bims-rimeca 2023-08-20 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023‒08‒20
nineteen papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

METTL14 Suppresses Tumor Stemness and Metastasis of Colon Cancer Cells by Modulating m6A-Modified SCD1.
Down-regulated FTO and ALKBH5 co-operatively activates FOXO signaling through m6A methylation modification in HK2 mRNA mediated by IGF2BP2 to enhance glycolysis in colorectal cancer.
Methyltransferase-like 3 facilitates the stem cell properties of esophageal cancer by upregulating Patched homolog 1 via N6-methyladenosine methylation.
Gemcitabine Inhibits the Progression of Pancreatic Cancer by Restraining the WTAP/MYC Chain in an m6A-dependent Manner.
The role of m6A RNA methylation in autoimmune diseases: Novel therapeutic opportunities.
Construction of Multiple DNAzymes Driven by Single Base Elongation and Ligation for Single-Molecule Monitoring of FTO in Cancer Tissues.
m6A genotypes and prognostic signature for assessing the prognosis of patients with acute myeloid leukemia.
FTO-mediated epigenetic upregulation of LINC01559 confers cell resistance to docetaxel in breast carcinoma by suppressing miR-1343-3p.
ALKBH5-mediated RNA m6 A methylation regulates the migration, invasion and proliferation of rheumatoid fibroblast-like synoviocytes.
RNA m6A reader YTHDF2 facilitates precursor miR-126 maturation to promote acute myeloid leukemia progression.
MiR-183-5p promotes renal cell carcinoma metastasis by targeting TET1.
LncRNA FOXD3-AS1/miR-128-3p axis-mediated IGF2BP3 in glioma stimulates cancer angiogenesis and progression.
A cleaved METTL3 potentiates the METTL3-WTAP interaction and breast cancer progression.
RNA modification-mediated translational control in immune cells.
IL-33 Downregulates Hepatic Carboxylesterase 1 in Acute Liver Injury via Macrophage-derived Exosomal miR-27b-3p.
The m6A Reader YTHDF1 Improves Sevoflurane-Induced Neuronal Pyroptosis and Cognitive Dysfunction Through Augmenting CREB-BDNF Signaling.
Benzo[a]pyrene-induced up-regulation of circ_0003552 via ALKBH5-mediated m6A modification promotes DNA damage in human bronchial epithelial cells.
METTL14 drives growth and metastasis of non-small cell lung cancer by regulating pri-miR-93-5p maturation and TXNIP expression.
Malat1 promotes macrophage-associated inflammation by increasing PPAR-γ methylation through binding to EZH2 in acute myocardial infarction.

Mol Biotechnol. 2023 Aug 17.

METTL14 Suppresses Tumor Stemness and Metastasis of Colon Cancer Cells by Modulating m6A-Modified SCD1.

Dehua Xu, Shuguang Han, Xiaoguang Yue, Xiangyu Xu, Tieao Huang.

  Colon cancer (CC) is a malignant disease of the digestive tract, and its rising prevalence poses a grave threat to people's health. N6-methyladenosine (m6A) modification is essential for various crucial life processes through modulating gene expression. Methyltransferase-like 14 (METTL14), the m6A methylation transferase core protein, and its aberrant expression is intimately correlated to tumor development. This study was conducted to probe the impacts and specific mechanisms of METTL14 on the biological process of CC. Bioinformatics data disclosed that METTL14 was significantly attenuated in CC. Functional assays were executed to ascertain how METTL14 affected CC tumorigenicity, and METTL14 overexpression caused a notable decline in viability, migration, invasion, and stemness phenotype of CC cells. Then, in-depth mechanistic studies displayed that stearoyl-CoA desaturase 1 (SCD1) was a downstream target gene of METTL14-mediated m6A modification. METTL14 overexpression substantially augmented the m6A modification of SCD1 mRNA and diminished the SCD1 mRNA level. In addition, we revealed that YTHDF2 was the m6A reader to recognize METTL14 m6A-modified SCD1 mRNA and abolish its stability. Finally, we also validated that METTL14 might impede the tumorigenic process of CC through SCD1 mediated Wnt/β-catenin signaling. Taken together, this study presented that METTL14 performed as a potential therapeutic target in CC with important implications for the prognosis amelioration of CC patients.

