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Xie M, Gu Y, Xu T, Jing X, Shu Y. Circular RNA Circ_0000119 promotes gastric cancer progression via circ_0000119/miR-502-5p/MTBP axis. Gene 2024; 908:148296. [PMID: 38378131 DOI: 10.1016/j.gene.2024.148296] [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: 10/22/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 02/22/2024]
Abstract
Dysregulated circular RNAs (circRNAs) are significantly related with tumor initiation and progression. However, biological activity and potential molecular mechanism of circRNAs in gastric cancer (GC) deserve further exploration. We carried out total RNA sequencing and acquired the expression profiles of circRNAs. Quantitative real-time PCR as well as RNA in situ hybridization helped to validate circ_0000119 dysregulation. Various in vitro experiments were utilized to investigate the biological activities of circ_0000119 in GC, and the clinical relation of circ_0000119 in vivo was identified through nude mouse xenograft models. Finally, the molecular mechanism of circ_0000119 was clarified via luciferase assays, western blot, and rescue experiments. Compared with adjacent normal tissues, the study found an increase in the expression of circ_0000119 as well as its host linear gene MAN1A2 in GC tissues. Circ_0000119 overexpression promoted proliferation and migration of GC cells in vitro and in vivo, whereas circ_0000119 suppression had the opposite effect. Mechanistically, circ_0000119 sponged miR-502-5p which played an inhibitory role in tumors. Furthermore, we found that miR-502-5p alleviated GC progression through targeting MTBP and downregulating its expression at mRNA and protein levels. In conclusion, our findings reveal a new regulatory mechanism for circ_0000119, which sponges the miR-502-5p, suppresses MTBP expression, and finally promotes GC progression.
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Affiliation(s)
- Mengyan Xie
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yunru Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Tingting Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Xinming Jing
- Daping Hospital, Army Medical University, Chongqing, People's Republic of China
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China.
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2
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Gao R, Zhou D, Qiu X, Zhang J, Luo D, Yang X, Qian C, Liu Z. Cancer Therapeutic Potential and Prognostic Value of the SLC25 Mitochondrial Carrier Family: A Review. Cancer Control 2024; 31:10732748241287905. [PMID: 39313442 PMCID: PMC11439189 DOI: 10.1177/10732748241287905] [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: 05/23/2024] [Revised: 08/29/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Transporters of the solute carrier family 25 (SLC25) regulate the intracellular distribution and concentration of nucleotides, amino acids, dicarboxylates, and vitamins within the mitochondrial and cytoplasmic matrices. This mechanism involves changes in mitochondrial function, regulation of cellular metabolism, and the ability to provide energy. In this review, important members of the SLC25 family and their pathways affecting tumorigenesis and progression are elucidated, highlighting the diversity and complexity of these pathways. Furthermore, the significant potential of the members of SLC25 as both cancer therapeutic targets and biomarkers will be emphasized.
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Affiliation(s)
- Renzhuo Gao
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Dan Zhou
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xingpeng Qiu
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jiayi Zhang
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Daya Luo
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaohong Yang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Caiyun Qian
- Department of Blood Transfusion, Key Laboratory of Jiangxi Province for Transfusion Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhuoqi Liu
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
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3
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Zhang C, Lin Q, Li C, Qiu Y, Chen J, Zhu X. Comprehensive analysis of the prognostic implication and immune infiltration of CISD2 in diffuse large B-cell lymphoma. Front Immunol 2023; 14:1277695. [PMID: 38155967 PMCID: PMC10754510 DOI: 10.3389/fimmu.2023.1277695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Background Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell lymphoma in adults. CDGSH iron sulfur domain 2 (CISD2) is an iron-sulfur protein and plays a critical role of cell proliferation. The aberrant expression of CISD2 is associated with the progression of multiple cancers. However, its role in DLBCL remains unclear. Methods The differential expression of CISD2 was identified via public databases, and quantitative real-time PCR (qRT-PCR) and western blot were used to identifed the expression of CISD2. We estimated the impact of CISD2 on clinical prognosis using the Kaplan-Meier plotter. Meanwhile, the drug sensitivity of CISD2 was assessed using CellMiner database. The 100 CISD2-related genes from STRING obtained and analyzed using the LASSO Cox regression. A CISD2 related signature for risk model (CISD2Risk) was established. The PPI network of CISD2Risk was performed, and functional enrichment was conducted through the DAVID database. The impacts of CISD2Risk on clinical features were analyzed. ESTIMATE, CIBERSORT, and MCP-counter algorithm were used to identify CISD2Risk associated with immune infiltration. Subsequently, Univariate and multivariate Cox regression analysis were applied, and a prognostic nomogram, accompanied by a calibration curve, was constructed to predict 1-, 3-, and 5-years survival probabilities. Results CISD2 was upregulated in DLBCL patients comparing with normal controls via public datasets, similarly, CISD2 was highly expressed in DLBCL cell lines. Overexpression of CISD2 was associated with poor prognosis in DLBCL patients based on the GSE31312, the GSE32918, and GSE93984 datasets (P<0.05). Nine drugs was considered as a potential therapeutic agents for CISD2. By using the LASSO cox regression, twenty seven genes were identified to construct CISD2Risk, and biological functions of these genes might be involved in apoptosis and P53 signaling pathway. The high CISD2Risk value had a worse prognosis and therapeutic effect (P<0.05). The higher stromal score, immune score, and ESTIMATE score were associated with lowe CISD2Risk value, CISD2Risk was negatively correlated with several immune infiltrating cells (macrophages M0 and M1, CD8 T cells, CD4 naïve T cells, NK cell, etc) that might be correlated with better prognosis. Additionally, The high CISD2Risk was identified as an independent prognostic factor for DLBCL patients using both univariate and multivariate Cox regression. The nomogram produced accurate predictions and the calibration curves were in good agreement. Conclusion Our study demonstrates that high expression of CISD2 in DLBCL patients is associated with poor prognosis. We have successfully constructed and validated a good prognostic prediction and efficacy monitoring for CISD2Risk that included 27 genes. Meanwhile, CISD2Risk may be a promising evaluator for immune infiltration and serve as a reference for clinical decision-making in DLBCL patients.
