bims-rimeca 2022-12-25 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022‒12‒25
twenty-six papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

N6-methyladenosine Modification of Noncoding RNAs: Mechanisms and Clinical Applications in Cancer.
ALKBH1-mediated m1 A demethylation of METTL3 mRNA promotes the metastasis of colorectal cancer by downregulating SMAD7 expression.
The regulatory role of N6-methyladenosine RNA modification in gastric cancer: Molecular mechanisms and potential therapeutic targets.
METTL3 is aberrantly expressed in endometriosis and suppresses proliferation, invasion, and migration of endometrial stromal cells.
Exon junction complex shapes the m6A epitranscriptome.
Transcriptome-wide profiling of mRNA N6-methyladenosine modification in rice panicles and flag leaves.
The Role of the m6A RNA Methyltransferase METTL16 in Gene Expression and SAM Homeostasis.
Diagnostic signature, subtype classification, and immune infiltration of key m6A regulators in osteomyelitis patients.
The N6-Methyladenosine Regulator ALKBH5 Mediated Stromal Cell-Macrophage Interaction via VEGF Signaling to Promote Recurrent Spontaneous Abortion: A Bioinformatic and In Vitro Study.
Bone Marrow Mesenchymal Stem Cell-Derived Exosomes Inhibit Triple-Negative Breast Cancer Cell Stemness and Metastasis via an ALKBH5-Dependent Mechanism.
Overexpression of FTO alleviates osteoarthritis by regulating the processing of miR-515-5p and the TLR4/MyD88/NF-κB axis.
Analysis of N 6 -methyladenosine RNA Modification Levels by Dot Blotting.
Engineering m6A demethylation-activated DNAzyme for visually and sensitively sensing fat mass and obesity-associated protein.
METTL3-Mediated N6-Methyladenosine Methylation Modifies Foxp3 mRNA Levels and Affects the Treg Cells Proportion in Peripheral Blood of Patients with Asthma.
HNRNPC, a predictor of prognosis and immunotherapy response based on bioinformatics analysis, is related to proliferation and invasion of NSCLC cells.
Predicting N6-Methyladenosine Sites in Multiple Tissues of Mammals through Ensemble Deep Learning.
Increased levels of N6-methyladenosine in peripheral blood RNA: a perspective diagnostic biomarker and therapeutic target for non-small cell lung cancer.
m5C regulator-mediated modification patterns and tumor microenvironment infiltration characterization in colorectal cancer: One step closer to precision medicine.
HDAC1 overexpression promoted by METTL3-IGF2BP2 inhibits FGF21 expression in metabolic syndrome-related liver injury.
N6-methyladenosine-modified USP13 induces pro-survival autophagy and imatinib resistance via regulating the stabilization of autophagy-related protein 5 in gastrointestinal stromal tumors.
Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation.
METTL3 Regulates the Inflammatory Response in CPB2 Toxin-Exposed IPEC-J2 Cells through the TLR2/NF-κB Signaling Pathway.
Role of m6A modification and novel circ_0066715/ miR-486-5p/ ETS1 axis in rheumatoid arthritis macrophage polarization progression.
Artemisitene suppresses rheumatoid arthritis progression via modulating METTL3-mediated N6-methyladenosine modification of ICAM2 mRNA in fibroblast-like synoviocytes.
RNA methylation in vascular disease: a systematic review.
Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation.

Diagnostics (Basel). 2022 Nov 30. pii: 2996. [Epub ahead of print]12(12):

N6-methyladenosine Modification of Noncoding RNAs: Mechanisms and Clinical Applications in Cancer.

Mingyang Ma, Tong Ye, Jiewei Wang, Haiying Zhao, Shutian Zhang, Peng Li, Guiping Zhao.

  N6-methyladenosine (m6A) modification remains the most pivotal epigenetic modification on RNA. As we know, m6A not only affects physiological processes but is also involved in carcinoma. Noncoding RNAs play an indispensable role in the occurrence and development of carcinoma. However, a large amount of research is focused on mRNA currently. Insufficient research has been done on the relationship between noncoding RNA (ncRNA) methylation and cancer. Therefore, this review aims to introduce the theoretical knowledge of m6A modification in noncoding RNA, discuss its function in tumorigenesis and progression, and ultimately summarize its potential clinical applications.

Keywords:  N6-methyladenosine; cancer; noncoding RNA

DOI:  https://doi.org/10.3390/diagnostics12122996
Mol Oncol. 2022 Dec 22.

ALKBH1-mediated m1 A demethylation of METTL3 mRNA promotes the metastasis of colorectal cancer by downregulating SMAD7 expression.

Wenwen Chen, Hao Wang, Shuyi Mi, Liming Shao, Zhipeng Xu, Meng Xue.

  Colorectal cancer (CRC) is one of the most common malignancies, and the main cause of death from CRC is tumor metastasis. m1 A RNA modification plays critical roles in many biological processes. However, the role of m1 A modification in CRC remains unclear. Here, we find that the m1 A demethylase alkB homolog 1, histone H2A dioxygenase (ALKBH1) is overexpressed in CRC and is associated with metastasis and poor prognosis. Upregulation of ALKBH1 expression promotes CRC metastasis in vitro and in vivo. Mechanistically, knockdown of ALKBH1 results in a decrease in methyltransferase 3, N6-adenosine-methyltransferase complex catalytic subunit (METTL3) expression, probably due to m1 A modification of METTL3 mRNA, followed by m6 A demethylation of SMAD family member 7 (SMAD7) mRNA. In addition, downregulation of SMAD7 establishes an aggressive phenotype. More importantly, the cell migration and invasion defects caused by ALKBH1 depletion or METTL3 depletion are significantly reversed by SMAD7 silencing. Considering these results collectively, we propose that ALKBH1 promotes CRC metastasis by destabilizing SMAD7 through METTL3.

Keywords:  ALKBH1; METTL3; colorectal cancer metastasis; m1A modification; m6A modification

DOI:  https://doi.org/10.1002/1878-0261.13366
Front Oncol. 2022 ;12 1074307

The regulatory role of N6-methyladenosine RNA modification in gastric cancer: Molecular mechanisms and potential therapeutic targets.

Gaofeng Li, Qiru Fu, Cong Liu, Yuxi Peng, Jun Gong, Shilan Li, Yan Huang, Haiyuan Zhang.

  N6-methyladenosinen (m6A) methylation is a frequent RNA methylation modification that is regulated by three proteins: "writers", "erasers", and "readers". The m6A modification regulates RNA stability and other mechanisms, including translation, cleavage, and degradation. Interestingly, recent research has linked m6A RNA modification to the occurrence and development of cancers, such as hepatocellular carcinoma and non-small cell lung cancer. This review summarizes the regulatory role of m6A RNA modification in gastric cancer (GC), including targets, the mechanisms of action, and the potential signaling pathways. Our present findings can facilitate our understanding of the significance of m6A RNA modification in GC.

