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Mesquita FCP, King M, da Costa Lopez PL, Thevasagayampillai S, Gunaratne PH, Hochman-Mendez C. Laminin Alpha 2 Enhances the Protective Effect of Exosomes on Human iPSC-Derived Cardiomyocytes in an In Vitro Ischemia-Reoxygenation Model. Int J Mol Sci 2024; 25:3773. [PMID: 38612582 PMCID: PMC11011704 DOI: 10.3390/ijms25073773] [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: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Ischemic heart disease, a leading cause of death worldwide, manifests clinically as myocardial infarction. Contemporary therapies using mesenchymal stromal cells (MSCs) and their derivative (exosomes, EXOs) were developed to decrease the progression of cell damage during ischemic injury. Laminin alpha 2 (LAMA2) is an important extracellular matrix protein of the heart. Here, we generated MSC-derived exosomes cultivated under LAMA2 coating to enhance human-induced pluripotent stem cell (hiPSC)-cardiomyocyte recognition of LAMA2-EXOs, thus, increasing cell protection during ischemia reoxygenation. We mapped the mRNA content of LAMA2 and gelatin-EXOs and identified 798 genes that were differentially expressed, including genes associated with cardiac muscle development and extracellular matrix organization. Cells were treated with LAMA2-EXOs 2 h before a 4 h ischemia period (1% O2, 5% CO2, glucose-free media). LAMA2-EXOs had a two-fold protective effect compared to non-treatment on plasma membrane integrity and the apoptosis activation pathway; after a 1.5 h recovery period (20% O2, 5% CO2, cardiomyocyte-enriched media), cardiomyocytes treated with LAMA2-EXOs showed faster recovery than did the control group. Although EXOs had a protective effect on endothelial cells, there was no LAMA2-enhanced protection on these cells. This is the first report of LAMA2-EXOs used to treat cardiomyocytes that underwent ischemia-reoxygenation injury. Overall, we showed that membrane-specific EXOs may help improve cardiomyocyte survival in treating ischemic cardiovascular disease.
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Affiliation(s)
- Fernanda C. P. Mesquita
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
| | - Madelyn King
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
| | - Patricia Luciana da Costa Lopez
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
| | | | - Preethi H. Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Camila Hochman-Mendez
- Department of Regenerative Medicine Research, The Texas Heart Institute, Houston, TX 77030, USA; (F.C.P.M.); (M.K.); (P.L.d.C.L.)
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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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Cohen E, Johnson CN, Wasikowski R, Billi AC, Tsoi LC, Kahlenberg JM, Gudjonsson JE, Coulombe PA. Significance of stress keratin expression in normal and diseased epithelia. iScience 2024; 27:108805. [PMID: 38299111 PMCID: PMC10828818 DOI: 10.1016/j.isci.2024.108805] [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: 09/06/2023] [Revised: 11/30/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
A group of keratin intermediate filament genes, the type II KRT6A-C and type I KRT16 and KRT17, are deemed stress responsive as they are induced in keratinocytes of surface epithelia in response to environmental stressors, in skin disorders (e.g., psoriasis) and in carcinomas. Monitoring stress keratins is widely used to identify keratinocytes in an activated state. Here, we analyze single-cell transcriptomic data from healthy and diseased human skin to explore the properties of stress keratins. Relative to keratins occurring in healthy skin, stress-induced keratins are expressed at lower levels and show lesser type I-type II pairwise regulation. Stress keratins do not "replace" the keratins expressed during normal differentiation nor reflect cellular proliferation. Instead, stress keratins are consistently co-regulated with genes with roles in differentiation, inflammation, and/or activation of innate immunity at the single-cell level. These findings provide a roadmap toward explaining the broad diversity and contextual regulation of keratins.
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Affiliation(s)
- Erez Cohen
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Craig N. Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rachael Wasikowski
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Allison C. Billi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - J. Michelle Kahlenberg
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Rheumatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Johann E. Gudjonsson
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Rheumatology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Pierre A. Coulombe
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
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Zhou X, Xue F, Li T, Xue J, Yue S, Zhao S, Lu H, He C. Exploration of potential biomarkers for early bladder cancer based on urine proteomics. Front Oncol 2024; 14:1309842. [PMID: 38410113 PMCID: PMC10894981 DOI: 10.3389/fonc.2024.1309842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Background Bladder cancer is a common malignant tumor of the urinary system. The progression of the condition is associated with a poor prognosis, so it is necessary to identify new biomarkers to improve the diagnostic rate of bladder cancer. Methods In this study, 338 urine samples (144 bladder cancer, 123 healthy control, 32 cystitis, and 39 upper urinary tract cancer samples) were collected, among which 238 samples (discovery group) were analyzed by LC-MS. The urinary proteome characteristics of each group were compared with those of bladder cancer, and the differential proteins were defined by bioinformatics analysis. The pathways and functional enrichments were annotated. The selected proteins with the highest AUC score were used to construct a diagnostic panel. One hundred samples (validation group) were used to test the effect of the panel by ELISA. Results Compared with the healthy control, cystitis and upper urinary tract cancer samples, the number of differential proteins in the bladder cancer samples was 325, 158 and 473, respectively. The differentially expressed proteins were mainly related to lipid metabolism and iron metabolism and were involved in the proliferation, metabolism and necrosis of bladder cancer cells. The AUC of the panel of APOL1 and ITIH3 was 0.96 in the discovery group. ELISA detection showed an AUC of 0.92 in the validation group. Conclusion This study showed that urinary proteins can reflect the pathophysiological changes in bladder cancer and that important molecules can be used as biomarkers for bladder cancer screening. These findings will benefit the application of the urine proteome in clinical research.
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Affiliation(s)
- Xu Zhou
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Fei Xue
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Tingmiao Li
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jiangshan Xue
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Siqi Yue
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Shujie Zhao
- Department of Laboratory Medicine, Changchun Infectious Diseases Hospital, Changchun, China
| | - Hezhen Lu
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Chengyan He
- Department of Laboratory Medicine, China-Japan Union Hospital of Jilin University, Changchun, China
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Chiang CY, Zhang M, Huang J, Zeng J, Chen C, Pan D, Yang H, Zhang T, Yang M, Han Q, Wang Z, Xiao T, Chen Y, Zou Y, Yin F, Li Z, Zhu L, Zheng D. A novel selective ERK1/2 inhibitor, Laxiflorin B, targets EGFR mutation subtypes in non-small-cell lung cancer. Acta Pharmacol Sin 2024; 45:422-435. [PMID: 37816856 PMCID: PMC10789733 DOI: 10.1038/s41401-023-01164-w] [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: 02/08/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Extracellular regulated protein kinases 1/2 (ERK1/2) are key members of multiple signaling pathways, including the ErbB axis. Ectopic ERK1/2 activation contributes to various types of cancer, especially drug resistance to inhibitors of RTK, RAF and MEK, and specific ERK1/2 inhibitors are scarce. In this study, we identified a potential novel covalent ERK inhibitor, Laxiflorin B, which is a herbal compound with anticancer activity. However, Laxiflorin B is present at low levels in herbs; therefore, we adopted a semi-synthetic process for the efficient production of Laxiflorin B to improve the yield. Laxiflorin B induced mitochondria-mediated apoptosis via BAD activation in non-small-cell lung cancer (NSCLC) cells, especially in EGFR mutant subtypes. Transcriptomic analysis suggested that Laxiflorin B inhibits amphiregulin (AREG) and epiregulin (EREG) expression through ERK inhibition, and suppressed the activation of their receptors, ErbBs, via a positive feedback loop. Moreover, mass spectrometry analysis combined with computer simulation revealed that Laxiflorin B binds covalently to Cys-183 in the ATP-binding pocket of ERK1 via the D-ring, and Cys-178 of ERK1 through non-inhibitory binding of the A-ring. In a NSCLC tumor xenograft model in nude mice, Laxiflorin B also exhibited strong tumor suppressive effects with low toxicity and AREG and EREG were identified as biomarkers of Laxiflorin B efficacy. Finally, Laxiflorin B-4, a C-6 analog of Laxiflorin B, exhibited higher binding affinity for ERK1/2 and stronger tumor suppression. These findings provide a new approach to tumor inhibition using natural anticancer compounds.