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Affiliation(s)
- ChaoFeng Zhang
- Department of Haematology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
- Department of Hematology and Rheumatology, The Affiliated Hospital of Putian University, Putian, China
- The School of Basic Medicine, Putian University, Putian, China
| | - Qi Lin
- Department of Pharmacy, The Affiliated Hospital of Putian University, Putian, China
| | - ChunTuan Li
- Department of Haematology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yang Qiu
- The School of Basic Medicine, Putian University, Putian, China
| | - JingYu Chen
- The School of Basic Medicine, Putian University, Putian, China
| | - XiongPeng Zhu
- Department of Haematology, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
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Kelesoglu N, Kori M, Yilmaz BK, Duru OA, Arga KY. Differential co-expression network analysis elucidated genes associated with sensitivity to farnesyltransferase inhibitor and prognosis of acute myeloid leukemia. Cancer Med 2023; 12:22420-22436. [PMID: 38069522 PMCID: PMC10757125 DOI: 10.1002/cam4.6804] [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: 05/05/2023] [Revised: 11/13/2023] [Accepted: 11/27/2023] [Indexed: 12/31/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease and the most common form of acute leukemia with a poor prognosis. Due to its complexity, the disease requires the identification of biomarkers for reliable prognosis. To identify potential disease genes that regulate patient prognosis, we used differential co-expression network analysis and transcriptomics data from relapsed, refractory, and previously untreated AML patients based on their response to treatment in the present study. In addition, we combined functional genomics and transcriptomics data to identify novel and therapeutically potential systems biomarkers for patients who do or do not respond to treatment. As a result, we constructed co-expression networks for response and non-response cases and identified a highly interconnected group of genes consisting of SECISBP2L, MAN1A2, PRPF31, VASP, and SNAPC1 in the response network and a group consisting of PHTF2, SLC11A2, PDLIM5, OTUB1, and KLRD1 in the non-response network, both of which showed high prognostic performance with hazard ratios of 4.12 and 3.66, respectively. Remarkably, ETS1, GATA2, AR, YBX1, and FOXP3 were found to be important transcription factors in both networks. The prognostic indicators reported here could be considered as a resource for identifying tumorigenesis and chemoresistance to farnesyltransferase inhibitor. They could help identify important research directions for the development of new prognostic and therapeutic techniques for AML.
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Affiliation(s)
| | - Medi Kori
- Department of BioengineeringMarmara UniversityIstanbulTürkiye
| | - Betul Karademir Yilmaz
- Genetic and Metabolic Diseases Research and Investigation CenterMarmara UniversityIstanbulTürkiye
- Department of Biochemistry, Faculty of MedicineMarmara UniversityIstanbulTürkiye
| | - Ozlem Ates Duru
- Department of Nutrition and Dietetics, School of Health SciencesNişantaşı UniversityIstanbulTürkiye
- Department of Chemical Engineering, Faculty of EngineeringBolu Abant İzzet Baysal UniversityBoluTürkiye
| | - Kazim Yalcin Arga
- Department of BioengineeringMarmara UniversityIstanbulTürkiye
- Genetic and Metabolic Diseases Research and Investigation CenterMarmara UniversityIstanbulTürkiye
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5
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BAO WEI, HAN QIANGUANG, GUAN XIAO, WANG ZIJIE, GU MIN. Solute carrier-related signature for assessing prognosis and immunity in patients with clear-cell renal cell carcinoma. Oncol Res 2023; 31:181-192. [PMID: 37304236 PMCID: PMC10208045 DOI: 10.32604/or.2023.028051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/07/2023] [Indexed: 06/13/2023] Open
Abstract
Background Clear-cell renal cell carcinoma (ccRCC) is the most common malignant kidney cancer. However, the tumor microenvironment and crosstalk involved in metabolic reprogramming in ccRCC are not well-understood. Methods We used The Cancer Genome Atlas to obtain ccRCC transcriptome data and clinical information. The E-MTAB-1980 cohort was used for external validation. The GENECARDS database contains the first 100 solute carrier (SLC)-related genes. The predictive value of SLC-related genes for ccRCC prognosis and treatment was assessed using univariate Cox regression analysis. An SLC-related predictive signature was developed through Lasso regression analysis and used to determine the risk profiles of patients with ccRCC. Patients in each cohort were separated into high- and low-risk groups based on their risk scores. The clinical importance of the signature was assessed through survival, immune microenvironment, drug sensitivity, and nomogram analyses using R software. Results SLC25A23, SLC25A42, SLC5A1, SLC3A1, SLC25A37, SLC5A6, SLCO5A1, and SCP2 comprised the signatures of the eight SLC-related genes. Patients with ccRCC were separated into high- and low-risk groups based on the risk value in the training and validation cohorts; the high-risk group had a significantly worse prognosis (p < 0.001). The risk score was an independent predictive indicator of ccRCC in the two cohorts according to univariate and multivariate Cox regression (p < 0.05). Analysis of the immune microenvironment showed that immune cell infiltration and immune checkpoint gene expression differed between the two groups (p < 0.05). Drug sensitivity analysis showed that compared to the low-risk group, the high-risk group was more sensitive to sunitinib, nilotinib, JNK-inhibitor-VIII, dasatinib, bosutinib, and bortezomib (p < 0.001). Survival analysis and receiver operating characteristic curves were validated using the E-MTAB-1980 cohort. Conclusions SLC-related genes have predictive relevance in ccRCC and play roles in the immunological milieu. Our results provide insight into metabolic reprogramming in ccRCC and identify promising treatment targets for ccRCC.
