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Fan J, Xue L, Lin H, Luo J. Depletion of NUAK2 blocks the stemness and angiogenesis and facilitates senescence of lung adenocarcinoma cells via enhancing ferroptosis. Cell Div 2024; 19:23. [PMID: 39068449 PMCID: PMC11283724 DOI: 10.1186/s13008-024-00128-8] [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: 03/15/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND NUAK family kinase 2 (NUAK2) has been identified as an important mediator for tumor progression in multiple malignancies. Nevertheless, its role in lung adenocarcinoma (LUAD) remains unclear. METHODS Bioinformatic analysis was performed to assess the expression and prognosis of NUAK2 in patients with LUAD. The NUAK2 expression was measured in multiple LUAD cell lines, and the loss-of-function experiment was conducted. Cell proliferation ability was assessed using CCK-8 and colony formation assays. Spheroid formation, alkaline phosphatase (AP) staining, tube formation and SA-β-gal staining assays were performed to examine stemness, angiogenesis and senescence. Lipid peroxidase was assessed by TBARS production and lipid ROS. Western blot was used to detect critical proteins. In addition, A549 cells were treated with ferroptosis inhibitor ferrostatin-1 (Fer-1) for a rescue assay. Finally, A549 cells were subcutaneously injected into the right flank of mice to establish LUAD-bearing mouse model, and the tumor weight and size were detected. RESULTS NUAK2 was upregulated in patients with LUAD and LUAD cell lines. NUAK2 depletion inhibited cell viability, colonies, tumor spheres and decreased Oct4 and Nanog expression, confirming NUAK2 depletion inhibited proliferation and stemness of A549 cells. Meanwhile, NUAK2 depletion blocked angiogenesis via reducing formed tubes and VEGFR1/2 expression, and promoted senescence of A549 cells by elevating SA-β-gal-positive cells and p16, p21 and p53 expression. Moreover, NUAK2 depletion elevated lipid ROS, TBARS production and Fe2+ level, demonstrating that NUAK2 depletion could trigger ferroptosis in A549 cells. Furthermore, the rescue experiments revealed that the impacts of NUAK2 depletion on malignant behaviors in A549 cells were partly weakened by additional Fer-1 treatment. Finally, in vivo experiments demonstrated that NUAK2 knockdown greatly inhibited tumor growth in LUAD-bearing mice. CONCLUSION In summary, NUAK2 depletion impeded oncogenic phenotypes of A549 cells partly via triggering ferroptosis, suggesting NUAK2 as a novel target for treating LUAD.
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Affiliation(s)
- Jun Fan
- Department of Thoracic Surgery, the First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Gulou District, Nanjing, 210000, Jiangsu, China
| | - Lei Xue
- Department of Thoracic Surgery, the First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Gulou District, Nanjing, 210000, Jiangsu, China
| | - Haoran Lin
- Department of Thoracic Surgery, the First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Gulou District, Nanjing, 210000, Jiangsu, China
| | - Jinhua Luo
- Department of Thoracic Surgery, the First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Gulou District, Nanjing, 210000, Jiangsu, China.
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2
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Wang Y, Chen Y, Zhao M. N6-methyladenosine modification and post-translational modification of epithelial-mesenchymal transition in colorectal cancer. Discov Oncol 2024; 15:209. [PMID: 38834851 DOI: 10.1007/s12672-024-01048-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 05/20/2024] [Indexed: 06/06/2024] Open
Abstract
Colorectal cancer is a leading cause of cancer-related mortality worldwide. Traditionally, colorectal cancer has been recognized as a disease caused by genetic mutations. However, recent studies have revealed the significant role of epigenetic alterations in the progression of colorectal cancer. Epithelial-mesenchymal transition, a critical step in cancer cell metastasis, has been found to be closely associated with the tumor microenvironment and immune factors, thereby playing a crucial role in many kinds of biological behaviors of cancers. In this review, we explored the impact of N6-methyladenosine and post-translational modifications (like methylation, acetylation, ubiquitination, SUMOylation, glycosylation, etc.) on the process of epithelial-mesenchymal transition in colorectal cancer and the epigenetic regulation for the transcription factors and pathways correlated to epithelial-mesenchymal transition. Furthermore, we emphasized that the complex regulation of epithelial-mesenchymal transition by epigenetics can provide new strategies for overcoming drug resistance and improving treatment outcomes. This review aims to provide important scientific evidence for the prevention and treatment of colorectal cancer based on epigenetic modifications.
