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Wu X, Chen H, Li K, Zhang H, Li K, Tan H. The biological function of the N6-Methyladenosine reader YTHDC2 and its role in diseases. J Transl Med 2024; 22:490. [PMID: 38790013 PMCID: PMC11119022 DOI: 10.1186/s12967-024-05293-6] [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: 03/25/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
N6-methyladenosine (m6A) stands as the most prevalent modified form of RNA in eukaryotes, pivotal in various biological processes such as regulating RNA stability, translation, and transcription. All members within the YT521-B homology (YTH) gene family are categorized as m6A reading proteins, capable of identifying and binding m6A modifications on RNA, thereby regulating RNA metabolism and functioning across diverse physiological processes. YTH domain-containing 2 (YTHDC2), identified as the latest member of the YTH family, has only recently started to emerge for its biological function. Numerous studies have underscored the significance of YTHDC2 in human physiology, highlighting its involvement in both tumor progression and non-tumor diseases. Consequently, this review aims to further elucidate the pathological mechanisms of YTHDC2 by summarizing its functions and roles in tumors and other diseases, with a particular focus on its downstream molecular targets and signaling pathways.
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Affiliation(s)
- Xudong Wu
- Department of Thoracic Surgery, The Third Hospital of Changsha, Changsha, 410015, Hunan, People's Republic of China
| | - Hui Chen
- Department of Thoracic Surgery, The Third Hospital of Changsha, Changsha, 410015, Hunan, People's Republic of China
| | - Kai Li
- Department of Thoracic Surgery, The Third Hospital of Changsha, Changsha, 410015, Hunan, People's Republic of China
| | - Hong Zhang
- Department of Thoracic Surgery, The Third Hospital of Changsha, Changsha, 410015, Hunan, People's Republic of China
| | - Kai Li
- Department of Thoracic Surgery, Xiangxi Autonomous Prefecture People's Hospital, Jishou, 410015, Hunan, People's Republic of China
| | - Haoyu Tan
- Department of Cardio-vascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, People's Republic of China.
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2
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Chen Y, Wang W, Zhang W, He M, Li Y, Qu G, Tong J. Emerging roles of biological m 6A proteins in regulating virus infection: A review. Int J Biol Macromol 2023; 253:126934. [PMID: 37722640 DOI: 10.1016/j.ijbiomac.2023.126934] [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: 07/16/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent chemical modifications of intracellular RNA, which recently emerging as a multifaceted effector of viral genomic RNA. As a dynamic process, three groups of biological proteins control the levels of m6A modification in eukaryocyte, designed as m6A writers, erasers, and readers. The m6A writers comprising of methyltransferases complex initiate the modification process. On the contrary, the m6A erasers ALKBH5 or FTO abolish the modification through three-step demethylation: m6A to N6-hydroxymethyl adenosine (hm6A), then hm6A to N6-methyladenosine (f6A), and finally f6A to adenosine. The known m6A readers include the YTH family and the hnRNP family. As m6A modification regulates RNA nuclear exportation, stability, and translation, m6A proteins commonly participate in virus infection by regulating viral genomic RNA synthesis. Moreover, m6A proteins establish molecular linkages between virus genome/viral encode proteins and host cells proteins via their multifunctional roles in cellular RNA metabolism. The m6A writers and erasers directly impact interferon expression and macrophage innate immune responses, facilitating them to act as anti-/pro-viral factors. The m6A readers enable to alter cell metabolism and stress granules (SGs) production to regulate virus-host interactions. Here, the latest progress of m6A proteins in regulating viral infection is reviewed. Demonstrating the roles of m6A proteins will enhance the understanding of epigenetic regulation of virus infection and stimulate the development of novel antiviral strategies.
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Affiliation(s)
- Yuran Chen
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wenjing Wang
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Mei He
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yuming Li
- School of Public Health, Shandong First Medical University, Shandong Academy of Medical Sciences, Ji'nan 250117, China; Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, Shandong Academy of Medical Sciences, Tai'an 271000, China.
| | - Guosheng Qu
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| | - Jie Tong
- College of Life Science, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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3
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Song J, You G, Yin X, Zhu G, Wang W, Yu Y, Zhu J. Overexpression of YTHDC2 contributes to the progression of prostate cancer and predicts poor outcomes in patients with prostate cancer. J Biochem Mol Toxicol 2023; 37:e23308. [PMID: 36644951 DOI: 10.1002/jbt.23308] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/23/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
YTH domain-containing protein 2 (YTHDC2), a member of N6-methyladenosine (m6A) readers, has been reported to be closely associated with multiple cancer types. However, very little is known about the YTHDC2 gene and its involvement in prostate cancer. YTHDC2 protein expression level was analyzed and correlated to clinical outcomes in prostate cancer patients who underwent prostatectomy in Guizhou Provincial People's Hospital. The YTHDC2 expression level was also detected in prostate cancer cell lines and an immortalized prostate epithelial cell line BPH-1 and RWPE1 by quantitative real-time reverse transcription polymerase chain reaction. Furthermore, we established stable cell lines (DU145 and PC-3) transfected with either empty vector or the full-length YTHDC2 gene and conducted cell function assays in vitro. Fisher's exact test and Pearson χ2 test were employed, Kaplan-Meier method was used for the survival analysis. Of 32 patient samples who enrolled in this study, YTHDC2 was significantly upregulated in prostate cancer (PCa) patients with higher Gleason scores and serum prostate-specific antigen levels. YTHDC2 expression was significantly elevated in all PCa cell lines compared to BPH-1 and RWPE1 (all p < 0.05). Functionally, the enforced expression of YTHDC2 markedly promoted cell growth, migration, and invasion efficacies in prostate cancer cells. Our data indicate that YTHDC2 upregulation may be potentially associated with the prognosis of prostate cancer patients.
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Affiliation(s)
- Jukun Song
- School Of Medicine, Guizhou University, Guizhou, China.,Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Guizhou Medical University, Guiyang, China
| | - Ganhua You
- The Second People's Hospital of Guizhou Province, Guizhou, China
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Guizhou Medical University, Guiyang, China
| | - Guohua Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Wei Wang
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
| | - Yongwei Yu
- Department of Pathology, Changhai Hospital, Shanghai, China
| | - Jianguo Zhu
- Department of Urology, Guizhou Provincial People's Hospital, Guizhou, China
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YTHDC2 Promotes Malignant Phenotypes of Breast Cancer Cells. JOURNAL OF ONCOLOGY 2022; 2022:9188920. [PMID: 36245989 PMCID: PMC9568362 DOI: 10.1155/2022/9188920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 12/03/2022]
Abstract
YTH domain-containing 2 (YTHDC2) is known to be an important regulator for RNA metabolism. Here, we show that YTHDC2 is essential for breast cancer tumorigenesis and metastasis. We examined YTHDC2 expression levels by immunohistochemistry in human breast tumor tissues from 99 patients and found a significantly positive correlation between the YTHDC2 expression level and the tumor stage. We established YTHDC2-knocked-down cell lines using four breast cancer cell lines with different subtypes. Knockdown of YTHDC2 attenuated the sphere-forming and the metastatic ability of breast cancer cells. Although stemness and EMT markers, such as SOX2, c-MYC, and NANOG, were downregulated in several YTHDC2-knocked-down breast cancer cells, a common target gene of YTHDC2 in breast cancer cells was not identified. These findings suggest that while YTHDC2 is involved in malignant progression of breast cancers, the mechanism by which YTHDC2 regulates those phenotypes is different between subtypes of breast cancers.
