bims-rimeca 2023-06-25 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023–06–25
twenty-two papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

METTL3-mediated m6A modification of SIRT1 mRNA inhibits progression of endometriosis by cellular senescence enhancing.
METTL3 regulates N6-methyladenosine modification of ANGPTL3 mRNA and potentiates malignant progression of stomach adenocarcinoma.
Exon junction complex modulates the formation of the m6A epitranscriptome.
METTL16 promotes glycolytic metabolism reprogramming and colorectal cancer progression.
Mettl3-mediated m6A modification plays a role in lipid metabolism disorders and progressive liver damage in mice by regulating lipid metabolism-related gene expression.
RBM15 m6 A modification-mediated OTUB2 upregulation promotes cervical cancer progression via the AKT/mTOR signaling.
M6A modification promotes blood-brain barrier breakdown during cerebral ischemia/reperfusion injury through increasing matrix metalloproteinase 3 expression.
Molecular features, biological behaviors and clinical implications of m5C RNA methylation modification regulators in gastrointestinal cancers.
N6-methyladenosine profiling reveals that Xuefu Zhuyu decoction upregulates METTL14 and BDNF in a rat model of traumatic brain injury.
YTHDF2/m6 A/NF-κB axis controls anti-tumor immunity by regulating intratumoral Tregs.
Roles and implications of mRNA N6 -methyladenosine in cancer.
Effects of N6-methyladenosine modification on the function of the female reproductive system.
Smoking and tetramer tryptase accelerate intervertebral disc degeneration by inducing METTL14-mediated DIXDC1 m6 modification.
Fufang Zhenzhu Tiaozhi (FTZ) capsule ameliorates diabetes-accelerated atherosclerosis via suppressing YTHDF2-mediated m6A modification of SIRT3 mRNA.
Targeting m6A binding protein YTHDFs for cancer therapy.
Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis.
Qinzhu Liangxue inhibits IL-6-induced hyperproliferation and inflammation in HaCaT cells by regulating METTL14/SOCS3/STAT3 axis.
m6A-mediated upregulation of lncRNA RMRP boosts the progression of bladder cancer via epigenetically suppressing SCARA5.
Serum exosomal m6A demethylase FTO promotes gefitinib resistance in non-small cell lung cancer by up-regulating FLRT3, PTGIS and SIRPα expression.
Exploration of m6A methylation regulators as epigenetic targets for immunotherapy in advanced sepsis.
CircNFATC3 promotes the proliferation of gastric cancer through binding to IGF2BP3 and restricting its ubiquitination to enhance CCND1 mRNA stability.
m6A methylation reader IGF2BP2 activates endothelial cells to promote angiogenesis and metastasis of lung adenocarcinoma.

J Transl Med. 2023 Jun 23. 21(1): 407

METTL3-mediated m6A modification of SIRT1 mRNA inhibits progression of endometriosis by cellular senescence enhancing.

Xiaotong Wang, Jing Wang, Xibo Zhao, Han Wu, Jixin Li, Yan Cheng, Qiuyan Guo, Xuejiao Cao, Tian Liang, Liyuan Sun, Guangmei Zhang.

   BACKGROUND: Endometriosis (EMs), the ectopic planting of functional endometrium outside of the uterus, is a leading cause of infertility and pelvic pain. As a fundamental mRNA modification, N6-methyladenosine (m6A) participates in various pathological processes. However, the role of m6A RNA modification in endometriosis remains unclear. The present study explores METTL3-mediated m6A modification and the mechanisms involved in endometriosis.
METHODS: The dominant m6A regulators in EMs were analysed using RT‒PCR. Candidate targets and possible mechanisms of METTL3 were assessed by m6A-mRNA epitranscriptomic microarray and RNA sequencing. A primary ESCs model was employed to verify the effect of METTL3 on m6A modification of SIRT1 mRNA, and the mechanism was elucidated by RT‒PCR, Western blotting, MeRIP, and RIP assays. CCK-8 viability assays, Transwell invasion assays, EdU proliferation assays, wound healing migration assays, and senescence-associated β-galactosidase staining were performed to illuminate the potential biological mechanism of METTL3 and SIRT1 in ESCs in vitro. An in vivo PgrCre/ + METTL3 -/- female homozygous mouse model and a nude mouse xenograft model were employed to further investigate the physiologic consequences of METTL3-mediated m6A alteration on EMs.
RESULTS: Our data show that decreased METTL3 expression significantly downregulates m6A RNA methylation levels in ESCs. Silencing m6A modifications mediated by METTL3 accelerates ESCs viability, proliferation, migration, and invasion in vitro. The m6A reader protein YTHDF2 binds to m6A modifications to induce the degradation of SIRT1 mRNA. SIRT1/FOXO3a signalling pathway activation is subsequently inhibited, promoting the cellular senescence of ESCs and inhibiting the ectopic implantation of ESCs in vitro and in vivo.
CONCLUSIONS: Our findings demonstrate that METTL3-mediated m6A methylation epigenetically regulates the ectopic implantation of ESCs, resulting in the progression of endometriosis. Our study establishes METTL3-YTHDF2-SIRT1/FOXO3a as a critical axis and potential mechanism in endometriosis.

Keywords:  Cellular senescence; Endometriosis; Epigenetic modification; METTL3; SIRT1; m6A

DOI:  https://doi.org/10.1186/s12967-023-04209-0
BMC Gastroenterol. 2023 Jun 21. 23(1): 217

METTL3 regulates N6-methyladenosine modification of ANGPTL3 mRNA and potentiates malignant progression of stomach adenocarcinoma.

Zhijin Zhang, Jun Fu, Yuhao Zhang, Xianju Qin, Yuexia Wang, Chungen Xing.

