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Wu Q, Liao R, Miao C, Hasnat M, Li L, Sun L, Wang X, Yuan Z, Jiang Z, Zhang L, Yu Q. Oncofetal SNRPE promotes HCC tumorigenesis by regulating the FGFR4 expression through alternative splicing. Br J Cancer 2024; 131:77-89. [PMID: 38796598 PMCID: PMC11231362 DOI: 10.1038/s41416-024-02689-5] [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: 12/25/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Due to insufficient knowledge about key molecular events, Hepatocellular carcinoma (HCC) lacks effective treatment targets. Spliceosome-related genes were significantly altered in HCC. Oncofetal proteins are ideal tumor therapeutic targets. Screening of differentially expressed Spliceosome-related oncofetal protein in embryonic liver development and HCC helps discover effective therapeutic targets for HCC. METHODS Differentially expressed spliceosome genes were analysis in fetal liver and HCC through bioinformatics analysis. Small nuclear ribonucleoprotein polypeptide E (SNRPE) expression was detected in fetal liver, adult liver and HCC tissues. The role of SNRPE in HCC was performed multiple assays in vitro and in vivo. SNRPE-regulated alternative splicing was recognized by RNA-Seq and confirmed by multiple assays. RESULTS We herein identified SNRPE as a crucial oncofetal splicing factor, significantly associated with the adverse prognosis of HCC. SOX2 was identified as the activator for SNRPE reactivation. Efficient knockdown of SNRPE resulted in the complete cessation of HCC tumorigenesis and progression. Mechanistically, SNRPE knockdown reduced FGFR4 mRNA expression by triggering nonsense-mediated RNA decay. A partial inhibition of SNRPE-induced malignant progression of HCC cells was observed upon FGFR4 knockdown. CONCLUSIONS Our findings highlight SNRPE as a novel oncofetal splicing factor and shed light on the intricate relationship between oncofetal splicing factors, splicing events, and carcinogenesis. Consequently, SNRPE emerges as a potential therapeutic target for HCC treatment. Model of oncofetal SNRPE promotes HCC tumorigenesis by regulating the AS of FGFR4 pre-mRNA.
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MESH Headings
- Animals
- Humans
- Mice
- Alternative Splicing
- Carcinogenesis/genetics
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Mice, Nude
- Prognosis
- Receptor, Fibroblast Growth Factor, Type 4/genetics
- Receptor, Fibroblast Growth Factor, Type 4/metabolism
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Affiliation(s)
- Qipeng Wu
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Ruyan Liao
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Chunmeng Miao
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Muhammad Hasnat
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Outfall Road, Lahore, Pakistan
| | - Le Li
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Lixin Sun
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Xinru Wang
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Ziqiao Yuan
- Key Laboratory of Advanced Drug Preparation Technologies, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenzhou Jiang
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China.
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing, China.
| | - Luyong Zhang
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China.
- The Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, China.
| | - Qinwei Yu
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China.
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing, China.
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2
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Subramani PG, Fraszczak J, Helness A, Estall JL, Möröy T, Di Noia JM. Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation. EMBO Rep 2024; 25:2662-2697. [PMID: 38744970 PMCID: PMC11169469 DOI: 10.1038/s44319-024-00152-3] [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: 10/05/2023] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
The multifunctional RNA-binding protein hnRNPL is implicated in antibody class switching but its broader function in B cells is unknown. Here, we show that hnRNPL is essential for B cell activation, germinal center formation, and antibody responses. Upon activation, hnRNPL-deficient B cells show proliferation defects and increased apoptosis. Comparative analysis of RNA-seq data from activated B cells and another eight hnRNPL-depleted cell types reveals common effects on MYC and E2F transcriptional programs required for proliferation. Notably, while individual gene expression changes are cell type specific, several alternative splicing events affecting histone modifiers like KDM6A and SIRT1, are conserved across cell types. Moreover, hnRNPL-deficient B cells show global changes in H3K27me3 and H3K9ac. Epigenetic dysregulation after hnRNPL loss could underlie differential gene expression and upregulation of lncRNAs, and explain common and cell type-specific phenotypes, such as dysfunctional mitochondria and ROS overproduction in mouse B cells. Thus, hnRNPL is essential for the resting-to-activated B cell transition by regulating transcriptional programs and metabolism, at least in part through the alternative splicing of several histone modifiers.
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Affiliation(s)
- Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
| | - Jennifer Fraszczak
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Anne Helness
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Jennifer L Estall
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada.
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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3
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Salib A, Jayatilleke N, Seneviratne JA, Mayoh C, De Preter K, Speleman F, Cheung BB, Carter DR, Marshall GM. MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression. Oncogene 2024; 43:363-377. [PMID: 38049564 PMCID: PMC10824661 DOI: 10.1038/s41388-023-02897-y] [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: 11/17/2022] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023]
Abstract
Many of the pro-tumorigenic functions of the oncogene MYCN are attributed to its regulation of global gene expression programs. Alternative splicing is another important regulator of gene expression and has been implicated in neuroblastoma development, however, the molecular mechanisms remain unknown. We found that MYCN up-regulated the expression of the core spliceosomal protein, SNRPD3, in models of neuroblastoma initiation and progression. High mRNA expression of SNRPD3 in human neuroblastoma tissues was a strong, independent prognostic factor for poor patient outcome. Repression of SNRPD3 expression correlated with loss of colony formation in vitro and reduced tumorigenicity in vivo. The effect of SNRPD3 on cell viability was in part dependent on MYCN as an oncogenic co-factor. RNA-sequencing revealed a global increase in the number of genes being differentially spliced when MYCN was overexpressed. Surprisingly, depletion of SNRPD3 in the presence of overexpressed MYCN further increased differential splicing, particularly of cell cycle regulators, such as BIRC5 and CDK10. MYCN directly bound SNRPD3, and the protein arginine methyltransferase, PRMT5, consequently increasing SNRPD3 methylation. Indeed, the PRMT5 inhibitor, JNJ-64619178, reduced cell viability and SNRPD3 methylation in neuroblastoma cells with high SNRPD3 and MYCN expression. Our findings demonstrate a functional relationship between MYCN and SNRPD3, which maintains the fidelity of MYCN-driven alternative splicing in the narrow range required for neuroblastoma cell growth. SNRPD3 methylation and its protein-protein interface with MYCN represent novel therapeutic targets. Hypothetical model for SNRPD3 as a co-factor for MYCN oncogenesis. SNRPD3 and MYCN participate in a regulatory loop to balance splicing fidelity in neuroblastoma cells. First MYCN transactivates SNRPD3 to lead to high-level expression. Second, SNRPD3 and MYCN form a protein complex involving PRMT5. Third, this leads to balanced alterative splicing (AS) activitiy that is favorable to neuroblastoma. Together this forms as a therapeutic vulnerability where SNRPD3 perturbation or PRMT5 inhibitors are selectively toxic to neuroblastoma by conditionally disturbing splicing activity.
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Affiliation(s)
- Alice Salib
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Nisitha Jayatilleke
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Katleen De Preter
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), Ghent, Belgium
| | - Belamy B Cheung
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Daniel R Carter
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, 2031, Australia.
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4
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JiaXin Y, XiaoFeng C, PengFei C, Songchen Z, Ziling L. Repeatedly next-generation sequencing during treatment follow-up of patients with small cell lung cancer. Medicine (Baltimore) 2023; 102:e34143. [PMID: 37390276 PMCID: PMC10313243 DOI: 10.1097/md.0000000000034143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 06/08/2023] [Indexed: 07/02/2023] Open
Abstract
Somatic alterations in tumors are a frequent occurrence. In small cell lung cancer (SCLC), these include mutations in the tumor suppressors TP53 and retinoblastoma (RB1). We used next generation sequencing (NGS) to study specific genetic variants and compare genetic and clinicopathological features of SCLC with healthy control genome. Ten SCLC patients receiving standard chemotherapy, between 2018 and 2019, from the First Hospital of Jilin University were included in this study. Prior patient treatment, NGS was performed using DNA isolated from blood plasma. New NGS analyses were performed after 2 and 4 treatment cycles. Four patients presented with different metastases at diagnosis. Overall, most genes tested presented missense or frameshift variants. TP53, RB1, CREBBP, FAT1 genes presented gain of stop codons. At the single-gene level, the most frequently altered genes were TP53 (8/10 patients, 80%) and RB1 (4/10 patients, 40%), followed by bromodomain containing 4 (BRD4), CREBBP, FAT1, FMS-like tyrosine kinase 3 (FLT3), KDR, poly ADP-ribose polymerase (PARP1), PIK3R2, ROS1, and splicing factor 3b subunit 1 (SF3B1) (2/10 patients, 20%). We identified 5 genes, which have not been previously reported to bear mutations in the context of SCLC. These genes include BRD4, PARP1, FLT3, KDR, and SF3B1. We observed that among the studied individuals, patients with a high number of genetic events, and in which such mutations were not eradicated after treatment, showed a worse prognosis. There has not yet been given enough attention to the above-mentioned genes in SCLC, which will have great clinical prospects for treatment.
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Affiliation(s)
- Yin JiaXin
- First Hospital of Jilin University, Changchun, China
| | - Cong XiaoFeng
- First Hospital of Jilin University, Changchun, China
| | - Cui PengFei
- First Hospital of Jilin University, Changchun, China
| | - Zhao Songchen
- First Hospital of Jilin University, Changchun, China
| | - Liu Ziling
- First Hospital of Jilin University, Changchun, China
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5
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Chang J, Yan S, Geng Z, Wang Z. Inhibition of splicing factors SF3A3 and SRSF5 contributes to As 3+/Se 4+ combination-mediated proliferation suppression and apoptosis induction in acute promyelocytic leukemia cells. Arch Biochem Biophys 2023; 743:109677. [PMID: 37356608 DOI: 10.1016/j.abb.2023.109677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/28/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
The low-dose combination of Arsenite (As3+) and selenite (Se4+) has the advantages of lower biological toxicity and better curative effects for acute promyelocytic leukemia (APL) therapy. However, the underlying mechanisms remain unclear. Here, based on the fact that the combination of 2 μM A3+ plus 4 μM Se4+ possessed a stronger anti-leukemic effect on APL cell line NB4 as compared with each individual, we employed iTRAQ-based quantitative proteomics to identify a total of 58 proteins that were differentially expressed after treatment with As3+/Se4+ combination rather than As3+ or Se4+ alone, the majority of which were involved in spliceosome pathway. Among them, eight proteins stood out by virtue of their splicing function and significant changes. They were validated as being decreased in mRNA and protein levels under As3+/Se4+ combination treatment. Further functional studies showed that only knockdown of two splicing factors, SF3A3 and SRSF5, suppressed the growth of NB4 cells. The reduction of SF3A3 was found to cause G1/S cell cycle arrest, which resulted in proliferation inhibition. Moreover, SRSF5 downregulation induced cell apoptosis through the activation of caspase-3. Taken together, these findings indicate that SF3A3 and SRSF5 function as pro-leukemic factors and can be potential novel therapeutic targets for APL.
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Affiliation(s)
- Jiayin Chang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, PR China
| | - Shihai Yan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, PR China
| | - Zhirong Geng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210046, PR China.
| | - Zhilin Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, PR China.
