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Majed SO, Mustafa SA. The profiles of miR-4510 expression level in breast cancer. Sci Rep 2023; 13:2262. [PMID: 36755123 PMCID: PMC9908886 DOI: 10.1038/s41598-022-25292-1] [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: 03/05/2022] [Accepted: 11/28/2022] [Indexed: 02/10/2023] Open
Abstract
MicroRNA that is abnormally produced in breast cells can disrupt biological processes, which can lead to cancer. This study aims to screen differentially expressed genes (DEGs) and ncRNAs (DEncRNAs) in the formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer (BC) as compared with the normal adjacent tissues (NAT), and identify miR-4510 as a novel biomarker of BC. This study looked at differentially expressed genes (DEGs) using MACE-Seq and differentially expressed ncRNAs (DEncRNAs) using the small RNA-Seq. Real-time qPCR was used to determine the level of expression of miR-4510. In this study, MACE-Seq results showed that 26,795 genes, with a p-value < 0.05, were differentially expressed in BC paraffin tissues as compared with NAT. Small RNA-Seq results revealed that 1326 ncRNAs, with a p-value < 0.05, were differentially expressed. We confirmed that miR-4510 was significantly down-expressed (p-value = 0.001) by qRT-PCR in the paraffin tissue of 120 BC patients. Based on eleven computational prediction programs, TP53, TP53INP1, MMP11, and COL1A1 for the miR-4510 were identified as miR-4510 targets. The MACE-seq result showed that the gene of TP53 (p-value = 0.001) and TP53INP1 (p-value = 0.02) was significantly down-regulated, but the gene of MMP11 (p-value = 0.004) and COL1A1 (p-value = 0.0001) was significantly over-expressed in 20 paired specimens of the BC and NAT. We discovered that a single SNP inside the miR-4510 binding site occurred only in BC, in which Guanine (G) changed into Adenine (A). Two SNPs outside the miR-4510 binding site occurred, and Guanine (G) in both BC and NAT was changed into Thymine (T), as compared to the reference sequence (RefSeq). Overall, our results suggested that miR-4510 functions as a tumor suppressor in the BC. Mir-4510 may act as a tumor suppressor, however additional experimental data is needed to corroborate these assumptions and can be exploited as a biomarker for BC.
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Affiliation(s)
- Sevan Omer Majed
- Biology Department, College of Education, Salahaddin University-Erbil, Erbil, Iraq
| | - Suhad Asad Mustafa
- General Directorate of Scientific Research Center, Salahaddin University-Erbil, Erbil, Iraq.
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2
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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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Mao C, Xu X, Ding Y, Xu N. Optimization of BCG Therapy Targeting Neutrophil Extracellular Traps, Autophagy, and miRNAs in Bladder Cancer: Implications for Personalized Medicine. Front Med (Lausanne) 2021; 8:735590. [PMID: 34660642 PMCID: PMC8514698 DOI: 10.3389/fmed.2021.735590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/05/2021] [Indexed: 01/07/2023] Open
Abstract
Bladder cancer (BC) is the ninth most common cancer and the thirteenth most common cause of mortality worldwide. Bacillus Calmette Guerin (BCG) instillation is a common treatment option for BC. BCG therapy is associated with the less adversary effects, compared to chemotherapy, radiotherapy, and other conventional treatments. BCG could inhibit the progression and recurrence of BC by triggering apoptosis pathways, arrest cell cycle, autophagy, and neutrophil extracellular traps (NETs) formation. However, BCG therapy is not efficient for metastatic cancer. NETs and autophagy were induced by BCG and help to suppress the growth of tumor cells especially in the primary stages of BC. Activated neutrophils can stimulate autophagy pathway and release NETs in the presence of microbial pathogenesis, inflammatory agents, and tumor cells. Autophagy can also regulate NETs formation and induce production of reactive oxygen species (ROS) and NETs. Moreover, miRNAs are important regulator of gene expression. These small non-coding RNAs are also considered as an essential factor to control the levels of tumor development. However, the interaction between BCG and miRNAs has not been well-understood yet. Therefore, the present study discusses the roles of miRNAs in regulations of autophagy and NETs formation in BCG therapy in the treatment of BC. The roles of autophagy and NETs formation in BC treatment and efficiency of BCG are also discussed.