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Affiliation(s)
- WEI BAO
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - QIANGUANG HAN
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - XIAO GUAN
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - ZIJIE WANG
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - MIN GU
- Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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6
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Berger AH, Bratland E, Sjøgren T, Heimli M, Tyssedal T, Bruserud Ø, Johansson S, Husebye ES, Oftedal BE, Wolff ASB. Transcriptional Changes in Regulatory T Cells From Patients With Autoimmune Polyendocrine Syndrome Type 1 Suggest Functional Impairment of Lipid Metabolism and Gut Homing. Front Immunol 2021; 12:722860. [PMID: 34526996 PMCID: PMC8435668 DOI: 10.3389/fimmu.2021.722860] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/12/2021] [Indexed: 01/22/2023] Open
Abstract
Autoimmune polyendocrine syndrome type I (APS-1) is a monogenic model disorder of organ-specific autoimmunity caused by mutations in the Autoimmune regulator (AIRE) gene. AIRE facilitates the expression of organ-specific transcripts in the thymus, which is essential for efficient removal of dangerous self-reacting T cells and for inducing regulatory T cells (Tregs). Although reduced numbers and function of Tregs have been reported in APS-I patients, the impact of AIRE deficiency on gene expression in these cells is unknown. Here, we report for the first time on global transcriptional patterns of isolated Tregs from APS-1 patients compared to healthy subjects. Overall, we found few differences between the groups, although deviant expression was observed for the genes TMEM39B, SKIDA1, TLN2, GPR15, FASN, BCAR1, HLA-DQA1, HLA-DQB1, HLA-DRA, GPSM3 and AKR1C3. Of significant interest, the consistent downregulation of GPR15 may indicate failure of Treg gut homing which could be of relevance for the gastrointestinal manifestations commonly seen in APS-1. Upregulated FASN expression in APS-1 Tregs points to increased metabolic activity suggesting a putative link to faulty Treg function. Functional studies are needed to determine the significance of these findings for the immunopathogenesis of APS-1 and for Treg immunobiology in general.
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Affiliation(s)
- Amund Holte Berger
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eirik Bratland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Thea Sjøgren
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Marte Heimli
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torgeir Tyssedal
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Øyvind Bruserud
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Anesthesiology and Intensive Care, Haukeland University Hospital, Bergen, Norway
| | - Stefan Johansson
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eystein Sverre Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bergithe Eikeland Oftedal
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette Susanne Bøe Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Kristian Gerhard (KG) Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Barresi V, Di Bella V, Andriano N, Privitera AP, Bonaccorso P, La Rosa M, Iachelli V, Spampinato G, Pulvirenti G, Scuderi C, Condorelli DF, Lo Nigro L. NUP-98 Rearrangements Led to the Identification of Candidate Biomarkers for Primary Induction Failure in Pediatric Acute Myeloid Leukemia. Int J Mol Sci 2021; 22:ijms22094575. [PMID: 33925480 PMCID: PMC8123909 DOI: 10.3390/ijms22094575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/17/2022] Open
Abstract
Conventional chemotherapy for acute myeloid leukemia regimens generally encompass an intensive induction phase, in order to achieve a morphological remission in terms of bone marrow blasts (<5%). The majority of cases are classified as Primary Induction Response (PIR); unfortunately, 15% of children do not achieve remission and are defined Primary Induction Failure (PIF). This study aims to characterize the gene expression profile of PIF in children with Acute Myeloid Leukemia (AML), in order to detect molecular pathways dysfunctions and identify potential biomarkers. Given that NUP98-rearrangements are enriched in PIF-AML patients, we investigated the association of NUP98-driven genes in primary chemoresistance. Therefore, 85 expression arrays, deposited on GEO database, and 358 RNAseq AML samples, from TARGET program, were analyzed for “Differentially Expressed Genes” (DEGs) between NUP98+ and NUP98-, identifying 110 highly confident NUP98/PIF-associated DEGs. We confirmed, by qRT-PCR, the overexpression of nine DEGs, selected on the bases of the diagnostic accuracy, in a local cohort of PIF patients: SPINK2, TMA7, SPCS2, CDCP1, CAPZA1, FGFR1OP2, MAN1A2, NT5C3A and SRP54. In conclusion, the integrated analysis of NUP98 mutational analysis and transcriptome profiles allowed the identification of novel putative biomarkers for the prediction of PIF in AML.
