bims-rimeca 2022-09-25 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022–09–25
thirty-one papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

Reduced N6-methyladenosine mediated by METTL3 acetylation promotes MTF1 expression and hepatocellular carcinoma cell growth.
New roles of N6-methyladenosine methylation system regulating the occurrence of non-alcoholic fatty liver disease with N6-methyladenosine-modified MYC.
Role of WTAP in Cancer: From Mechanisms to the Therapeutic Potential.
The role of RNA modification in hepatocellular carcinoma.
Novel Roles of RNA m6A Methylation Regulators in the Occurrence of Alzheimer's Disease and the Subtype Classification.
N6-Methyladenosine RNA Modification Landscape in the Occurrence and Recurrence of Nasopharyngeal Carcinoma.
m6A-modified circFOXK2 targets GLUT1 to accelerate oral squamous cell carcinoma aerobic glycolysis.
Interaction between m6A and ncRNAs and Its Association with Diseases.
The pattern of expression and prognostic value of key regulators for m7G RNA methylation in hepatocellular carcinoma.
m6A-related lncRNAs are potential biomarkers for the prognosis of COAD patients.
Pan-cancer analysis identifies YTHDF2 as an immunotherapeutic and prognostic biomarker.
RBM15 condensates modulate m6A modification of STYK1 to promote tumorigenesis.
The role and regulatory mechanism of m6A methylation in the nervous system.
Exercise training ameliorates myocardial phenotypes in heart failure with preserved ejection fraction by changing N6-methyladenosine modification in mice model.
Crosstalk of Oxidative Phosphorylation-Related Subtypes, Establishment of a Prognostic Signature and Immune Infiltration Characteristics in Colorectal Adenocarcinoma.
Molecular subtype identification and predictive power of N6-methyladenosine regulator in unexplained recurrent pregnancy loss.
Unveiling the m6A Methylation Regulator Links between Prostate Cancer and Periodontitis by Transcriptomic Analysis.
RNA modification writer expression profiles predict clinical outcomes and guide neoadjuvant immunotherapy in non-small cell lung cancer.
Cross-talk of four types of RNA modification proteins with adenosine reveals the landscape of multivariate prognostic patterns in breast cancer.
m7G regulator-mediated molecular subtypes and tumor microenvironment in kidney renal clear cell carcinoma.
N6-methyladenosine modification of circ_0003215 suppresses the pentose phosphate pathway and malignancy of colorectal cancer through the miR-663b/DLG4/G6PD axis.
Implications of m6A methylation and microbiota interaction in non-small cell lung cancer: From basics to therapeutics.
YAP 5-methylcytosine modification increases its mRNA stability and promotes the transcription of exosome secretion-related genes in lung adenocarcinoma.
Expression and prognostic signatures of m6A-related lncRNAs in hepatocellular carcinoma.
Prognostic value of m6A regulators and the nomogram construction in glioma patients.
Identification and validation of the role of c-Myc in head and neck squamous cell carcinoma.
Slow RNAPII Transcription Elongation Rate, Low Levels of RNAPII Pausing, and Elevated Histone H1 Content at Promoters Associate with Higher m6A Deposition on Nascent mRNAs.
Immune dysregulation and RNA N6-methyladenosine modification in sepsis.
MicroRNA-1306-5p Regulates the METTL14-Guided m6A Methylation to Repress Acute Myeloid Leukemia.
Integrated bioinformatical analysis, machine learning and in vitro experiment-identified m6A subtype, and predictive drug target signatures for diagnosing renal fibrosis.
NAT10: An RNA cytidine transferase regulates fatty acid metabolism in cancer cells.

Chem Biodivers. 2022 Sep 23.

Reduced N6-methyladenosine mediated by METTL3 acetylation promotes MTF1 expression and hepatocellular carcinoma cell growth.

Ying Yang, Qian Qian Cai, Li Sheng Fu, Yi Wei Dong, Fei Fan, Xing Zhong Wu.

  N6-methyladenosine (m6A), one of the post-transcriptional modifications of RNA, is important in hepatocellular carcinoma (HCC). However, the mechanism of its regulation remains elusive. We here show that exposure of HCC cells to sulfatide significantly reduced the total mRNA m6A modification. Interestingly, METTL3 protein was robustly acetylated and the binding of METTL3 to MTF1 mRNA, METTL14 or WTAP was weakened in cells treated with sulfatide. Further investigation of the METTL3 complex revealed recruitment of the deacetylase scaffold SIN3B, but a diminished level of histone deacetylase HDAC2, which might enhance the acetylation of METTL3. The m6A abundance in MTF1 mRNA was markedly decreased in cells after sulfatide treatment. The expression of MTF1, a zinc-dependent transcription factor, was significantly strengthened with reduced m6A modification. Sulfatide prolonged the half-life of MTF1 mRNA, while the mutation (A to C) on 7 methylation sites in the 3'UTR of MTF1 mRNA enhanced MTF1 mRNA stability. 3-deaza-adenosine, an m6A methylation inhibitor, significantly reduced the m6A modification of MTF1 mRNA but extended its half-life time. Importantly, overexpression of MTF1 prompted HCC cell proliferation and was associated with poor prognosis. In conclusion, the METTL3-METTL14-WTAP complex was regulated by acetylation induced by sulfatide to control MTF1 m6A methylation and its mRNA transcription, which was important for the tumor growth and migration of HCC.

Keywords:  METTL3 complex; MTF1; N6-methyladenosine; methyltransferase; sulfatide

DOI:  https://doi.org/10.1002/cbdv.202200333
Front Pharmacol. 2022 ;13 973116

New roles of N6-methyladenosine methylation system regulating the occurrence of non-alcoholic fatty liver disease with N6-methyladenosine-modified MYC.

Wenli Cheng, Min Li, Luyun Zhang, Cheng Zhou, Susu Yu, Xinyue Peng, Wenji Zhang, Wenjuan Zhang.

  Non-alcoholic fatty liver disease (NAFLD) has become a major chronic disease in contemporary society, affected by N6-methyladenosine (m6A) RNA methylation, one of the most common RNA modifications. Compared with healthy control, m6A RNA methyltransferase 3 (METTL3) and METTL14 increased, while Wilms tumor 1-associated protein (WTAP) and RNA-binding motif protein 15 (RBM15) decreased significantly in NAFLD, and the m6A demethylases fat mass and obesity-associated protein (FTO) elevated. Meanwhile, the m6A binding proteins, YT521-B homology (YTH) domain-containing 1 (YTHDC1), YTHDC2, insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), and HNRNPA2B1 were decreased, while eukaryotic translation initiation factor 3 subunit H (EIF3H) was increased significantly. All these changes of m6A regulators had significant differences between healthy control and NAFLD, but no differences between the NAFL and NASH group. The expression level of RBM15, HNRNPC, and HNRNPA2B1 were related to body fat index. RBM15, YTHDC2, HNRNPC, HNRNPA2B1, and EIF3H were related to steatosis. Also, KIAA1429 and YTH domain family 1 (YTHDF1) were related to lobular inflammation. Taken together, m6A regulators were involved in the occurrence of NAFLD. More importantly, abnormal MYC was determined as a key link to m6A regulation of NAFLD. The higher MYC mRNA level was accompanied by higher HDL cholesterol and unsaturated fatty acid proportions, as well as lower fat mass, glucose, and transaminase. Taken together, dysregulation of m6A methylation caused steatosis and fibrosis, affecting the occurrence of NAFLD, and MYC might be its potential target.