   BACKGROUND: N6-methyladenosine (m6A) is associated with mammalian mRNA biogenesis, decay, translation and metabolism, and also contributes greatly to gastrointestinal tumor formation and development. Therefore, the specific mechanisms and signaling pathways mediated by methyltransferase-like 3 (METTL3), which catalyzes the formation of m6A chemical labeling in stomach adenocarcinoma (STAD), are still worth exploring.
METHODS: Quantitative real-time PCR (qRT-PCR) was constructed to detect the expression of METTL3 in gastric cancer cell lines and patient tissues. The biological function of METTL3 was investigated in vitro/in vivo by Cell Counting Kit-8, colony formation assay, Transwell assay and nude mouse tumorigenesis assay. Based on the LinkedOmics database, the genes co-expressed with METTL3 in the TCGA STAD cohort were analyzed to clarify the downstream targets of METTL3. Methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) and RNA stability analysis were employed to explore the mechanism of METTL3 in gastric cancer progression.
RESULTS: We analyzed TCGA data and found that METTL3 was frequently elevated in STAD, and demonstrated that METTL3 was present at high levels in clinical STAD tissues and cells. High METTL3 expression was more likely to have advanced TNM tumors and distant metastasis. On the other hand, METTL3 silencing effectively impeded the higher oncogenic capacity of AGS and HGC27 cells in vivo and in vitro, as reflected by slowed cell growth and diminished migration and invasion capacities. Continued mining of the TCGA dataset identified the co-expression of angiopoietin-like 3 (ANGPTL3) and METTL3 in STAD. Lower level of ANGPTL3 was related to increased level of METTL3 in STAD samples and shorter survival times in STAD patients. ANGPTL3 enrichment limited the growth and metastasis of STAD cells. Besides, ANGPTL3 mRNA levels could be decreased by METTL3-dominated m6A modifications, a result derived from a combination of MeRIP-qPCR and RNA half-life experiments. Importantly, the inhibitory effect of METTL3 silencing on cancer could be reversed to some extent by ANGPTL3 inhibition.
CONCLUSIONS: Overall, our findings suggested that METTL3 functioned an oncogenic role in STAD by reducing ANGPTL3 expression in an m6A-dependent manner. The discovery of the METTL3-ANGPTL3 axis and its effect on STAD tumor growth will contribute to further studies on the mechanisms of gastric adenocarcinoma development.

Keywords:  ANGPTL3; METTL3; N6-methyladenosine; Stomach adenocarcinoma

DOI:  https://doi.org/10.1186/s12876-023-02844-x
Yi Chuan. 2023 Jun 20. 45(6): 464-471

Exon junction complex modulates the formation of the m6A epitranscriptome.

Peng-Hui Song, Li-Juan Ma, Dong Yan.

  N6-methyladenosine (m6A) is one of the most abundant chemical modifications in mRNA and plays essential roles in diverse physiological and pathological processes. m6A is highly enriched near stop codons and in long internal exons of mRNA, but the mechanism leading to this specific distribution has been unclear. Recently, three papers have solved this major problem by revealing that exon junction complexes (EJCs) act as m6A suppressors and shape the formation of the m6A epitranscriptome. Here, we briefly introduce the m6A pathway, elaborate the roles of EJC on the formation of m6A modification based on these results, and describe the effect of exon-intron structure on mRNA stability via m6A, which will help us better understand the latest progress in the m6A RNA modification field.

Keywords:  RNA modification; RNA stability; exon junction complexes; m6A; splicing

DOI:  https://doi.org/10.16288/j.yczz.23-051
J Exp Clin Cancer Res. 2023 Jun 20. 42(1): 151

METTL16 promotes glycolytic metabolism reprogramming and colorectal cancer progression.

Wei Wei, Zhong-Yuan Zhang, Bin Shi, Yike Cai, Hou-Shun Zhang, Chun-Lei Sun, Yun-Fei Fei, Wen Zhong, Shuang Zhang, Chen Wang, Bing He, Guan-Min Jiang, Hao Wang.

   BACKGROUND: Glycolysis is the key hallmark of cancer and maintains malignant tumor initiation and progression. The role of N6-methyladenosine (m6A) modification in glycolysis is largely unknown. This study explored the biological function of m6A methyltransferase METTL16 in glycolytic metabolism and revealed a new mechanism for the progression of Colorectal cancer (CRC).
METHODS: The expression and prognostic value of METTL16 was evaluated using bioinformatics and immunohistochemistry (IHC) assays. The biological functions of METTL16 in CRC progression was analyzed in vivo and in vitro. Glycolytic metabolism assays were used to verify the biological function of METTL16 and Suppressor of glucose by autophagy (SOGA1). The protein/RNA stability, RNA immunoprecipitation (RIP), Co-immunoprecipitation (Co-IP) and RNA pull-down assays were used to explore the potential molecular mechanisms.
RESULTS: SOGA1 is a direct downstream target of METTL16 and involved in METTL16 mediated glycolysis and CRC progression. METTL16 significantly enhances SOGA1 expression and mRNA stability via binding the "reader" protein insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1). Subsequently, SOGA1 promotes AMP-activated protein kinase (AMPK) complex ubiquitination, inhibits its expression and phosphorylation, thus upregulates pyruvate dehydrogenase kinase 4 (PDK4), a crucial protein controlling glucose metabolism. Moreover, Yin Yang 1 (YY1) can transcriptionally inhibit the expression of METTL16 in CRC cells by directly binding to its promoter. Clinical data showed that METTL16 expression is positively correlated to SOGA1 and PDK4, and is associated with poor prognosis of CRC patients.
CONCLUSIONS: Our findings suggest that METTL16/SOGA1/PDK4 axis might be promising therapeutic targets for CRC.

Keywords:  Colorectal cancer; METTL16; PDK4; SOGA1; m6A

DOI:  https://doi.org/10.1186/s13046-023-02732-y
Aging (Albany NY). 2023 06 16. 15

Mettl3-mediated m6A modification plays a role in lipid metabolism disorders and progressive liver damage in mice by regulating lipid metabolism-related gene expression.

