bims-rimeca 2023-04-02 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023–04–02
twenty-one papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

METTL3 relieved the injury of SH-SY5Y cells treated with lipopolysaccharide and exposed to sevoflurane through regulating the m6A levels of Sox2.
N6-methyladenosine reader YTHDF1 regulates the proliferation and migration of airway smooth muscle cells through m6A/cyclin D1 in asthma.
Bibliometric analysis of METTL3: Current perspectives, highlights, and trending topics.
Epitranscriptome Mapping of N6-Methyladenosine Using m6A Immunoprecipitation with High Throughput Sequencing in Skeletal Muscle Stem Cells.
Epitranscriptic regulation of HRAS by N6-methyladenosine drives tumor progression.
METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation.
Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14.
WTAP contributes to the tumorigenesis of osteosarcoma via modulating ALB in an m6A-dependent manner.
The critical roles of m6A RNA methylation in lung cancer: from mechanism to prognosis and therapy.
N7-methylguanosin regulators-mediated methylation modification patterns and characterization of the immune microenvironment in lower-grade glioma.
METTL3-Mediated LncRNA EN_42575 m6A Modification Alleviates CPB2 Toxin-Induced Damage in IPEC-J2 Cells.
FERMT1 Is a Prognostic Marker Involved in Immune Infiltration of Pancreatic Adenocarcinoma Correlating with m6A Modification and Necroptosis.
PLAGL2 promotes Snail expression and gastric cancer progression via UCA1/miR-145-5p/YTHDF1 axis.
N6-methyladenosine reader YTHDF family in biological processes: Structures, roles, and mechanisms.
M6A-Related Long Non-Coding RNA Displays Utility in Predicting Prognosis, Portraying the Tumor Immune Microenvironment and Guiding Immunotherapy in Pancreatic Ductal Adenocarcinoma.
Identification of m6A-associated LncRNAs as predict factors for the immune infiltration and prognosis of thyroid cancer.
DNA 6mA demethylase ALKBH1 regulates DDX18 expression to promote proliferation of human head and neck squamous cell carcinoma.
The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer.
Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation.
The N6-methyladenine DNA demethylase ALKBH1 promotes gastric carcinogenesis by disrupting NRF1 binding capacity.
A metabolic vulnerability of pancreatic cancer.

Brain Behav. 2023 Mar 28. e2936

METTL3 relieved the injury of SH-SY5Y cells treated with lipopolysaccharide and exposed to sevoflurane through regulating the m6A levels of Sox2.

Yilong Wang, Zeyong Yang.

   INTRODUCTION: Postoperative cognitive dysfunction (POCD) is a common complication of the central nervous system in elderly patients. The objective of this study was to investigate the role of methyltransferase 3 (METTL3) in the POCD progression.
METHODS: The SH-SY5Y cells were treated with lipopolysaccharide (LPS) and exposed to sevoflurane to establish a POCD cell model. The cell viability and proliferation were assessed with MTT and EdU assays. Besides, the cell apoptosis was determined with TUNEL staining and flow cytometry. Additionally, the inflammatory factors were measured with ELISA. N6-methyladenosine (m6A) RNA Methylation Quantification Kit was used to detect the m6A levels. The relative expressions of methyltransferase 3 (METTL3) and Sex-determining region Y-box-2 (Sox2) was measured with RT-qPCR and western blot assays. RNA methylation immunoprecipitation-real-time quantitative PCR was performed to detect the RNA that was m6A modified.
RESULTS: After LPS treatment and sevoflurane exposure, the cell viability and proliferation were decreased and the cell apoptosis was elevated. The m6A and the METTL3 expression levels in the POCD cell model were declined. METTL3 overexpression promoted the cell growth and inhibited the cell apoptosis in the POCD cell model. Besides, the Sox2 levels were reduced in the POCD cell model. METTL3 silencing declined the m6A and mRNA levels of Sox2, while overexpression of METTL3 elevated it. The relationship between METTL3 and Sox2 was confirmed with double luciferase assay. Finally, Sox2 silencing neutralized the role of METTTL3 overexpression in the POCD cell model.
CONCLUSION: METTL3 relieved the injury of the SH-SY5Y cells induced by LPS treatment and sevoflurane exposure through regulating the m6A and mRNA levels of Sox2.

Keywords:  METTL3; Sox2; postoperative cognitive dysfunction; sevoflurane

DOI:  https://doi.org/10.1002/brb3.2936
PeerJ. 2023 ;11 e14951

N6-methyladenosine reader YTHDF1 regulates the proliferation and migration of airway smooth muscle cells through m6A/cyclin D1 in asthma.

Juan Wang, Lei Wang, Xingfeng Tian, Lingping Luo.

