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Deng X, Liu Z, Wang B, Ma J, Meng X. The DDX6/KIFC1 signaling axis, as regulated by YY1, contributes to the malignant behavior of pancreatic cancer. FASEB J 2024; 38:e23581. [PMID: 38551642 DOI: 10.1096/fj.202400166r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024]
Abstract
Human DEAD/H box RNA helicase DDX6 acts as an oncogene in several different types of cancer, where it participates in RNA processing. Nevertheless, the role of DDX6 in pancreatic cancer (PC), together with the underlying mechanism, has yet to be fully elucidated. In the present study, compared with adjacent tissues, the level of DDX6 was abnormally increased in human PC tissues, and this increased level of expression was associated with poor prognosis. Furthermore, the role of DDX6 in PC was investigated by overexpressing or silencing the DDX6 in the PC cell lines, SW1990 and PaTu-8988t. A xenograft model was established by injecting nude mice with either DDX6-overexpressing or DDX6-silenced SW1990 cells. DDX6 overexpression promoted the proliferation and cell cycle transition, inhibited the cell apoptosis of PC cells, and accelerated tumor formation, whereas DDX6 knockdown elicited the opposite effects. DDX6 exerted positive effects on PC. RNA immunoprecipitation assay showed that DDX6 bound to kinesin family member C1 (KIFC1) mRNA, which was further confirmed by RNA pull-down assay. These results suggested that DDX6 positively regulated the expression of KIFC1. KIFC1 overexpression enhanced the proliferative capability of PC cells with DDX6 knockdown and inhibited their apoptosis. By contrast, DDX6 overexpression reversed the inhibitory effect of KIFC1 silencing on tumor proliferation. Subsequently, the transcription factor Yin Yang 1 (YY1) was shown to negatively regulate DDX6 at both the mRNA and protein levels. Dual-luciferase reporter assay verified that YY1 targeted the promoter of DDX6 and inhibited its transcription. High expression levels of YY1 decreased the proliferation of PC cells and promoted cell apoptosis, although these effects were reversed by DDX6 overexpression. Taken together, YY1 may target the DDX6/KIFC1 axis, thereby negatively regulating its expression, leading to an inhibitory effect on pancreatic tumor.
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Affiliation(s)
- Xin Deng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhen Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Baosheng Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jia Ma
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiangpeng Meng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Lee SG, Eom SY, Lim JA, Choi BS, Kwon HJ, Hong YS, Kim YD, Kim H, Park JD. Association between urinary arsenic concentration and genetic polymorphisms in Korean adults. Toxicol Res 2024; 40:179-188. [PMID: 38223675 PMCID: PMC10786758 DOI: 10.1007/s43188-023-00216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/10/2023] [Accepted: 10/25/2023] [Indexed: 01/16/2024] Open
Abstract
Arsenic (As) is a human carcinogen widely distributed in the environment. This study evaluated the association between the urinary As concentration and single nucleotide polymorphisms (SNPs) in Korean adults to determine the genetic factors related to As concentration. The study included 496 participants for the genome-wide association study (GWAS) and 1483 participants for the candidate gene approach study. Participants were 19 years and older. The concentrations of total As (Tot As) and total As metabolites (Tmet As, the sum of inorganic As and their metabolites; arsenite, arsenate, monomethylarsonic, and dimethylarsinic acid) in the urine were analyzed. The GWAS identified four SNPs (rs1432523, rs3776006, rs11171747, and rs807573) associated with urinary Tot As and four SNPs (rs117605537, rs3776006, rs11171747, and rs148103384) significantly associated with urinary Tmet As concentration (P < 1 × 10-4). The candidate gene study identified two SNPs (PRDX2 rs10427027 and GLRX rs3822751) in genes related to the reduction reaction associated with urinary Tot As and Tmet As. This study suggests that genetic factors may play a role in regulating As metabolism in the human body, affecting both exposure levels and its potential health risks in the general Korean population, even at low exposure levels. Supplementary Information The online version contains supplementary material available at 10.1007/s43188-023-00216-x.
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Affiliation(s)
- Seul-Gi Lee
- Department of Preventive Medicine, College of Medicine, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
| | - Sang-Yong Eom
- Department of Preventive Medicine, College of Medicine, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Ji-Ae Lim
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, 16890 Republic of Korea
| | - Byung-Sun Choi
- Department of Preventive Medicine, College of Medicine, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
| | - Ho-Jang Kwon
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, 16890 Republic of Korea
| | - Young-Seoub Hong
- Department of Preventive Medicine, College of Medicine, Dong-A University, Busan, 49201 Republic of Korea
| | - Yong-Dae Kim
- Department of Preventive Medicine, College of Medicine, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Heon Kim
- Department of Preventive Medicine, College of Medicine, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Jung-Duck Park
- Department of Preventive Medicine, College of Medicine, Chung-Ang University, 84 Heukseok-Ro, Dongjak-Gu, Seoul, 06974 Republic of Korea
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Ma Z, Song J, Hua Y, Wang Y, Cao W, Wang H, Hou L. The role of DDX46 in breast cancer proliferation and invasiveness: A potential therapeutic target. Cell Biol Int 2023; 47:283-291. [PMID: 36200534 DOI: 10.1002/cbin.11930] [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: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/24/2022] [Indexed: 01/19/2023]
Abstract
DDX46, a member of DEAD-box (DDX) proteins, is associated with various cancers, while its involvement in the pathogenesis of breast cancer hasn't been reported so far. The study demonstrated the overexpression of DDX46 in human breast cancer cells and tissue samples, and correlated with high histological grade and lymph node metastasis. Downregulation of DDX46 in the breast cancer cell lines inhibited their proliferation and invasiveness in vitro. Furthermore, the growth of MDA-MB-231 xenografts was suppressed in nude mice by DDX46 knockingdown. Taken together, our findings suggest that DDX46 is an oncogenic factor in human breast cancer, and a potential therapeutic target.
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Affiliation(s)
- Zhongliang Ma
- Department of Breast Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jinlian Song
- Department of Laboratory, Qingdao University Affiliated Qingdao Women and Childrens Hospital, Qingdao, China
| | - Yanan Hua
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu Wang
- Department of Breast Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Weihong Cao
- Department of Breast Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Haibo Wang
- Department of Breast Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lin Hou
- Department of Biochemistry and Molecular Biology, Qingdao University Medical College
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Hobani YH, Almars AI, Alelwani W, Toraih EA, Nemr NA, Shaalan AAM, Fawzy MS, Attallah SM. Genetic Variation in DEAD-Box Helicase 20 as a Putative Marker of Recurrence in Propensity-Matched Colon Cancer Patients. Genes (Basel) 2022; 13:genes13081404. [PMID: 36011315 PMCID: PMC9407271 DOI: 10.3390/genes13081404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 12/04/2022] Open
Abstract
Variants of the DEAD-Box Helicase 20 (DDX20), one of the microRNAs (miRNAs) machinery genes, can modulate miRNA/target gene expressions and, hence, influence cancer susceptibility and prognosis. Here, we aimed to unravel the association of DDX20 rs197412 T/C variant with colon cancer risk and/or prognosis in paired samples of 122 colon cancer and non-cancer tissue specimens by TaqMan allelic discrimination analysis. Structural/functional bioinformatic analyses were carried out, followed by a meta-analysis. We found that the T allele was more frequent in cancer tissues compared to control tissues (60.2% vs. 35.7%, p < 0.001). Furthermore, the T variant was highly frequent in primary tumors with evidence of recurrence (73% vs. 47.5%, p < 0.001). Genetic association models, adjusted by age and sex, revealed that the T allele was associated with a higher risk of developing colon cancer under heterozygote (T/C vs. C/C: OR = 2.35, 95%CI = 1.25−4.44, p < 0.001), homozygote (T/T vs. C/C: OR = 7.6, 95%CI = 3.5−16.8, p < 0.001), dominant (T/C-T/T vs. C/C: OR = 3.4, 95%CI = 1.87−8.5, p < 0.001), and recessive (T/T vs. C/C-T/C: OR = 4.42, 95%CI = 2.29−8.54, p = 0.001) models. Kaplan−Meier survival curves showed the shift in the C > T allele to be associated with poor disease-free survival. After adjusting covariates using a multivariate cox regression model, patients harboring C > T somatic mutation were 3.5 times more likely to develop a recurrence (p < 0.001). A meta-analysis of nine studies (including ours) showed a higher risk of CRC (81%) in subjects harboring the T/T genotype than in T/C + C/C genotypes, supporting the potential clinical utility of the specified study variant as a biomarker for risk stratification in CRC cases. However, results were not significant in non-colorectal cancers. In conclusion, the DDX20 rs197412 variant is associated with increased colon cancer risk and a higher likelihood of recurrence in the study population.