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Affiliation(s)
- Chenyu Mao
- Department of Medical Oncology Cancer Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xin Xu
- Department of Medical Oncology Cancer Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology Cancer Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Nong Xu
- Department of Medical Oncology Cancer Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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4
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Stempor PA, Avni D, Leibowitz R, Sidi Y, Stępień M, Dzieciątkowski T, Dobosz P. Comprehensive Analysis of Correlations in the Expression of miRNA Genes and Immune Checkpoint Genes in Bladder Cancer Cells. Int J Mol Sci 2021; 22:2553. [PMID: 33806327 PMCID: PMC7961343 DOI: 10.3390/ijms22052553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Personalised medicine is the future and hope for many patients, including those with cancers. Early detection, as well as rapid, well-selected treatment, are key factors leading to a good prognosis. MicroRNA mediated gene regulation is a promising area of development for new diagnostic and therapeutic methods, crucial for better prospects for patients. Bladder cancer is a frequent neoplasm, with high lethality and lacking modern, advanced therapeutic modalities, such as immunotherapy. MicroRNAs are involved in bladder cancer pathogenesis, proliferation, control and response to treatment, which we summarise in this perspective in response to lack of recent review publications in this field. We further performed a correlation-based analysis of microRNA and gene expression data in bladder cancer (BLCA) TCGA dataset. We identified 27 microRNAs hits with opposite expression profiles to genes involved in immune response in bladder cancer, and 24 microRNAs hits with similar expression profiles. We discuss previous studies linking the functions of these microRNAs to bladder cancer and assess if they are good candidates for personalised medicine therapeutics and diagnostics. The discussed functions include regulation of gene expression, interplay with transcription factors, response to treatment, apoptosis, cell proliferation and angiogenesis, initiation and development of cancer, genome instability and tumour-associated inflammatory reaction.
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Affiliation(s)
- Przemysław A. Stempor
- SmartImmune Ltd, Accelerate Cambridge, University of Cambridge Judge Business School, Cambridge CB4 1EE, UK;
| | - Dror Avni
- Laboratory of Molecular Cell Biology, Center for Cancer Research and Department of Medicine C, Sheba Medical Center, Tel Hashome 52621, Israel;
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center, Be’er Yaakov, Tel Hashome 52621, Israel;
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Yechezkel Sidi
- Faculty of Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel;
| | - Maria Stępień
- Faculty of Medicine, Medical University of Lublin, 20-059 Lublin, Poland;
| | | | - Paula Dobosz
- Department of Hematology, Transplantationand Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
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The immune-related biomarker TEK inhibits the development of clear cell renal cell carcinoma (ccRCC) by regulating AKT phosphorylation. Cancer Cell Int 2021; 21:119. [PMID: 33602230 PMCID: PMC7890987 DOI: 10.1186/s12935-021-01830-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 12/19/2022] Open
Abstract
Background High immunogenicity is an important feature of ccRCC, but its underlying immune-related molecular mechanisms remain unclear. This study aimed to investigate the effect of immune-related gene TEK on ccRCC and its prognostic value. Methods The immune-related differentially expressed genes (DEGs) and transcription factors (TFs) in ccRCC were screened based on The Cancer Genome Atlas (TCGA) database, and a regulatory network of TF was constructed. Prognostic-related immune genes were screened by univariate Cox regression analysis and functional annotation was performed. Univariate and multivariate Cox regression analyses were performed to construct the immune gene risk model and identify the hub gene TEK that independently affected the prognosis of ccRCC. The effectiveness of the TEK was verified by external microarray datasets. The relationship between TEK and immune cells in ccRCC was evaluated based on Tumor Immune Estimation Resource (TIMER). The expression of TEK in clinical specimens was verified by qRT-PCR and immunohistochemical (IHC) staining. MTT and cloning formation assay were used to evaluate cell proliferation. Transwell assays were used to assess cell migration. Apoptosis was assessed by flow cytometry, and the expression of related proteins was detected by Western blot and immunofluorescence. Results We constructed a prognostic model consisting of 12 hub genes and performed risk scores to determine the relationship between these scores and prognosis. Through Cox regression analysis and survival analysis, TEK, an immune marker highly related to survival prognosis, was obtained and validated. In vitro experiments showed that knockdown of TEK promoted the proliferation and migration of ccRCC cells, and we found that TEK promoted apoptosis by regulating the phosphorylation of AKT, thereby inhibiting cell proliferation. Conclusions TEK plays an important role in risk assessment and survival prediction for ccRCC patients as a new immune gene and maybe an emerging target for immunotherapy for ccRCC patients.