  Asthma is a chronic inflammatory respiratory disease, which is involved in multiple pathologic molecular mechanisms and presents a huge challenge to clinic nursing. Emerging evidence suggests that N6-methyladenosine (m6A) plays critical roles in respiratory system disease. Thus, present work tried to investigate the functions of m6A reader YTHDF 1 in asthma. The results indicated that YTHDF1 significantly upregulated in platelet-derived growth factor (PDGF) induced airway smooth muscle cells (ASMCs). Functionally, overexpression of YTHDF1 promoted the proliferation and migration of ASMCs, while YTHDF1 knockdown repressed the proliferation and migration. Mechanistically, there was a m6A modification site on cyclin D1 RNA (CCND1 genome) and YTHDF1 combined with cyclin D1 mRNA, thereby enhancing its mRNA stability via m6A-dependent manner. Collectively, these findings reveal a novel axis of YTHDF1/m6A/cyclin D1 in asthma's airway remodeling, which may provide novel therapeutic strategy for asthma.

Keywords:  Airway smooth muscle cells; Asthma; N6-methyladenosine

DOI:  https://doi.org/10.7717/peerj.14951
Open Life Sci. 2023 ;18(1): 20220586

Bibliometric analysis of METTL3: Current perspectives, highlights, and trending topics.

Hanqi Liu, Yanqing Huang, Shanshan Lu, Didi Yuan, Junwen Liu.

  N6-methyladenosine (m6A) is a representative of RNA methylation modification, which plays a critical role in the epigenetic modification process of regulating human diseases. As a key protein for m6A, methyltransferase 3 (METTL3) had been identified to be associated with a variety of diseases. The publications related to METTL3 were searched in the Web of Science Core Collection from the earliest mention to July 1st, 2022. Being screened by the retrieval strategy, a total of 1,738 articles related to METTL3 were retrieved. Much of our work focused on collecting the data of annual publication outputs, high-yielding countries/regions/authors, keywords, citations, and journals frequently published for qualitative and quantitative analysis. We found that diseases with high correlations to METTL3 not only included various known cancers but also obesity and atherosclerosis. In addition to m6A-related enzyme molecules, the most frequent key molecules were MYC proto-oncogene (C-MYC), Enhancer of zeste homolog 2 (EZH2), and Phosphatase and tensin homolog deleted on chromosome 10 (PTEN). METTL3 and methyltransferase 14 (METTL14) may function through opposite regulatory pathways in the same disease. "Leukemia," "Liver Cancer," and "Glioblastoma" were speculated to be potential hotspots in METTL3 related study. The number of publications had significantly surged year by year, demonstrating the growing importance of the research on epigenetic modification in the pathology of various diseases.

Keywords:  METTL3; RNA methylation; bibliometrics; epigenetics; publications

DOI:  https://doi.org/10.1515/biol-2022-0586
Methods Mol Biol. 2023 ;2640 431-443

Epitranscriptome Mapping of N6-Methyladenosine Using m6A Immunoprecipitation with High Throughput Sequencing in Skeletal Muscle Stem Cells.

Justin Law, Stefan Günther, Shuichi Watanabe.

  N6-Methyladenosine (m6A), one of the most abundant chemical modifications in mRNA (epitranscriptome), contributes to the regulation of biological processes by iterating gene expression post-transcriptionally. A number of publications on m6A modification have escalated in the recent past, due to the advancements in profiling m6A along the transcriptome using different approaches. The vast majority of studies primarily focused on m6A modification on cell lines but not primary cells. We present in this chapter a protocol for m6A immunoprecipitation with high throughput sequencing (MeRIP-Seq) that profiles m6A on mRNA with merely 100 μg total RNA worth of muscle stem cells as starting material. With this MeRIP-Seq, we observed epitranscriptome landscape in muscle stem cells.

Keywords:  Epitranscriptome; Immunoprecipitation; Mettl3/14; RNA metabolism; YTH RNA binding proteins; m6A

DOI:  https://doi.org/10.1007/978-1-0716-3036-5_29
Proc Natl Acad Sci U S A. 2023 Apr 04. 120(14): e2302291120

Epitranscriptic regulation of HRAS by N6-methyladenosine drives tumor progression.

Yongbo Pan, Yinmin Gu, Tihui Liu, Qingqing Zhang, Facai Yang, Liqiang Duan, Shuwen Cheng, Xiaofeng Zhu, Yibo Xi, Xiaoli Chang, Qinong Ye, Shan Gao.

  Overexpression of Ras, in addition to the oncogenic mutations, occurs in various human cancers. However, the mechanisms for epitranscriptic regulation of RAS in tumorigenesis remain unclear. Here, we report that the widespread N6-methyladenosine (m6A) modification of HRAS, but not KRAS and NRAS, is higher in cancer tissues compared with the adjacent tissues, which results in the increased expression of H-Ras protein, thus promoting cancer cell proliferation and metastasis. Mechanistically, three m6A modification sites of HRAS 3' UTR, which is regulated by FTO and bound by YTHDF1, but not YTHDF2 nor YTHDF3, promote its protein expression by the enhanced translational elongation. In addition, targeting HRAS m6A modification decreases cancer proliferation and metastasis. Clinically, up-regulated H-Ras expression correlates with down-regulated FTO and up-regulated YTHDF1 expression in various cancers. Collectively, our study reveals a linking between specific m6A modification sites of HRAS and tumor progression, which provides a new strategy to target oncogenic Ras signaling.

