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Meta-Analysis of MS-Based Proteomics Studies Indicates Interferon Regulatory Factor 4 and Nucleobindin1 as Potential Prognostic and Drug Resistance Biomarkers in Diffuse Large B Cell Lymphoma. Cells 2023; 12:cells12010196. [PMID: 36611989 PMCID: PMC9818977 DOI: 10.3390/cells12010196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The prognosis of diffuse large B cell lymphoma (DLBCL) is inaccurately predicted using clinical features and immunohistochemistry (IHC) algorithms. Nomination of a panel of molecules as the target for therapy and predicting prognosis in DLBCL is challenging because of the divergences in the results of molecular studies. Mass spectrometry (MS)-based proteomics in the clinic represents an analytical tool with the potential to improve DLBCL diagnosis and prognosis. Previous proteomics studies using MS-based proteomics identified a wide range of proteins. To achieve a consensus, we reviewed MS-based proteomics studies and extracted the most consistently significantly dysregulated proteins. These proteins were then further explored by analyzing data from other omics fields. Among all significantly regulated proteins, interferon regulatory factor 4 (IRF4) was identified as a potential target by proteomics, genomics, and IHC. Moreover, annexinA5 (ANXA5) and nucleobindin1 (NUCB1) were two of the most up-regulated proteins identified in MS studies. Functional enrichment analysis identified the light zone reactions of the germinal center (LZ-GC) together with cytoskeleton locomotion functions as enriched based on consistent, significantly dysregulated proteins. In this study, we suggest IRF4 and NUCB1 proteins as potential biomarkers that deserve further investigation in the field of DLBCL sub-classification and prognosis.
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Guo C, Trivedi R, Tripathi AK, Nandy RR, Wagner DC, Narra K, Chaudhary P. Higher Expression of Annexin A2 in Metastatic Bladder Urothelial Carcinoma Promotes Migration and Invasion. Cancers (Basel) 2022; 14:cancers14225664. [PMID: 36428758 PMCID: PMC9688257 DOI: 10.3390/cancers14225664] [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: 10/19/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
In this study, we aim to evaluate the significance of AnxA2 in BLCA and establish its metastatic role in bladder cancer cells. Analysis of TCGA data showed that AnxA2 mRNA expression was significantly higher in BLCA tumors than in normal bladder tissues. High mRNA expression of AnxA2 in BLCA was significantly associated with high pathological grades and stages, non-papillary tumor histology, and poor overall survival (OS), progression-free survival (PFS), and diseases specific survival (DSS). Similarly, we found that AnxA2 expression was higher in bladder cancer cells derived from high-grade metastatic carcinoma than in cells derived from low-grade urothelial carcinoma. AnxA2 expression significantly mobilized to the surface of highly metastatic bladder cancer cells compared to cells derived from low-grade tumors and associated with high plasmin generation and AnxA2 secretion. In addition, the downregulation of AnxA2 cells significantly inhibited the proliferation, migration, and invasion in bladder cancer along with the reduction in proangiogenic factors and cytokines such as PDGF-BB, ANGPT1, ANGPT2, Tie-2, bFGF, GRO, IL-6, IL-8, and MMP-9. These findings suggest that AnxA2 could be a promising biomarker and therapeutic target for high-grade BLCA.
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Affiliation(s)
- Christina Guo
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Rucha Trivedi
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Amit K. Tripathi
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Rajesh R. Nandy
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Diana C. Wagner
- Department of Anatomic Pathology, JPS Health Network, Fort Worth, TX 76104, USA
| | - Kalyani Narra
- JPS Oncology and Infusion Center, JPS Health Network, Fort Worth, TX 76104, USA
| | - Pankaj Chaudhary
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Correspondence: ; Tel.: +1-817-735-5178
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Prieto-Fernández L, Menéndez ST, Otero-Rosales M, Montoro-Jiménez I, Hermida-Prado F, García-Pedrero JM, Álvarez-Teijeiro S. Pathobiological functions and clinical implications of annexin dysregulation in human cancers. Front Cell Dev Biol 2022; 10:1009908. [PMID: 36247003 PMCID: PMC9554710 DOI: 10.3389/fcell.2022.1009908] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Annexins are an extensive superfamily of structurally related calcium- and phospholipid-binding proteins, largely conserved and widely distributed among species. Twelve human annexins have been identified, referred to as Annexin A1-13 (A12 remains as of yet unassigned), whose genes are spread throughout the genome on eight different chromosomes. According to their distinct tissue distribution and subcellular localization, annexins have been functionally implicated in a variety of biological processes relevant to both physiological and pathological conditions. Dysregulation of annexin expression patterns and functions has been revealed as a common feature in multiple cancers, thereby emerging as potential biomarkers and molecular targets for clinical application. Nevertheless, translation of this knowledge to the clinic requires in-depth functional and mechanistic characterization of dysregulated annexins for each individual cancer type, since each protein exhibits varying expression levels and phenotypic specificity depending on the tumor types. This review specifically and thoroughly examines the current knowledge on annexin dysfunctions in carcinogenesis. Hence, available data on expression levels, mechanism of action and pathophysiological effects of Annexin A1-13 among different cancers will be dissected, also further discussing future perspectives for potential applications as biomarkers for early diagnosis, prognosis and molecular-targeted therapies. Special attention is devoted to head and neck cancers (HNC), a complex and heterogeneous group of aggressive malignancies, often lately diagnosed, with high mortality, and scarce therapeutic options.