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Affiliation(s)
- Cheng-Yao Chiang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Min Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Junrong Huang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Juan Zeng
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, 523808, China
| | - Chunlan Chen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Dongmei Pan
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Heng Yang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Tiantian Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Min Yang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Qiangqiang Han
- SpecAlly Life Technology Co., Ltd, Wuhan, 430075, China
- Wuhan Biobank Co., Ltd, Wuhan, 430074, China
| | - Zou Wang
- Wuhan Biobank Co., Ltd, Wuhan, 430074, China
| | - Tian Xiao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Yongdong Zou
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China
| | - Feng Yin
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Xili, Shenzhen, 518055, China
| | - Zigang Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen University Town, Xili, Shenzhen, 518055, China
| | - Lizhi Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China.
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China.
| | - Duo Zheng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, International Cancer Center, Department of Cell Biology and Genetics, Shenzhen University Medical School; College of Life Sciences and Oceanography, Shenzhen University; Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, 518055, China.
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Whitehead CA, Fang H, Su H, Morokoff AP, Kaye AH, Hanssen E, Nowell CJ, Drummond KJ, Greening DW, Vella LJ, Mantamadiotis T, Stylli SS. Small extracellular vesicles promote invadopodia activity in glioblastoma cells in a therapy-dependent manner. Cell Oncol (Dordr) 2023:10.1007/s13402-023-00786-w. [PMID: 37014551 DOI: 10.1007/s13402-023-00786-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 04/05/2023] Open
Abstract
PURPOSE The therapeutic efficacy of radiotherapy/temozolomide treatment for glioblastoma (GBM) is limited by the augmented invasiveness mediated by invadopodia activity of surviving GBM cells. As yet, however the underlying mechanisms remain poorly understood. Due to their ability to transport oncogenic material between cells, small extracellular vesicles (sEVs) have emerged as key mediators of tumour progression. We hypothesize that the sustained growth and invasion of cancer cells depends on bidirectional sEV-mediated cell-cell communication. METHODS Invadopodia assays and zymography gels were used to examine the invadopodia activity capacity of GBM cells. Differential ultracentrifugation was utilized to isolate sEVs from conditioned medium and proteomic analyses were conducted on both GBM cell lines and their sEVs to determine the cargo present within the sEVs. In addition, the impact of radiotherapy and temozolomide treatment of GBM cells was studied. RESULTS We found that GBM cells form active invadopodia and secrete sEVs containing the matrix metalloproteinase MMP-2. Subsequent proteomic studies revealed the presence of an invadopodia-related protein sEV cargo and that sEVs from highly invadopodia active GBM cells (LN229) increase invadopodia activity in sEV recipient GBM cells. We also found that GBM cells displayed increases in invadopodia activity and sEV secretion post radiation/temozolomide treatment. Together, these data reveal a relationship between invadopodia and sEV composition/secretion/uptake in promoting the invasiveness of GBM cells. CONCLUSIONS Our data indicate that sEVs secreted by GBM cells can facilitate tumour invasion by promoting invadopodia activity in recipient cells, which may be enhanced by treatment with radio-chemotherapy. The transfer of pro-invasive cargos may yield important insights into the functional capacity of sEVs in invadopodia.
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Affiliation(s)
- Clarissa A Whitehead
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Haoyun Fang
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Huaqi Su
- Centre for Stem Cell Systems, The University of Melbourne, Parkville, VIC, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew P Morokoff
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Level 5, Clinical Sciences Building, Parkville, VIC, 3050, Australia
| | - Andrew H Kaye
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Neurosurgery, Hadassah Hebrew University Medical Centre, Jerusalem, Israel
| | - Eric Hanssen
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Advanced Microscopy Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cameron J Nowell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, 3052, Australia
| | - Katharine J Drummond
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Level 5, Clinical Sciences Building, Parkville, VIC, 3050, Australia
| | - David W Greening
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia
- Central Clinical School, Monash University, Melbourne, VIC, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, VIC, Australia
| | - Laura J Vella
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Centre for Stem Cell Systems, The University of Melbourne, Parkville, VIC, Australia
| | - Theo Mantamadiotis
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- Centre for Stem Cell Systems, The University of Melbourne, Parkville, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
| | - Stanley S Stylli
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia.
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Level 5, Clinical Sciences Building, Parkville, VIC, 3050, Australia.
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Tabaei S, Haghshenas MR, Webster TJ, Ghaderi A. Proteomics strategies for urothelial bladder cancer diagnosis, prognosis and treatment: Trends for tumor biomarker sources. Anal Biochem 2023; 666:115074. [PMID: 36738874 DOI: 10.1016/j.ab.2023.115074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Urothelial bladder cancer (UBC) is a heterogeneous multifactorial malignancy with a high recurrence rate. Current procedures for UBC diagnosis suffering from the lack of clinical sensitivity and specificity screening tests. Therefore, biomarkers have promising values to predict pathological conditions and can be considered as effective targets for early diagnosis, prognosis and antitumor immunotherapy. Recently, researchers have been interested for tumor proteins as biomarkers for different diseases. At present, proteomics methods have rapidly progressive that has potential identified biomarkers of UBC. Specifically, there has been several studies on the potential application of proteomics for the identification, quantification, and profiling of proteins for UBC in different sources. Based on these studies, using the panel of biomarkers as proteomic patterns may achieve higher sensitivity and specificity than single proteins in the diagnosis of UBC. In the present review, we evaluate recent literature related to the UBC proteome focusing especially on new proteomics techniques. Moreover, we classify UBC tumor biomarkers as diagnostic, prognostic, and therapeutic targets based on their sources (urine, serum/plasm, cell line, and tumor tissue) and we also discuss the advantages and limitations of each source. In this manner, this review article provides a critical assessment presentation of the advances in proteomics for all aspects of UBC diagnosis, prognosis, and treatment based on sources.