Keywords:  FTO; HRAS; YTHDF1; epitranscriptome; m6A

DOI:  https://doi.org/10.1073/pnas.2302291120
Cell Death Dis. 2023 Mar 28. 14(3): 221

METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation.

Chengjie Lin, Ting Li, Yan Wang, Shihui Lai, Yue Huang, Zhenyun Guo, Xiang Zhang, Shangeng Weng.

The aim of the present study was to clarify the mechanism of how METTL3 regulated pancreatic ductal adenocarcinoma (PDAC) progression by m6A modification of its downstream target mRNA and signaling pathway. Immunoblotting and qRT-PCR assays was employed to determine the expression levels of METTL3. In situ fluorescence hybridization was conducted to localize the cellular distribution of METTL3 and DEAD-box helicase 23 (DDX23). CCK8, colony formation, EDU incorporation, TUNEL, wound healing and Transwell assays were carried out accordingly to study the viability, proliferation, apoptosis, and mobility of cells under different treatments in vitro. Xenograft and animal lung metastasis experiments were also conducted to study the functional role of METTL3 or DDX23 on tumor growth and lung metastasis in vivo. MeRIP-qPCR and bioinformatical analyses were used to obtain the potential direct targets of METTL3. It was shown that m6A methyltransferase METTL3 was upregulated in PDAC tissues with gemcitabine resistance, and its knockdown sensitized pancreatic cancer cells to chemotherapy. Furthermore, silencing METTL3 remarkably reduced pancreatic cancer cell proliferation, migration, and invasion both in vitro and in vivo. Mechanistically, validation experiments confirmed that DDX23 mRNA was a direct target of METTL3 in YTHDF1-dependent manner. Additionally, DDX23 silence resulted in the suppression of pancreatic cancer cell malignancy and PIAK/Akt signaling inactivation. Strikingly, rescuse experiments demonstrated the inhibitive effects of METTL3 silence on cell phenotypes and gemcitabine resistance were partially reversed by forcibly expressed DDX23. In summary, METTL3 promotes PDAC progression and gemcitabine resistance by modifying DDX23 mRNA m6A methylation and enhancing PI3K/Akt signaling activation. Our findings establish a potential tumor promotive and chemo-resistant role for METTL3/DDX23 axis in PDAC.

DOI: https://doi.org/10.1038/s41419-023-05715-1
bioRxiv. 2023 Mar 16. pii: 2023.03.16.532618. [Epub ahead of print]

Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14.

Chi Zhang, Luiza Tunes, Meng-Hsiung Hsieh, Ping Wang, Ashwani Kumar, Brijesh B Khadgi, YenYu Yang, Katelyn A Doxtader, Emily Herrell, Oliwia Koczy, Rohit Setlem, Xunzhi Zhang, Bret Evers, Yinsheng Wang, Chao Xing, Hao Zhu, Yunsun Nam.

Chemical modification of RNAs is important for post-transcriptional gene regulation. The METTL3-METTL14 complex generates most N 6 -methyladenosine (m 6 A) modifications in mRNAs, and dysregulated methyltransferase expression has been linked to numerous cancers. Here we show that changes in m 6 A modification location can impact oncogenesis. A gain-of-function missense mutation found in cancer patients, METTL14 R298P , promotes malignant cell growth in culture and in transgenic mice. The mutant methyltransferase preferentially modifies noncanonical sites containing a GGAU motif and transforms gene expression without increasing global m 6 A levels in mRNAs. The altered substrate specificity is intrinsic to METTL3-METTL14, helping us to propose a structural model for how the METTL3-METTL14 complex selects the cognate RNA sequences for modification. Together, our work highlights that sequence-specific m 6 A deposition is important for proper function of the modification and that noncanonical methylation events can impact aberrant gene expression and oncogenesis.

DOI: https://doi.org/10.1101/2023.03.16.532618
Environ Toxicol. 2023 Mar 29.

WTAP contributes to the tumorigenesis of osteosarcoma via modulating ALB in an m6A-dependent manner.

Qiyong Pan, Jigang Lou, Penghui Yan, Xiaobiao Kang, Pengfei Li, Zongqiang Huang.

   PURPOSE: Osteosarcoma (OS) is a prevalent bone malignancy mainly occurred in adolescents. WTAP/N6-methyladenosine (m6A) modification is confirmed to be involved in OS progression. This study is conducted to bring some novel insights to the action mechanism of WTAP/m6A under the hidden pathogenesis of OS.
METHODS: qRT-PCR was executed to evaluate the expression levels of WTAP and ALB. ALB protein level in OS cells was measured by western blotting. The content of m6A in total RNA was assessed by m6A quantification assay. Me-RIP, dual luciferase reporter, and mRNA stability assays confirmed the target relationship of WTAP with ALB. With the use of the wound healing, CCK-8, and transwell invasion assays, the functional relationship between WTAP and ALB in OS cells was confirmed. The influences of WTAP on tumor growth in vivo were performed in the xenograft model of mouse.
RESULTS: WTAP was increased but ALB was diminished in OS tissues and/or cell lines. WTAP modulated ALB expression in an m6A-dependent manner. Silencing of WTAP retarded the development of OS via inhibiting cell viability, migration, invasion, and tumor growth. Knockdown of ALB exerted the opposite effects on OS progression. Additionally, ALB deficiency partially eliminated the inhibiting effects of WTAP silencing on cellular processes in OS.
CONCLUSIONS: This is the first report to clarify the interaction of WTAP/m6A with ALB in OS progression. These experimental data to some extent broadened the horizons of WTAP/m6A in the development of OS.

