bims-rimeca 2022-11-06 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022‒11‒06
28 papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

N6-methyladenosine (m6A) writer KIAA1429 accelerates gastric cancer oxaliplatin chemoresistance by targeting FOXM1.
WTAP Targets the METTL3 m6A-Methyltransferase Complex to Cytoplasmic Hepatitis C Virus RNA to Regulate Infection.
Downregulation of METTL14 improves postmenopausal osteoporosis via IGF2BP1 dependent posttranscriptional silencing of SMAD1.
N6-methyladenosine functions and its role in skin cancer.
IGF2BP3 promotes progression of gallbladder carcinoma by stabilizing KLK5 mRNA in N6-methyladenosine-dependent binding.
Characterization of m6A-related lncRNA signature in neuroblastoma.
Transcriptome-wide N6-methyladenosine modification profiling of mRNAs during infection of Newcastle disease virus in chicken macrophages.
Cerebroprotective Role of N6-Methyladenosine Demethylase FTO (Fat Mass and Obesity-Associated Protein) After Experimental Stroke.
PARP1 Is Upregulated by Hyperglycemia Via N6-methyladenosine Modification and Promotes Diabetic Retinopathy.
N6-methyladenosine reader YTHDF3 regulates melanoma metastasis via its 'executor'LOXL3.
Identification of genes modified by N6-methyladenosine in patients with colorectal cancer recurrence.
The development of a novel signature based on the m6A RNA methylation regulator-related ceRNA network to predict prognosis and therapy response in sarcomas.
N6 -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation.
Modulation of gene expression by YTH domain family (YTHDF) proteins in human physiology and pathology.
Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection.
FTO inhibits oxidative stress by mediating m6A demethylation of Nrf2 to alleviate cerebral ischemia/reperfusion injury.
RNA m6A methylation regulators in endometrial cancer (Review).
m6A Methyltransferase METTL3 Reduces Hippocampal Neuron Apoptosis in a Mouse Model of Autism Through the MALAT1/SFRP2/Wnt/β-catenin Axis.
Alteration of the N6-methyladenosine epitranscriptomic profile in synthetic phthalate-treated human induced pluripotent stem cell-derived endothelial cells.
N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer.
NRP1 contributes to stemness and potentiates radioresistance via WTAP-mediated m6A methylation of Bcl-2 mRNA in breast cancer.
m6A/ m1A /m5C/m7G-related methylation modification patterns and immune characterization in prostate cancer.
Emerging functions of tRNA modifications in mRNA translation and diseases.
m6A-immune-related lncRNA prognostic signature for predicting immune landscape and prognosis of bladder cancer.
3-Methylation alters excited state decay in photoionised uracil.
Comprehensive Analysis and Functional Characteristics of Differential Expression of N6-Methyladenosine Methylation Modification in the Whole Transcriptome of Rheumatoid Arthritis.
N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection.
A comprehensive investigation discovered the novel methyltransferase METTL24 as one presumably prognostic gene for kidney renal clear cell carcinoma potentially modulating tumor immune microenvironment.

J Cancer Res Clin Oncol. 2022 Nov 03.

N6-methyladenosine (m6A) writer KIAA1429 accelerates gastric cancer oxaliplatin chemoresistance by targeting FOXM1.

Bingxi Tang, Mingdong Li, Yanbing Xu, Xinli Li.

  PURPOSE: Chemical modification plays a critical role in regulating human cancer progression, especially N6-methyladenosine (m6A). However, m6A writer KIAA1429-mediated m6A modification in gastric cancer (GC) tumorigenesis remains largely unknown.METHODS: The levels of mRNA and protein were detected using RT-qPCR and western blot. The half maximal inhibitory concentration (IC50) of oxaliplatin (OXA) resistance is detected using CCK-8 assay. The binding within moleculars was identified using RIP-PCR.
RESULTS: Results found that KIAA1429 was upregulated in GC tissue samples and its high expression acted as a prognostic factor of poor survival in patients with GC. Functional assays indicated that KIAA1429 promoted the proliferation of GC cells, besides, KIAA1429 accelerated the half maximal inhibitory concentration (IC50) of oxaliplatin (OXA) resistance. Mechanistically, online prediction found that there was possible m6A modification site on FOXM1 mRNA. KIAA1429 could target the m6A modification site on FOXM1. Notably, KIAA1429 facilitated the GC OXA resistance in GC cells by promoting FOXM1 mRNA stability.
CONCLUSIONS: Taken together, our study reveals the functions and mechanism for KIAA1429 and exposes KIAA1429 as a key player in GC chemoresistance.

Keywords:  FOXM1; Gastric cancer; KIAA1429; N6-methyladenosine (m6A); Oxaliplatin

DOI:  https://doi.org/10.1007/s00432-022-04426-y
J Virol. 2022 Oct 31. e0099722

WTAP Targets the METTL3 m6A-Methyltransferase Complex to Cytoplasmic Hepatitis C Virus RNA to Regulate Infection.

Matthew T Sacco, Katherine M Bland, Stacy M Horner.

  Modification of the hepatitis C virus (HCV) positive-strand RNA genome by N6-methyladenosine (m6A) regulates the viral life cycle. This life cycle takes place solely in the cytoplasm, while m6A addition on cellular mRNA takes place in the nucleus. Thus, the mechanisms by which m6A is deposited on the viral RNA have been unclear. In this work, we find that m6A modification of HCV RNA by the m6A-methyltransferase proteins methyltransferase-like 3 and 14 (METTL3 and METTL14) is regulated by Wilms' tumor 1-associating protein (WTAP). WTAP, a predominantly nuclear protein, is an essential member of the cellular mRNA m6A-methyltransferase complex and known to target METTL3 to mRNA. We found that HCV infection induces localization of WTAP to the cytoplasm. Importantly, we found that WTAP is required for both METTL3 interaction with HCV RNA and m6A modification across the viral RNA genome. Further, we found that WTAP, like METTL3 and METTL14, negatively regulates the production of infectious HCV virions, a process that we have previously shown is regulated by m6A. Excitingly, WTAP regulation of both HCV RNA m6A modification and virion production was independent of its ability to localize to the nucleus. Together, these results reveal that WTAP is critical for HCV RNA m6A modification by METTL3 and METTL14 in the cytoplasm. IMPORTANCE Positive-strand RNA viruses such as HCV represent a significant global health burden. Previous work has described that HCV RNA contains the RNA modification m6A and how this modification regulates viral infection. Yet, how this modification is targeted to HCV RNA has remained unclear due to the incompatibility of the nuclear cellular processes that drive m6A modification with the cytoplasmic HCV life cycle. In this study, we present evidence for how m6A modification is targeted to HCV RNA in the cytoplasm by a mechanism in which WTAP recruits the m6A-methyltransferase METTL3 to HCV RNA. This targeting strategy for m6A modification of cytoplasmic RNA viruses is likely relevant for other m6A-modified positive-strand RNA viruses with cytoplasmic life cycles such as enterovirus 71 and SARS-CoV-2 and provides an exciting new target for potential antiviral therapies.