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Affiliation(s)
- Yingnan Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Yufan Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China
| | - Miaomiao Zhao
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou, 310000, China.
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3
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Kim MW, Moon S, Lee S, Lee H, Kim Y, Kim JY, Kim JY, Kim SI. Exploring miRNA‑target gene profiles associated with drug resistance in patients with breast cancer receiving neoadjuvant chemotherapy. Oncol Lett 2024; 27:158. [PMID: 38426156 PMCID: PMC10902752 DOI: 10.3892/ol.2024.14291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Exosomal microRNAs (miRNAs) are closely related to drug resistance in patients with breast cancer (BC); however, only a few roles of the exosomal miRNA-target gene networks have been clinically implicated in drug resistance in BC. Therefore, the present study aimed to identify the differential expression of exosomal miRNAs associated with drug resistance and their target mRNAs. In vitro microarray analysis was used to verify differentially expressed miRNAs (DEMs) in drug-resistant BC. Next, tumor-derived exosomes (TDEs) were isolated. Furthermore, it was determined whether the candidate drug-resistant miRNAs were also significant in TDEs, and then putative miRNAs in TDEs were validated in plasma samples from 35 patients with BC (20 patients with BC showing no response and 15 patients with BC showing a complete response). It was confirmed that the combination of five exosomal miRNAs, including miR-125b-5p, miR-146a-5p, miR-484, miR-1246-5p and miR-1260b, was effective for predicting therapeutic response to neoadjuvant chemotherapy, with an area under the curve value of 0.95, sensitivity of 75%, and specificity of 95%. Public datasets were analyzed to identify differentially expressed genes (DEGs) related to drug resistance and it was revealed that BAK1, NOVA1, PTGER4, RTKN2, AGO1, CAP1, and ETS1 were the target genes of exosomal miRNAs. Networks between DEMs and DEGs were highly correlated with mitosis, metabolism, drug transport, and immune responses. Consequently, these targets could be used as predictive markers and therapeutic targets for clinical applications to enhance treatment outcomes for patients with BC.
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Affiliation(s)
- Min Woo Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Sol Moon
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Suji Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hyojung Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Young Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Joon Ye Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jee Ye Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Il Kim
- Department of Surgery, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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4
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Negrutskii BS, Porubleva LV, Malinowska A, Novosylna OV, Dadlez M, Knudsen CR. Understanding functions of eEF1 translation elongation factors beyond translation. A proteomic approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:67-99. [PMID: 38220433 DOI: 10.1016/bs.apcsb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Mammalian translation elongation factors eEF1A1 and eEF1A2 are 92% homologous isoforms whose mutually exclusive tissue-specific expression is regulated during development. The isoforms have similar translation functionality, but show differences in spatial organization and participation in various processes, such as oncogenesis and virus reproduction. The differences may be due to their ability to interact with isoform-specific partner proteins. We used the identified sets of eEF1A1 or eEF1A2 partner proteins to identify cell complexes and/or processes specific to one particular isoform. As a result, we found isoform-specific interactions reflecting the involvement of different eEF1A isoforms in different cellular processes, including actin-related, chromatin-remodeling, ribonuclease H2, adenylyl cyclase, and Cul3-RING ubiquitin ligase complexes as well as initiation of mitochondrial transcription. An essential by-product of our analysis is the elucidation of a number of cellular processes beyond protein biosynthesis, where both isoforms appear to participate such as large ribosomal subunit biogenesis, mRNA splicing, DNA mismatch repair, 26S proteasome activity, P-body and exosomes formation, protein targeting to the membrane. This information suggests that a relatively high content of eEF1A in the cell may be necessary not only to maintain efficient translation, but also to ensure its participation in various cellular processes, where some roles of eEF1A have not yet been described. We believe that the data presented here will be useful for deciphering new auxiliary functions of eEF1A and its isoforms, and provide a new look at the known non-canonical functions of this main component of the human translation-elongation machinery.