Keywords:  ALB; N6-methyladenosine; WTAP; osteosarcoma

DOI:  https://doi.org/10.1002/tox.23780
Br J Cancer. 2023 Mar 30.

The critical roles of m6A RNA methylation in lung cancer: from mechanism to prognosis and therapy.

Mei-Ning Diao, Xiao-Jing Zhang, Yin-Feng Zhang.

Lung cancer, a highly malignant disease, greatly affects patients' quality of life. N6-methyladenosine (m6A) is one of the most common posttranscriptional modifications of various RNAs, including mRNAs and ncRNAs. Emerging studies have demonstrated that m6A participates in normal physiological processes and that its dysregulation is involved in many diseases, especially pulmonary tumorigenesis and progression. Among these, regulators including m6A writers, readers and erasers mediate m6A modification of lung cancer-related molecular RNAs to regulate their expression. Furthermore, the imbalance of this regulatory effect adversely affects signalling pathways related to lung cancer cell proliferation, invasion, metastasis and other biological behaviours. Based on the close association between m6A and lung cancer, various prognostic risk models have been established and novel drugs have been developed. Overall, this review comprehensively elaborates the mechanism of m6A regulation in the development of lung cancer, suggesting its potential for clinical application in the therapy and prognostic assessment of lung cancer.

DOI: https://doi.org/10.1038/s41416-023-02246-6
Eur J Med Res. 2023 Mar 30. 28(1): 144

N7-methylguanosin regulators-mediated methylation modification patterns and characterization of the immune microenvironment in lower-grade glioma.

Aierpati Maimaiti, Zhaohai Feng, Yanwen Liu, Mirzat Turhon, Zhihao Xie, Yilimire Baihetiyaer, Xixian Wang, Maimaitijiang Kasimu, Lei Jiang, Yongxin Wang, Zengliang Wang, Yinan Pei.

  N7-methylguanosine (m7G) modification signature has recently emerged as a crucial regulator of tumor progression and treatment in cancer. However, there is limited information available on the genomic profile of lower-grade gliomas (LGGs) related to m7G methylation modification genes' function in tumorigenesis and progression. In this study, we employed bioinformatics methods to characterize m7G modifications in individuals with LGG from The Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). We used gene set enrichment analysis (GSEA), single sample GSEA (ssGSEA), CIBERSORT algorithm, ESTIMATE algorithm, and TIDE to evaluate the association between m7G modification patterns, tumor microenvironment (TME) cell infiltration properties, and immune infiltration markers. The m7G scoring scheme using principal component analysis (PCA) was employed to investigate the m7G modification patterns quantitatively. We examined the m7G modification hub genes' expression levels in normal samples, refractory epilepsy samples, and LGG samples using immunohistochemistry, western-blotting, and qRT-PCR. Our findings revealed that individuals with LGG could be categorized into two groups based on m7G scores (high and low) according to the properties of m7G. Moreover, we observed that high m7G score was associated with significant clinical benefit and prolonged survival duration in the anti-PD-1 cohort, while low m7G score was associated with improved prognostic outcomes and increased likelihood of complete or partial response in the anti-PD-L1 cohort. Different m7G subtypes also showed varying Tumor Mutational Burden (TMB) and immune profiles and might have distinct responses to immunotherapy. Furthermore, we identified five potential genetic markers that were highly correlated with the m7G score signature index. These findings provide insight into the features and classification associated with m7G methylation modifications and may aid in improving the clinical outcome of LGG.

Keywords:  Anti-PD-1/L1 immunotherapy; Lower-grade glioma; N7-methylguanosine; Prognostic signature; Tumor microenvironment

DOI:  https://doi.org/10.1186/s40001-023-01108-4
Int J Mol Sci. 2023 Mar 16. pii: 5725. [Epub ahead of print]24(6):

METTL3-Mediated LncRNA EN_42575 m6A Modification Alleviates CPB2 Toxin-Induced Damage in IPEC-J2 Cells.

Jiaojiao Yang, Qiaoli Yang, Xiaoyu Huang, Zunqiang Yan, Pengfei Wang, Xiaoli Gao, Jie Li, Shuangbao Gun.