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Affiliation(s)
- Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy; (V.B.); (V.D.B.); (A.P.P.); (G.S.); (C.S.)
| | - Virginia Di Bella
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy; (V.B.); (V.D.B.); (A.P.P.); (G.S.); (C.S.)
| | - Nellina Andriano
- Cytogenetic-Cytofluorimetric-Molecular Biology Lab, 95123 Catania, Italy; (N.A.); (P.B.); (M.L.R.); (V.I.); (G.P.); (L.L.N.)
- Center of Pediatric Hematology-Oncology, Azienda Policlinico–San Marco, 95123 Catania, Italy
| | - Anna Provvidenza Privitera
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy; (V.B.); (V.D.B.); (A.P.P.); (G.S.); (C.S.)
| | - Paola Bonaccorso
- Cytogenetic-Cytofluorimetric-Molecular Biology Lab, 95123 Catania, Italy; (N.A.); (P.B.); (M.L.R.); (V.I.); (G.P.); (L.L.N.)
- Center of Pediatric Hematology-Oncology, Azienda Policlinico–San Marco, 95123 Catania, Italy
| | - Manuela La Rosa
- Cytogenetic-Cytofluorimetric-Molecular Biology Lab, 95123 Catania, Italy; (N.A.); (P.B.); (M.L.R.); (V.I.); (G.P.); (L.L.N.)
- Center of Pediatric Hematology-Oncology, Azienda Policlinico–San Marco, 95123 Catania, Italy
| | - Valeria Iachelli
- Cytogenetic-Cytofluorimetric-Molecular Biology Lab, 95123 Catania, Italy; (N.A.); (P.B.); (M.L.R.); (V.I.); (G.P.); (L.L.N.)
- Center of Pediatric Hematology-Oncology, Azienda Policlinico–San Marco, 95123 Catania, Italy
| | - Giorgia Spampinato
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy; (V.B.); (V.D.B.); (A.P.P.); (G.S.); (C.S.)
| | - Giulio Pulvirenti
- Cytogenetic-Cytofluorimetric-Molecular Biology Lab, 95123 Catania, Italy; (N.A.); (P.B.); (M.L.R.); (V.I.); (G.P.); (L.L.N.)
- Center of Pediatric Hematology-Oncology, Azienda Policlinico–San Marco, 95123 Catania, Italy
| | - Chiara Scuderi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy; (V.B.); (V.D.B.); (A.P.P.); (G.S.); (C.S.)
| | - Daniele F. Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123 Catania, Italy; (V.B.); (V.D.B.); (A.P.P.); (G.S.); (C.S.)
- Correspondence:
| | - Luca Lo Nigro
- Cytogenetic-Cytofluorimetric-Molecular Biology Lab, 95123 Catania, Italy; (N.A.); (P.B.); (M.L.R.); (V.I.); (G.P.); (L.L.N.)
- Center of Pediatric Hematology-Oncology, Azienda Policlinico–San Marco, 95123 Catania, Italy
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8
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Shao X, Cheng Z, Xu M, Tan Z, Gao L, Wang J, Zhou C. Pooled analysis of prognostic value and clinical significance of Rab1A expression in human solid tumors. Medicine (Baltimore) 2019; 98:e18370. [PMID: 31852145 PMCID: PMC6922505 DOI: 10.1097/md.0000000000018370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 10/16/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND This study aims to assess the relationship between Rab1A expression and clinicopathological parameters and prognosis of patients with human solid cancer by summarizing the studies included. METHODS PubMed, EMBASE, The Cochrane Library, and other sources were searched for relative studies. The risk ratios (RRs) and confidence interval (CI) were used to assess association between Rab1A expression and clinical parameters and prognosis in solid cancer patients. RESULTS Eight studies were included in the final analysis with 800 patients. The results revealed that expression of Rab1A was significantly related with differentiation (RR = 0.883, 95%CI = 0.782-0.997, P = .044), lymph node metastasis (RR = 0.835, 95%CI = 0.753-0.926, P = .001), tumor-lymph node-metastasis (TNM) stage (RR = 1.190, 95%CI = 1.071-1.322, P < .001) and tumor size (RR = 0.818, 95%CI = 0.730-0.915, P < .001). What is more, no significant difference was seen in 1-year survival between high and low expression of Rab1A in multiple malignancies (RR = 0.855, 95%CI = 0.697-1.050, P = .136). However, increased Rab1A revealed poorer prognosis with 2-year survival (RR = 0.760, 95%CI = 0.701-0.824, P < .001), 3-year survival (RR = 0.669, 95%CI = 0.604-0.742, P < .001), 4-year survival (RR = 0.622, 95%CI = 0.554-0.698, P < .001) and 5-year survival (RR = 0.525, 95%CI = 0.458-0.698, P < .001). Expression of Rab1A was increased obviously in solid cancer tissues compared with the adjacent normal tissue (RR = 4.78, 95%CI 4.05-5.63, P = .015). CONCLUSION This study revealed Rab1A expression links closely with tumor size, differentiation, lymph node metastasis, TNM stage and poor prognosis of human solid cancer patients. It may act as a biomarker of prognosis and a novel therapeutic target in solid cancer.