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Affiliation(s)
- Boris S Negrutskii
- Institute of Molecular Biology and Genetics, Kyiv, Ukraine; Aarhus Institute of Advanced Sciences, Høegh-Guldbergs, Aarhus C, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark.
| | | | - Agata Malinowska
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | | | - Michal Dadlez
- Institute of Biochemistry and Biophysics, PAN, Pawinskiego, Warsaw, Poland
| | - Charlotte R Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen, Aarhus C, Denmark
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Xie J, Quan L, Wang X, Wu H, Jin Z, Pan D, Chen T, Wu T, Lyu Q. DeepMPSF: A Deep Learning Network for Predicting General Protein Phosphorylation Sites Based on Multiple Protein Sequence Features. J Chem Inf Model 2023; 63:7258-7271. [PMID: 37931253 DOI: 10.1021/acs.jcim.3c00996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Phosphorylation, as one of the most important post-translational modifications, plays a key role in various cellular physiological processes and disease occurrences. In recent years, computer technology has been gradually applied to the prediction of protein phosphorylation sites. However, most existing methods rely on simple protein sequence features that provide limited contextual information. To overcome this limitation, we propose DeepMPSF, a phosphorylation site prediction model based on multiple protein sequence features. There are two types of features: sequence semantic features, which comprise protein residue type information and relative position information within protein sequence, and protein background biophysical features, which include global semantic information containing more comprehensive protein background information obtained from pretrained models. To extract these features, DeepMPSF employs two separate subnetworks: the S71SFE module and the BBFE module, which automatically extract high-level semantic features. Our model incorporates a learning strategy for handling imbalanced datasets through ensemble learning during training and prediction. DeepMPSF is trained and evaluated on a well-established dataset of human proteins. Comparing the analysis with other benchmark methods reveals that DeepMPSF outperforms in predicting both S/T residues and Y residues. In particular, DeepMPSF showed excellent generalization performance in cross-species blind test performance, with an average improvement of 5.63%/5.72%, 22.28%/25.94%, 20.11%/17.49%, and 26.40%/28.33% for Mus musculus/Rattus norvegicus test sets in area under curves (AUCs) of ROC curve, AUC of the PR curve, F1-score, and MCC metrics, respectively. Furthermore, it also shows excellent performance in the latest updated case of natural proteins with functional phosphorylation sites. Through an ablation study and visual analysis, we uncover that the design of different feature modules significantly contributes to the accurate classification of DeepMPSF, which provides valuable insights for predicting phosphorylation sites and offers effective support for future downstream research.
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Affiliation(s)
- Jingxin Xie
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Lijun Quan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Xuejiao Wang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Hongjie Wu
- Suzhou University of Science and Technology, Suzhou 215006, China
| | - Zhi Jin
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Deng Pan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Taoning Chen
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Tingfang Wu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Qiang Lyu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
- Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China
- Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
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Nikhil K, Shah K. CDK5: an oncogene or an anti-oncogene: location location location. Mol Cancer 2023; 22:186. [PMID: 37993880 PMCID: PMC10666462 DOI: 10.1186/s12943-023-01895-8] [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: 08/01/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
Recent studies have uncovered various physiological functions of CDK5 in many nonneuronal tissues. Upregulation of CDK5 and/or its activator p35 in neurons promotes healthy neuronal functions, but their overexpression in nonneuronal tissues is causally linked to cancer of many origins. This review focuses on the molecular mechanisms by which CDK5 recruits diverse tissue-specific substrates to elicit distinct phenotypes in sixteen different human cancers. The emerging theme suggests that CDK5's role as an oncogene or anti-oncogene depends upon its subcellular localization. CDK5 mostly acts as an oncogene, but in gastric cancer, it is a tumor suppressor due to its unique nuclear localization. This indicates that CDK5's access to certain nuclear substrates converts it into an anti-oncogenic kinase. While acting as a bonafide oncogene, CDK5 also activates a few cancer-suppressive pathways in some cancers, presumably due to the mislocalization of nuclear substrates in the cytoplasm. Therefore, directing CDK5 to the nucleus or exporting tumor-suppressive nuclear substrates to the cytoplasm may be promising approaches to combat CDK5-induced oncogenicity, analogous to neurotoxicity triggered by nuclear CDK5. Furthermore, while p35 overexpression is oncogenic, hyperactivation of CDK5 by inducing p25 formation results in apoptosis, which could be exploited to selectively kill cancer cells by dialing up CDK5 activity, instead of inhibiting it. CDK5 thus acts as a molecular rheostat, with different activity levels eliciting distinct functional outcomes. Finally, as CDK5's role is defined by its substrates, targeting them individually or in conjunction with CDK5 should create potentially valuable new clinical opportunities.