Keywords:  RNA methylation; gastric cancer; m6A RNA modification; mRNA; ncRNA

DOI:  https://doi.org/10.3389/fonc.2022.1074307
Kaohsiung J Med Sci. 2022 Dec 22.

METTL3 is aberrantly expressed in endometriosis and suppresses proliferation, invasion, and migration of endometrial stromal cells.

Qian-Chen Zhang.

  Endometriosis (EM) is one of the leading gynecological disorders, and associated with excessive functioning of endometrial stromal cells (ESCs). The current study was conducted to determine the expression and role of methyltransferase-like 3 (METTL3) in the proliferation, invasion, and migration of ESCs in EM. The documented expression levels of METTL3, microRNA (miR)-21-5p, and WNT inhibitory factor 1 (WIF1) in eutopic (Eut) and ectopic (Ect) endometrial tissues and ESCs were determined by a combination of real-time quantitative polymerase chain reaction and Western blot assay. After transfection with pcDNA3.1-METTL3, miR-21-5p mimic, and WIF1 small interfering RNA, cell counting kit-8, colony formation, and Transwell assays were performed in the Ect ESCs (Ect-ESCs). Subsequently, the binding of miR-21-5p to METTL3 was analyzed, along with quantification of the N6-methyladenosine (m6A) level, the enrichments of METTL3 and m6A on WIF1, and the mRNA stability of WIF1. In our findings, METTL3 was downregulated in the EM tissues and cells. METTL3 overexpression intrinsically reduced the proliferation, invasion, and migration of Ect-ESCs. miR-21-5p inhibited the METTL3 expression while METTL3 enhanced the mRNA stability and expression of WIF1 via m6A modification. Additionally, a negative correlation of METTL3 was identified with miR-21-5p along with a positive correlation with the WIF1 mRNA in EM tissues. The miR-21-5p overexpression or WIF1 downregulation enhanced the proliferation, invasion, and migration of Ect-ESCs. Collectively, miR-21-5p inhibited the METTL3-mediated m6A modification and mRNA stability of WIF1, thereby facilitating the proliferation, invasion, and migration of Ect-ESCs.

Keywords:  METTL3; WIF1; endometrial stromal cells; endometriosis; m6A modification

DOI:  https://doi.org/10.1002/kjm2.12626
Nat Commun. 2022 Dec 23. 13(1): 7904

Exon junction complex shapes the m6A epitranscriptome.

Xin Yang, Robinson Triboulet, Qi Liu, Erdem Sendinc, Richard I Gregory.

N6-methyladenosine (m6A), the most abundant modification of mRNA, is essential for normal development and dysregulation promotes cancer. m6A is highly enriched in the 3' untranslated region (UTR) of a large subset of mRNAs to influence mRNA stability and/or translation. However, the mechanism responsible for the observed m6A distribution remains enigmatic. Here we find the exon junction complex shapes the m6A landscape by blocking METTL3-mediated m6A modification close to exon junctions within coding sequence (CDS). Depletion of EIF4A3, a core component of the EJC, causes increased METTL3 binding and m6A modification of short internal exons, and sites close to exon-exon junctions within mRNA. Reporter gene experiments further support the role of splicing and EIF4A3 deposition in controlling m6A modification via the local steric blockade of METTL3. Our results explain how characteristic patterns of m6A mRNA modification are established and uncover a role of the EJC in shaping the m6A epitranscriptome.

DOI: https://doi.org/10.1038/s41467-022-35643-1
Genomics. 2022 Dec 16. pii: S0888-7543(22)00289-0. [Epub ahead of print] 110542

Transcriptome-wide profiling of mRNA N6-methyladenosine modification in rice panicles and flag leaves.

Li Wang, Chenhui Yang, Qianru Shan, Miao Zhao, Juanjuan Yu, Yong-Fang Li.

  N6-methyladenosine (m6A) modification is essential for plant growth and development. Exploring m6A methylation patterns in rice tissues is fundamental to understanding the regulatory effects of this modification. Here, we profiled the transcriptome-wide m6A landscapes of rice panicles at the booting stage (PB) and flowering stage (PF), and of flag leaves at the flowering stage (LF). The global m6A level differed significantly among the three tissues and was closely associated with the expression of writer and eraser genes. The methylated gene ratio was higher in the flag leaves than in the panicles. Compared with commonly methylated genes, tissue-specific methylated genes showed lower levels of both m6A modification and expression, and a preference for m6A deposition in the coding sequence region. The m6A profiles of the two organs had more distinct differences than the profiles of the same organ at different stages. A negative correlation between m6A levels and gene expression was observed in PF vs. PB but not in PF vs. LF, indicting the complicated regulatory effect of m6A on gene expression. The distinct expression patterns of m6A reader genes in different tissues indicate that readers may affect gene stability through binding. Overall, our findings demonstrated that m6A modification influences tissue function by regulating gene expression. Our findings provide valuable insights on the regulation and biological functions of m6A modifications in rice.

Keywords:  Flag leaf; Gene expression; Methylation pattern; N(6)-methyladenosine; Panicle; Rice

DOI:  https://doi.org/10.1016/j.ygeno.2022.110542
Genes (Basel). 2022 Dec 08. pii: 2312. [Epub ahead of print]13(12):

The Role of the m6A RNA Methyltransferase METTL16 in Gene Expression and SAM Homeostasis.

Jacqueline E Mermoud.

  The RNA methylation of adenosine at the N6-position (m6A) has attracted significant attention because of its abundance and dynamic nature. It accounts for more than 80% of all RNA modifications present in bacteria and eukaryotes and regulates crucial aspects of RNA biology and gene expression in numerous biological processes. The majority of m6A found in mammals is deposited by a multicomponent complex formed between methyltransferase-like (METTL) proteins METTL3 and METTL14. In the last few years, the list of m6A writers has grown, resulting in an expansion of our understanding of the importance of m6A and the methylation machinery. The characterization of the less familiar family member METTL16 has uncovered a new function of the m6A methylation apparatus, namely the fine-tuning of the cellular levels of the major methyl donor S-adenosylmethionine (SAM). METTL16 achieves this by adjusting the levels of the enzyme that synthesizes SAM in direct response to fluctuations in the SAM availability. This review summarizes recent progress made in understanding how METTL16 can sense and relay metabolic information and considers the wider implications. A brief survey highlights similarities and differences between METTL16 and the better-known METTL3/14 complex, followed by a discussion of the target specificity, modes of action and potential roles of METTL16.