Keywords:  MYC; N6-methyladenosine (m6A); RNA methylation; non-alcoholic fatty liver disease (NAFLD); non-alcoholic steatohepatitis (NASH)

DOI:  https://doi.org/10.3389/fphar.2022.973116
Biomolecules. 2022 Sep 02. pii: 1224. [Epub ahead of print]12(9):

Role of WTAP in Cancer: From Mechanisms to the Therapeutic Potential.

Yongfei Fan, Xinwei Li, Huihui Sun, Zhaojia Gao, Zheng Zhu, Kai Yuan.

  Wilms' tumor 1-associating protein (WTAP) is required for N6-methyladenosine (m6A) RNA methylation modifications, which regulate biological processes such as RNA splicing, cell proliferation, cell cycle, and embryonic development. m6A is the predominant form of mRNA modification in eukaryotes. WTAP exerts m6A modification by binding to methyltransferase-like 3 (METTL3) in the nucleus to form the METTL3-methyltransferase-like 14 (METTL14)-WTAP (MMW) complex, a core component of the methyltransferase complex (MTC), and localizing to the nuclear patches. Studies have demonstrated that WTAP plays a critical role in various cancers, both dependent and independent of its role in m6A modification of methyltransferases. Here, we describe the recent findings on the structural features of WTAP, the mechanisms by which WTAP regulates the biological functions, and the molecular mechanisms of its functions in various cancers. By summarizing the latest WTAP research, we expect to provide new directions and insights for oncology research and discover new targets for cancer treatment.

Keywords:  WTAP; cancer; m6A; methyltransferase; molecular mechanisms

DOI:  https://doi.org/10.3390/biom12091224
Front Pharmacol. 2022 ;13 984453

The role of RNA modification in hepatocellular carcinoma.

Qiang Feng, Dongxu Wang, Tianyi Xue, Chao Lin, Yongjian Gao, Liqun Sun, Ye Jin, Dianfeng Liu.

  Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.

Keywords:  RNA modification; hepatocellular carcinoma; m1A; m3C; m5C; m6A; m7G; ψ

DOI:  https://doi.org/10.3389/fphar.2022.984453
Int J Mol Sci. 2022 Sep 15. pii: 10766. [Epub ahead of print]23(18):

Novel Roles of RNA m6A Methylation Regulators in the Occurrence of Alzheimer's Disease and the Subtype Classification.

Min Li, Wenli Cheng, Luyun Zhang, Cheng Zhou, Xinyue Peng, Susu Yu, Wenjuan Zhang.

  Alzheimer's disease (AD) is one of the most common forms of dementia, closely related to epigenetic factors. N6-methyladenosine (m6A) is the most abundant RNA modification, affecting the pathogenesis and development of neurodegenerative diseases. This study was the first exploration of the combined role of 25 common m6A RNA methylation regulators in AD through the integrated bioinformatics approaches. The 14 m6A regulators related to AD were selected by analyzing differences between AD patients and normal controls. Based on the selected m6A regulators, AD patients could be well classified into two m6A models using consensus clustering. The two clusters of patients had different immune profiles, and m6A regulators were associated with the components of immune cells. Additionally, there were 19 key AD genes obtained by screening differential genes through weighted gene co-expression network and least absolute shrinkage and selection operator regression analysis, which were highly associated with important m6A regulators during the occurrence of AD. More interestingly, NOTCH2 and NME1 could be potential targets for m6A regulation of AD. Taken together, these findings indicate that dysregulation of m6A methylation affects the occurrence of AD and is vital for the subtype classification and immune infiltration of AD.

Keywords:  Alzheimer’s disease; biomarker; consensus clustering; m6A methylation

DOI:  https://doi.org/10.3390/ijms231810766
World J Oncol. 2022 Aug;13(4): 205-215

N6-Methyladenosine RNA Modification Landscape in the Occurrence and Recurrence of Nasopharyngeal Carcinoma.

Yu Min Wang, Zhou Ying Peng, Lu Yuan Zhang, Ya Xuan Wang, Ruo Hao Fan, Hua Zhang, Wei Hong Jiang.

   Background: Nasopharyngeal carcinoma (NPC) is a type of squamous head and neck cancer with variable geographic distributions, with the highest incidence in Southeast Asia. Its primary treatment is radiotherapy due to its high radio sensitivity. However, the N6-methyladenosine (m6A) landscape in NPC, including recurrent NPC, has not been reported.
Methods: In this study, m6A RNA immunoprecipitation (RIP) sequencing and microarray sequencing were performed on 12 tissue samples tissues of patients with primary and recurrent NPC. The expression profiles of m6A-related and non-coding RNAs were constructed and explored. Then, function experiments were performed to evaluate the effects of methyltransferase (METTL)3, METTL14 and WT1 associated protein (WTAP) on progressions of NPC. Finally, immunohistochemistry (IHC) and survival analysis were performed to confirm the correlation between METTL3, METTL14 and WTAP and NPC patients' clinical outcomes.
Results: This study mapped m6A RNA modification and RNA expression profiles in normal nasopharynx, primary NPC, and recurrent NPC tissues. This study also explored the role of m6A modificators in NPC development and recurrence. METTL3, METTL14, and WTAP could promote invasion and metastasis of NPC, and that these three proteins could induce radiotherapy resistance in NPC cells through DNA repair. Moreover, we found that METTL3, METTL14, and WTAP promoted an increase in exosomes within NPC microenvironment.
Conclusions: This study suggests that the alteration of m6A modification in primary and recurrent NPCs may play an important role in the development and progression of NPC.

Keywords:  N6-methyladenosine; Nasopharyngeal carcinoma; Occurrence; RNA modification; Recurrence

DOI:  https://doi.org/10.14740/wjon1491
Cancer Gene Ther. 2022 Sep 20.

m6A-modified circFOXK2 targets GLUT1 to accelerate oral squamous cell carcinoma aerobic glycolysis.

Yameng Cui, Jingwen Liu, Lina Liu, Xiaozhou Ma, Yu Gui, Hao Liu, Wei Zhao.

N6-methyladenosine (m6A) is an abundant nucleotide modification in mRNA, and its emerging roles have been gradually identified. However, the potential function of m6A and m6A-modified circular RNA (circRNA) is still unclear. Here, m6A-circRNA epitranscriptomic microarray analysis revealed a high-expressed m6A-modified circFOXK2 (hsa_circ_0000816, from FOXK2 gene) in oral squamous cell carcinoma (OSCC). For the biofunctions of OSCC, results revealed that circFOXK2 promoted the malignant phenotypes of OSCC cells. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) demonstrated that a remarkable m6A modified site was installed on glucose transporter 1 (GLUT1) mRNA. Mechanistically, circFOXK2 promoted the GLUT1 mRNA stability through cooperating with insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) in a m6A-dependent manner. In summary, the present study explored the oncogenic role of m6A-modified circFOXK2 in OSCC through the m6A-dependent IGF2BP3/GLUT1 axis, indicating a potential therapeutic target for OSCC.

DOI: https://doi.org/10.1038/s41417-022-00526-6
Cytogenet Genome Res. 2022 Sep 19. 1-17

Interaction between m6A and ncRNAs and Its Association with Diseases.

Shuangyi Chen, Jianxiang Dong, Xinjie Luo, Zixiong Nie, Shanshan Lu, Hanqi Liu, Junwen Liu.