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Affiliation(s)
- Kumar Nikhil
- Department of Chemistry, Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India
| | - Kavita Shah
- Department of Chemistry, Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA.
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7
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Li Y, Zhang R, Hei H. Advances in post-translational modifications of proteins and cancer immunotherapy. Front Immunol 2023; 14:1229397. [PMID: 37675097 PMCID: PMC10477431 DOI: 10.3389/fimmu.2023.1229397] [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: 05/26/2023] [Accepted: 07/21/2023] [Indexed: 09/08/2023] Open
Abstract
Protein post-translational modification (PTM) is a regulatory mechanism for protein activity modulation, localization, expression, and interactions with other cellular molecules. It involves the addition or removal of specific chemical groups on the amino acid residues of proteins. Its common forms include phosphorylation, ubiquitylation, methylation, and acetylation. Emerging research has highlighted lactylation, succinylation, and glycosylation. PTMs are involved in vital biological processes. The occurrence and development of diseases depends on protein abundance and is regulated by various PTMs. In addition, advancements in tumor immunotherapy have revealed that protein PTM is also involved in the proliferation, activation, and metabolic reprogramming of immune cells in tumor microenvironment. These PTMs play an important role in tumor immunotherapy. In this review, we comprehensively summarize the role of several types of PTMs in tumor immunotherapy. This review could provide new insights and future research directions for tumor immunotherapy.
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Affiliation(s)
| | | | - Hu Hei
- Department of Thyroid and Neck, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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8
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Gulhane P, Singh S. Unraveling the Post-Translational Modifications and therapeutical approach in NSCLC pathogenesis. Transl Oncol 2023; 33:101673. [PMID: 37062237 PMCID: PMC10133877 DOI: 10.1016/j.tranon.2023.101673] [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: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/18/2023] Open
Abstract
Non-Small Cell Lung Cancer (NSCLC) is the most prevalent kind of lung cancer with around 85% of total lung cancer cases. Despite vast therapies being available, the survival rate is low (5 year survival rate is 15%) making it essential to comprehend the mechanism for NSCLC cell survival and progression. The plethora of evidences suggests that the Post Translational Modification (PTM) such as phosphorylation, methylation, acetylation, glycosylation, ubiquitination and SUMOylation are involved in various types of cancer progression and metastasis including NSCLC. Indeed, an in-depth understanding of PTM associated with NSCLC biology will provide novel therapeutic targets and insight into the current sophisticated therapeutic paradigm. Herein, we reviewed the key PTMs, epigenetic modulation, PTMs crosstalk along with proteogenomics to analyze PTMs in NSCLC and also, highlighted how epi‑miRNA, miRNA and PTM inhibitors are key modulators and serve as promising therapeutics.
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Affiliation(s)
- Pooja Gulhane
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SPPU Campus, Pune 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SPPU Campus, Pune 411007, India.