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Affiliation(s)
- Samira Tabaei
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Haghshenas
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Thomas J Webster
- School of Biomedical Engineering and Health Sciences, Hebei University of Technology, Tianjin, China
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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Wei L, Han Y, Tu C. Molecular Pathways of Diabetic Kidney Disease Inferred from Proteomics. Diabetes Metab Syndr Obes 2023; 16:117-128. [PMID: 36760602 PMCID: PMC9842482 DOI: 10.2147/dmso.s392888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023] Open
Abstract
Diabetic kidney disease (DKD) affects an estimated 20-40% of type 2 diabetes patients and is among the most prevalent microvascular complications in this patient population, contributing to high morbidity and mortality rates. Currently, changes in albuminuria status are thought to be a primary indicator of the onset or progression of DKD, yet progressive nephropathy and renal impairment can occur in certain diabetic individuals who exhibit normal urinary albumin levels, emphasizing the lack of sensitivity and specificity associated with the use of albuminuria as a biomarker for detecting diabetic kidney disease and predicting DKD risk. According to the study, a non-invasive method for early detection or prediction of DKD may involve combining proteomic analytical techniques such second generation sequencing, mass spectrometry, two-dimensional gel electrophoresis, and other advanced system biology algorithms. Another category of proteins of relevance may now be provided by renal tissue biomarkers. The establishment of reliable proteomic biomarkers of DKD represents a novel approach to improving the diagnosis, prognostic evaluation, and treatment of affected patients. In the present review, a series of protein biomarkers that have been characterized to date are discussed, offering a theoretical foundation for future efforts to aid patients suffering from this debilitating microvascular complication.
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Affiliation(s)
- Lan Wei
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Chao Tu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
- Correspondence: Chao Tu, Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, 213000, People’s Republic of China, Email
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Araumi A, Osaki T, Ichikawa K, Kudo K, Suzuki N, Watanabe S, Watanabe M, Konta T. Urinary and plasma proteomics to discover biomarkers for diagnosing between diabetic nephropathy and minimal change nephrotic syndrome or membranous nephropathy. Biochem Biophys Rep 2021; 27:101102. [PMID: 34458592 PMCID: PMC8379417 DOI: 10.1016/j.bbrep.2021.101102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022] Open
Abstract
The choice of treatment for primary nephrotic syndrome depends on the pathologic type of the disorder. Renal biopsy is necessary for a definitive diagnosis, but it is burdensome for the patients, and can be avoided if tests could be performed using urine or plasma. In this study, we analyzed 100 urinary proteins, 141 plasma proteins, and 57 urine/plasma ratios in cases of diabetic nephropathy (DN; n = 11), minimal change nephrotic syndrome (MCNS; n = 14), and membranous nephropathy (MN; n = 23). We found that the combination of urinary retinol-binding protein 4 and SH3 domain-binding glutamic acid-rich-like protein 3 could distinguish between MCNS and DN, with an area under the curve (AUC) of 0.9740. On the other hand, a selectivity index (SI) based on serotransferrin and immunoglobulin G, which is often used in clinical practice, distinguished them with an AUC of 0.9091. Similarly, the combination of urinary afamin and complement C3 urine/plasma ratio could distinguish between MN and DN with an AUC of 0.9842, while SI distinguished them with an AUC of 0.8538. Evidently, the candidates identified in this study were superior to the SI method. Thus, the aim was to test these biomarkers for accurate diagnosis and to greatly reduce the burden on patients. Renal biopsy is necessary for a definitive diagnosis of primary nephrotic syndrome. Renal biopsy is a heavy burden for patients, and a less burdensome test is desired. We discovered at least 6 diagnostic biomarkers using urinary and plasma proteomics. Combination allowed to judge the disease more accurately than selectivity index.
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Affiliation(s)
- Akira Araumi
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, Yamagata, Japan
| | - Tsukasa Osaki
- Department of Public Health and Hygiene, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Kazunobu Ichikawa
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, Yamagata, Japan
| | - Kosuke Kudo
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, Yamagata, Japan
| | - Natsuko Suzuki
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, Yamagata, Japan
| | - Sayumi Watanabe
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, Yamagata, Japan
| | - Masafumi Watanabe
- Department of Cardiology, Pulmonology, and Nephrology, Yamagata University School of Medicine, Yamagata, Japan
| | - Tsuneo Konta
- Department of Public Health and Hygiene, Yamagata University Faculty of Medicine, Yamagata, Japan
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10
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Di Pisa F, Pesenti E, Bono M, Mazzarello AN, Bernardi C, Lisanti MP, Renzone G, Scaloni A, Ciccone E, Fais F, Bruno S, Scartezzini P, Ghiotto F. SH3BGRL3 binds to myosin 1c in a calcium dependent manner and modulates migration in the MDA-MB-231 cell line. BMC Mol Cell Biol 2021; 22:41. [PMID: 34380438 PMCID: PMC8356473 DOI: 10.1186/s12860-021-00379-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
Background The human SH3 domain Binding Glutamic acid Rich Like 3 (SH3BGRL3) gene is highly conserved in phylogeny and widely expressed in human tissues. However, its function is largely undetermined. The protein was found to be overexpressed in several tumors, and recent work suggested a possible relationship with EGFR family members. We aimed at further highlighting on these issues and investigated SH3BGRL3 molecular interactions and its role in cellular migration ability. Results We first engineered the ErbB2-overexpressing SKBR3 cells to express exogenous SH3BGRL3, as well as wild type Myo1c or different deletion mutants. Confocal microscopy analysis indicated that SH3BGRL3 co-localized with Myo1c and ErbB2 at plasma membranes. However, co-immunoprecipitation assays and mass spectrometry demonstrated that SH3BGRL3 did not directly bind ErbB2, but specifically recognized Myo1c, on its IQ-bearing neck region. Importantly, the interaction with Myo1c was Ca2+-dependent. A role for SH3BGRL3 in cell migration was also assessed, as RNA interference of SH3BGRL3 in MDA-MB-231 cells, used as a classical migration model, remarkably impaired the migration ability of these cells. On the other side, its over-expression increased cell motility. Conclusion The results of this study provide insights for the formulation of novel hypotheses on the putative role of SH3BGRL3 protein in the regulation of myosin-cytoskeleton dialog and in cell migration. It could be envisaged the SH3BGRL3-Myo1c interaction as a regulation mechanism for cytoskeleton dynamics. It is well known that, at low Ca2+ concentrations, the IQ domains of Myo1c are bound by calmodulin. Here we found that binding of Myo1c to SH3BGRL3 requires instead the presence of Ca2+. Thus, it could be hypothesized that Myo1c conformation may be modulated by Ca2+-driven mechanisms that involve alternative binding by calmodulin or SH3BGRL3, for the regulation of cytoskeletal activity. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00379-1.
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Affiliation(s)
- Filippo Di Pisa
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy.,Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester, UK
| | - Elisa Pesenti
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy.,Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Maria Bono
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy
| | - Andrea N Mazzarello
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, 11030, USA
| | - Cinzia Bernardi
- Molecular Pathology Unit, IRCCS Policlinico San Martino, 16132, Genoa, Italy
| | - Michael P Lisanti
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester, UK
| | - Giovanni Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM-National Research Council, 80147, Naples, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM-National Research Council, 80147, Naples, Italy
| | - Ermanno Ciccone
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy
| | - Franco Fais
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy.,Molecular Pathology Unit, IRCCS Policlinico San Martino, 16132, Genoa, Italy
| | - Silvia Bruno
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy
| | | | - Fabio Ghiotto
- Department of Experimental Medicine, University of Genoa, 16132, Genoa, Italy. .,Molecular Pathology Unit, IRCCS Policlinico San Martino, 16132, Genoa, Italy.