  Noncoding RNAs (ncRNA) are a kind of endogenous RNA that regulate many vital bioprocesses with limited ability to encode polypeptides. Most of them are involved in transcriptional and posttranscriptional regulations, thus showing some biological effects. N6-methyladenosine (m6A) RNA modification is a reversible modification that adjusts RNA's functions and stability. The enzymes that regulate m6A can be divided into "writers," "readers," and "erasers." Mechanically, m6A modification of microRNA is mainly identified by DGVR8, participating in the processing of primary micro-RNAs, while m6A modification on long noncoding RNA (lnc-RNA) can change its spatial structure and stability to regulate its RNA- or protein-binding ability. The m6A-modified lnc-RNA and circular RNA can act as competing endogenous RNAs, sponge downstream miRNA. Moreover, ncRNA can also regulate m6A level of downstream molecules. Here, we elaborate on recent advances about pathways and underlying molecular mechanisms of how the interaction between m6A and ncRNA is involved in the occurrence and development of various diseases, especially cancer.

Keywords:  Cancer; Disease; Eraser; Reader; Writer; m6A; ncRNA

DOI:  https://doi.org/10.1159/000526035
Front Genet. 2022 ;13 894325

The pattern of expression and prognostic value of key regulators for m7G RNA methylation in hepatocellular carcinoma.

Jianxing Chen, Shibin Yao, Zhijuan Sun, Yanjun Wang, Jili Yue, Yongkang Cui, Chengping Yu, Haozhi Xu, Linqiang Li.

  N7-methylguanosine (m7G) modification on internal RNA positions plays a vital role in several biological processes. Recent research shows m7G modification is associated with multiple cancers. However, in hepatocellular carcinoma (HCC), its implications remain to be determined. In this place, we need to interrogate the mRNA patterns for 29 key regulators of m7G RNA modification and assess their prognostic value in HCC. Initial, the details from The Cancer Genome Atlas (TCGA) database concerning transcribed gene data and clinical information of HCC patients were inspected systematically. Second, according to the mRNA profiles of 29 m7G RNA methylation regulators, two clusters (named 1 and 2, respectively) were identified by consensus clustering. Furthermore, robust risk signature for seven m7G RNA modification regulators was constructed. Last, we used the Gene Expression Omnibus (GEO) dataset to validate the prognostic associations of the seven-gene risk signature. We figured out that 24/29 key regulators of m7G RNA modification varied remarkably in their grades of expression between the HCC and the adjacent tumor control tissues. Cluster one compared with cluster two had a substandard prognosis and was also positively correlated with T classification (T), pathological stage, and vital status (fustat) significantly. Consensus clustering results suggested the expression pattern of m7G RNA modification regulators was correlated with the malignancy of HCC strongly. In addition, cluster one was extensively enriched in metabolic-related pathways. Seven optimal genes (METTL1, WDR4, NSUN2, EIF4E, EIF4E2, NCBP1, and NCBP2) were selected to establish the risk model for HCC. Indicating by further analyses and validation, the prognostic model has fine anticipating command and this probability signature might be a self supporting presage factor for HCC. Finally, a new prognostic nomogram based on age, gender, pathological stage, histological grade, and prospects were established to forecast the prognosis of HCC patients accurately. In essence, we detected association of HCC severity and expression levels of m7G RNA modification regulators, and developed a risk score model for predicting prognosis of HCC patients' progression.

Keywords:  bioinformatics; hepatocellular carcinoma; m7G; prognosis; risk signature

DOI:  https://doi.org/10.3389/fgene.2022.894325
Front Oncol. 2022 ;12 920023

m6A-related lncRNAs are potential biomarkers for the prognosis of COAD patients.

Chenyang Xu, Tingting He, Xinxin Shao, Ling Gao, Lei Cao.

   Background: Colon adenocarcinoma (COAD) is the most common subtype of colon cancer. However, the 5-year survival rate of COAD patients remains unsatisfactory. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play essential roles in the occurrence and development of COAD. Herein, we are committed to establish and validate a prognostic m6A-related lncRNA signature.
Methods: We obtained m6A-related lncRNAs by coexpression. The m6A-related lncRNA risk signature (m6ALncSig) was developed via univariate, LASSO, and multivariate Cox regression analyses. Kaplan-Meier (KM) survival curves, gene set enrichment analysis (GSEA), and nomogram generation were conducted to assess m6ALncSig. In addition, the potential immunotherapeutic signatures were also discussed. Real-time PCR and CCK8 analysis were performed to evaluate the expression and functions of lncRNA UBA6-AS1, which was selected.
Results: The risk signature comprising 14 m6A-related lncRNAs (m6ALncSig) was established, which possessed a superior predictive ability of prognosis. Meanwhile, m6ALncSig was linked to immune cell infiltration. The level of UBA6-AS1 expression was validated in 17 pairs of COAD samples. In cell function experiments, UBA6-AS1 knockdown attenuated cell proliferation capacity.
Conclusions: Collectively, m6ALncSig could serve as an independent predictive factor for COAD and accurately estimate the outcome for COAD patients. Importantly, UBA6-AS1 was first identified as an oncogene in COAD.

Keywords:  biomarker; cell function assays; colon adenocarcinoma; lncRNA; m6A modification

DOI:  https://doi.org/10.3389/fonc.2022.920023
Front Cell Dev Biol. 2022 ;10 954214

Pan-cancer analysis identifies YTHDF2 as an immunotherapeutic and prognostic biomarker.

Weiwei Liu, Chaoqun Liu, Jia You, Zilin Chen, Cheng Qian, Wandie Lin, Lina Yu, Lele Ye, Liang Zhao, Rui Zhou.

  Background: N6-methyladenosine (m6A) modification is a dynamic and reversible post-transcriptional RNA modification prevalent in eukaryotic cells. YT521-B homology domain family 2 (YTHDF2) has been identified as a member of m6A reader protein involving in many vital biological processes, whereas its role and functional mechanisms in cancers remain unclear. Methods: Bioinformatics analyses were performed on multiple databases including GTEx, TCGA, GEO and Cbioportal to explore the connection between YTHDF2 expression and its genomic changes including tumor mutation burden, microsatellite instability and mismatch repair in 33 different cancer types. We also investigated the association of YTHDF2 expression with prognosis, immune infiltration, tumor microenvironment, immune checkpoints and chemokines. Besides, the correlation of YTHDF2 expression with copy number variation and promoter methylation was also studied in tumors compared with normal tissues. At last, we analyzed the protein-protein interacting network and related genes of YTHDF2 to enrich its potential functional mechanism in tumor development and progression. Real-time qPCR was used to verify the expression of YTHDF2-related genes in colorectal cancer cells, and immunohistochemical staining was adopted to verify immune infiltration in tissue sections from 51 hepatocellular carcinoma patients. Results: YTHDF2 was overexpressed in a majority of tumor types and associated with their poor overall survival, progression-free interval, and disease-specific survival. The correlation of YTHDF2 expression with tumor mutation burden, microsatellite instability and mismatch repair was also detected in most of the tumor types. Moreover, YTHDF2 might participate in the immune regulation through influencing the expression of immune checkpoint genes and the infiltration of immunocytes in tumor microenvironment. Notably, we demonstrated a positive correlation between YTHDF2 expression and the infiltration of CD8+ T cells and macrophages in many tumors, and it was verified in 51 clinic hepatocellular carcinoma tissues. In addition, the involvement of YTHDF2 in "Spliceosome" and "RNA degradation" were two potential functional mechanisms underlying its influence on tumor progression. The regulation of YTHDF2 on predicted genes has been verified in CRC cells. Conclusion: YTHDF2 might be a new therapeutic target and a potential biomarker of cancer immune evasion and poor prognosis.

Keywords:  YTHDF2; immune cell infiltration; immunotherapy; prognosis; tumor microenvironment

DOI:  https://doi.org/10.3389/fcell.2022.954214
Comput Struct Biotechnol J. 2022 ;20 4825-4836

RBM15 condensates modulate m6A modification of STYK1 to promote tumorigenesis.