Keywords:  CC; METTL14; SCD1; Stemness; m6A

DOI:  https://doi.org/10.1007/s12033-023-00843-7
Cell Biosci. 2023 Aug 14. 13(1): 148

Down-regulated FTO and ALKBH5 co-operatively activates FOXO signaling through m6A methylation modification in HK2 mRNA mediated by IGF2BP2 to enhance glycolysis in colorectal cancer.

Mujie Ye, Jinhao Chen, Feiyu Lu, Minghui Zhao, Suwen Wu, Chunhua Hu, Ping Yu, Jingbao Kan, Jianan Bai, Ye Tian, Qiyun Tang.

  BACKGROUND: N6-methyladenosine (m6A) modification is the most abundant reversible methylation modification in eukaryotes, and it is reportedly closely associated with a variety of cancers progression, including colorectal cancer (CRC). This study showed that activated lipid metabolism and glycolysis play vital roles in the occurrence and development of CRC. However, only a few studies have reported the biological mechanisms underlying this connection.METHODS: Protein and mRNA levels of FTO and ALKBH5 were measured using western blot and qRT-PCR. The effects of FTO and ALKBH5 on cell proliferation were examined using CCK-8, colony formation, and EdU assays, and the effects on cell migration and invasion were tested using a transwell assay. m6A RNA immunoprecipitation (MeRIP) and RNA-seq was used to explore downstream target gene. RIP was performed to verify the interaction between m6A and HK2. The function of FTO and ALKBH5 in vivo was determined by xenograft in nude mice.
RESULTS: In this study, FTO and ALKBH5 were significantly down-regulated in CRC patients and cells both in vivo and in vitro in a high-fat environment. Moreover, FTO and ALKBH5 over-expression hampered cell proliferation both in vitro and in vivo. Conversely, FTO and ALKBH5 knockdown accelerated the malignant biological behaviors of CRC cells. The mechanism of action of FTO and ALKBH5 involves joint regulation of HK2, a key enzyme in glycolysis, which was identified by RNA sequencing and MeRIP-seq. Furthermore, reduced expression of FTO and ALKBH5 jointly activated the FOXO signaling pathway, which led to enhanced proliferation ability in CRC cells. IGF2BP2, as a m6A reader, positively regulated HK2 mRNA in m6A dependent manner. Additionally, down-regulation of FTO/ALKBH5 increased METTL3 and decreased METTL14 levels, further promoting CRC progression.
CONCLUSION: In conclusion, our study revealed the FTO-ALKBH5/IGF2BP2/HK2/FOXO1 axis as a mechanism of aberrant m6A modification and glycolysis regulation in CRC.

Keywords:  Colorectal cancer; Glycolysis; N6-methyladenosine; RNA demethylase

DOI:  https://doi.org/10.1186/s13578-023-01100-9
Am J Physiol Cell Physiol. 2023 Aug 14.

Methyltransferase-like 3 facilitates the stem cell properties of esophageal cancer by upregulating Patched homolog 1 via N6-methyladenosine methylation.

Hao Liang, Chengyuan Fang, Luquan Zhang.

  Patched homolog 1 (PTCH1) has been proved to facilitate cell proliferation and self-renewal in esophageal cancer (EC). The present study intended to exploit the influence of PTCH1 on EC cells and the potential mechanisms. PTCH1 and methyltransferase-like 3 (METTL3) expression was examined by qRT-PCR and western blot in EC cell lines. Following the loss- and gain-of-function assays, cell proliferation was examined by CCK-8 and clone formation assays, invasion and migration by Transwell and scratch assays, and the sphere-forming ability of stem cells by cell sphere-forming assay. The expression of stemness genes NANOG, Oct4, and SOX2 was detected by western blot. Me-RIP assay was performed to test N6-methyladenosine (m6A) modification levels of PTCH1 mRNA, RIP and PAR-CLIP assays to assess the binding of METTL3 to PTCH1, and actinomycin D treatment to examine PTCH1 mRNA stability. A xenograft tumor model in nude mice was established for further in vivo verification. PTCH1 and METTL3 expression was high in EC cells. Knockdown of METTL3 reduced m6A level and stability of PTCH1 mRNA. Knockdown of PTCH1 or METTL3 declined invasion, proliferation, migration, and NANOG, Oct4, and SOX2 levels in EC cells, and reduced sphere-forming abilities of EC stem cells. Overexpression of PTCH1 abolished the suppressive effect of METTL3 knockdown on EC cells in vitro. METTL3 knockdown repressed tumor growth in nude mice, which was negated by further overexpressing PTCH1. METTL3 facilitated growth and stemness of EC cells via upregulation of PTCH1 expression by enhancing PTCH1 m6A modification.