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11
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SH3BGRL3, transcribed by STAT3, facilitates glioblastoma tumorigenesis by activating STAT3 signaling. Biochem Biophys Res Commun 2021; 556:114-120. [PMID: 33839406 DOI: 10.1016/j.bbrc.2021.03.165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/19/2022]
Abstract
Glioblastoma (GBM) is the most aggressive tumors of the central nervous system. Here, we report that SH3 binding glutamic acid-rich protein like 3 (SH3BGRL3) was extremely highly expressed in GBM and glioma stem cells. SH3BGRL3 high expression associates with worse survival of GBM patients. Functionally, Targeting SH3BGRL3 obviously impairs GSCs self-renewal in vitro. Most importantly, we first report that SH3BGRL3 is a direct transcriptional target gene of signal transducer and activator of transcription 3 (STAT3) and thereby activating STAT3 signaling in turn. Additionally, forced expression of the constitutively activated STAT3 (STAT3-C) rescued GSCs self-renewal inhibited by SH3BGRL3 silencing. Collectively, we first identified a critical positive feedback loop between SH3BGRL3 and STAT3, which facilitates the tumorigenic potential of GBM.
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12
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Cheng HL, Chou LP, Tsai HW, Lee CT, Wang YW, Chung-Liang H, Ou JH, Tsai YS, Chow NH. Urothelial carcinoma with trophoblastic differentiation: Reappraisal of the clinical implication and immunohistochemically features. Urol Oncol 2021; 39:732.e17-732.e23. [PMID: 33773916 DOI: 10.1016/j.urolonc.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/21/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE To investigate the clinical implications of identifying urothelial carcinoma (UC) with trophoblastic differentiation (UCTD). MATERIALS AND METHODS A prospective cohort study was performed from 2010 to 2016 to examine the incidence of UCTD in urinary tract cancer and association with clinicopathological indicators and patient outcome. RESULTS UCTD was detected in 47 of 859 (5.5%) cases of UC of the bladder and 65 of 635 (10.2%) cases in the upper urinary tract. UCTD of the bladder was significantly associated with non-papillary, multiple, larger size ( > 3 cm), muscle invasion, and nodal metastasis (P ≤ 0.0001, respectively). A higher risk of recurrence (P = 0.005), progression (P < 0.0001), and patient death (P < 0.0001) was observed for UCTD than those with traditional, high-grade UC of the bladder. Among four patterns of expression, focal expression of β-human chorionic gonadotropin was frequently detected in papillary tumor (P < 0.005) and UCs of smaller than 3 cm (P = 0.03). Significant indicators in predicting poor disease-specific overall survival in multivariate statistical model were tumor staging (P = 0.001), followed by non-focal β-hCG expression (P = 0.049). CONCLUSION UCTD is more often identified in the upper urinary tract than in the bladder. UCTD of the bladder was significantly associated with higher risk of recurrence, progression, and patient death. Expression of β-hCG in non-focal patterns predicts a worse prognosis for patients with UCTD and deserves an individualized treatment planning.
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Affiliation(s)
- Hong-Ling Cheng
- Departments of Urology, College of Medicine, National Cheng Kung University, Tainan, TW
| | - Lien-Ping Chou
- Department of Urology, National Cheng Kung University Hospital, Tainan, TW
| | - Hung-Wen Tsai
- Departments of Pathology, College of Medicine, National Cheng Kung University, Tainan, TW
| | - Chung-Ta Lee
- Departments of Pathology, College of Medicine, National Cheng Kung University, Tainan, TW
| | - Yi-Wen Wang
- Departments of Pathology, College of Medicine, National Cheng Kung University, Tainan, TW
| | - Ho Chung-Liang
- Departments of Pathology, College of Medicine, National Cheng Kung University, Tainan, TW; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, TW
| | - Jiann-Hui Ou
- Departments of Urology, College of Medicine, National Cheng Kung University, Tainan, TW
| | - Yuh-Shyan Tsai
- Departments of Urology, College of Medicine, National Cheng Kung University, Tainan, TW.
| | - Nan-Haw Chow
- Departments of Pathology, College of Medicine, National Cheng Kung University, Tainan, TW; Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, TW.
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13
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Jiang M, Lash GE, Zeng S, Liu F, Han M, Long Y, Cai M, Hou H, Ning F, Hu Y, Yang H. Differential expression of serum proteins before 20 weeks gestation in women with hypertensive disorders of pregnancy: A potential role for SH3BGRL3. Placenta 2020; 104:20-30. [PMID: 33217630 DOI: 10.1016/j.placenta.2020.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 09/19/2020] [Accepted: 10/26/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The objective of this study was to explore serum levels of differentially abundant proteins between women with hypertensive disorders of pregnancy (HDP) and women with normal-term pregnancy, and to explore the contribution of SH3BGRL3 to the pathogenesis of HDP. METHODS At 6-20 weeks gestation 48 pregnant women who later developed HDP (HDP group) and 48 women with normal-term pregnancy (normal group) were recruited based on maternal age and gestational age at a 1:1 ratio. Total serum protein was extracted, denatured, deoxidized, and subjected to enzymolysis. The sample was labeled with Tandem Mass Tags and analyzed via mass spectroscopy to identify differentially abundant proteins. The role of SH3BGRL3 in trophoblast invasion, proliferation and apoptosis was examined using the HTR-8/SVneo cell line and primary isolates of extravillous trophoblast (EVT) cells. RESULTS In the proteomic profiling analysis, there were 19 proteins that showed significant differential abundance (P < 0.05). Among them, 13 proteins were more abundant and 6 proteins were less abundant in the serum from the HDP group compared with the normal group. The function of one of the more abundant proteins, SH3BGRL3, in trophoblast cell invasion, proliferation and apoptosis was investigated. Treatment of the EVT cells or the HTR-8/SVneo cell line with anti-SH3BGRL3 inhibited proliferation, but stimulated both apoptosis and invasion. MMP2 and p-ERK levels were also decreased in EVT after anti-SH3BGRL3 treatment. DISCUSSION The SH3BGRL3 protein can regulate various aspects of trophoblast biology, and may be useful in the clinical diagnosis of HDP.
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Affiliation(s)
- Min Jiang
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Gendie E Lash
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China.
| | - Shanshui Zeng
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Fei Liu
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Mengru Han
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Yan Long
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Minmin Cai
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Huomei Hou
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Feng Ning
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China
| | - Yanwei Hu
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China.
| | - Hongling Yang
- Department of Clinical Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, PR China.
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14
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Wu J, Xiao Y, Sun J, Sun H, Chen H, Zhu Y, Fu H, Yu C, E W, Lai S, Ma L, Li J, Fei L, Jiang M, Wang J, Ye F, Wang R, Zhou Z, Zhang G, Zhang T, Ding Q, Wang Z, Hao S, Liu L, Zheng W, He J, Huang W, Wang Y, Xie J, Li T, Cheng T, Han X, Huang H, Guo G. A single-cell survey of cellular hierarchy in acute myeloid leukemia. J Hematol Oncol 2020; 13:128. [PMID: 32977829 PMCID: PMC7517826 DOI: 10.1186/s13045-020-00941-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a fatal hematopoietic malignancy and has a prognosis that varies with its genetic complexity. However, there has been no appropriate integrative analysis on the hierarchy of different AML subtypes. Methods Using Microwell-seq, a high-throughput single-cell mRNA sequencing platform, we analyzed the cellular hierarchy of bone marrow samples from 40 patients and 3 healthy donors. We also used single-cell single-molecule real-time (SMRT) sequencing to investigate the clonal heterogeneity of AML cells. Results From the integrative analysis of 191727 AML cells, we established a single-cell AML landscape and identified an AML progenitor cell cluster with novel AML markers. Patients with ribosomal protein high progenitor cells had a low remission rate. We deduced two types of AML with diverse clinical outcomes. We traced mitochondrial mutations in the AML landscape by combining Microwell-seq with SMRT sequencing. We propose the existence of a phenotypic “cancer attractor” that might help to define a common phenotype for AML progenitor cells. Finally, we explored the potential drug targets by making comparisons between the AML landscape and the Human Cell Landscape. Conclusions We identified a key AML progenitor cell cluster. A high ribosomal protein gene level indicates the poor prognosis. We deduced two types of AML and explored the potential drug targets. Our results suggest the existence of a cancer attractor.