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Zhang X, Ma L, Zhai L, Chen D, Li Y, Shang Z, Zhang Z, Gao Y, Yang W, Li Y, Pan Y. Construction and validation of a three-microRNA signature as prognostic biomarker in patients with hepatocellular carcinoma. Int J Med Sci 2021; 18:984-999. [PMID: 33456356 PMCID: PMC7807177 DOI: 10.7150/ijms.49126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC), a common type of primary liver cancer, is one of the most aggressive malignant tumors worldwide. Although overall survival (OS) rates for HCC has significantly improved in recent years, however, the exact predictive value of microRNA (miRNA) for the prognosis of HCC has not yet been recognized. Here, we aimed to identify potential prognostic miRNAs involved in HCC by bioinformatics analysis and validated expression levels through quantitative polymerase chain reaction (qPCR) and GEO database. The RNA expression profiles and corresponding clinical information of HCC were available from The Cancer Genome Atlas (TCGA) datasets. Differentially expression and standardization analysis of miRNAs, Kaplan-Meier curve and time dependent ROC curve were performed by using R tools. Differentially expressed miRNAs (DEmiRNAs) and clinical parameters involved in the OS of HCC were confirmed by Cox regression models. And functional enrichment analysis was used to establish functions of the targeted genes of DEmiRNAs. A total of 300 DEmiRNAs were significantly related with HCC, of which 40 were down-regulated and 260 were up-regulated. A total of 344 patients with DEmiRNAs, status, overall survival (OS) time were randomized into training group (172) and test group (172). Multivariate Cox regression analyses revealed that 3 miRNA (hsa-miR-139-3p, hsa-miR-760, hsa-miR-7-5p) had independent prognostic significance for the OS of HCC in both training and test group. Moreover, according to Kaplan Meier analysis, the OS of HCC patients with high-risk score was shorter in validation and entire series. The time dependent ROC curve demonstrated high accuracy of the signature for OS. Besides, target genes of three miRNAs were analyzed by functional enrichment analysis and 20 genes associated with OS were verified by using Kaplan-Meier method. Compared with normal and benign group, the relative expression level of hsa-miR-139-3p was significantly decreased, while hsa-miR-7-5p and hsa-miR-760 were distinctly increased in the plasma of HCC patients. The same results were observed in the independent cohort. Collectively, our research suggested that three-miRNA signature could serve as an independent prognostic indicator for HCC patients.