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Affiliation(s)
- Yahya H. Hobani
- Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan 82911, Saudi Arabia
| | - Amany I. Almars
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Walla Alelwani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 80203, Saudi Arabia
| | - Eman A. Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Genetics Unit, Department of Histology and Cell Biology, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: (E.A.T.); or (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +966-58-3241944 (M.S.F.)
| | - Nader A. Nemr
- Endemic and Infectious Diseases Department, Suez Canal University, Ismailia 41522, Egypt
| | - Aly A. M. Shaalan
- Department of Anatomy, Faculty of Medicine, Jazan University, Jazan 45142, Saudi Arabia
- Department of Histology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
- Correspondence: (E.A.T.); or (M.S.F.); Tel.: +1-346-907-4237 (E.A.T.); +966-58-3241944 (M.S.F.)
| | - Samy M. Attallah
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
- Clinical Pathology Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
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Zheng Z, Liu H, Shi Y, Liu Z, Teng H, Deng S, Wei L, Wang Y, Zhang F. Comparative transcriptome analysis reveals the resistance regulation mechanism and fungicidal activity of the fungicide phenamacril in Fusarium oxysporum. Sci Rep 2022; 12:11081. [PMID: 35773469 PMCID: PMC9247061 DOI: 10.1038/s41598-022-15188-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/20/2022] [Indexed: 12/21/2022] Open
Abstract
Fusarium oxysporum (Fo) is an important species complex of soil-borne pathogenic fungi that cause vascular wilt diseases of agricultural crops and some opportunistic diseases of humans. The fungicide phenamacril has been extensively reported to have antifungal activity against Fusarium graminearum and Fusarium fujikuroi. In this study, we found that the amino acid substitutions (V151A and S418T) in Type I myosin FoMyo5 cause natural low resistance to phenamacril in the plant pathogenic Fo isolates. Therefore, we compared the transcriptomes of two phenamacril-resistant Fo isolates FoII5, Fo1st and one phenamacril-sensitive isolate Fo3_a after 1 μg/mL phenamacril treatment. Among the 2728 differentially expressed genes (DEGs), 14 DEGs involved in oxidation–reduction processes and MFS transporters, were significantly up-regulated in phenamacril-resistant isolates. On the other hand, 14 DEGs involved in ATP-dependent RNA helicase and ribosomal biogenesis related proteins, showed significantly down-regulated expression in both phenamacril-resistant and -sensitive isolates. These results indicated that phenamacril not only seriously affected the cytoskeletal protein binding and ATPase activity of sensitive isolate, but also suppressed ribosome biogenesis in all the isolates. Hence, this study helps us better understand resistance regulation mechanism and fungicidal activity of phenamacril and provide reference for the development of new fungicides to control Fo.
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Affiliation(s)
- Zhitian Zheng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, People's Republic of China.
| | - Huaqi Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, People's Republic of China
| | - Yunyong Shi
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, People's Republic of China
| | - Zao Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, People's Republic of China
| | - Hui Teng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, People's Republic of China
| | - Sheng Deng
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
| | - Lihui Wei
- Institute of Plant Protection, Key Lab of Food Quality and Safety of Jiangsu Province-State, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Yunpeng Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, People's Republic of China.
| | - Feng Zhang
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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SNORA42 promotes oesophageal squamous cell carcinoma development through triggering the DHX9/p65 axis. Genomics 2021; 113:3015-3029. [PMID: 34182081 DOI: 10.1016/j.ygeno.2021.06.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are an important group of non-coding RNAs that have been reported to play a key role in the occurrence and development of various cancers. Here we demonstrate that Small nucleolar RNA 42 (SNORA42) enhanced the proliferation and migration of Oesophageal squamous carcinoma cells (ESCC) via the DHX9/p65 axis. Our results found that SNORA42 was significantly upregulated in ESCC cell lines, tissues and serum of ESCC patients. The high expression level of SNORA42 was positively correlated with malignant characteristics and over survival probability of patients with ESCC. Through in vitro and in vivo approaches, we demonstrated that knockdown of SNORA42 significantly impeded ESCC growth and metastasis whereas overexpression of SNORA42 got opposite effects. Mechanically, SNORA42 promoted DHX9 expression by attenuating DHX9 transports into the cytoplasm, to protect DHX9 from being ubiquitinated and degraded. From the KEGG analysis of Next-Generation Sequencing, the NF-κB pathway was one of the most regulated pathways by SNORA42. SNORA42 enhanced phosphorylation of p65 and this effect could be reversed by NF-κB inhibitor, BAY11-7082. Moreover, SNORA42 activated NF-κB signaling through promoting the transcriptional co-activator DHX9 interacted with p-p65, inducing NF-κB downstream gene expression. In summary, our study highlights the potential of SNORA42 is up-regulated in ESCC and promotes ESCC development partly via interacting with DHX9 and triggering the DHX9/p65 axis.
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Maheshvara regulates JAK/STAT signaling by interacting and stabilizing hopscotch transcripts which leads to apoptosis in Drosophila melanogaster. Cell Death Dis 2021; 12:363. [PMID: 33824299 PMCID: PMC8024297 DOI: 10.1038/s41419-021-03649-0] [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: 12/14/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 02/01/2023]
Abstract
Maheshvara (mahe), an RNA helicase that is widely conserved across taxa, regulates Notch signaling and neuronal development in Drosophila. In order to identify novel components regulated by mahe, transcriptome profiling of ectopic mahe was carried out and this revealed striking upregulation of JAK/STAT pathway components like upd1, upd2, upd3, and socs36E. Further, significant downregulation of the pathway components in mahe loss-of-function mutant as well as upon lowering the level of mahe by RNAi, supported and strengthened our transcriptome data. Parallelly, we observed that mahe, induced caspase-dependent apoptosis in photoreceptor neurons, and this phenotype was significantly modulated by JAK/STAT pathway components. RNA immunoprecipitation unveiled the presence of JAK/STAT tyrosine kinase hopscotch (hop) transcripts in the complex immunoprecipitated with Mahe, which ultimately resulted in stabilization and elevation of hop transcripts. Additionally, we also observed the surge in activity of downstream transcription factor Stat92E, which is indicative of activation of the JAK/STAT signaling, and this in turn led to apoptosis via upregulation of hid. Taken together, our data provide a novel regulation of JAK/STAT pathway by RNA helicase Maheshvara, which ultimately promotes apoptosis.
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The DEAD-box protein family of RNA helicases: sentinels for a myriad of cellular functions with emerging roles in tumorigenesis. Int J Clin Oncol 2021; 26:795-825. [PMID: 33656655 DOI: 10.1007/s10147-021-01892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/20/2021] [Indexed: 02/06/2023]
Abstract
DEAD-box RNA helicases comprise a family within helicase superfamily 2 and make up the largest group of RNA helicases. They are a profoundly conserved family of RNA-binding proteins, carrying a generic Asp-Glu-Ala-Asp (D-E-A-D) motif that gives the family its name. Members of the DEAD-box family of RNA helicases are engaged in all facets of RNA metabolism from biogenesis to decay. DEAD-box proteins ordinarily function as constituents of enormous multi-protein complexes and it is believed that interactions with other components in the complexes might be answerable for the various capacities ascribed to these proteins. Therefore, their exact function is probably impacted by their interacting partners and to be profoundly context dependent. This may give a clarification to the occasionally inconsistent reports proposing that DEAD-box proteins have both pro- and anti-proliferative functions in cancer. There is emerging evidence that DEAD-box family of RNA helicases play pivotal functions in various cellular processes and in numerous cases have been embroiled in cellular proliferation and/or neoplastic transformation. In various malignancy types, DEAD-box RNA helicases have been reported to possess pro-proliferation or even oncogenic roles as well as anti-proliferative or tumor suppressor functions. Clarifying the exact function of DEAD-box helicases in cancer is probably intricate, and relies upon the cellular milieu and interacting factors. This review aims to summarize the current data on the numerous capacities that have been ascribed to DEAD-box RNA helicases. It also highlights their diverse actions upon malignant transformation in the various tumor types.