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Qin S, Liu G, Jin H, Chen X, He J, Xiao J, Qin Y, Mao Y, Zhao L. The comprehensive expression and functional analysis of m6A modification "readers" in hepatocellular carcinoma. Aging (Albany NY) 2022; 14:6269-6298. [PMID: 35963644 PMCID: PMC9417225 DOI: 10.18632/aging.204217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
Abstract
N6-methyladenosine (m6A) modification regulators are essential for the diagnosis and treatment of various cancers. However, the comprehensive analysis about roles of m6A "readers" in hepatocellular carcinoma (HCC) remains unclear. UALCAN, GEPIA2, HPA, Kaplan Meier plotter, cBioPortal, STRING WebGestalt, Metascape and TIMER 2.0 database and Cytoscape software were used to comprehensively analyze the bioinformatic data. We found that m6A "readers" were upregulated at the mRNA level and protein level in HCC patients. Highly expressed YTHDF1, IGF2BP3 and NKAP were positively correlated with advanced HCC stage and had a poor prognosis in OS and PFS. The gene alterations of m6A "readers" happened frequently, and YTHDF3 had the highest mutation rate. The function of m6A "readers" on HCC may be closely correlated with splicing related proteins (including HNRNP family, SNRP family, and SR family), metabolic process, protein binding and RNA splicing related signaling pathways. Moreover, although the correlation of YTHDF3 and CD8+ T cell infiltration, and the correlation of IGF2BP3 and infiltration of mast cells and CAF are negative, most m6A "readers" had a positive correlation with immune cells (including CD8+ T cell, CD4+ T cell, Tregs, B cell, neutrophil, monocyte, macrophage, myeloid dendritic cell, nature killer cell, mast cell, and CAF). Macrophages, CD4+ T cell, Treg, B cell, monocyte, and myeloid dendritic cell had a positively strong correlation (Rho>0.4) with most m6A "readers" (such as YTHDC1, YTHDC2, YTHDF1, IGF2BP3, HNRNPA2B1 and HNRNPC). In conclusion, by comprehensive analysis of m6A "readers", we found that they were involved in the prognosis of HCC, and m6A "readers" might regulate the development and progression of HCC by participating in some metabolism-related and RNA splicing-related signaling pathways as well as immune cell infiltration.
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Affiliation(s)
- Sha Qin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Gaoming Liu
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haoer Jin
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xue Chen
- Early Clinical Trial Center, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jiang He
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Juxiong Xiao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Qin
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yitao Mao
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Luqing Zhao
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pathology, School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Ha T, DiPrima M, Koparde V, Jailwala P, Ohnuki H, Feng JX, Palangat M, Larson D, Tosato G. Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:877-891. [PMID: 35694213 PMCID: PMC9163427 DOI: 10.1016/j.omtn.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/12/2022] [Indexed: 11/10/2022]
Abstract
Advances in gene therapy research have resulted in the successful development of new therapies for clinical use. Here, we explored a gene targeting approach to deplete ephrinB2 from colorectal cancer cells using an inducible lentiviral vector. EphrinB2, a transmembrane ephrin ligand, promotes colorectal cancer cell growth and viability and predicts poor patient survival when expressed at high levels in colorectal cancer tissues. We discovered that lentiviral vector integration and expression in the host DNA frequently drive divergent host gene transcription, generating antisense reads coupled with splicing events and generation of chimeric vector/host transcripts. Antisense transcription of host DNA was linked to development of an integrated stress response and cell death. Despite recent successes, off-target effects remain a concern in genetic medicine. Our results provide evidence that divergent gene transcription is a previously unrecognized off-target effect of lentiviral vector integration with built-in properties for regulation of gene expression.
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Liao J, Wei Y, Liang J, Wen J, Chen X, Zhang B, Chu L. Insight into the structure, physiological function, and role in cancer of m6A readers—YTH domain-containing proteins. Cell Death Dis 2022; 8:137. [PMID: 35351856 PMCID: PMC8964710 DOI: 10.1038/s41420-022-00947-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022]
Abstract
YT521-B homology (YTH) domain-containing proteins (YTHDF1-3, YTHDC1-2) are the most crucial part of N6-methyladenosine (m6A) readers and play a regulatory role in almost all stages of methylated RNA metabolism and the progression of various cancers. Since m6A is identified as an essential post-transcriptional type, YTH domain-containing proteins have played a key role in the m6A sites of RNA. Hence, it is of great significance to study the interaction between YTH family proteins and m6A-modified RNA metabolism and tumor. In this review, their basic structure and physical functions in RNA transcription, splicing, exporting, stability, and degradation as well as protein translation are introduced. Then we discussed the expression regulation of YTH domain-containing proteins in cancers. Furthermore, we introduced the role of the YTH family in cancer biology and systematically demonstrated their functions in various aspects of tumorigenesis and development. To provide a more institute understanding of the role of YTH family proteins in cancers, we summarized their functions and specific mechanisms in various cancer types and presented their involvement in cancer-related signaling pathways.
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Yuan J, Liu Y, Zhou L, Xue Y, Lu Z, Gan J. YTHDC2-Mediated circYTHDC2 N6-Methyladenosine Modification Promotes Vascular Smooth Muscle Cells Dysfunction Through Inhibiting Ten-Eleven Translocation 2. Front Cardiovasc Med 2021; 8:686293. [PMID: 34660707 PMCID: PMC8517116 DOI: 10.3389/fcvm.2021.686293] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/31/2021] [Indexed: 01/11/2023] Open
Abstract
Type 2 diabetes condition mediated vascular smooth muscle cell (VSMCs) dysfunction. However, the mechanism of VSMCs dysfunction in diabetic patients needs further elucidation. VSMCs are an important component of the vascular wall, participate in the process of vascular remodeling, and play a vital role in the vascular complications of diabetes. Studies have found that circular RNAs (circRNAs) play a key regulatory role in the occurrence and development of VSMCs dysfunction. In this study, we stimulated VSMCs with high glucose and identified a new circular RNA, circYTHDC2, using circRNA chip analysis. circYTHDC2 was highly expressed in VSMCs treated with high glucose. Knockout of circYTHDC2 significantly inhibited the proliferation and migration of VSMCs. Metformin treatment significantly inhibited the expression of YTHDC2 and circYTHDC2. The upstream mechanism analysis revealed that the stability of circYTHDC2 was regulated by YTHDC2-mediated m6A modification. Furthermore, circYTHDC2 negatively regulates the expression of Ten-Eleven Translocation 2 (TET2) by targeting the unstable motif of TET2 3′UTR, thereby promoting dedifferentiated “synthetic type” transformation of VSMC. Taken together, these results suggest that the YTHDC2/circYTHDC2/TET2 pathway is an important target of metformin in preventing the progression of VSMCs dysfunction under high glucose.
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Affiliation(s)
- Jun Yuan
- Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yu Liu
- Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Lizhen Zhou
- Health Management Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yan Xue
- Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zhengde Lu
- Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jianting Gan
- Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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Takemoto S, Nakano M, Fukami T, Nakajima M. m 6A modification impacts hepatic drug and lipid metabolism properties by regulating carboxylesterase 2. Biochem Pharmacol 2021; 193:114766. [PMID: 34536357 DOI: 10.1016/j.bcp.2021.114766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 10/20/2022]
Abstract
Methylation of adenosine at the N6 position to form N6-methyladenosine (m6A) is the most prevalent epitranscriptomic modification of mammalian mRNA. This modification is catalyzed by a methyltransferase-like 3 (METTL3)-METTL14 complex and is erased by demethylases such as fat mass and obesity-associated protein (FTO) or AlkB homolog 5 (ALKBH5). m6A modification regulates mRNA stability, nuclear export, splicing, and/or protein translation via recognition by reader proteins such as members of YT521-B homology (YTH) family. Carboxylesterase 2 (CES2) is a serine esterase responsible for the hydrolysis of drugs and endogenous substrates, such as triglycerides and diacylglycerides. Here, we examined the potential regulation of human CES2 expression by m6A modification. CES2 mRNA level was significantly increased by double knockdown of METTL3 and METTL14 but was decreased by knockdown of FTO or ALKBH5 in HepaRG and HepG2 cells, leading to changes in its protein level and hydrolase activity for 7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxycamptothecin (CPT-11), suggesting that m6A modification negatively regulates CES2 expression. Consistent with the changes in CES2 expression, lipid accumulation in the cells was decreased by double knockdown of METTL3 and METTL14 but was increased by knockdown of FTO or ALKBH5. RNA immunoprecipitation assays using an anti-m6A antibody showed that adenosines in the 5'-untranslated region (UTR) and the last exon of CES2 are methylated. Luciferase assays revealed that YTHDC2, which degrades m6A-containing mRNA, downregulates CES2 expression by recognition of m6A in the 5'-UTR of CES2. Collectively, we demonstrated that m6A modification has a great impact on the regulation of CES2, affecting pharmacokinetics, drug response and lipid metabolism.