Keywords:  HCV; METTL14; METTL3; N6-methyladenosine; RNA modification; WTAP

DOI:  https://doi.org/10.1128/jvi.00997-22
Cell Death Dis. 2022 Nov 01. 13(11): 919

Downregulation of METTL14 improves postmenopausal osteoporosis via IGF2BP1 dependent posttranscriptional silencing of SMAD1.

Chaoqing Huang, Yuan Wang.

Osteoporosis (OP) tends to occur in postmenopausal women, making them prone to fractures. N6-methyladenosine (m6A) methylation plays a crucial role in OP. Herein, we aimed to explore the effects of METTL14 on osteogenesis and the underlying mechanism. Osteogenic differentiation was assessed through osteoblast markers expression, cell proliferation, ALP activity, and mineralization, which were detected by qRT-PCR, CCK-8, EdU assay, ALP staining assay, and ARS staining assay, respectively. Osteoporosis was evaluated in OVX mice using qRT-PCR, microcomputed tomography, and H&E staining assay. The levels of METTL14 and SMAD1 were measured using qRT-PCR and western blot, and their interaction was assessed using RIP and luciferase reporter assay. M6A methylation was analyzed using the Me-RIP assay. The results indicated that m6A, METTL14, and SMAD1 levels were downregulated in patients with OP and OVX mice, and upregulated in osteogenic BMSCs. Knockdown of METTL14 suppressed osteogenesis of BMSCs and reduced bone mass of OVX mice. Moreover, silencing of METTL14 positively related to SMAD1 and inhibited m6A modification of SMAD1 by suppressing its stability. IGF2BP1 was identified as the methylation reader, and which knockdown reversed the upregulation induced by SMAD1. Overexpression of SMAD1 reversed the suppression of osteogenic differentiation induced by METTL14 knockdown. In conclusion, interference with METTL14 inhibited osteogenic differentiation of BSMCs by m6A modification of SMAD1 in an IGFBP1 manner, suggesting that METTL14 might be a novel approach for improving osteoporosis.

DOI: https://doi.org/10.1038/s41419-022-05362-y
Exp Dermatol. 2022 Oct 31.

N6-methyladenosine functions and its role in skin cancer.

Yanqin Ran, Zhuoxian Yan, Bimei Jiang, Pengfei Liang.

  N6-methyladenosine (m6A) methylation is the most abundant mammalian mRNA modification. m6A regulates RNA processing, splicing, nucleation, translation, and stability by transferring, removing, and recognizing m6A methylation sites, which are critical for cancer initiation, progression, metabolism, and metastasis. m6A is involved in pathophysiological tumor development by altering m6A modification and expression levels in tumor oncogenes and suppressor genes. Skin cancers are by far the most common malignancies in humans, with well over a million cases diagnosed each year. Skin cancers are grouped into two main categories: melanoma and non-melanoma skin cancers (NMSC), based on cell origin and clinical behavior. In this review, we summarize m6A methylation functions in different skin cancers, and discuss how m6A methylation is involved in disease development and progression. Moreover, we review potential prognostic biomarkers and molecular targets for early skin cancer diagnosis and treatment.

Keywords:  N6-methyladenosine; RNA Epigenetics; molecular mechanisms; skin cancer

DOI:  https://doi.org/10.1111/exd.14696
Front Oncol. 2022 ;12 1035871

IGF2BP3 promotes progression of gallbladder carcinoma by stabilizing KLK5 mRNA in N6-methyladenosine-dependent binding.

Junzhe Zhang, Kaini Yang, Junfeng Bu, Jiayan Yan, Xiaoqiang Hu, Ke Liu, Si Gao, Shuibin Tang, Lili Gao, Wei Chen.

  Background: Recent studies have reported that IGF2BP3 is linked to the pathogenesis of various malignancies. Since IGF2BP3 is associated with poor outcomes of gallbladder carcinoma (GBC), we aimed to explore the association between its N6-methyladenosine (m6A) RNA methylation and GBC progression.Methods: Bioinformatic analysis of GSE136982, GSE104165, and RNA-seq was performed. In vitro and in vivo gain- and loss-of-function assays were done. qPCR, Western blotting, and IHC were conducted in cells or in collected clinical tissue samples. RNA immunoprecipitation, RNA stability measurement, methylated RNA immunoprecipitation, and dual-luciferase reporter assays were performed in this study.
Results: The expression of IGF2BP3 was higher in GBC tissues than in peritumoral tissues. Functions such as cell proliferation and migration, both in vitro and in vivo, were inhibited by downregulation of IGF2BP3. The analysis of RNA-seq indicated that KLK5 was a downstream target of IGF2BP3. The expression of KLK5 was measured in GBC cells and tumor samples. It was found to be positively correlated with IGF2BP3 level. Upon IGF2BP3 depletion, ectopic expression of KLK5 could rescue cell function in part. Mechanistically, we found that IGF2BP3 directly binds to KLK5 mRNA and regulates its stability in an m6A-dependent manner. As a result, inhibition of KLK5 decreased the expression of PAR2, and deregulated phospho-Akt. Using bioinformatic prediction combined with miRNA microarray analysis, we identified that let-7g-5p is an inhibitor of IGF2BP3, and let-7g-5p expression was negatively correlated with IGF2BP3. Overexpression of let-7g-5p affected the aggressive phenotype of GBC cells by deregulating IGF2BP3, and inhibiting the KLK5/PAR2/AKT axis.
Conclusions: Our data showed that IGF2BP3 is associated with the aggressive phenotype of GBC. Mechanistically, IGF2BP3 activated the PAR2/AKT axis by stabilizing KLK5 mRNA in an m6A-dependent manner. The loss of let-7g-5p enhanced the expression of IGF2BP3 and improved GBC progression. Thus, IGF2BP3 plays a crucial role in GBC, and the let-7g-5p/IGF2BP3/KLK5/PAR2 axis may be a therapeutic target for GBC.

Keywords:  IGF2BP3; KLK5; gallbladder carcinoma; let-7g-5p; m6A reader

DOI:  https://doi.org/10.3389/fonc.2022.1035871
Front Pediatr. 2022 ;10 927885

Characterization of m6A-related lncRNA signature in neuroblastoma.

Liming Li, Sisi Chen, Jianhong Li, Guochou Rong, Juchao Yang, Yunquan Li.

  N6-methyladenosine (m6A) constitutes one of the most common modifications in mRNA, rRNA, tRNA, microRNA, and long-chain noncoding RNA. The influence of modifications of m6A on the stability of RNA depends upon the expression of methyltransferase ("writer") and demethylase ("eraser") and m6A binding protein ("reader"). In this study, we identified a set of m6A-related lncRNA expression profiles in neuroblastoma (NBL) based on the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) program. Thereupon, we identified two subgroups of neuroblastoma (high-risk group and low-risk group) by applying consensus clustering to m6A RNA methylation regulators ("Readers,", "Writer," and "Erase"). Relative to the low-risk group, the high-risk group correlates with a poorer prognosis. Moreover, the present study also revealed that the high-risk group proves to be significantly positively enriched in the tumor-related signaling pathways, including the P53 signaling pathway, cell cycle, and DNA repair. This finding indicates that these molecular prognostic markers may also be potentially valuable in early diagnosis, which provides a new research direction for the study of molecular mechanisms underlying the development of NBL. In conclusion, this study constructed a new model of NBL prognosis based on m6a-associated lncRNAs. Ultimately, this model is helpful for stratification of prognosis and development of treatment strategies.