Amin Jiang, Siwei Zhang, Xinyu Wang, Dong Li.

  RBM15 expression is recurrently upregulated in several types of malignant tissues, and its high expression level is typically associated with poor prognosis. However, whether and how RBM15 is involved in the tumor progression remains unclear. In this study, we found that overexpressing RBM15 in NIH3T3 cells was able to enhance proliferation rate in vitro and induced subcutaneous tumor formation in vivo. Moreover, we imaged the subcellular localization of RBM15 with our home-built structured illumination super-resolution microscopy, and revealed that RBM15 formed substantial condensates dispersed in the nucleus, undergoing dynamic fusion and fission activities. These condensates were partially colocalized with m6A-modified transcripts in the nucleus. In addition, we confirmed that RBM15 formed "liquid-like" droplets in a protein/salt concentration-dependent manner in vitro, and the addition of RNA further enhanced its phase-separation propensity. To identify downstream targets of RBM15, we performed meRIP-seq and RNA-seq, revealing that RBM15 preferentially bound to and promoted the m6A modification on the mRNA of Serine/threonine/tyrosine kinase 1 (STYK1), thereby enhancing its stability. The upregulated STYK1 expression caused MAPK hyperactivation, thereby leading to oncogenic transformation of NIH3T3 cells.

Keywords:  N6-methyladenine modification; Phase separation; RBM15; STYK1

DOI:  https://doi.org/10.1016/j.csbj.2022.08.068
Front Genet. 2022 ;13 962774

The role and regulatory mechanism of m6A methylation in the nervous system.

Lingling Jiang, Xiaoheng Li, Shasha Wang, Zengqiang Yuan, Jinbo Cheng.

  N6-methyladenosine (m6A) modification regulates RNA translation, splicing, transport, localization, and stability at the post-transcriptional level. The m6A modification has been reported to have a wide range of effects on the nervous system, including neurogenesis, cerebellar development, learning, cognition, and memory, as well as the occurrence and development of neurological disorders. In this review, we aim to summarize the findings on the role and regulatory mechanism of m6A modification in the nervous system, to reveal the molecular mechanisms of neurodevelopmental processes, and to promote targeted therapy for nervous system-related diseases.

Keywords:  development; m6A methylation; mechanism; nervous system; neurological disorders

DOI:  https://doi.org/10.3389/fgene.2022.962774
Front Cell Dev Biol. 2022 ;10 954769

Exercise training ameliorates myocardial phenotypes in heart failure with preserved ejection fraction by changing N6-methyladenosine modification in mice model.

Kai Liu, Wenhao Ju, Shengrong Ouyang, Zhuo Liu, Feng He, Jingyi Hao, Hongyan Guan, Jianxin Wu.

  Heart failure with preserved ejection fraction (HFpEF) shows complicated and not clearly defined etiology and pathogenesis. Although no pharmacotherapeutics have improved the survival rate in HFpEF, exercise training has become an efficient intervention to improve functional outcomes. Here, we investigated N6-methyladenosine (m6A) RNA methylation modification in a "two-hit" mouse model with HFpEF and HFpEF with exercise (HFpEF + EXT). The manner of m6A in HFpEF and HFpEF + EXT hearts was explored via m6A-specific methylated RNA immunoprecipitation followed by high-throughput and RNA sequencing methods. A total amount of 3992 novel m6A peaks were spotted in HFpEF + EXT, and 426 differently methylated sites, including 371 hypermethylated and 55 hypomethylated m6A sites, were singled out for further analysis (fold change >2, p < 0.05). According to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, unique m6A-modified transcripts in HFpEF + EXT were associated with apoptosis-related pathway and myocardial energy metabolism. HFpEF + EXT had higher total m6A levels and downregulated fat mass and obesity-related (FTO) protein levels. Overexpression of FTO cancels out the benefits of exercise in HFpEF + EXT mice by promoting myocyte apoptosis, myocardial fibrosis and myocyte hypertrophy. Totally, m6A is a significant alternation of epitranscriptomic processes, which is also a potentially meaningful therapeutic target.

Keywords:  FTO; HFPEF; apoptosis; m6A; myocardial energy metabolism

DOI:  https://doi.org/10.3389/fcell.2022.954769
Cancers (Basel). 2022 Sep 16. pii: 4503. [Epub ahead of print]14(18):

Crosstalk of Oxidative Phosphorylation-Related Subtypes, Establishment of a Prognostic Signature and Immune Infiltration Characteristics in Colorectal Adenocarcinoma.

Can Wang, Guoliang Cui, Dan Wang, Min Wang, Qi Chen, Yunshan Wang, Mengjie Lu, Xinyi Tang, Bolin Yang.

  Oxidative phosphorylation (OXPHOS) is an emerging target in cancer therapy. However, the prognostic signature of OXPHOS in colorectal adenocarcinoma (COAD) remains non-existent. We comprehensively investigated the expression pattern of OXPHOS-related genes (ORGs) in COAD from public databases. Based on four ORGs, an OXPHOS-related prognostic signature was established in which COAD patients were assigned different risk scores and classified into two different risk groups. It was observed that the low-risk group had a better prognosis but lower immune activities including immune cells and immune-related function in the tumor microenvironment. Combining with relevant clinical features, a nomogram for clinical application was also established. Receiver operating characteristic (ROC) and calibration curves were constructed to demonstrate the predictive ability of this risk signature. Moreover, a higher risk score was significantly positively correlated with higher tumor mutation burden (TMB) and generally higher gene expression of immune checkpoint, N6-methyladenosine (m6A) RNA methylation regulators and mismatch repair (MMR) related proteins. The results also indicated that the high-risk group was more sensitive to immunotherapy and certain chemotherapy drugs. In conclusion, OXPHOS-related prognostic signature can be utilized to better understand the roles of ORGs and offer new perspectives for clinical prognosis and personalized treatment.

Keywords:  colorectal adenocarcinoma; oxidative phosphorylation; prognosis predicting; tumor microenvironment

DOI:  https://doi.org/10.3390/cancers14184503
Front Genet. 2022 ;13 925652

Molecular subtype identification and predictive power of N6-methyladenosine regulator in unexplained recurrent pregnancy loss.

Jiahui Huo, Qian Chen, Yutong Zhang, Nuo Li, Zhiyu Fu, Ning Ma, Nan Zheng, Nan Cui, Lu Li.

  The etiology of recurrent pregnancy loss (RPL) is complicated and effective clinical preventive measures are lacking. Identifying biomarkers for RPL has been challenging, and to date, little is known about the role of N6-methyladenosine (m6A) regulators in RPL. Expression data for m6A regulators in 29 patients with RPL and 29 healthy controls were downloaded from the Gene Expression Omnibus (GEO) database. To establish a diagnostic model for unexplained RPL, differential gene expression analysis was conducting for 36 m6A regulators using least absolute shrinkage and selection operator (LASSO) regression. Unsupervised cluster analysis was conducted on hub genes, and probable mechanisms were explored using gene set enrichment analysis (GSEA) and gene ontology (GO) analysis. Correlations between m6A-related differentially expressed genes and immune infiltration were analyzed using single-sample GSEA. A total of 18 m6A regulators showed significant differences in expression in RPL: 10 were upregulated and eight were downregulated. Fifteen m6A regulators were integrated and used to construct a diagnostic model for RPL that had good predictive efficiency and robustness in differentiating RPL from control samples, with an overall area under the curve (AUC) value of 0.994. Crosstalk was identified between 10 hub genes, miRNAs, and transcription factors (TFs). For example, YTHDF2 was targeted by mir-1-3p and interacted with embryonic development-related TFs such as FOXA1 and GATA2. YTHDF2 was also positively correlated with METTL14 (r = 0.5983, p < 0.001). Two RPL subtypes (Cluster-1 and Cluster-2) with distinct hub gene signatures were identified. GSEA and GO analysis revealed that the differentially expressed genes were mainly associated with immune processes and cell cycle signaling pathway (normalized enrichment score, NES = -1.626, p < 0.001). Immune infiltration was significantly higher in Cluster-1 than in Cluster-2 (p < 0.01). In conclusion, we demonstrated that m6A modification plays a critical role in RPL. We also developed and validated a diagnostic model for RPL prediction based on m6A regulators. Finally, we identified two distinct RPL subtypes with different biological processes and immune statuses.