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Affiliation(s)
- Seiya Takemoto
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Masataka Nakano
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPINano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Tatsuki Fukami
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPINano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Miki Nakajima
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPINano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability. Genes (Basel) 2021; 12:genes12081228. [PMID: 34440402 PMCID: PMC8394865 DOI: 10.3390/genes12081228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
To date, the knowledge of the genetic determinants behind the modulation of hearing ability is relatively limited. To investigate this trait, we performed Genome-Wide Association Study (GWAS) meta-analysis using genotype and audiometric data (hearing thresholds at 0.25, 0.5, 1, 2, 4, and 8 kHz, and pure-tone averages of thresholds at low, medium, and high frequencies) collected in nine cohorts from Europe, South-Eastern USA, Caucasus, and Central Asia, for an overall number of ~9000 subjects. Three hundred seventy-five genes across all nine analyses were tagged by single nucleotide polymorphisms (SNPs) reaching a suggestive p-value (p < 10−5). Amongst these, 15 were successfully replicated using a gene-based approach in the independent Italian Salus in the Apulia cohort (n = 1774) at the nominal significance threshold (p < 0.05). In addition, the expression level of the replicated genes was assessed in published human and mouse inner ear datasets. Considering expression patterns in humans and mice, eleven genes were considered particularly promising candidates for the hearing function: BNIP3L, ELP5, MAP3K20, MATN2, MTMR7, MYO1E, PCNT, R3HDM1, SLC9A9, TGFB2, and YTHDC2. These findings represent a further contribution to our understanding of the genetic basis of hearing function and its related diseases.
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11
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Zhang C, Guo C, Li Y, Ouyang L, Zhao Q, Liu K. The role of YTH domain containing 2 in epigenetic modification and immune infiltration of pan-cancer. J Cell Mol Med 2021; 25:8615-8627. [PMID: 34312987 PMCID: PMC8435423 DOI: 10.1111/jcmm.16818] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/11/2021] [Accepted: 07/15/2021] [Indexed: 12/17/2022] Open
Abstract
YTH domain containing 2 (YTHDC2) is the largest N6‐Methyladenosine (m6A) binding protein of the YTH protein family and the only member containing ATP‐dependent RNA helicase activity. For further analysing its biological role in epigenetic modification, we comprehensively explored YTHDC2 from gene expression, genetic alteration, protein‐protein interaction (PPI) network, immune infiltration, diagnostic value and prognostic value in pan‐cancer, using a series of databases and bioinformatic tools. We found that YTHDC2 with Missense mutation could cause a different prognosis in uterine corpus endometrial carcinoma (UCEC), and its different methylation level could lead to a totally various prognosis in adrenocortical carcinoma (ACC), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), lung squamous cell carcinoma (LUSC) and UCEC. The main molecular mechanisms of YTHDC2 focused on catalytic activity, helicase activity, snRNA binding, spliceosome and mRNA surveillance. Additionally, YTHDC2 was notably correlated with tumour immune infiltration. Moreover, YTHDC2 had a high diagnostic value for seven cancer types and a prognostic value for brain lower grade glioma (LGG), rectum adenocarcinoma (READ) and skin cutaneous melanoma (SKCM). Collectively, YTHDC2 plays a significant role in epigenetic modification and immune infiltration and maybe a potential biomarker for diagnosis and prognosis in certain cancers.
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Affiliation(s)
- Chiyuan Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cuishan Guo
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yan Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ling Ouyang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, China
| | - Kuiran Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
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Hu Y, Zhao X. Role of m6A in osteoporosis, arthritis and osteosarcoma (Review). Exp Ther Med 2021; 22:926. [PMID: 34306195 PMCID: PMC8281110 DOI: 10.3892/etm.2021.10358] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/11/2021] [Indexed: 12/18/2022] Open
Abstract
RNA modification is a type of post-transcriptional modification that regulates important cellular pathways, such as the processing and metabolism of RNA. The most abundant form of methylation modification is RNA N6-methyladenine (m6A), which plays various post-transcriptional regulatory roles in cellular biological functions, including cell differentiation, embryonic development and disease occurrence. Bones play a pivotal role in the skeletal system as they support and protect muscles and other organs, facilitate movement and ensure haematopoiesis. The development and remodelling of bones require a delicate and accurate regulation of gene expression by epigenetic mechanisms that involve modifications of histone, DNA and RNA. The present review discusses the enzymes and proteins involved in mRNA m6A methylation modification and summarises current research progress and the mechanisms of mRNA m6A methylation in common orthopaedic diseases, including osteoporosis, arthritis and osteosarcoma.
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Affiliation(s)
- Yibo Hu
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Xining, Qinghai 810000, P.R. China
| | - Xiaohui Zhao
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Xining, Qinghai 810000, P.R. China
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Wang J, Tan L, Jia B, Yu X, Yao R, OUYang N, Yu X, Cao X, Tong J, Chen T, Chen R, Li J. Downregulation of m 6A Reader YTHDC2 Promotes the Proliferation and Migration of Malignant Lung Cells via CYLD/NF-κB Pathway. Int J Biol Sci 2021; 17:2633-2651. [PMID: 34326699 PMCID: PMC8315025 DOI: 10.7150/ijbs.58514] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/08/2021] [Indexed: 12/18/2022] Open
Abstract
Lung cancer is one of the most common types of carcinoma worldwide. Cigarette smoking is considered the leading cause of lung cancer. Aberrant expression of several YT521-B homology (YTH) family proteins has been reported to be closely associated with multiple cancer types. The present study aims to evaluate the function and regulatory mechanisms of the N6-methyladenosine (m6A) reader protein YTH domain containing 2 (YTHDC2) by in vitro, in vivo and bioinformatics analyses. The results revealed that YTHDC2 was reduced in lung cancer and cigarette smoke-exposed cells. Notably, bioinformatics and tissue arrays analysis demonstrated that decreased YTHDC2 was highly associated with smoking history, pathological stage, invasion depth, lymph node metastasis and poor outcomes. The in vivo and in vitro studies revealed that YTHDC2 overexpression inhibited the proliferation and migration of lung cancer cells as well as tumor growth in nude mice. Furthermore, YTHDC2 decreased expression was modulated by copy number deletion in lung cancer. Importantly, the cylindromatosis (CYLD)/NF-κB pathways were confirmed as the downstream signaling of YTHDC2, and this axis was mediated by m6A modification. The present results indicated that smoking-related downregulation of YTHDC2 was associated with enhanced proliferation and migration in lung cancer cells, and appeared to be regulated by DNA copy number variation. Importantly, YTHDC2 functions as a tumor suppressor through the CYLD/NF-κB signaling pathway, which is mediated by m6A modification.