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6
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Evaluation of a Novel Oncolytic Adenovirus Silencing SYVN1. Int J Mol Sci 2022; 23:ijms232315430. [PMID: 36499754 PMCID: PMC9737683 DOI: 10.3390/ijms232315430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/23/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Oncolytic adenoviruses are promising new anticancer agents. To realize their full anticancer potential, they are being engineered to express therapeutic payloads. Tumor suppressor p53 function contributes to oncolytic adenovirus activity. Many cancer cells carry an intact TP53 gene but express p53 inhibitors that compromise p53 function. Therefore, we hypothesized that oncolytic adenoviruses could be made more effective by suppressing p53 inhibitors in selected cancer cells. To investigate this concept, we attenuated the expression of the established p53 inhibitor synoviolin (SYVN1) in A549 lung cancer cells by RNA interference. Silencing SYVN1 inhibited p53 degradation, thereby increasing p53 activity, and promoted adenovirus-induced A549 cell death. Based on these observations, we constructed a new oncolytic adenovirus that expresses a short hairpin RNA against SYVN1. This virus killed A549 cells more effectively in vitro and inhibited A549 xenograft tumor growth in vivo. Surprisingly, increased susceptibility to adenovirus-mediated cell killing by SYVN1 silencing was also observed in A549 TP53 knockout cells. Hence, while the mechanism of SYVN1-mediated inhibition of adenovirus replication is not fully understood, our results clearly show that RNA interference technology can be exploited to design more potent oncolytic adenoviruses.
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GEMIN6 Overexpression Correlates with the Low Immune Cell Infiltration and Poor Prognosis in Lung Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:1930604. [PMID: 36284636 PMCID: PMC9588342 DOI: 10.1155/2022/1930604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/27/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Background. Gem nuclear organelle-associated protein 6 (GEMIN6) is a component of the GEMINS protein family involved in the survival of motor neuron (SMN) complex. SMN interfered with snRNP assembly and mRNA processing resulting in tumorigenesis. We performed this study to explore the association between GEMIN6 and lung adenocarcinoma (LUAD). Methods. We used The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to collect transcriptomic expression data of LUAD patients and analyze the difference in GEMIN6 expression between normal and tumor tissues of LUAD. qRT-PCR analysis was also performed to detect the expression of GEMIN6 in normal and LUAD cells. The expression of GEMIN6 on the LUAD patient survival outcome was estimated by the Kaplan–Meier curves and Cox analyses. In addition, the Metascape online tool and single-sample GSEA were employed to find out the underlying biological mechanisms of GEMIN6. Furthermore, the correlations of GEMIN6 expression with immune cell infiltration in LUAD were analyzed by ssGSEA and Spearman correlation analysis. Results. Compared with the normal tissues and cells, the expression of GEMIN6 was significantly higher in LUAD tissues and cells; the high expression GEMIN6 was also found in the advanced pathologic stage and advanced N and T stages of LUAD. GEMIN6 high expression was significantly associated with inferior overall survival. The heat map revealed the top 20 coexpressed genes with GEMIN6, including SF3B6, CPSF3, and PSMB3. Functional enrichment analysis demonstrated that enrichment genes are associated with the cell cycle, mRNA processing, and energy metabolism. Additionally, GEMIN6 was negatively related to the immune cell infiltration in LUAD. Conclusions. This study demonstrated that GEMIN6 was involved in the tumorigenesis and progression of LUAD. GEMIN6 could be an important molecular marker of poor prognosis and a therapeutic target of LUAD.
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Ma H, Liu G, Yu B, Wang J, Qi Y, Kou Y, Hu Y, Wang S, Wang F, Chen D. RNA-binding protein CELF6 modulates transcription and splicing levels of genes associated with tumorigenesis in lung cancer A549 cells. PeerJ 2022; 10:e13800. [PMID: 35910766 PMCID: PMC9336609 DOI: 10.7717/peerj.13800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/06/2022] [Indexed: 01/18/2023] Open
Abstract
CELF6 (CUGBP Elav-Like Family Member 6), a canonical RNA binding protein (RBP), plays important roles in post-transcriptional regulation of pre-mRNAs. However, the underlying mechanism of lower expressed CELF6 in lung cancer tissues is still unclear. In this study, we increased CELF6 manually in lung cancer cell line (A549) and utilized transcriptome sequencing (RNA-seq) technology to screen out differentially expressed genes (DEGs) and alternative splicing events (ASEs) after CELF6 over-expression (CELF6-OE). We found that CELF6-OE induced 417 up-regulated and 1,351 down-regulated DEGs. Functional analysis of down-regulated DEGs showed that they were highly enriched in immune/inflammation response- related pathways and cell adhesion molecules (CAMs). We also found that CELF6 inhibited the expression of many immune-related genes, including TNFSF10, CCL5, JUNB, BIRC3, MLKL, PIK3R2, CCL20, STAT1, MYD88, and CFS1, which mainly promote tumorigenesis in lung cancer. The dysregulated DEGs were also validated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) experiment. In addition, CELF6 regulates the splicing pattern of large number of genes that are enriched in p53 signaling pathway and apoptosis, including TP53 and CD44. In summary, we made an extensive analysis of the transcriptome profile of gene expression and alternative splicing by CELF6-OE, providing a global understanding of the target genes and underlying regulation mechanisms mediated by CELF6 in the pathogenesis and development of lung cancer.
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Affiliation(s)
- HuSai Ma
- Department of thoracic Surgery, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China,Department of Thoracic Surgery, Qinghai Red Cross Hospital, Xining, Qinghai Province, P. R. China
| | - GuoWei Liu
- Department of thoracic Surgery, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China
| | - Bin Yu
- Department of thoracic Surgery, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China
| | - Joshua Wang
- Wuhan Ruixing Biotechnology Co. Ltd., Wuhan, Hubei Province, China
| | - YaLi Qi
- Department of Respiratory Medicine, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China
| | - YiYing Kou
- Qinghai University School of Medicine, Qinghai University School of Medicine, Xining, Qinghai Province, China
| | - Ying Hu
- Qinghai University School of Medicine, Qinghai University School of Medicine, Xining, Qinghai Province, China
| | - ShunJun Wang
- Department of thoracic Surgery, Qinghai Provincial People’s Hospital, Xining, Qinghai Province, China
| | - Fei Wang
- Qinghai University, Xining, Qinghai Province, China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co. Ltd., Wuhan, Hubei Province, China
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9
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Li FP, Liu GH, Zhang XQ, Kong WJ, Mei J, Wang M, Dai YH. Overexpressed SNRPB/D1/D3/E/F/G correlate with poor survival and immune infiltration in hepatocellular carcinoma. Am J Transl Res 2022; 14:4207-4228. [PMID: 35836882 PMCID: PMC9274562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Prior reports have indicated that the abnormal expression of small nuclear ribonucleoproteins (snRNPs) genes is related to malignant tumors. However, in hepatocellular carcinoma (HCC), the precise role of snRNPs is not well understood. Therefore, the purpose of this study was to evaluate the prognostic roles of SNRPB/D1/D2/D3/E/F/G and their correlation to immune infiltration in HCC. METHODS The study was carried out via the following databases, software, and experimental validation: ONCOMINE, GEPIA2, UALCAN, The Cancer Genome Atlas, Gene Expression Omnibus, ArrayExpress, Kaplan-Meier plotter, cBioPortal, STRING, DAVID 6.8, TIMER, Cytoscape software, and immunohistochemistry experiments. RESULTS Overexpressed SNRPB/D1/D2/D3/E/F/G proteins were found in HCC tissues. The transcription levels of 7 snRNPs genes were related to the TP53 mutation and tumor grades. SNRPB/D1/D2/D3/F/G expression was significantly correlated with cancer staging, whereas SNRPE was not. Moreover, Kaplan-Meier survival analysis showed that upregulation of SNRPB/D1/D2/E/G was relevant to worse OS in HCC patients, especially in patients with alcohol consumption and those without viral hepatitis. Multivariate Cox regression analysis indicated that expression of SNRPB/D1/D3/E/F/G were independent prognostic factors for unfavorable OS in HCC. In addition, a high mutation rate of snRNPs genes (44%) was also found in HCC. The mRNA expression levels of snRNPs were meaningfully and positively related to six types of infiltrating immune cells (B cells, CD4+ T cells, CD8+ T cells, neutrophil, macrophage, and dendritic cells). Also, SNRPB/D1/G genes were significantly associated with molecular markers of various immune cells in HCC. CONCLUSIONS SNRPB/D1/D3/E/F/G are potential prognostic biomarkers for a short OS in HCC, and SNRPB/D1/G were novel immune therapy targets in HCC patients.
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Affiliation(s)
- Fu-Ping Li
- Department of Clinical Medicine, Shaanxi University of Chinese MedicineXianyang 712046, Shaanxi, China
| | - Gao-Hua Liu
- Department of Oncology, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
| | - Xue-Qin Zhang
- Jincheng Institute of Sichuan UniversityChengdu 610000, Sichuan, China
| | - Wei-Jie Kong
- Department of Clinical Medicine, Shaanxi University of Chinese MedicineXianyang 712046, Shaanxi, China
| | - Jian Mei
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Fujian Medical UniversityFuzhou 350005, China
| | - Mao Wang
- Department of Surgical Oncology Medicine, Second Affiliated Hospital of Shaanxi University of Chinese MedicineXianyang 712000, Shaanxi, China
| | - Yin-Hai Dai
- Department of Clinical Medicine, Shaanxi University of Chinese MedicineXianyang 712046, Shaanxi, China
- Department of Surgical Oncology Medicine, Second Affiliated Hospital of Shaanxi University of Chinese MedicineXianyang 712000, Shaanxi, China
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Chen D, Zhou H, Cai Z, Cai K, Liu J, Wang W, Miao H, Li H, Li R, Li X, Chen Y, Wang HY, Wen Z. CircSCAP interacts with SF3A3 to inhibit the malignance of non-small cell lung cancer by activating p53 signaling. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:120. [PMID: 35365208 PMCID: PMC8973551 DOI: 10.1186/s13046-022-02299-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/23/2022] [Indexed: 12/18/2022]
Abstract
BACKGROUND Circular RNA (circRNA) has been recently identified as a critical regulator during carcinogenesis. However, the biological function and potential underlying mechanisms of circRNAs in lung cancer remain to be further elucidated. METHODS Here, we first evaluated the differentially expressed circRNAs between tumor and the matched adjacent nontumor tissues (3 pairs) of lung cancer patients via circRNA microarray. The expression of top five dysregulated circRNAs were tested in lung cancer cell lines and the circSCAP with concordant alteration in microarray data and cell lines was selected for further investigation. Then we validated the expression level of circSCAP in tumor and corresponding adjacent tissues (161 pairs) from a lung cancer cohort by RT-PCR analysis followed by correlation and prognosis analysis between circSCAP and clinical characteristics. Non-small cell lung cancer (NSCLC) accounts for the majority of lung cancer diagnosis (about 80% in the cohort used in this study). Therefore, we focused the role of circSCAP in NSCLC in the present study. In vitro and in vivo assays were performed to study the biological function of circSCAP in NSCLC. Biotin-labeled RNA pulldown and RNA immunoprecipitation (RIP) assays were carried out to identify the proteins directly interacting with circSCAP. The molecular mechanism of circSCAP-driven tumor suppression was demonstrated by immunoblotting, immunoprecipitation and luciferase reporter assays. In vitro and in vivo rescue experiments were conducted to verify the role of the circSCAP/SF3A3/p53 signaling axis in NSCLC. RESULTS We screened the expression profiles of human circRNAs in lung cancer tissues and found that hsa_circ_0065214 (termed as circSCAP) was significantly decreased. Kaplan-Meier analysis showed that patients with low level of circSCAP had a significantly poor prognosis. Gain- and loss-of-function experiments suggested that circSCAP played an important role in NSCLC cell proliferation, cell migration and apoptosis. Mechanistically, circSCAP directly binds to the SF3A3 protein, facilitating the reduction of SF3A3 by promoting its ubiquitin-proteasome-mediated degradation, which enhances the expression of MDM4-S to finally activate its downstream p53 signaling. CONCLUSION These findings illustrate a novel circSCAP/SF3A3/p53 signaling axis involved in suppressing the malignance of NSCLC and provide a promising target for NSCLC prognosis prediction and treatment.