Guanqi Dai, Shihao Huang, Yonglong Li, Xueyi Tu, Jiawei Xia, Zhihao Zhou, Wanyi Chen, Ao Zhang, Jintao Lin, Yingchun Li, Danhua He, Taoyan Lin, Jinge Cong, Ye Lei, Liuxin Han, Zhenxia Yao, Weiwei Liu, Ying Zhou, Qiwen Li, Jing Li, Yuqin Zhang, Aibing Wu, Dong Xiao, Wanshan Wang, Wentao Zhao, Junshuang Jia, Xiaolin Lin.

   AIMS: N6-methyladenosine (m6A), the most abundant and conserved epigenetic modification of mRNA, participates in various physiological and pathological processes. However, the roles of m6A modification in liver lipid metabolism have yet to be understood entirely. We aimed to investigate the roles of the m6A "writer" protein methyltransferase-like 3 (Mettl3) in liver lipid metabolism and the underlying mechanisms.
MAIN METHODS: We assessed the expression of Mettl3 in liver tissues of diabetes (db/db) mice, obese (ob/ob) mice, high saturated fat-, cholesterol-, and fructose-induced non-alcoholic fatty liver disease (NAFLD) mice, and alcohol abuse and alcoholism (NIAAA) mice by quantitative reverse-transcriptase PCR (qRT-PCR). Hepatocyte-specific Mettl3 knockout mice were used to evaluate the effects of Mettl3 deficiency in mouse liver. The molecular mechanisms underlying the roles of Mettl3 deletion in liver lipid metabolism were explored by multi-omics joint analysis of public data from the Gene Expression Omnibus database and further validated by qRT-PCR and Western blot.
KEY FINDINGS: Significantly decreased Mettl3 expression was associated with NAFLD progression. Hepatocyte-specific knockout of Mettl3 resulted in significant lipid accumulation in the liver, increased serum total cholesterol levels, and progressive liver damage in mice. Mechanistically, loss of Mettl3 significantly downregulated the expression levels of multiple m6A-modified mRNAs related to lipid metabolism, including Adh7, Cpt1a, and Cyp7a1, further promoting lipid metabolism disorders and liver injury in mice.
SIGNIFICANCE: In summary, our findings demonstrate that the expression alteration of genes related to lipid metabolism by Mettl3-mediated m6A modification contributes to the development of NAFLD.

Keywords:  Mettl3; NAFLD; epigenetics; lipid metabolism; m6A modification

DOI:  https://doi.org/10.18632/aging.204810
Environ Toxicol. 2023 Jun 19.

RBM15 m6 A modification-mediated OTUB2 upregulation promotes cervical cancer progression via the AKT/mTOR signaling.

Yan Song, Qiongwei Wu.

  Cervical cancer (CC) is a deadly gynecological tumor worldwide. Otubain 2 (OTUB2) has been recently identified as an oncogene in human malignancies. However, its expression and function remain unclear. This work aims to explore the role of OTUB2 in CC progression. Herein, The Cancer Genome Atlas data revealed that OTUB2 expression was significantly upregulated in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) and gradually increased with CESC progression; moreover, OTUB2 expression predicted poor outcomes of CESC patients. Then, RT-qPCR and Western blotting were applied to determine mRNA and protein expression in CC and normal cells. Our results confirmed that OTUB2 was highly expressed in CC cell lines. As indicated by CCK-8, Transwell, and flow cytometry results, OTUB2 silencing attenuated proliferative and metastatic capacities of CC cells but promoted CC cell apoptosis. Then, RBM15, an N6-methyladenosine (m6 A) methyltransferase "writer," was also demonstrated to be upregulated in CESC and CC cells. Mechanistically, m6 A RNA immunoprecipitation (Me-RIP) results showed that RBM15 inhibition reduced the m6 A methylation level of OTUB2 in CC cells, leading to the decline of OTUB2 expression. In addition, OTUB2 inhibition deactivated the AKT/mTOR signaling in CC cells. Furthermore, SC-79 (AKT/mTOR activator) partially abated the inhibitory effects of OTUB2 knockdown on the AKT/mTOR signaling pathway and the malignant phenotypes of CC cells. In summary, this work showed that RBM15-mediated m6 A modification led to OTUB2 upregulation, thereby promoting malignant behaviors of CC cells via the AKT/mTOR signaling pathway.

Keywords:  AKT/mTOR; OTUB2; RBM15; cervical cancer; m6A

DOI:  https://doi.org/10.1002/tox.23852
Heliyon. 2023 Jun;9(6): e16905

M6A modification promotes blood-brain barrier breakdown during cerebral ischemia/reperfusion injury through increasing matrix metalloproteinase 3 expression.

En Liang, Shaorong Xiao, Changtong Zhao, Yu Zhang, Guanglei Fu.

  Blood-brain barrier (BBB) breakdown is a critical event in cerebral ischemia-reperfusion (I/R) injury, and matrix metalloproteinases (MMPs), which are proteolytic enzymes, play essential roles in BBB breakdown through degrading the extracellular matrix. N6-Methyladenosine (m6A), the most common and reversible mRNA modification, has an important role in the progression of cerebral I/R injury. However, whether m6A is related to BBB breakdown and MMPs expression in cerebral I/R injury is still not clear. In this study, we explored the potential effects of m6A modification on BBB breakdown in cerebral I/R injury and its underlying mechanisms using mice subjected to transient middle cerebral artery occlusion and reperfusion (MCAO/R), and mouse brain endothelial cells treated with oxygen-glucose deprivation and reoxygenation (OGD/R). We find that MMP3 expression is highly expressed and positively associated with the m6A writer CBLL1 (Cbl proto-oncogene like 1) in cerebral I/R injury in vivo and in vitro. Furthermore, MMP3 mRNA occurs m6A modification in mouse brain endothelial cells, and the m6A modification level of MMP3 mRNA is significantly increased in cerebral I/R injury. Moreover, inhibition of m6A modification reduces MMP3 expression and ameliorates BBB breakdown in cerebral I/R in vivo and in vitro. In conclusion, m6A modification promotes BBB breakdown in cerebral I/R injury through increasing MMP3 expression, indicating that m6A may be a potential therapeutic target for cerebral I/R injury.