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Affiliation(s)
- Junqing Wu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yanyu Xiao
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Yuanyuan Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Huarui Fu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Guodong Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tingyue Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiong Ding
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Zou Wang
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Sheng Hao
- Wuhan Biobank Co., LTD, Wuhan, 430075, China
| | - Lizhen Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weiyan Zheng
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jingsong He
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yungui Wang
- Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jin Xie
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, 310058, China
| | - Tiefeng Li
- Institute of Applied Mechanics, Zhejiang University, Hangzhou, 310027, China
| | - Tao Cheng
- Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300000, China.,Alliance for Atlas of Blood Cells, Tianjin, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
| | - He Huang
- Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Alliance for Atlas of Blood Cells, Tianjin, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China. .,Institute of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China. .,Stem Cell Institute, Zhejiang University, Hangzhou, 310058, China. .,Alliance for Atlas of Blood Cells, Tianjin, China. .,Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, 311121, China.
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15
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Singh N, Sahu DK, Tripathi RK, Mishra A, Shyam H, Shankar P, Jain M, Alam N, Kumar A, Mishra A, Chowdhry R, Singh A, Gupta S, Mehrotra D, Agarwal P, Goel MM, Chaturvedi A, Agarwal SP, Bajpai M, Gupta DK, Bhatt MLB, Kant R. Differentially expressed full-length, fusion and novel isoforms transcripts-based signature of well-differentiated keratinized oral squamous cell carcinoma. Oncotarget 2020; 11:3227-3243. [PMID: 32922662 PMCID: PMC7456611 DOI: 10.18632/oncotarget.27693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022] Open
Abstract
Highly keratinized oral squamous cell carcinoma (OSCC) exhibits an improved response to treatment and prognosis compared with weakly keratinized OSCC. Therefore, we aimed to develop gene transcript signature and to identify novel full-length isoforms, fusion transcript and non-coding RNA to differentiate well-differentiated (WD) with Moderately Differentiated (MD)/Poorly Differentiated (PD)/WD-lymphadenopathy OSCC through, HTA, Isoform sequencing, and NanoString. Additionally, specific copy number gain and loss were also identify in WD keratinized OSCC through Oncoscan array and validated through Real-time PCR in histopathologically characterized FFPE-WD keratinized OSCC. Three-hundred-thirty-eight (338) differentially expressed full-length (FL) transcript isoforms (317 upregulated and 21 down-regulated in OSCC) were identified through Isoform Sequencing using the PacBio platform. Thirty-four (34) highly upregulated differentially expressed transcripts from IsoSeq data were also correlated with HTA2.0 and validated in 42 OSCC samples. We were able to identify 18 differentially expressed transcripts, 12 fusion transcripts, and two long noncoding RNAs. These transcripts were involved in increased cell proliferation, dysregulated metabolic reprogramming, oxidative stress, and immune system markers with enhanced immune rearrangements, suggesting a cancerous nature. However, an increase in proteasomal activity and hemidesmosome proteins suggested an improved prognosis and tumor cell stability in keratinized OSCC and helped to characterize WD with MD/PD/WD with lymphadenopathy OSCC. Additionally, novel isoforms of IL37, NAA10, UCHL3, SPAG7, and RAB24 were identified while in silico functionally validated SPAG7 represented the premalignant phenotype of keratinized (K4) OSCC. Most importantly we found copy number gain and overexpression of EGFR suggest that TKIs may also be used as therapeutics in WD-OSCCs.
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Affiliation(s)
- Neetu Singh
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Dinesh Kumar Sahu
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Ratnesh Kumar Tripathi
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,These authors contributed equally to this work
| | - Archana Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India.,Department of Surgery, King George's Medical University, Lucknow, India
| | - Hari Shyam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Pratap Shankar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Mayank Jain
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Nawazish Alam
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Anil Kumar
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Abhishek Mishra
- Department of Molecular Biology, Center for Advance Research, King George's Medical University, Lucknow, India
| | - Rebecca Chowdhry
- Department of Periodontology, All India Institute of Medical Sciences, Rishikesh, India
| | - Anjana Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | - Divya Mehrotra
- Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow, India
| | - Preeti Agarwal
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Madhu Mati Goel
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Arun Chaturvedi
- Department of Surgical Oncology, King George's Medical University, Lucknow, India
| | | | - Manish Bajpai
- Department of Physiology, King George's Medical University, Lucknow, India
| | - Devendra Kumar Gupta
- Department of Pediatric Surgery, Super Speciality Pediatric Hospital and Post Graduate Teaching Institute, Noida, India
| | | | - Ravi Kant
- Department of Surgical Oncology, All India Institute of Medical Sciences, Rishikesh, India
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16
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Logotheti S, Marquardt S, Gupta SK, Richter C, Edelhäuser BA, Engelmann D, Brenmoehl J, Söhnchen C, Murr N, Alpers M, Singh KP, Wolkenhauer O, Heckl D, Spitschak A, Pützer BM. LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1. Am J Cancer Res 2020; 10:9620-9643. [PMID: 32863950 PMCID: PMC7449907 DOI: 10.7150/thno.44176] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as integral components of E2F1-regulated gene regulatory networks (GRNs), but their implication in advanced or treatment-refractory malignancy is unknown. Methods: We combined high-throughput transcriptomic approaches with bioinformatics and structure modeling to search for lncRNAs that participate in E2F1-activated prometastatic GRNs and their phenotypic targets in the highly-relevant case of E2F1-driven aggressive bladder cancer (BC). RNA immunoprecipitation was performed to verify RNA-protein interactions. Functional analyses including qRT-PCR, immunoblotting, luciferase assays and measurement of extracellular fluxes were conducted to validate expression and target gene regulation. Results: We identified E2F1-responsive lncRNA-SLC16A1-AS1 and its associated neighboring protein-coding gene, SLC16A1/MCT1, which both promote cancer invasiveness. Mechanistically, upon E2F1-mediated co-transactivation of the gene pair, SLC16A1-AS1 associates with E2F1 in a structure-dependent manner and forms an RNA-protein complex that enhances SLC16A1/MCT1 expression through binding to a composite SLC16A1-AS1:E2F1-responsive promoter element. Moreover, SLC16A1-AS1 increases aerobic glycolysis and mitochondrial respiration and fuels ATP production by fatty acid β-oxidation. These metabolic changes are accompanied by alterations in the expression of the SLC16A1-AS1:E2F1-responsive gene PPARA, a key mediator of fatty acid β-oxidation. Conclusions: Our results unveil a new gene regulatory program by which E2F1-induced lncRNA-SLC16A1-AS1 forms a complex with its transcription factor that promotes cancer metabolic reprogramming towards the acquisition of a hybrid oxidative phosphorylation/glycolysis cell phenotype favoring BC invasiveness.