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Affiliation(s)
- Dongni Chen
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510089, China
| | - Hongli Zhou
- Key Laboratory of Tropical Disease Control, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Zhuochen Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510089, China
| | - Ji Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Weidong Wang
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Huikai Miao
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Hongmu Li
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Rongzhen Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xiaodong Li
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Youfang Chen
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Hui-Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Zhesheng Wen
- Department of Thoracic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
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11
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Liu G, Li F, Chen M, Luo Y, Dai Y, Hou P. SNRPD1/E/F/G Serve as Potential Prognostic Biomarkers in Lung Adenocarcinoma. Front Genet 2022; 13:813285. [PMID: 35356432 PMCID: PMC8959887 DOI: 10.3389/fgene.2022.813285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/14/2022] [Indexed: 12/30/2022] Open
Abstract
Objectives: Sm proteins (SNRPB/D1/D2/D3/E/F/G), involved in pre-mRNA splicing, were previously reported in the tumorigenesis of several cancers. However, their specific role in lung adenocarcinoma (LUAD) remains obscure. Our study aims to feature abnormal expressions and mutations of genes for Sm proteins and assess their potential as therapeutic targets via integrated bioinformatics analysis. Methods: In this research, we explored the expression pattern and prognostic worth of genes for Sm proteins in LUAD across TCGA, GEO, UALCAN, Oncomine, Metascape, David 6.8, and Kaplan-Meier Plotter, and confirmed its independent prognostic value via univariate and multivariate cox regression analysis. Meanwhile, their expression patterns were validated by RT-qPCR. Gene mutations and co-expression of genes for Sm proteins were analyzed by the cBioPortal database. The PPI network for Sm proteins in LUAD was visualized by the STRING and Cytoscape. The correlations between genes for Sm proteins and immune infiltration were analyzed by using the “GSVA” R package. Results: Sm proteins genes were found upregulated expression in both LUAD tissues and LUAD cell lines. Moreover, highly expressed mRNA levels for Sm proteins were strongly associated with short survival time in LUAD. Genes for Sm proteins were positively connected with the infiltration of Th2 cells, but negatively connected with the infiltration of mast cells, Th1 cells, and NK cells. Importantly, Cox regression analysis showed that high SNRPD1/E/F/G expression were independent risk factors for the overall survival of LUAD. Conclusion: Our study showed that SNRPD1/E/F/G could independently predict the prognostic outcome of LUAD and was correlated with immune infiltration. Also, this report laid the foundation for additional exploration on the potential treatment target’s role of SNRPD1/E/F/G in LUAD.
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Affiliation(s)
- Gaohua Liu
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Fuping Li
- Department of Clinical Medicine, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Meichun Chen
- Department of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yang Luo
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yinhai Dai
- Department of Surgical Oncology Medicine, Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
- *Correspondence: Yinhai Dai, ; Peifeng Hou,
| | - Peifeng Hou
- Department of Oncology Medicine, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Medical University Stem Cell Research Institute, Fuzhou, China
- Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, China
- *Correspondence: Yinhai Dai, ; Peifeng Hou,
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12
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Kumar D, Kashyap MK, Yu Z, Spaanderman I, Villa R, Kipps TJ, La Clair JJ, Burkart MD, Castro JE. Modulation of RNA splicing associated with Wnt signaling pathway using FD-895 and pladienolide B. Aging (Albany NY) 2022; 14:2081-2100. [PMID: 35230971 PMCID: PMC8954975 DOI: 10.18632/aging.203924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alterations in RNA splicing are associated with different malignancies, including leukemia, lymphoma, and solid tumors. The RNA splicing modulators such as FD-895 and pladienolide B have been investigated in different malignancies to target/modulate spliceosome for therapeutic purpose. Different cell lines were screened using an RNA splicing modulator to test in vitro cytotoxicity and the ability to modulate RNA splicing capability via induction of intron retention (using RT-PCR and qPCR). The Cignal Finder Reporter Array evaluated [pathways affected by the splice modulators in HeLa cells. Further, the candidates associated with the pathways were validated at protein level using western blot assay, and gene-gene interaction studies were carried out using GeneMANIA. We show that FD-895 and pladienolide B induces higher apoptosis levels than conventional chemotherapy in different solid tumors. In addition, both agents modulate Wnt signaling pathways and mRNA splicing. Specifically, FD-895 and pladienolide B significantly downregulates Wnt signaling pathway-associated transcripts (GSK3β and LRP5) and both transcript and proteins including LEF1, CCND1, LRP6, and pLRP6 at the transcript, total protein, and protein phosphorylation's levels. These results indicate FD-895 and pladienolide B inhibit Wnt signaling by decreasing LRP6 phosphorylation and modulating mRNA splicing through induction of intron retention in solid tumors.
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Affiliation(s)
- Deepak Kumar
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- ThermoFisher Scientific, Carlsbad, CA 92008, USA
| | - Manoj K. Kashyap
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon (Manesar), Haryana 122413, India
| | - Zhe Yu
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Ide Spaanderman
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Reymundo Villa
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas J. Kipps
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Januario E. Castro
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- CLL Research Consortium and Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Hematology-Oncology Division, Mayo Clinic, Phoenix, AZ 85054, USA
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13
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Bryzgalov LO, Korbolina EE, Damarov IS, Merkulova TI. The functional insight into the genetics of cardiovascular disease: results from the post-GWAS study. Vavilovskii Zhurnal Genet Selektsii 2022; 26:65-73. [PMID: 35342858 PMCID: PMC8892170 DOI: 10.18699/vjgb-22-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Cardiovascular diseases (CVDs), the leading cause of death worldwide, generally refer to a range of pathological conditions with the involvement of the heart and the blood vessels. A sizable fraction of the susceptibility loci is known, but the underlying mechanisms have been established only for a small proportion. Therefore, there is an increasing need to explore the functional relevance of trait-associated variants and, moreover, to search for novel risk genetic variation. We have reported the bioinformatic approach allowing effective identification of functional non-coding variants by integrated analysis of genome-wide data. Here, the analysis of 1361 previously identified regulatory SNPs (rSNPs) was performed to provide new insights into cardiovascular risk. We found 773,471 coding co-segregating markers for input rSNPs using the 1000 Genomes Project. The intersection of GWAS-derived SNPs with a relevance to cardiovascular traits with these markers was analyzed within a window of 10 Kbp. The effects on the transcription factor (TF) binding sites were explored by DeFine models. Functional pathway enrichment and protein– protein interaction (PPI) network analyses were performed on the targets and the extended genes by STRING and DAVID. Eighteen rSNPs were functionally linked to cardiovascular risk. A significant impact on binding sites of thirteen TFs including those involved in blood cells formation, hematopoiesis, macrophage function, inflammation, and vasoconstriction was found in K562 cells. 21 rSNP gene targets and 5 partners predicted by PPI were enriched for spliceosome and endocytosis KEGG pathways, endosome sorting complex and mRNA splicing REACTOME pathways. Related Gene Ontology terms included mRNA splicing and processing, endosome transport and protein catabolic processes. Together, the findings provide further insight into the biological basis of CVDs and highlight the importance of the precise regulation of splicing and alternative splicing.
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Affiliation(s)
- L. O. Bryzgalov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. E. Korbolina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. S. Damarov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - T. I. Merkulova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
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14
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Strybol PP, Larmuseau M, de Schaetzen van Brienen L, Van den Bulcke T, Marchal K. Extracting functional insights from loss-of-function screens using deep link prediction. CELL REPORTS METHODS 2022; 2:100171. [PMID: 35474966 PMCID: PMC9017186 DOI: 10.1016/j.crmeth.2022.100171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/09/2021] [Accepted: 01/25/2022] [Indexed: 11/10/2022]
Abstract
We present deep link prediction (DLP), a method for the interpretation of loss-of-function screens. Our approach uses representation-based link prediction to reprioritize phenotypic readouts by integrating screening experiments with gene-gene interaction networks. We validate on 2 different loss-of-function technologies, RNAi and CRISPR, using datasets obtained from DepMap. Extensive benchmarking shows that DLP-DeepWalk outperforms other methods in recovering cell-specific dependencies, achieving an average precision well above 90% across 7 different cancer types and on both RNAi and CRISPR data. We show that the genes ranked highest by DLP-DeepWalk are appreciably more enriched in drug targets compared to the ranking based on original screening scores. Interestingly, this enrichment is more pronounced on RNAi data compared to CRISPR data, consistent with the greater inherent noise of RNAi screens. Finally, we demonstrate how DLP-DeepWalk can infer the molecular mechanism through which putative targets trigger cell line mortality.
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Affiliation(s)
- Pieter-Paul Strybol
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
| | - Maarten Larmuseau
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
| | - Louise de Schaetzen van Brienen
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
| | | | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, 9000 Gent, Belgium
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15
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Zhang J, He P, Wang X, Wei S, Ma L, Zhao J. A Novel Model of Tumor-Infiltrating B Lymphocyte Specific RNA-Binding Protein-Related Genes With Potential Prognostic Value and Therapeutic Targets in Multiple Myeloma. Front Genet 2021; 12:778715. [PMID: 34976013 PMCID: PMC8719635 DOI: 10.3389/fgene.2021.778715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/16/2021] [Indexed: 11/28/2022] Open
Abstract
Background: RNA-binding proteins (RBPs) act as important regulators in the progression of tumors. However, their role in the tumorigenesis and prognostic assessment in multiple myeloma (MM), a B-cell hematological cancer, remains elusive. Thus, the current study was designed to explore a novel prognostic B-cell-specific RBP signature and the underlying molecular mechanisms. Methods: Data used in the current study were obtained from the Gene Expression Omnibus (GEO) database. Significantly upregulated RBPs in B cells were defined as B cell-specific RBPs. The biological functions of B-cell-specific RBPs were analyzed by the cluster Profiler package. Univariate and multivariate regressions were performed to identify robust prognostic B-cell specific RBP signatures, followed by the construction of the risk classification model. Gene set enrichment analysis (GSEA)-identified pathways were enriched in stratified groups. The microenvironment of the low- and high-risk groups was analyzed by single-sample GSEA (ssGSEA). Moreover, the correlations among the risk score and differentially expressed immune checkpoints or differentially distributed immune cells were calculated. The drug sensitivity of the low- and high-risk groups was assessed via Genomics of Drug Sensitivity in Cancer by the pRRophetic algorithm. In addition, we utilized a GEO dataset involving patients with MM receiving bortezomib therapy to estimate the treatment response between different groups. Results: A total of 56 B-cell-specific RBPs were identified, which were mainly enriched in ribonucleoprotein complex biogenesis and the ribosome pathway. ADAR, FASTKD1 and SNRPD3 were identified as prognostic B-cell specific RBP signatures in MM. The risk model was constructed based on ADAR, FASTKD1 and SNRPD3. Receiver operating characteristic (ROC) curves revealed the good predictive capacity of the risk model. A nomogram based on the risk score and other independent prognostic factors exhibited excellent performance in predicting the overall survival of MM patients. GSEA showed enrichment of the Notch signaling pathway and mRNA cis-splicing via spliceosomes in the high-risk group. Moreover, we found that the infiltration of diverse immune cell subtypes and the expression of CD274, CD276, CTLA4 and VTCN1 were significantly different between the two groups. In addition, the IC50 values of 11 drugs were higher in the low-risk group. Patients in the low-risk group exhibited a higher complete response rate to bortezomib therapy. Conclusion: Our study identified novel prognostic B-cell-specific RBP biomarkers in MM and constructed a unique risk model for predicting MM outcomes. Moreover, we explored the immune-related mechanisms of B cell-specific RBPs in regulating MM. Our findings could pave the way for developing novel therapeutic strategies to improve the prognosis of MM patients.