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Cui F, Luo P, Bai Y, Meng J. Silencing of Long Non-Coding RNA FGD5-AS1 Inhibits the Progression of Non-Small Cell Lung Cancer by Regulating the miR-493-5p/DDX5 Axis. Technol Cancer Res Treat 2021; 20:1533033821990007. [PMID: 33550957 PMCID: PMC7876571 DOI: 10.1177/1533033821990007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background: Long non-coding RNA FGD5 antisense RNA 1 (FGD5-AS1), identified to be a carcinogenic lncRNA, exhibits a regulatory role in some malignancies including non-small cell lung cancer (NSCLC). The aim of the present research is to decipher the function and underlying mechanism of FGD5-AS1 in progression of NSCLC. Methods: Expression of FGD5-AS1, miR-493-5p and DEAD-box protein 5 (DDX5) in NSCLC tissues and cells was quantified utilizing qRT-PCR. Cell proliferation was assessed by CCK-8 method. Scratch healing test and Transwell assay were used for assaying cell migration and invasion. Expressions of DDX5 and epithelial-mesenchymal transition (EMT)-related proteins were examined by Western blot. Additionally, targeting relationships between FGD5-AS1 and miR-493-5p, miR-493-5p and DDX5 were verified by dual-luciferase reporter gene assay. Results: Expression of FGD5-AS1 in NSCLC tissues and cell lines was up-regulated. Expression of FGD5-AS1 was in association with enlarged tumor size and lymph node metastasis of the patients. Knockdown of FGD5-AS1 led to the inhibition of proliferation, migration, invasion and EMT of NSCLC cells. FGD5-AS1 directly targeted miR-493-5p, while DDX5 was the target of miR-493-5p in NSCLC cells. Additionally, FGD5-AS1 could positively regulate the expression of DDX5 via suppressing miR-493-5p. Conclusion: FGD5-AS1 facilitates the proliferation, migration, invasion and EMT of NSCLC cells by sponging miR-493-5p and up-regulating DDX5.
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Affiliation(s)
- Fang Cui
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Luo
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yao Bai
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiangping Meng
- Assisted Reproductive Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Qin K, Jian D, Xue Y, Cheng Y, Zhang P, Wei Y, Zhang J, Xiong H, Zhang Y, Yuan X. DDX41 regulates the expression and alternative splicing of genes involved in tumorigenesis and immune response. Oncol Rep 2021; 45:1213-1225. [PMID: 33650667 PMCID: PMC7859996 DOI: 10.3892/or.2021.7951] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
DEAD‑box helicase 41 (DDX41) is an RNA helicase and accumulating evidence has suggested that DDX41 is involved in pre‑mRNA splicing during tumor development. However, the role of DDX41 in tumorigenesis remains unclear. In order to determine the function of DDX41, the human DDX41 gene was cloned and overexpressed in HeLa cells. The present study demonstrated that DDX41 overexpression inhibited proliferation and promoted apoptosis in HeLa cells. RNA‑sequencing analysis of the transcriptomes in overexpressed and normal control samples. DDX41 regulated 959 differentially expressed genes compared with control cells. Expression levels of certain oncogenes were also regulated by DDX41. DDX41 selectively regulated the alternative splicing of genes in cancer‑associated pathways including the EGFR and FGFR signaling pathways. DDX41 selectively upregulated the expression levels of five antigen processing and presentation genes (HSPA1A, HSPA1B, HSPA6, HLA‑DMB and HLA‑G) and downregulated other immune‑response genes in HeLa cells. Additionally, DDX41‑regulated oncogenes and antigen processing and presentation genes were associated with patient survival rates. Moreover, DDX41 expression was associated with immune infiltration in cervical and endocervical squamous cancer. The present findings showed that DDX41 regulated the cancer cell transcriptome at both the transcriptional and alternative splicing levels. The DDX41 regulatory network predicted the biological function of DDX41 in suppressing tumor cell growth and regulating cancer immunity, which may be important for developing anticancer therapeutics.
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Affiliation(s)
- Kai Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Danni Jian
- Department of Otolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yaqiang Xue
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, Wuhan, Hubei 430075, P.R. China
| | - Yi Cheng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, Wuhan, Hubei 430075, P.R. China
| | - Jing Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yi Zhang
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, Wuhan, Hubei 430075, P.R. China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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Abdelkrim YZ, Banroques J, Kyle Tanner N. Known Inhibitors of RNA Helicases and Their Therapeutic Potential. Methods Mol Biol 2021; 2209:35-52. [PMID: 33201461 DOI: 10.1007/978-1-0716-0935-4_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA helicases are proteins found in all kingdoms of life, and they are associated with all processes involving RNA from transcription to decay. They use NTP binding and hydrolysis to unwind duplexes, to remodel RNA structures and protein-RNA complexes, and to facilitate the unidirectional metabolism of biological processes. Viral, bacterial, and eukaryotic parasites have an intimate need for RNA helicases in their reproduction. Moreover, various disorders, like cancers, are often associated with a perturbation of the host's helicase activity. Thus, RNA helicases provide a rich source of targets for the development of therapeutic or prophylactic drugs. In this review, we provide an overview of the different targeting strategies against helicases, the different types of compounds explored, the proposed inhibitory mechanisms of the compounds on the proteins, and the therapeutic potential of these compounds in the treatment of various disorders.
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Affiliation(s)
- Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France.,Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis/Université de Tunis el Manar, Tunis-Belvédère, Tunisia
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France.,PSL Research University, Paris, France
| | - N Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France.
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12
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Zhou B, Sun Q, Kong DX. Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach. Oncotarget 2017; 7:32394-407. [PMID: 27083051 PMCID: PMC5078021 DOI: 10.18632/oncotarget.8716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/28/2016] [Indexed: 12/15/2022] Open
Abstract
In this study, we proposed an improved algorithm for identifying proteins relevant to cancer. The algorithm was named two-layer molecular similarity ensemble approach (TL-SEA). We applied TL-SEA to analyzing the correlation between anticancer compounds (against cell lines K562, MCF7 and A549) and active compounds against separate target proteins listed in BindingDB. Several associations between cancer types and related proteins were revealed using this chemoinformatics approach. An analysis of the literature showed that 26 of 35 predicted proteins were correlated with cancer cell proliferation, apoptosis or differentiation. Additionally, interactions between proteins in BindingDB and anticancer chemicals were also predicted. We discuss the roles of the most important predicted proteins in cancer biology and conclude that TL-SEA could be a useful tool for inferring novel proteins involved in cancer and revealing underlying molecular mechanisms.
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Affiliation(s)
- Bin Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - De-Xin Kong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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13
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Nyagwange J, Tijhaar E, Ternette N, Mobegi F, Tretina K, Silva JC, Pelle R, Nene V. Characterization of the Theileria parva sporozoite proteome. Int J Parasitol 2017; 48:265-273. [PMID: 29258832 PMCID: PMC5854367 DOI: 10.1016/j.ijpara.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/16/2017] [Accepted: 09/21/2017] [Indexed: 12/29/2022]
Abstract
2007 Theileria parva proteins expressed in the sporozoite were identified. Proteins include known T. parva antigens targeted by antibodies and cytotoxic T cells. Proteins predicted to be orthologs of Plasmodium falciparum sporozoite surface molecules were identified. Proteins predicted to be orthologs of P. falciparum invasion organelle proteins were identified. Proteins that may contribute to the phenomenon of bovine lymphocyte transformation were identified.
East Coast fever is a lymphoproliferative disease caused by the tick-borne protozoan parasite Theileria parva. The sporozoite stage of this parasite, harboured and released from the salivary glands of the tick Rhipicephalus appendiculatus during feeding, invades and establishes infection in bovine lymphocytes. Blocking this initial stage of invasion presents a promising vaccine strategy for control of East Coast fever and can in part be achieved by targeting the major sporozoite surface protein p67. To support research on the biology of T. parva and the identification of additional candidate vaccine antigens, we report on the sporozoite proteome as defined by LC–MS/MS analysis. In total, 4780 proteins were identified in an enriched preparation of sporozoites. Of these, 2007 were identified as T. parva proteins, representing close to 50% of the total predicted parasite proteome. The remaining 2773 proteins were derived from the tick vector. The identified sporozoite proteins include a set of known T. parva antigens targeted by antibodies and cytotoxic T cells from cattle that are immune to East Coast fever. We also identified proteins predicted to be orthologs of Plasmodium falciparum sporozoite surface molecules and invasion organelle proteins, and proteins that may contribute to the phenomenon of bovine lymphocyte transformation. Overall, these data establish a protein expression profile of T. parva sporozoites as an important starting point for further study of a parasitic species which has considerable agricultural impact.
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Affiliation(s)
- James Nyagwange
- International Livestock Research Institute, P.O. Box 30709, Nairobi, Kenya; Cell Biology and Immunology Group, Wageningen University, The Netherlands
| | - Edwin Tijhaar
- Cell Biology and Immunology Group, Wageningen University, The Netherlands
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK
| | - Fredrick Mobegi
- Department of Infection and Immunity, South Australian Health and Medical Research Institute, North Terrace, Adelaide 5000, South Australia, Australia
| | - Kyle Tretina
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roger Pelle
- International Livestock Research Institute, P.O. Box 30709, Nairobi, Kenya
| | - Vishvanath Nene
- International Livestock Research Institute, P.O. Box 30709, Nairobi, Kenya.