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Affiliation(s)
- Xinyu Shao
- Department of gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou
| | - Zhengwu Cheng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College
| | - Menglin Xu
- Department of Oncology, The First Affiliated Hospital of Wannan Medical College, Wuhu
| | - Zhuqing Tan
- Department of Medicine, The Affiliated Infectious Diseases Hospital of Soochow University, The Fifth People's Hospital of Suzhou
| | - Ling Gao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Junfeng Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College
| | - Chunli Zhou
- Department of gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou
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9
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Rafieenia F, Abbaszadegan MR, Poursheikhani A, Razavi SMS, Jebelli A, Molaei F, Aghaee‐Bakhtiari SH. In silico evidence of high frequency of miRNA‐related SNPs in Esophageal Squamous Cell Carcinoma. J Cell Physiol 2019; 235:966-978. [DOI: 10.1002/jcp.29012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/31/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Fatemeh Rafieenia
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
- Student Research Committee Mashhad University of Medical Sciences Mashhad Iran
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
- Immunology Research Center Mashhad University of Medical Sciences Mashhad Iran
| | - Arash Poursheikhani
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
| | | | - Amir Jebelli
- Stem Cell and Regenerative Medicine Research Department Iranian Academic Center for Education, Culture and Research (ACECR), Mashhad Branch Mashhad Iran
| | - Fatemeh Molaei
- Medical Genetics Research Center Mashhad University of Medical Sciences Mashhad Iran
| | - Seyed Hamid Aghaee‐Bakhtiari
- Bioinformatics Research Group Mashhad University of Medical Sciences Mashhad Iran
- Department of Medical Biotechnology, Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran
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10
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Li H, Wang G, Yu Y, Jian W, Zhang D, Wang Y, Wang T, Meng Y, Yuan C, Zhang C. α-1,2-Mannosidase MAN1C1 Inhibits Proliferation and Invasion of Clear Cell Renal Cell Carcinoma. J Cancer 2018; 9:4618-4626. [PMID: 30588245 PMCID: PMC6299394 DOI: 10.7150/jca.27673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/01/2018] [Indexed: 01/08/2023] Open
Abstract
Background: This study investigated the biological function of the gene MAN1C1 α-mannosidase in renal cell carcinoma. It has been reported that MAN1C1 is probably a potential tumor suppressor gene in Wilms. However, the role of MAN1C1 in human clear cell renal cell carcinoma (ccRCC) has not been reported. Methods: In this study, MAN1C1 gene over-expression was used to transfect human renal cancer cell lines 786-O and OS-RC-2 to study apoptosis and the underlying mechanisms which influence epithelial-mesenchymal transition. Results: MAN1C1 was down-regulated in ccRCC and related to the clinicopathological factors and prognosis of ccRCC. We revealed that over-expression MAN1C1 showed anti-tumor effect by inducing apoptosis, as determined by Cell Counting Kit-8 (CCK-8) assay, cell cycle analysis, and western blot analysis. What's more, MAN1C1 over-expression remarkably increased the ratio of Bax/Bcl-2 and inhibited epithelial-mesenchymal transition by increasing the expression of E-CA. In addition, the ratio of Bax/Bcl-2 and E-CA were also increased in MAN1C1 gene over-expression renal cancer cells compared with the control cells. Conclusion: We find that re-expression of silenced MAN1C1 in ccRCC cell lines inhibited cell viability, colony formation, induced apoptosis, suppressed cell invasion and migration. In conclusion, MAN1C1 is a novel functional tumor suppressor in renal carcinogenesis. This is the first time that the function of MAN1C1 gene has been verified in the renal tumor tissue so far.
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Affiliation(s)
- Haoming Li
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Gang Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yipeng Yu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Wengang Jian
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Daming Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yongquan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Tengda Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yuyang Meng
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chao Yuan
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
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11
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Janikowska G, Janikowski T, Pyka-Pająk A, Mazurek U, Janikowski M, Gonciarz M, Lorenc Z. Potential biomarkers for the early diagnosis of colorectal adenocarcinoma - transcriptomic analysis of four clinical stages. Cancer Biomark 2018; 22:89-99. [PMID: 29562499 DOI: 10.3233/cbm-170984] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUNDS Colorectal cancer is the third most common cancer in economically developed countries. Molecular studies and, in particular, gene expression have contributed to advances in the diagnosis and treatment of many cancers. Genes can be molecular and therapeutic markers, but because of the large molecular diversity in colorectal cancer the knowledge is not yet fully established. Probably one of the most crucial processes during early cancer development is inflammation. The inflammatory response in the tumor is an important indicator of molecular etiology and later of cancer progression. OBJECTIVE The aim of this work is to identify potential biomarkers for early stage of colorectal adenocarcinoma in patients' bowel tissues using transcriptomic analysis. METHODS Expression of the inflammatory response genes of colorectal cancer at all clinical stages (I-IV) and control of the bowel were evaluated by oligonucleotide microarrays. RESULTS Based on statistical analysis many differentially expressed genes were selected. LCK (LCK Proto-Oncogene, Src Family Tyrosine Kinase), GNLY (granulysin), SLC6A6 (Solute-Carrier Family 6 Member 6) and LAMP2 (Lysosomal Associated Membrane Protein 2) were specific for the early stage of the disease. These genes had the properties of the good biomarkers. CONCLUSIONS The expression of LCK, GNLY, SLC6A6 and LAMP2 genes could be valuable potential diagnostic biomarkers of the early stage of colorectal adenocarcinoma.