Keywords:  DNA methylation; MAT2A; METTL16; N6-methyladenosine; S-adenosyl-methionine; chromatin; epigenetics; epitranscriptome; histone methylation; metabolism

DOI:  https://doi.org/10.3390/genes13122312
Front Genet. 2022 ;13 1044264

Diagnostic signature, subtype classification, and immune infiltration of key m6A regulators in osteomyelitis patients.

Xiangwen Shi, Haonan Ni, Yipeng Wu, Minzheng Guo, Bin Wang, Yue Zhang, Bihuan Zhang, Yongqing Xu.

  Background: As a recurrent inflammatory bone disease, the treatment of osteomyelitis is always a tricky problem in orthopaedics. N6-methyladenosine (m6A) regulators play significant roles in immune and inflammatory responses. Nevertheless, the function of m6A modification in osteomyelitis remains unclear. Methods: Based on the key m6A regulators selected by the GSE16129 dataset, a nomogram model was established to predict the incidence of osteomyelitis by using the random forest (RF) method. Through unsupervised clustering, osteomyelitis patients were divided into two m6A subtypes, and the immune infiltration of these subtypes was further evaluated. Validating the accuracy of the diagnostic model for osteomyelitis and the consistency of clustering based on the GSE30119 dataset. Results: 3 writers of Methyltransferase-like 3 (METTL3), RNA-binding motif protein 15B (RBM15B) and Casitas B-lineage proto-oncogene like 1 (CBLL1) and three readers of YT521-B homology domain-containing protein 1 (YTHDC1), YT521-B homology domain-containing family 3 (YTHDF2) and Leucine-rich PPR motif-containing protein (LRPPRC) were identified by difference analysis, and their Mean Decrease Gini (MDG) scores were all greater than 10. Based on these 6 significant m6A regulators, a nomogram model was developed to predict the incidence of osteomyelitis, and the fitting curve indicated a high degree of fit in both the test and validation groups. Two m6A subtypes (cluster A and cluster B) were identified by the unsupervised clustering method, and there were significant differences in m6A scores and the abundance of immune infiltration between the two m6A subtypes. Among them, two m6A regulators (METTL3 and LRPPRC) were closely related to immune infiltration in patients with osteomyelitis. Conclusion: m6A regulators play key roles in the molecular subtypes and immune response of osteomyelitis, which may provide assistance for personalized immunotherapy in patients with osteomyelitis.

Keywords:  N6-methyladenosine (m6A); diagnosis; immune infiltration; osteomyelitis; subtype

DOI:  https://doi.org/10.3389/fgene.2022.1044264
Int J Mol Sci. 2022 Dec 13. pii: 15819. [Epub ahead of print]23(24):

The N6-Methyladenosine Regulator ALKBH5 Mediated Stromal Cell-Macrophage Interaction via VEGF Signaling to Promote Recurrent Spontaneous Abortion: A Bioinformatic and In Vitro Study.

Yongbo Zhao, Jiani Sun, Liping Jin.

  Successful conception requires the synchrony of multiple systems and organs. Dysregulation of stromal cell-immune cell interactions has been proposed to be associated with recurrent spontaneous abortion. However, the mechanism of this regulation has not been well elucidated. N6-methyladenosine is one of the most common RNA modifications, and is involved in many pathological processes. Our group has demonstrated that abnormal patterns of m6A modification inhibit trophoblast invasion and contribute to adverse pregnancy outcomes. The association between m6A regulators and stromal cell-immune cell interactions is unclear. We obtained RNA-seq profiles from a GEO dataset and identified differentially expressed m6A regulators between healthy controls and patients with a recurrent spontaneous abortion history. ROC curves, functional enrichment and subclassification analysis were applied to elucidate the role of m6A regulators in pregnancy. We verified the expression of m6A regulators and constructed an overexpression cell line in a coculture system to reveal ALKBH5 function in stromal cell-macrophage interactions. We identified 11 differentially expressed m6A regulators between healthy controls and patients with a recurrent spontaneous abortion history. Then, we identified the correlation between "eraser" genes and "writer" genes. We tested the predictive abilities of the 11 m6A regulators based on another dataset and verified their expression in primary human endometrial stromal cells. We then subclassified three distinct patterns using the 11 genes and visualized genes related to immune infiltration and macrophage function in each cluster. ALKBH5 was proven to be correlated with recurrent spontaneous abortion. To verify the role of ALKBH5 in RSA, we constructed an ALKBH5-overexpression cell line. Finally, we cocultured the overexpression cell line with THP-1 cells. A decrease in M2 differentiation was observed, and this bias could be attributed to the hyposecretion of VEGF in stromal cells. N6-methyladenosine regulators play a pivotal role in stromal cell-immune cell interactions at the maternal-fetal interface. Overexpression of the m6A "eraser" gene ALKBH5 in stromal cells resulted in the hyposecretion of VEGF. Dysregulation of VEGF might impair macrophage recruitment and M2 differentiation, which could be the potential cause of recurrent spontaneous abortion.

Keywords:  ALKBH5; N6-methyladenosine; VEGF; macrophage; recurrent spontaneous abortion

DOI:  https://doi.org/10.3390/ijms232415819
Cancers (Basel). 2022 Dec 09. pii: 6059. [Epub ahead of print]14(24):

Bone Marrow Mesenchymal Stem Cell-Derived Exosomes Inhibit Triple-Negative Breast Cancer Cell Stemness and Metastasis via an ALKBH5-Dependent Mechanism.

Yun Hu, Hanyuan Liu, Xiudi Xiao, Qiao Yu, Rong Deng, Lixin Hua, Jinhua Wang, Xinwei Wang.

  BACKGROUND: Abnormal N6-methyladenosine (m6A) modification caused by m6A regulators is a common characteristic in various tumors. However, little is known about the role of m6A regulator AlkB homolog 5 (ALKBH5) in triple-negative breast cancer (TNBC). In this study, we analyzed the influence of ALKBH5 on the stemness of TNBC and the molecular mechanism using bioinformatics analysis and in vivo animal experiments.METHODS: RNA expression data and single-cell RNA sequencing (scRNA-seq) data were downloaded from the TCGA and GEO databases. Following intersection analysis, key genes involved in the TNBC cell stemness were determined, which was followed by functional enrichment analysis, PPI and survival analysis. Exosomes were extracted from bone marrow mesenchymal stem cells (BMSC-Exos) where ALKBH5 inhibition assay was conducted to verify their function in the biological characteristics of TNBC cells.
RESULTS: Bioinformatics analysis revealed 45 key genes of ALKBH5 regulating TNBC cell stemness. In addition, UBE2C was predicted as a key downstream gene and p53 was predicted as a downstream signaling of ALKBH5. In vivo data confirmed that ALKBH5 upregulated UBE2C expression by regulating the m6A modification of UBE2C and reduced p53 expression, thus promoting the stemness, growth and metastasis of TNBC cells. BMSC-Exos suppressed the tumor stemness, growth and metastasis of TNBC cells and ALKBH5 shRNA-loaded BMSC-Exos showed a more significant suppressive role.
CONCLUSION: Taken together, our findings indicated that ALKBH5 shRNA-loaded BMSC-Exos reduced TNBC cell stemness, growth and metastasis and define a promising strategy to treat TNBC.

