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Sarhadi S, Armani A, Jafari-Gharabaghlou D, Sadeghi S, Zarghami N. Cross-platform gene expression profiling of breast cancer: Exploring the relationship between breast cancer grades and gene expression pattern. Heliyon 2024; 10:e29736. [PMID: 38681607 PMCID: PMC11053269 DOI: 10.1016/j.heliyon.2024.e29736] [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: 05/12/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
Gene expression profiling is a powerful tool that has been extensively used to investigate the underlying biology and etiology of diseases, including cancer. Microarray gene expression analysis enables simultaneous measurement of thousands of mRNA levels. Sophisticated computational approaches have evolved in parallel with the rapid progress in bioassay technologies, enabling more effective analysis of the large and complex datasets that these technologies produce. In this study, we utilized systems biology approaches to examine gene expression profiles across different grades of breast cancer progression. We conducted a meta-analysis of publicly available microarray data to elucidate the molecular mechanisms underlying breast cancer grade classification. Our results suggest that while grade index is commonly used for evaluating cancer progression status in the clinic, the complexity of molecular mechanisms, histological characteristics, and other factors related to patient outcomes raises doubts about the utility of breast cancer grades as a foundation for formulating treatment protocols. Our study underscores the importance of advancing personalized strategies for breast cancer classification and management. More research is crucial to refine diagnostic tools and treatment modalities, aiming for greater precision and tailored care in patient outcomes.
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Affiliation(s)
- Shamim Sarhadi
- Institute of Clinical Chemistry and Pathobiochemistry, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Arta Armani
- Department of Medical Biology and Genetic, Faculty of Medicine, Istanbul Aydin University, Istanbul, Turkey
| | - Davoud Jafari-Gharabaghlou
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Somayeh Sadeghi
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nosratollah Zarghami
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Aydin University, Istanbul, Turkey
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Long Noncoding RNAs and Circular RNAs Regulate AKT and Its Effectors to Control Cell Functions of Cancer Cells. Cells 2022; 11:cells11192940. [PMID: 36230902 PMCID: PMC9563963 DOI: 10.3390/cells11192940] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/06/2022] [Accepted: 09/17/2022] [Indexed: 11/29/2022] Open
Abstract
AKT serine-threonine kinase (AKT) and its effectors are essential for maintaining cell proliferation, apoptosis, autophagy, endoplasmic reticulum (ER) stress, mitochondrial morphogenesis (fission/fusion), ferroptosis, necroptosis, DNA damage response (damage and repair), senescence, and migration of cancer cells. Several lncRNAs and circRNAs also regulate the expression of these functions by numerous pathways. However, the impact on cell functions by lncRNAs and circRNAs regulating AKT and its effectors is poorly understood. This review provides comprehensive information about the relationship of lncRNAs and circRNAs with AKT on the cell functions of cancer cells. the roles of several lncRNAs and circRNAs acting on AKT effectors, such as FOXO, mTORC1/2, S6K1/2, 4EBP1, SREBP, and HIF are explored. To further validate the relationship between AKT, AKT effectors, lncRNAs, and circRNAs, more predicted AKT- and AKT effector-targeting lncRNAs and circRNAs were retrieved from the LncTarD and circBase databases. Consistently, using an in-depth literature survey, these AKT- and AKT effector-targeting database lncRNAs and circRNAs were related to cell functions. Therefore, some lncRNAs and circRNAs can regulate several cell functions through modulating AKT and AKT effectors. This review provides insights into a comprehensive network of AKT and AKT effectors connecting to lncRNAs and circRNAs in the regulation of cancer cell functions.
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Dioguardi M, Spirito F, Sovereto D, La Femina L, Campobasso A, Cazzolla AP, Di Cosola M, Zhurakivska K, Cantore S, Ballini A, Lo Muzio L, Troiano G. Biological Prognostic Value of miR-155 for Survival Outcome in Head and Neck Squamous Cell Carcinomas: Systematic Review, Meta-Analysis and Trial Sequential Analysis. BIOLOGY 2022; 11:biology11050651. [PMID: 35625379 PMCID: PMC9138061 DOI: 10.3390/biology11050651] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide; in fact, it is among the top six neoplasms, with an incidence of about 370,000 new cases per year. The 5-year survival rate, despite chemotherapy, radiotherapy, and surgery for stages 3 and 4 of the disease, is low. MicroRNAs (miRNAs) are a large group of small single-stranded non-coding endogenous RNAs, approximately 18-25 nucleotides in length, that play a significant role in the post-transcriptional regulation of genes. Recent studies investigated the tissue expression of miR-155 as a prognostic biomarker of survival in HNSCC. The purpose of this systematic review is, therefore, to investigate and summarize the current findings in the literature concerning the potential prognostic expression of tissue miR-155 in patients with HNSCC. The revision was performed according to PRISMA indications: three databases (PubMed, Scopus, and the Cochrane Register) were consulted through the use of keywords relevant to the revision topic. Totally, eight studies were included and meta-analyzed. The main results report for the aggregate HR values of 1.40 for OS, 1.36 for DFS, and 1.09 for DPS. Finally, a trial sequencing analysis was also conducted to test the robustness of the proposed meta-analysis.
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Affiliation(s)
- Mario Dioguardi
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
- Correspondence:
| | - Francesca Spirito
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Diego Sovereto
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Lucia La Femina
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Alessandra Campobasso
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Angela Pia Cazzolla
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Michele Di Cosola
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Khrystyna Zhurakivska
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Stefania Cantore
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari “Aldo Moro”, 70124 Bari, Italy; (S.C.); (A.B.)
- Faculty of Dentistry (Fakulteti i Mjekësisë Dentare-FMD), University of Medicine, 1001 Tirana, Albania
| | - Andrea Ballini
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari “Aldo Moro”, 70124 Bari, Italy; (S.C.); (A.B.)
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy; (F.S.); (D.S.); (L.L.F.); (A.C.); (A.P.C.); (M.D.C.); (K.Z.); (L.L.M.); (G.T.)
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