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Affiliation(s)
- Jin Wang
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Lirong Tan
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Beibei Jia
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xiaofan Yu
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ruixin Yao
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Nan OUYang
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xueting Yu
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xiyuan Cao
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Jian Tong
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tao Chen
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Rui Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital of Soochow University, Suzhou Jiangsu, 215004, China
| | - Jianxiang Li
- Department of Toxicology, School of Public Health, Medicine College, Soochow University, Suzhou, Jiangsu, 215123, China
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m 6A RNA Methylation Regulators Elicit Malignant Progression and Predict Clinical Outcome in Hepatocellular Carcinoma. DISEASE MARKERS 2021; 2021:8859590. [PMID: 34234878 PMCID: PMC8218914 DOI: 10.1155/2021/8859590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/22/2021] [Indexed: 12/29/2022]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide, and N6-methyladenosine (m6A) is a predominant internal modification of RNA in various cancers. We obtained the expression profiles of m6A-related genes for HCC patients from the International Cancer Genome Consortium and The Cancer Genome Atlas datasets. Most of the m6A RNA methylation regulators were confirmed to be differentially expressed among groups stratified by clinical characteristics and tissues. The clinical factors (including stage, grade, and gender) were correlated with the two subgroups (cluster 1/2). We identified an m6A RNA methylation regulator-based signature (including METTL3, YTHDC2, and YTHDF2) that could effectively stratify a high-risk subset of these patients by univariate and LASSO Cox regression, and receiver operating characteristic (ROC) analysis indicated that the signature had a powerful predictive ability. Immune cell analysis revealed that the genes in the signature were correlated with B cell, CD4 T cell, CD8 T cell, dendritic cell, macrophage, and neutrophil. Functional enrichment analysis suggested that these three genes may be involved in genetic and epigenetic events with known links to HCC. Moreover, the nomogram was established based on the signature integrated with clinicopathological features. The calibration curve and the area under ROC also demonstrated the good performance of the nomogram in predicting 3- and 5-year OS in the ICGC and TCGA cohorts. In summary, we demonstrated the vital role of m6A RNA methylation regulators in the initial presentation and progression of HCC and constructed a nomogram which would predict the clinical outcome and provide a basis for individualized therapy.
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Tang S, Liu Q, Xu M. LINC00857 promotes cell proliferation and migration in colorectal cancer by interacting with YTHDC1 and stabilizing SLC7A5. Oncol Lett 2021; 22:578. [PMID: 34122629 PMCID: PMC8190780 DOI: 10.3892/ol.2021.12839] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/12/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal malignances in humans. Hence, it is of great significance to identify regulatory molecules in CRC progression. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are involved in cancer malignancy. It has been reported that long intergenic non-protein coding RNA 857 (LINC00857) acts as a vital oncogene in many types of cancer by promoting cell proliferation and migration. However, the role of LINC00857 in CRC remains unclear. In the present study, LINC00857 was upregulated in CRC tissue samples and cells. Next, in vitro loss-of-function experiments demonstrated that LINC00857 knockdown suppressed CRC cell viability, proliferation and migration, as well as epithelial-mesenchymal transition and increased cell apoptosis. Mechanistically, LINC00857 abundantly interacted with the RNA-binding protein YTH domain containing 1 (YTHDC1). YTHDC1 ultimately combined with solute carrier family 7 member 5 (SLC7A5) and increased SLC7A5 mRNA stability. Finally, a series of rescue experiments indicated that LINC00857 promoted the proliferation and migration of CRC cells by regulating mRNA stability. Thus, the present findings illustrated that LINC00857 functions as an oncogene in CRC cells via the YTHDC1/SLC7A5 axis.
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Affiliation(s)
- Shu Tang
- Department of Internal Medicine-Oncology, Chenzhou No. 1 People's Hospital, Chenzhou, Hunan 423000, P.R. China
| | - Qi Liu
- Hospital Medical Department, Chenzhou No. 1 People's Hospital, Chenzhou, Hunan 423000, P.R. China
| | - Ming Xu
- Department of Gastrointestinal Surgery, Chenzhou No. 1 People's Hospital, Chenzhou, Hunan 423000, P.R. China
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16
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Lin Y, Yao Y, Wang Y, Wang L, Cui H. PD-L1 and Immune Infiltration of m 6A RNA Methylation Regulators and Its miRNA Regulators in Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5516100. [PMID: 34055974 PMCID: PMC8147529 DOI: 10.1155/2021/5516100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/01/2021] [Indexed: 01/27/2023]
Abstract
BACKGROUND The aim of this study was to systematically evaluate the relationship between the expression of m6A RNA methylation regulators and prognosis in HCC. METHODS We compared the expression of m6A methylation modulators and PD-L1 between HCC and normal in TCGA database. HCC samples were divided into two subtypes by consensus clustering of data from m6A RNA methylation regulators. The differences in PD-L1, immune infiltration, and prognosis between the two subtypes were further compared. The LASSO regression was used to build a risk score for m6A modulators. In addition, we identified miRNAs that regulate m6A regulators. RESULTS We found that fourteen m6A regulatory genes were significantly differentially expressed between HCC and normal. HCC samples were divided into two clusters. Of these, there are higher PD-L1 expression and poorer overall survival (OS) in cluster 1. There was a significant difference in immune cell infiltration between cluster 1 and cluster 2. Through the LASSO model, we obtained 12 m6A methylation regulators to construct a prognostic risk score. Compared with patients with a high-risk score, patients with a low-risk score had upregulated PD-L1 expression and worse prognosis. There was a significant correlation between risk score and tumor-infiltrating immune cells. Finally, we found that miR-142 may be the important regulator for m6A RNA methylation in HCC. CONCLUSION Our results suggest that m6A RNA methylation modulators may affect the prognosis through PD-L1 and immune cell infiltration in HCC patients. In addition, the two clusters may be beneficial for prognostic stratification and improving immunotherapeutic efficacy.
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Affiliation(s)
- Yingxue Lin
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Yinhui Yao
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Ying Wang
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Lingdi Wang
- Department of Medicine, Affiliated Hospital of Chengde Medical University, Nanyingzi Road, Shuangqiao District, Chengde, Hebei, China
| | - Haipeng Cui
- Department of Pathophysiology, Chengde Medical University, Anyuan Road, Shuangqiao District, Chengde, Hebei, China
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Liu J, Wang D, Zhou J, Wang L, Zhang N, Zhou L, Zeng J, Liu J, Yang M. N6-methyladenosine reader YTHDC2 and eraser FTO may determine hepatocellular carcinoma prognoses after transarterial chemoembolization. Arch Toxicol 2021; 95:1621-1629. [PMID: 33713148 DOI: 10.1007/s00204-021-03021-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/03/2021] [Indexed: 02/05/2023]
Abstract
Transarterial chemoembolization (TACE) has significantly improved overall survival (OS) of unresectable hepatocellular carcinoma (HCC) patients. Unfortunately, a portion of patients show no therapeutic responses to TACE. N6-methyladenosine (m6A) as well as its epigenetic writers, erasers, and readers play a crucial role in HCC development. However, it is still largely unclear how functional small nucleotide polymorphisms (SNPs) in m6A-regulating genes contribute to prognosis of TACE-treated HCC patients. In this study, potential functional SNPs were systematically evaluated to identify their roles in the prognosis of HCC patients after TACE in a Chinese Han population. Employing multiple databases, we successfully annotated 55 candidate SNPs. After genotyping these SNPs in our TACE cohort, we identified three genetic variants in YTHDC2 (rs6594732, rs10071816, and rs2303718) and one SNP in FTO (rs7202116) having statistically significant associations with the OS of HCC patients treated with TACE. For example, multivariate Cox proportional hazards model indicated that the rs7202116 GG genotype carriers had markedly shorter OS and an 87% increased death risk compared with the AA carriers after TACE therapy (P = 0.002). When investigating functional relevance of these SNPs, we observed an allelic regulation of rs7202116 on FTO expression in HCC tissue samples, with higher tumor suppressor FTO expression among the A allele carriers. Our findings reported the first evidence supporting the prognostic value of m6A reader YTHDC2 and m6A eraser FTO SNPs in TACE-treated HCC patients. Importantly, our data implicated that m6A-regulating genes may be targets to improve therapeutic strategy for unresectable HCC patients.