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17
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Dufies M. SH3BGRL2, a new downregulated tumor suppressor in clear cell renal cell carcinomas. EBioMedicine 2020; 52:102641. [PMID: 32014821 PMCID: PMC6997511 DOI: 10.1016/j.ebiom.2020.102641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/13/2020] [Indexed: 11/03/2022] Open
Affiliation(s)
- Maeva Dufies
- Centre Scientifique de Monaco, Biomedical Department, Principality of Monaco, Monaco.
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18
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Yin L, Li W, Xu A, Shi H, Wang K, Yang H, Wang R, Peng B. SH3BGRL2 inhibits growth and metastasis in clear cell renal cell carcinoma via activating hippo/TEAD1-Twist1 pathway. EBioMedicine 2020; 51:102596. [PMID: 31911271 PMCID: PMC7000347 DOI: 10.1016/j.ebiom.2019.12.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignancies in the world, and tumor metastasis is still the main reason for disease progression. Accumulating evidence shows that SH3BGRL2 may play a key role in tumor progression and metastasis. However, the role of SH3BGRL2 in ccRCC has not been systematically investigated and remains elusive. Methods The clinical significance of SH3BGRL2 was evaluated by bioinformatic analysis and tissue microarray (TMA) samples. SH3BGRL2 expression was determined by RT-PCR, western blot and immunohistochemistry staining. Tumor suppressive effect of SH3BGRL2 was determined by both in vitro and in vivo studies. Western blot, chromatin immunoprecipitation assay and luciferase report assay were applied for mechanism dissection. Findings SH3BGRL2 was crucial for epithelial-mesenchymal transition (EMT) progression and metastasis in ccRCC. Clinically, SH3BGRL2 was identified as an independent prognostic factor for ccRCC patients. Gain- and loss-of-function results suggested that SH3BGRL2 played a critical role in cell proliferation, migration and invasion. Mechanistically, we found that SH3BGRL2 acted as a tumor suppressor through Hippo/TEAD1 signaling, then TEAD1 altered Twist1 expression at the transcriptional level via directly binding to its promoter region. Interpretation Our findings established that SH3BGRL2 performed as a tumor suppressor and modulator via Hippo/TEAD1-Twist1 signaling in ccRCC, and the alteration of SH3BGRL2 could serve as a functional response biomarker of tumor progression and metastasis in ccRCC.
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Affiliation(s)
- Lei Yin
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Wenjia Li
- Shanghai Institute of Cardiovascular Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Aiming Xu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Shi
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Keyi Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Huan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Ronghao Wang
- School of basic medical sciences, Southwest Medical University, Luzhou, China.
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China.
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19
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Gellert M, Hossain MF, Berens FJF, Bruhn LW, Urbainsky C, Liebscher V, Lillig CH. Substrate specificity of thioredoxins and glutaredoxins - towards a functional classification. Heliyon 2019; 5:e02943. [PMID: 31890941 PMCID: PMC6928294 DOI: 10.1016/j.heliyon.2019.e02943] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
The spatio-temporal reduction and oxidation of protein thiols is an essential mechanism in signal transduction in all kingdoms of life. Thioredoxin (Trx) family proteins efficiently catalyze thiol-disulfide exchange reactions and the proteins are widely recognized for their importance in the operation of thiol switches. Trx family proteins have a broad and at the same time very distinct substrate specificity – a prerequisite for redox switching. Despite of multiple efforts, the true nature for this specificity is still under debate. Here, we comprehensively compare the classification/clustering of various redoxins from all domains of life based on their similarity in amino acid sequence, tertiary structure, and their electrostatic properties. We correlate these similarities to the existence of common interaction partners, identified in various previous studies and suggested by proteomic screenings. These analyses confirm that primary and tertiary structure similarity, and thereby all common classification systems, do not correlate to the target specificity of the proteins as thiol-disulfide oxidoreductases. Instead, a number of examples clearly demonstrate the importance of electrostatic similarity for their target specificity, independent of their belonging to the Trx or glutaredoxin subfamilies.
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Affiliation(s)
- Manuela Gellert
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Md Faruq Hossain
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Felix Jacob Ferdinand Berens
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany.,Institute for Mathematics and Informatics, University of Greifswald, Germany
| | - Lukas Willy Bruhn
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany.,Institute for Mathematics and Informatics, University of Greifswald, Germany
| | - Claudia Urbainsky
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
| | - Volkmar Liebscher
- Institute for Mathematics and Informatics, University of Greifswald, Germany
| | - Christopher Horst Lillig
- Institute for Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Germany
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20
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Proteomic Technology "Lens" for Epithelial-Mesenchymal Transition Process Identification in Oncology. Anal Cell Pathol (Amst) 2019; 2019:3565970. [PMID: 31781477 PMCID: PMC6855076 DOI: 10.1155/2019/3565970] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/20/2019] [Accepted: 09/10/2019] [Indexed: 02/08/2023] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a complex transformation process that induces local and distant progression of many malignant tumours. Due to its complex array of proteins that are dynamically over-/underexpressed during this process, proteomic technologies gained their place in the EMT research in the last years. Proteomics has identified new molecular pathways of this process and brought important insights to develop new therapy targets. Various proteomic tools and multiple combinations were developed in this area. Out of the proteomic technology armentarium, mass spectrometry and array technologies are the most used approaches. The main characteristics of the proteomic technology used in this domain are high throughput and detection of minute concentration in small samples. We present herein, using various proteomic technologies, the identification in cancer cell lines and in tumour tissue EMT-related proteins, proteins that are involved in the activation of different cellular pathways. Proteomics has brought besides standard EMT markers (e.g., cell-cell adhesion proteins and transcription factors) other future potential markers for improving diagnosis, monitoring evolution, and developing new therapy targets. Future will increase the proteomic role in clinical investigation and validation of EMT-related biomarkers.
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21
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Seervi M, Sumi S, Chandrasekharan A, Sharma AK, SanthoshKumar TR. Molecular profiling of anastatic cancer cells: potential role of the nuclear export pathway. Cell Oncol (Dordr) 2019; 42:645-661. [PMID: 31147963 DOI: 10.1007/s13402-019-00451-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2019] [Indexed: 01/11/2023] Open
Abstract
PURPOSE Anastasis is newly discovered process by which cells recover from late-stage apoptosis upon removal of a death stimulus. Recent reports suggest that cells may recover, even after the initiation of mitochondrial outer-membrane permeabilization (MOMP) and caspase activation. Here, we specifically studied the reversibility of late-stage apoptosis in cervical (HeLa) and breast (MDA-MB-231) cancer cells in relation to the extent of MOMP (limited or widespread). In addition, we explored the molecular factors involved in the anastatic process. METHODS The extent of MOMP was assessed using time lapse confocal microscopic imaging, considering mitochondrial cytochrome c-GFP release as a marker for MOMP. Anastatic cells were generated by specifically recovering late-stage apoptotic (annexin V/PI positive) cervical and breast cancer cells. Molecular signaling events involved in death reversal were assessed using LC-MS/MS and qRT-PCR. Targeted chemical inhibition and shRNA-based gene silencing studies were employed to explore the role of the nuclear export pathway in anastasis and increased oncogenicity. RESULTS Time-lapse imaging of drug-treated Cyt-c-GFP expressing cancer cells revealed cell recovery despite widespread MOMP. A few recovered anastatic cells were noted and these were found to proliferate through a selection-type of survival. They showed increased drug-resistance, migration and invasive potential compared to non-anastatic cancer cells. Network analysis using 49 proteins uniquely expressed in anastatic cells indicated upregulation of nuclear export/import, redox and Ras signaling pathways in both HeLa and MDA-MB-231 anastatic cells, indicating common molecular mechanisms in different cell types. Inhibition of XPO1 significantly reduced the recovery of apoptotic cells and abrogated acquired oncogenic transformation in the anastatic cancer cells. CONCLUSIONS Our study indicates that cancer cells can revert from apoptosis even after the induction of widespread MOMP. We noted a significant role of the nuclear-export pathway in the anastatic process of cancer cells. Inhibition of anastasis through the nuclear export pathway may be a potential therapeutic strategy for targeting drug-resistance, metastasis and recurrence problems during cancer treatment.