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Affiliation(s)
- Grażyna Janikowska
- Department of Analytical Chemistry, Medical University of Silesia, Sosnowiec, Poland
| | - Tomasz Janikowski
- Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland
| | - Alina Pyka-Pająk
- Department of Analytical Chemistry, Medical University of Silesia, Sosnowiec, Poland
| | - Urszula Mazurek
- Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland
| | - Marcin Janikowski
- Department of Molecular Biology, Medical University of Silesia, Sosnowiec, Poland
| | - Maciej Gonciarz
- Department of Gastroenterology and Gastrointestinal Oncology, St Barbara's Main District Hospital, Sosnowiec, Poland
| | - Zbigniew Lorenc
- Chair and Clinical Department of General, Colorectal and Trauma Surgery, Medical University of Silesia, Sosnowiec, Poland
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12
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Hou P, Kang Y, Luo J. Hypoxia-mediated miR-212-3p downregulation enhances progression of intrahepatic cholangiocarcinoma through upregulation of Rab1a. Cancer Biol Ther 2018; 19:984-993. [PMID: 29672195 DOI: 10.1080/15384047.2018.1456608] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Rab1a, a member RAS oncogene family, has been reported playing important role in tumor proliferation and migration. However, the role of Rab1a in intrahepatic cholangiocarcinoma (ICC) is not clear. In this study, we found Rab1a was overexpressed in ICC tissues both in mRNA and protein level. Kaplan-meier analysis showed that high expression of Rab1a was associated with poor prognosis of ICC patients. Suppression of Rab1a led to lower proliferation rate and migration ability both in vitro and in vivo by inhibiting process of cell cycle and Epithelial-Mesenchymal Transition (EMT). Further study showed that Rab1a was targeting regulated by miR-212-3p.In addition, expression of Rab1a was increased while miR-212-3p was decreased under hypoxia condition. In conclusion, these findings extend our understanding of Rab1a in progression of ICC, and we found hypoxia/miR-212-3p/Rab1a pathway played important role for progression of ICC. This newly identified pathway should promote the development of novel therapeutic biomarker for ICC.
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Affiliation(s)
- Panzhang Hou
- a Radiotherapy department , Henan Provicial people's Hospital , Zhengzhou , Henan province , China
| | - Yi Kang
- b Infectious Diseases department , Henan Provicial people's Hospital , Zhengzhou , China
| | - Jianchao Luo
- a Radiotherapy department , Henan Provicial people's Hospital , Zhengzhou , Henan province , China
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13
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Lytovchenko O, Kunji ERS. Expression and putative role of mitochondrial transport proteins in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2017; 1858:641-654. [PMID: 28342810 DOI: 10.1016/j.bbabio.2017.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/20/2017] [Accepted: 03/21/2017] [Indexed: 02/07/2023]
Abstract
Cancer cells undergo major changes in energy and biosynthetic metabolism. One of them is the Warburg effect, in which pyruvate is used for fermentation rather for oxidative phosphorylation. Another major one is their increased reliance on glutamine, which helps to replenish the pool of Krebs cycle metabolites used for other purposes, such as amino acid or lipid biosynthesis. Mitochondria are central to these alterations, as the biochemical pathways linking these processes run through these organelles. Two membranes, an outer and inner membrane, surround mitochondria, the latter being impermeable to most organic compounds. Therefore, a large number of transport proteins are needed to link the biochemical pathways of the cytosol and mitochondrial matrix. Since the transport steps are relatively slow, it is expected that many of these transport steps are altered when cells become cancerous. In this review, changes in expression and regulation of these transport proteins are discussed as well as the role of the transported substrates. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.
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Affiliation(s)
- Oleksandr Lytovchenko
- Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.
