use in biomarker assays is presented.
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Affiliation(s)
- Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, MUSC Proteomics Center, Medical University of South Carolina , Charleston, SC , USA
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