Keywords:  Blood-brain barrier; Cerebral ischemia-reperfusion injury; Matrix metalloproteinase 3; N6-methyladenosine; Oxygen-glucose deprivation and reoxygenation

DOI:  https://doi.org/10.1016/j.heliyon.2023.e16905
Cancer Biol Ther. 2023 Dec 31. 24(1): 2223382

Molecular features, biological behaviors and clinical implications of m5C RNA methylation modification regulators in gastrointestinal cancers.

Mengyao Zhan, Huan Song, Dan Tian, Qin Wen, Xinling Shi, Yuting Wang, Xuhua Mao, Jianming Wang.

  Epitranscriptome studies have shown that critical RNA modifications drive tumorigenicity; however, the role of 5-methylcytosine (m5C) RNA methylation remains poorly understood. We extracted 17 m5C regulators and clustered distinct m5C modification patterns by consensus clustering analysis. Gene set variation and single-sample gene set enrichment analysis were applied to quantify functional analysis and immune infiltration. The least absolute shrinkage and selection operator was employed to develop a prognostic risk score. Kaplan-Meier with log-rank test was used for survival analysis. Differential expression analysis was performed with the "limma" R package. Wilcoxon signed ranked test or Kruskal-Wallis test was used to compare groups. We observed that m5C RNA methylation was commonly upregulated in gastrointestinal cancer and related to prognosis. Clusters were identified for m5C patterns, with distinct immune infiltrations and functional pathways. The risk scores of m5C regulators were independent risk factors. Differentially expressed mRNAs (DEmRNAs) in m5C clusters were involved in cancer-related pathways. The methylation-based m5Cscore showed a significant effect on the prognosis. Patients with a lower m5Cscore exhibited more therapeutic efficiency on anti-CTLA4 therapy in liver cancer, while the combination of anti-CTLA4 therapy and pd1 was more efficient for patients with a lower m5Cscore in pancreatic cancer. We uncovered dysregulations of m5C-related regulators in gastrointestinal cancer and their associations with overall survival. Some immune cells were differently infiltrated in distinct m5C modification patterns, indicating their potential impacts on gastrointestinal cancer cell-immune. Moreover, an m5Cscore, derived from DEmRNAs in specific clusters, can serve as a classifier for immunotherapy.

Keywords:  5-methylcytosine; Epigenetics; gastrointestinal cancer; immunotherapy; methylation; prognostic biomarker; transcriptome

DOI:  https://doi.org/10.1080/15384047.2023.2223382
J Ethnopharmacol. 2023 Jun 20. pii: S0378-8741(23)00691-8. [Epub ahead of print] 116823

N6-methyladenosine profiling reveals that Xuefu Zhuyu decoction upregulates METTL14 and BDNF in a rat model of traumatic brain injury.

Dandan Feng, Pengfei Li, Wei Xiao, Zhuan Pei, Peishun Chen, Mingrui Hu, Zhaoyu Yang, Teng Li, Zian Xia, Hanjin Cui, Haigang Li, Qing Huang, Wei Zhang, Tao Tang, Yang Wang.

   ETHNOPHARMACOLOGICAL RELEVANCE: The traditional Chinese herbal formula Xuefu Zhuyu decoction (XFZYD) is a classic formula in the category of invigorating blood circulation and resolving blood stasis. It has been proven to improve the neurological and ethological prognosis of traumatic brain injury. XFZYD promotes synaptic and axonal regeneration after traumatic brain injury, which is functionally modulated by the N6-methyladenosine (m6A) modification of RNA. However, the epigenetic effects of XFZYD on m6A modification remain unknown.
AIM OF THE STUDY: To explore how XFZYD protected against traumatic brain injury induced by controlled cortical impact (CCI) injury by altering RNA m6A modification.
MATERIALS AND METHODS: The modified neurological severity scoring and Morris water maze were performed to evaluate the neuroprotective effects of XFZYD for 14 days and screen the dose. Then, dot blot, western blotting, and methylated RNA immunoprecipitation sequencing (MeRIP-Seq) were used to explore changes in RNA m6A modification in the perilesional cortex. The Metascape platform was used to analyze the Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome pathway of the differential m6A-tagged genes. Furthermore, MeRIP-qPCR was conducted to quantify differences in the hub differential m6A modification gene brain-derived neurotrophic factor (Bdnf).
RESULTS: XFZYD significantly ameliorated the neurological deficits, spatial learning, and memory impairments in rats post-CCI on day 14. XFZYD enhanced the m6A level, and the expression of METTL14 and YTHDC2 in the perilesional cortex of CCI rats. In all three groups, the 3'-untranslated regions and coding sequence were primarily enriched for m6A peaks. XFZYD reversed the increased proportion of 3'-untranslated regions, and the decreased proportion of coding sequence and 5'-untranslated regions post-CCI. Moreover, XFZYD markedly downregulated 41 elevated m6A-tagged transcripts and upregulated 119 decreased m6A-tagged transcripts following CCI. Gene ontology and KEGG pathway analysis revealed that XFZYD-regulated m6A-tagged transcripts were predominantly enriched in synapse assembly, synaptic plasticity, learning or memory, and MAPK signaling pathway. Then, the hub-regulated m6A-tagged gene BDNF was identified. Both the m6A methylation level and the protein level of BDNF were ascended by XFZYD treatment.
CONCLUSION: XFZYD improves neurological deficits, spatial learning and memory impairments in rats post-TBI probably through increasing the expression of METTL14 and BDNF in the cortex. Our study highlights a novel post-transcriptional regulation mechanism mediated by herbal medicine for traumatic brain injury treatment.

Keywords:  Brain-derived neurotrophic factor; Epitranscriptional regulation; METTL14; N(6)-methyladenosine; Traumatic brain injury; Xuefu Zhuyu decoction

DOI:  https://doi.org/10.1016/j.jep.2023.116823
EMBO J. 2023 Jun 22. e113126

YTHDF2/m6 A/NF-κB axis controls anti-tumor immunity by regulating intratumoral Tregs.