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Affiliation(s)
- JingJing Zhang
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Pengcheng He
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xiaoning Wang
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Suhua Wei
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Le Ma
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jing Zhao
- Department of Hematology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Jing Zhao,
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16
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Czarnek M, Sarad K, Karaś A, Kochan J, Bereta J. Non-targeting control for MISSION shRNA library silences SNRPD3 leading to cell death or permanent growth arrest. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:711-731. [PMID: 34703654 PMCID: PMC8517100 DOI: 10.1016/j.omtn.2021.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 09/03/2021] [Indexed: 12/15/2022]
Abstract
In parallel with the expansion of RNA interference (RNAi) techniques, accumulating evidence indicates that RNAi analyses might be seriously biased due to the off-target effects of gene-specific short hairpin RNAs (shRNAs). Our findings indicated that off-target effects of non-targeting shRNA comprise another source of misinterpreted shRNA-based data. We found that SHC016, which is one of two non-targeting shRNA controls for the MISSION (commercialized TRC) library, exerts deleterious effects that lead to elimination of the shRNA-coding cassette from the genomes of cultured murine and human cells. Here, we used a lentiviral vector with inducible SHC016 expression to confirm that this shRNA induces apoptosis in murine cells and senescence or mitotic catastrophe depending on the p53 status in human tumor cells. We identified the core spliceosomal protein, small nuclear ribonucleoprotein Sm D3 (SNRPD3), as a major SHC016 target in several cell lines and confirmed that CRISPRi knockdown of SNRPD3 mimics the effects of SHC016 expression in A549 and U251 cells. The overexpression of SNRPD3 rescued U251 cells from SHC016-induced mitotic catastrophe. Our findings disqualified non-targeting SHC016 shRNA and added a new premise to the discussion about the sources of uncertainty in RNAi results.
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Affiliation(s)
- Maria Czarnek
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Katarzyna Sarad
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Agnieszka Karaś
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna Bereta
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Gronostajowa 7, 30-387 Kraków, Poland
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17
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Khan R, Palo A, Dixit M. Role of FRG1 in predicting the overall survivability in cancers using multivariate based optimal model. Sci Rep 2021; 11:22505. [PMID: 34795329 PMCID: PMC8602605 DOI: 10.1038/s41598-021-01665-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/02/2021] [Indexed: 12/20/2022] Open
Abstract
FRG1 has a role in tumorigenesis and angiogenesis. Our preliminary analysis showed that FRG1 mRNA expression is associated with overall survival (OS) in certain cancers, but the effect varies. In cervix and gastric cancers, we found a clear difference in the OS between the low and high FRG1 mRNA expression groups, but the difference was not prominent in breast, lung, and liver cancers. We hypothesized that FRG1 expression level could affect the functionality of the correlated genes or vice versa, which might mask the effect of a single gene on the OS analysis in cancer patients. We used the multivariate Cox regression, risk score, and Kaplan Meier analyses to determine OS in a multigene model. STRING, Cytoscape, HIPPIE, Gene Ontology, and DAVID (KEGG) were used to deduce FRG1 associated pathways. In breast, lung, and liver cancers, we found a distinct difference in the OS between the low and high FRG1 mRNA expression groups in the multigene model, suggesting an independent role of FRG1 in survival. Risk scores were calculated based upon regression coefficients in the multigene model. Low and high-risk score groups showed a significant difference in the FRG1 mRNA expression level and OS. HPF1, RPL34, and EXOSC9 were the most common genes present in FRG1 associated pathways across the cancer types. Validation of the effect of FRG1 mRNA expression level on these genes by qRT-PCR supports that FRG1 might be an upstream regulator of their expression. These genes may have multiple regulators, which also affect their expression, leading to the masking effect in the survival analysis. In conclusion, our study highlights the role of FRG1 in the survivability of cancer patients in tissue-specific manner and the use of multigene models in prognosis.
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Affiliation(s)
- Rehan Khan
- grid.419643.d0000 0004 1764 227XSchool of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, P.O. Jatni, Khurda, 752050 Odisha India
| | - Ananya Palo
- grid.419643.d0000 0004 1764 227XSchool of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, P.O. Jatni, Khurda, 752050 Odisha India
| | - Manjusha Dixit
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, HBNI, P.O. Jatni, Khurda, 752050, Odisha, India. .,School of Biological Sciences, NISER, Room No.- 203, P.O. Jatni, Khurda, Odisha, 752050, India.
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18
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Zhou Y, Wang S, Yin X, Gao G, Wang Q, Zhi Q, Han Y, Kuang Y. TSHZ3 functions as a tumor suppressor by DNA methylation in colorectal cancer. Clin Res Hepatol Gastroenterol 2021; 45:101725. [PMID: 34089916 DOI: 10.1016/j.clinre.2021.101725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/22/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Teashirt zinc finger homeobox 3 (TSHZ3) is currently reported to be aberrantly expressed in several tumors, but the detailed functions and epigenetic mechanisms of TSHZ3 in colorectal cancer (CRC) remain unclear. MATERIALS AND METHODS In this study, the TSHZ3 expression in 118 CRC and normal adjacent tissues (NATs) was evaluated, and the methylation status of the TSZH3 promoter region in CRC tissues and cell lines was also analyzed. RESULTS The results of PCR analysis showed that TSHZ3 was significantly down-regulated in CRC tissues, and patients with low TSHZ3 levels had a poorer 5-year overall survival (OS) rate. Analyzing the promoter sequence (-1000∼0) by MethPrimer, TSHZ3 promoter was found to harbor abundant of CpG islands. The methylation specific PCR (MSP) analysis presented a relatively hypermethylated status of THSZ3 promoter in CRC samples. The data of MSP and bisulfite sequencing PCR (BSP) also confirmed that CpG sites of TSHZ3 promoter were methylated in CRC cells, and the DNA methyltransferase (DNMT) inhibitor 5-aza-2'-deoxycytidine (5-Aza) could effectively restored the TSHZ3 expression in vitro. Functionally, the proliferation, apoptosis and metastasis of CRC cells were regulated by TSZH3 over-expression, and the suppressing effects of TSHZ3 in CRC were also confirmed in a xenograft mouse model. CONLUSIONS Our results indicated that promoter methylation was one of the mechanisms contributing to the down-regulation of TSHZ3 in CRC, and TSZH3 might served as a potential tumor suppressor gene in the development and progression of CRC.
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Affiliation(s)
- Youxin Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Sentai Wang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Xuequn Yin
- Department of Anesthesia Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Guanzhuang Gao
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Qiang Wang
- Department of General Surgery, Jiangsu Shengze Hospital, Wujiang, Jiangsu, 215228, China
| | - Qiaoming Zhi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Ye Han
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| | - Yuting Kuang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
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19
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Feng Q, Xia W, Wang S, Dai G, Jiao W, Guo N, Li H, Zhang G. Etodolac improves collagen induced rheumatoid arthritis in rats by inhibiting synovial inflammation, fibrosis and hyperplasia. MOLECULAR BIOMEDICINE 2021; 2:33. [PMID: 35006449 PMCID: PMC8607370 DOI: 10.1186/s43556-021-00052-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Synovial hyperplasia is the main cause of chronic rheumatoid arthritis (RA), but the mechanism of synovial hyperplasia is still unclear. Etodolac (ETD) is a selective COX-2 inhibitor for relieving pain and stiffness in RA, but the disease modifying effect is still lack of evidence. Proteomics method was used to study the differential proteome of synovial tissue in collagen induced arthritis (CIA) in rats. With the help of STRING analysis, the upregulated proteins enriched in the cluster of complement and coagulation cascades and platelet degranulation were highlighted, these proteins with fibrogenic factors Lum, CIV, CXI and Tgfbi participated in the synovial inflammation, fibrosis and hyperplasia in CIA. Based on KOG function class analysis, the proteins involved in the events of the central dogma was explored. They might be hyperplasia related proteins for most of them are related to the proliferation of cancer. ETD significantly attenuated synovial inflammation, fibrosis and hyperplasia in CIA rats by downregulating these proteins. Several proteins have not been observed in RA so far, such as Tmsb4x, Pura, Nfic, Ruvbl1, Snrpd3, U2af2, Srrm2, Srsf7, Elavl1, Hnrnph1, Wars, Yars, Bzw2, Mcts1, Eif4b, Ctsh, Lamp1, Dpp7, Ptges3, Cdc37 and Septin9, they might be potentials targets for RA. Blood biochemistry tests showed the safety of 7 months use of ETD on rats. In conclusion, present study displayed a comprehensive mechanism of synovial hyperplasia in CIA rats, on this basis, the clinical value of ETD in the treatment of RA was well confirmed.
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Affiliation(s)
- Qin Feng
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China.,National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Wenkai Xia
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Shenglan Wang
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Guoxin Dai
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Weimei Jiao
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Na Guo
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Honghua Li
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Guimin Zhang
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China. .,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China. .,National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China.
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20
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Stemm-Wolf AJ, O’Toole ET, Sheridan RM, Morgan JT, Pearson CG. The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis. Mol Biol Cell 2021; 32:ar4. [PMID: 34406792 PMCID: PMC8684746 DOI: 10.1091/mbc.e21-06-0305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022] Open
Abstract
Control of centrosome assembly is critical for cell division, intracellular trafficking, and cilia. Regulation of centrosome number occurs through the precise duplication of centrioles that reside in centrosomes. Here we explored transcriptional control of centriole assembly and find that the RNA splicing factor SON is specifically required for completing procentriole assembly. Whole genome mRNA sequencing identified genes whose splicing and expression are affected by the reduction of SON, with an enrichment in genes involved in the microtubule (MT) cytoskeleton, centrosome, and centriolar satellites. SON is required for the proper splicing and expression of CEP131, which encodes a major centriolar satellite protein and is required to organize the trafficking and MT network around the centrosomes. This study highlights the importance of the distinct MT trafficking network that is intimately associated with nascent centrioles and is responsible for procentriole development and efficient ciliogenesis.
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Affiliation(s)
- Alexander J. Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | | | - Ryan M. Sheridan
- RNA Biosciences Initiative (RBI), University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Jacob T. Morgan
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Chad G. Pearson
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
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21
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Yu X, Cao F, Yu Y, Li Y, Zhang J, Xu T, Di Q, Wu G, Zhang Z, Wang R, Li Y. HNRNPL Is Identified and Validated as a Prognostic Biomarker Associated with Microsatellite Instability in Human Gastric Cancer. DNA Cell Biol 2021; 40:1251-1260. [PMID: 34491823 DOI: 10.1089/dna.2021.0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microsatellite instability (MSI) is emerging as a promising subtype related to immunotherapy in gastric cancer (GC). However, the underlying mechanism between MSI and microsatellite stability (MSS) remains unclear. In this study, we conducted a weighted gene co-expression network analysis and found that the expression of heterogeneous nuclear ribonucleoprotein L (HNRNPL) was significantly increased in MSI GC compared with MSS GC. This finding was further validated in public GC cohorts and commercialized human GC tissue microarray. The significant negative correlation with the expression of mismatch repair protein mutL homolog 1 (MLH1) may be one of the potential mechanisms for the upregulation of HNRNPL expression in MSI GC (R = -0.689, p = 8.59e-11). In addition, HNRNPL expression was markedly upregulated in GC tissues compared with adjacent normal tissues. High HNRNPL expression also predicted a poor prognosis in GC patients. Finally, gene set enrichment analysis revealed that high HNRNPL MSI GC samples were highly positive associated with the biological functions of inflammation and cell proliferation, such as interferon gamma response, MYC targets, E2F targets, and G2/M checkpoints. In conclusion, HNRNPL could be a new MSI-associated prognostic biomarker in GC and could be a new target for the MSI GC treatment.