Keywords:  N6-methyladenosine; lncRNAs; neuroblastoma; prognosis; risk score

DOI:  https://doi.org/10.3389/fped.2022.927885
Virus Res. 2022 Oct 27. pii: S0168-1702(22)00322-7. [Epub ahead of print]323 198993

Transcriptome-wide N6-methyladenosine modification profiling of mRNAs during infection of Newcastle disease virus in chicken macrophages.

Jindou Li, Jiaxin Ding, Minghua Chen, Kainan Chen, Yinxue Zou, Xiaohong Xu, Di Zhang, Xibing Yu, Zhuang Ding.

  N6-methyladenosine (m6A) modification, the most prevalent post-transcriptional modification of eukaryotic mRNAs, is reported to play a crucial role in viral infection. However, the role of m6A modification during Newcastle disease virus (NDV) infection has remained unclear. In this study, we performed MeRIP-seq to investigate the transcriptome-wide m6A methylome and m6A-modified genes in NDV-infected chicken macrophages. A total of 9496 altered peaks were identified, of which 7015 peaks were significantly upregulated across 3320 genes, and 2481 peaks were significantly down-regulated across 1264 genes. Combined analysis of m6A peaks and mRNA expression showed that 1234 mRNAs had significantly altered levels of methylation and expression after NDV infection, and m6A modification tended to have a negative relationship with mRNA expression, suggesting that m6A modification may regulate the process of NDV infection by regulating gene expression, particularly of the genes important in the innate immune response. To the best of our knowledge, this is the first comprehensive characterization of m6A patterns in chicken macrophage mRNA after NDV infection, providing a valuable basis for further exploring the role of m6A modification mechanisms during the course of NDV infection.

Keywords:  Chicken macrophages; MeRIP-seq; N6-methyladenosine; Newcastle disease virus; mRNA

DOI:  https://doi.org/10.1016/j.virusres.2022.198993
Stroke. 2022 Nov 02.

Cerebroprotective Role of N6-Methyladenosine Demethylase FTO (Fat Mass and Obesity-Associated Protein) After Experimental Stroke.

Anil K Chokkalla, Soomin Jeong, Suresh L Mehta, Charles K Davis, Kahlilia C Morris-Blanco, Saivenkateshkomal Bathula, Simran S Qureshi, Raghu Vemuganti.

  BACKGROUND: FTO (fat mass and obesity-associated protein) demethylates N6-methyladenosine (m6A), which is a critical epitranscriptomic regulator of neuronal function. We previously reported that ischemic stroke induces m6A hypermethylation with a simultaneous decrease in FTO expression in neurons. Currently, we evaluated the functional significance of restoring FTO with an adeno-associated virus 9, and thus reducing m6A methylation in poststroke brain damage.METHODS: Adult male and female C57BL/6J mice were injected with FTO adeno-associated virus 9 (intracerebral) at 21 days prior to inducing transient middle cerebral artery occlusion. Poststroke brain damage (infarction, atrophy, and white matter integrity) and neurobehavioral deficits (motor function, cognition, depression, and anxiety-like behaviors) were evaluated between days 1 and 28 of reperfusion.
RESULTS: FTO overexpression significantly decreased the poststroke m6A hypermethylation. More importantly, exogenous FTO substantially decreased poststroke gray and white matter damage and improved motor function recovery, cognition, and depression-like behavior in both sexes.
CONCLUSIONS: These results demonstrate that FTO-dependent m6A demethylation minimizes long-term sequelae of stroke independent of sex.

Keywords:  brain injury; ischemic stroke; methylation; neuroprotection; obesity

DOI:  https://doi.org/10.1161/STROKEAHA.122.040401
Discov Med. 2022 Sep-Oct;34(172):34(172): 115-129

PARP1 Is Upregulated by Hyperglycemia Via N6-methyladenosine Modification and Promotes Diabetic Retinopathy.

Jinghui Sun, Guodong Liu, Rui Chen, Jibin Zhou, Ting Chen, Yalan Cheng, Qiyang Lou, Hao Wang.

Poly (ADP-ribose) polymerase 1 (PARP1) plays an irreplaceable role in the progression of diabetic retinopathy (DR). The m6A methylation in mRNA controls gene expression under various physiological and pathological conditions. However, effects of m6A methylation on PARP1 expression and DR progression at molecular level have not been documented. This study shows that the levels of PARP1, inflammatory factors, and fibrosis markers were significantly upregulated via evaluation by real-time PCR, western blotting, and immunofluorescence in both in vivo and in vitro experiments. EdU, CCK8, and apoptosis assays demonstrate that knockdown of PARP1 not only significantly improved the vitality of hRMECs (human retinal microvascular endothelial cells) even under high glucose conditions but also prevented glucose-induced inflammation, fibrosis, and angiogenesis in vivo. Mechanistically, dot blot, RNA pull-down, and immunoblots were implemented to explore the mechanism of m6A-mediated PARP1 stability and function. PARP1 is identified as a target of YTHDF2-mediated m6A modification. Overexpression of YTHDF2 substantially suppressed PARP1 mRNA m6A modification and inhibited its mRNA expression. Collectively, it has been demonstrated that PARP1 is frequently upregulated in human retinas and contributes to DR progression, and that YTHDF2-mediated m6A modification epigenetically regulates diabetes-induced PARP1 expression. Findings from this work may engender therapeutic targets for treating diabetic retinopathy.
Clin Transl Med. 2022 Nov;12(11): e1075

N6-methyladenosine reader YTHDF3 regulates melanoma metastasis via its 'executor'LOXL3.

Hao-Ze Shi, Jing-Shu Xiong, Lu Gan, Ying Zhang, Cong-Cong Zhang, Ying-Qi Kong, Qiu-Ju Miao, Cui-Cui Tian, Rong Li, Jin-Quan Liu, Er-Jia Zhang, Wen-Bo Bu, Yan Wang, Xian-Feng Cheng, Jian-Fang Sun, Hao Chen.

