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Berta D, Girma M, Melku M, Adane T, Birke B, Yalew A. Role of RNA Splicing Mutations in Diffuse Large B Cell Lymphoma. Int J Gen Med 2023; 16:2469-2480. [PMID: 37342407 PMCID: PMC10278864 DOI: 10.2147/ijgm.s414106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Ribonucleic acid splicing is a crucial process to create a mature mRNA molecule by removing introns and ligating exons. This is a highly regulated process, but any alteration in splicing factors, splicing sites, or auxiliary components affects the final products of the gene. In diffuse large B-cell lymphoma, splicing mutations such as mutant splice sites, aberrant alternative splicing, exon skipping, and intron retention are detected. The alteration affects tumor suppression, DNA repair, cell cycle, cell differentiation, cell proliferation, and apoptosis. As a result, malignant transformation, cancer progression, and metastasis occurred in B cells at the germinal center. B-cell lymphoma 7 protein family member A (BCL7A), cluster of differentiation 79B (CD79B), myeloid differentiation primary response gene 88 (MYD88), tumor protein P53 (TP53), signal transducer and activator of transcription (STAT), serum- and glucose-regulated kinase 1 (SGK1), Pou class 2 associating factor 1 (POU2AF1), and neurogenic locus notch homolog protein 1 (NOTCH) are the most common genes affected by splicing mutations in diffuse large B cell lymphoma.
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Affiliation(s)
- Dereje Berta
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mekonnen Girma
- Department of Quality Assurance and Laboratory Management, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mulugeta Melku
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tiruneh Adane
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Bisrat Birke
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Aregawi Yalew
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Bayır Ö, Aşık MD, Saylam G, Pınarlı FA, Tatar EÇ, Han Ü, Şimşek E, Korkmaz MH. Differentially expressed genes related to lymph node metastasis in advanced laryngeal squamous cell cancers. Oncol Lett 2022; 24:409. [PMID: 36245825 PMCID: PMC9555062 DOI: 10.3892/ol.2022.13529] [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: 01/02/2022] [Accepted: 07/19/2022] [Indexed: 11/06/2022] Open
Abstract
Understanding the molecular mechanisms and gene expression in laryngeal squamous cell carcinoma (LSCC) may explain its aggressive biological behavior and regional metastasis pathways. In the present study, patients with locally advanced LSCC tumors were examined for differential gene expression in the normal mucosa (non-tumoral mucosa), tumors and lymph node tissues. The aim was to identify possible predictive genes for lymph node metastasis. A total of 16 patients who had undergone total laryngectomy with neck dissection for advanced LSCC were randomly selected from a hospital database: Eight of the patients had lymph node metastasis (Group 1) and the other eight patients did not have metastasis (Group 2). Overall survival (OS), disease-free survival (DFS) and disease-specific survival (DSS) were analyzed. For each patient, paraffin-embedded tissue samples were collected from non-tumoral mucosa, tumoral lesions and lymph node tissues. RNA was extracted from the tissue samples and used for complementary DNA synthesis, and microarray analysis was subsequently performed on each sample. Gene expression levels were determined in each specimen, and Groups 1 and 2 were compared and statistically analyzed. The microarray results for lymph node metastasis-positive and -negative groups, indicated the differential expression of 312 genes in the lymph nodes, 691 genes in the normal mucosal tissue and 93 genes in the tumor tissue. Transgelin (TAGLN) and cofilin 1 (CFL1) were identified as possible target genes and validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The RT-qPCR results for TAGLN and CFL1 supported the microarray data. OS, DFS and DSS times were longer in Group 2 than in Group 1 (P=0.002, 0.015 and 0.009, respectively). In addition, TAGLN and CFL1 were associated with DFS and DSS. On the basis of these results, it is suggested that TAGLN and CFL1 expression may play an important role in the pathogenesis of regional metastasis and poor prognosis in advanced LSCC.