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Affiliation(s)
- Xi Zhang
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Li Ma
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Li Zhai
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Dong Chen
- Department of Ultrasound, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Yong Li
- Department of Abdominal Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Zhongjun Shang
- Department of Hospital Affairs, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Zongmei Zhang
- Department of Pathology, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Yanzhang Gao
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Wei Yang
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, P.R. China
| | - Yixun Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Experimental Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan, P.R. China
| | - Yuqing Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Yunnan Institute of Experimental Diagnosis, Yunnan Key Laboratory of Laboratory Medicine, Kunming, Yunnan, P.R. China
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7
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Gaber DA, Wassef RM, El-Ayat WM, El-Moazen MI, Montasser KA, Swar SA, Amin HAA. Role of a schistosoma haematobium specific microRNA as a predictive and prognostic tool for bilharzial bladder cancer in Egypt. Sci Rep 2020; 10:18844. [PMID: 33139749 PMCID: PMC7606480 DOI: 10.1038/s41598-020-74807-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
Urinary bladder cancer is a common malignancy in Egypt, thus reliable methodologies are required for screening and early detection. In this study, we analyzed the gene expression of a Schistosoma hematobium specific microRNA "Sha-miR-71a" and mitogen-associated protein kinase-3 (MAPK-3) in the urine samples of 50 bladder cancer patients and 50 patients with benign bilharzial cystitis. Fifty control subjects were also tested. Indirect hemagglutination test (IHA) diagnosed 70% of studied cancer cases as bilharzial associated bladder cancer (BBC), while histopathological examination detected only 18%. Urinary Sha-miR-71a & MAPK-3 revealed enhanced expression in BBC (p-value = 0.001) compared to non-bilharzial bladder cancer (NBBC) cases. Patients with chronic bilharzial cystitis exhibited a significant increase in gene expression compared to those with acute infection (p-value = 0.001). Sha-miR-71a and MAPK-3 showed good sensitivity and specificity in the diagnosis of BBC when analyzed by the receiver operating characteristic (ROC) curve. They were also prognostic regarding malignancy grade. Both biomarkers showed a positive correlation. Our results revealed that IHA is a reliable test in the diagnosis of bilharziasis associated with bladder cancer, and that Sha-miR-71a and MAPK-3 provide non-invasive specific biomarkers to diagnose BBC, as well as a potential role in testing bilharzial patients for risk to develop cancer.
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Affiliation(s)
- Dalia A Gaber
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Helwan University, Cairo, Egypt.
| | - Rita M Wassef
- Parasitology Department, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Wael M El-Ayat
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Karim A Montasser
- Clinical Pathology Department, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Sherif A Swar
- Urology Department, National Institute of Urology and Nephrology, Cairo, Egypt
| | - Hebat Allah A Amin
- Pathology Department, Faculty of Medicine, Helwan University, Cairo, Egypt
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Involvement of Differentially Expressed microRNAs in the PEGylated Liposome Encapsulated 188Rhenium-Mediated Suppression of Orthotopic Hypopharyngeal Tumor. Molecules 2020; 25:molecules25163609. [PMID: 32784458 PMCID: PMC7463599 DOI: 10.3390/molecules25163609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/11/2022] Open
Abstract
Hypopharyngeal cancer (HPC) accounts for the lowest survival rate among all types of head and neck cancers (HNSCC). However, the therapeutic approach for HPC still needs to be investigated. In this study, a theranostic 188Re-liposome was prepared to treat orthotopic HPC tumors and analyze the deregulated microRNA expressive profiles. The therapeutic efficacy of 188Re-liposome on HPC tumors was evaluated using bioluminescent imaging followed by next generation sequencing (NGS) analysis, in order to address the deregulated microRNAs and associated signaling pathways. The differentially expressed microRNAs were also confirmed using clinical HNSCC samples and clinical information from The Cancer Genome Atlas (TCGA) database. Repeated doses of 188Re-liposome were administrated to tumor-bearing mice, and the tumor growth was apparently suppressed after treatment. For NGS analysis, 13 and 9 microRNAs were respectively up-regulated and down-regulated when the cutoffs of fold change were set to 5. Additionally, miR-206-3p and miR-142-5p represented the highest fold of up-regulation and down-regulation by 188Re-liposome, respectively. According to Differentially Expressed MiRNAs in human Cancers (dbDEMC) analysis, most of 188Re-liposome up-regulated microRNAs were categorized as tumor suppressors, while down-regulated microRNAs were oncogenic. The KEGG pathway analysis showed that cancer-related pathways and olfactory and taste transduction accounted for the top pathways affected by 188Re-liposome. 188Re-liposome down-regulated microRNAs, including miR-143, miR-6723, miR-944, and miR-136 were associated with lower survival rates at a high expressive level. 188Re-liposome could suppress the HPC tumors in vivo, and the therapeutic efficacy was associated with the deregulation of microRNAs that could be considered as a prognostic factor.