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14
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Fidaleo M, De Paola E, Paronetto MP. The RNA helicase A in malignant transformation. Oncotarget 2017; 7:28711-23. [PMID: 26885691 PMCID: PMC5053757 DOI: 10.18632/oncotarget.7377] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
The RNA helicase A (RHA) is involved in several steps of RNA metabolism, such as RNA processing, cellular transit of viral molecules, ribosome assembly, regulation of transcription and translation of specific mRNAs. RHA is a multifunctional protein whose roles depend on the specific interaction with different molecular partners, which have been extensively characterized in physiological situations. More recently, the functional implication of RHA in human cancer has emerged. Interestingly, RHA was shown to cooperate with both tumor suppressors and oncoproteins in different tumours, indicating that its specific role in cancer is strongly influenced by the cellular context. For instance, silencing of RHA and/or disruption of its interaction with the oncoprotein EWS-FLI1 rendered Ewing sarcoma cells more sensitive to genotoxic stresses and affected tumor growth and maintenance, suggesting possible therapeutic implications. Herein, we review the recent advances in the cellular functions of RHA and discuss its implication in oncogenesis, providing a perspective for future studies and potential translational opportunities in human cancer.
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Affiliation(s)
- Marco Fidaleo
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
| | - Elisa De Paola
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Laboratory of Cellular and Molecular Neurobiology, CERC, Fondazione Santa Lucia, Rome, Italy
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15
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Ito S, Koso H, Sakamoto K, Watanabe S. RNA helicase DHX15 acts as a tumour suppressor in glioma. Br J Cancer 2017; 117:1349-1359. [PMID: 28829764 PMCID: PMC5672939 DOI: 10.1038/bjc.2017.273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 06/22/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common form of malignant brain cancer and has a poor prognosis in adults. We identified Dhx15 as a candidate tumour suppressor gene in glioma by transposon-based mutagenesis. Dhx15 is an adenosine triphosphate (ATP)-dependent RNA helicase belonging to the DEAH-box (DHX) helicase family, but its role in cancer remains elusive. METHODS DHX15 expression levels were examined in glioma cell lines. DHX15 functions were examined by gain- and loss-of-function analyses. Protein motifs required for the function of DHX15 were investigated by the analysis of mutant proteins. RESULTS DHX15 expression was lower in human glioma cell lines than in normal neural stem cells. Dhx15 knockdown resulted in enhanced proliferation of primary immortalised mouse astrocytes, supporting the notion that DHX15 is a tumour suppressor. Retroviral-mediated transduction of DHX15 into glioma cell lines suppressed proliferation and foci formation in vitro. Moreover, DHX15 suppressed tumour formation in a xenograft mouse model. ATPase activity was not required for the growth-inhibitory function of DHX15; however, the Ia, Ib, IV, and V motifs, which act as RNA-binding domains in DHX15, were essential. qPCR analysis revealed that DHX15 suppressed expression of NF-κB downstream target genes as well as the genes involved in splicing. CONCLUSIONS These findings provide evidence that DHX15 acts as a tumour suppressor gene in glioma.
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Affiliation(s)
- Shingo Ito
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 1088639, Japan
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University, Tokyo 1138421, Japan
| | - Hideto Koso
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 1088639, Japan
| | - Kazuhiro Sakamoto
- Department of Coloproctological Surgery, Faculty of Medicine, Juntendo University, Tokyo 1138421, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, University of Tokyo, Tokyo 1088639, Japan
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16
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Liang S, Ju X, Zhou Y, Chen Y, Ke G, Wen H, Wu X. Downregulation of eukaryotic initiation factor 4A1 improves radiosensitivity by delaying DNA double strand break repair in cervical cancer. Oncol Lett 2017; 14:6976-6982. [PMID: 29163714 DOI: 10.3892/ol.2017.7040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/27/2017] [Indexed: 12/31/2022] Open
Abstract
Expression of eukaryotic initiation factor 4A1 (eIF4A1) following brachytherapy has been reported to predict improved radiosensitivity and tumor-specific survival in cervical cancer. Therefore, the present study investigated the function of eIF4A1 in cervical cancer and the mechanism by which eIF4A1 regulates cervical cancer radiosensitivity. It was determined that the downregulation of eIF4A1 in HeLa and SiHa cells notably attenuated cell proliferation, in addition to repressing cervical cancer migration and invasion, and promoting cell apoptosis. In vitro and in vivo studies have demonstrated that silencing eIF4A1 improves cervical cancer radiosensitivity. Detection of γ-H2AX using western blot analysis at 0, 0.5, 1, 6 and 24 h following the exposure of cervical cancer cells to X-rays illustrated that eIF4A1-knockdown results in postponed radiation-induced DNA double strand break (DSB) repair. Overall, the results of the present study demonstrated that downregulated eIF4A1 improves cervical cancer radiosensitivity by delaying cancer cell DSB repair. In conclusion, the data indicated that eIF4A1 performs a vital role in cervical cancer progression and radiosensitivity. Therefore, eIF4A1 may be a potential therapeutic target in patients with cervical cancer.
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Affiliation(s)
- Shanhui Liang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xingzhu Ju
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yuqi Zhou
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yiran Chen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Guihao Ke
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Hao Wen
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, P.R. China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
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17
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18
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Lin H, Fang Z, Su Y, Li P, Wang J, Liao H, Hu Q, Ye C, Fang Y, Luo Q, Lin Z, Pan C, Wang F, Zhang ZY. DHX32 Promotes Angiogenesis in Colorectal Cancer Through Augmenting β-catenin Signaling to Induce Expression of VEGFA. EBioMedicine 2017; 18:62-72. [PMID: 28330603 PMCID: PMC5405167 DOI: 10.1016/j.ebiom.2017.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 03/03/2017] [Accepted: 03/07/2017] [Indexed: 12/29/2022] Open
Abstract
We previously reported that overexpression of DHX32 contributes to the growth and metastasis of colorectal cancer (CRC). However, the underlying mechanism is not largely characterized. Herein, we reported that DHX32 in CRC cells upregulated expression of vascular endothelial growth factor A (VEGFA) at the transcription level through interacting with and stabilizing β-catenin. This promoted the recruitment of host endothelial cells to the tumor, and therefore, formation of microvessel in the tumor. Xenograft model revealed that depletion of DHX32 in CRC cells significantly reduced the microvessel density in the grafts and suppressed the growth of grafts. Furthermore, the expression level of DHX32 was positively associated with microvessel density in human CRC and poor outcome of CRC patients. Therefore, the report demonstrates that DHX32 is a pro-angiogenic factor, that inhibition of DHX32-β-catenin pathway can provide a strategy for CRC treatment, and that the expression level of DHX32 has the potential to serve as a biomarker for CRC diagnosis and prognosis. DHX32 upregulates VEGFA expression through interacting with and stabilizing β-catenin. DHX32 promotes colorectal cancer cells to recruit endothelial cells and induces angiogenesis. DHX32 is associated with tumor angiogenesis and poor prognosis of colorectal cancer patients.
Tumor angiogenesis is required for cancer growth and metastasis. Understanding the molecular mechanism by which cancer cells promote angiogenesis is required to develop effective cancer treatment. In this study, we reported that DHX32 is a pro-angiogenic factor in colorectal cancer. Aberrantly expressed DHX32 promoted tumor angiogenesis by stabilizing β-catenin and increasing the expression of vascular endothelial growth factor. The results suggested that suppression of DHX32 can be of therapeutic value for colorectal cancer and that expression level of DHX32 has the potential to serve as a biomarker for colorectal cancer diagnosis and prognosis.
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Affiliation(s)
- Huayue Lin
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Zanxi Fang
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Yuanhui Su
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Peihua Li
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Jingkun Wang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Hongfeng Liao
- Department of Pathology, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Qing Hu
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Chunlei Ye
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Yizhen Fang
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Qing Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Zhiyuan Lin
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China
| | - Chao Pan
- Department of Pathology, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China.
| | - Fen Wang
- Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, United States.
| | - Zhong-Ying Zhang
- Center for Clinical Laboratory, Xiamen University Affiliated Zhongshan Hospital, Xiamen, China; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China.