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9
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Herrera JA, Dingle LA, Monetero MA, Venkateswaran RV, Blaikley JF, Granato F, Pearson S, Lawless C, Thornton DJ. Morphologically intact airways in lung fibrosis have an abnormal proteome. Respir Res 2023; 24:99. [PMID: 37005656 PMCID: PMC10066954 DOI: 10.1186/s12931-023-02400-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/16/2023] [Indexed: 04/04/2023] Open
Abstract
Honeycombing is a histological pattern consistent with Usual Interstitial Pneumonia (UIP). Honeycombing refers to cystic airways located at sites of dense fibrosis with marked mucus accumulation. Utilizing laser capture microdissection coupled mass spectrometry (LCM-MS), we interrogated the fibrotic honeycomb airway cells and fibrotic uninvolved airway cells (distant from honeycomb airways and morphologically intact) in specimens from 10 patients with UIP. Non-fibrotic airway cell specimens from 6 patients served as controls. Furthermore, we performed LCM-MS on the mucus plugs found in 6 patients with UIP and 6 patients with mucinous adenocarcinoma. The mass spectrometry data were subject to both qualitative and quantitative analysis and validated by immunohistochemistry. Surprisingly, fibrotic uninvolved airway cells share a similar protein profile to honeycomb airway cells, showing deregulation of the slit and roundabout receptor (Slit and Robo) pathway as the strongest category. We find that (BPI) fold-containing family B member 1 (BPIFB1) is the most significantly increased secretome-associated protein in UIP, whereas Mucin-5AC (MUC5AC) is the most significantly increased in mucinous adenocarcinoma. We conclude that fibrotic uninvolved airway cells share pathological features with fibrotic honeycomb airway cells. In addition, fibrotic honeycomb airway cells are enriched in mucin biogenesis proteins with a marked derangement in proteins essential for ciliogenesis. This unbiased spatial proteomic approach generates novel and testable hypotheses to decipher fibrosis progression.
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Affiliation(s)
- Jeremy A Herrera
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK.
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK.
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Lewis A Dingle
- Blond McIndoe Laboratories, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - M Angeles Monetero
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Rajamiyer V Venkateswaran
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - John F Blaikley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Felice Granato
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Stella Pearson
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - Craig Lawless
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - David J Thornton
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
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10
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Ercan H, Resch U, Hsu F, Mitulovic G, Bileck A, Gerner C, Yang JW, Geiger M, Miller I, Zellner M. A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection. Cells 2023; 12:747. [PMID: 36899884 PMCID: PMC10000902 DOI: 10.3390/cells12050747] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.
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Affiliation(s)
- Huriye Ercan
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
- Immunology Outpatient Clinic, 1090 Vienna, Austria
| | - Ulrike Resch
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Felicia Hsu
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Goran Mitulovic
- Proteomics Core Facility, Clinical Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Jae-Won Yang
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Margarethe Geiger
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ingrid Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Maria Zellner
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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11
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Kakurina G, Stakheeva M, Sereda E, Sidenko E, Cheremisina O, Choinzonov E, Kondakova I. A pilot study of the relative number of circulating tumor cells and leukocytes containing actin-binding proteins in head and neck cancer patients. J Biomed Res 2022; 37:213-224. [PMID: 37226274 PMCID: PMC10226087 DOI: 10.7555/jbr.36.20220182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/25/2023] Open
Abstract
Circulating tumor cells (CTCs) play an important role in tumor metastases, which is positively correlated with an increased risk of death. Actin-binding proteins, including cofilin (CFL1), profilin 1 (PFN1), and adenylate cyclase-associated protein 1 (CAP1), are thought to be involved in tumor cell motility and metastasis, specifically in head and neck squamous cell carcinoma (HNSCC). However, currently, there are no published studies on CFL1, PFN1, and CAP1 in CTCs and leukocytes in HNSCC patients. We assessed serum levels of CFL1, PFN1, and CAP1 and the number of CTCs and leukocytes containing these proteins in blood from 31 HNSCC patients (T1-4N0-2M0). The analysis used flow cytometry and an enzyme-linked immunosorbent assay kit. We found that CAP1 + CTCs and CAP1 + leukocyte subpopulations were prevalent in these HNSCC patient samples, while the prevalence rates of CFL1 + and PFN1 + CTCs were relatively low. Patients with stage T2-4N1-2M0 had CFL1 + and PFN1 + CTCs with an elevated PFN1 serum level, compared with the T1-3N0M0 group. In summary, the PFN1 serum level and the relative number of PFN1 +CD326 + CTCs could be valuable prognostic markers for HNSCC metastases. The current study is the first to obtain data regarding the contents of actin-binding proteins (ABPs) in CTCs, and leukocytes in blood from HNSCC patients. This is also the first to assess the relationship between the number of CTCs subgroups and disease characteristics.