  Long non-coding RNAs (lncRNAs) modified by n6-methyladenosine (m6A) have been implicated in the development and progression of several diseases. However, the mechanism responsible for the role of m6A-modified lncRNAs in Clostridium perfringens type C piglet diarrhea has remained largely unknown. We previously developed an in vitro model of CPB2 toxin-induced piglet diarrhea in IPEC-J2 cells. In addition, we previously performed RNA immunoprecipitation sequencing (MeRIP-seq), which demonstrated lncRNA EN_42575 as one of the most regulated m6A-modified lncRNAs in CPB2 toxin-exposed IPEC-J2 cells. In this study, we used MeRIP-qPCR, FISH, EdU, and RNA pull-down assays to determine the function of lncRNA EN_42575 in CPB2 toxin-exposed IPEC-J2 cells. LncRNA EN_42575 was significantly downregulated at different time points in CPB2 toxin-treated cells. Functionally, lncRNA EN_42575 overexpression reduced cytotoxicity, promoted cell proliferation, and inhibited apoptosis and oxidative damage, whereas the knockdown of lncRNA EN_42575 reversed these results. Furthermore, the dual-luciferase analysis revealed that METTL3 regulated lncRNA EN_42575 expression in an m6A-dependent manner. In conclusion, METTL3-mediated lncRNA EN_42575 exerted a regulatory effect on IPEC-J2 cells exposed to CPB2 toxins. These findings offer novel perspectives to further investigate the function of m6A-modified lncRNAs in piglet diarrhea.

Keywords:  CPB2 toxin; IPEC-J2 cell; METTL3; lncRNA EN_42575; m6A

DOI:  https://doi.org/10.3390/ijms24065725
Genes (Basel). 2023 Mar 16. pii: 734. [Epub ahead of print]14(3):

FERMT1 Is a Prognostic Marker Involved in Immune Infiltration of Pancreatic Adenocarcinoma Correlating with m6A Modification and Necroptosis.

Qian Wu, Jin Li, Pei Wang, Qihang Peng, Zhongcui Kang, Yiting Deng, Jiayi Li, Dehong Yan, Feng Ge, Ying Chen.

  As an important member of the kindlin family, fermitin family member 1 (FERMT1) can interact with integrin and its aberrant expression involves multiple tumors. However, there are few systematic studies on FERMT1 in pancreatic carcinoma (PAAD). We used several public databases to analyze the expression level and clinicopathological characteristics of FERMT1 in PAAD. Meanwhile, the correlation between FERMT1 expression and diagnostic and prognostic value, methylation, potential biological function, immune infiltration, and sensitivity to chemotherapy drugs in PAAD patients were investigated. FERMT1 was significantly up-regulated in PAAD and correlated with T stage, and histologic grade. High FERMT1 expression was closely connected with poor prognosis and can be used to diagnose PAAD. Moreover, the methylation of six CpG sites of FERMT1 was linked to prognosis, and FERMT1 expression was significantly related to N6-methyladenosine (m6A) modification. Functional enrichment analysis revealed that FERMT1 co-expression genes participated in diverse biological functions including necroptosis. In addition, the expression of FERMT1 was associated with immune cell infiltration and the expression of immune checkpoint molecules. Finally, FERMT1 overexpression may be sensitive to chemotherapy drugs such as Palbociclib, AM-5992 and TAE-226. FERMT1 can serve as a diagnostic and prognostic marker of PAAD, which is connected with immune cell infiltration and the modulation of m6A and necroptosis.

Keywords:  FERMT1; immune infiltration; m6A modification; necroptosis; pancreatic adenocarcinoma; prognosis

DOI:  https://doi.org/10.3390/genes14030734
Carcinogenesis. 2023 Mar 31. pii: bgad016. [Epub ahead of print]

PLAGL2 promotes Snail expression and gastric cancer progression via UCA1/miR-145-5p/YTHDF1 axis.

Wen Chen, Qunjun He, Jingjing Liu, Ni Li, Kai Xiao, Honghui Chen.

   BACKGROUND: Although great progress has made in gastric cancer (GC) in the past years, the overall 5-year survival rate remains to be low for advanced GC patients. A recent study showed that PLAGL2 was increased in GC and enhanced the proliferation and metastasis of GC. Nevertheless, the underlying mechanism still needs to be investigated.
METHODS: Gene and protein expressions were assessed using RT-qPCR and western blot. The migration, proliferation and invasion of GC cells were examined using scratch assay, CCK-8 assay and Transwell assay, respectively. ChIP-PCR, dual luciferase assay, RIP-qPCR and CoiP were utilized to confirm the interaction among PLAGL2, UCA1, miR-145-5p and YTHDF1 as well as METTL3, YTHDF1 and eEF-2. A mouse xenograft model was used utilized to further confirm the regulatory network.
RESULTS: PLAGL2 bound to the upstream promoter of UCA1, which regulated YTHDF1 by sponging miR-145-5p. METTL3 can mediate the m6A modification level of Snail. YTHDF1 recognized m6A-modified Snail by interacting with eEF-2 and thus promoted Snail expression, which eventually induced epithelial-mesenchymal transition (EMT) in GC cells and metastasis of GC.
CONCLUSION: Overall, our study demonstrates that PLAGL2 enhances Snail expression and GC progression via the UCA1/miR-145-5p/YTHDF1 axis, suggesting that PLAGL2 may become a therapeutic target for GC treatment.