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14
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Tu HC, Hsiao YC, Yang WY, Tsai SL, Lin HK, Liao CY, Lu JW, Chou YT, Wang HD, Yuh CH. Up-regulation of golgi α-mannosidase IA and down-regulation of golgi α-mannosidase IC activates unfolded protein response during hepatocarcinogenesis. Hepatol Commun 2017; 1:230-247. [PMID: 29404456 PMCID: PMC5721452 DOI: 10.1002/hep4.1032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/27/2017] [Accepted: 03/09/2017] [Indexed: 12/27/2022] Open
Abstract
α‐1,2 mannosidases, key enzymes in N‐glycosylation, are required for the formation of mature glycoproteins in eukaryotes. Aberrant regulation of α‐1,2 mannosidases can result in cancer, although the underlying mechanisms are unclear. Here, we report the distinct roles of α‐1,2 mannosidase subtypes (MAN1A, MAN1B, ERMAN1, MAN1C) in the formation of hepatocellular carcinoma (HCC). Clinicopathological analyses revealed that the clinical stage, tumor size, α‐fetoprotein level, and invasion status were positively correlated with the expression levels of MAN1A1, MAN1B1, and MAN1A2. In contrast, the expression of MAN1C1 was decreased as early as stage I of HCC. Survival analyses showed that high MAN1A1, MAN1A2, and MAN1B1 expression levels combined with low MAN1C1 expression levels were significantly correlated with shorter overall survival rates. Functionally, the overexpression of MAN1A1 promoted proliferation, migration, and transformation as well as in vivo migration in zebrafish. Conversely, overexpression of MAN1C1 reduced the migration ability both in vitro and in vivo, decreased the colony formation ability, and shortened the S phase of the cell cycle. Furthermore, the expression of genes involved in cell cycle/proliferation and migration was increased in MAN1A1‐overexpressing cells but decreased in MAN1C1‐overexpressing cells. MAN1A1 activated the expression of key regulators of the unfolded protein response (UPR), while treatment with endoplasmic reticulum stress inhibitors blocked the expression of MAN1A1‐activated genes. Using the MAN1A1 liver‐specific overexpression zebrafish model, we observed steatosis and inflammation at earlier stages and HCC formation at a later stage accompanied by the increased expression of the UPR modulator binding immunoglobulin protein (BiP). These data suggest that the up‐regulation of MAN1A1 activates the UPR and might initiate metastasis. Conclusion: MAN1A1 represents a novel oncogene while MAN1C1 plays a role in tumor suppression in hepatocarcinogenesis. (Hepatology Communications 2017;1:230‐247)
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Affiliation(s)
- Hsiao-Chen Tu
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan.,Institute of Biotechnology National Tsing-Hua University Hsinchu Taiwan
| | - Yung-Chun Hsiao
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan.,Institute of Biotechnology National Tsing-Hua University Hsinchu Taiwan
| | - Wan-Yu Yang
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan
| | - Shin-Lin Tsai
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan
| | - Hua-Kuo Lin
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan
| | - Chong-Yi Liao
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan.,Institute of Biotechnology National Tsing-Hua University Hsinchu Taiwan
| | - Jeng-Wei Lu
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan.,Department of Life Sciences National Central University Jhongli City Taoyuan Taiwan
| | - Yu-Ting Chou
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan.,Institute of Biotechnology National Tsing-Hua University Hsinchu Taiwan
| | - Horng-Dar Wang
- Institute of Biotechnology National Tsing-Hua University Hsinchu Taiwan
| | - Chiou-Hwa Yuh
- Institute of Molecular and Genomic Medicine National Health Research Institutes Zhunan Miaoli Taiwan.,Institute of Bioinformatics and Structural Biology National Tsing-Hua University Hsinchu Taiwan.,Department of Biological Science and Technology National Chiao Tung University Hsinchu Taiwan.,Kaohsiung Medical University Kaohsiung Taiwan
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15
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Hong JY, Ryu KJ, Lee JY, Park C, Ko YH, Kim WS, Kim SJ. Serum level of CXCL10 is associated with inflammatory prognostic biomarkers in patients with diffuse large B-cell lymphoma. Hematol Oncol 2016; 35:480-486. [PMID: 27943355 DOI: 10.1002/hon.2374] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/12/2016] [Accepted: 11/13/2016] [Indexed: 12/19/2022]
Abstract
Inflammatory biomarkers, such as the neutrophil to lymphocyte ratio (NLR), lymphocyte to monocyte ratio (LMR), and Glasgow Prognostic Score (GPS) have been proposed to predict prognosis in diffuse large B-cell lymphoma (DLBCL). C-X-C motif ligand 10 (CXCL10) is a chemokine released from inflammatory cells in the tumor microenvironment and is known to promote tumor cell migration and invasion. In this study, we investigated the clinical impact of pretreatment serum level of CXCL10 on the prognostic value of inflammatory biomarkers in 313 patients with DLBCL who were enrolled into a prospective cohort study. Serum level of CXCL10 was measured in archived pretreatment frozen samples. The high CXCL10 (>median value) group was significantly associated with high tumor burden status, including advanced stage (III-IV), elevated serum lactic dehydrogenase, and a higher risk International Prognostic Index. Progression-free survival of the high CXCL10 group was significantly worse than that of the low CXCL10 group, and secondary central nervous system involvement was more frequent in the high CXCL10 group. High CXCL10 was associated with high C-reactive protein level (r = 0.246), low albumin level (r = -0.289), low absolute lymphocyte count (r = -0.185), and risk stratification according to NLR, LMR, and GPS. C-X-C motif ligand 10 promoted cell migration of patient-derived cells and several DLBCL cell lines. However, the prognostic value of high CXCL10 was lost in the multivariate analyses. Nevertheless, we suggest serum CXCL10 may have clinical value if it can be more easily assessed because of its contribution to the prognostic value of NLR, LMR, and GPS in DLBCL.