Linda Zhang, Xiaoyang Dou, Zhong Zheng, Chang Ye, Thomas X Lu, Hua L Liang, Liangliang Wang, Ralph R Weichselbaum, Chuan He.

  N6 -methyladenosine (m6 A) in messenger RNA (mRNA) regulates immune cells in homeostasis and in response to infection and inflammation. The function of the m6 A reader YTHDF2 in the tumor microenvironment (TME) in these contexts has not been explored. We discovered that the loss of YTHDF2 in regulatory T (Treg) cells reduces tumor growth in mice. Deletion of Ythdf2 in Tregs does not affect peripheral immune homeostasis but leads to increased apoptosis and impaired suppressive function of Treg cells in the TME. Elevated tumor necrosis factor (TNF) signaling in the TME promotes YTHDF2 expression, which in turn regulates NF-κB signaling by accelerating the degradation of m6 A-modified transcripts that encode NF-κB-negative regulators. This TME-specific regulation of Treg by YTHDF2 points to YTHDF2 as a potential target for anti-cancer immunotherapy, where intratumoral Treg cells can be targeted to enhance anti-tumor immune response while avoiding Treg cells in the periphery to minimize undesired inflammations.

Keywords:  Anti-tumor immunity; Intratumoral Tregs; NF-κB regulation; YTHDF2; m6A

DOI:  https://doi.org/10.15252/embj.2022113126
Cancer Commun (Lond). 2023 Jun 23.

Roles and implications of mRNA N6 -methyladenosine in cancer.

Lingxing Zeng, Xudong Huang, Jialiang Zhang, Dongxin Lin, Jian Zheng.

  RNA N6 -methyladenosine modification is the most prevalent internal modification of eukaryotic RNAs and has emerged as a novel field of RNA epigenetics, garnering increased attention. To date, m6 A modification has been shown to impact multiple RNA metabolic processes and play a vital role in numerous biological processes. Recent evidence suggests that aberrant m6 A modification is a hallmark of cancer, and it plays a critical role in cancer development and progression through multiple mechanisms. Here, we review the biological functions of mRNA m6 A modification in various types of cancers, with a particular focus on metabolic reprogramming, programmed cell death and tumor metastasis. Furthermore, we discuss the potential of targeting m6 A modification or its regulatory proteins as a novel approach of cancer therapy and the progress of research on m6 A modification in tumor immunity and immunotherapy. Finally, we summarize the development of different m6 A detection methods and their advantages and disadvantages.

Keywords:  N6-methyladenosine; cancer therapy; immunotherapy; m6A methylation

DOI:  https://doi.org/10.1002/cac2.12458
Yi Chuan. 2023 Jun 20. 45(6): 472-487

Effects of N6-methyladenosine modification on the function of the female reproductive system.

Shan He, Jian Zhao, Xiao-Feng Song.

  In recent years, the rate of female infertility in China has been increasing, posing an urgent challenge to improve fertility. A healthy reproductive system is essential for successful reproduction, and N6-methyladenosine (m6A) is the most abundant chemical modification in eukaryotes and plays a critical role in cellular processes. Recent studies have shown that m6A modifications also have a keying effect in various physiological and pathological processes in the female reproductive system, although their regulatory mechanisms and biological functions remain unclear. In this review, we first introduce the reversible regulatory mechanisms of m6A and its functions, discuss the role of m6A in female reproductive function and disorders of the reproductive system, and present recent advances in m6A detection technologies and methods. Our review provides new insights into the biological role of m6A and its potential application in the treatment of female reproductive disorders.

Keywords:  development and aging; diseases; female reproductive system; m6A; methylation modification

DOI:  https://doi.org/10.16288/j.yczz.23-071
Mol Ther. 2023 Jun 19. pii: S1525-0016(23)00321-0. [Epub ahead of print]

Smoking and tetramer tryptase accelerate intervertebral disc degeneration by inducing METTL14-mediated DIXDC1 m6 modification.

Ji Tu, Wentian Li, Philip M Hansbro, Qi Yan, Xupeng Bai, Chantal Donovan, Richard Y Kim, Izabela Galvao, Abhirup Das, Cao Yang, Jun Zou, Ashish Diwan.

Although cigarette smoke (CS) and low back pain (LBP) are common worldwide, their correlations and the mechanisms of action remain unclear. We had shown that excessive activation of Mast Cells (MCs) and their proteases play key roles in CS associated diseases, like asthma, chronic obstructive pulmonary disease (COPD), blood coagulation and lung cancer. Previous studies also show that MCs and their proteases induce degenerative musculoskeletal disease. By using mice custom-designed smoke-exposure system, we demonstrated that CS results in intervertebral disc (IVDs) degeneration and the release of MC-restricted tetramer tryptases (TT) inside the IVDs. TT was found to regulate the expression of methyltransferase 14 (METTL14) at the epigenetic level by inducing N6-methyladenosine (m6A) deposition in the 3'-untranslated region (3'-UTR) of the transcript that encodes DIX Domain Containing 1 (DIXDC1). That reaction increases the mRNA stability and expression of Dixdc1. DIXDC1 functionally interacts with 'Disrupted in Schizophrenia-1' (DISC1) to accelerate the degeneration and senescence of nucleus pulposus (NP) cells by activating a canonical Wnt pathway. Our study demonstrates the association between CS, MC-derived TTs, and LBP. These findings raise the possibility that METTL14-medicated DIXDC1 m6A modification could serve as a potential therapeutic target to block the development of degeneration of the NP in LBP patients.

DOI: https://doi.org/10.1016/j.ymthe.2023.06.010
J Ethnopharmacol. 2023 Jun 19. pii: S0378-8741(23)00634-7. [Epub ahead of print] 116766

Fufang Zhenzhu Tiaozhi (FTZ) capsule ameliorates diabetes-accelerated atherosclerosis via suppressing YTHDF2-mediated m6A modification of SIRT3 mRNA.