Keywords:  ALKBH5; UBE2C; bone marrow mesenchymal stem cells; exosomes; m6A demethylase; p53; stemness; triple-negative breast cancer

DOI:  https://doi.org/10.3390/cancers14246059
Int Immunopharmacol. 2022 Dec 18. pii: S1567-5769(22)01009-8. [Epub ahead of print]114 109524

Overexpression of FTO alleviates osteoarthritis by regulating the processing of miR-515-5p and the TLR4/MyD88/NF-κB axis.

Dongfeng Cai, Jing Zhang, Jin Yang, Qi Lv, Chao Zhong.

  OBJECTIVE: Osteoarthritis (OA) is regarded as the most prevalent chronic joint disease. Fat-mass and obesity-associated gene (FTO) is involved in OA alleviation. This study elucidated the role of FTO in OA and the associated mechanism.METHODS: We established a cell injury model by stimulating human normal chondrocytes (C28/I2) with lipopolysaccharide (LPS), and measured cell viability, apoptosis, and inflammatory cytokines using CCK-8, flow cytometry, Western blot, and ELISA. TLR4, MyD88, p/t-p65, and p/t-IκBα levels, FTO, COX-2, and iNOS mRNA levels, and m6A methylation levels were measured by Western blot, RT-qPCR, and colorimetry. RNA immunoprecipitation and co-immunoprecipitation were conducted to confirm the interaction between FTO and DGCR8. pri-miR-515-5p process was regulated in an m6A-dependent manner. After predicting the presence of several binding sites between miR-515-5p and TLR4 on Targetscan, we further confirmed their relationship by dual-luciferase assay. OA rat models were established by monosodium iodoacetate injection. The pathological changes in knee joint were observed by HE staining.
RESULTS: FTO was diminished in LPS-induced C28/I2 cells. With the increase of LPS concentration, cell viability was repressed, apoptosis rate was increased, and inflammatory markers were promoted, which were annulled by FTO overexpression. FTO interacted with DGCR8 and modulated the pri-miR-515-5p processing in an m6A-dependent manner. miR-515-5p silencing partially averted the inhibitory effect of FTO on LPS-induced cell injury. Given that TLR4 was a direct target of miR-515-5p, miR-515-5p inactivated the MyD88/NF-κB pathway by targeting TLR4. FTO overexpression improved cartilage structure in OA rats, reduced apoptosis, inhibited inflammation in synovial fluid, and repressed the TLR4/MyD88/NF-κB axis.
CONCLUSION: FTO alleviated OA in an m6A-dependent manner via the miR-515-5p/TLR4/MyD88/NF-κB axis.

Keywords:  Cell injury; Lipopolysaccharide; N6-methyladenosine; NF-κB; Obesity-associated gene; Osteoarthritis; TLR4; miR-515-5p

DOI:  https://doi.org/10.1016/j.intimp.2022.109524
Bio Protoc. 2022 Dec 05. pii: e4565. [Epub ahead of print]12(23):

Analysis of N 6 -methyladenosine RNA Modification Levels by Dot Blotting.

Yu Du, Mingyue Xia, Zhigang Hu.

  N 6 -methyladenosine (m 6 A) is the most prevalent internal modification of eukaryotic messenger RNAs (mRNAs), affecting their fold, stability, degradation, and cellular interaction(s) and implicating them in processes such as splicing, translation, export, and decay. The m 6 A modification is also extensively present in non-coding RNAs, including microRNAs (miRNAs), ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs). Common m 6 A methylation detection techniques play an important role in understanding the biological function and potential mechanism of m 6 A, mainly including the quantification and specific localization of m 6 A modification sites. Here, we describe in detail the dot blotting method for detecting m 6 A levels in RNA (mRNA as an example), including total RNA extraction, mRNA purification, dot blotting, and data analysis. This protocol can also be used to enrich specific RNAs (such as tRNA, rRNA, or miRNA) by isolation technology to detect the m 6 A level of single RNA species, so as to facilitate further studies of the role of m 6 A in biological processes. This protocol was validated in: eLife (2022), DOI: 10.7554/eLife.75231.

Keywords:   Dot blot ; METTL3 ; N 6 -methyladenosine ; Non-coding RNAs ; RNA m 6 A ; RNA modification ; mRNA

DOI:  https://doi.org/10.21769/BioProtoc.4565
Biosens Bioelectron. 2022 Dec 13. pii: S0956-5663(22)01047-8. [Epub ahead of print]222 115007

Engineering m6A demethylation-activated DNAzyme for visually and sensitively sensing fat mass and obesity-associated protein.

Liu Shi, Xuemei Ma, Haojie Xie, Yujia Qin, Yue Huang, Yuanyuan Zhang, Lizhou Sun, Jie Yang, Genxi Li.

  Fat mass and obesity-associated protein (FTO) regulating the N6-methyladenine (m6A, the most pervasive epigenetic modification) levels within the nucleus has been identified as a potential biomarker for cancer diagnosis and prognosis. However, current methods for FTO detection are complicated or/and not sensitive enough for practical application. Herein, we propose a colorimetric biosensor for detecting FTO based on a delicate design of m6A demethylation-activated DNAzyme. Specifically, an m6A-blocked DNAzyme is constructed as a switch of the biosensor that can be turned on by target FTO. The decreased thermal stability resulting from substrate cleavage leads to a DNAzyme recycling to produce multiple primers. Then the rolling circle amplification (RCA) reactions can be initiated to generate G-quadruplex-DNAzymes catalyzing 2,2-azino-bis-(3-ethylben-zthiazoline-6-sulfonic acid (ABTS) oxidation which can be readily observed by the naked eye. Quantitative detection can also be achieved with a limit of detection (LOD) down to 69.9 fM, exhibiting higher sensitivity than previous reports. Therefore, this biosensor opens a simple and sensitive way to achieve visual assay of FTO via triple signal amplification. In addition, our biosensor has been successfully applied to FTO detection in clinical samples, which shows great potential in clinical molecular diagnostics.