Keywords:  METTL3; PLAGL2; Snail; YTHDF1; gastric cancer; m 6A modification

DOI:  https://doi.org/10.1093/carcin/bgad016
Front Immunol. 2023 ;14 1162607

N6-methyladenosine reader YTHDF family in biological processes: Structures, roles, and mechanisms.

Lin Chen, Yang Gao, Simiao Xu, Jinxiong Yuan, Min Wang, Tianyu Li, Jun Gong.

  As the most abundant and conserved internal modification in eukaryote RNAs, N6-methyladenosine (m6A) is involved in a wide range of physiological and pathological processes. The YT521-B homology (YTH) domain-containing family proteins (YTHDFs), including YTHDF1, YTHDF2, and YTHDF3, are a class of cytoplasmic m6A-binding proteins defined by the vertebrate YTH domain, and exert extensive functions in regulating RNA destiny. Distinct expression patterns of the YTHDF family in specific cell types or developmental stages result in prominent differences in multiple biological processes, such as embryonic development, stem cell fate, fat metabolism, neuromodulation, cardiovascular effect, infection, immunity, and tumorigenesis. The YTHDF family mediates tumor proliferation, metastasis, metabolism, drug resistance, and immunity, and possesses the potential of predictive and therapeutic biomarkers. Here, we mainly summary the structures, roles, and mechanisms of the YTHDF family in physiological and pathological processes, especially in multiple cancers, as well as their current limitations and future considerations. This will provide novel angles for deciphering m6A regulation in a biological system.

Keywords:  M6A; YTHDF; biological process; cancer; clinical applications

DOI:  https://doi.org/10.3389/fimmu.2023.1162607
Vaccines (Basel). 2023 Feb 21. pii: 499. [Epub ahead of print]11(3):

M6A-Related Long Non-Coding RNA Displays Utility in Predicting Prognosis, Portraying the Tumor Immune Microenvironment and Guiding Immunotherapy in Pancreatic Ductal Adenocarcinoma.

Guangyu Xu, Yutian Ji, Lufeng Wang, Hao Xu, Chaodong Shen, Haihao Ye, Xiangchou Yang.

  N6-methyladenosine (m6A) lncRNA plays a pivotal role in cancer. However, little is known about its role in pancreatic ductal adenocarcinoma (PDAC) and its tumor immune microenvironment (TIME). Based on The Cancer Genome Atlas (TCGA) cohort, m6A-related lncRNAs (m6A-lncRNA) with prognostic value were filtered using Pearson analysis and univariate Cox regression analysis. Distinct m6A-lncRNA subtypes were divided using unsupervised consensus clustering. Least absolute shrinkage and selection operator (LASSO) Cox regression was applied to establish an m6A-lncRNA-based risk score signature. The CIBERSORT and ESTIMATE algorithms were employed to analyze the TIME. The expression pattern of TRAF3IP2-AS1 was examined using qRT-PCR. The influence of TRAF3IP2-AS1 knockdown on cell proliferation was estimated by performing CCK8, EdU and colony-formation assays. Flow cytometry was applied to measure the effect of TRAF3IP2-AS1 knockdown on cell cycle and apoptosis. The in vivo anti-tumor effect of TRAF3IP2-AS1 was validated in a tumor-bearing mouse model. Two m6A-lncRNA subtypes with different TIME features were clarified. A risk score signature was constructed as a prognostic predictor based on m6A-lncRNAs. The risk score also correlated with TIME characterization, which facilitated immunotherapy. Finally, the m6A-lncRNA TRAF3IP2-AS1 was proved to be a tumor suppressor in PDAC. We comprehensively demonstrated m6A-lncRNAs to be useful tools for prognosis prediction, TIME depiction and immunotherapeutic guidance in PDAC.

Keywords:  N6-methyladenosine; immune checkpoint blockade; immunotherapy; lncRNA; pancreatic ductal adenocarcinoma; tumor immune microenvironment; tumor immunology

DOI:  https://doi.org/10.3390/vaccines11030499
Ann Med. 2023 Dec;55(1): 1298-1316

Identification of m6A-associated LncRNAs as predict factors for the immune infiltration and prognosis of thyroid cancer.

Yongcheng Su, Beibei Xu, Jiangquan Li, Qianwen Shen, Ziyu Lei, Miaomiao Ma, Fuxing Zhang, Tianhui Hu.