Keywords:  N6-methyladenosine; YTHDF2; diagnostic model; immune cell infiltration; recurrent pregnancy loss

DOI:  https://doi.org/10.3389/fgene.2022.925652
Dis Markers. 2022 ;2022 4030046

Unveiling the m6A Methylation Regulator Links between Prostate Cancer and Periodontitis by Transcriptomic Analysis.

Dexin Ding, Guobin Liu, Jianing Gao, Muyang Cao.

Objective: To identify the N6-methyladenosine (m6A) methylation regulator genes linking prostate adenocarcinoma (PRAD) and periodontitis (PD).
Materials and Methods: PD and TCGA-PRAD GEO datasets were downloaded and analyzed through differential expression analysis to determine the differentially expressed genes (DEGs) deregulated in both conditions. Twenty-three m6A RNA methylation-related genes were downloaded in total. The m6A-related genes that overlapped between PRAD and PD were identified as crosstalk genes. Survival analysis was performed on these genes to determine their prognostic values in the overall survival outcomes of prostate cancer. The KEGG pathways were the most significantly enriched by m6A-related crosstalk genes. We also performed lasso regression analysis and univariate survival analysis to identify the most important m6A-related crosstalk genes, and a protein-protein interaction (PPI) network was built from these genes.
Results: Twenty-three m6A methylation-related regulator genes were differentially expressed and deregulated in PRAD and PD. Among these, seven (i.e., ALKBH5, FMR1, IGFBP3, RBM15B, YTHDF1, YTHDF2, and ZC3H13) were identified as m6A-related cross-talk genes. Survival analysis showed that only the FMR1 gene was a prognostic indicator for PRAD. All other genes had no significant influence on the overall survival of patients with PRAD. Lasso regression analysis and univariate survival analysis identified four m6A-related cross-talk genes (i.e., ALKBH5, IGFBP3, RBM15B, and FMR1) that influenced risk levels. A PPI network was constructed from these genes, and 183 genes from this network were significantly enriched in pathogenic Escherichia coli infection, p53 signaling pathway, nucleocytoplasmic transport, and ubiquitin-mediated proteolysis.
Conclusion: Seven m6A methylation-related genes (ALKBH5, FMR1, IGFBP3, RBM15B, YTHDF1, YTHDF2, and ZC3H13) were identified as cross-talk genes between prostate cancer and PD.

DOI: https://doi.org/10.1155/2022/4030046
EBioMedicine. 2022 Sep 15. pii: S2352-3964(22)00450-9. [Epub ahead of print]84 104268

RNA modification writer expression profiles predict clinical outcomes and guide neoadjuvant immunotherapy in non-small cell lung cancer.

Bolun Zhou, Fenglong Bie, Ruochuan Zang, Moyan Zhang, Peng Song, Lei Liu, Yue Peng, Guangyu Bai, Jun Zhao, Shugeng Gao.

   BACKGROUND: RNA modifications, including adenosine-to-inosine RNA editing, alternative polyadenylation, m1A and m6A, play a significant role in tumorigenesis and tumor immunity. However, the functions of RNA modification enzymes (writers) in immunotherapy and tumor microenvironment (TME) remain unknown.
METHODS: Nonnegative matrix factorization clustering was applied to identify RNA modification clusters in lung adenocarcinoma, one of the most prevalent subtypes of non-small cell lung cancer (NSCLC). CIBERSORT and ESTIMATE algorithms were performed to depict TME characteristics. Additionally, a scoring system called Writer-Score was established to quantify RNA modification patterns and subsequently predict clinical outcomes. We subsequently used RNA sequencing, targeted DNA sequencing and multiplex immunofluorescence to further evaluate the efficacy of Writer-Score in NSCLC patients receiving neoadjuvant immunotherapy.
FINDINGS: We identified three distinct RNA modification clusters and two DEGclusters, which were shown to be strongly associated with a variety of TME features and biological processes. Additionally, the Writer-Score served as an important factor in post-transcriptional events and immunotherapy. The Writer-Score was capable of properly predicting the prognosis of NSCLC patients receiving neoadjuvant PD-1 inhibitor therapy.
INTERPRETATION: Our work systematically analyzed four types of RNA modifications and constructed a scoring system to guide neoadjuvant immunotherapy in NSCLC, which highlighted the writers' roles in post-transcriptional events, TME and neoadjuvant immunotherapy.
FUNDING: A full list of funding bodies that supported this study can be found in the Acknowledgements section.

Keywords:  Neoadjuvant immunotherapy; Non-small cell lung cancer; RNA modification; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.ebiom.2022.104268
Front Genet. 2022 ;13 943378

Cross-talk of four types of RNA modification proteins with adenosine reveals the landscape of multivariate prognostic patterns in breast cancer.

Xuliren Wang, Fangdie Ye, Min Xiong, Bingqiu Xiu, Weiru Chi, Qi Zhang, Jingyan Xue, Ming Chen, Liyi Zhang, Jiong Wu, Yayun Chi.

  Background: Breast cancer (BC) is the most common malignant tumour, and its heterogeneity is one of its major characteristics. N6-methyladenosine (m6A), N1-methyladenosine (m1A), alternative polyadenylation (APA), and adenosine-to-inosine (A-to-I) RNA editing constitute the four most common adenosine-associated RNA modifications and represent the most typical and critical forms of epigenetic regulation contributing to the immunoinflammatory response, tumorigenesis and tumour heterogeneity. However, the cross-talk and potential combined profiles of these RNA-modified proteins (RMPs) in multivariate prognostic patterns of BC remain unknown. Methods: A total of 48 published RMPs were analysed and found to display significant expression alterations and genomic mutation rates between tumour and normal tissues in the TCGA-BRCA cohort. Data from 4188 BC patients with clinical outcomes were downloaded from the Gene Expression Omnibus (GEO), the Cancer Genome Atlas (TCGA), and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), normalized and merged into one cohort. The prognostic value and interconnections of these RMPs were also studied. The four prognosis-related genes (PRGs) with the greatest prognostic value were then selected to construct diverse RMP-associated prognostic models through univariate Cox (uniCox) regression analysis, differential expression analysis, Least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox (multiCox) regression. Alterations in biological functional pathways, genomic mutations, immune infiltrations, RNAss scores and drug sensitivities among different models, as well as their prognostic value, were then explored. Results: Utilizing a large number of samples and a comprehensive set of genes contributing to adenosine-associated RNA modification, our study revealed the joint potential bio-functions and underlying features of these diverse RMPs and provided effective models (PRG clusters, gene clusters and the risk model) for predicting the clinical outcomes of BC. The individuals with higher risk scores showed poor prognoses, cell cycle function enrichment, upregulation of stemness scores, higher tumour mutation burdens (TMBs), immune activation and specific drug resistance. This work highlights the significance of comprehensively examining post-transcriptional RNA modification genes. Conclusion: Here, we designed and verified an advanced forecasting model to reveal the underlying links between BC and RMPs and precisely predict the clinical outcomes of multivariate prognostic patterns for individuals.