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Affiliation(s)
- Gelena Kakurina
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and Biology, Siberian State Medical University, Tomsk 634050, Russia
| | - Marina Stakheeva
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and Biology, Siberian State Medical University, Tomsk 634050, Russia
| | - Elena Sereda
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine and Biology, Siberian State Medical University, Tomsk 634050, Russia
| | - Evgenia Sidenko
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
| | - Olga Cheremisina
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
| | - Evgeny Choinzonov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
| | - Irina Kondakova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634009, Russia
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Phosphorylated Proteins from Serum: A Promising Potential Diagnostic Biomarker of Cancer. Int J Mol Sci 2022; 23:ijms232012359. [PMID: 36293212 PMCID: PMC9604268 DOI: 10.3390/ijms232012359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is a fatal disease worldwide. Each year ten million people are diagnosed around the world, and more than half of patients eventually die from it in many countries. A majority of cancer remains asymptomatic in the earlier stages, with specific symptoms appearing in the advanced stages when the chances of adequate treatment are low. Cancer screening is generally executed by different imaging techniques like ultrasonography (USG), mammography, CT-scan, and magnetic resonance imaging (MRI). Imaging techniques, however, fail to distinguish between cancerous and non-cancerous cells for early diagnosis. To confirm the imaging result, solid and liquid biopsies are done which have certain limitations such as invasive (in case of solid biopsy) or missed early diagnosis due to extremely low concentrations of circulating tumor DNA (in case of liquid biopsy). Therefore, it is essential to detect certain biomarkers by a noninvasive approach. One approach is a proteomic or glycoproteomic study which mostly identifies proteins and glycoproteins present in tissues and serum. Some of these studies are approved by the Food and Drug Administration (FDA). Another non-expensive and comparatively easier method to detect glycoprotein biomarkers is by ELISA, which uses lectins of diverse specificities. Several of the FDA approved proteins used as cancer biomarkers do not show optimal sensitivities for precise diagnosis of the diseases. In this regard, expression of phosphoproteins is associated with a more specific stage of a particular disease with high sensitivity and specificity. In this review, we discuss the expression of different serum phosphoproteins in various cancers. These phosphoproteins are detected either by phosphoprotein enrichment by immunoprecipitation using phosphospecific antibody and metal oxide affinity chromatography followed by LC-MS/MS or by 2D gel electrophoresis followed by MALDI-ToF/MS analysis. The updated knowledge on phosphorylated proteins in clinical samples from various cancer patients would help to develop these serum phophoproteins as potential diagnostic/prognostic biomarkers of cancer.
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13
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Xie Y, Liu Y, Ding J, Li G, Ni B, Pang H, Hu X, Wu L. Identification of DDX31 as a Potential Oncogene of Invasive Metastasis and Proliferation in PDAC. Front Cell Dev Biol 2022; 10:762372. [PMID: 35237592 PMCID: PMC8883474 DOI: 10.3389/fcell.2022.762372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/11/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignant tumors worldwide and has poor prognosis. DEAD box proteins31 (DDX31) participate in cellular processes involving RNA secondary structure changes. However, the functions of DDX31 in PDAC remain to be elucidated. Methods: The key gene DDX31 was identified using a combination of a risk model and weighted gene co-expression network analysis (WGCNA) with R software. The biological functions of DDX31 in PDAC were investigated through bioinformatics analysis and in vitro experiments. Results: Combining with WGCNA and risk model, DDX31 was identified as a potential factor of the invasive metastasis properties of PDAC, and its expression was closely related to the malignant differentiation of PDAC. The results of gene set enrichment analysis (GSEA) showed that DDX31 was correlated with cell invasive metastasis and proliferation by activating MAPK signaling pathway. The inhibition of DDX31 inhibited the invasion and migration of PDAC cells. Survival analysis showed that DDX31 expression was negatively associated with the poor prognosis in patients with PDAC. Interpretation:DDX31 may be a potential factor for PDAC. The inhibition of DDX31 may be a potential way to treat PDAC.
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Affiliation(s)
- Yongjie Xie
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Yang Liu
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Jinsheng Ding
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Guangming Li
- Department of General Surgery, Tianjin General Surgery Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Ni
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,The Graduate School, Tianjin Medical University, Tianjin, China
| | - Huifang Pang
- Department of Gastroenterology, Digestive Endoscopy Unit, Tongliao City Hospital, Tongliao, China
| | - Xin Hu
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology, Tianjin, China
| | - Liangliang Wu
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention, Department of Gastric Cancer, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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