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Ghousein A, Mosca N, Cartier F, Charpentier J, Dupuy JW, Raymond AA, Bioulac-Sage P, Grosset CF. miR-4510 blocks hepatocellular carcinoma development through RAF1 targeting and RAS/RAF/MEK/ERK signalling inactivation. Liver Int 2020; 40:240-251. [PMID: 31612616 DOI: 10.1111/liv.14276] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/20/2019] [Accepted: 10/04/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Therapeutic outcomes using the multikinase inhibitors, sorafenib and regorafenib, remain unsatisfactory for patients with advanced hepatocellular carcinoma (HCC). Thus, new drug modalities are needed. We recently reported the remarkable capacity of miR-4510 to impede the growth of HCC and hepatoblastoma through Glypican-3 (GPC3) targeting and Wnt pathway inactivation. METHODS To identify new targets of miR-4510, we used a label-free proteomic approach and reported down-regulation of RAF proto-oncogene serine/threonine-protein kinase (RAF1) by miR-4510. Because the tumourigenic role of RAF1 in HCC is controversial, we further studied RAF1:miR-4510 interactions using cellular, molecular as well as functional approaches and a chicken chorioallantoic membrane (CAM) xenograft model. RESULTS We found an increase in RAF1 protein in 59.3% of HCC patients and a specific up-regulation of its transcript in proliferative tumours. We showed that miR-4510 inactivates the RAS/RAF/MEK/ERK pathway and reduces the expression of downstream targets (ie c-Fos proto-oncogene [FOS]) through RAF1 direct targeting. At a cellular level, miR-4510 inhibited HCC cell proliferation and migration and induced senescence in part by lowering RAF1 messenger RNA (mRNA) and protein expression. Finally, we confirmed the pro-tumoural function of RAF1 protein in HCC cells and its ability to sustain HCC tumour progression in vitro and in vivo. CONCLUSIONS In this work, we confirm that RAF1 acts as an oncogene in HCC and further demonstrate that miR-4510 acts as a strong tumour suppressor in the liver by targeting many proto-oncogenes, including GPC3 and RAF1, and subsequently controlling key biological and signalling pathways among which Wnt and RAS/RAF/MEK/ERK signals.
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Affiliation(s)
| | - Nicola Mosca
- Inserm, BMGIC, U1035, Univ. Bordeaux, Bordeaux, France
| | - Flora Cartier
- Inserm, BMGIC, U1035, Univ. Bordeaux, Bordeaux, France
| | | | - Jean-William Dupuy
- Centre de Génomique Fonctionnelle de Bordeaux, Plateforme Proteome, Univ. Bordeaux, Bordeaux, France
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Qian GF, Yuan LS, Chen M, Ye D, Chen GP, Zhang Z, Li CJ, Vijayan V, Xiao Y. PPWD1 is associated with the occurrence of postmenopausal osteoporosis as determined by weighted gene co‑expression network analysis. Mol Med Rep 2019; 20:3202-3214. [PMID: 31432133 PMCID: PMC6755193 DOI: 10.3892/mmr.2019.10570] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 06/21/2019] [Indexed: 12/17/2022] Open
Abstract
Postmenopausal osteoporosis (PMO) is the most common type of primary osteoporosis (OP), a systemic skeletal disease. Although many factors have been revealed to contribute to the occurrence of PMO, specific biomarkers for the early diagnosis and therapy of PMO are not available. In the present study, a weighted gene co-expression network analysis (WGCNA) was performed to screen gene modules associated with menopausal status. The turquoise module was verified as the clinically significant module, and 12 genes (NUP133, PSMD12, PPWD1, RBM8A, CRNKL1, PPP2R5C, RBM22, PIK3CB, SKIV2L2, PAPOLA, SRSF1 and COPS2) were identified as ‘real’ hub genes in both the protein-protein interaction (PPI) network and co-expression network. Furthermore, gene expression analysis by microarray in blood monocytes from pre- and post-menopausal women revealed an increase in the expression of these hub genes in postmenopausal women. However, only the expression of peptidylprolyl isomerase domain and WD repeat containing 1 (PPWD1) was correlated with bone mineral density (BMD) in postmenopausal women. In the validation set, a similar expression pattern of PPWD1 was revealed. Functional enrichment analysis revealed that the fatty acid metabolism pathway was significantly abundant in the samples that exhibited a higher expression of PPWD1. Collectively, PPWD1 is indicated as a potential diagnostic biomarker for the occurrence of PMO.