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Affiliation(s)
- Ömer Bayır
- Department of Otolaryngology, Head and Neck Surgery, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara 06110, Turkey
| | - Mehmet Doğan Aşık
- Department of Medical Biology, School of Medicine, Ankara Yıldırım Beyazıt University, Ankara 06010, Turkey
| | - Güleser Saylam
- Department of Otolaryngology, Head and Neck Surgery, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara 06110, Turkey
| | | | - Emel Çadallı Tatar
- Department of Otolaryngology, Head and Neck Surgery, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara 06110, Turkey
| | - Ünsal Han
- Department of Pathology, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara 06110, Turkey
| | - Ender Şimşek
- Department of Medical Biology, School of Medicine, Ankara Yıldırım Beyazıt University, Ankara 06010, Turkey
| | - Mehmet Hakan Korkmaz
- Department of Otolaryngology, Head and Neck Surgery, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara 06110, Turkey
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine, Ankara Yıldırım Beyazıt University, Ankara 06010, Turkey
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Naakka E, Barros-Filho MC, Adnan-Awad S, Al-Samadi A, Marchi FA, Kuasne H, Korelin K, Suleymanova I, Brown AL, Scapulatempo-Neto C, Lourenço SV, Castilho RM, Kowalski LP, Mäkitie A, Araújo VC, Leivo I, Rogatto SR, Salo T, Passador-Santos F. miR-22 and miR-205 Drive Tumor Aggressiveness of Mucoepidermoid Carcinomas of Salivary Glands. Front Oncol 2022; 11:786150. [PMID: 35223452 PMCID: PMC8864291 DOI: 10.3389/fonc.2021.786150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
Objectives To integrate mRNA and miRNA expression profiles of mucoepidermoid carcinomas (MECs) and normal salivary gland (NSGs) tissue samples and identify potential drivers. Material and Methods Gene and miRNA expression arrays were performed in 35 MECs and six NSGs. Results We found 46 differentially expressed (DE) miRNAs and 3,162 DE mRNAs. Supervised hierarchical clustering analysis of the DE transcripts revealed two clusters in both miRNA and mRNA profiles, which distinguished MEC from NSG samples. The integrative miRNA-mRNA analysis revealed a network comprising 696 negatively correlated interactions (44 miRNAs and 444 mRNAs) involving cell signaling, cell cycle, and cancer-related pathways. Increased expression levels of miR-205-5p and miR-224-5p and decreased expression levels of miR-139-3p, miR-145-3p, miR-148a-3p, miR-186-5p, miR-338-3p, miR-363-3p, and miR-4324 were significantly related to worse overall survival in MEC patients. Two overexpressed miRNAs in MEC (miR-22 and miR-205) were selected for inhibition by the CRISPR-Cas9 method. Cell viability, migration, and invasion assays were performed using an intermediate grade MEC cell line. Knockout of miR-205 reduced cell viability and enhanced ZEB2 expression, while miR-22 knockout reduced cell migration and invasion and enhanced ESR1 expression. Our results indicate a distinct transcriptomic profile of MEC compared to NSG, and the integrative analysis highlighted miRNA-mRNA interactions involving cancer-related pathways, including PTEN and PI3K/AKT. Conclusion The in vitro functional studies revealed that miR-22 and miR-205 deficiencies reduced the viability, migration, and invasion of the MEC cells suggesting they are potential oncogenic drivers in MEC.
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Affiliation(s)
- Erika Naakka
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | | | - Shady Adnan-Awad
- Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland.,Hematology Research Unit, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Ahmed Al-Samadi
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | | | - Hellen Kuasne
- Centro Internacional de Pesquisa (CIPE) - A.C.Camargo Cancer Center, São Paulo, Brazil
| | - Katja Korelin
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - Ilida Suleymanova
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - Amy Louise Brown
- Department of Oral Pathology, Faculdade São Leopoldo Mandic, Campinas, Brazil
| | | | - Silvia Vanessa Lourenço
- Department of Pathology, A.C.Camargo Cancer Center, São Paulo, Brazil.,Department of General Pathology, Dental School, University of São Paulo, São Paulo, Brazil
| | - Rogério Moraes Castilho
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, United States
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo, Brazil.,Department of Head and Neck Surgery, University of Sao Paulo Medical School, São Paulo, Brazil
| | - Antti Mäkitie
- Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska Hospital, Stockholm, Sweden
| | | | - Ilmo Leivo
- Institute of Biomedicine, Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland.,Department of Pathology, Helsinki University Hospital, Helsinki, Finland.,Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, Oulu, Finland
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The impact of glutamine deprivation on the expression of MEIS3, SPAG4, LHX1, LHX2, and LHX6 genes in ERN1 knockdown U87 glioma cells. Endocr Regul 2022; 56:38-47. [PMID: 35180817 DOI: 10.2478/enr-2022-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Objective. The aim of the current study was to investigate the expression of genes encoded homeobox proteins such as MEIS3 (Meis homeobox 3), SPAG4 (sperm associated antigen 4), LHX1 (LIM homeobox 1), LHX2, and LHX6 in U87 glioma cells in response to glutamine deprivation in control glioma cells and cells with knockdown of ERN1 (endoplasmic reticulum to nucleus signaling 1), the major pathway of the endoplasmic reticulum stress signaling, for evaluation of a possible dependence on the expression of these important regulatory genes from glutamine supply and ERN1 signaling. Methods. The expression level of MEIS3, SPAG4, LHX, LHX2, and LHX6 genes was studied by real-time quantitative polymerase chain reaction in control U87 glioma cells (transfected by vector) and cells with ERN1 knockdown after exposure to glutamine deprivation. Results. It was shown that the expression level of MEIS3 and LHX1 genes was up-regulated in control glioma cells treated by glutamine deprivation. At the same time, the expression level of three other genes (LHX2, LHX6, and SPAG4) was down-regulated. Furthermore, ERN1 knockdown significantly modified the effect of glutamine deprivation on LHX1 gene expression in glioma cells, but did not change significantly the sensitivity of all other genes expression to this experimental condition. Conclusion. The results of this investigation demonstrate that the exposure of U87 glioma cells under glutamine deprivation significantly affected the expression of all genes studied encoding the homeobox proteins and that this effect of glutamine deprivation was independent of the endoplasmic reticulum stress signaling mediated by ERN1, except LHX1 gene.