  BACKGROUND: A number of studies have demonstrated that N6-methyladenosine (m6A) plays a vital role in the pathological process of various tumours. Recently, it was found that m6A writers or erasers affect the tumourigenesis of melanoma. However, the relationship between m6A readers such as YTH domain family (YTHDF) proteins and melanoma was still elusive.METHODS: RT-qPCR, Western blot and immunohistochemistry were conducted to measure the expression level of YTH N6-methyladenosine RNA binding protein 3 (YTHDF3) and lysyl oxidase-like 3 (LOXL3) in melanoma tissues and cells. The effects of YTHDF3 and LOXL3 on melanoma were verified in vitro and in vivo. Multi-omics analysis including RNA-seq, MeRIP-seq, RIP-seq and mass spectrometry analyses was performed to identify the target. The interaction between YTHDF3 and LOXL3 was verified by RT-PCR, Western blot, MeRIP-qPCR, RIP-qPCR and CRISPR-Cas13b-based epitranscriptome engineering.
RESULTS: In this study, we found that m6A reader YTHDF3 could affect the metastasis of melanoma both in vitro and in vivo. The downstream targets of YTHDF3, such as LOXL3, phosphodiesterase 3A (PDE3A) and chromodomain helicase DNA-binding protein 7 (CHD7) were identified by means of RNA-seq, MeRIP-seq, RIP-seq and mass spectrometry analyses. Besides, RT-qPCR, Western blot, RIP-qPCR and MeRIP-qPCR were performed for subsequent validation. Among various targets of YTHDF3, LOXL3 was found to be the optimal target of YTHDF3. With the application of CRISPR-Cas13b-based epitranscriptome engineering, we further confirmed that the transcript of LOXL3 was captured and regulated by YTHDF3 via m6A binding sites. YTHDF3 augmented the protein expression of LOXL3 without affecting its mRNA level via the enrichment of eukaryotic translation initiation factor 3 subunit A (eIF3A) on the transcript of LOXL3. LOXL3 downregulation inhibited the metastatic ability of melanoma cells, and overexpression of LOXL3 ameliorated the inhibition of melanoma metastasis caused by YTHDF3 downregulation.
CONCLUSIONS: The YTHDF3-LOXL3 axis could serve as a promising target to be interfered with to inhibit the metastasis of melanoma.

Keywords:  Lysyl oxidase-like 3 (LOXL3); N6-methyladenosine; YTH N6-methyladenosine RNA binding protein 3 (YTHDF3); melanoma; metastasis

DOI:  https://doi.org/10.1002/ctm2.1075
Front Genet. 2022 ;13 1043297

Identification of genes modified by N6-methyladenosine in patients with colorectal cancer recurrence.

Qianru Zhu, Xingxing Huang, Shuxian Yu, Lan Shou, Ruonan Zhang, Han Xie, Zimao Liang, Xueni Sun, Jiao Feng, Ting Duan, Mingming Zhang, Yu Xiang, Xinbing Sui, Weiwei Jin, Lili Yu, Qibiao Wu.

  Background: Recent studies demonstrate that N6-methyladenosine (m6A) methylation plays a crucial role in colorectal cancer (CRC). Therefore, we conducted a comprehensive analysis to assess the m6A modification patterns and identify m6A-modified genes in patients with CRC recurrence. Methods: The m6A modification patterns were comprehensively evaluated by the NMF algorithm based on the levels of 27 m6A regulators, and tumor microenvironment (TME) cell-infiltrating characteristics of these modification patterns were systematically assessed by ssGSEA and CIBERSORT algorithms. The principal component analysis algorithm based on the m6A scoring scheme was used to explore the m6A modification patterns of individual tumors with immune responses. The weighted correlation network analysis and univariable and multivariable Cox regression analyses were applied to identify m6A-modified gene signatures. The single-cell expression dataset of CRC samples was used to explore the tumor microenvironment affected by these signatures. Results: Three distinct m6A modification patterns with significant recurrence-free survival (RFS) were identified in 804 CRC patients. The TME characterization revealed that the m6A modification pattern with longer RFS exhibited robust immune responses. CRC patients were divided into high- and low-score subgroups according to the m6A score individually, which was obtained from the m6A-related signature genes. The patients with low m6A scores had both longer RFS and overall survival (OS) with altered immune cell infiltration. Notably, m6A-modified genes showed significant differences related to the prognosis of CRC patients in the meta-GEO cohort and TCGA cohort. Single-cell expression indicated that ALVRL1 was centrally distributed in endothelial tip cells and stromal cells. Conclusion: The m6A modification plays an indispensable role in the formation of TME diversity and complexity. Importantly, the signatures (TOP2A, LRRC58, HAUS6, SMC4, ACVRL1, and KPNB1) were identified as m6A-modified genes associated with CRC recurrence, thereby serving as a promising predictive biomarker or therapeutic target for patients with CRC recurrence.

Keywords:  colorectal cancer; m6A methylation modification; overall survival; recurrence; tumor immune microenvironment

DOI:  https://doi.org/10.3389/fgene.2022.1043297
Front Genet. 2022 ;13 894080

The development of a novel signature based on the m6A RNA methylation regulator-related ceRNA network to predict prognosis and therapy response in sarcomas.

Huling Li, Dandan Lin, Xiaoyan Wang, Zhiwei Feng, Jing Zhang, Kai Wang.

  Background: N6 methyladenosine (m6A)-related noncoding RNAs (including lncRNAs and miRNAs) are closely related to the development of cancer. However, the gene signature and prognostic value of m6A regulators and m6A-associated RNAs in regulating sarcoma (SARC) development and progression remain largely unexplored. Therefore, further research is required. Methods: We obtained expression data for RNA sequencing (RNA-seq) and miRNAs of SARC from The Cancer Genome Atlas (TCGA) datasets. Correlation analysis and two target gene prediction databases (miRTarBase and LncBase v.2) were used to deduce m6A-related miRNAs and lncRNAs, and Cytoscape software was used to construct ceRNA-regulating networks. Based on univariate Cox regression and least absolute shrinkage and selection operator (LASSO) Cox regression analyses, an m6A-associated RNA risk signature (m6Ascore) model was established. Prognostic differences between subgroups were explored using Kaplan-Meier (KM) analysis. Risk score-related biological phenotypes were analyzed in terms of functional enrichment, tumor immune signature, and tumor mutation signature. Finally, potential immunotherapy features and drug sensitivity predictions for this model were also discussed. Results: A total of 16 miRNAs, 104 lncRNAs, and 11 mRNAs were incorporated into the ceRNA network. The risk score was obtained based on RP11-283I3.6, hsa-miR-455-3p, and CBLL1. Patients were divided into two risk groups using the risk score, with patients in the low-risk group having longer overall survival (OS) than those in the high-risk group. The receiver operating characteristic (ROC) curves indicated that risk characteristic performed well in predicting the prognosis of patients with SARC. In addition, lower m6Ascore was also positively correlated with the abundance of immune cells such as monocytes and mast cells activated, and several immune checkpoint genes were highly expressed in the low-m6Ascore group. According to our analysis, lower m6Ascore may lead to better immunotherapy response and OS outcomes. The risk signature was significantly associated with the chemosensitivity of SARC. Finally, a nomogram was constructed to predict the OS in patients with SARC. The concordance index (C-index) for the nomogram was 0.744 (95% CI: 0.707-0.784). The decision curve analysis (DCA), calibration plot, and ROC curve all showed that this nomogram had good predictive performance. Conclusion: This m6Ascore risk model based on m6A RNA methylation regulator-related RNAs may be promising for clinical prediction of prognosis and might contain potential biomarkers for treatment response prediction for SARC patients.