Keywords:  Colorimetric biosensor; DNAzyme; Demethylation; Fat mass and obesity-associated protein; N6-methyladenosine

DOI:  https://doi.org/10.1016/j.bios.2022.115007
Ann Clin Lab Sci. 2022 Nov;52(6): 884-894

METTL3-Mediated N6-Methyladenosine Methylation Modifies Foxp3 mRNA Levels and Affects the Treg Cells Proportion in Peripheral Blood of Patients with Asthma.

Linxia Fan, Jiqiang Wu, Hongjuan Wang, Qizhang Chen, Xiaomin He, Qiong Wang, Zhian Yang.

OBJECTIVE: To investigate the regulatory effect and mechanism of methyltransferase-like protein 3 (METTL3)-mediated N6-methyladenosine methylation (m6A) on forkhead box protein 3 (Foxp3) levels and the proportion of regulatory T (Treg) cells in the peripheral blood of patients with asthma.METHODS: Flow cytometry and ELISA were used to detect the differences in the proportions of Treg cells and serum interleukins (ILs) 4 and 7, respectively, in the peripheral blood between healthy individuals and patients with different asthma conditions. Reverse transcription-quantitative PCR (RT-qPCR) and Western blotting were used to detect the mRNA and protein expression levels, respectively, of METTL3 and Foxp3 in CD4+ T cells in the peripheral blood samples of different groups. M6A blot and m6A coimmunoprecipitation-PCR were used to detect the global and Foxp3 mRNA m6A levels, respectively, in the peripheral blood CD4+ T cells. CD4+ T cells collected from the peripheral blood of patients with asthma were subjected to in vitro transfection to knockdown the METTL3 levels and observe changes in the Foxp3 mRNA, protein, m6A levels, and RNA stability. Flow cytometry and ELISA were used to detect the changes in the Treg cell proportion and IL-4 and IL-17 levels in the cell culture supernatant.
RESULTS: Compared with the healthy individuals, the ratio of Treg cells to peripheral blood CD4+ T cells was significantly decreased and the Foxp3 mRNA and protein expression was downregulated in patients with asthma with disease progression. The Foxp3 mRNA and protein expression levels were positively correlated with the Treg cell proportion and negatively correlated with IL-17 expression. The global and Foxp3 mRNA m6A levels were increased in the peripheral blood CD4+ T cells of patients with asthma. METTL3 expression was significantly higher in the peripheral blood CD4+ T cells of patients with asthma compared with healthy individuals. After METTL3 knockdown, the Foxp3 mRNA m6A level was reduced, and the stability of Foxp3 mRNA and protein expression was increased. YTHDF2 could bind to the m6A site in 3'UTR of Foxp3 mRNA. Knockdown of YTHDF2 regulated the level and stability of Foxp3 mRNA. METTL3 knockdown reduced the ratio of Treg cells to CD4+ T cells and the IL-4 and IL-17 secretion levels from CD4+ T cells in the peripheral blood of patients with asthma.
CONCLUSIONS: High METTL3 expression in the peripheral blood CD4+ T cells of patients with asthma increased the m6A level and reduced the stability of Foxp3 mRNA in a YTHDF2-dependent way, thereby reducing the expression of Foxp3 and the proportion of Treg cells.

Keywords: Methyltransferase-like protein 3 (METTL3); N6-methyladenosine methylation (m6A); asthma; forkhead box protein 3 (Foxp3); regulatory T (Treg) cells
Respir Res. 2022 Dec 19. 23(1): 362

HNRNPC, a predictor of prognosis and immunotherapy response based on bioinformatics analysis, is related to proliferation and invasion of NSCLC cells.

Zhuoyu Gu, Yang Yang, Qian Ma, Hui Wang, Song Zhao, Yu Qi, Yixin Li.

  BACKGROUND: Little is known about the relationship between N6-methyladenosine (m6A)-related genes and tumor immune microenvironment (TIME) in non-small cell lung cancer (NSCLC). It is unclear which m6A regulators are essential for NSCLC progression. The aim of this work was to excavate the role of m6A-related genes in the TIME and progression of NSCLC.METHODS: Based on bioinformatics analysis, heterogeneous nuclear ribonucleoprotein C (HNRNPC) was considered as the most influential m6A regulator. Further study was investigated using patient samples, stable cell lines, and xenograft mice models.
RESULTS: The differentially expressed profiles of m6A-related genes were established in NSCLC, and the NSCLC samples were clustered into two subtypes with different immune infiltration and survival time. Next, we found that the risk score (RS) based on m6A-related genes was a predictor of prognosis and immunotherapy response for NSCLC, in which HNRNPC was considered as the most influential m6A regulator. In NSCLC patients, we confirmed that HNRNPC predicted poor prognosis and correlated with tumor invasion and lymph node metastasis. RNA-seq data revealed that HNRNPC was involved in cell growth, cell migration, extracellular matrix organization and angiogenesis. In vitro, we verified that HNRNPC knockdown attenuated the cell proliferation, clonogenicity, invasion and migration. In vivo, HNRNPC knockdown inhibited the tumor growth and lung metastasis. Additionally, HNRNPC knockdown was associated with high CD8 + T cell infiltration, along with elevated CD4 + T cell infiltration, collagen production and angiogenesis.
CONCLUSIONS: M6A regulator HNRNPC, a predictor of prognosis and immunotherapy response based on bioinformatics analysis, is related to proliferation and invasion of NSCLC cells.

Keywords:  HNRNPC; Invasion; NSCLC; Proliferation; m6A methylation

DOI:  https://doi.org/10.1186/s12931-022-02227-y
Int J Mol Sci. 2022 Dec 07. pii: 15490. [Epub ahead of print]23(24):

Predicting N6-Methyladenosine Sites in Multiple Tissues of Mammals through Ensemble Deep Learning.

Zhengtao Luo, Liliang Lou, Wangren Qiu, Zhaochun Xu, Xuan Xiao.