Yue Zhang, Ruonan Wang, Huiling Tan, Kaili Wu, Yaju Hu, Hongtao Diao, Dongwei Wang, Xinyuan Tang, Mingyang Leng, Xu Li, Zhenlu Cai, Duosheng Luo, Xiaoqi Shao, Meiling Yan, Yingyu Chen, Xianglu Rong, Jiao Guo.

   ETHNOPHARMACOLOGICAL RELEVANCE: Fufang Zhenzhu TiaoZhi (FTZ), a Chinese medicinal decoction, has continuously been used to treat metabolic syndrome. Atherosclerosis is the main pathological basis of cardiovascular disease. The N6 methyladenosine (m6A) modification is a highly dynamic and reversible process involving a variety of important biological processes.
AIM OF THE STUDY: Here, we investigated the therapeutic effects and mechanism of FTZ in diabetes-accelerated atherosclerosis.
MATERIALS AND METHODS: Doppler ultrasonography was used to examine the carotid intima-media thickness and plaque area in diabetic atherosclerosis patients. HFD mice were injected with streptozotocin to induce diabetes. HE and Oil red O staining were used to assess the effect of FTZ on lipid deposition. HUVECs were induced with HG/ox-LDL as a model of diabetic atherosclerosis. Furthermore, application of m6A methylation level kit, qRT-PCR, Western blot, tunel staining, reactive oxygen species staining and mPTP staining were performed to analyze the detailed mechanism.
RESULTS: Clinical trials of FTZ have shown obvious effect of lowering blood glucose and blood lipids. These effects were reversed after FTZ intervention. Compared with the control, lipid deposition decreased significantly after FTZ administration. FTZ reduced endothelial cell apoptosis. At the same time, we found that FTZ reversed the increase of methylation reader YTHDF2 caused by ox-LDL treatment. Subsequently, we discovered that YTHDF2 degraded SIRT3 mRNA, leading to endothelial cell apoptosis and oxidative stress.
CONCLUSION: FTZ attenuated diabetes-accelerated atherosclerosis by decreasing blood glucose and serum lipids levels, and increased endothelial cell antioxidant capacity, inhibited endothelial cell apoptosis via inhibiting YTHDF2-mediated m6A modification of SIRT3 mRNA, which reduced mRNA degradation.

Keywords:  Diabetes-accelerated atherosclerosis; Fufang Zhenzhu TiaoZhi; SIRT3; YTHDF2; m(6)A RNA methylation

DOI:  https://doi.org/10.1016/j.jep.2023.116766
Bioorg Med Chem. 2023 Jun 12. pii: S0968-0896(23)00221-3. [Epub ahead of print]90 117373

Targeting m6A binding protein YTHDFs for cancer therapy.

Weikun Zhang, Tingting Wu, Yuejiao Zhang, Wenjing Kang, Chenyu Du, Qidong You, Xuetao Chen, Zhengyu Jiang.

  N6-methyladenosine (m6A) is the most common mRNA modification in mammalians. The function and dynamic regulation of m6A depends on the "writer", "readers" and "erasers". YT521-B homology domain family (YTHDF) is a class of m6A binding proteins, including YTHDF1, YTHDF2 and YTHDF3. In recent years, the modification of m6A and the molecular mechanism of YTHDFs have been further understood. Growing evidence has shown that YTHDFs participate in multifarious bioprocesses, particularly tumorigenesis. In this review, we summarized the structural characteristics of YTHDFs, the regulation of mRNA by YTHDFs, the role of YTHDF proteins in human cancers and inhibition of YTHDFs.

Keywords:  Cancer therapy; YTHDF proteins; YTHDFs inhibition; m(6)A modification; m(6)A readers

DOI:  https://doi.org/10.1016/j.bmc.2023.117373
J Periodontal Res. 2023 Jun 22.

Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis.

Margaux Vignon, Amandine Bastide, Aurore Attina, Alexandre David, Philippe Bousquet, Valérie Orti, Jérôme Vialaret, Sylvain Lehmann, Dominique DevilleDe Periere, Christophe Hirtz.

   OBJECTIVE: To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS).
BACKGROUND: The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date.
MATERIALS AND METHODS: Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS.
RESULTS: Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary.
CONCLUSION: The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.

Keywords:  biomarker; epitranscriptomics; mass spectrometry; periodontitis; saliva

DOI:  https://doi.org/10.1111/jre.13155
J Ethnopharmacol. 2023 Jun 17. pii: S0378-8741(23)00677-3. [Epub ahead of print] 116809

Qinzhu Liangxue inhibits IL-6-induced hyperproliferation and inflammation in HaCaT cells by regulating METTL14/SOCS3/STAT3 axis.

Yiran Chen, Xiao Miao, Yanwei Xiang, Le Kuai, Xiaojie Ding, Tian Ma, Bin Li, Bin Fan.

   ETHNOPHARMACOLOGICAL RELEVANCE: Psoriasis, an immune-mediated chronic inflammatory skin condition, is treatable with Qinzhu Liangxue (QZLX), a therapeutic medicinal plant formula used in clinical practice. However, further investigation is needed to clarify its molecular mechanisms of action.
AIM OF THE STUDY: The potential biological mechanisms of QZLX to alleviate psoriasis involving IL-6-induced hyperproliferation and inflammation by regulating METTL14/SOCS3/STAT3 axis.
MATERIALS AND METHODS: HaCaT cell model was induced by IL-6, and dealt with serum containing QZLX. In addition, shRNAs and siRNAs were used for gene silencing, viruses were collected 48 h post-transfection and infected HaCaT cells. Cell viability was detected by CCK-8 assay, cell cycle was determined by flow cytometry. Finally, psoriasis mice model was induced by IMQ cream, then back skin tissue was used for hematoxylin and eosin (H&E). The content of IL-1β, IL-6, and IL-8 in cell supernatants were analyzed using ELISA kits. Analysis of SOCS3 was used by quantitative RT-PCR, the expression level of SOCS3, METTL3, METTL14, WTAP, SOCS3, YTHDF2, p-STAT3 and STAT3 in HaCaT cells transduced with METTL14 overexpression was detected by Western blot.
RESULTS: All results indicated that QZLX could significantly alleviate IL-6-induced HaCaT cell viability, cell cycle progression, and inhibit the level of IL-1β, IL-6, and IL-8. The m6A levels and level of METTL14 in HaCaT cells treated with IL-6 were enhanced, while it was reversed by QZLX. METTL14 silencing could inhibit IL-6-induced HaCaT cell viability, cell cycle progression and inflammation response, while SOCS3 overexpression also suppressed METTL14-induced HaCaT cell viability, cell cycle progression and inflammation. QZLX could significantly enhance the expression level of SOCS3, while inhibit the level of METTL14, and p-STAT3/STAT3. In addition, QZLX inhibits METTL14-induced HaCaT cell viability, cell cycle progression, and inhibits the level of IL-1β, IL-6, and IL-8.
CONCLUSIONS: Our finding suggested that QZLX ameliorated the inflammation response of psoriasis and performed the potential anti-psoriasis effect by regulating METTL14/SOCS3/STAT3 axis in both mice and HaCaT cells psoriasis model. Therefore, our study demonstrated a significant strategy for inhibiting psoriasis inflammation via targeting METTL14/SOCS3/STAT3 axis.