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Affiliation(s)
- Llara Prieto-Fernández
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía T. Menéndez
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - María Otero-Rosales
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Irene Montoro-Jiménez
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Hermida-Prado
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Juana M. García-Pedrero
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | - Saúl Álvarez-Teijeiro
- Department of Otolaryngology, Hospital Universitario Central de Asturias and Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Instituto Universitario de Oncología Del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
- CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
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Sarafidis M, Lambrou GI, Zoumpourlis V, Koutsouris D. An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. Cancers (Basel) 2022; 14:cancers14143358. [PMID: 35884419 PMCID: PMC9319344 DOI: 10.3390/cancers14143358] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Bladder cancer is evidently a challenge as far as its prognosis and treatment are concerned. The investigation of potential biomarkers and therapeutic targets is indispensable and still in progress. Most studies attempt to identify differential signatures between distinct molecular tumor subtypes. Therefore, keeping in mind the heterogeneity of urinary bladder tumors, we attempted to identify a consensus gene-related signature between the common expression profile of bladder cancer and control samples. In the quest for substantive features, we were able to identify key hub genes, whose signatures could hold diagnostic, prognostic, or therapeutic significance, but, primarily, could contribute to a better understanding of urinary bladder cancer biology. Abstract Bladder cancer (BCa) is one of the most prevalent cancers worldwide and accounts for high morbidity and mortality. This study intended to elucidate potential key biomarkers related to the occurrence, development, and prognosis of BCa through an integrated bioinformatics analysis. In this context, a systematic meta-analysis, integrating 18 microarray gene expression datasets from the GEO repository into a merged meta-dataset, identified 815 robust differentially expressed genes (DEGs). The key hub genes resulted from DEG-based protein–protein interaction and weighted gene co-expression network analyses were screened for their differential expression in urine and blood plasma samples of BCa patients. Subsequently, they were tested for their prognostic value, and a three-gene signature model, including COL3A1, FOXM1, and PLK4, was built. In addition, they were tested for their predictive value regarding muscle-invasive BCa patients’ response to neoadjuvant chemotherapy. A six-gene signature model, including ANXA5, CD44, NCAM1, SPP1, CDCA8, and KIF14, was developed. In conclusion, this study identified nine key biomarker genes, namely ANXA5, CDT1, COL3A1, SPP1, VEGFA, CDCA8, HJURP, TOP2A, and COL6A1, which were differentially expressed in urine or blood of BCa patients, held a prognostic or predictive value, and were immunohistochemically validated. These biomarkers may be of significance as prognostic and therapeutic targets for BCa.
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Affiliation(s)
- Michail Sarafidis
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780 Athens, Greece;
- Correspondence: ; Tel.: +30-210-772-2430
| | - George I. Lambrou
- Choremeio Research Laboratory, First Department of Pediatrics, National and Kapodistrian University of Athens, 8 Thivon & Levadeias Str., 11527 Athens, Greece;
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, 8 Thivon & Levadeias Str., 11527 Athens, Greece
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vas. Konstantinou Ave., 11635 Athens, Greece;
| | - Dimitrios Koutsouris
- Biomedical Engineering Laboratory, School of Electrical and Computer Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., 15780 Athens, Greece;
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Zhao J, Chang L, Tu J, Sun B, Wei X. Evaluation of Annexins Family as Potential Biomarker for Predicting Progression and Prognosis in Clear Renal Cell Carcinoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:8748434. [PMID: 39290334 PMCID: PMC11407897 DOI: 10.1155/2022/8748434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 09/19/2024]
Abstract
Background Annexins family (ANXAs), as a Ca2+-dependent phospholipid-binding protein superfamily, participates in a wide variety of biological activities and has been reported to be dysregulated in numerous types of human cancers. Evidence from cell lines and human tissues indicates that ANAXs are involved in kidney clear renal cell carcinoma (KIRC) tumorigenesis. However, their prognostic value and expression pattern associated with KIRC remain to be elucidated. Methods We visited public databases, including ONCOMINE, Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier plotter, cBioPortal, and GeneMANIA, to conduct comprehensive bioinformatics analysis and tried to detect basic relationships between each Annexins family member and KIRC. Results We found that the expression level of ANXA1/2/4/5/6/7/8/13 in clear renal cell carcinoma tissue was higher than that in the kidney tissue, while the expression level of ANXA3/9/11 in the former was lower than that in the latter. The expression level of ANXA7/8/13 is related to the stage of the tumour. Survival analysis using the Kaplan-Meier plotter database showed that a high transcription level of ANXA2/5/8/10 is related to a low overall survival rate (OS) in predicting KIRC patients. In contrast, high ANXA3/4/7/9/11/13 levels are associated with a high OS in these patients. Conclusions Our study implies that ANXA4/8/13 are potential targets of precision therapy for patients with KIRC and that ANXA2/5/8/10 are new biomarkers for the prognosis of KIRC.
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Affiliation(s)
- Jiyu Zhao
- Department of Urology, ChuiYangLiu Hospital Affiliated to Tsinghua University, 100021 Beijing, China
| | - Luchen Chang
- Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, 300060 Tianjin, China
| | - Jianping Tu
- Department of Urology, The Third Hospital of Xiamen, 361199 Xiamen, Fujian, China
| | - Bei Sun
- Department of Outpatient Office, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, 300060 Tianjin, China
| | - Xi Wei
- Department of Diagnostic and Therapeutic Ultrasonography, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, 300060 Tianjin, China
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Wan S, Jiang C, Li S, Fan Y. Special Issue on Bioinformatics and Machine Learning for Cancer Biology. BIOLOGY 2022; 11:biology11030361. [PMID: 35336735 PMCID: PMC8945039 DOI: 10.3390/biology11030361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
Abstract
Cancer is a leading cause of death worldwide, claiming millions of lives each year [...]
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Affiliation(s)
- Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
- Correspondence: ; Tel.: +1-901-595-1905
| | - Chunjie Jiang
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Shengli Li
- School of Medicine, Shanghai Jiao Tong University, Shanghai 201620, China;
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
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