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Affiliation(s)
- Jung Yong Hong
- Department of Oncology, Asan Medical Center, Ulsan University College of Medicine, Seoul, Korea
| | - Kyung Ju Ryu
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea
| | - Ji Yean Lee
- Division of Hematology-Oncology, Department of Medicine, G SAM Hospital, Gunpo-si, Gyeonggi-do, Korea
| | - Chaehwa Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Seog Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, Korea.,Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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16
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Musella V, Callari M, Di Buduo E, Scuro M, Dugo M, Miodini P, Bianchini G, Paolini B, Gianni L, Daidone MG, Cappelletti V. Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients. PLoS One 2015; 10:e0123194. [PMID: 25844937 PMCID: PMC4386823 DOI: 10.1371/journal.pone.0123194] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/18/2015] [Indexed: 01/16/2023] Open
Abstract
To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalin-fixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P<2.2 E-16,) and larger fold changes. The Affymetrix chips were used to run a pilot study on 60 fixed breast cancers. By including in the workflow the sample pre-assessment steps, 96% of the samples predicted to give good results (44/46), were in fact rated as satisfactory from the point of view of technical and biological meaningfulness. Our gene expression profiles showed strong agreement with immunohistochemistry data, were able to reproduce breast cancer molecular subtypes, and allowed the validation of an estrogen receptor status classifier derived in frozen samples. The approach is therefore suitable to profile formalin-fixed paraffin-embedded samples collected in clinical trials, provided that quality controls are run both before (sample pre-assessment) and after hybridization on the array.
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Affiliation(s)
- Valeria Musella
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maurizio Callari
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Eleonora Di Buduo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Manuela Scuro
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Patrizia Miodini
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Biagio Paolini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luca Gianni
- Department of Medical Oncology, Ospedale San Raffaele, Milan, Italy
| | - Maria Grazia Daidone
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- * E-mail:
| | - Vera Cappelletti
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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17
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Ferber K, Archer KJ. Modeling discrete survival time using genomic feature data. Cancer Inform 2015; 14:37-43. [PMID: 25861216 PMCID: PMC4360712 DOI: 10.4137/cin.s17275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/18/2014] [Accepted: 12/25/2014] [Indexed: 01/31/2023] Open
Abstract
Researchers have recently shown that penalized models perform well when applied to high-throughput genomic data. Previous researchers introduced the generalized monotone incremental forward stagewise (GMIFS) method for fitting overparameterized logistic regression models. The GMIFS method was subsequently extended by others for fitting several different logit link ordinal response models to high-throughput genomic data. In this study, we further extended the GMIFS method for ordinal response modeling using a complementary log-log link, which allows one to model discrete survival data. We applied our extension to a publicly available microarray gene expression dataset (GSE53733) with a discrete survival outcome. The dataset included 70 primary glioblastoma samples from patients of the German Glioma Network with long-, intermediate-, and short-term overall survival. We tested the performance of our method by examining the prediction accuracy of the fitted model. The method has been implemented as an addition to the ordinalgmifs package in the R programming environment.
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Affiliation(s)
- Kyle Ferber
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Kellie J Archer
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
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18
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Hong JY, Yoon DH, Suh C, Huh J, Do IG, Sohn I, Jo J, Jung SH, Hong ME, Yoon H, Ko YH, Kim SJ, Kim WS. EBV-positive diffuse large B-cell lymphoma in young adults: is this a distinct disease entity? Ann Oncol 2015; 26:548-55. [PMID: 25475080 DOI: 10.1093/annonc/mdu556] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) of the elderly is defined only in adults older than 50 years. However, EBV-positive DLBCL can affect younger patients. We investigated the prevalence, clinical characteristics and survival outcomes of EBV-positive DLBCL in young adults. PATIENTS AND METHODS We analyzed patients with de novo DLBCL who were registered in the Samsung Medical Center (SMC) retrospective lymphoma cohort and prospective SMC Lymphoma Cohort Study I (ClinicalTrials.gov: NCT00822731). RESULTS A total of 571 cases were included in the analysis. The prevalence of EBV positivity was 6.7% (13/195) and 9.3% (35/376) in the young group (≤50 years) and in the elderly group (>50 years), respectively. EBV status was closely associated with unique unfavorable clinical characteristics [older age, more advanced stage, two or more sites of extranodal involvement, higher International Prognostic Index (IPI), and age-adjusted IPI risk] only in the elderly group. Poor prognostic impact of EBV positivity on overall survival was observed only in the elderly group [hazard ratio (HR) 2.86; 95% confidence interval (CI) 1.83-4.47; P < 0.001], but not in the young group (HR 1.17; 95% CI 0.35-3.89; P = 0.801). CONCLUSION A substantial proportion of EBV-positive DLBCL of the elderly can occur in young adults. EBV positivity of DLBCL in young adults was not associated with unfavorable clinical characteristics or worse outcomes. We suggest that EBV-positive DLBCL should not be confined only in the elderly and 'EBV-positive DLBCL in young adults' needs to be considered as a clinically distinct disease entity. ClinicalTrials.gov: NCT02060435.
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Affiliation(s)
- J Y Hong
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul
| | | | | | - J Huh
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul
| | - I-G Do
- Department of Samsung Cancer Research Institute, Samsung Medical Center, Seoul, Korea
| | - I Sohn
- Department of Samsung Cancer Research Institute, Samsung Medical Center, Seoul, Korea
| | - J Jo
- Department of Samsung Cancer Research Institute, Samsung Medical Center, Seoul, Korea
| | - S-H Jung
- Department of Samsung Cancer Research Institute, Samsung Medical Center, Seoul, Korea Department of Biostatistics and Bioinformatics, Duke University, Durham, USA
| | | | | | | | - S J Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - W S Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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