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Affiliation(s)
- Xiongjie Yu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Fengjun Cao
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Yuandong Yu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Yong Li
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Jun Zhang
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Tao Xu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Quanshu Di
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Guang Wu
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Zhe Zhang
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Ran Wang
- Department of Oncology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
| | - Yanli Li
- Department of Endocrinology, Renmin Hospital, Hubei University of Medicine, Shiyan, P.R. China
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22
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High-Throughput Screen of Natural Compounds and Biomarkers for NSCLC Treatment by Differential Expression and Weighted Gene Coexpression Network Analysis (WGCNA). BIOMED RESEARCH INTERNATIONAL 2021; 2021:5955343. [PMID: 34485520 PMCID: PMC8416370 DOI: 10.1155/2021/5955343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/24/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
Lung cancer is known as the leading cause which presents the highest fatality rate worldwide; non-small-cell lung cancer (NSCLC) is the most prevalent type of lung carcinoma with high severity and affects 80% of patients with lung malignancies. Up to now, the general treatment for NSCLC includes surgery, chemotherapy, and radiotherapy; however, some therapeutic drugs and approaches could cause side effects and weaken the immune system. The combination of conventional therapies and traditional Chinese medicine (TCM) significantly improves treatment efficacy in lung cancer. Therefore, it is necessary to investigate the chemical composition and underlying antitumor mechanisms of TCM, so as to get a better understanding of the potential natural ingredient for lung cancer treatment. In this study, we selected 78 TCM to treat NSCLC cell line (A549) and obtained 92 transcriptome data; differential expression and WGCNA were applied to screen the potential natural ingredient and target genes. The sample which was treated with A. pierreana generated the most significant DEG set, including 6130 DEGs, 2479 upregulated, and 3651 downregulated. KEGG pathway analyses found that four pathways (MAPK, NF-kappa B, p53, and TGF-beta signaling pathway) were significantly enriched; 16 genes were significantly regulated in these four pathways. Interestingly, some of them such as EGFR, DUSP4, IL1R1, IL1B, MDM2, CDKNIA, and IDs have been used as the target biomarkers for cancer diagnosis and therapy. In addition, classified samples into 14 groups based on their pharmaceutical effects, WGCNA was used to identify 27 modules. Among them, green and darkgrey were the most relevant modules. Eight genes in the green module and four in darkgrey were identified as hub genes. In conclusion, we screened out three new TCM (B. fruticose, A. pierreana, and S. scandens) that have the potential to develop natural anticancer drugs and obtained the therapeutic targets for NSCLC therapy. Our study provides unique insights to screen the natural components for NSCLC therapy using high-throughput transcriptome analysis.
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23
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Li J, Tong H, Li D, Jiang Q, Zhang Y, Tang W, Jin D, Chen S, Qin X, Zhang S, Xue R. The long non-coding RNA DKFZp434J0226 regulates the alternative splicing process through phosphorylation of SF3B6 in PDAC. Mol Med 2021; 27:95. [PMID: 34470609 PMCID: PMC8411526 DOI: 10.1186/s10020-021-00347-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/29/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs), a type of pervasive genes that regulates various biological processes, are differentially expressed in different types of malignant tumors. The role of lncRNAs in the carcinogenesis of pancreatic ductal adenocarcinoma (PDAC) remains unclear. Here, we investigated the role of the lncRNA DKFZp434J0226 in PDAC. METHODS Aberrantly expressed mRNAs and lncRNAs among six PDAC and paired non-tumorous tissues were profiled using microarray analysis. Quantitative real-time polymerase chain reaction was used to evaluate DKFZp434J0226 expression in PDAC tissues. CCK-8 assay, wound-healing assay, soft agar colony formation assay, and transwell assay were performed to assess the invasiveness and proliferation of PDAC cells. Furthermore, RNA pull-down, immunofluorescence, RNA immunoprecipitation, and western blotting assays were performed to investigate the association between DKFZp434J0226 and SF3B6. Tumor xenografts in mice were used to test for tumor formation in vivo. RESULTS In our study, 222 mRNAs and 128 lncRNAs were aberrantly expressed (≥ twofold change). Of these, 66 mRNAs and 53 lncRNAs were upregulated, while 75 lncRNAs and 156 mRNAs were downregulated. KEGG pathway analysis and the Gene ontology category indicated that these genes were associated with the regulation of mRNA alternative splicing and metabolic balance. Clinical analyses revealed that overexpression of DKFZp434J0226 was associated with worse tumor grading, frequent perineural invasion, advanced tumor-node-metastasis stage, and decreased overall survival and time to progression. Functional assays demonstrated that DKFZp434J0226 promoted PDAC cell migration, invasion, and growth in vitro and accelerated tumor proliferation in vivo. Mechanistically, DKFZp434J0226 interacted with the splicing factor SF3B6 and promoted its phosphorylation, which further regulated the alternative splicing of pre-mRNA. CONCLUSIONS This study indicates that DKFZp434J0226 regulates alternative splicing through phosphorylation of SF3B6 in PDAC and leads to an oncogenic phenotype in PDAC.
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Affiliation(s)
- Jinglei Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Hanxing Tong
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Dongping Li
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Qiuyu Jiang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Wenqing Tang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Dayong Jin
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - She Chen
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 130 DongAn Road, Shanghai, 200032, China
| | - Xinyu Qin
- Department of General Surgery, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China.
| | - Si Zhang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 130 DongAn Road, Shanghai, 200032, China.
| | - Ruyi Xue
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Shanghai Institute of Liver Disease, Fudan University, 180 FengLin Road, Shanghai, 200032, China.
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24
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Kurkowiak M, Grasso G, Faktor J, Scheiblecker L, Winniczuk M, Mayordomo MY, O'Neill JR, Oster B, Vojtesek B, Al-Saadi A, Marek-Trzonkowska N, Hupp TR. An integrated DNA and RNA variant detector identifies a highly conserved three base exon in the MAP4K5 kinase locus. RNA Biol 2021; 18:2556-2575. [PMID: 34190025 PMCID: PMC8632122 DOI: 10.1080/15476286.2021.1932345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
RNA variants that emerge from editing and alternative splicing form important regulatory stages in protein signalling. In this report, we apply an integrated DNA and RNA variant detection workbench to define the range of RNA variants that deviate from the reference genome in a human melanoma cell model. The RNA variants can be grouped into (i) classic ADAR-like or APOBEC-like RNA editing events and (ii) multiple-nucleotide variants (MNVs) including three and six base pair in-frame non-canonical unmapped exons. We focus on validating representative genes of these classes. First, clustered non-synonymous RNA edits (A-I) in the CDK13 gene were validated by Sanger sequencing to confirm the integrity of the RNA variant detection workbench. Second, a highly conserved RNA variant in the MAP4K5 gene was detected that results most likely from the splicing of a non-canonical three-base exon. The two RNA variants produced from the MAP4K5 locus deviate from the genomic reference sequence and produce V569E or V569del isoform variants. Low doses of splicing inhibitors demonstrated that the MAP4K5-V569E variant emerges from an SF3B1-dependent splicing event. Mass spectrometry of the recombinant SBP-tagged MAP4K5V569E and MAP4K5V569del proteins pull-downs in transfected cell systems was used to identify the protein-protein interactions of these two MAP4K5 isoforms and propose possible functions. Together these data highlight the utility of this integrated DNA and RNA variant detection platform to detect RNA variants in cancer cells and support future analysis of RNA variant detection in cancer tissue.
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Affiliation(s)
- Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland
| | - Giuseppa Grasso
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Lisa Scheiblecker
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Małgorzata Winniczuk
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland
| | - Marcos Yebenes Mayordomo
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - J Robert O'Neill
- Cambridge Oesophagogastric Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Bodil Oster
- QIAGEN Aarhus, Silkeborgvej 2, 8000 Aarhus, Denmark
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ali Al-Saadi
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, 80-822 Gdańsk, Poland.,University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
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25
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Riquier S, Mathieu M, Bessiere C, Boureux A, Ruffle F, Lemaitre JM, Djouad F, Gilbert N, Commes T. Long non-coding RNA exploration for mesenchymal stem cell characterisation. BMC Genomics 2021; 22:412. [PMID: 34088266 PMCID: PMC8178833 DOI: 10.1186/s12864-020-07289-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a potential for high tissue specificity and function. Therefore, we tested the biomarker potential of lncRNAs on Mesenchymal Stem Cells (MSCs), a complex type of adult multipotent stem cells of diverse tissue origins, that is frequently used in clinics but which is lacking extensive characterization. RESULTS We developed a dedicated bioinformatics pipeline for the purpose of building a cell-specific catalogue of unannotated lncRNAs. The pipeline performs ab initio transcript identification, pseudoalignment and uses new methodologies such as a specific k-mer approach for naive quantification of expression in numerous RNAseq data. We next applied it on MSCs, and our pipeline was able to highlight novel lncRNAs with high cell specificity. Furthermore, with original and efficient approaches for functional prediction, we demonstrated that each candidate represents one specific state of MSCs biology. CONCLUSIONS We showed that our approach can be employed to harness lncRNAs as cell markers. More specifically, our results suggest different candidates as potential actors in MSCs biology and propose promising directions for future experimental investigations.
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Affiliation(s)
- Sébastien Riquier
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Marc Mathieu
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Chloé Bessiere
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Anthony Boureux
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Florence Ruffle
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Jean-Marc Lemaitre
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Farida Djouad
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Nicolas Gilbert
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
| | - Thérèse Commes
- IRMB, University of Montpellier, INSERM, 80 rue Augustin Fliche, Montpellier, France
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26
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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27
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Peng W, Tu G, Zhao Z, He B, Cai Q, Zhang P, Peng X, Shi S, Wang X. DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection. PeerJ 2021; 9:e11355. [PMID: 34012728 PMCID: PMC8109010 DOI: 10.7717/peerj.11355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/05/2021] [Indexed: 12/14/2022] Open
Abstract
Background Esophageal carcinogenesis involves in alterations of DNA methylation and gene transcription. This study profiled genomic DNA methylome vs. gene expression using transcriptome data on esophageal adenocarcinoma (EAC) tissues from the online databases in order to identify methylation biomarkers in EAC early diagnosis. Materials and Methods The DNA methylome and transcriptome data were downloaded from the UCSC Xena, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases and then bioinformatically analyzed for the differentially methylated positions (DMPs) vs. gene expression between EAC and normal tissues. The highly methylated DMPs vs. reduced gene expression in EAC were selected and then stratified with those of the corresponding normal blood samples and other common human cancers to construct an EAC-specific diagnostic model. The usefulness of this model was further verified in other three GEO datasets of EAC tissues. Result A total of 841 DMPs were associated with expression of 320 genes, some of which were aberrantly methylated in EAC tissues. Further analysis showed that four (cg07589773, cg10474350, cg13011388 and cg15208375 mapped to gene IKZF1, HOXA7, EFS and TSHZ3, respectively) of these 841 DMPs could form and establish a diagnostic model after stratified them with the corresponding normal blood samples and other common human cancers. The data were further validated in other three GEO datasets on EAC tissues in early EAC diagnosis. Conclusion This study revealed a diagnostic model of four genes methylation to diagnose EAC early. Further study will confirm the usefulness of this model in a prospective EAC cases.