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Affiliation(s)
- Guo-Feng Qian
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Lu-Shun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Min Chen
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Dan Ye
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Guo-Ping Chen
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Zhe Zhang
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Cheng-Jiang Li
- Department of Endocrinology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Vijith Vijayan
- Institute for Transfusion Medicine, Hannover Medical School, D‑30625 Hannover, Germany
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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11
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Wang L, Chen S, Luo Y, Yuan L, Peng T, Qian K, Liu X, Xiao Y, Wang X. Identification of several cell cycle relevant genes highly correlated with the progression and prognosis of human bladder urothelial tumor. J Cell Physiol 2019; 234:13439-13451. [PMID: 30618079 DOI: 10.1002/jcp.28023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/30/2018] [Indexed: 01/03/2023]
Abstract
The incidence of bladder cancer (BCa) in China is the highest among genitourinary system tumors, and its progression is affected by multitudinous pathways, of which cell cycle progress plays an important role. This study screened and enriched differentially expressed genes (DEGs) from four gene expression profiles using bioinformatics analysis methods. The enrichment and analysis of gene function showed that these genes were highly correlated with cell cycle regulation. Identification of candidate small molecules was conducted to evaluate the application of clinical transformation in these DEGs. Prognostic and stage-related expression analysis further sorted five highly expressed genes associated with worse prognosis and higher stages in patients with BCa. Further analysis revealed their interaction in cell cycle regulation and genetical alteration. Meanwhile, we validated the elevated expression of these genes through transcription and translation levels. Taking the results together, we could infer that these five genes are valuable in diagnosis, prediction, and providing candidate therapeutic targets for patients with BCa in different stages.
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Affiliation(s)
- Lu Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Song Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongwen Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lushun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Tianchen Peng
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Xuefeng Liu
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington DC
| | - Yu Xiao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Research Institute, Wuhan University, Wuhan, China
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12
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Yuan L, Qian G, Chen L, Wu CL, Dan HC, Xiao Y, Wang X. Co-expression Network Analysis of Biomarkers for Adrenocortical Carcinoma. Front Genet 2018; 9:328. [PMID: 30158955 PMCID: PMC6104177 DOI: 10.3389/fgene.2018.00328] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 07/31/2018] [Indexed: 01/08/2023] Open
Abstract
Adrenocortical carcinoma (ACC) is a rare malignancy with a poor prognosis. And currently, there are no specific diagnostic biomarkers for ACC. In our study, we aimed to screen biomarkers for disease diagnosis, progression and prognosis. We firstly used the microarray data from public database Gene Expression Omnibus database to construct a weighted gene co-expression network, and then to identify gene modules associated with clinical features of ACC. Though this algorithm, a significant module with R2 = 0.64 (P = 9 × 10-5) was identified. Co-expression network and protein–protein interaction network were performed for screen the candidate hub genes. Checked by The Cancer Genome Atlas (TCGA) database, another independent dataset GSE19750, and GEPIA database, using one-way ANOVA, Pearson’s correlation, survival analysis, diagnostic capacity (ROC curve) and expression level revalidation, a total 12 real hub genes were identified. Gene ontology and KEGG pathway analysis of genes in the significant module revealed that the hub genes are significantly enriched in cell cycle regulation. Moreover, gene set enrichment analysis suggests that the samples with highly expressed hub genes are correlated with cell cycle. Taken together, our integrated analysis has identified 12 hub genes that are associated with the progression and prognosis of ACC; these hub genes might lead to poor outcomes by regulating the cell cycle.
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Affiliation(s)
- Lushun Yuan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guofeng Qian
- Department of Endocrinology, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Liang Chen
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chin-Lee Wu
- Department of Urology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Han C Dan
- Greenebaum Cancer Center, School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
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