   OBJECTIVE: This study aims to evaluate the prognostic value of m6A-associated long noncoding RNAs (lncRNAs) and their interaction with tumour microenvironment in thyroid cancer (THCA).
METHODS: The clinical and gene expression data of tumours from 502 patients with THCA and 58 adjacent normal tissues were retrieved from The Cancer Genome Atlas (TCGA)-THCA dataset. The Pearson test was utilized to identify potential m6A-associated lncRNAs (p < 0.001 and Pearson correlation coefficient > 0.4). Quantitative real-time polymerase chain reaction was performed to verify the expression levels of lncRNAs in tissues. MTT, EdU, colony formation and wound-healing assays were performed to determine the functions of m6A-associated lncRNAs in THCA cell proliferation and metastasis.
RESULTS: M6A-associated lncRNAs were identified in three cluster groups. A significant survival difference was found among them, with cluster 1 patients showing worse survival. Moreover, lower immune and estimate scores were correlated to poorer prognosis, and CD8+ T cell and memory CD4+ T cell levels were increased in cluster 1. Cluster 2, with better overall survival, had high expression of PD-L1 and CTLA-4. Eleven of the m6A-associated lncRNAs were screened to establish the risk model, including AC007365.1, AC008555.1, AC040160.1, AC064807.1, AC126773.4, AL023583.1, AL512306.2, EIF2AK3-DT, LINC00667, LYPLAL1-DT and MIR181A2HG. Based on the median risk score, THCA patients were stratified into low-risk and high-risk groups. Overall survival analysis showed a dramatic difference between the two groups. qRCR was performed to verify the expression levels of lncRNA (LYPLAL1-DT, EIF2AK3-DT and MIR181A2HG) in THCA and adjacent normal tissues. Furthermore, functional experiments showed that knockdown of MIR181A2HG obviously inhibited the proliferation and migration of papillary thyroid cancer (PTC) cells in vitro, whereas LYPLAL1-DT overexpression promoted PTC cell proliferation and migration.
CONCLUSIONS: Eleven of the m6A-associated lncRNAs were identified as a risk model to predict clinical outcomes and provide a novel and efficient immunotherapeutic strategy for THCA patients.Key messagesm6A-associated lncRNAs can be used to predict the clinical outcomes of thyroid cancer patients.An m6A-associated lncRNAs risk model, which can accurately evaluate the immune status and risk stratification in individual thyroid cancer patients, was established.Knockdown/overexpression of representative lncRNAs in the risk model significantly affected the proliferation and migration of papillary thyroid cancer cells.

Keywords:  immunotherapy; lncRNA; m6A; thyroid cancer

DOI:  https://doi.org/10.1080/07853890.2023.2192049
Cell Oncol (Dordr). 2023 Mar 28.

DNA 6mA demethylase ALKBH1 regulates DDX18 expression to promote proliferation of human head and neck squamous cell carcinoma.

Chengli Guo, Zheming Liu, Haojian Zhang.

   PURPOSE: Human head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Currently, surgical resection plus a combination of chemotherapy and radiotherapy is the standard treatment for HNSCC, and the 5-year survival rate of patients with HNSCC remains very low because of the higher incidence of metastasis with consequent recurrence. Here, we aimed to investigate the potential role of DNA N6-methyladenine (6mA) demethylase ALKBH1 in tumor cell proliferation in HNSCC.
METHODS: The expression of ALKBH1 in 10 pairs of HNSCC/normal tissues and 3 HNSCC cell lines were measured by qRT‒PCR and western blotting. Colony formation, flow cytometry, patient-derived HNSCC organoid assays were used to assess the role of ALKBH1 in HNSCC cell proliferation in cell lines and human HNSCC patients. MeDIP-seq, RNA sequencing, Dot blotting and western blotting were used to evaluate the regulatory effect of ALKBH1 on the expression of DEAD-box RNA helicase DDX18. A dual-luciferase reporter assay was used to assess the putative effect of DNA 6mA levels on DDX18 transcription.
RESULTS: ALKBH1 was highly expressed in HNSCC cells and patient tissues. Functional experiments revealed that ALKBH1 knockdown in SCC9, SCC25, and CAL27 cells inhibited their proliferation in vitro. Using patient-derived HNSCC organoid assay, we found that knockdown of ALKBH1 inhibited the proliferation and colony formation of HNSCC patients-derived organoids. Moreover, we found that ALKBH1 can enhance DDX18 expression by erasing DNA 6mA level and regulating its promoter activity. ALKBH1 deficiency blocked tumor cell proliferation by inhibiting DDX18 expression. Exogenous overexpression of DDX18 rescued the cell proliferation arrest caused by ALKBH1 knockdown.
CONCLUSION: Our data reveal the important role of ALKBH1 in regulating proliferation of HNSCC.

Keywords:  ALKBH1; DDX18; DNA 6mA; Head and neck carcinoma

DOI:  https://doi.org/10.1007/s13402-023-00800-1
Front Oncol. 2023 ;13 1063636

The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer.

Vincenza Ylenia Cusenza, Annalisa Tameni, Antonino Neri, Raffaele Frazzi.