  N6-methyladenosine (m6A) is the most abundant within eukaryotic messenger RNA modification, which plays an essential regulatory role in the control of cellular functions and gene expression. However, it remains an outstanding challenge to detect mRNA m6A transcriptome-wide at base resolution via experimental approaches, which are generally time-consuming and expensive. Developing computational methods is a good strategy for accurate in silico detection of m6A modification sites from the large amount of RNA sequence data. Unfortunately, the existing computational models are usually only for m6A site prediction in a single species, without considering the tissue level of species, while most of them are constructed based on low-confidence level data generated by an m6A antibody immunoprecipitation (IP)-based sequencing method, thereby restricting reliability and generalizability of proposed models. Here, we review recent advances in computational prediction of m6A sites and construct a new computational approach named im6APred using ensemble deep learning to accurately identify m6A sites based on high-confidence level data in multiple tissues of mammals. Our model im6APred builds upon a comprehensive evaluation of multiple classification methods, including four traditional classification algorithms and three deep learning methods and their ensembles. The optimal base-classifier combinations are then chosen by five-fold cross-validation test to achieve an effective stacked model. Our model im6APred can produce the area under the receiver operating characteristic curve (AUROC) in the range of 0.82-0.91 on independent tests, indicating that our model has the ability to learn general methylation rules on RNA bases and generalize to m6A transcriptome-wide identification. Moreover, AUROCs in the range of 0.77-0.96 were achieved using cross-species/tissues validation on the benchmark dataset, demonstrating differences in predictive performance at the tissue level and the need for constructing tissue-specific models for m6A site prediction.

Keywords:  RNA modification; ensemble deep learning; m6A site identification

DOI:  https://doi.org/10.3390/ijms232415490
Clin Chem Lab Med. 2022 Dec 22.

Increased levels of N6-methyladenosine in peripheral blood RNA: a perspective diagnostic biomarker and therapeutic target for non-small cell lung cancer.

Haofan Yin, Honghai Hong, Ping Yin, Wenhua Lu, Shiqiong Niu, Xinchun Chen, Yong Xia, Ping Jiang, Zhijian Huang.

  OBJECTIVES: Due to lack of effective biomarkers for non-small cell lung cancer (NSCLC), many patients are diagnosed at an advanced stage, which leads to poor prognosis. Dysregulation of N6-methyladenosine (m6A) RNA contributes significantly to tumorigenesis and tumor progression. However, the diagnostic value of m6A RNA status in peripheral blood to screen NSCLC remains unclear.METHODS: Peripheral blood samples from 152 NSCLC patients and 64 normal controls (NCs) were applied to assess the m6A RNA levels. Bioinformatics and qRT-PCR analysis were performed to identify the specific immune cells in peripheral blood cells and investigate the mechanism of the alteration of m6A RNA levels.
RESULTS: Robust elevation of m6A RNA levels of peripheral blood cells was exhibited in the NSCLC group. Moreover, the m6A levels increased as NSCLC progressed, and reduced after treatment. The m6A levels contained area under the curve (AUC) was 0.912, which was remarkably greater than the AUCs for CEA (0.740), CA125 (0.743), SCC (0.654), and Cyfra21-1 (0.730). Furthermore, the combination of these traditional biomarkers with m6A levels elevated the AUC to 0.970. Further analysis established that the expression of m6A erasers FTO and ALKBH5 were both markedly reduced and negatively correlated with m6A levels in peripheral blood of NSCLC. Additionally, GEO database and flow cytometry analysis implied that FTO and ALKBH5 attributes to peripheral CD4+ T cells proportion and activated the immune functions of T cells.
CONCLUSIONS: These findings unraveled that m6A RNA of peripheral blood immune cells was a prospective biomarker for the diagnosis of NSCLC.

Keywords:  N6-methyladenosine; biomarker; non-small cell lung cancer; peripheral blood; therapeutic target

DOI:  https://doi.org/10.1515/cclm-2022-1033
Front Immunol. 2022 ;13 1049435

m5C regulator-mediated modification patterns and tumor microenvironment infiltration characterization in colorectal cancer: One step closer to precision medicine.

Baoxiang Chen, Yiqing Xi, Jianhong Zhao, Yuntian Hong, Shunhua Tian, Xiang Zhai, Quanjiao Chen, Xianghai Ren, Lifang Fan, Xiaoyu Xie, Congqing Jiang.

  Background: The RNA modification 5-methylcytosine (m5C) is one of the most prevalent post-transcriptional modifications, with increasing evidence demonstrating its extensive involvement in the tumorigenesis and progression of various cancers. Colorectal cancer (CRC) is the third most common cancer and second leading cause of cancer-related deaths worldwide. However, the role of m5C modulators in shaping tumor microenvironment (TME) heterogeneity and regulating immune cell infiltration in CRC requires further clarification.Results: The transcriptomic sequencing data of 18 m5C regulators and clinical data of patients with CRC were obtained from The Cancer Genome Atlas (TCGA) and systematically evaluated. We found that 16 m5C regulators were differentially expressed between CRC and normal tissues. Unsupervised cluster analysis was then performed and revealed two distinct m5C modification patterns that yielded different clinical prognoses and biological functions in CRC. We demonstrated that the m5C score constructed from eight m5C-related genes showed excellent prognostic performance, with a subsequent independent analysis confirming its predictive ability in the CRC cohort. Then we developed a nomogram containing five clinical risk factors and the m5C risk score and found that the m5C score exhibited high prognostic prediction accuracy and favorable clinical applicability. Moreover, the CRC patients with low m5C score were characterized by "hot" TME exhibiting increased immune cell infiltration and higher immune checkpoint expression. These characteristics were highlighted as potential identifiers of suitable candidates for anticancer immunotherapy. Although the high m5C score represented the non-inflammatory phenotype, the CRC patients in this group exhibited high level of sensitivity to molecular-targeted therapy.
Conclusion: Our comprehensive analysis indicated that the novel m5C clusters and scoring system accurately reflected the distinct prognostic signature, clinicopathological characteristics, immunological phenotypes, and stratifying therapeutic opportunities of CRC. Our findings, therefore, offer valuable insights into factors that may be targeted in the development of precision medicine-based therapeutic strategies for CRC.

Keywords:  5-methylcytosine; RNA methylation; colorectal cancer; immune infiltrates; precision medicine; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2022.1049435
Biochem Cell Biol. 2022 Dec 21.

HDAC1 overexpression promoted by METTL3-IGF2BP2 inhibits FGF21 expression in metabolic syndrome-related liver injury.

Yunjiang Chen, Kaiyu Cai, Yueling Du, Zixiong Liu, Yanchun Gong.

Metabolic syndrome (MetS) represents a cluster of diseases that include diabetes and insulin resistance. A combination of these metabolic disorders damages liver function. We hypothesized here that HDAC1 inhibits FGF21 expression through histone deacetylation, thereby accentuating liver injury in rats with MetS. MetS rats induced by a high-fat diet were monitored weekly for blood pressure and body weight. The changes of hepatic injury parameters were also measured. The pathological changes in the liver were observed by HE staining and oil red O staining. We found that HDAC1 was increased in the liver of rats with MetS, while sh-HDAC1 reduced blood pressure, body weight and hepatic injury parameters. Improvement of structural pathological alterations and reduction of lipid deposition were observed after HDAC1 inhibition. Notably, HDAC1 inhibited FGF21 expression through histone deacetylation. The hepatoprotective effects of sh-HDAC1 on rats were reversed by adenovirus-mediated knockdown of FGF21. Moreover, METTL3 mediated the m6A modification of HDAC1 mRNA and increased its binding to IGF2BP2. Consistently, sh-METTL3 inhibited HDAC1 and increased FGF21 expression, thereby ameliorating liver injury in MetS rats. This study discovered that HDAC1 is capable of managing liver injury in MetS. Targeting HDAC1 may be an optimal treatment for MetS-related liver injury.