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19
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Wang M, Zhang G, Wang Y, Ma R, Zhang L, Lv H, Fang F, Kang X. DHX32 expression is an indicator of poor breast cancer prognosis. Oncol Lett 2016; 13:942-948. [PMID: 28356982 DOI: 10.3892/ol.2016.5503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence suggests that DEAH-box polypeptide 32 (DHX32) serves an important role in the progression and metastasis of cancer. However, the role of DHX32 in breast cancer remains to be completely elucidated. The aim of the present study was to evaluate the expression and clinical significance of DHX32 in breast cancer. The reverse transcription-quantitative polymerase chain reaction was performed to analyze DHX32 messenger (m)RNA expression, and western blotting and immunohistochemistry were performed to examine DHX32 protein expression in breast cancer and adjacent non-cancerous tissues. The association in breast cancer between DHX32 expression, clinicopathological features and prognosis was analyzed using 193 breast cancer tissue samples. The results of the present study demonstrated that breast cancer tissues exhibited increased DHX32 mRNA and protein expression compared with adjacent non-cancerous tissues (P<0.001). In addition, DHX32 expression was significantly associated with breast cancer clinical stage (P=0.006), histological grade (P=0.029), lymph node metastasis (P<0.001) and expression of the proliferation marker Ki-67 (P=0.004). Kaplan-Meier estimator analysis indicated that increased DHX32 expression is associated with poor prognosis in patients with breast cancer. Furthermore, the Cox proportional hazards model indicated that DHX32 expression is an independent prognostic factor for decreased overall survival and disease-free survival in patients with breast cancer. In conclusion, the results of the present study suggest that DHX32 overexpression is an unfavorable prognostic biomarker in breast cancer and a potential therapeutic target of future breast cancer treatments.
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Affiliation(s)
- Meng Wang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Guojun Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China; Beijing Engineering Research Center of Immunological Reagents and Clinical Research, Beijing 100050, P.R. China
| | - Yajie Wang
- Core Laboratory for Clinical Medical Research, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Ruimin Ma
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Limin Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Hong Lv
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Fang Fang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Xixiong Kang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China; Beijing Engineering Research Center of Immunological Reagents and Clinical Research, Beijing 100050, P.R. China
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20
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Mi J, Ray P, Liu J, Kuan CT, Xu J, Hsu D, Sullenger BA, White RR, Clary BM. In Vivo Selection Against Human Colorectal Cancer Xenografts Identifies an Aptamer That Targets RNA Helicase Protein DHX9. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e315. [PMID: 27115840 PMCID: PMC5014527 DOI: 10.1038/mtna.2016.27] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/10/2016] [Indexed: 12/25/2022]
Abstract
The ability to selectively target disease-related tissues with molecules is critical to the design of effective therapeutic and diagnostic reagents. Recognizing the differences between the in vivo environment and in vitro conditions, we employed an in vivo selection strategy to identify RNA aptamers (targeting motifs) that could localize to tumor in situ. One of the selected molecules is an aptamer that binds to the protein DHX9, an RNA helicase that is known to be upregulated in colorectal cancer. Upon systemic administration, the aptamer preferentially localized to the nucleus of cancer cells in vivo and thus has the potential to be used for targeted delivery.
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Affiliation(s)
- Jing Mi
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Partha Ray
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Jenny Liu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Chien-Tsun Kuan
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Jennifer Xu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - David Hsu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Rebekah R White
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Bryan M Clary
- Department of Surgery, University of California at San Diego, La Jolla, California, USA
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21
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Wilky BA, Kim C, McCarty G, Montgomery EA, Kammers K, DeVine LR, Cole RN, Raman V, Loeb DM. RNA helicase DDX3: a novel therapeutic target in Ewing sarcoma. Oncogene 2015; 35:2574-83. [PMID: 26364611 DOI: 10.1038/onc.2015.336] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/29/2015] [Accepted: 08/03/2015] [Indexed: 02/08/2023]
Abstract
RNA helicase DDX3 has oncogenic activity in breast and lung cancers and is required for translation of complex mRNA transcripts, including those encoding key cell-cycle regulatory proteins. We sought to determine the expression and function of DDX3 in sarcoma cells, and to investigate the antitumor activity of a novel small molecule DDX3 inhibitor, RK-33. Utilizing various sarcoma cell lines, xenografts and human tissue microarrays, we measured DDX3 expression at the mRNA and protein levels, and evaluated cytotoxicity of RK-33 in sarcoma cell lines. To study the role of DDX3 in Ewing sarcoma, we generated stable DDX3-knockdown Ewing sarcoma cell lines using DDX3-specific small hairpin RNA (shRNA), and assessed oncogenic activity. DDX3-knockdown and RK-33-treated Ewing sarcoma cells were compared with wild-type cells using an isobaric mass-tag quantitative proteomics approach to identify target proteins impacted by DDX3 inhibition. Overall, we found high expression of DDX3 in numerous human sarcoma subtypes compared with non-malignant mesenchymal cells, and knockdown of DDX3 by RNA interference inhibited oncogenic activity in Ewing sarcoma cells. Treatment with RK-33 was preferentially cytotoxic to sarcoma cells, including chemotherapy-resistant Ewing sarcoma stem cells, while sparing non-malignant cells. Sensitivity to RK-33 correlated with DDX3 protein expression. Growth of human Ewing sarcoma xenografts expressing high DDX3 was inhibited by RK-33 treatment in mice, without overt toxicity. DDX3 inhibition altered the Ewing sarcoma cellular proteome, especially proteins involved in DNA replication, mRNA translation and proteasome function. These data support further investigation of the role of DDX3 in sarcomas, advancement of RK-33 to Ewing sarcoma clinical trials and development of RNA helicase inhibition as a novel anti-neoplastic strategy.
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Affiliation(s)
- B A Wilky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - C Kim
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - G McCarty
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - E A Montgomery
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - K Kammers
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - L R DeVine
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - R N Cole
- Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - V Raman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Radiology, Johns Hopkins University, Baltimore, MD, USA
| | - D M Loeb
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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22
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Shi D, Dai C, Qin J, Gu W. Negative regulation of the p300-p53 interplay by DDX24. Oncogene 2015; 35:528-36. [PMID: 25867071 PMCID: PMC4603993 DOI: 10.1038/onc.2015.77] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 12/15/2022]
Abstract
Numerous studies indicate that p300 acts as a key transcriptional cofactor in vivo, at least, in part, through modulating activities of p53 by acetylation. Nevertheless, the regulation of the p53-p300 interplay is not completely understood. Here, we have identified the DEAD box RNA helicase DDX24 as a novel regulator of the p300-p53 axis. We found that DDX24 interacts with p300, and this interaction leads to suppression of p300 mediated acetylation of p53. Notably, RNAi-mediated knockdown of endogenous DDX24 significantly increases the acetylation levels of endogenous p53 in human cancer cells and subsequently promotes p53-mediated activation of its transcriptional targets such as p21 and PUMA. In contrast, DDX24 expression inhibits the p300-p53 interaction and suppresses p300-mediated acetylation of p53. Moreover, DDX24 is overexpressed in human cancer cells and reduction of DDX24 protein levels by RNAi induces cell cycle arrest and senescence in a p53 dependent manner. These results reveal DDX24 as an important regulator of p300 and suggest that the modulation of the p53-p300 interplay by DDX24 is critical in controlling p53 activities in human cancer cells.
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Affiliation(s)
- D Shi
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - C Dai
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - J Qin
- Departments of Biochemistry and Cell Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - W Gu
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, College of Physicians & Surgeons, Columbia University, New York, NY, USA
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23
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Overexpression of DHX32 contributes to the growth and metastasis of colorectal cancer. Sci Rep 2015; 5:9247. [PMID: 25782664 PMCID: PMC4363870 DOI: 10.1038/srep09247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/25/2015] [Indexed: 12/28/2022] Open
Abstract
Our previous work demonstrates that DHX32 is upregulated in colorectal cancer (CRC) compared to its adjacent normal tissues. However, how overexpressed DHX32 contributes to CRC remains largely unknown. In this study, we reported that DHX32 was overexpressed in human colon cancer cells. Overexpressed DHX32 promoted SW480 cancer cells proliferation, migration, and invasion, as well as decreased the susceptibility to chemotherapy agent 5-Fluorouracil. Furthermore, PCR array analyses revealed that depleting DHX32 in SW480 colon cancer cells suppressed expression of WISP1, MMP7 and VEGFA in the Wnt pathway, and anti-apoptotic gene BCL2 and CA9, however, elevated expression of pro-apoptotic gene ACSL5. The findings suggested that overexpressed DHX32 played an important role in CRC progression and metastasis and that DHX32 has the potential to serve as a biomarker and a novel therapeutic target for CRC.