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Affiliation(s)
- Jiandong Liu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Dongyang Wang
- Department of Endoscopy, Shandong Cancer Hospital and Institute, Jinan, Shandong, China
| | - Jianyuan Zhou
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Leirong Wang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan, Shandong, China
| | - Liqing Zhou
- Department of Radiation Oncology, Huaian No. 2 Hospital, Huaian, Jiangsu, China
| | - Jiajia Zeng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Jibing Liu
- Department of Intervention Surgery, Shandong Cancer Hospital and Institute, Jinan, 250117, Shandong, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.
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18
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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19
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Jing JJ, Zhao X, Li H, Sun LP, Yuan Y. Expression profiles and prognostic roles of m6A writers, erasers and readers in gastric cancer. FUTURE ONCOLOGY (LONDON, ENGLAND) 2021; 17:2605-2620. [PMID: 33878934 DOI: 10.2217/fon-2020-0630] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Aim: To explore the expression profiles of N6-methyladenosine (m6A) enzymes (writers, erasers and readers) and their associations with gastric cancer (GC) prognosis. Methods: Gene expression was analyzed using the UALCAN and Oncomine web resources. The prognostic roles of these genes in GC were analyzed using data from The Cancer Genome Atlas. Results: Thirteen m6A enzymes were found to be upregulated in GC tissues. The expression of m6A writers METTL3, RBM15 and WTAP was associated with pathological stage. The m6A eraser FTO was related to tumor stage and ALKBH5 expression was related to GC prognosis. The m6A reader YTHDF3 expression was associated with tumor stage. YTHDC2 was associated with survival of GC patients. Conclusion: Abnormal changes of key genes involved in m6A RNA methylation may have an important impact on GC development and prognosis.
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Affiliation(s)
- Jing-Jing Jing
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Xu Zhao
- Mathematical Computer Teaching & Research Office, Liaoning Vocational College of Medicine, Shenyang, 110101, China
| | - Hao Li
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Li-Ping Sun
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yuan Yuan
- Tumor Etiology & Screening Department of Cancer Institute & General Surgery, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of Cancer Etiology & Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology & Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
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20
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Li Y, Zheng JN, Wang EH, Gong CJ, Lan KF, Ding X. The m6A reader protein YTHDC2 is a potential biomarker and associated with immune infiltration in head and neck squamous cell carcinoma. PeerJ 2020; 8:e10385. [PMID: 33304653 PMCID: PMC7700739 DOI: 10.7717/peerj.10385] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Background Increasing evidence has shown that N6-methyladenosine (m6A) RNA methylation regulators have important biological functions in human cancers. However, there are few studies on the value of m6A reader protein YTHDC2 in the diagnosis and tumor-infiltrating of head and neck squamous cell carcinoma (HNSCC). Therefore, it is important to understand the potential clinical value of YTHDC2 in the prognosis and immune infiltration of HNSCC. Methods In this study, gene expression profiles and the corresponding clinical information of 270 HNSCC patients were downloaded from the Gene Expression Omnibus (GEO) database. The gene co-expression network was established to verify whether YTHDC2 was related to the prognosis of HNSCC and verified again in the public database. The correlations between YTHDC2 and immune infiltration was investigated via Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA). Results The results showed that YTHDC2 appeared in the blue module related to survival time and survival state and had a close correlation with the prognosis and immune infiltration level of HNSCC in public database. Patients with low expression of YTHDC2 had poor overall survival (OS) and recurrence-free survival (RFS) than those with high expression. In addition, the expression of YTHDC2 was positively correlated with the level of CD4+ T cell subpopulations infiltration in HNSCC. Conclusions Through this study, we found that YTHDC2 is a tumor suppressor gene with high expression in normal tissues and low expression in tumor tissues. In addition, YTHDC2 is correlated with the immune infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells in HNSCC, which may become a potential marker for prognosis and immune infiltration of HNSCC.
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Affiliation(s)
- Yang Li
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
| | - Ji-Na Zheng
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - En-Hao Wang
- Department of Otolaryngology, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chan-Juan Gong
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Keng-Fu Lan
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - XiaoJun Ding
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
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21
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Xu Z, Peng B, Cai Y, Wu G, Huang J, Gao M, Guo G, Zeng S, Gong Z, Yan Y. N6-methyladenosine RNA modification in cancer therapeutic resistance: Current status and perspectives. Biochem Pharmacol 2020; 182:114258. [PMID: 33017575 DOI: 10.1016/j.bcp.2020.114258] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023]
Abstract
Several strategies, including chemotherapy and radiotherapy, have improved therapeutic outcomes among cancer patients in clinical practice. However, due to their heterogeneity, cancer cells frequently display primary or acquired therapeutic resistance, thereby resulting in treatment failure. The mechanisms underlying cancer therapeutic resistance are complex and varied. Among them, N6-methyladenosine (m6A) RNA modification has gained increasing attention as a potential determinant of therapy resistance within various cancers. In this review, we primarily describe evidence for the effect of the m6A epitranscriptome on RNA homeostasis modulation, which has been shown to alter multiple cellular pathways in cancer research and treatment. Additionally, we discuss the profiles and biological implications of m6A RNA methylation, which is undergoing intensive investigation for its effect on the control of therapeutic resistance.
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Affiliation(s)
- Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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22
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Sun S, Han Q, Liang M, Zhang Q, Zhang J, Cao J. Downregulation of m 6 A reader YTHDC2 promotes tumor progression and predicts poor prognosis in non-small cell lung cancer. Thorac Cancer 2020; 11:3269-3279. [PMID: 32956555 PMCID: PMC7606000 DOI: 10.1111/1759-7714.13667] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/03/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Background m6A modification affects the pathological progress of many diseases by affecting RNA stability and translocation. YTHDC2, a m6A reader, is associated with multiple cancers; however, little is known of its role in non‐small cell lung cancer (NSCLC). Methods The GEPIA, Oncomine and GEO databases were analyzed to assess expression of YTHDC2 in NSCLC patients. Quantitative polymerase chain reaction, western blot and immunohistochemistry were used to detect YTHDC2 expression in different NSCLC cell lines (H1299, H460, H292 and A549) and patients. The effects of YTHDC2 on NSCLC cell lines (A549 and H1299) proliferation and migration were employed using CCK8 and transwell assays. The potential target RNAs of YTHDC2 were obtained from the POSTAR database. Functional enrichment analysis of YTHDC2 targeted RNAs was performed using the Metascape database. Results GEPIA, Oncomine and GEO databases showed low expression of YTHDC2 in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. YTHDC2 expression was significantly decreased in different NSCLC cell lines and our clinical samples. Moreover, low expression of YTHDC2 was significantly associated with poor differentiation, lymph node metastasis, tumor size and stage. In addition, YTHDC2 could suppress the proliferation and migration ability of A549 and H1299 cell lines. Kaplan‐Meier Plotter database analysis revealed that patients with low level of YTHDC2 had a significantly poor prognosis. Finally, functional enrichment analysis of YTHDC2 targeted RNAs indicated several enriched pathways related to cancer. Conclusions These findings elucidate that YTHDC2 suppresses tumorigenesis in NSCLC, indicating that YTHDC2 may be a promising therapeutic target for NSCLC. Key points Significant findings of the study This study demonstrated that the downregulation of YTHDC2 promotes tumor progression and predicts poor prognosis in non‐small cell lung cancer (NSCLC). What this study adds YTHDC2 might be a promising therapeutic target for non‐small cell lung cancer (NSCLC).