Keywords:  Esophageal cancer; METTL3; N6-methyladenosine; PTCH1; Stemness

DOI:  https://doi.org/10.1152/ajpcell.00136.2023
Cancer Res Treat. 2023 Aug 16.

Gemcitabine Inhibits the Progression of Pancreatic Cancer by Restraining the WTAP/MYC Chain in an m6A-dependent Manner.

Pei Cao, Weigang Zhang, Junyi Qiu, Zuxiong Tang, Xiaofeng Xue, Tingting Feng.

  Purpose: Pancreatic cancer (PC) is a common malignant tumor of the digestive system, and its five-year survival rate is only 4%. N6-methyladenosine (m6A) RNA methylation is the most common post-transcriptional modification and dynamically regulates cancer development, while its role in PC treatment remains unclear.Materials and Methods: We treated PC cells with gemcitabine and quantified the overall m6A level with m6A methylation quantification. qRT-PCR and Western blot (WB) analyses were used to detect expression changes of m6A regulators. We verified the m6A modification on the target genes through m6A-immunoprecipitation (IP), and further in vivo experiments and immunofluorescence (IF) assays were applied to verify regulation of gemcitabine on WTAP and MYC.
Results: Gemcitabine inhibited the proliferation and migration of PC cells and reduced the overall level of m6A modification. Additionally, the expression of the "writer" WTAP was significantly downregulated after gemcitabine treatment. We knocked down WTAP in cells and found target gene MYC expression was significantly downregulated, m6A-IP also confirmed the m6A modification on MYC. Our experiments showed that m6A-MYC may be recognized by the "reader" IGF2BP1. In vivo experiments revealed gemcitabine inhibited the tumorigenic ability of PC cells. IF analysis also showed that gemcitabine inhibited the expression of WTAP and MYC, which displayed a significant trend of co-expression.
Conclusion: Our study confirmed that gemcitabine interferes with WTAP protein expression in PC, reduces m6A modification on MYC and RNA stability, thereby inhibiting the downstream pathway of MYC, and inhibits the progression of PC.

Keywords:  Gemcitabine; MYC; Pancreatic neoplasms; RNA methylation; WTAP

DOI:  https://doi.org/10.4143/crt.2022.1600
Genes Dis. 2024 Jan;11(1): 252-267

The role of m6A RNA methylation in autoimmune diseases: Novel therapeutic opportunities.

Yunan Shan, Wei Chen, Yanbin Li.

  N6-methyladenosine (m6A) modifications, as one of the most common forms of internal RNA chemical modifications in eukaryotic cells, have gained increasing attention in recent years. The m6A RNA modifications exert various crucial roles in various biological processes, such as embryonic development, neurogenesis, circadian rhythms, and tumorigenesis. Recent advances have highlighted that m6A RNA modification plays an important role in immune response, especially in the initiation and progression of autoimmune diseases. In this review, we summarized the regulatory mechanisms of m6A methylation and its biological functions in the immune system and mainly focused on recent progress in research on the potential role of m6A RNA methylation in the pathogenesis of autoimmune diseases, thus providing possible biomarkers and potential targets for the prevention and treatment of autoimmune diseases.

Keywords:  Adaptive immunity; Autoimmune diseases; Immune response; Innate immunity; m6A RNA methylation

DOI:  https://doi.org/10.1016/j.gendis.2023.02.013
Anal Chem. 2023 Aug 17.

Construction of Multiple DNAzymes Driven by Single Base Elongation and Ligation for Single-Molecule Monitoring of FTO in Cancer Tissues.

Ning-Ning Zhao, Ya-Zhen Liu, Lingfei Zhang, Wenjing Liu, Xiaoran Zou, Qinfeng Xu, Chun-Yang Zhang.