Keywords:  IL-6; Inflammation; METTL14; Qinzhu Liangxue; SOCS3

DOI:  https://doi.org/10.1016/j.jep.2023.116809
Epigenomics. 2023 Jun 20.

m6A-mediated upregulation of lncRNA RMRP boosts the progression of bladder cancer via epigenetically suppressing SCARA5.

Xinsheng Lu, Libo Chen, Shucheng Liu, Youhan Cao, Zhongxin Huang.

  Aim: This study aimed to elucidate the relationship between SCARA5 and RMRP in bladder cancer and their underlying mechanism. Methods: Biological functions were evaluated using cell-counting kit 8 assay, 5-ethynyl-2'-deoxyuridine incorporation, wound healing and Transwell assays. RNA immunoprecipitation, RNA pull-down and chromatin immunoprecipitation were employed. A xenograft tumor model in nude mice was also conducted. Results & conclusion: RMRP and SCARA5 exhibited an inverse correlation. Downregulation of RMRP significantly suppressed bladder cancer cell proliferation, migration and invasion, which was reversed by SCARA5 overexpression. RMRP recruited DNA methyltransferases to the promoter region of SCARA5, thereby triggering the methylation of the SCARA5 promoter to epigenetically suppress its expression. Our findings elucidate the machinery by which RMRP, stabilized by METTL3, exerts a promoter role in bladder cancer tumorigenesis by triggering SCARA5 methylation.

Keywords:  DNMTs; RMRP; SCARA5; bladder cancer; hypermethylation; tumorigenesis

DOI:  https://doi.org/10.2217/epi-2023-0062
Pulm Pharmacol Ther. 2023 Jun 15. pii: S1094-5539(23)00039-1. [Epub ahead of print] 102227

Serum exosomal m6A demethylase FTO promotes gefitinib resistance in non-small cell lung cancer by up-regulating FLRT3, PTGIS and SIRPα expression.

Qi Wang, Lin Zhang, Zhenzhong Su, Wei Li, Yuxi Jia, Jie Zhang.

  This study investigates the molecular mechanism of FTO m6A demethylase in non-small cell lung cancer (NSCLC) and gefitinib resistance using GEO and TCGA databases. Differentially expressed genes (DEGs) were screened from RNA-seq data sets of serum exosomes of gefitinib-resistant NSCLC patients in the GEO database and the NSCLC data set in the GEPIA2 database. From this analysis, FTO m6A demethylase was found to be significantly upregulated in the serum exosomes of gefitinib-resistant NSCLC patients. To identify downstream genes affected by FTO m6A demethylase, weighted correlation network analysis and differential expression analysis were performed, resulting in the identification of three key downstream genes (FLRT3, PTGIS, and SIRPA). Using these genes, the authors constructed a prognostic risk assessment model. Patients with high-risk scores exhibited a significantly worse prognosis. The model could predict the prognosis of NSCLC with high accuracy measured by AUC values of 0.588, 0.608, and 0.603 at 1, 3, and 5 years respectively. Furthermore, m6A sites were found in FLRT3, PTGIS, and SIRPA genes, and FTO was significantly positively correlated with the expression of these downstream genes. Overall, FTO m6A demethylase promotes gefitinib resistance in NSCLC patients by upregulating downstream FLRT3, PTGIS, and SIRPA expression, with these three downstream genes serving as strong prognostic indicators.

Keywords:  FLRT3; FTO; Gefitinib resistance; Non-small cell lung cancer; PTGIS; SIRPα; Serum exosome

DOI:  https://doi.org/10.1016/j.pupt.2023.102227
BMC Bioinformatics. 2023 Jun 17. 24(1): 257

Exploration of m6A methylation regulators as epigenetic targets for immunotherapy in advanced sepsis.

Weiwei Qian, Jian Zhou, Songtao Shou.

   BACKGROUND: This study aims to deeply explore the relationship between m6A methylation modification and peripheral immune cells in patients with advanced sepsis and mine potential epigenetic therapeutic targets by analyzing the differential expression patterns of m6A-related genes in healthy subjects and advanced sepsis patients.
METHODS: A single cell expression dataset of peripheral immune cells containing blood samples from 4 patients with advanced sepsis and 5 healthy subjects was obtained from the gene expression comprehensive database (GSE175453). Differential expression analysis and cluster analysis were performed on 21 m6A-related genes. The characteristic gene was identified based on random forest algorithm, and the correlation between the characteristic gene METTL16 and 23 immune cells in patients with advanced sepsis was evaluated using single-sample gene set enrichment analysis.
RESULTS: IGFBP1, IGFBP2, IGF2BP1, and WTAP were highly expressed in patients with advanced sepsis and m6A cluster B. IGFBP1, IGFBP2, and IGF2BP1 were positively correlated with Th17 helper T cells. The characteristic gene METTL16 exhibited a significant positive correlation with the proportion of various immune cells.
CONCLUSION: IGFBP1, IGFBP2, IGF2BP1, WTAP, and METTL16 may accelerate the development of advanced sepsis by regulating m6A methylation modification and promoting immune cell infiltration. The discovery of these characteristic genes related to advanced sepsis provides potential therapeutic targets for the diagnosis and treatment of sepsis.