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Affiliation(s)
- Weilin Peng
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Guangxu Tu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Zhenyu Zhao
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Boxue He
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Qidong Cai
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Pengfei Zhang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Xiong Peng
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Shuai Shi
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Xiang Wang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
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Liew K, Yu GQS, Wei Pua LJ, Wong LZ, Tham SY, Hii LW, Lim WM, OuYong BM, Looi CK, Mai CW, Fei-Lei Chung F, Tan LP, Ahmad M, Soo-Beng Khoo A, Leong CO. Parallel genome-wide RNAi screens identify lymphocyte-specific protein tyrosine kinase (LCK) as a targetable vulnerability of cell proliferation and chemoresistance in nasopharyngeal carcinoma. Cancer Lett 2021; 504:81-90. [PMID: 33587980 DOI: 10.1016/j.canlet.2021.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/08/2021] [Indexed: 02/05/2023]
Abstract
Despite recent in advances in the management of nasopharyngeal carcinoma (NPC), development of targeted therapy remains challenging particularly in patients with recurrent or metastatic disease. To search for clinically relevant targets for the treatment of NPC, we carried out parallel genome-wide functional screens to identified essential genes that are required for NPC cells proliferation and cisplatin resistance. We identified lymphocyte-specific protein tyrosine kinase (LCK) as a key vulnerability of both proliferation and cisplatin resistance. Depletion of endogenous LCK or treatment of cells with LCK inhibitor induced tumor-specific cell death and synergized cisplatin sensitivity in EBV-positive C666-1 and EBV-negative SUNE1 cells. Further analyses demonstrated that LCK is regulating the proliferation and cisplatin resistance through activation of signal transducer and activator of transcription 5 (STAT5). Taken together, our study provides a molecular basis for targeting LCK and STAT5 signaling as potential druggable targets for the management of NPC.
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Affiliation(s)
- Kitson Liew
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Gibson Qi Sheng Yu
- School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Lesley Jia Wei Pua
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia; School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Li Zhe Wong
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
| | - Shiau Ying Tham
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Ling-Wei Hii
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia; School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Wei-Meng Lim
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Brian Ming OuYong
- School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Chin King Looi
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia
| | - Chun-Wai Mai
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Felicia Fei-Lei Chung
- Mechanisms of Carcinogenesis Section (MCA), Epigenetics Group (EGE), International Agency for Research on Cancer World Health Organization, Lyon CEDEX 08, France
| | - Lu Ping Tan
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Munirah Ahmad
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Alan Soo-Beng Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia; Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Postgraduate Studies, International Medical University, Kuala Lumpur, Malaysia.
| | - Chee-Onn Leong
- Center for Cancer and Stem Cell Research, Institute for Research, Development and Innovation (IRDI), International Medical University, Kuala Lumpur, Malaysia; School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia.
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Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle ADL, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W. Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. Gastroenterology 2021; 160:1164-1178.e6. [PMID: 33058866 PMCID: PMC7956223 DOI: 10.1053/j.gastro.2020.08.062] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes. METHODS Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted. RESULTS We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis. CONCLUSIONS Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Weiqiang Lin
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeroen Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Tabitha Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yuan Yuan
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangqin Wang
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqiu Bai
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | | | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - David V Conti
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Mark Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | | | - Soo Chin Lee
- National University Cancer Institute, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Neil Murphy
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; School of Public Health, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Xiaoliang Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St John's, Newfoundland and Labrador, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen B Gruber
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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Zhan YT, Li L, Zeng TT, Zhou NN, Guan XY, Li Y. SNRPB-mediated RNA splicing drives tumor cell proliferation and stemness in hepatocellular carcinoma. Aging (Albany NY) 2020; 13:537-554. [PMID: 33289700 PMCID: PMC7834993 DOI: 10.18632/aging.202164] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading malignant diseases worldwide, but therapeutic targets for HCC are lacking. Here, we characterized a significant upregulation of Small Nuclear Ribonucleoprotein Polypeptides B and B1 (SNRPB) in HCC via qRT-PCR, western blotting, tissue microarray and public database analyses. Increased SNRPB expression was positively associated with adjacent organ invasion, tumor size, serum AFP level and poor HCC patient survival. Next, we transfected SNRPB into HCC cells to construct SNRPB-overexpressing cell lines, and short hairpin RNA targeting SNRPB was used to silence SNRPB in HCC cells. Functional studies showed that SNRPB overexpression could promote HCC cell malignant proliferation and stemness maintenance. Inversely, SNRPB knockdown in HCC cells caused inverse effects. Importantly, analysis of alternative splicing by RNA sequencing revealed that SNRPB promoted the formation of AKT3-204 and LDHA-220 splice variants, which activated the Akt pathway and aerobic glycolysis in HCC cells. In conclusion, SNRPB could serve as a prognostic predictor for patients with HCC, and it promotes HCC progression by inducing metabolic reprogramming.
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Affiliation(s)
- Yu-Ting Zhan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Lei Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China.,Department of Clinical Oncology, The University of Hong Kong, Hong Kong 852, P. R. China
| | - Ting-Ting Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Ning-Ning Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
| | - Xin-Yuan Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China.,Department of Clinical Oncology, The University of Hong Kong, Hong Kong 852, P. R. China
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, P. R. China
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Shao XY, Dong J, Zhang H, Wu YS, Zheng L. Systematic Analyses of the Role of the Reader Protein of N 6-Methyladenosine RNA Methylation, YTH Domain Family 2, in Liver Hepatocellular Carcinoma. Front Mol Biosci 2020; 7:577460. [PMID: 33344502 PMCID: PMC7738478 DOI: 10.3389/fmolb.2020.577460] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background YTH domain family (YTHDF) 2 acts as a "reader" protein for RNA methylation, which is important in tumor regulation. However, the effect of YTHDF2 in liver hepatocellular carcinoma (LIHC) has yet to be elucidated. Methods We explored the role of YTHDF2 in LIHC based on publicly available datasets [The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO)]. A bioinformatics approach was employed to analyze YTHDF2. Logistic regression analyses were applied to analyze the correlation between YTHDF2 expression and clinical characteristics. To evaluate the effect of YTHDF2 on the prognosis of LIHC patients, we used Kaplan-Meier (K-M) curves. Gene set enrichment analysis (GSEA) was undertaken using TCGA dataset. Univariate and multivariate Cox analyses were used to ascertain the correlations between YTHDF2 expression and clinicopathologic characteristics with survival. Genes co-expressed with YTHDF2 were identified and detected using publicly available datasets [LinkedOmics, University of California, Santa Cruz (UCSC), Gene Expression Profiling Interactive Analysis (GEPIA), and GEO]. Correlations between YTHDF2 and infiltration of immune cells were investigated by Tumor Immune Estimation Resource (TIMER) and GEPIA. Results mRNA and protein expression of YTHDF2 was significantly higher in LIHC tissues than in non-cancerous tissues. High YTHDF2 expression in LIHC was associated with poor prognostic clinical factors (high stage, grade, and T classification). K-M analyses indicated that high YTHDF2 expression was correlated with an unfavorable prognosis. Univariate and multivariate Cox analyses revealed that YTHDF2 was an independent factor for a poor prognosis in LIHC patients. GSEA revealed that the high-expression phenotype of YTHDF2 was consistent with the molecular pathways implicated in LIHC carcinogenesis. Analyses of receiver operating characteristic curves showed that YTHDF2 might have a diagnostic value in LIHC patients. YTHDF2 expression was associated positively with SF3A3 expression, which implied that they may cooperate in LIHC progression. YTHDF2 expression was associated with infiltration of immune cells and their marker genes. YTHDF2 had the potential to regulate polarization of tumor-associated macrophages, induce T-cell exhaustion, and activate T-regulatory cells. Conclusion YTHDF2 may be a promising biomarker for the diagnosis and prognosis of LIHC and may provide new directions and strategies for LIHC treatment.
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Affiliation(s)
- Xiang-Yang Shao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Dong
- Department of Nephrology, Renmin Hospital of Wuhan University (Eastern Hospital), Wuhan, China
| | - Han Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying-Song Wu
- School of Laboratory Medicine and Biotechnology, Institute of Antibody Engineering, Southern Medical University, Guangzhou, China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Mao CG, Jiang SS, Shen C, Long T, Jin H, Tan QY, Deng B. BCAR1 promotes proliferation and cell growth in lung adenocarcinoma via upregulation of POLR2A. Thorac Cancer 2020; 11:3326-3336. [PMID: 33001583 PMCID: PMC7606008 DOI: 10.1111/1759-7714.13676] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This study was designed to investigate the effects of a novel carcinogenetic molecule, p130cas (breast cancer antiestrogen resistance protein 1 or BCAR1) on proliferation and cell growth in lung adenocarcinoma. The study also aimed to identify the possible underlying signal networks of BCAR1. METHODS First, we evaluated proliferation, cell colony formation, apoptosis, and cell cycle after BCAR1 was knocked out (KO) using CRISPR-Cas9 technology in H1975 and H1299 human lung adenocarcinoma cells. Subsequently, BCAR1 was upregulated in 293T cells and immunoprecipitation-mass spectrometry (IP-MS) was used with bioinformatics analysis to screen for potential networks of BCAR1 interacting proteins. Ultimately, we validated the correlated expressions of BCAR1 and a selected hub gene, RNA polymerase II subunit A (POLR2A), in 54 lung adenocarcinoma tissues, as well as in H1975 and H1299 cells. RESULTS Cell proliferation of H1975 and H1299 was significantly inhibited following BCAR1-KO. Colony formation of H1975 cells was also significantly decreased following BCAR1-KO. IP-MS demonstrated 419 potential proteins that may interact with BCAR1. Among them, 68 genes were significantly positively correlated to BCAR1 expression, as verified by TCGA. Six hub genes were revealed by PPI String. High expression of POLR2A, MAPK3, MOV10, and XAB2 predicted poor prognosis in lung adenocarcinoma, as verified by the K-M plotter database. POLR2A and MAPK3 are involved in both catalytic activity and transferase activity. POLR2A and BCAR1 were significantly increased in lung cancer tissues as compared with matched normal tissues. High expression of POLR2A was significantly positively correlated to BCAR1 overexpression and predicted poor prognosis in 54 lung cancer cases. POLR2A expression was significantly decreased following BCAR1-KO in H1975 and H1299 cells. CONCLUSIONS BCAR1 promotes proliferation and cell growth, probably via upregulation of POLR2A and subsequent enhancement of catalytic and transferase activities. However, additional robust studies are required to elucidate the mechanisms involved.