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Dong YJ, Feng W, Li Y. HOTTIP-miR-205-ZEB2 Axis Confers Cisplatin Resistance to Ovarian Cancer Cells. Front Cell Dev Biol 2021; 9:707424. [PMID: 34322490 PMCID: PMC8311351 DOI: 10.3389/fcell.2021.707424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Ovarian cancer is a deadly gynecological malignancy with resistance to cisplatin a major clinical problem. We evaluated a role of long non-coding (lnc) RNA HOTTIP (HOXA transcript at the distal tip) in the cisplatin resistance of ovarian cancer cells, using paired cisplatin sensitive and resistant A2780 cells along with the SK-OV-3 cells. HOTTIP was significantly elevated in cisplatin resistant cells and its silencing reversed the cisplatin resistance of resistant cells. HOTTIP was found to sponge miR-205 and therefore HOTTIP silenced cells had higher levels of miR-205. Downregulation of miR-205 could attenuate HOTTIP-silencing effects whereas miR-205 upregulation in resistant cells was found to re-sensitize cells to cisplatin. HOTTIP silencing also led to reduced NF-κB activation, clonogenic potential and the reduced expression of stem cell markers SOX2, OCT4, and NANOG, an effect that could be attenuated by miR-205. Finally, ZEB2 was identified as the gene target of miR-205, thus completing the elucidation of HOTTIP-miR-205-ZEB2 as the novel axis which is functionally involved in the determination of cisplatin resistance in ovarian cancer cells.
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Affiliation(s)
- Yu-Jie Dong
- Department of Emergency, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Wei Feng
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yan Li
- Department of Emergency, China-Japan Union Hospital of Jilin University, Changchun, China
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ERN1 knockdown modifies the effect of glucose deprivation on homeobox gene expressions in U87 glioma cells. Endocr Regul 2021; 54:196-206. [PMID: 32857719 DOI: 10.2478/enr-2020-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE The aim of the present investigation was to study the expression of genes encoding homeobox proteins ZEB2 (zinc finger E-box binding homeobox 2), TGIF1 (TGFB induced factor homeobox 1), SPAG4 (sperm associated antigen 4), LHX1 (LIM homeobox 1), LHX2, LHX6, NKX3-1 (NK3 homeobox 1), and PRRX1 (paired related homeobox 1) in U87 glioma cells in response to glucose deprivation in control glioma cells and cells with knockdown of ERN1 (endoplasmic reticulum to nucleus signaling 1), the major pathway of the endoplasmic reticulum stress signaling, for evaluation of it possible significance in the control of glioma growth through ERN1 signaling and chemoresistance. METHODS The expression level of homeobox family genes was studied in control (transfected by vector) and ERN1 knockdown U87 glioma cells under glucose deprivation condition by real-time quantitative polymerase chain reaction. RESULTS It was shown that the expression level of ZEB2, TGIF1, PRRX1, and LHX6 genes was up-regulated in control glioma cells treated by glucose deprivation. At the same time, the expression level of three other genes (NKX3-1, LHX1, and LHX2) was down-regulated. Furthermore, ERN1 knockdown of glioma cells significantly modified the effect glucose deprivation condition on the expression almost all studied genes. Thus, treatment of glioma cells without ERN1 enzymatic activity by glucose deprivation condition lead to down-regulation of the expression level of ZEB2 and SPAG4 as well as to more significant up-regulation of PRRX1 and TGIF1 genes. Moreover, the expression of LHX6 and NKX3-1 genes lost their sensitivity to glucose deprivation but LHX1 and LHX2 genes did not change it significantly. CONCLUSIONS The results of this investigation demonstrate that ERN1 knockdown significantly modifies the sensitivity of most studied homeobox gene expressions to glucose deprivation condition and that these changes are a result of complex interaction of variable endoplasmic reticulum stress related and unrelated regulatory factors and contributed to glioma cell growth and possibly to their chemoresistance.
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