Keywords:  chemotherapy; immunotherapy; m6A; prognosis; risk score; sarcomas

DOI:  https://doi.org/10.3389/fgene.2022.894080
Adv Sci (Weinh). 2022 Oct 30. e2205091

N6 -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation.

Yin Zhao, Shengyan Huang, Xirong Tan, Liufen Long, Qingmei He, Xiaoyu Liang, Jiewen Bai, Qingjie Li, Jiayi Lin, Yingqin Li, Na Liu, Jun Ma, Yupei Chen.

  Epitranscriptomic remodeling such as N6 -methyladenosine (m6 A) modification plays a critical role in tumor development. However, little is known about the underlying mechanisms connecting m6 A modification and nasopharyngeal carcinoma (NPC) progression. Here, CBX1 is identified, a histone methylation regulator, to be significantly upregulated with m6 A hypomethylation in metastatic NPC tissues. The m6 A-modified CBX1 mRNA transcript is recognized and destabilized by the m6 A reader YTHDF3. Furthermore, it is revealed that CBX1 promotes NPC cell migration, invasion, and proliferation through transcriptional repression of MAP7 via H3K9me3-mediated heterochromatin formation. In addition to its oncogenic effect, CBX1 can facilitate immune evasion through IFN-γ-STAT1 signaling-mediated PD-L1 upregulation. Clinically, CBX1 serves as an independent predictor for unfavorable prognosis in NPC patients. The results reveal a crosstalk between epitranscriptomic and epigenetic regulation in NPC progression, and shed light on the functions of CBX1 in tumorigenesis and immunomodulation, which may provide an appealing therapeutic target in NPC.

Keywords:  CBX1; MAP7; PD-L1; heterochromatin; m6A; nasopharyngeal carcinoma

DOI:  https://doi.org/10.1002/advs.202205091
J Cell Physiol. 2022 Nov 03.

Modulation of gene expression by YTH domain family (YTHDF) proteins in human physiology and pathology.

Aju Kisan, Ravindresh Chhabra.

  The advent of high throughput techniques in the past decade has significantly advanced the field of epitranscriptomics. The internal chemical modification of the target RNA at a specific site is a basic feature of epitranscriptomics and is critical for its structural stability and functional property. More than 170 modifications at the transcriptomic level have been reported so far, among which m6A methylation is one of the more conserved internal RNA modifications, abundantly found in eukaryotic mRNAs and frequently involved in enhancing the target messenger RNA's (mRNA) stability and translation. m6A modification of mRNAs is essential for multiple physiological processes including stem cell differentiation, nervous system development and gametogenesis. Any aberration in the m6A modification can often result in a pathological condition. The deregulation of m6A methylation has already been described in inflammation, viral infection, cardiovascular diseases and cancer. The m6A modification is reversible in nature and is carried out by specialized m6A proteins including writers (m6A methyltransferases) that add methyl groups and erasers (m6A demethylases) that remove methyl groups selectively. The fate of m6A-modified mRNA is heavily reliant on the various m6A-binding proteins ("readers") which recognize and generate a functional signal from m6A-modified mRNA. In this review, we discuss the role of a family of reader proteins, "YT521-B homology domain containing family" (YTHDF) proteins, in human physiology and pathology. In addition, we critically evaluate the potential of YTHDF proteins as therapeutic targets in human diseases.

Keywords:  RNA methylation; YT521-B homology domain; epitranscriptomics; m6A; reader

DOI:  https://doi.org/10.1002/jcp.30907
Abiotech. 2022 Sep;3(3): 197-211

Transcriptome-wide N6-methyladenosine (m6A) methylation in soybean under Meloidogyne incognita infection.

Xue Han, Qianqian Shi, Ziyi He, Wenwen Song, Qingshan Chen, Zhaoming Qi.

  N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita.Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-022-00077-2.

Keywords:  Meloidogyne incognita; Metabolome; RNA-seq; Soybean; m6A methylation; m6A-seq

DOI:  https://doi.org/10.1007/s42994-022-00077-2
J Physiol Biochem. 2022 Nov 03.

FTO inhibits oxidative stress by mediating m6A demethylation of Nrf2 to alleviate cerebral ischemia/reperfusion injury.

Lijing Hou, Shuang Li, Shasha Li, Ru Wang, Mengke Zhao, Xiaomin Liu.

  Current therapies are of limited efficacy in cerebral ischemia/reperfusion (I/R) injury. Based on the important role of oxidative stress in cerebral I/R injury, this study aimed to explore how the N6-adenosine methylation (m6A) demethylase FTO affects oxidative stress. Middle cerebral artery occlusion/reperfusion (MCAO/R)-induced rat model and oxygen and glucose deprivation/re-oxygenation (OGD/R)-induced SH-SY5Y cells were established as in vivo and in vitro model, respectively. The neurological score of rats was measured, and the volume of cerebral infarction was measured by TTC staining. The levels of FTO, nuclear factor-erythroid 2-related factor (Nrf2), and the activity of m6A demethylase FTO were detected. The m6A methylation level of Nrf2 mRNA was detected by MeRIP experiment. Flow cytometry and MTT assay were used to detect apoptosis and proliferation in vitro. TUNEL assay was used to detect apoptosis in brain tissues. FTO and Nrf2 expressions were decreased in the MCAO/R rat brain tissues and OGD/R SH-SY5Y cells, while the m6A methylation level of Nrf2 mRNA was significantly increased. Overexpression of FTO upregulated Nrf2 expression by decreasing the m6A methylation level of Nrf2 mRNA. m6A binding protein YT521-B homology (YTH) domain family protein 2 (YTHDF2) promoted the degradation of Nrf2 by promoting the m6A methylation level of Nrf2 mRNA. Furthermore, SH-SY5Y cell apoptosis was increased and cell viability was decreased after the addition of methyltransferases METTL 3/14, thus blocking FTO to protect SH-SY5Y cells from oxidative stress injury. In vivo, overexpression of FTO decreased the area of cerebral ischemia infarction and the extent of cell apoptosis. In conclusion, FTO increases Nrf2 expression by mediating m6A demethylation of Nrf2 mRNA, thereby inhibiting oxidative stress response and ultimately alleviating cerebral I/R injury.

Keywords:  Cerebral ischemia/reperfusion injury; FTO; Nrf2; Oxidative stress; m6A demethylation

DOI:  https://doi.org/10.1007/s13105-022-00929-x
Int J Oncol. 2022 Dec;pii: 155. [Epub ahead of print]61(6):

RNA m6A methylation regulators in endometrial cancer (Review).

Siyi Shen, Jialu Guo, Nengyuan Lv, Qianying Chen, Jinyi Tong.