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Affiliation(s)
- Chun-Guo Mao
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
| | - Sha-Sha Jiang
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
| | - Cheng Shen
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
| | - Tan Long
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
| | - Hua Jin
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
| | - Qun-You Tan
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
| | - Bo Deng
- Thoracic Surgery Department, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing, China
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Caccamo D, Currò M, Ientile R, Verderio EAM, Scala A, Mazzaglia A, Pennisi R, Musarra-Pizzo M, Zagami R, Neri G, Rosmini C, Potara M, Focsan M, Astilean S, Piperno A, Sciortino MT. Intracellular Fate and Impact on Gene Expression of Doxorubicin/Cyclodextrin-Graphene Nanomaterials at Sub-Toxic Concentration. Int J Mol Sci 2020; 21:ijms21144891. [PMID: 32664456 PMCID: PMC7402311 DOI: 10.3390/ijms21144891] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
The graphene road in nanomedicine still seems very long and winding because the current knowledge about graphene/cell interactions and the safety issues are not yet sufficiently clarified. Specifically, the impact of graphene exposure on gene expression is a largely unexplored concern. Herein, we investigated the intracellular fate of graphene (G) decorated with cyclodextrins (CD) and loaded with doxorubicin (DOX) and the modulation of genes involved in cancer-associated canonical pathways. Intracellular fate of GCD@DOX, tracked by FLIM, Raman mapping and fluorescence microscopy, evidenced the efficient cellular uptake of GCD@DOX and the presence of DOX in the nucleus, without graphene carrier. The NanoString nCounter™ platform provided evidence for 34 (out of 700) differentially expressed cancer-related genes in HEp-2 cells treated with GCD@DOX (25 µg/mL) compared with untreated cells. Cells treated with GCD alone (25 µg/mL) showed modification for 16 genes. Overall, 14 common genes were differentially expressed in both GCD and GCD@DOX treated cells and 4 of these genes with an opposite trend. The modification of cancer related genes also at sub-cytotoxic G concentration should be taken in consideration for the rational design of safe and effective G-based drug/gene delivery systems. The reliable advantages provided by NanoString® technology, such as sensibility and the direct RNA measurements, could be the cornerstone in this field.
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Affiliation(s)
- Daniela Caccamo
- Department of Biomedical Sciences, Dental Sciences and Morpho-Functional Imaging, Polyclinic Hospital University, 98125 Messina, Italy; (D.C.); (M.C.); (R.I.)
| | - Monica Currò
- Department of Biomedical Sciences, Dental Sciences and Morpho-Functional Imaging, Polyclinic Hospital University, 98125 Messina, Italy; (D.C.); (M.C.); (R.I.)
| | - Riccardo Ientile
- Department of Biomedical Sciences, Dental Sciences and Morpho-Functional Imaging, Polyclinic Hospital University, 98125 Messina, Italy; (D.C.); (M.C.); (R.I.)
| | - Elisabetta AM Verderio
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham NG11 8NS, UK;
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Antonino Mazzaglia
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.M.); (R.Z.)
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
- Department of Innate Immunology, Shenzhen International Institute for Biomedical Research, 140 Jinye Ave, Building A10, Life Science Park, Dapeng New District, Shenzhen 518119, China
| | - Maria Musarra-Pizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Roberto Zagami
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.M.); (R.Z.)
| | - Giulia Neri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Consolato Rosmini
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Monica Potara
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271 Cluj-Napoca, Romania; (M.P.); (M.F.); (S.A.)
| | - Monica Focsan
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271 Cluj-Napoca, Romania; (M.P.); (M.F.); (S.A.)
| | - Simion Astilean
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271 Cluj-Napoca, Romania; (M.P.); (M.F.); (S.A.)
- Department of Biomolecular Physics, Faculty of Physics, Babes-Bolyai University, M Kogalniceanu Str. 1, 400084 Cluj-Napoca, Romania
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
- Correspondence: (A.P.); (M.T.S.); Tel.: +39-090-6765173 (A.P.); +39-090-6765217 (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
- Correspondence: (A.P.); (M.T.S.); Tel.: +39-090-6765173 (A.P.); +39-090-6765217 (M.T.S.)
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Fan Y, Wang K. miR‑205 suppresses cell migration, invasion and EMT of colon cancer by targeting mouse double minute 4. Mol Med Rep 2020; 22:633-642. [PMID: 32467998 PMCID: PMC7339668 DOI: 10.3892/mmr.2020.11150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Colon cancer is one of the most frequent malignant tumors, and microRNA (miR)‑205 is involved in the tumor progression. The present study aimed to explore the effects of miR‑205 on human colon cancer and its targeting mechanism. The levels of miR‑205 and mouse double minute 4 (MDM4) were determined via reverse transcription‑quantitative (RT‑q)PCR and western blot analysis. A luciferase activity assay was performed to analyze the association between miR‑205 and MDM4. Cell viability, migration and invasion were determined via Cell Counting Kit‑8, wound healing and Transwell assays, respectively. The levels of epithelial‑mesenchymal transition (EMT)‑associated factors were determined by RT‑qPCR and western blot analysis. It was identified that MDM4 was overexpressed in colon cancer tissues and cells, and that there was a negative correlation between miR‑205 and MDM4 expression in colon cancer. Similarly, miR‑205 inhibited MDM4 expression by binding to its 3'untranslated region. in addition, miR‑205 directly targeted MDM4, accompanied by suppressed proliferation, migration and invasion of HCT116 cells. EMT processes were suppressed in miR‑205‑overexpressed cells; upregulation of E‑cadherin, and downregulation of N‑cadherin, vimentin, matrix metalloproteinase (MMP)2 and MMP9 were observed. Collectively, miR‑205 conspicuously depressed the viability, migration, invasion and EMT process of human colon cancer cells via targeting MDM4. miR‑205 could be potentially used in the treatment of human colon cancer.
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Affiliation(s)
- Yujing Fan
- Department of Gastroenterology, Beijing Jishuitan Hospital, Beijing 100036, P.R. China
| | - Kuanyu Wang
- Department of The Second Surgery, First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang 150040, P.R. China
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Gu J, Chen Z, Chen X, Wang Z. Heterogeneous nuclear ribonucleoprotein (hnRNPL) in cancer. Clin Chim Acta 2020; 507:286-294. [PMID: 32376323 DOI: 10.1016/j.cca.2020.04.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNPL) is a type of RNA binding protein that is mainly located in the nucleus. hnRNPL protein, encoded by the gene located at 19q13.2, is an important member of the hnRNP family. In recent years, studies have shown that hnRNPL is highly expressed in a variety of tumors and plays a vital role in tumor progression. hnRNPL promotes various biological processes of tumor cells, including proliferation, migration and invasion. In this review, we discuss the clinical significance of hnRNPL by reviewing the mechanism of hnRNPL in the tumorigenesis of various cancers.
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Affiliation(s)
- Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Zhenyao Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, PR China.
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Prusinkiewicz MA, Gameiro SF, Ghasemi F, Dodge MJ, Zeng PYF, Maekebay H, Barrett JW, Nichols AC, Mymryk JS. Survival-Associated Metabolic Genes in Human Papillomavirus-Positive Head and Neck Cancers. Cancers (Basel) 2020; 12:E253. [PMID: 31968678 PMCID: PMC7017314 DOI: 10.3390/cancers12010253] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Human papillomavirus (HPV) causes an increasing number of head and neck squamous cell carcinomas (HNSCCs). Altered metabolism contributes to patient prognosis, but the impact of HPV status on HNSCC metabolism remains relatively uncharacterized. We hypothesize that metabolism-related gene expression differences unique to HPV-positive HNSCC influences patient survival. The Cancer Genome Atlas RNA-seq data from primary HNSCC patient samples were categorized as 73 HPV-positive, 442 HPV-negative, and 43 normal-adjacent control tissues. We analyzed 229 metabolic genes and identified numerous differentially expressed genes between HPV-positive and negative HNSCC patients. HPV-positive carcinomas exhibited lower expression levels of genes involved in glycolysis and higher levels of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and β-oxidation than the HPV-negative carcinomas. Importantly, reduced expression of the metabolism-related genes SDHC, COX7A1, COX16, COX17, ELOVL6, GOT2, and SLC16A2 were correlated with improved patient survival only in the HPV-positive group. This work suggests that specific transcriptional alterations in metabolic genes may serve as predictive biomarkers of patient outcome and identifies potential targets for novel therapeutic intervention in HPV-positive head and neck cancers.
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Affiliation(s)
- Martin A. Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Steven F. Gameiro
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Farhad Ghasemi
- Department of Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Peter Y. F. Zeng
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
| | - Hanna Maekebay
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - John W. Barrett
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
| | - Anthony C. Nichols
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
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Li N, Zhao L, Guo C, Liu C, Liu Y. Identification of a novel DNA repair-related prognostic signature predicting survival of patients with hepatocellular carcinoma. Cancer Manag Res 2019; 11:7473-7484. [PMID: 31496805 PMCID: PMC6689532 DOI: 10.2147/cmar.s204864] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is the sixth most lethal neoplasm worldwide. Traditional biomarkers often exploit the relationship between a certain gene and cancer progression, but they cannot predict patient survival or prognosis accurately. We aim to construct a new DNA repair-related gene signature that combines several genes to improve prognosis prediction in HCC. Methods We selected an HCC mRNA sequencing (mRNA-seq) dataset (n=365) from The Cancer Genome Atlas (TCGA), and gene set enrichment analysis (GSEA) was used to explore bioinformatics information and further screen genes. We then built a gene signature based on the Cox proportional hazards regression model. Results GSEA revealed that the hallmark DNA repair gene set was significantly upregulated in the tumor phenotype. A set of seven genes, namely, ADA, FEN1, POLR2G, SAC3D1, SEC61A1, SF3A3, and UPF3B, were significantly a
ssociated with overall survival (OS) and used to form a gene signature. The signature risk score was calculated and used to divide patients into high‐ and low‐risk groups. The high-risk group showed worse prognosis (log-rank test p<0.0001). Univariate and multivariate Cox regression analysis showed that the prognostic performance of this risk score signature was robust in different subgroups based on clinicopathological features, with p-values <0.05 (HR=2.38, 95% CI (confidence interval) =1.355–4.184), indicating that it can serve as an independent prognostic indicator. Conclusion We developed and identified a seven‐gene signature related to the DNA repair process that can predict survival in HCC. It can be used as an effective classification tool and to guide clinical treatment.
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Affiliation(s)
- Na Li
- Department of Central Laboratory, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, People's Republic of China
| | - Lan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Chunyan Guo
- Department of Pharmacy, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, People's Republic of China
| | - Chang Liu
- Department of Thoracic Surgery, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, People's Republic of China
| | - Yongyu Liu
- Department of Thoracic Surgery, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, People's Republic of China
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Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P. Proteomic analysis of meningiomas reveals clinically distinct molecular patterns. Neuro Oncol 2019; 21:1028-1038. [PMID: 31077268 PMCID: PMC6682208 DOI: 10.1093/neuonc/noz084] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Meningiomas represent one of the most common brain tumors and exhibit a clinically heterogeneous behavior, sometimes difficult to predict with classic histopathologic features. While emerging molecular profiling efforts have linked specific genomic drivers to distinct clinical patterns, the proteomic landscape of meningiomas remains largely unexplored. METHODS We utilize liquid chromatography tandem mass spectrometry with an Orbitrap mass analyzer to quantify global protein abundances of a clinically well-annotated formalin-fixed paraffin embedded (FFPE) cohort (n = 61) of meningiomas spanning all World Health Organization (WHO) grades and various degrees of clinical aggressiveness. RESULTS In total, we quantify 3042 unique proteins comparing patterns across different clinical parameters. Unsupervised clustering analysis highlighted distinct proteomic (n = 106 proteins, Welch's t-test, P < 0.01) and pathway-level (eg, Notch and PI3K/AKT/mTOR) differences between convexity and skull base meningiomas. Supervised comparative analyses of different pathological grades revealed distinct patterns between benign (grade I) and atypical/malignant (grades II‒III) meningiomas with specific oncogenes enriched in higher grade lesions. Independent of WHO grade, clinically aggressive meningiomas that rapidly recurred (<3 y) had distinctive protein patterns converging on mRNA processing and impaired activation of the matrisome complex. Larger sized meningiomas (>3 cm maximum tumor diameter) and those with previous radiation exposure revealed perturbed pro-proliferative (eg, epidermal growth factor receptor) and metabolic as well as inflammatory response pathways (mitochondrial activity, interferon), respectively. CONCLUSIONS Our proteomic study demonstrates that meningiomas of different grades and clinical parameters present distinct proteomic profiles. These proteomic variations offer potential future utility in helping better predict patient outcome and in nominating novel therapeutic targets for personalized care.