Fat mass and obesity-associated proteins (FTO) play an essential role in the reversible regulation of N6-methyladenosine (m6A) epigenetic modification, and the overexpression of FTO is closely associated with the occurrence of diverse human diseases (e.g., obesity and cancers). Herein, we demonstrate the construction of multiple DNAzymes driven by single base elongation and ligation for the single-molecule monitoring of FTO in cancer tissues. When target FTO is present, the m6A-RNA is specifically demethylated and subsequently acts as a primer to combine with the padlock probe, initiating single-base elongation and ligation reaction to generate a closed template probe. Upon the addition of phi29 DNA polymerase, a rolling circle amplification (RCA) reaction is initiated to produce large numbers of Mg2+-dependent DNAzyme repeats. Subsequently, the DNAzymes cyclically digest the signal probes, liberating numerous Cy5 molecules that can be precisely counted by single-molecule imaging. Taking advantage of the sequence specificity of the polymerase/ligase-mediated gap-filling and ligation as well as the high amplification efficiency of RCA, this biosensor shows excellent specificity and high sensitivity with a detection limit of 5.96 × 10-16 M. It can be applied to screen FTO inhibitors and quantify FTO activity at the single-cell level. Moreover, the proposed strategy can accurately distinguish the FTO expression level in tissues of healthy individuals and breast cancer patients, providing a new platform for drug discovery, m6A modification-related research, and clinical diagnostics.

DOI: https://doi.org/10.1021/acs.analchem.3c02989
BMC Med Genomics. 2023 Aug 18. 16(1): 191

m6A genotypes and prognostic signature for assessing the prognosis of patients with acute myeloid leukemia.

Caizhu Fu, Ruirui Kou, Jie Meng, Duanfeng Jiang, Ruilan Zhong, Min Dong.

  BACKGROUND: N6-methyladenosine (m6A) has been confirmed to function critically in acute myeloid leukemia (AML) progression. Hitherto, the subtyping and prognostic predictive significance of m6A-correlated genes in AML is unclear.METHOD: From The Cancer Genome Atlas (TCGA-LAML), Therapeutically Applicable Research to Generate Effective Treatments (TARGET-AML) and Gene Expression Omnibus (GEO, GSE71014) databases, we collected the sequencing data of AML patients. The batch effect was removed via limma package for TCGA-LAML and TARGET-AML, and the aggregated samples were AML cohorts. Samples in the AML cohort identified m6A models in AML by consensus clustering based on 23-m6A-related modulators. M6A-related differentially expressed genes (m6ARDEGs) influencing the overall survival (OS) of AML were determined by performing differential expression analysis and univariate COX analysis, and consensus-based clustering was utilized to access AML molecular subtypes. LASSO and multivariate COX analyses were performed to obtain the optimized m6ARDEGs to construct the m6A Prognostic Risk Score (m6APR_Score). Whether the model was robust was evaluated according to Kaplan-Meier (K-M) and receiver operator characteristic (ROC) curves. Further, the abundance of immune cell infiltration was explored in different m6A modification patterns and molecular subtypes and m6APR_Score groupings. Finally, nomogram was constructed to predict OS in AML. Quantitative real-time polymerase chain reaction (RT-qPCR) and cell counting kit-8 (CCK-8) assay were used to validate the genes in m6APR_Score in AML cells.
RESULTS: The m6A models (m6AM1, m6AM2, m6AM3) and molecular subtypes (C1, C2, C3) were identified in the AML cohort, exhibiting different prognosis and immunoreactivity. We recognized novel prognostic biomarkers of AML such as CD83, NRIP1, ACSL1, METTL7B, OGT, and C4orf48. AML patients were grouped into high-m6APR_Score and low-m6APR_Score groups, with the later group showing a better prognosis than former one. Both the AML cohort and the validation cohort GSE71014 demonstrated excellent prediction. Finally, the nomogram accurately predicted the survival of patients suffering from AML. Further, the decision curves showed that both nomogram and m6APR_Score showed excellent prediction. It was confirmed in vitro experiments that mRNA expressions of NRIP1, ACSL1, METTL7B and OGT were elevated, while CD83 and C4orf48 mRNA expressions downregulated in AML cells. A significant increase in the viability of U937 and THP-1 cell lines after inhibition of CD83, while siMETTL7B had contrast results.
CONCLUSION: Our study demonstrated that m6APR_Score and CD83, NRIP1, ACSL1, METTL7B, OGT, and C4orf48 potentially provided novel and promising prognostic support for AML patients.

Keywords:  Acute myeloid leukemia; Immune; N6-methyladenosine; Prognostic; TCGA

DOI:  https://doi.org/10.1186/s12920-023-01629-1
Kaohsiung J Med Sci. 2023 Aug 16.

FTO-mediated epigenetic upregulation of LINC01559 confers cell resistance to docetaxel in breast carcinoma by suppressing miR-1343-3p.

Wei Lin, Cai-Qin Mo, Ling-Jun Kong, Ling Chen, Kun-Lin Wu, Xian Wu.