Keywords:  RNA-modifying proteins; breast cancer; drug sensitivity; immune infiltration; mutation burden; prognosis; risk score; stemness score

DOI:  https://doi.org/10.3389/fgene.2022.943378
Front Pharmacol. 2022 ;13 900006

m7G regulator-mediated molecular subtypes and tumor microenvironment in kidney renal clear cell carcinoma.

Mei Chen, Zhenyu Nie, Yuanhui Gao, Hui Cao, Linlin Zheng, Na Guo, Yanling Peng, Shufang Zhang.

  Background: RNA methylation modification plays an important role in immune regulation. m7G RNA methylation is an emerging research hotspot in the RNA methylation field. However, its role in the tumor immune microenvironment of kidney renal clear cell carcinoma (KIRC) is still unclear. Methods: We analyzed the expression profiles of 29 m7G regulators in KIRC, integrated multiple datasets to identify a novel m7G regulator-mediated molecular subtype, and developed the m7G score. We evaluated the immune tumor microenvironments in m7G clusters and analyzed the correlation of the m7G score with immune cells and drug sensitivity. We tested the predictive power of the m7G score for prognosis of patients with KIRC and verified the predictive accuracy of the m7G score by using the GSE40912 and E-MTAB-1980 datasets. The genes used to develop the m7G score were verified by qRT-PCR. Finally, we experimentally analyzed the effects of WDR4 knockdown on KIRC proliferation, migration, invasion, and drug sensitivity. Results: We identified three m7G clusters. The expression of m7G regulators was higher in cluster C than in other clusters. m7G cluster C was related to immune activation, low tumor purity, good prognosis, and low m7G score. Cluster B was related to drug metabolism, high tumor purity, poor survival, and high m7G score. Cluster A was related to purine metabolism. The m7G score can well-predict the prognosis of patients with KIRC, and its prediction accuracy based on the m7G score nomogram was very high. Patients with high m7G scores were more sensitive to rapamycin, gefitinib, sunitinib, and vinblastine than other patients. Knocking down WDR4 can inhibit the proliferation, migration, and invasion of 786-0 and Caki-1 cells and increase sensitivity to sorafenib and sunitinib. Conclusion: We proposed a novel molecular subtype related to m7G modification and revealed the immune cell infiltration characteristics of different subtypes. The developed m7G score can well-predict the prognosis of patients with KIRC, and our research provides a basis for personalized treatment of patients with KIRC.

Keywords:  drug sensitivity; kidney renal clear cell carcinoma; m7G; molecular subtype; prognosis; tumor microenvironment

DOI:  https://doi.org/10.3389/fphar.2022.900006
Cell Death Dis. 2022 Sep 20. 13(9): 804

N6-methyladenosine modification of circ_0003215 suppresses the pentose phosphate pathway and malignancy of colorectal cancer through the miR-663b/DLG4/G6PD axis.

Baoxiang Chen, Yuntian Hong, Rui Gui, Huabin Zheng, Shunhua Tian, Xiang Zhai, Xiaoyu Xie, Quanjiao Chen, Qun Qian, Xianghai Ren, Lifang Fan, Congqing Jiang.

Circular RNAs (circRNAs) are a recently discovered kind of regulatory RNAs that have emerged as critical biomarkers of various types of cancers. Metabolic reprogramming has gradually been identified as a distinct hallmark of cancer cells. The pentose phosphate pathway (PPP) plays an indispensable role in satisfying the bioenergetic and biosynthetic demands of cancer cells. However, little is known about the role of circRNAs and PPP in colorectal cancer (CRC). The novel circ_0003215 was identified at low levels in CRC and was negatively correlated with larger tumor size, higher TNM stage, and lymph node metastasis. The decreased level of circ_0003215 was resulted from the RNA degradation by m6A writer protein YTHDF2. A series of functional assays demonstrated that circ_0003215 inhibited cell proliferation, migration, invasion, and CRC tumor metastasis in vivo and in vitro. Moreover, circ_0003215 regulated the expression of DLG4 via sponging miR-663b, thereby inducing the metabolic reprogramming in CRC. Mechanismly, DLG4 inhibited the PPP through the K48-linked ubiquitination of glucose-6-phosphate dehydrogenase (G6PD). Taken together, we have identified m6A-modified circ_0003215 as a novel regulator of metabolic glucose reprogramming that inhibited the PPP and the malignant phenotype of CRC via the miR-663b/DLG4/G6PD axis.

DOI: https://doi.org/10.1038/s41419-022-05245-2
Front Cell Infect Microbiol. 2022 ;12 972655

Implications of m6A methylation and microbiota interaction in non-small cell lung cancer: From basics to therapeutics.

Fen-Sheng Qiu, Jia-Qi He, Yu-Sen Zhong, Mei-Ying Guo, Chen-Huan Yu.

  N6-methyladenine (m6A) is one of the most common RNA epigenetic modifications in all higher eukaryotes. Increasing evidence demonstrated that m6A-related proteins, acted as oncogenes or tumor suppressors, are abnormally expressed in the cell lines and tissues of non-small cell lung cancer (NSCLC). In addition, lung as the special immune organ contacts with the outer environments and thereby inevitably suffers from different types of microbial pathogen attack. Those microbial pathogens affect the development, progression, and clinical outcomes of NSCLC via altering host m6A modification to disrupt pulmonary immune homeostasis and increase the susceptibility; conversely, host cells modulate m6A modification to repress bacterial colonization. Therefore, m6A harbors the potential to be the novel biomarkers and targets for predicting poor prognosis and chemotherapy sensitivity of patients with lung cancer. In this paper, we provided an overview of the biological properties of m6A-modifying enzymes, and the mechanistic links among lung microbiota, m6A modification and NSCLC. Although the flood of novel m6A-related inhibitors represents many dramatic improvements in NSCLC therapy, their efficacy and toxicity in NSCLC are explored to address these pivotal gaps in the field.

Keywords:  FTO; METTL3; biomarker; epigenetics; inhibitor; m6A

DOI:  https://doi.org/10.3389/fcimb.2022.972655
Cancer Gene Ther. 2022 Sep 19.

YAP 5-methylcytosine modification increases its mRNA stability and promotes the transcription of exosome secretion-related genes in lung adenocarcinoma.

Wenjun Yu, Congcong Zhang, Yikun Wang, Xiaoting Tian, Yayou Miao, Fanyu Meng, Lifang Ma, Xiao Zhang, Jinjing Xia.

YAP is a transcriptional co-activator with critical roles in tumorigenesis. However, its upstream regulatory mechanism, especially how its mRNA stability is regulated, remains to be further studied. Here, we validated that YAP expression was higher in lung adenocarcinoma (LUAD) tissues compared to adjacent normal tissues, and found that YAP m5C modification occurred in its 328-331 3' UTR region under the promotion NSUN2 and ALYREF, and increased the stability of YAP mRNA. This m5C modification also inhibited miR-582-3p binding and m6A modification in the nearby region. In addition, YAP m5C modification enhanced the exosome secretion effect, which was caused by two YAP-dependent transcription factors, Mycn and SOX10, and then stimulating the transcription of seven downstream exosome-promoting genes. Furthermore, we found that YAP m5C modification and its exosome-secretion-promoting function contributed to the malignant phenotype and AZD9291 (a third-generation EGFR-TKI) resistance of LUAD cells. Collectively, YAP is promoted by its m5C modification, and blocking YAP m5C modification will be helpful for future LUAD treatment.