  As one of the three major malignant tumor types of the female reproductive system, endometrial cancer (EC) is the most prevalent gynecologic cancer in developed countries. In recent years, the incidence of EC has increased worldwide, threatening the health and well‑being of women. Recent research has indicated that the expression of multiple N6‑methyladenosine (m6A) regulators is up‑ or downregulated in EC and that abnormalities in m6A methylation and the expression of associated regulators are critical to the pathogenesis and progression of EC. m6A is the most abundant internal modification of mRNA. Several studies have demonstrated a close association between the development and progression of malignant tumors and the epigenetic phenomenon of m6A methylation. In the present study, the current status of research on m6A methylation in EC was reviewed. The mechanisms of methyltransferase, demethylase and m6A binding protein in regulating the development and progression of EC by modifying mRNA were introduced. The related research results will provide novel methods and approaches for the prevention and treatment of EC.

Keywords:  N6‑methyladenosine; endometrial cancer; methylation; regulator

DOI:  https://doi.org/10.3892/ijo.2022.5445
Psychiatry Investig. 2022 Oct;19(10): 771-787

m6A Methyltransferase METTL3 Reduces Hippocampal Neuron Apoptosis in a Mouse Model of Autism Through the MALAT1/SFRP2/Wnt/β-catenin Axis.

Yue Ming, Zhihui Deng, Xianhua Tian, Yuerong Jia, Meng Ning, Shuhua Cheng.

  OBJECTIVE: Hippocampal neuron apoptosis contributes to autism, while METTL3 has been documented to possess great potentials in neuron apoptosis. Our study probed into the role of METTL3 in neuron apoptosis in autism and to determine the underlying mechanism.METHODS: Bioinformatics analysis was used to analyze expressed genes in autism samples. Institute of Cancer Research mice were treated with valproic acid to develop autism models. The function of METTL3 in autism-like symptoms in mice was analyzed with behavioral tests and histological examination of their hippocampal tissues. Primary mouse hippocampal neurons were extracted for in vitro studies. Downstream factors of METTL3 were explored and validated.
RESULTS: METTL3, MALAT1, and Wnt/β-catenin signaling were downregulated, while SFRP2 was upregulated in the hippocampal tissues of a mouse model of autism. METTL3 stabilized MALAT1 expression by promoting m6A modification of MALAT1. MALAT1 promoted SFRP2 methylation and led to reduced SFRP2 expression by recruiting DNMT1, DNMT3A, and DNMT3B to the promoter region of SFRP2. Furthermore, SFRP2 facilitated activation of the Wnt/β-catenin signaling. By this mechanism, METTL3 suppressed autism-like symptoms and hippocampal neuron apoptosis.
CONCLUSION: This research suggests that METTL3 can reduce autism-like symptoms and hippocampal neuron apoptosis by regulating the MALAT1/SFRP2/Wnt/β-catenin axis.

Keywords:  Autism; DNA methyltransferase; Hippocampal neurons; Long noncoding RNA MALAT1; Methyltransferase like-3; Secreted Frizzled Related Protein 2; Wnt/β-catenin signaling

DOI:  https://doi.org/10.30773/pi.2021.0370
Epigenomics. 2022 Oct 31.

Alteration of the N6-methyladenosine epitranscriptomic profile in synthetic phthalate-treated human induced pluripotent stem cell-derived endothelial cells.

Jordan Jousma, Zhenbo Han, Gege Yan, Sarath Babu Nukala, Youjeong Kwon, Hoai Huong Thi Le, Ya Li, Sang-Bing Ong, Won Hee Lee, Sang-Ging Ong.

  Background: This study aimed to characterize the N6-methyladenosine epitranscriptomic profile induced by mono(2-ethylhexyl) phthalate (MEHP) exposure using a human-induced pluripotent stem cell-derived endothelial cell model. Methods: A multiomic approach was employed by performing RNA sequencing in parallel with an N6-methyladenosine-specific microarray to identify mRNAs, lncRNAs, and miRNAs affected by MEHP exposure. Results: An integrative multiomic analysis identified relevant biological features affected by MEHP, while functional assays provided a phenotypic characterization of these effects. Transcripts regulated by the epitranscriptome were validated with quantitative PCR and methylated RNA immunoprecipitation. Conclusion: The authors' profiling of the epitranscriptome expands the scope of toxicological insights into known environmental toxins to under surveyed cellular contexts and emerging domains of regulation and is, therefore, a valuable resource to human health.

Keywords:  N6-methyladenosine; epitranscriptomic; iPSCs; mono(2-ethylhexyl) phthalate; synthetic phthalate; toxicology screening

DOI:  https://doi.org/10.2217/epi-2022-0110
Transl Oncol. 2022 Oct 31. pii: S1936-5233(22)00240-6. [Epub ahead of print]27 101581

N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer.

Ziye Huang, Guang Wang, Yuyun Wu, Tongxin Yang, Lishi Shao, Bowei Yang, Pei Li, Jiongming Li.

  OBJECTIVES: Identification of m6A- related lncRNAs associated with BC diagnosis and prognosis.METHODS: From the TCGA database, we obtained transcriptome data and corresponding clinical information (including histopathological and CT imaging data) for 408 patients. And bioinformatics, computational histopathology, and radiomics were used to identify and analyze diagnostic and prognostic biomarkers of m6A-related lncRNAs in BC.
RESULTS: 3 significantly high-expressed m6A-related lncRNAs were significantly associated with the prognosis of BC. The BC samples were divided into two subgroups based on the expression of the 3 lncRNAs. The overall survival of patients in cluster 2 was significantly lower than that in cluster 1. The immune landscape results showed that the expression of PD-L1, T cells follicular helper, NK cells resting, and mast cells activated in cluster 2 were significantly higher, and naive B cells, plasma cells, T cells regulatory (Tregs), and mast cells resting were significantly lower. Computational histopathology results showed a significantly higher percentage of tumor-infiltrating lymphocytes (TILs) in cluster 2. The radiomics results show that the 3 eigenvalues of diagnostics image-original minimum, diagnostics image-original maximum, and original GLCM inverse variance are significantly higher in cluster 2. High expression of 2 bridge genes in the PPI network of 30 key immune genes predicts poorer disease-free survival, while immunohistochemistry showed that their expression levels were significantly higher in high-grade BC than in low-grade BC and normal tissue.
CONCLUSION: Based on the results of immune landscape, computational histopathology, and radiomics, these 3 m6A-related lncRNAs may be diagnostic and prognostic biomarkers for BC.

Keywords:  Biomarker; Diagnosis; Prognosis; Radiomics; Urinary bladder neoplasms

DOI:  https://doi.org/10.1016/j.tranon.2022.101581
Apoptosis. 2022 Nov 04.

NRP1 contributes to stemness and potentiates radioresistance via WTAP-mediated m6A methylation of Bcl-2 mRNA in breast cancer.

Yang Wang, Lin Zhang, Xiao-Lin Sun, Ya-Chun Lu, Si Chen, Dong-Sheng Pei, Lan-Sheng Zhang.