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Ratnoglik SL, Jiang DP, Aoki C, Sudarmono P, Shoji I, Deng L, Hotta H. Induction of cell-mediated immune responses in mice by DNA vaccines that express hepatitis C virus NS3 mutants lacking serine protease and NTPase/RNA helicase activities. PLoS One 2014; 9:e98877. [PMID: 24901478 PMCID: PMC4046998 DOI: 10.1371/journal.pone.0098877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 05/07/2014] [Indexed: 12/14/2022] Open
Abstract
Effective therapeutic vaccines against virus infection must induce sufficient levels of cell-mediated immune responses against the target viral epitopes and also must avoid concomitant risk factors, such as potential carcinogenic properties. The nonstructural protein 3 (NS3) of hepatitis C virus (HCV) carries a variety of CD4(+) and CD8(+) T cell epitopes, and induces strong HCV-specific T cell responses, which are correlated with viral clearance and resolution of acute HCV infection. On the other hand, NS3 possesses serine protease and nucleoside triphosphatase (NTPase)/RNA helicase activities, which not only play important roles in viral life cycle but also concomitantly interfere with host defense mechanisms by deregulating normal cellular functions. In this study, we constructed a series of DNA vaccines that express NS3 of HCV. To avoid the potential harm of NS3, we introduced mutations to the catalytic triad of the serine protease (H57A, D81A and S139A) and the NTPase/RNA helicase domain (K210N, F444A, R461Q and W501A) to eliminate the enzymatic activities. Immunization of BALB/c mice with each of the DNA vaccine candidates (pNS3[S139A/K210N], pNS3[S139A/F444A], pNS3[S139A/R461Q] and pNS3[S139A/W501A]) that expresses an NS3 mutant lacking both serine protease and NTPase/helicase activities induced T cell immune responses to the degree comparable to that induced by the wild type NS3 and the NS3/4A complex, as demonstrated by interferon-γ production and cytotoxic T lymphocytes activities against NS3. The present study has demonstrated that plasmids expressing NS3 mutants, NS3(S139A/K210N), NS3(S139A/F444A), NS3(S139A/R461Q) and NS3(S139A/W501A), which lack both serine protease and NTPase/RNA helicase activities, would be good candidates for safe and efficient therapeutic DNA vaccines against HCV infection.
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Affiliation(s)
- Suratno Lulut Ratnoglik
- Division of Microbiology, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Da-Peng Jiang
- Division of Microbiology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Chie Aoki
- Division of Microbiology, Kobe University Graduate School of Medicine, Kobe, Japan
- JST/JICA SATREPS Laboratory of Kobe University, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | | | - Ikuo Shoji
- Division of Microbiology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Lin Deng
- Division of Microbiology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hak Hotta
- Division of Microbiology, Kobe University Graduate School of Medicine, Kobe, Japan
- * E-mail:
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25
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Bish R, Vogel C. RNA binding protein-mediated post-transcriptional gene regulation in medulloblastoma. Mol Cells 2014; 37:357-64. [PMID: 24608801 PMCID: PMC4044306 DOI: 10.14348/molcells.2014.0008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/02/2014] [Indexed: 12/21/2022] Open
Abstract
Medulloblastoma, the most common malignant brain tumor in children, is a disease whose mechanisms are now beginning to be uncovered by high-throughput studies of somatic mutations, mRNA expression patterns, and epigenetic profiles of patient tumors. One emerging theme from studies that sequenced the tumor genomes of large cohorts of medulloblastoma patients is frequent mutation of RNA binding proteins. Proteins which bind multiple RNA targets can act as master regulators of gene expression at the post-transcriptional level to co-ordinate cellular processes and alter the phenotype of the cell. Identification of the target genes of RNA binding proteins may highlight essential pathways of medulloblastomagenesis that cannot be detected by study of transcriptomics alone. Furthermore, a subset of RNA binding proteins are attractive drug targets. For example, compounds that are under development as anti-viral targets due to their ability to inhibit RNA helicases could also be tested in novel approaches to medulloblastoma therapy by targeting key RNA binding proteins. In this review, we discuss a number of RNA binding proteins, including Musashi1 (MSI1), DEAD (Asp-Glu-Ala-Asp) box helicase 3 X-linked (DDX3X), DDX31, and cell division cycle and apoptosis regulator 1 (CCAR1), which play potentially critical roles in the growth and/or maintenance of medulloblastoma.
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Affiliation(s)
- Rebecca Bish
- New York University, Center for Genomics and Systems Biology, New York, NY,
USA
| | - Christine Vogel
- New York University, Center for Genomics and Systems Biology, New York, NY,
USA
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26
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Chen CY, Liu X, Boris-Lawrie K, Sharma A, Jeang KT. Cellular RNA helicases and HIV-1: insights from genome-wide, proteomic, and molecular studies. Virus Res 2013; 171:357-65. [PMID: 22814432 PMCID: PMC3493675 DOI: 10.1016/j.virusres.2012.06.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 06/25/2012] [Accepted: 06/25/2012] [Indexed: 11/24/2022]
Abstract
RNA helicases are ubiquitous in plants and animals and function in many cellular processes. Retroviruses, such as human immunodeficiency virus (HIV-1), encode no RNA helicases in their genomes and utilize host cellular RNA helicases at various stages of their life cycle. Here, we briefly summarize the roles RNA helicases play in HIV-1 replication that have been identified recently, in part, through genome-wide screenings, proteomics, and molecular studies. Some of these helicases augment virus propagation while others apparently participate in antiviral defenses against viral replication.
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Affiliation(s)
- Chia-Yen Chen
- Molecular Virology Section1, Laboratory of Molecular, Microbiology, the National Institute of Allergy and Infectious Diseases, the National Institutes of Health, Bethesda, MD, USA 20892
| | - Xiang Liu
- Molecular Virology Section1, Laboratory of Molecular, Microbiology, the National Institute of Allergy and Infectious Diseases, the National Institutes of Health, Bethesda, MD, USA 20892
| | - Kathleen Boris-Lawrie
- Department of Veterinary Biosciences, Center for Retrovirus Research, Ohio State University, Columbus, OH USA 43210
| | - Amit Sharma
- Department of Veterinary Biosciences, Center for Retrovirus Research, Ohio State University, Columbus, OH USA 43210
| | - Kuan-Teh Jeang
- Molecular Virology Section1, Laboratory of Molecular, Microbiology, the National Institute of Allergy and Infectious Diseases, the National Institutes of Health, Bethesda, MD, USA 20892
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27
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Abstract
Members of the DEAD box family of RNA helicases are known to be involved in most cellular processes that require manipulation of RNA structure and, in many cases, exhibit other functions in addition to their established ATP-dependent RNA helicase activities. They thus play critical roles in cellular metabolism and in many cases have been implicated in cellular proliferation and/or neoplastic transformation. These proteins generally act as components of multi-protein complexes; therefore their precise role is likely to be influenced by their interacting partners and to be highly context-dependent. This may also provide an explanation for the sometimes conflicting reports suggesting that DEAD box proteins have both pro- and anti-proliferative roles in cancer.
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Affiliation(s)
- Frances V Fuller-Pace
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland.
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28
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Henn A, Bradley MJ, De La Cruz EM. ATP utilization and RNA conformational rearrangement by DEAD-box proteins. Annu Rev Biophys 2012; 41:247-67. [PMID: 22404686 DOI: 10.1146/annurev-biophys-050511-102243] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA helicase enzymes catalyze the in vivo folding and conformational re-arrangement of RNA. DEAD-box proteins (DBPs) make up the largest family of RNA helicases and are found across all phyla. DBPs are molecular motor proteins that utilize chemical energy in cycles of ATP binding, hydrolysis, and product release to perform mechanical work resulting in reorganization of cellular RNAs. DBPs contain a highly conserved motor domain helicase core. Auxiliary domains, enzymatic adaptations, and regulatory partner proteins contribute to the diversity of DBP function throughout RNA metabolism. In this review we focus on the current understanding of the DBP ATP utilization mechanism in rearranging and unwinding RNA structures. We discuss DBP structural properties, kinetic pathways, and thermodynamic features of nucleotide-dependent interactions with RNA. We highlight recent advances in the DBP field derived from biochemical and molecular biophysical investigations aimed at developing a quantitative mechanistic understanding of DBP molecular motor function.
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Affiliation(s)
- Arnon Henn
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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29
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Bradley MJ, De La Cruz EM. Analyzing ATP utilization by DEAD-Box RNA helicases using kinetic and equilibrium methods. Methods Enzymol 2012; 511:29-63. [PMID: 22713314 PMCID: PMC7768905 DOI: 10.1016/b978-0-12-396546-2.00002-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DEAD-box proteins (DBPs) couple ATP utilization to conformational rearrangement of RNA. In this chapter, we outline a combination of equilibrium and kinetic methods that have been developed and applied to the analysis of ATP utilization and linked RNA remodeling by DBPs, specifically Escherichia coli DbpA and Saccharomyces cerevisiae Mss116. Several important considerations are covered, including solution conditions, DBP assembly/aggregation, and RNA substrate properties. We discuss practical experimental methods for determination of DBP-RNA-nucleotide binding affinities and stoichiometries, steady-state ATPase activity, ATP binding, hydrolysis and product release rate constants, and RNA unwinding. We present general methods to integrate and analyze this combination of experimental data to identify the preferred kinetic pathway of ATP utilization and linked dsRNA unwinding.