DOI: https://doi.org/10.1139/bcb-2022-0314
Cell Death Differ. 2022 Dec 17.

N6-methyladenosine-modified USP13 induces pro-survival autophagy and imatinib resistance via regulating the stabilization of autophagy-related protein 5 in gastrointestinal stromal tumors.

Zhishuang Gao, Chao Li, Haoyu Sun, Yibo Bian, Zhiwei Cui, Nuofan Wang, Zhangjie Wang, Yang Yang, Zonghang Liu, Zhongyuan He, Bowen Li, Fengyuan Li, Zheng Li, Linjun Wang, Diancai Zhang, Li Yang, Zekuan Xu, Xueming Li, Hao Xu.

Secondary resistance to imatinib (IM) represents a major challenge for therapy of gastrointestinal stromal tumors (GISTs). Aberrations in oncogenic pathways, including autophagy, correlate with IM resistance. Regulation of autophagy-related protein 5 (ATG5) by the ubiquitin-proteasome system is critical for autophagic activity, although the molecular mechanisms that underpin reversible deubiquitination of ATG5 have not been deciphered fully. Here, we identified USP13 as an essential deubiquitinase that stabilizes ATG5 in a process that depends on the PAK1 serine/threonine-protein kinase and which enhances autophagy and promotes IM resistance in GIST cells. USP13 preferentially is induced in GIST cells by IM and interacts with ATG5, which leads to stabilization of ATG5 through deubiquitination. Activation of PAK1 promoted phosphorylation of ATG5 thereby enhancing the interaction of ATG5 with USP13. Furthermore, N6-methyladenosine methyltransferase-like 3 (METTL3) mediated stabilization of USP13 mRNA that required the m6A reader IGF2BP2. Moreover, an inhibitor of USP13 caused ATG5 decay and co-administration of this inhibitor with 3-methyladenine boosted treatment efficacy of IM in murine xenograft models derived from GIST cells. Our findings highlight USP13 as an essential regulator of autophagy and IM resistance in GIST cells and reveal USP13 as a novel potential therapeutic target for GIST treatment.

DOI: https://doi.org/10.1038/s41418-022-01107-8
PLoS Pathog. 2022 Dec;18(12): e1010972

Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation.

Cassandra Catacalos, Alexander Krohannon, Sahiti Somalraju, Kate D Meyer, Sarath Chandra Janga, Kausik Chakrabarti.

"Epitranscriptomics" is the new RNA code that represents an ensemble of posttranscriptional RNA chemical modifications, which can precisely coordinate gene expression and biological processes. There are several RNA base modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), etc. that play pivotal roles in fine-tuning gene expression in almost all eukaryotes and emerging evidences suggest that parasitic protists are no exception. In this review, we primarily focus on m6A, which is the most abundant epitranscriptomic mark and regulates numerous cellular processes, ranging from nuclear export, mRNA splicing, polyadenylation, stability, and translation. We highlight the universal features of spatiotemporal m6A RNA modifications in eukaryotic phylogeny, their homologs, and unique processes in 3 unicellular parasites-Plasmodium sp., Toxoplasma sp., and Trypanosoma sp. and some technological advances in this rapidly developing research area that can significantly improve our understandings of gene expression regulation in parasites.

DOI: https://doi.org/10.1371/journal.ppat.1010972
Int J Mol Sci. 2022 Dec 13. pii: 15833. [Epub ahead of print]23(24):

METTL3 Regulates the Inflammatory Response in CPB2 Toxin-Exposed IPEC-J2 Cells through the TLR2/NF-κB Signaling Pathway.

Juanli Zhang, Jiaojiao Yang, Xiaoli Gao, Xiaoyu Huang, Ruirui Luo, Qiaoli Yang, Zunqiang Yan, Pengfei Wang, Wei Wang, Kaihui Xie, Jie Li, Bo Zhang, Shuangbao Gun.

  Clostridium perfringens beta2 (CPB2) toxin is one of the main pathogenic toxins produced by Clostridium perfringens, which causes intestinal diseases in animals and humans. The N6-methyladenosine (m6A) modification is the most common reversible modification in eukaryotic disease processes. Methyltransferase-like 3 (METTL3) regulates immunity and inflammatory responses induced by the bacterial infections in animals. However, METTL3's involvement in CPB2-treated intestinal porcine epithelial cell line-J2 (IPEC-J2) remains unclear. In the current study, we used methylated RNA immunoprecipitation-quantitative polymerase chain reaction, Western blotting and immunofluorescence assay to determine the role of METTL3 in CPB2-exposed IPEC-J2 cells. The findings revealed that m6A and METTL3 levels were increased in CPB2 treated IPEC-J2 cells. Functionally, METTL3 overexpression promoted the release of inflammatory factors, increased cytotoxicity, decreased cell viability and disrupted tight junctions between cells, while the knockdown of METTL3 reversed these results. Furthermore, METTL3 was involved in the inflammatory response of IPEC-J2 cells by activating the TLR2/NF-κB signaling pathway through regulating TLR2 m6A levels. In conclusion, METTL3 overexpression triggered the TLR2/NF-κB signaling pathway and promoted CPB2-induced inflammatory responses in IPEC-J2 cells. These findings may provide a new strategy for the prevention and treatment of diarrhea caused by Clostridium perfringens.

Keywords:  CPB2 toxin; IPEC-J2; METTL3; TLR2/NF-κB; inflammatory response

DOI:  https://doi.org/10.3390/ijms232415833
Aging (Albany NY). 2022 Dec 20. 14

Role of m6A modification and novel circ_0066715/ miR-486-5p/ ETS1 axis in rheumatoid arthritis macrophage polarization progression.

Lei Wan, Jian Liu, Chuanbing Huang, Ziheng Zhu, Fangze Li, Guanghan Sun, Kun Wang, Shu Li, Ximeng Ma, Xi Chen, Wang Yuan.