  NRP1 is a transmembrane glycoprotein that is highly expressed in a variety of tumors. There is evidence that NRP1 can enhance the stem cell properties of tumor cells, which are thought to be resistant to radiotherapy. This study aims to elucidate the potential mechanism of NRP1 in radiation resistance. We transfected NRP1 siRNA and plasmid in breast cancer cells to detect the expression of cancer stem cell markers by western blot and qRT-PCR. The effect of NRP1 on radiotherapy resistance was assesses by immunofluorescence and flow cytometry. In vivo, we established xenograft tumor model treating with shRNA-NRP1 to assess radiotherapy sensitivity. We found that NRP1 could enhance the stem cell properties and confer radioresistance of breast cancer cells. Mechanistically, we proved that NRP1 reduced IR-induced apoptosis by downregulation of Bcl-2 via methyltransferase WTAP in m6A-depentent way. It is suggested that these molecules may be the therapeutic targets for improving the efficacy of radiotherapy for breast cancer.

Keywords:  Apoptosis; Breast cancer; NRP1; Radioresistance; m6A

DOI:  https://doi.org/10.1007/s10495-022-01784-3
Front Pharmacol. 2022 ;13 1030766

m6A/ m1A /m5C/m7G-related methylation modification patterns and immune characterization in prostate cancer.

Xin Ye, Ruyi Wang, Xiaoqian Yu, Zili Wang, Haifeng Hu, Hanchao Zhang.

  Methylation has a close relationship with immune reactions, metastasis, and cancer cell growth. Additionally, RNA methylation-related proteins have emerged as potential cancer therapeutic targets. The connection between the tumor microenvironment (TME) and methylation-related genes (MRGs) remains unclear. We explored the expression patterns of the MRGs in the genome and transcriptional fields of 796 prostate cancer (PCa) samples using two separate data sets. We identified a relationship between patient clinicopathological characteristics, prognosis, TME cell infiltrating qualities, and different MRG changes, as well as the identification of two distinct molecular groupings. Then, we formed an MRGs model to predict overall survival (OS), and we tested the accuracy of the model in patients with PCa. In addition, we developed a very accurate nomogram to improve the MRG model's clinical applicability. The low-risk group had fewer tumor mutational burden (TMB), greater tumor immune dysfunction and exclusion (TIDE) ratings, fewer mutant genes, and better OS prospects. We discuss how MGRs may affect the prognosis, clinically important traits, TME, and immunotherapy responsiveness in PCa. In order to get a better understanding of MRGs in PCa, we could further explore the prognosis and create more effective immunotherapy regimens to open new avenues.

Keywords:  Methylation modification; Molecular subtype; Prognostic model; Prostate cancer; Tumor microenvironment

DOI:  https://doi.org/10.3389/fphar.2022.1030766
J Genet Genomics. 2022 Oct 26. pii: S1673-8527(22)00243-0. [Epub ahead of print]

Emerging functions of tRNA modifications in mRNA translation and diseases.

Lu Wang, Shuibin Lin.

  tRNAs are essential modulators that recognize mRNA codons and bridge amino acids for mRNA translation. The tRNAs are heavily modified, which is essential for forming a complex secondary structure that facilitates codon recognition and mRNA translation. In recent years, studies have identified the regulatory roles of tRNA modifications in mRNA translation networks. Misregulation of tRNA modifications is closely related to the progression of developmental diseases and cancers. In this review, we summarize the tRNA biogenesis process and then discuss the effects and mechanisms of tRNA modifications on tRNA processing and mRNA translation. Finally, we provide a comprehensive overview of tRNA modifications' physiological and pathological functions, focusing on diseases including cancers.

Keywords:  Cancer; Developmental diseases; Translation; tRNA modification; tRNA processing

DOI:  https://doi.org/10.1016/j.jgg.2022.10.002
J Transl Med. 2022 Oct 29. 20(1): 492

m6A-immune-related lncRNA prognostic signature for predicting immune landscape and prognosis of bladder cancer.

Zi-Hao Feng, Yan-Ping Liang, Jun-Jie Cen, Hao-Hua Yao, Hai-Shan Lin, Jia-Ying Li, Hui Liang, Zhu Wang, Qiong Deng, Jia-Zheng Cao, Yong Huang, Jin-Huan Wei, Jun-Hang Luo, Wei Chen, Zhen-Hua Chen.

  BACKGROUND: N6-methyladenosine (m6A) related long noncoding RNAs (lncRNAs) may have prognostic value in bladder cancer for their key role in tumorigenesis and innate immunity.METHODS: Bladder cancer transcriptome data and the corresponding clinical data were acquired from the Cancer Genome Atlas (TCGA) database. The m6A-immune-related lncRNAs were identified using univariate Cox regression analysis and Pearson correlation analysis. A risk model was established using least absolute shrinkage and selection operator (LASSO) Cox regression analyses, and analyzed using nomogram, time-dependent receiver operating characteristics (ROC) and Kaplan-Meier survival analysis. The differences in infiltration scores, clinical features, and sensitivity to Talazoparib of various immune cells between low- and high-risk groups were investigated.
RESULTS: Totally 618 m6A-immune-related lncRNAs and 490 immune-related lncRNAs were identified from TCGA, and 47 lncRNAs of their intersection demonstrated prognostic values. A risk model with 11 lncRNAs was established by Lasso Cox regression, and can predict the prognosis of bladder cancer patients as demonstrated by time-dependent ROC and Kaplan-Meier analysis. Significant correlations were determined between risk score and tumor malignancy or immune cell infiltration. Meanwhile, significant differences were observed in tumor mutation burden and stemness-score between the low-risk group and high-risk group. Moreover, high-risk group patients were more responsive to Talazoparib.
CONCLUSIONS: An m6A-immune-related lncRNA risk model was established in this study, which can be applied to predict prognosis, immune landscape and chemotherapeutic response in bladder cancer.

Keywords:  Bladder cancer (BLCA); Immune cell infiltration; Immune microenvironment; Long noncoding RNA (lncRNA); Prognosis prediction; m6A (N6-methyladenosine)

DOI:  https://doi.org/10.1186/s12967-022-03711-1
Phys Chem Chem Phys. 2022 Nov 02.

3-Methylation alters excited state decay in photoionised uracil.

Javier Segarra-Martí, Thierry Tran, Michael J Bearpark.

UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the events following photoionisation and electronic excitation in uracil, methylated in the 1' and 3' positions, using the correlated XMS-CASPT2 method. We compare our results against those for uracil and 5-methyl-uracil (thymine) previously published. We find 3-methylation, an epigenetic modification in non-negligible amounts, shows the largest differences in photoionised decay of all three derivatives studied compared to uracil itself. At the S0 minimum, 3-methyl-uracil (3mUra) shows almost degenerate excited cation states. Upon populating the cation manifold, a crossing is predicted featuring different topography compared to other methylated uracil species in this study. We find an effective 3-state conical intersection accessible for 3mUra+, which points towards an additional pathway for radiationless decay. 3-Methylation reduces the potential energy barrier mediating decay to the cation ground state, making it vanish and leading to a pathway that we expect will contribute to the fastest radiationless decay amongst all methylated uracil species studied to date. 1- and 5-methylation, on the other hand, give differences from uracil in detail only: ionisation potentials are slightly red-shifted and the potential energy barrier mediating decay to the cation ground state is small but almost unchanged. By comparing against CASSCF calculations, we establish XMS-CASPT2 is essential to correctly describe conical intersections for 3mUra+. Our calculations show how a chemical modification that seems relatively small electronically can nevertheless have a significant impact on the behaviour of electronic excited states: a single methylation in the 3' position alters the behaviour of the RNA base uracil and appears to open an additional pathway for radiationless decay following ionisation and electronic excitation.