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Affiliation(s)
- Michael J Bradley
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
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30
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Oxidative stress induced carbonylation in human plasma. J Proteomics 2011; 74:2395-416. [PMID: 21856457 DOI: 10.1016/j.jprot.2011.07.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 07/01/2011] [Accepted: 07/13/2011] [Indexed: 02/02/2023]
Abstract
The focus of this study was on the assessment of technology that might be of clinical utility in identification, quantification, characterization of carbonylation in human plasma proteins. Carbonylation is widely associated with oxidative stress diseases. Breast cancer patient samples were chosen as a stress positive case based on the fact that oxidative stress has been reported to be elevated in this disease. Measurements of 8-isoprostane in plasma confirmed that breast cancer patients in this study were indeed experiencing significant oxidative stress. Carbonyl groups in proteins from freshly drawn blood were derivatized with biotin hydrazide after which the samples were dialyzed and the biotinylated proteins subsequently selected, digested and labeled with iTRAQ™ heavy isotope coding reagent(s). Four hundred sixty proteins were identified and quantified, 95 of which changed 1.5 fold or more in concentration. Beyond confirming the utility of the analytical method, association of protein carbonylation was examined as well. Nearly one fourth of the selected proteins were of cytoplasmic, nuclear, or membrane origin. Analysis of the data by unbiased knowledge assembly methods indicated the most likely disease associated with the proteins was breast neoplasm. Pathway analysis showed the proteins which changed in carbonylation were strongly associated with Brca1, the breast cancer type-1 susceptibility protein. Pathway analysis indicated the major molecular functions of these proteins are defense, immunity and nucleic acid binding.
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31
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Linder P, Jankowsky E. From unwinding to clamping - the DEAD box RNA helicase family. Nat Rev Mol Cell Biol 2011; 12:505-16. [PMID: 21779027 DOI: 10.1038/nrm3154] [Citation(s) in RCA: 778] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA helicases of the DEAD box family are present in all eukaryotic cells and in many bacteria and Archaea. These highly conserved enzymes are required for RNA metabolism from transcription to degradation and are therefore important players in gene expression. DEAD box proteins use ATP to unwind short duplex RNA in an unusual fashion and remodel RNA-protein complexes, but they can also function as ATP-dependent RNA clamps to provide nucleation centres that establish larger RNA-protein complexes. Structural, mechanistic and molecular biological studies have started to reveal how these conserved proteins can perform such diverse functions and how accessory proteins have a central role in their regulation.
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Affiliation(s)
- Patrick Linder
- Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1, rue Michel Servet, 1211 Genève 4, Switzerland.
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32
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Jankowsky E. RNA helicases at work: binding and rearranging. Trends Biochem Sci 2011; 36:19-29. [PMID: 20813532 DOI: 10.1016/j.tibs.2010.07.008] [Citation(s) in RCA: 380] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/20/2010] [Accepted: 07/23/2010] [Indexed: 12/22/2022]
Abstract
RNA helicases are ubiquitous, highly conserved enzymes that participate in nearly all aspects of RNA metabolism. These proteins bind or remodel RNA or RNA-protein complexes in an ATP-dependent fashion. How RNA helicases physically perform their cellular tasks has been a longstanding question, but in recent years, intriguing models have started to link structure, mechanism and biological function for some RNA helicases. This review outlines our current view on major structural and mechanistic themes of RNA helicase function, and on emerging physical models for cellular roles of these enzymes.
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Affiliation(s)
- Eckhard Jankowsky
- Center for RNA Molecular Biology & Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA.
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33
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Kondaskar A, Kondaskar S, Kumar R, Fishbein JC, Muvarak N, Lapidus RG, Sadowska M, Edelman MJ, Bol GM, Vesuna F, Raman V, Hosmane RS. Novel, Broad Spectrum Anti-Cancer Agents Containing the Tricyclic 5:7:5-Fused Diimidazodiazepine Ring System. ACS Med Chem Lett 2010; 2:252-256. [PMID: 21572541 DOI: 10.1021/ml100281b] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Synthesis of a series of novel, broad-spectrum anti-cancer agents containing the tricyclic 5:7:5-fused diimidazo[4,5-d:4',5'-f][1,3]diazepine ring system is reported. Compounds 1, 2, 8, 11, and 12 in the series show promising in vitro antitumor activity with low micromolar IC(50)'s against prostate, lung, breast, and ovarian cancer cell lines. Some notions about structure-activity relationships and a possible mechanism of biological activity are presented. Also presented are preliminary in vivo toxicity studies of 1 using SCID mice.
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Affiliation(s)
- Atul Kondaskar
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Shilpi Kondaskar
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Raj Kumar
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - James C. Fishbein
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
| | - Nidal Muvarak
- Translational Core Laboratory, University of Maryland Marlene & Stewart Greenbaum Cancer Center, 22 South Greene Street, Baltimore, Maryland 21201, United States
| | - Rena G. Lapidus
- Translational Core Laboratory, University of Maryland Marlene & Stewart Greenbaum Cancer Center, 22 South Greene Street, Baltimore, Maryland 21201, United States
| | - Mariola Sadowska
- Translational Core Laboratory, University of Maryland Marlene & Stewart Greenbaum Cancer Center, 22 South Greene Street, Baltimore, Maryland 21201, United States
| | - Martin J. Edelman
- Translational Core Laboratory, University of Maryland Marlene & Stewart Greenbaum Cancer Center, 22 South Greene Street, Baltimore, Maryland 21201, United States
| | - Guus M. Bol
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Farhad Vesuna
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Venu Raman
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Ramachandra S. Hosmane
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United States
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34
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Abstract
RNA helicases are ubiquitous and essential enzymes that function in nearly all aspects of RNA metabolism. The RNA helicase database (www.rnahelicase.org) integrates the wealth of accumulating information on RNA helicases in a readily accessible format. The database is a portal that allows straightforward retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most widely used model organisms Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mouse and human. Also included are RNA helicases from other organisms that are subject to specific investigation. The database is structured according to the most recent helicase classification into helicase superfamilies (SFs) and families, and thus emphasizes phyologenetic relations between RNA helicases as well. Information on individual RNA helicases can be accessed through various browsing routes or through text-based searches of the database.
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Affiliation(s)
- Anja Jankowsky
- Department of Biochemistry, Center for RNA Molecular Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
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35
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Abstract
DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.
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36
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Fairman-Williams ME, Guenther UP, Jankowsky E. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 2010; 20:313-24. [PMID: 20456941 DOI: 10.1016/j.sbi.2010.03.011] [Citation(s) in RCA: 662] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 03/29/2010] [Indexed: 12/25/2022]
Abstract
Helicases of the superfamily (SF) 1 and 2 are involved in virtually all aspects of RNA and DNA metabolism. SF1 and SF2 helicases share a catalytic core with high structural similarity, but different enzymes even within each SF perform a wide spectrum of distinct functions on diverse substrates. To rationalize similarities and differences between these helicases, we outline a classification based on protein families that are characterized by typical sequence, structural, and mechanistic features. This classification complements and extends existing SF1 and SF2 helicase categorizations and highlights major structural and functional themes for these proteins. We discuss recent data in the context of this unifying view of SF1 and SF2 helicases.
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Affiliation(s)
- Margaret E Fairman-Williams
- Center for RNA Molecular Biology & Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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37
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Real-time monitoring of RNA helicase activity using fluorescence resonance energy transfer in vitro. Biochem Biophys Res Commun 2010; 393:131-6. [PMID: 20117090 DOI: 10.1016/j.bbrc.2010.01.100] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Accepted: 01/23/2010] [Indexed: 11/20/2022]
Abstract
We have developed a continuous fluorescence assay based on fluorescence resonance energy transfer (FRET) for the monitoring of RNA helicase activity in vitro. The assay is tested using the hepatitis C virus (HCV) NS3 helicase as a model. We prepared a double-stranded RNA (dsRNA) substrate with a 5' fluorophore-labeled strand hybridized to a 3' quencher-labeled strand. When the dsRNA is unwound by helicase, the fluorescence of the fluorophore is emitted following the separation of the strands. Unlike in conventional gel-based assays, this new assay eliminates the complex and time-consuming steps, and can be used to simply measure the real-time kinetics in a single helicase reaction. Our results demonstrate that Alexa Fluor 488 and BHQ1 are an effective fluorophore-quencher pair, and this assay is suitable for the quantitative measurement of the RNA helicase activity of HCV NS3. Moreover, we found that several extracts of marine organisms exhibited different inhibitory effects on the RNA and DNA helicase activities of HCV NS3. We propose that this assay will be useful for monitoring the detailed kinetics of RNA unwinding mechanisms and screening RNA helicase inhibitors at high throughput.