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Affiliation(s)
- Shulei Sun
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiang Han
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Maoli Liang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Qian Zhang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Zhang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Jie Cao
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
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23
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Wang W, Sun B, Xia Y, Sun S, He C. RNA N6-Methyladenosine-Related Gene Contribute to Clinical Prognostic Impact on Patients With Liver Cancer. Front Genet 2020; 11:306. [PMID: 32391046 PMCID: PMC7190981 DOI: 10.3389/fgene.2020.00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/13/2020] [Indexed: 12/24/2022] Open
Abstract
Liver cancer (LC) is the fourth leading cause of cancer-related deaths worldwide. There is an urgent need to identify novel and reliable prognostic biomarkers for LC in order to improve patient outcomes. N6-methyladenosine (m6A) is the most common internal modification in eukaryotic mRNA and has been associated with various cancers, although its roles in the prognosis of LC remains to be elucidated. We analyzed the expression profiles of 15 m6A-related genes in the International Cancer Genome Consortium (ICGC) LIRI-JP dataset, and applied consensus clustering to stratify LC patients into two subgroups (Cluster 1 and Cluster 2). Cluster1 was significantly correlated to lower tumor stage and longer overall survival (OS). Gene set enrichment analysis showed that tumorigenic markers, including DNA repair, E2F targets, G2M checkpoint, and MYC targets V1, were enriched in Cluster2. We then constructed a prognostic risk model using three m6A-related genes that were identified as independent factors affecting OS. The nomogram based on the risk model score indicated good performance in predicting the 1-, 2- and 3-year survival of the LC patients. In conclusion, m6A-related genes are potential prognostic markers and therapeutic targets for LC.
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Affiliation(s)
- Wei Wang
- Department of Gastroenterology, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Bo Sun
- Department of Gastroenterology, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Yang Xia
- Department of Gastroenterology, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Shenghong Sun
- Department of Gastroenterology, Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Chiyi He
- Department of Gastroenterology, Yijishan Hospital, Wannan Medical College, Wuhu, China
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Deciphering N 6-Methyladenosine-Related Genes Signature to Predict Survival in Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2514230. [PMID: 32258108 PMCID: PMC7066421 DOI: 10.1155/2020/2514230] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/08/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Lung cancer is the most commonly diagnosed cancer and the leading cause of cancer-related death. Among these, lung adenocarcinoma (LUAD) accounts for most cases. Due to the improvement of precision medicine based on molecular characterization, the treatment of LUAD underwent significant changes. With these changes, the prognosis of LUAD becomes diverse. N6-methyladenosine (m6A) is the most predominant modification in mRNAs, which has been a research hotspot in the field of oncology. Nevertheless, little has been studied to reveal the correlations between the m6A-related genes and prognosis in LUAD. Thus, we conducted a comprehensive analysis of m6A-related gene expressions in LUAD patients based on The Cancer Genome Atlas (TCGA) database by revealing their relationship with prognosis. Different expressions of the m6A-related genes in tumor tissues and non-tumor tissues were confirmed. Furthermore, their relationship with prognosis was studied via Consensus Clustering Analysis, Principal Components Analysis (PCA), and Least Absolute Shrinkage and Selection Operator (LASSO) Regression. Based on the above analyses, a m6A-based signature to predict the overall survival (OS) in LUAD was successfully established. Among the 479 cases, we found that most of the m6A-related genes were differentially expressed between tumor and non-tumor tissues. Six genes, HNRNPC, METTL3, YTHDC2, KIAA1429, ALKBH5, and YTHDF1 were screened to build a risk scoring signature, which is strongly related to the clinical features pathological stages (p < 0.05), M stages (p < 0.05), T stages (p < 0.05), gender (p = 0.04), and survival outcome (p = 0.02). Multivariate Cox analysis indicated that risk value could be used as an independent prognostic factor, revealing that the m6A-related genes signature has great predictive value. Its efficacy was also validated by data from the Gene Expression Omnibus (GEO) database.
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Multiple m 6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis. BMC Cancer 2020; 20:165. [PMID: 32111180 PMCID: PMC7047390 DOI: 10.1186/s12885-020-6638-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death in the world. N6-methyladenosine (m6A) RNA methylation is dynamically regulated by m6A RNA methylation modulators (“writer,” “eraser,” and “reader” proteins), which are associated with cancer occurrence and development. The purpose of this study was to explore the relationships between m6A RNA methylation modulators and HCC. Methods First, using data from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases, we compared the expression levels of 13 major m6A RNA methylation modulators between HCC and normal tissues. Second, we applied consensus clustering to the expression data on the m6A RNA methylation modulators to divide the HCC tissues into two subgroups (clusters 1 and 2), and we compared the clusters in terms of overall survival (OS), World Health Organization (WHO) stage, and pathological grade. Third, using least absolute shrinkage and selection operator (LASSO) regression, we constructed a risk signature involving the m6A RNA methylation modulators that affected OS in TCGA and ICGC analyses. Results We found that the expression levels of 12 major m6A RNA methylation modulators were significantly different between HCC and normal tissues. After dividing the HCC tissues into clusters 1 and 2, we found that cluster 2 had poorer OS, higher WHO stage, and higher pathological grade. Four m6A RNA methylation modulators (YTHDF1, YTHDF2, METTL3, and KIAA1429) affecting OS in the TCGA and ICGC analyses were selected to construct a risk signature, which was significantly associated with WHO stage and was also an independent prognostic marker of OS. Conclusions In summary, m6A RNA methylation modulators are key participants in the malignant progression of HCC and have potential value in prognostication and treatment decisions.
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Zhuang J, Lin C, Ye J. m 6 A RNA methylation regulators contribute to malignant progression in rectal cancer. J Cell Physiol 2020; 235:6300-6306. [PMID: 32043594 DOI: 10.1002/jcp.29626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/09/2020] [Indexed: 12/27/2022]
Abstract
N6,2'-O-dimethyladenosine (m6 A) RNA methylation, which is correlated with cancer initiation and progression, is dynamically regulated by m6 A RNA methylation regulators, including writers, erasers, and readers. Two subgroups of rectal cancer, including cluster1 and cluster2, were identified based on consensus clustering to m6 A RNA methylation regulators. A protein-protein interaction network was constructed and hub genes were identified. The results demonstrated that the expression of WTAP was significantly associated with YTHDC1 and YTHDF2. The principal component analysis was used to compare the transcriptional profile between cluster1 and cluster2 subgroups. By using two identified m6 A RNA methylation regulators, we constructed a risk signature to predict the survival outcomes of rectal cancer. The results revealed that YTHDC2 and YTHDF2 were protective genes with HR < 1. The coefficients obtained from the least absolute shrinkage and selection operator algorithm were used to calculate the risk score. Patients were then divided into low- and high-risk groups based on the median risk score. The survival analysis demonstrated that there were significant differences in overall survival between these two groups (p < .05). The results of the univariate analysis showed that the risk score, AJCC stage, M stage, and age were associated with overall survival. The results of the multivariate Cox regression analysis showed that the risk score and age were still significantly associated with the overall survival (p < .05). To conclude, m6 A RNA methylation regulators can be regarded as potentially useful biomarkers for predicting the prognosis and designing a treatment strategy in rectal cancer.