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Affiliation(s)
- Mahendra Seervi
- DBT-PU-IPLS, Department of Botany/Biotechnology, Patna University, Patna, Bihar, India.
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat, India.
| | - S Sumi
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Aneesh Chandrasekharan
- Cancer Research Division 1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Abhay K Sharma
- DBT-PU-IPLS, Department of Botany/Biotechnology, Patna University, Patna, Bihar, India
| | - T R SanthoshKumar
- Cancer Research Division 1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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22
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Yin L, Gao S, Shi H, Wang K, Yang H, Peng B. TIP-B1 promotes kidney clear cell carcinoma growth and metastasis via EGFR/AKT signaling. Aging (Albany NY) 2019; 11:7914-7937. [PMID: 31562290 PMCID: PMC6782011 DOI: 10.18632/aging.102298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/14/2019] [Indexed: 12/14/2022]
Abstract
Kidney clear cell carcinoma (KIRC) is the most prevalent kidney malignancy. Accumulating evidence shows that high expression of TIP-B1 correlates with development of tumor progression. However, the detailed functions of TIP-B1 in the KIRC remain to be further elucidated. Here, we firstly found TIP-B1 expression was significantly increased in KIRC compared with adjacent normal tissues. What’s more, higher expression of TIP-B1 were correlated with aggressive clinico-pathological characteristics. In vitro assay found TIP-B1 knockdown dramatically inhibited KIRC cells proliferation, migration and invasion. In vivo assay found down regulated TIP-B1 could suppress tumor growth and metastasis. Mechanism analysis indicated that TIP-B1 could bind EGFR and suppress EGFR degradation, then promoted EGF-induced AKT signaling. Together, TIP-B1 could be applied as an independent risk factor to predict KIRC progression and metastasis. Targeting TIP-B1 might be a new potential therapeutic strategy for KIRC treatment.
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Affiliation(s)
- Lei Yin
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Shenglin Gao
- Department of Urology, Changzhou No. 2 People's Hospital, Nanjing Medical University, Changzhou, Jiangsu, China
| | - Heng Shi
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China.,Department of Urology, Shanghai Tenth People's Hospital, Nanjing Medical University, Nanjing, China
| | - Keyi Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
| | - Huan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, China
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23
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Krochmal M, van Kessel KEM, Zwarthoff EC, Belczacka I, Pejchinovski M, Vlahou A, Mischak H, Frantzi M. Urinary peptide panel for prognostic assessment of bladder cancer relapse. Sci Rep 2019; 9:7635. [PMID: 31114012 PMCID: PMC6529475 DOI: 10.1038/s41598-019-44129-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Non-invasive tools stratifying bladder cancer (BC) patients according to the risk of relapse are urgently needed to guide clinical intervention. As a follow-up to the previously published study on CE-MS-based urinary biomarkers for BC detection and recurrence monitoring, we expanded the investigation towards BC patients with longitudinal data. Profiling datasets of BC patients with follow-up information regarding the relapse status were investigated. The peptidomics dataset (n = 98) was split into training and test set. Cox regression was utilized for feature selection in the training set. Investigation of the entire training set at the single peptide level revealed 36 peptides being strong independent prognostic markers of disease relapse. Those features were further integrated into a Random Forest-based model evaluating the risk of relapse for BC patients. Performance of the model was assessed in the test cohort, showing high significance in BC relapse prognosis [HR = 5.76, p-value = 0.0001, c-index = 0.64]. Urinary peptide profiles integrated into a prognostic model allow for quantitative risk assessment of BC relapse highlighting the need for its incorporation in prospective studies to establish its value in the clinical management of BC.
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Affiliation(s)
| | - Kim E M van Kessel
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Urology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens (BRFAA), Athens, Greece
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24
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Wu Y, Zhang J, Wang M, Yang L, Wang Y, Hu T, Liu A, Cheng Q, Fu Z, Zhang P, Cao L. Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects. J Cell Physiol 2019; 234:13544-13556. [PMID: 30635921 DOI: 10.1002/jcp.28033] [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: 05/26/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Abnormal development of embryonic conus arteriosus could lead to conotruncal defects in fetal heart, and increase the incidence of fetal congenital heart disease. Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. It may be helpful for us to solve this clinical problem through exploring the molecular mechanisms of development in embryonic congenital heart disease. Proteomics has attracted much attention in understanding the development of human diseases during the past decades. However, there is still little information about the relationship between protein expression pattern and TOF. In this study, we aimed to explore the potential linkage of proteomics and TOF development. Briefly, 121 differentially expressed proteins were identified from a TOF group, compared with a control group. The expression levels of 34 of these proteins were significantly different (>1.5 absolute fold change, p < 0.05) between the two groups. Gene ontology (GO) and pathway analysis showed that these proteins were mainly associated with carbon metabolism, biosynthesis of antibodies, positive regulation of transcription from RNA polymerase II promoter, nucleus, ATP binding, and so on. The ingenuity pathway analysis (IPA) results indicated that 435 of upstream regulators were identified of these differentially expressed proteins, which might be involved in the development of TOF. Data of string analysis showed the protein-protein interaction network among the differentially expressed proteins and regulators, which are related to TOF. In conclusion, our study explored the protein expression pattern of TOF, which might provide new insights into understanding the mechanism of TOF development and afford potential targets for TOF diagnosis and therapy.