DOI: https://doi.org/10.1039/d2cp03460c
Mediators Inflamm. 2022 ;2022 4766992

Comprehensive Analysis and Functional Characteristics of Differential Expression of N6-Methyladenosine Methylation Modification in the Whole Transcriptome of Rheumatoid Arthritis.

Lei Wan, Jian Liu, Chuanbing Huang, Ziheng Zhu, Kun Wang, Guanghan Sun, Lei Zhu, Zhongxiang Hu.

N6-methyladenosine (m6A) modification is the most prevalent chemical modification in eukaryotic mRNA and is associated with the development of various immune diseases. However, the role of m6A methylation in rheumatoid arthritis (RA) development is unclear. We preliminarily explored the role of m6A methylation-related mRNAs in RA for its clinical application. The discovery of m6A methylation-modifying genes in this study may provide a fresh perspective on the development of drugs for RA treatment. High-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to assess whole-transcriptome m6A modifications in the synovium of patients with RA. The relationship between m6A-modified target genes and RA inflammation and macrophages was determined. The expression of the m6A-modified significant transcript-enriched inflammatory signaling pathway was assessed through animal experiments. Differentially expressed m6A genes were correlated with macrophage activation involved in immune response, vascular endothelium, MAPK signaling pathway, PI3K - Akt signaling pathway, and other inflammatory processes. Furthermore, combined analysis with m6A-seq and RNA-seq revealed 120 genes with significant changes in both m6A modification and mRNA expression. We selected the top 3 candidate mRNAs that were upregulated and downregulated simultaneously. The expression of phosphatase and tensin homolog deleted on chromosome ten (PTEN) mRNA and protein in RA patients was lower than that in healthy control (HC). SHC-binding protein 1 (SHCBP1) and neurexophilin-3 (NXPH3) mRNA expressions were increased in RA patients. The expression of M1 macrophages was increased in RA patients. RA markers are such as rheumatoid factor (RF) and peptide containing citrulline (CCP). Further animal experiments showed that the expression of synovial MAPK, PI3K, and Akt1 proteins in the RA model was increased, and the PTEN, p-PTEN protein expression was decreased. PI3K, Akt1, PTEN, and p-PTEN were correlated to RA joint inflammation. This study revealed a unique pattern of differential m6A methylation modifications in RA and concluded that m6A modification is related to the occurrence of RA synovial inflammation.

DOI: https://doi.org/10.1155/2022/4766992
Nat Commun. 2022 Nov 02. 13(1): 6576

N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection.

Tianye Zhang, Chaonan Shi, Haichao Hu, Zhuo Zhang, Ziqiong Wang, Zhiqing Chen, Huimin Feng, Peng Liu, Jun Guo, Qisen Lu, Kaili Zhong, ZhiHui Chen, Jiaqian Liu, Jiancheng Yu, Jianping Chen, Feng Chen, Jian Yang.

Molecular manipulation of susceptibility (S) genes that are antipodes to resistance (R) genes has been adopted as an alternative strategy for controlling crop diseases. Here, we show the S gene encoding Triticum aestivum m6A methyltransferase B (TaMTB) is identified by a genome-wide association study and subsequently shown to be a positive regulator for wheat yellow mosaic virus (WYMV) infection. TaMTB is localized in the nucleus, is translocated into the cytoplasmic aggregates by binding to WYMV NIb to upregulate the m6A level of WYMV RNA1 and stabilize the viral RNA, thus promoting viral infection. A natural mutant allele TaMTB-SNP176C is found to confer an enhanced susceptibility to WYMV infection through genetic variation analysis on 243 wheat varieties. Our discovery highlights this allele can be a useful target for the molecular wheat breeding in the future.

DOI: https://doi.org/10.1038/s41467-022-34362-x
Front Immunol. 2022 ;13 926461

A comprehensive investigation discovered the novel methyltransferase METTL24 as one presumably prognostic gene for kidney renal clear cell carcinoma potentially modulating tumor immune microenvironment.

Zhongji Jiang, Wei Zhang, Zhipeng Zeng, Donge Tang, Chujiao Li, Wanxia Cai, Yumei Chen, Ya Li, Qiu Jin, Xinzhou Zhang, Lianghong Yin, Xueyan Liu, Yong Xu, Yong Dai.

  Background: Recently, an increasing number of studies have uncovered the aberrant expression of methyltransferase-like family (METTL) plays an important role in tumorigenesis, such as METTL3 (an m6A writer). In our recent work, we discovered METTL24 expression was highly associated with the hazard ratio (HR) of kidney renal clear cell carcinoma (KIRC) compared to other tumors, implying a special function of METTL24 in KIRC carcinogenesis. Until now, the functions and mechanisms of METTL24 in KIRC have remained mostly unknown.Methods: The mRNA expression of METTL24 in KIRC was analyzed using the TIMER 2.0, GEPIA, and UALCAN databases. The immunohistochemical assay was performed to validate METTL24 expression in our self-built Chinese cohort (n tumor = 88, n normal = 85). The gene set enrichment analysis (GSEA) was used to investigate the biological processes in which METTL24 might be engaged. The Spearman analysis was used to evaluate the expression correlations between METTL24 and a range of immunological variables, and the effects of METTL24 on the infiltration levels of multiple immune cells were explored using TCGA data. The upstream transcription factors of METTL24 were screened through a multi-omics analysis.
Results: METTL24 expression in KIRC tissues was significantly decreased compared to normal adjacent kidney tissues, which was associated with the lower survival rate of KIRC patients. METTL24 potentially participated in the immune-relevant biological processes such as cytokine binding, NF-kappa B binding, MHC protein complex, and interleukin-12 action. Besides, METTL24 expression was linked to a number of immune checkpoints, cytokines, chemokines, and chemokine receptors, and also correlated with the infiltration levels of 10 types of immune cells in KIRC. Meanwhile, METTL24 expression differently affected the overall survival rates (OS) of KIRC patients with high or low levels of immune infiltration. Finally, CTCF and EP300 were discovered to be the probable transcription factors of METTL24 in KIRC.
Conclusion: This study revealed that METTL24 might serve as a prognostic marker in KIRC and as one immune-relevant target for clinical treatment.

Keywords:  METTL24; immune microenvironment; kidney cancer; methyltransferase; prognostic biomarker

DOI:  https://doi.org/10.3389/fimmu.2022.926461