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Affiliation(s)
- Michail-Dimitrios Papaioannou
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Ugljesa Djuric
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Jennifer Kao
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shirin Karimi
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Kenneth Aldape
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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Co-expression of key gene modules and pathways of human breast cancer cell lines. Biosci Rep 2019; 39:BSR20181925. [PMID: 31285391 PMCID: PMC6639467 DOI: 10.1042/bsr20181925] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 06/30/2019] [Accepted: 07/06/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer (BC) is the most common leading cause of cancer-related death in women worldwide. Gene expression profiling analysis for human BCs has been studied previously. However, co-expression analysis for BC cell lines is still devoid to date. The aim of the study was to identify key pathways and hub genes that may serve as a biomarker for BC and uncover potential molecular mechanism using weighted correlation network analysis. We analyzed microarray data of BC cell lines (GSE 48213) listed in the Gene Expression Omnibus database. Gene co-expression networks were used to construct and explore the biological function in hub modules using the weighted correlation network analysis algorithm method. Meanwhile, Gene ontology and KEGG pathway analysis were performed using Cytoscape plug-in ClueGo. The network of the key module was also constructed using Cytoscape. A total of 5000 genes were selected, 28 modules of co-expressed genes were identified from the gene co–expression network, one of which was found to be significantly associated with a subtype of BC lines. Functional enrichment analysis revealed that the brown module was mainly involved in the pathway of the autophagy, spliceosome, and mitophagy, the black module was mainly enriched in the pathway of colorectal cancer and pancreatic cancer, and genes in midnightblue module played critical roles in ribosome and regulation of lipolysis in adipocytes pathway. Three hub genes CBR3, SF3B6, and RHPN1 may play an important role in the development and malignancy of the disease. The findings of the present study could improve our understanding of the molecular pathogenesis of breast cancer.
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Label propagation defines signaling networks associated with recurrently mutated cancer genes. Sci Rep 2019; 9:9401. [PMID: 31253832 PMCID: PMC6599034 DOI: 10.1038/s41598-019-45603-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Human tumors have distinct profiles of genomic alterations, and each of these alterations has the potential to cause unique changes to cellular homeostasis. Detailed analyses of these changes could reveal downstream effects of genomic alterations, contributing to our understanding of their roles in tumor development and progression. Across a range of tumor types, including bladder, lung, and endometrial carcinoma, we determined genes that are frequently altered in The Cancer Genome Atlas patient populations, then examined the effects of these alterations on signaling and regulatory pathways. To achieve this, we used a label propagation-based methodology to generate networks from gene expression signatures associated with defined mutations. Individual networks offered a large-scale view of signaling changes represented by gene signatures, which in turn reflected the scope of molecular events that are perturbed in the presence of a given genomic alteration. Comparing different networks to one another revealed common biological pathways impacted by distinct genomic alterations, highlighting the concept that tumors can dysregulate key pathways through multiple, seemingly unrelated mechanisms. Finally, altered genes inducing common changes to the signaling network were used to search for genomic markers of drug response, connecting shared perturbations to differential drug sensitivity.
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Chandramouli B, Melino G, Chillemi G. Smyd2 conformational changes in response to p53 binding: role of the C-terminal domain. Mol Oncol 2019; 13:1450-1461. [PMID: 31069954 PMCID: PMC6547616 DOI: 10.1002/1878-0261.12502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/01/2019] [Accepted: 05/08/2019] [Indexed: 12/24/2022] Open
Abstract
Smyd2 lysine methyltransferase regulates monomethylation of histone and nonhistone lysine residues using S‐adenosylmethionine cofactor as the methyl donor. The nonhistone interactors include several tumorigenic targets, including p53. Understanding this interaction would allow the structural principles that underpin Smyd2‐mediated p53 methylation to be elucidated. Here, we performed μ‐second molecular dynamics (MD) simulations on binary Smyd2‐cofactor and ternary Smyd2‐cofactor‐p53 peptide complexes. We considered both unmethylated and monomethylated p53 peptides (at Lys370 and Lys372). The results indicate that (a) the degree of conformational freedom of the C‐terminal domain of Smyd2 is restricted by the presence of the p53 peptide substrate, (b) the Smyd2 C‐terminal domain shows distinct dynamic properties when interacting with unmethylated and methylated p53 peptides, and (c) Lys372 methylation confines the p53 peptide conformation, with detectable influence on Lys370 accessibility to the cofactor. These MD results are therefore of relevance for studying the biology of p53 in cancer progression.
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Affiliation(s)
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome 'Tor Vergata', Italy.,Medical Research Council, Toxicology Unit, Department of Pathology, Cambridge University, Cambridge, UK
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy.,National Council of Research, CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
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High-throughput RNAi screening reveals cancer-selective lethal targets in the RNA spliceosome. Oncogene 2019; 38:4142-4153. [PMID: 30705407 DOI: 10.1038/s41388-019-0711-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/21/2018] [Accepted: 01/16/2019] [Indexed: 12/23/2022]
Abstract
Novel therapeutic strategies for non-small-cell lung cancer (NSCLC) are urgently needed. RNA splicing, orchestrated by the spliceosome, is deregulated in many forms of cancer, including NSCLC. Here, we performed high-throughput screening with a small interfering RNA library targeting all annotated human spliceosome proteins to identify cancer-selective lethal targets in the RNA splicing machinery. Silencing of several spliceosome proteins reduced cell viability in a panel of NSCLC cell lines, but not in non-malignant lung fibroblasts and epithelial cells. Interestingly, the cancer-selective lethal target set comprised all seven Sm proteins that, together with small nuclear RNA, form the core structure of most spliceosome subunits. Interfering with Sm protein expression induced apoptosis in NSCLC cells, but not in non-malignant cells. In silico analysis revealed that Sm proteins are frequently upregulated in NSCLC. For several Sm proteins, increased expression showed a positive correlation with disease severity. Together, our results suggest that the Sm proteins represent particularly useful novel targets for selective treatment of NSCLC.
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Wu YY, Hsieh CT, Chiu YM, Chou SC, Kao JT, Shieh DC, Lee YJ. GSK-3 inhibitors enhance TRAIL-mediated apoptosis in human gastric adenocarcinoma cells. PLoS One 2018; 13:e0208094. [PMID: 30557366 PMCID: PMC6296518 DOI: 10.1371/journal.pone.0208094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023] Open
Abstract
Resistance to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis has been reported in some cancer cells, including AGS human gastric adenocarcinoma cells. Reducing this resistance might shed light on the treatment of human gastric adenocarcinoma. In this study, we examined whether glycogen synthase kinase-3 (GSK-3) inhibitors can restore TRAIL responsiveness in gastric adenocarcinoma cells. The effect of two GSK-3 inhibitors, SB-415286, and LiCl, on apoptosis signaling of TRAIL in human gastric adenocarcinoma cell lines and primary gastric epithelial cells was analyzed. Both inhibitors can sensitize gastric adenocarcinoma cells, but not primary gastric epithelial cells, to TRAIL-induced apoptosis by increasing caspase-8 activity and its downstream signal transmission. Adding p53 siRNA can downregulate GSK-3 inhibitor-related sensitization to TRAIL-induced apoptosis and caspase-3 activity. GSK-3 inhibitors strongly activate the phosphorylation of JNK. Inhibition of JNK leads to earlier and more intense apoptosis, showing that the activation of JNK may provide anti-apoptotic equilibrium of pro-apoptotic cells. Our observations indicate that GSK-3 inhibitors can sentize AGS gastric adenocarcinoma cells to TRAIL-induced apoptosis. Therefore, in certain types of gastric adenocarcinoma, GSK-3 inhibitor might enhance the antitumor activity of TRAIL and mightbe a promising candidate for the treatment of certain types of gastric adenocarcinoma.
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Affiliation(s)
- Yi-Ying Wu
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung, Taiwan
- Research Center for Chinese Herbal Medicine, China Medical University, Taichung, Taiwan
- * E-mail:
| | - Chin-Tung Hsieh
- Department of Pediatrics, Lo-Hsu Medical Foundation Lotung Poh-Ai Hospital, I-Lan, Taiwan
| | - Ying-Ming Chiu
- Department of Nursing, College of Medicine and Nursing, Hungkuang University, Taichung, Taiwan
- Division of Allergy, Immunology & Rheumatology, Changhua Christian Hospital, Changhua, Taiwan
| | - Shen-Chieh Chou
- Department of Biological Science and Technology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Jung-Ta Kao
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
- Department of Internal Medicine, School of Medicine, China Medical University Hospital and China Medical University, Taichung, Taiwan
| | - Dong-Chen Shieh
- Department of Nursing, College of Medicine and Nursing, Hungkuang University, Taichung, Taiwan
| | - Yi-Ju Lee
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan
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Brachtlova T, van Beusechem VW. Unleashing the Full Potential of Oncolytic Adenoviruses against Cancer by Applying RNA Interference: The Force Awakens. Cells 2018; 7:cells7120228. [PMID: 30477117 PMCID: PMC6315459 DOI: 10.3390/cells7120228] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/23/2022] Open
Abstract
Oncolytic virus therapy of cancer is an actively pursued field of research. Viruses that were once considered as pathogens threatening the wellbeing of humans and animals alike are with every passing decade more prominently regarded as vehicles for genetic and oncolytic therapies. Oncolytic viruses kill cancer cells, sparing healthy tissues, and provoke an anticancer immune response. Among these viruses, recombinant adenoviruses are particularly attractive agents for oncolytic immunotherapy of cancer. Different approaches are currently examined to maximize their therapeutic effect. Here, knowledge of virus–host interactions may lead the way. In this regard, viral and host microRNAs are of particular interest. In addition, cellular factors inhibiting viral replication or dampening immune responses are being discovered. Therefore, applying RNA interference is an attractive approach to strengthen the anticancer efficacy of oncolytic viruses gaining attention in recent years. RNA interference can be used to fortify the virus’ cancer cell-killing and immune-stimulating properties and to suppress cellular pathways to cripple the tumor. In this review, we discuss different ways of how RNA interference may be utilized to increase the efficacy of oncolytic adenoviruses, to reveal their full potential.
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Affiliation(s)
- Tereza Brachtlova
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1007 MB Amsterdam, The Netherlands.
| | - Victor W van Beusechem
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, 1007 MB Amsterdam, The Netherlands.
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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Williams SP, Barthorpe AS, Lightfoot H, Garnett MJ, McDermott U. High-throughput RNAi screen for essential genes and drug synergistic combinations in colorectal cancer. Sci Data 2017; 4:170139. [PMID: 28972570 PMCID: PMC5625556 DOI: 10.1038/sdata.2017.139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/14/2017] [Indexed: 12/19/2022] Open
Abstract
Metastatic colorectal cancer is a leading cause of cancer death. However, current therapy options are limited to chemotherapy, with the addition of anti-EGFR antibodies for patients with RAS wild-type tumours. Novel drug targets, or drug combinations that induce a synergistic response, would be of great benefit to patients. The identification of genes that are essential for cell survival can be undertaken using functional genomics screens. Furthermore, performing such screens in the presence of a targeted agent would allow the identification of combinations that result in a synthetic lethal interaction. Here, we present a dataset containing the results of a large scale RNAi screen (815 genes) to detect essential genes as well as synergistic combinations with targeted therapeutic agents using a panel of 27 colorectal cancer cell lines. These data identify genes that are essential for colorectal cancer cell survival as well as synthetic lethal treatment combinations using novel computational approaches. Moreover, this dataset could be utilised in combination with genomic profiling to identify predictive biomarkers of response.
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