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Affiliation(s)
- Yun Wu
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Mei Wang
- Department of Pathology, Nanjing Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Yang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yongmei Wang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tao Hu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - An Liu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Qing Cheng
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Ziyi Fu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pingyang Zhang
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Li Cao
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
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25
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Xiang Z, Huang X, Wang J, Zhang J, Ji J, Yan R, Zhu Z, Cai W, Yu Y. Cross-Database Analysis Reveals Sensitive Biomarkers for Combined Therapy for ERBB2+ Gastric Cancer. Front Pharmacol 2018; 9:861. [PMID: 30123134 PMCID: PMC6085474 DOI: 10.3389/fphar.2018.00861] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
Exploring ERBB2-related pathways will help us finding sensitive molecules and potential combined therapeutic targets of ERBB2-targeted therapy for ERBB2+ gastric cancer (GC). In this study, we performed a cross-databases study focused on ERBB2+ GC. The data of ERBB2+ GC deposited in the cancer genome atlas (TCGA), gene expression omnibus (GEO), InBio MapTM, cancer cell line encyclopedia (CCLE), and cancer therapeutics response portal (CTRP) were analyzed. The correlation of expression levels of candidate and IC50 of candidate genes-targeted drugs were verified on NCI-N87 and MKN-45 GC cell lines. We found that RARA, THRA, CACNB1, and TOP2A are drug sensitive biomarkers of ERBB2-targeted treatment with FDA-approved drugs. All these genes act through Myc signaling pathway. Myc is the downstream hub gene of both ERBB2 and RARA. The expression of RARA, THRA, and CACNB1 were negatively correlated with Myc activation, while ERBB2 and TOP2A positively correlated with Myc activation. SH3BGRL3, SH3BGRL, and NRG2 were identified as potential ligands of ERBB2. The ERBB2+ GC with RARA amplification demonstrated better prognosis than those without RARA amplification, while overexpression of NRG2 and SH3BGRL correlated with poor prognosis in ERBB2+ GC. About 90% of ERBB2+ GC was compatible with chromosome instability (CIN) subtype of TCGA, which overlaps with intestinal-type GC in Lauren classification. In validating experiments, combination of Lapatinib and all-trans retinoic acid (ATRA) synergistically suppresses cell growth, and accompanied by decreased expression of MYC. In conclusions, we identified several predicting biomarkers for ERBB2-targeted therapy and corresponding histological features of ERBB2+ GC. Combination of ERBB2 antagonist or RARA agonist may be effective synergistic regimens for ERBB2+ GC.
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Affiliation(s)
- Zhen Xiang
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Xia Huang
- Department of Disease Prevention and Control, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiexuan Wang
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Jun Zhang
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Jun Ji
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Ranlin Yan
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Zhenggang Zhu
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Wei Cai
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
| | - Yingyan Yu
- Department of Surgery, Ruijin Hospital, Shanghai Institute of Digestive Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai, China
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26
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Wang W, Wang S, Zhang M. Identification of urine biomarkers associated with lung adenocarcinoma. Oncotarget 2018; 8:38517-38529. [PMID: 28404947 PMCID: PMC5503550 DOI: 10.18632/oncotarget.15870] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/24/2017] [Indexed: 12/16/2022] Open
Abstract
Lung adenocarcinoma (LAC) progression is accompanied by changes in protein levels that may be reflected in body fluids, such as urine. Urine collected from LAC patients (n=34) and healthy controls (n=36) was analyzed via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) combined with weak cationic exchange magnetic beads. The results revealed 76 urinary polypeptides significantly different between LAC patients and normal controls (P<0.05). Twenty-two of these peptides were up-regulated and 54 were down-regulated. Thirteen peptides had average peak intensities >600. Twelve of these 13 peptides were successfully identified using nano-liquid chromatography-tandem MS. Receiver operating characteristic analyses identified seven peptides with superior LAC diagnostic performances. Immunohistochemical staining in 20 paired LAC and adjacent normal tissues showed that IGKC, AAT, SH3BGRL3, osteopontin and gelsolin levels were higher in LAC tissues than in adjacent tissuesand were closely associated with LAC. Urinary peptides assessments may thus provide a novel, noninvasive, repeatable method for detecting and monitoring LAC. New, low-cost detection methods and bioinformatics tools are therefore urgently needed for the analysis of low abundance proteins and peptides in body fluids.
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Affiliation(s)
- Weiwei Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Shanshan Wang
- Department of Pulmonary and Critical Care Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Man Zhang
- Clinical Laboratory Medicine, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics, Beijing, China
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27
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Zhang H, Fan Y, Xia L, Gao C, Tong X, Wang H, Sun L, Ji T, Jin M, Gu B, Fan B. The impact of advanced proteomics in the search for markers and therapeutic targets of bladder cancer. Tumour Biol 2017; 39:1010428317691183. [PMID: 28345451 DOI: 10.1177/1010428317691183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bladder cancer is the most common cancer of the urinary tract and can be avoided through proper surveillance and monitoring. Several genetic factors are known to contribute to the progression of bladder cancer, many of which produce molecules that serve as cancer biomarkers. Blood, urine, and tissue are commonly analyzed for the presence of biomarkers, which can be derived from either the nucleus or the mitochondria. Recent advances in proteomics have facilitated the high-throughput profiling of data generated from bladder cancer-related proteins or peptides in parallel with high sensitivity and specificity, providing a wealth of information for biomarker discovery and validation. However, the transmission of screening results from one laboratory to another remains the main disadvantage of these methods, a fact that emphasizes the need for consistent and standardized procedures as suggested by the Human Proteome Organization. This review summarizes the latest discoveries and progress of biomarker identification for the early diagnosis, projected prognosis, and therapeutic response of bladder cancer, informs the readers of the current status of proteomic-based biomarker findings, and suggests avenues for future work.
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Affiliation(s)
- Hongshuo Zhang
- 1 Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, P.R. China
| | - Yue Fan
- 2 Department of Propaganda, Jinzhou Medical University, Jinzhou, P.R. China
| | - Lingling Xia
- 3 Graduate School, Guangzhou Medical University, Guangzhou, P.R. China.,4 Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, P.R. China
| | - Chunhui Gao
- 5 Department of Gastrointestinal Surgery, The Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Xin Tong
- 6 Department of Gastrointestinal Surgery, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P.R. China
| | - Hanfu Wang
- 7 Medical Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, P.R. China
| | - Lili Sun
- 8 Department of Ophthalmology, The Third Affiliated Hospital of Jinzhou Medical University, Jinzhou, P.R. China
| | - Tuo Ji
- 9 Department of Hospital Management, Jinzhou Medical University, Jinzhou, P.R. China
| | - Mingyu Jin
- 10 Graduate School, Dalian Medical University, Dalian, P.R. China
| | - Bing Gu
- 11 Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, P.R. China
| | - Bo Fan
- 12 Department of Urology, Second Affiliated Hospital, Dalian Medical University, Dalian, P.R. China
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28
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Hsu JL, Chen SH. Stable isotope dimethyl labelling for quantitative proteomics and beyond. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0364. [PMID: 27644970 PMCID: PMC5031631 DOI: 10.1098/rsta.2015.0364] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 05/21/2023]
Abstract
Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan City, Taiwan, Republic of China
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29
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Meo AD, Pasic MD, Yousef GM. Proteomics and peptidomics: moving toward precision medicine in urological malignancies. Oncotarget 2016; 7:52460-52474. [PMID: 27119500 PMCID: PMC5239567 DOI: 10.18632/oncotarget.8931] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
Urological malignancies are a major cause of morbidity and mortality worldwide. Advances in early detection, diagnosis, prognosis and prediction of treatment response can significantly improve patient care. Proteomic and peptidomic profiling studies are at the center of kidney, prostate and bladder cancer biomarker discovery and have shown great promise for improved clinical assessment. Mass spectrometry (MS) is the most widely employed method for proteomic and peptidomic analyses. A number of MS platforms have been developed to facilitate accurate identification of clinically relevant markers in various complex biological samples including tissue, urine and blood. Furthermore, protein profiling studies have been instrumental in the successful introduction of several diagnostic multimarker tests into the clinic. In this review, we will provide a brief overview of high-throughput technologies for protein and peptide based biomarker discovery. We will also examine the current state of kidney, prostate and bladder cancer biomarker research as well as review the journey toward successful clinical implementation.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Maria D. Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, Ontario, Canada
| | - George M. Yousef
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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