Keywords:  Advanced sepsis; Immunoregulation; m6A methylation modification

DOI:  https://doi.org/10.1186/s12859-023-05379-w
J Transl Med. 2023 Jun 20. 21(1): 402

CircNFATC3 promotes the proliferation of gastric cancer through binding to IGF2BP3 and restricting its ubiquitination to enhance CCND1 mRNA stability.

Feifei Yang, Qiang Ma, Bo Huang, Xiaolin Wang, Xiaojuan Pan, Ting Yu, Lingyu Ran, Shan Jiang, Haiping Li, Ye Chen, Yuying Liu, Ce Liang, Junwu Ren, Yuying Zhang, Shimin Wang, Wei Li, Bin Xiao.

   BACKGROUND: Insulin like growth factor II mRNA binding protein 3 (IGF2BP3) is an RNA binding protein with multiple roles in regulation of gene expression at the post-transcriptional level and is implicated in tumorigenesis and progression of numerous cancers including gastric cancer (GC). Circular RNAs (circRNAs) are a diverse endogenous noncoding RNA population that have important regulatory roles in cancer. However, circRNAs that regulate the expression of IGF2BP3 in GC is largely unknown.
METHODS: CircRNAs that bound to IGF2BP3 were screened in GC cells using RNA immunoprecipitation and sequencing (RIP-seq). The identification and localization of circular nuclear factor of activated T cells 3 (circNFATC3) were identified using Sanger sequencing, RNase R assays, qRT-PCR, nuclear-cytoplasmic fractionation and RNA-FISH assays. CircNFATC3 expression in human GC tissues and adjacent normal tissues were measured by qRT-PCR and ISH. The biological role of circNFATC3 in GC was confirmed by in vivo and in vitro experiments. Furthermore, RIP, RNA-FISH/IF, IP and rescue experiments were performed to uncover interactions between circNFATC3, IGF2BP3 and cyclin D1 (CCND1).
RESULTS: We identified a GC-associated circRNA, circNFATC3, that interacted with IGF2BP3. CircNFATC3 was significantly overexpressed in GC tissues and was positively associated with tumor volume. Functionally, the proliferation of GC cells decreased significantly after circNFATC3 knockdown in vivo and in vitro. Mechanistically, circNFATC3 bound to IGF2BP3 in the cytoplasm, which enhanced the stability of IGF2BP3 by preventing ubiquitin E3 ligase TRIM25-mediated ubiquitination, thereby enhancing the regulatory axis of IGF2BP3-CCND1 and promoting CCND1 mRNA stability.
CONCLUSIONS: Our findings demonstrate that circNFATC3 promotes GC proliferation by stabilizing IGF2BP3 protein to enhance CCND1 mRNA stability. Therefore, circNFATC3 is a potential novel target for the treatment of GC.

Keywords:  CCND1; Gastric cancer; IGF2BP3; TRIM25; circNFATC3

DOI:  https://doi.org/10.1186/s12967-023-04235-y
Mol Cancer. 2023 Jun 23. 22(1): 99

m6A methylation reader IGF2BP2 activates endothelial cells to promote angiogenesis and metastasis of lung adenocarcinoma.

Han Fang, Qi Sun, Jin Zhou, Huijuan Zhang, Qiong Song, Hua Zhang, Guohua Yu, Ying Guo, Chengyu Huang, Yakui Mou, Chuanliang Jia, Yingjian Song, Aina Liu, Kaiyu Song, Congxian Lu, Ruxian Tian, Shizhuang Wei, Dengfeng Yang, Yixuan Chen, Ting Li, Kejian Wang, Yilan Yu, Yufeng Lv, Ke Mo, Ping Sun, Xiaofeng Yu, Xicheng Song.

   BACKGROUND: Lung adenocarcinoma (LUAD) is a common type of lung cancer with a high risk of metastasis, but the exact molecular mechanisms of metastasis are not yet understood.
METHODS: This study acquired single-cell transcriptomics profiling of 11 distal normal lung tissues, 11 primary LUAD tissues, and 4 metastatic LUAD tissues from the GSE131907 dataset. The lung multicellular ecosystems were characterized at a single-cell resolution, and the potential mechanisms underlying angiogenesis and metastasis of LUAD were explored.
RESULTS: We constructed a global single-cell landscape of 93,610 cells from primary and metastatic LUAD and found that IGF2BP2 was specifically expressed both in a LUAD cell subpopulation (termed as LUAD_IGF2BP2), and an endothelial cell subpopulation (termed as En_IGF2BP2). The LUAD_IGF2BP2 subpopulation progressively formed and dominated the ecology of metastatic LUAD during metastatic evolution. IGF2BP2 was preferentially secreted by exosomes in the LUAD_IGF2BP2 subpopulation, which was absorbed by the En_IGF2BP2 subpopulation in the tumor microenvironment. Subsequently, IGF2BP2 improved the RNA stability of FLT4 through m6A modification, thereby activating the PI3K-Akt signaling pathway, and eventually promoting angiogenesis and metastasis. Analysis of clinical data showed that IGF2BP2 was linked with poor overall survival and relapse-free survival for LUAD patients.
CONCLUSIONS: Overall, these findings provide a novel insight into the multicellular ecosystems of primary and metastatic LUAD, and demonstrate that a specific LUAD_IGF2BP2 subpopulation is a key orchestrator promoting angiogenesis and metastasis, with implications for the gene regulatory mechanisms of LUAD metastatic evolution, representing themselves as potential antiangiogenic targets.

Keywords:  Angiogenesis; Exosomes; IGF2BP2; Lung adenocarcinoma; Metastasis; N6-methyladenosine; Single-cell RNA sequencing

DOI:  https://doi.org/10.1186/s12943-023-01791-1