  Most of our transcribed RNAs are represented by non-coding sequences. Long non-coding RNAs (lncRNAs) are transcripts with no or very limited protein coding ability and a length >200nt. They can be epigenetically modified. N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G) and 2'-O-methylation (Nm) are some of the lncRNAs epigenetic modifications. The epigenetic modifications of RNA are controlled by three classes of enzymes, each playing a role in a specific phase of the modification. These enzymes are defined as "writers", "readers" and "erasers". m6A and m5C are the most studied epigenetic modifications in RNA. These modifications alter the structure and properties, thus modulating the functions and interactions of lncRNAs. The aberrant expression of several lncRNAs is linked to the development of a variety of cancers and the epigenetic signatures of m6A- or m5C-related lncRNAs are increasingly recognized as potential biomarkers of prognosis, predictors of disease stage and overall survival. In the present manuscript, the most up to date literature is reviewed with the focus on m6A and m5C modifications of lncRNAs and their significance in cancer.

Keywords:  cancer; epigenetics; lncRNA; m5C; m6A

DOI:  https://doi.org/10.3389/fonc.2023.1063636
Nat Commun. 2023 Mar 27. 14(1): 1694

Rewired m6A epitranscriptomic networks link mutant p53 to neoplastic transformation.

An Xu, Mo Liu, Mo-Fan Huang, Yang Zhang, Ruifeng Hu, Julian A Gingold, Ying Liu, Dandan Zhu, Chian-Shiu Chien, Wei-Chen Wang, Zian Liao, Fei Yuan, Chih-Wei Hsu, Jian Tu, Yao Yu, Taylor Rosen, Feng Xiong, Peilin Jia, Yi-Ping Yang, Danielle A Bazer, Ya-Wen Chen, Wenbo Li, Chad D Huff, Jay-Jiguang Zhu, Francesca Aguilo, Shih-Hwa Chiou, Nathan C Boles, Chien-Chen Lai, Mien-Chie Hung, Zhongming Zhao, Eric L Van Nostrand, Ruiying Zhao, Dung-Fang Lee.

N6-methyladenosine (m6A), one of the most prevalent mRNA modifications in eukaryotes, plays a critical role in modulating both biological and pathological processes. However, it is unknown whether mutant p53 neomorphic oncogenic functions exploit dysregulation of m6A epitranscriptomic networks. Here, we investigate Li-Fraumeni syndrome (LFS)-associated neoplastic transformation driven by mutant p53 in iPSC-derived astrocytes, the cell-of-origin of gliomas. We find that mutant p53 but not wild-type (WT) p53 physically interacts with SVIL to recruit the H3K4me3 methyltransferase MLL1 to activate the expression of m6A reader YTHDF2, culminating in an oncogenic phenotype. Aberrant YTHDF2 upregulation markedly hampers expression of multiple m6A-marked tumor-suppressing transcripts, including CDKN2B and SPOCK2, and induces oncogenic reprogramming. Mutant p53 neoplastic behaviors are significantly impaired by genetic depletion of YTHDF2 or by pharmacological inhibition using MLL1 complex inhibitors. Our study reveals how mutant p53 hijacks epigenetic and epitranscriptomic machinery to initiate gliomagenesis and suggests potential treatment strategies for LFS gliomas.

DOI: https://doi.org/10.1038/s41467-023-37398-9
Cell Rep. 2023 Mar 22. pii: S2211-1247(23)00290-5. [Epub ahead of print]42(3): 112279

The N6-methyladenine DNA demethylase ALKBH1 promotes gastric carcinogenesis by disrupting NRF1 binding capacity.

Xiaohong Wang, Chi Chun Wong, Huarong Chen, Kaili Fu, Lingxue Shi, Hao Su, Shang Guo, Hongyan Gou, Xiaoxu Hu, Lianhai Zhang, Jiafu Ji, Jun Yu.

  DNA N6-methyladenine (6mA) is an epigenetic modification that regulates various biological processes. Here, we show that gastric cancer (GC) cells and tumors display a marked reduction in 6mA levels compared with normal gastric tissues and cells. 6mA is abundant in the surrounding transcription start sites and occurs at consensus motifs. Among the 6mA regulators, ALKBH1, a demethylase, is significantly overexpressed in GC tissues compared with adjacent normal tissues. Moreover, high ALKBH1 expression is associated with poor survival of patients with GC. ALKBH1 knockout in mice impairs chemically induced gastric carcinogenesis. Mechanistically, ALKBH1 mediates DNA 6mA demethylation to repress gene expression. In particular, the 6mA sites are enriched in NRF1 binding sequences and targeted for demethylation by ALKBH1. ALKBH1-induced 6mA demethylation inhibits NRF1-driven transcription of downstream targets, including multiple genes involved in the AMP-activated protein kinase (AMPK) signaling pathway. Accordingly, ALKBH1 suppresses AMPK signaling, causing a metabolic shift toward the Warburg effect, which facilitates tumorigenesis.

Keywords:  6mA; ALKBH1; AMPK signaling; CP: Cancer; CP: Molecular biology; NRF1; gastric cancer

DOI:  https://doi.org/10.1016/j.celrep.2023.112279
Nature. 2023 Mar 29.

A metabolic vulnerability of pancreatic cancer.

Daniel J Puleston.



Keywords:  Cancer; Medical research

DOI:  https://doi.org/10.1038/d41586-023-00848-x