DOI: https://doi.org/10.1038/s41417-022-00533-7
J Cancer Res Clin Oncol. 2022 Sep 19.

Expression and prognostic signatures of m6A-related lncRNAs in hepatocellular carcinoma.

Kenan Hao, Jincheng Li, Youao Zhang, Wei Zhao, Xiaojing Chen, Jiabin Xu, Ye Tian, Xinmin Li, Jianyu Fen, Xiaofeng He.

   BACKGROUND: N6-methyladenosine (m6A) is a common modification and plays an important role in various biological processes, but m6A-related lncRNA functions in hepatocellular carcinoma (HCC) have not been systematically clarified.
METHODS: The clinical data and RNA-seq transcriptome of 375 cases of HCC and 50 cases of normal tissues were obtained from the Cancer Gene Atlas database. Co-expression analysis was used to obtain m6A-related lncRNA. The independent prognostic factors were identified by univariate and multivariate Cox regression models. Kaplan-Meier method was used in survival analysis. The core gene of the mRNA-mRNA interaction network is related to m6A-related lncRNAs obtained by the CytoHubba plugin of Cytoscape. Gene ontology and Kyoto Gene Encyclopedia were analyzed to find out the potential mechanism. CIBERSORT algorithm was used to calculate the relative proportion of immune infiltrating cells.
RESULTS: We identified two subgroups (cluster 1 and cluster 2) according to the expression level. The survival analysis curve and receiver operating characteristic curve proved that this model could predict the prognosis of HCC patients. The univariate and multivariate Cox regression analyses showed the independent prognostic value. UBE2C was screened as the pivotal gene. The expression level of m6A-related lncRNAs causes changes in the tumor immune microenvironment.
CONCLUSION: The expression levels of m6A-related lncRNAs were significantly different and the prognostic value of m6A-related lncRNAs was confirmed. The m6A-related lncRNAs are expected to be prognostic signatures in HCC.

Keywords:  Hepatocellular carcinoma; Prognostic signatures; Tumor immune microenvironment; lncRNAs; m6A

DOI:  https://doi.org/10.1007/s00432-022-04338-x
Medicine (Baltimore). 2022 Sep 16. 101(37): e30643

Prognostic value of m6A regulators and the nomogram construction in glioma patients.

Pengdi Liu, Xianxia Yan, Chengwen Ma, Junxiang Gu, Fuyu Tian, Jianqiang Qu.

Although N6-methyladenosine (m6A) has been implicated in various biological functions in human cancers, its role in predicting the prognosis of glioma remains unclear. In this study, the transcriptome expression profiles and the clinical data of 961 patients were derived from the Chinese Glioma Genome Atlas (CGGA). We comprehensively evaluated the association between the expression of m6A regulators and the prognosis of glioma and established a 3-gene (YTHDF2, FTO, and ALKBH5) risk signature using least absolute shrinkage and selection operator (LASSO) analysis. Patients with a high-risk signature had significantly adverse prognoses. Gene set enrichment analysis (GSEA) analysis revealed that the G2M checkpoint, MTORC1 signaling, epithelial mesenchymal transition, and PI3K-AKT-mTOR signaling were significantly enriched in the high-risk group. Univariate and multivariate Cox regression analyses confirmed the independent prognostic value of this risk signature. We then constructed a nomogram for individualized prediction of overall survival (OS) by integrating clinicopathological features (age, World Health Organization [WHO] grade), treatment information (radiotherapy, temozolomide therapy), and m6A risk signature. The calibration curves showed excellent agreement between the predicted and actual probabilities for the 1-, 3-, and 5-year OS, with a C-index of 0.780 in the training cohort and 0.717 in the validation cohort. Altogether, our study elucidated the important role of m6A regulators in glioma prognosis, which is valuable for the selection of therapeutic methods and clinical management of patients with glioma.

DOI: https://doi.org/10.1097/MD.0000000000030643
Front Oncol. 2022 ;12 820587

Identification and validation of the role of c-Myc in head and neck squamous cell carcinoma.

Sufeng Zhao, Li An, Xudong Yang, Zheng Wei, He Zhang, Yufeng Wang.

   Background: Many studies have shown that c-Myc plays a critical role in tumorigenesis. However, the molecular role of c-Myc in head and neck squamous cell carcinoma (HNSC) remains unclear.
Methods: Several biological databases, including UALCAN, TIMER2.0, TCGAportal, GEPIA, KM plotter, OncoLnc, LinkedOmics, GSCA, and TCIA, were used to analyze the molecular role of c-Myc in HNSC. The expression levels of c-Myc were validated by real-time PCR (RT-PCR) and Western blot in CAL-27 cells.
Results: The expression of c-Myc mRNA were significantly increased in HPV-negative HNSC tissues. The expression of c-Myc gene level was correlated with TP53 mutation status. HNSC also showed hypomethylated c-Myc compared with normal tissues. c-Myc was identified as an ominous prognostic factor for HNSC patients and correlated with immune infiltrating levels. Moreover, high c-Myc expression was associated with decreased expression of a series of immune checkpoints, resulting in a dampened immune response. c-Myc potentially mediated IL-17 signaling pathway and Th1 and Th2 cell differentiation. Inhibition of c-Myc expression increased apoptosis of CAL-27 cells.
Conclusions: These findings suggest a new mechanism of c-Myc in the prognosis of HNSC, implying the potential of c-Myc as a therapeutic target for HNSC patients.

Keywords:  c-Myc; head and neck squamous cell carcinoma; mRNA; survival; triptonide

DOI:  https://doi.org/10.3389/fonc.2022.820587
Genes (Basel). 2022 Sep 14. pii: 1652. [Epub ahead of print]13(9):

Slow RNAPII Transcription Elongation Rate, Low Levels of RNAPII Pausing, and Elevated Histone H1 Content at Promoters Associate with Higher m6A Deposition on Nascent mRNAs.

Alicia Gallego, José Miguel Fernández-Justel, Sara Martín-Vírgala, Magdalena M Maslon, María Gómez.

  N6-methyladenosine modification (m6A) fine-tunes RNA fate in a variety of ways, thus regulating multiple fundamental biological processes. m6A writers bind to chromatin and interact with RNA polymerase II (RNAPII) during transcription. To evaluate how the dynamics of the transcription process impact m6A deposition, we studied RNAPII elongation rates in mouse embryonic stem cells with altered chromatin configurations, due to reductions in linker histone H1 content. We found that genes transcribed at slow speed are preferentially methylated and display unique signatures at their promoter region, namely high levels of histone H1, together with marks of bivalent chromatin and low RNAPII pausing. They are also highly susceptible to m6A loss upon histone H1 reduction. These results indicate that RNAPII velocity links chromatin structure and the deposition of m6A, highlighting the intricate relationship between different regulatory layers on nascent mRNA molecules.

Keywords:  RNAPII elongation rate; RNAPII pausing; bivalent chromatin; histone H1; m6A

DOI:  https://doi.org/10.3390/genes13091652
Wiley Interdiscip Rev RNA. 2022 Sep 23. e1764

Immune dysregulation and RNA N6-methyladenosine modification in sepsis.

Hongyan Chen, Xiaoting Zhang, Hao Su, Judeng Zeng, Hung Chan, Qing Li, Xiaodong Liu, Lin Zhang, William Ka Kei Wu, Matthew Tak Vai Chan, Huarong Chen.