  Rheumatoid arthritis (RA) is a systemic disease dominated by inflammatory synovitis. RA synovial macrophages tend undergo M1-type macrophage polarization. Then, polarized M1-type macrophages secrete abundant pro-inflammatory cytokines, causing joint and cartilage destruction. N6-methyladenosine (m6A) methylation modification, circular RNA (circRNA), microRNA (miRNA), messenger RNA (mRNA), etc. are involved in the inflammatory response of RA. We found that there is an imbalance of inflammatory polarization in RA, which is manifested by a sharp increase in inflammatory markers and a high inflammatory response. Here, we show that RA was closely associated with low expression of circ_0066715. The overexpression of circ_0066715 significantly increased the ETS1 levels in RA-FLS cells, decreased cytokine secretion by M1-type macrophages, elevated M2-type cytokines, and inhibited FLS proliferation. Interestingly, the overexpression of miR-486-5p significantly suppressed the attenuation of the cell function and the effect on M1 macrophage polarization caused by circ_0066715 positive expression. WTAP may be involved in the methylation process of ETS1 in RA. ETS1 m6A methylation levels were altered upon WTAP intervention. The overexpression or interference of circ_0066715 decreased or increased WTAP expression. Our findings provide a novel circRNA/miRNA/mRNA regulatory axis and m6A regulatory mechanism involved in the process of RA macrophage polarization, thereby providing a powerful diagnostic and therapeutic strategy for RA treatment.

Keywords:  N6-methyladenosine methylation modification; circular RNA; macrophage polarization; microRNA; rheumatoid arthritis

DOI:  https://doi.org/10.18632/aging.204439
Clin Transl Med. 2022 Dec;12(12): e1148

Artemisitene suppresses rheumatoid arthritis progression via modulating METTL3-mediated N6-methyladenosine modification of ICAM2 mRNA in fibroblast-like synoviocytes.

Jian Chen, Xian Lin, Juan He, Dandan Liu, Lianhua He, Miaomiao Zhang, Huijie Luan, Yiping Hu, Cheng Tao, Qingwen Wang.

  BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune disease. We previously revealed that the natural compound artemisitene (ATT) exhibits excellent broad anticancer activities without toxicity on normal tissues. Nevertheless, the effect of ATT on RA is undiscovered. Herein, we aim to study the effect and potential mechanism of ATT on RA management.METHODS: A collagen-induced arthritis (CIA) mouse model was employed to confirm the anti-RA potential of ATT. Cell Counting Kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) assays, cell cycle and apoptosis analysis, immunofluorescence, migration and invasion assays, quantitative real-time PCR (RT-qPCR), Western blot, RNA-sequencing (RNA-seq) analysis, plasmid construction and lentivirus infection, and methylated RNA immunoprecipitation and chromatin immunoprecipitation assays, were carried out to confirm the effect and potential mechanism of ATT on RA management.
RESULTS: ATT relieved CIA in mice. ATT inhibited proliferation and induced apoptosis of RA-fibroblast-like synoviocytes (FLSs). ATT restrained RA-FLSs migration and invasion via suppressing epithelial-mesenchymal transition. RNA-sequencing analysis and bioinformatics analysis identified intercellular adhesion molecule 2 (ICAM2) as a promoter of RA progression in RA-FLSs. ATT inhibits RA progression by suppressing ICAM2/phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/p300 pathway in RA-FLSs. Moreover, ATT inhibited methyltransferase-like 3 (METTL3)-mediated N6-methyladenosine methylation of ICAM2 mRNA in RA-FLSs. Interestingly, p300 directly facilitated METTL3 transcription, which could be restrained by ATT in RA-FLSs. Importantly, METTL3, ICAM2 and p300 expressions in synovium tissues of RA patients were related to clinical characteristics and therapy response.
CONCLUSIONS: We provided strong evidence that ATT has therapeutic potential for RA management by suppressing proliferation, migration and invasion, in addition to inducing apoptosis of RA-FLSs through modulating METTL3/ICAM2/PI3K/AKT/p300 feedback loop, supplying the fundamental basis for the clinical application of ATT in RA therapy. Moreover, METTL3, ICAM2 and p300 might serve as biomarkers for the therapy response of RA patients.

Keywords:  ICAM2; METTL3; artemisitene; fibroblast-like synoviocytes; rheumatoid arthritis

DOI:  https://doi.org/10.1002/ctm2.1148
J Cardiothorac Surg. 2022 Dec 19. 17(1): 323

RNA methylation in vascular disease: a systematic review.

Yue Shu, Yilong Guo, Yin Zheng, Shuwu He, Zhensu Shi.

  Despite the rise in morbidity and mortality associated with vascular diseases, the underlying pathophysiological molecular mechanisms are still unclear. RNA N6-methyladenosine modification, as the most common cellular mechanism of RNA regulation, participates in a variety of biological functions and plays an important role in epigenetics. A large amount of evidence shows that RNA N6-methyladenosine modifications play a key role in the morbidity caused by vascular diseases. Further research on the relationship between RNA N6-methyladenosine modifications and vascular diseases is necessary to understand disease mechanisms at the gene level and to provide new tools for diagnosis and treatment. In this study, we summarize the currently available data on RNA N6-methyladenosine modifications in vascular diseases, addressing four aspects: the cellular regulatory system of N6-methyladenosine methylation, N6-methyladenosine modifications in risk factors for vascular disease, N6-methyladenosine modifications in vascular diseases, and techniques for the detection of N6-methyladenosine-methylated RNA.

Keywords:  N6-methyladenosine; RNA-modifying enzymes; Risk factors of vascular disease; Vascular disease

DOI:  https://doi.org/10.1186/s13019-022-02077-1
Nucleic Acids Res. 2022 Dec 20. pii: gkac1185. [Epub ahead of print]

Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation.

Xavier Hernandez-Alias, Christopher D Katanski, Wen Zhang, Mahdi Assari, Christopher P Watkins, Martin H Schaefer, Luis Serrano, Tao Pan.

Transfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing data. How these properties are coordinated at the transcriptome level is an open question. Here, we develop a single-read tRNA analysis pipeline that takes advantage of the pseudo single-molecule nature of tRNA sequencing in NGS libraries. tRNAs are short enough that a single NGS read can represent one tRNA molecule, and can simultaneously report on the status of multiple modifications, aminoacylation, and fragmentation of each molecule. We find correlations among modification-modification, modification-aminoacylation and modification-fragmentation. We identify interdependencies among one of the most common tRNA modifications, m1A58, as coordinators of tissue-specific gene expression. Our method, SingLe-read Analysis of Crosstalks (SLAC), reveals tRNAome-wide networks of modifications, aminoacylation, and fragmentation. We observe changes of these networks under different stresses, and assign a function for tRNA modification in translational regulation and fragment biogenesis. SLAC leverages the richness of the tRNA-seq data and provides new insights on the coordination of tRNA properties.

DOI: https://doi.org/10.1093/nar/gkac1185