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38
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Huang C, Liang X, Huang R, Zhang Z. Up-regulation and clinical relevance of novel helicase homologue DHX32 in colorectal cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2009; 28:11. [PMID: 19161603 PMCID: PMC2642774 DOI: 10.1186/1756-9966-28-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 01/22/2009] [Indexed: 01/26/2023]
Abstract
Background This study aimed to find novel biomarkers for colorectal cancer. Methods Fluorescent mRNA differential display PCR (DD-PCR) was used to screen the genes differentially expressed in colorectal cancer tissues and their adjacent tissues. The differentially expressed genes were confirmed by real-time PCR and then their clinical relevance (such as association with tumor location and lymph gland metastasis) was further investigated. Results We identified by DD-PCR a novel RNA helicase, DHX32, which showed higher expression in colorectal cancer tissues than their adjacent tissues, and this result was confirmed by real time RT-PCR. In addition, we found that the level of DHX32 gene expression in colorectal cancer was significantly associated with cancer location, lymph gland metastasis, cancer nodal status, differentiation grade, and Dukes, stage. Conclusion DHX32 may play an important role in the development of colorectal cancer and could serve as a novel biomarker for colorectal cancer after additional investigation.
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Affiliation(s)
- Chunling Huang
- Xiamen Center for Clinical Laboratory, Xiamen Zhongshan Hospital, Xiamen University, Xiamen, PR China.
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39
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Savage SA, Giri N, Baerlocher GM, Orr N, Lansdorp PM, Alter BP. TINF2, a component of the shelterin telomere protection complex, is mutated in dyskeratosis congenita. Am J Hum Genet 2008; 82:501-9. [PMID: 18252230 DOI: 10.1016/j.ajhg.2007.10.004] [Citation(s) in RCA: 293] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 09/26/2007] [Accepted: 10/05/2007] [Indexed: 12/25/2022] Open
Abstract
Patients with dyskeratosis congenita (DC), a heterogeneous inherited bone marrow failure syndrome, have abnormalities in telomere biology, including very short telomeres and germline mutations in DKC1, TERC, TERT, or NOP10, but approximately 60% of DC patients lack an identifiable mutation. With the very short telomere phenotype and a highly penetrant, rare disease model, a linkage scan was performed on a family with autosomal-dominant DC and no mutations in DKCI, TERC, or TERT. Evidence favoring linkage was found at 2p24 and 14q11.2, and this led to the identification of TINF2 (14q11.2) mutations, K280E, in the proband and her five affected relatives and TINF2 R282H in three additional unrelated DC probands, including one with Revesz syndrome; a fifth DC proband had a R282S mutation. TINF2 mutations were not present in unaffected relatives, DC probands with mutations in DKC1, TERC, or TERT or 298 control subjects. We demonstrate that a fifth gene, TINF2, is mutated in classical DC and, for the first time, in Revesz syndrome. This represents the first shelterin complex mutation linked to human disease and confirms the role of very short telomeres as a diagnostic test for DC.
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40
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Alli Z, Ho M, Ackerley C, Abdelhaleem M. Characterization of murine Dhx32. Exp Mol Pathol 2007; 83:115-8. [PMID: 17239371 DOI: 10.1016/j.yexmp.2006.10.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 10/30/2006] [Accepted: 10/30/2006] [Indexed: 11/16/2022]
Abstract
In this report, we studied the expression of Dhx32, the murine counterpart of the human putative RNA helicase DHX32. Northern analysis showed widespread but variable level of expression among different tissues. RT-PCR detected the presence of two mRNA transcripts in several tissues that result from alternative usage of either exon 1 or exon 2 at the 5' UTR. Immunohistochemistry showed the presence of Dhx32 in all tissues examined including spleen, kidney and liver. The distribution of Dhx32 proteins was not uniform among different cell types within the same tissue, suggesting cell type-dependent regulation of expression. Finally, electron microscope immunocytochemistry detected the presence of Dhx32 in the mitochondria of hepatocytes.
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Affiliation(s)
- Zaman Alli
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Rm 3691, Atrium, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8
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41
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Chen Y, Alli Z, Ackerley C, Al-Saud B, Abdelhaleem M. Altered distribution of heat shock protein 60 (Hsp60) with dysregulated expression of DHX32. Exp Mol Pathol 2006; 82:256-61. [PMID: 17174952 DOI: 10.1016/j.yexmp.2006.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Accepted: 11/09/2006] [Indexed: 11/21/2022]
Abstract
DHX32 has an overall similarity to the DHX family of RNA helicases but with a novel helicase domain and nuclear and mitochondrial localizations. The expression of DHX32 is highly regulated during lymphocyte activation and is dysregulated in lymphoid malignancies. In this study, we report our finding of an altered subcellular localization of heat shock protein 60 (Hsp60) in Jurkat-DHX32 cell line in which DHX32 is constitutively expressed. Two-dimensional gel electrophoresis followed by mass spectrometry, electron microscopic immunocytochemistry, and immunoblot analysis showed mainly cytoplasmic localization of Hsp60 in Jurkat-DHX32 cells instead of its mainly mitochondrial localization in control cells. No significant changes were detected in the mitochondrial ultra-structure and the mitochondrial membrane potential activity as a result of dysregulated DHX32 expression. The subcellular distribution of several mitochondrial proteins including cytochrome c, peroxiredoxin 3, manganese superoxide dismutase, Leucine-Rich PentatricoPeptide Repeat Cassette and the 49-kDa subunit of the mitochondrial respiratory Complex I were similar in control and Jurkat-DHX32 cells ruling out non-specific cytoplasmic leakage of mitochondrial proteins. No significant changes in the expression of Hsp60 transcript or total cellular protein were detected. These findings suggest that dysregulated expression of DHX32 might lead to as of yet unknown changes in mitochondrial homeostasis manifested by cytoplasmic redistribution of the molecular chaperon Hsp60.
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Affiliation(s)
- Yong Chen
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
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Alli Z, Ackerley C, Chen Y, Al-Saud B, Abdelhaleem M. Nuclear and mitochondrial localization of the putative RNA helicase DHX32. Exp Mol Pathol 2006; 81:245-8. [PMID: 16959245 DOI: 10.1016/j.yexmp.2006.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
RNA helicases are involved in all aspects of RNA metabolism. We identified DHX32 as a novel gene with homology to the DHX family of RNA helicases. To gain insight into the role of DHX32 in RNA metabolism, we determined its subcellular localization. Electron microscopy immunocytochemistry detected DHX32 in the nucleus and mitochondria of the myeloid leukemia cell line HL-60. Confocal microscopy shows mitochondrial localization of DHX32 in HeLa cells. Double labeling showed close proximity of DHX32 to some of the newly synthesized RNA in the mitochondria. These results suggest that DHX32 is a putative RNA helicase that might be involved in regulating nuclear and mitochondrial gene expression.
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Affiliation(s)
- Zaman Alli
- Division of Haematopathology, Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
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Uhlmann-Schiffler H, Jalal C, Stahl H. Ddx42p--a human DEAD box protein with RNA chaperone activities. Nucleic Acids Res 2006; 34:10-22. [PMID: 16397294 PMCID: PMC1325199 DOI: 10.1093/nar/gkj403] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human gene ddx42 encodes a human DEAD box protein highly homologous to the p68 subfamily of RNA helicases. In HeLa cells, two ddx42 poly(A)+ RNA species were detected both encoding the nuclear localized 938 amino acid Ddx42p polypeptide. Ddx42p has been heterologously expressed and its biochemical properties characterized. It is an RNA binding protein, and ATP and ADP modulate its RNA binding affinity. Ddx42p is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase. Interestingly, RNA unwinding by Ddx42p is promoted in the presence of a single-strand (ss) binding protein (T4gp32). Ddx42p, particularly in the ADP-bound form (the state after ATP hydrolysis), also mediates efficient annealing of complementary RNA strands thereby displacing the ss binding protein. Ddx42p therefore represents the first example of a human DEAD box protein possessing RNA helicase, protein displacement and RNA annealing activities. The adenosine nucleotide cofactor bound to Ddx42p apparently acts as a switch that controls the two opposing activities: ATP triggers RNA strand separation, whereas ADP triggers annealing of complementary RNA strands.
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Affiliation(s)
- Heike Uhlmann-Schiffler
- FR 2.3 Medical Biochemistry and Molecular Biology, Theoretical Medicine, University of the Saarland, D-66421 Homburg, Germany.
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