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Affiliation(s)
- Jinfu Zhuang
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Chunlin Lin
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jianxin Ye
- Department of Gastrointestinal Surgery 2 Section, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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Methylation of adenosine at the N6 position post-transcriptionally regulates hepatic P450s expression. Biochem Pharmacol 2020; 171:113697. [DOI: 10.1016/j.bcp.2019.113697] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022]
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Heck AM, Wilusz CJ. Small changes, big implications: The impact of m 6A RNA methylation on gene expression in pluripotency and development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194402. [PMID: 31325527 PMCID: PMC6742438 DOI: 10.1016/j.bbagrm.2019.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022]
Abstract
In order to maintain a state of self-renewal, yet retain the ability to rapidly differentiate in response to external signals, pluripotent cells exert tight control over gene expression at many levels. Recent studies have suggested that N6-methyladenosine (m6A) RNA methylation, one of the most abundant post-transcriptional modifications, is important for both pluripotency and differentiation. In this review, we summarize the current state of the m6A field, with emphasis on the impact of writers, erasers and readers of m6A on RNA metabolism and stem cell biology.
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Affiliation(s)
- Adam M Heck
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America
| | - Carol J Wilusz
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America.
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Understanding m 6A Function Through Uncovering the Diversity Roles of YTH Domain-Containing Proteins. Mol Biotechnol 2019; 61:355-364. [PMID: 30637606 DOI: 10.1007/s12033-018-00149-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant-internal modification of eukaryotic mRNA. m6A can be installed and removed by specific enzymes. The "writer," "eraser," and "reader" of m6A modification have been reported. These discoveries facilitate our understanding of the functional significance of m6A. m6A plays an essential role in diverse biological processes by recruiting the corresponding YTH domain-containing proteins, as well as recruiting additional translation initiation factors. Here, we provide an update on the various aspects of YTH domain-containing proteins, including an introduction to the YTH domain, the categories, distribution in cells, and biological roles of YTH proteins. Then we focus on the mechanisms that YTH proteins recognize m6A and mediate the fate of methylated-RNAs in eukaryotic cells.
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30
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Berlivet S, Scutenaire J, Deragon JM, Bousquet-Antonelli C. Readers of the m 6A epitranscriptomic code. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:329-342. [PMID: 30660758 DOI: 10.1016/j.bbagrm.2018.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/20/2018] [Accepted: 12/28/2018] [Indexed: 12/21/2022]
Abstract
N6-methyl adenosine (m6A) is the most prevalent and evolutionarily conserved, modification of polymerase II transcribed RNAs. By post-transcriptionally controlling patterns of gene expression, m6A deposition is crucial for organism reproduction, development and likely stress responses. m6A mostly mediates its effect by recruiting reader proteins that either directly accommodate the modified residue in a hydrophobic pocket formed by their YTH domain, or otherwise have their affinity positively influenced by the presence of m6A. We firstly describe here the evolutionary history, and review known molecular and physiological roles of eukaryote YTH readers. In the second part, we present non YTH-proteins whose roles as m6A readers largely remain to be explored. The diversity and multiplicity of m6A readers together with the possibility to regulate their expression and function in response to various cues, offers a multitude of possible combinations to rapidly and finely tune gene expression patterns and hence cellular plasticity. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Soizik Berlivet
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jérémy Scutenaire
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jean-Marc Deragon
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France; Institut Universitaire de France (IUF), 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Cécile Bousquet-Antonelli
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France.
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31
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m⁶A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins. Genes (Basel) 2019; 10:genes10010049. [PMID: 30650668 PMCID: PMC6356822 DOI: 10.3390/genes10010049] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/04/2023] Open
Abstract
The control of gene expression is a multi-layered process occurring at the level of DNA, RNA, and proteins. With the emergence of highly sensitive techniques, new aspects of RNA regulation have been uncovered leading to the emerging field of epitranscriptomics dealing with RNA modifications. Among those post-transcriptional modifications, N6-methyladenosine (m6A) is the most prevalent in messenger RNAs (mRNAs). This mark can either prevent or stimulate the formation of RNA-protein complexes, thereby influencing mRNA-related mechanisms and cellular processes. This review focuses on proteins containing a YTH domain (for YT521-B Homology), a small building block, that selectively detects the m6A nucleotide embedded within a consensus motif. Thereby, it contributes to the recruitment of various effectors involved in the control of mRNA fates through adjacent regions present in the different YTH-containing proteins.
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32
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Chang G, Leu JS, Ma L, Xie K, Huang S. Methylation of RNA N 6-methyladenosine in modulation of cytokine responses and tumorigenesis. Cytokine 2018; 118:35-41. [PMID: 30017390 DOI: 10.1016/j.cyto.2018.06.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/25/2018] [Accepted: 06/12/2018] [Indexed: 12/19/2022]
Abstract
Among myriads of distinct chemical modification in RNAs, the dynamic, reversible and fine-tuned methylation of N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic mRNAs. This RNA mark is generated by proteins that act as m6A writers and can be reversed by proteins that act as m6A erasers. The RNA m6A modification is also mediated by another group of proteins capable of recognizing m6A that act as m6A readers. The m6A modification exerts direct control over the RNA metabolism including mRNA processing, mRNA exporting, translation initiation, mRNA stability and the biogenesis of long-non-coding RNA (LncRNA), thereby can influence various aspects of cell function. Evidently, m6A is intimately associated with cancer development and progression such as self-renewal capacity of cancer stem cells, proliferation, apoptosis and therapeutic resistance, and immune response. In this review, we will discuss the regulation and function of m6A, the various functions ascribed to these proteins and the emerging concepts that impact our knowledge of these proteins and their roles in the epitranscriptome. Conceivably, m6A may play pivotal roles in cytokine and immune response and carcinogenesis.
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Affiliation(s)
- Guoqiang Chang
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Jia-Shiun Leu
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Li Ma
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Keping Xie
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States; Program in Cancer Biology, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, United States
| | - Suyun Huang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States; Program in Cancer Biology, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, United States.
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33
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Jain D, Puno MR, Meydan C, Lailler N, Mason CE, Lima CD, Anderson KV, Keeney S. ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2. eLife 2018; 7:30919. [PMID: 29360036 PMCID: PMC5832417 DOI: 10.7554/elife.30919] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Abstract
Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YTHDC2 as a critical component. A screen yielded a sterile mutant, ‘ketu’, caused by a Ythdc2 missense mutation. Mutant germ cells enter meiosis but proceed prematurely to aberrant metaphase and apoptosis, and display defects in transitioning from spermatogonial to meiotic gene expression programs. ketu phenocopies mutants lacking MEIOC, a YTHDC2 partner. Consistent with roles in post-transcriptional regulation, YTHDC2 is cytoplasmic, has 3′→5′ RNA helicase activity in vitro, and has similarity within its YTH domain to an N6-methyladenosine recognition pocket. Orthologs are present throughout metazoans, but are diverged in nematodes and, more dramatically, Drosophilidae, where Bgcn is descended from a Ythdc2 gene duplication. We also uncover similarity between MEIOC and Bam, a Bgcn partner unique to schizophoran flies. We propose that regulation of gene expression by YTHDC2-MEIOC is an evolutionarily ancient strategy for controlling the germline transition into meiosis.
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Affiliation(s)
- Devanshi Jain
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - M Rhyan Puno
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States
| | - Nathalie Lailler
- Integrated Genomics Operation, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States.,The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, United States
| | - Christopher D Lima
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kathryn V Anderson
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
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34
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Patil DP, Pickering BF, Jaffrey SR. Reading m 6A in the Transcriptome: m 6A-Binding Proteins. Trends Cell Biol 2017; 28:113-127. [PMID: 29103884 DOI: 10.1016/j.tcb.2017.10.001] [Citation(s) in RCA: 409] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/26/2017] [Accepted: 10/02/2017] [Indexed: 01/28/2023]
Abstract
N6-Methyladenosine (m6A) is the most prevalent post-transcriptional modification of eukaryotic mRNA and long noncoding RNA. m6A mediates its effects primarily by recruiting proteins, including the multiprotein eukaryotic initiation factor 3 complex and a set of proteins that contain the YTH domain. Here we describe the mechanisms by which YTH domain-containing proteins bind m6A and influence the fate of m6A-containing RNA in mammalian cells. We discuss the diverse, and occasionally contradictory, functions ascribed to these proteins and the emerging concepts that are influencing our understanding of these proteins and their effects on the epitranscriptome.