  Sepsis is defined as life-threatening organ dysfunction caused by the host immune dysregulation to infection. It is a highly heterogeneous syndrome with complex pathophysiological mechanisms. The host immune response to sepsis can be divided into hyper-inflammatory and immune-suppressive phases which could exist simultaneously. In the initial stage, systemic immune response is activated after exposure to pathogens. Both innate and adaptive immune cells undergo epigenomic, transcriptomic, and functional reprogramming, resulting in systemic and persistent inflammatory responses. Following the hyper-inflammatory phase, the body is in a state of continuous immunosuppression, which is related to immune cell apoptosis, metabolic failure, and epigenetic reprogramming. Immunosuppression leads to increased susceptibility to secondary infections in patients with sepsis. RNA N6-Methyladenosine (m6A) has been recognized as an indispensable epitranscriptomic modification involved in both physiological and pathological processes. Recent studies suggest that m6A could reprogram both innate and adaptive immune cells through posttranscriptional regulation of RNA metabolism. Dysregulated m6A modifications contribute to the pathogenesis of immune-related diseases. In this review, we summarize immune cell changes and the potential role of m6A modification in sepsis. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > RNA Editing and Modification.

Keywords:  N6-methyladenosine; hyperinflammation; immunosuppression; reprogramming; sepsis

DOI:  https://doi.org/10.1002/wrna.1764
Comput Math Methods Med. 2022 ;2022 5787808

MicroRNA-1306-5p Regulates the METTL14-Guided m6A Methylation to Repress Acute Myeloid Leukemia.

Jiajia Li, Yanping Wu, Meng Wang, Xiaofeng Chen, Zhongyu Li, Xue Bai, Haotian Wu.

miRNA and m6A methylation are two key regulators in cancers. However, in acute myeloid leukemia (AML), the relationship of miRNA and m6A methylation remains unclear. The present work is aimed at determining the effect of m6A methylation induced by miRNAs on AML and its underlying mechanism. The expression of METTL14 was detected by qRT-PCR and western blot. The growth of HL-60 cells was analyzed by CCK-8, Transwell assay, and flow cytometry. Tumor-bearing mice were established, and Ki-67 staining assay was used to detect the proliferation in vivo. Dual luciferase reporter system detected the effect of miR-1306-5p on METTL14 luciferase activity. Dot blot analysis detected m6A methylation. We found that METTL14 was upregulated in AML patients and overexpressed METTL14 promoted AML development. Further analysis indicated that METTL14 was directly targeted by miR-1306-5p and overexpressed miR-1306-5p alleviated AML progression. In addition, m6A methylation level regulated by METTL14 could be affected by miR-1306-5p. In conclusion, we found that suppressed miR-1306-5p enhanced AML progression by elevating m6A methylation level via upregulating METTL14. These findings provided basis for the development of new strategies for treating AML.

DOI: https://doi.org/10.1155/2022/5787808
Front Pharmacol. 2022 ;13 909784

Integrated bioinformatical analysis, machine learning and in vitro experiment-identified m6A subtype, and predictive drug target signatures for diagnosing renal fibrosis.

Chunxiang Feng, Zhixian Wang, Chang Liu, Shiliang Liu, Yuxi Wang, Yuanyuan Zeng, Qianqian Wang, Tianming Peng, Xiaoyong Pu, Jiumin Liu.

  Renal biopsy is the gold standard for defining renal fibrosis which causes calcium deposits in the kidneys. Persistent calcium deposition leads to kidney inflammation, cell necrosis, and is related to serious kidney diseases. However, it is invasive and involves the risk of complications such as bleeding, especially in patients with end-stage renal diseases. Therefore, it is necessary to identify specific diagnostic biomarkers for renal fibrosis. This study aimed to develop a predictive drug target signature to diagnose renal fibrosis based on m6A subtypes. We then performed an unsupervised consensus clustering analysis to identify three different m6A subtypes of renal fibrosis based on the expressions of 21 m6A regulators. We evaluated the immune infiltration characteristics and expression of canonical immune checkpoints and immune-related genes with distinct m6A modification patterns. Subsequently, we performed the WGCNA analysis using the expression data of 1,611 drug targets to identify 474 genes associated with the m6A modification. 92 overlapping drug targets between WGCNA and DEGs (renal fibrosis vs. normal samples) were defined as key drug targets. A five target gene predictive model was developed through the combination of LASSO regression and stepwise logistic regression (LASSO-SLR) to diagnose renal fibrosis. We further performed drug sensitivity analysis and extracellular matrix analysis on model genes. The ROC curve showed that the risk score (AUC = 0.863) performed well in diagnosing renal fibrosis in the training dataset. In addition, the external validation dataset further confirmed the outstanding predictive performance of the risk score (AUC = 0.755). These results indicate that the risk model has an excellent predictive performance for diagnosing the disease. Furthermore, our results show that this 5-target gene model is significantly associated with many drugs and extracellular matrix activities. Finally, the expression levels of both predictive signature genes EGR1 and PLA2G4A were validated in renal fibrosis and adjacent normal tissues by using qRT-PCR and Western blot method.

Keywords:  drug sensitivity; immune microenvironment; logistic regression; prective model; renal fibrosis

DOI:  https://doi.org/10.3389/fphar.2022.909784
Clin Transl Med. 2022 Sep;12(9): e1045

NAT10: An RNA cytidine transferase regulates fatty acid metabolism in cancer cells.

Mahmood Hassan Dalhat, Mohammed Razeeth Shait Mohammed, Hind Ali Alkhatabi, Mohd Rehan, Aamir Ahmad, Hani Choudhry, Mohammad Imran Khan.

   BACKGROUND: N-4 cytidine acetylation (ac4C) is an epitranscriptomics modification catalyzed by N-acetyltransferase 10 (NAT10); important for cellular mRNA stability, rRNA biogenesis, cell proliferation and epithelial to mesenchymal transition (EMT). However, whether other crucial pathways are regulated by NAT10-dependent ac4C modification in cancer cells remains unclear. Therefore, in this study, we explored the impact of NAT10 depletion in cancer cells using unbiased RNA-seq.
METHODS: High-throughput sequencing of knockdown NAT10 in cancer cells was conducted to identify enriched pathways. Acetylated RNA immunoprecipitation-seq (acRIP-seq) and RIP-PCR were used to map and determine ac4C levels of RNA. Exogenous palmitate uptake assay was conducted to assess NAT10 knockdown cancer cells using Oil Red O staining and lipid content analysis. Gas-chromatography-tandem mass spectroscopy (GC/MS) was used to perform untargeted lipidomics.
RESULTS: High-throughput sequencing of NAT10 knockdown in cancer cells revealed fatty acid (FA) metabolism as the top enriched pathway through the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis in differentially downregulated genes. FA metabolic genes such as ELOLV6, ACSL1, ACSL3, ACSL4, ACADSB and ACAT1 were shown to be stabilised via NAT10-dependent ac4C RNA acetylation. Additionally, NAT10 depletion was shown to significantly reduce the levels of overall lipid content, triglycerides and total cholesterol. Further, NAT10 depletion in palmitate-loaded cancer cells showed decrease in ac4C levels across the RNA transcripts of FA metabolic genes. In untargeted lipidomics, 496 out of 2 279 lipids were statistically significant in NAT10 depleted cancer cells, of which pathways associated with FA metabolism are the most enriched.
CONCLUSIONS: Conclusively, our results provide novel insights into the impact of NAT10-mediated ac4C modification as a crucial regulatory factor during FA metabolism and showed the benefit of targeting NAT10 for cancer treatment.

Keywords:  NAT10; ac4C; cancer; fatty acid metabolism

DOI:  https://doi.org/10.1002/ctm2.1045