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Affiliation(s)
- Deepak P Patil
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA; These authors contributed equally
| | - Brian F Pickering
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA; These authors contributed equally
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA.
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35
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Tanabe A, Tanikawa K, Tsunetomi M, Takai K, Ikeda H, Konno J, Torigoe T, Maeda H, Kutomi G, Okita K, Mori M, Sahara H. RNA helicase YTHDC2 promotes cancer metastasis via the enhancement of the efficiency by which HIF-1α mRNA is translated. Cancer Lett 2016; 376:34-42. [DOI: 10.1016/j.canlet.2016.02.022] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 02/05/2023]
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36
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Wang YL, Fang M, Wang XM, Liu WY, Zheng YJ, Wu XB, Tao R. Proinflammatory effects and molecular mechanisms of interleukin-17 in intestinal epithelial cell line HT-29. World J Gastroenterol 2014; 20:17924-17931. [PMID: 25548490 PMCID: PMC4273142 DOI: 10.3748/wjg.v20.i47.17924] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 08/24/2014] [Accepted: 10/21/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the proinflammatory effects and molecular mechanisms of interleukin (IL)-17 in intestinal epithelial cell line HT-29.
METHODS: HT-29 cells were cultured with IL-17, tumor necrosis factor (TNF)-α, or the combination of both IL-17 and TNF-α. Real-time PCR and Western blot were used to measure the gene expression levels of neutrophil chemokines CXCL1, CXCL2, CXCL5, CXCL6, IL-8 and TH-17 cell chemokine CCL20, the phosphorylation levels of p38 and TNF-α, and the expression level of IL-8, after using the p38 inhibitor in HT-29 cells. The stable Act1 knockdown HT-29 cell line was established to further test the phosphorylation changes of p38, after using IL-17 and TNF-α.
RESULTS: After HT-29 cells were cultured with IL-17 and TNF-α, the expression levels of neutrophil chemokines (CXCL1, CXCL2, CXCL5, CXCL6, IL-8) and Th17 chemokine (CCL20) significantly improved (24.96 ± 2.53, 28.47 ± 2.87, 38.08 ± 2.72, 33.47 ± 2.41, 31.7 ± 2.38, 44.37 ± 2.73, respectively), and the differences were all statistically significant (P < 0.01). Western blot results showed that IL-17 obviously enhanced the phosphorylation level of p38, which was induced by TNF-α. Compared with the control group, the expression level of IL-8 significantly declined (9.47 ± 1.36 vs 3.06 ± 0.67, P < 0.01) when TH-29 cells were cultured with IL-17 and TNF-α. p38 inhibition assay showed that the p38 pathway played an essential role in the inflammatory response induced by IL-17. p38 phosphorylation levels could not be changed after using IL-17 and TNF-α in the stable Act1 knockdown HT-29 cell line.
CONCLUSION: IL-17 significantly promoted the gene expression levels of TNF-α-induced neutrophil chemokines and Th17 cell chemokine. It is obvious that IL-17 and TNF-α have synergistic effects on p38.
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Chai Y, Sun Y, Guo L, Li D, Ding Y. Investigating the role of introns in the regulation of regenerating gene 1 expression. Oncol Lett 2014; 9:875-880. [PMID: 25621062 PMCID: PMC4301469 DOI: 10.3892/ol.2014.2712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 10/31/2014] [Indexed: 01/15/2023] Open
Abstract
Gastrin is a hormone that physiologically regulates gastric acid secretion and contributes to the maintenance of gastric epithelial architecture by regulating the expression of genes such as regenerating gene 1 (Reg1). Reg1 is involved in gastric carcinogenesis as an antiapoptotic factor. The current study explores the molecular mechanism of gastrin-regulated Reg1 expression in human gastric cancer cells. In total, five intron fragments of the Reg1 gene were cloned by polymerase chain reaction and inserted into luciferase reporter vector pGL3 to construct intron-luciferase reporter vectors. After confirmation by Xho I/Hind III digestion and DNA sequencing, the five constructs were transfected into the SGC7901 gastric cancer cell line. The luciferase activity of the cells transfected with each of the five constructs was detected following incubation without or with gastrin. The five intron fragments of Reg1 were also randomly labeled with digoxin as a probe, and nuclear proteins of gastric cancer cells were extracted following treatment with or without gastrin. Southwestern blotting was subsequently performed to detect transcription factors that bind to the introns. The results indicated that the luciferase activity was significantly higher in cells transfected with recombinant vectors containing introns 2, 3, 4 or 5 than that in the cells transfected with an empty vector (P<0.05). However, no statistically significant difference in luciferase activity was identified between cells transfected with pGL3-intron 1 and those transfected with pGL3-Basic (P>0.05). Following incubation with gastrin, no significant difference was identified (P>0.05). The five introns of Reg1 can bind a number of transcription factors and gastrin may affect this interaction. Introns 2–5 of Reg1 potentially have transcriptional control over gene expression in gastric cancer cells. In conclusion, gastrin may regulate the expression of the Reg1 gene via the interaction of the introns by binding to the transcription factors.
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Affiliation(s)
- Yurong Chai
- Department of Histology and Embryology, College of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yun Sun
- Department of Histology and Embryology, College of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Linxia Guo
- Department of Histology and Embryology, College of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Dan Li
- Department of Histology and Embryology, College of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yi Ding
- Department of Histology and Embryology, College of Basic Medicine, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
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Fanale D, Iovanna JL, Calvo EL, Berthezene P, Belleau P, Dagorn JC, Bronte G, Cicero G, Bazan V, Rolfo C, Santini D, Russo A. Germline copy number variation in the YTHDC2 gene: does it have a role in finding a novel potential molecular target involved in pancreatic adenocarcinoma susceptibility? Expert Opin Ther Targets 2014; 18:841-50. [PMID: 24834797 DOI: 10.1517/14728222.2014.920324] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The vast majority of pancreatic cancers occurs sporadically. The discovery of frequent variations in germline gene copy number can significantly influence the expression levels of genes that predispose to pancreatic adenocarcinoma. We prospectively investigated whether patients with sporadic pancreatic adenocarcinoma share specific gene copy number variations (CNVs) in their germline DNA. PATIENTS AND METHODS DNA samples were analyzed from peripheral leukocytes from 72 patients with a diagnosis of sporadic pancreatic adenocarcinoma and from 60 controls using Affymetrix 500K array set. Multiplex ligation-dependent probe amplification (MLPA) assay was performed using a set of self-designed MLPA probes specific for seven target sequences. RESULTS We identified a CNV-containing DNA region associated with pancreatic cancer risk. This region shows a deletion of 1 allele in 36 of the 72 analyzed patients but in none of the controls. This region is of particular interest since it contains the YTHDC2 gene encoding for a putative DNA/RNA helicase, such protein being frequently involved in cancer susceptibility. Interestingly, 82.6% of Sicilian patients showed germline loss of one allele. CONCLUSIONS Our results suggest that the YTHDC2 gene could be a potential candidate for pancreatic cancer susceptibility and a useful marker for early detection as well as for the development of possible new therapeutic strategies.
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Affiliation(s)
- Daniele Fanale
- University of Palermo, Department of Surgical, Oncological and Stomatological Sciences, Section of Medical Oncology , Via del Vespro 129, 90127 Palermo , Italy +39 091 6552500 ; +011 39 091 6554529 ;
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