  This study was to explore the regulatory effect of long non-coding RNA LINC01559 on Docetaxel resistance in breast carcinoma (BCa) and its underlying mechanism. In the present study, we found that LINC01559 expression was elevated and LINC01559 overexpression facilitated docetaxel resistance in BCa cells. Moreover, it was revealed that the upregulation of LINC01559 in BCa cells was induced by FTO-mediated demethylation in an m6A-YTHDF2-dependent manner. Additionally, Dual-luciferase reporter assay confirmed the binding ability between LINC01559 and miR-1343-3p, and Pearson correlation analysis showed a negative correlation between them. Particularly, miR-1343-3p inhibition partly abolished the suppression on docetaxel resistance in BCa cells caused by LINC01559 knockdown. To sum up, FTO-mediated epigenetic upregulation of LINC01559 promoted cell resistance to Docetaxel in BCa by negatively regulating miR-1343-3p.

Keywords:  FTO; LINC01559; N6-methyladenosine; breast carcinoma; docetaxel resistance

DOI:  https://doi.org/10.1002/kjm2.12728
Arthritis Rheumatol. 2023 Aug 16.

ALKBH5-mediated RNA m6 A methylation regulates the migration, invasion and proliferation of rheumatoid fibroblast-like synoviocytes.

Yu Kuang, Ruiru Li, Jingnan Wang, Siqi Xu, Qian Qiu, Shuibin Lin, Di Liu, Chuyu Shen, Yingli Liu, Meilin Xu, Wei Lin, Shuoyang Zhang, Liuqin Liang, Hanshi Xu, Youjun Xiao.

OBJECTIVE: Fibroblast-like synoviocytes (FLS) are critical for promoting joint damage in rheumatoid arthritis (RA). N6-methyladenosine (m6 A) modification plays key roles in various diseases; however, its role in the pathogenesis of RA is largely unknown. Here, we investigated increased demethylase ALKBH5 promotes proliferation, migration and invasion of RA FLS via regulating JARID2 expression.METHODS: ALKBH5 expression in FLS was evaluated using RT-qPCR and WB. EdU, scratch wound healing, and transwell assays were implemented to determine the role of ALKBH5 on RA FLS proliferation, mobility, and migration. Then, m6 A-seq combined with RNA-seq was performed to identify the potential target of ALKBH5. The following RNA immunoprecipitation (RIP) and RNA pulldown was used to validate the interaction between protein and mRNA. CIA and DTHA models were further established to assess the therapeutic potency of ALKBH5 in vivo.
RESULTS: We demonstrated that ALKBH5 expression was increased in FLS and synovium from RA. Functionally, ALKBH5 knockdown inhibited the proliferation, migration and invasion of RA FLS, whereas overexpression of ALKBH5 displayed the opposite effect. Mechanistically, ALKBH5 mediated m6 A modification in the JARID2 mRNA and enhanced its mRNA stability in cooperation with IGF2BP3. Intriguingly, the severity of arthritis was attenuated in DTHA mice with ALKBH5 knockout (KO) or CIA rats with intra-articular injection of ALKBH5-shRNA.
CONCLUSION: Our findings suggest that ALKBH5-mediated m6 A modification is crucial for synovial hyperplasia and invasion in RA. ALKBH5 might be a potential therapeutic target for RA and even for dysregulated fibroblasts in a wide range of diseases.

DOI: https://doi.org/10.1002/art.42676
Genes Dis. 2024 Jan;11(1): 382-396

RNA m6A reader YTHDF2 facilitates precursor miR-126 maturation to promote acute myeloid leukemia progression.

Zheng Zhang, Keren Zhou, Li Han, Andrew Small, Jianhuang Xue, Huilin Huang, Hengyou Weng, Rui Su, Brandon Tan, Chao Shen, Wei Li, Zhicong Zhao, Ying Qing, Xi Qin, Kitty Wang, Keith Leung, Mark Boldin, Chun-Wei Chen, David Ann, Zhijian Qian, Xiaolan Deng, Jianjun Chen, Zhenhua Chen.

  As the most common internal modification of mRNA, N6-methyladenosine (m6A) and its regulators modulate gene expression and play critical roles in various biological and pathological processes including tumorigenesis. It was reported previously that m6A methyltransferase (writer), methyltransferase-like 3 (METTL3) adds m6A in primary microRNAs (pri-miRNAs) and facilitates its processing into precursor miRNAs (pre-miRNAs). However, it is unknown whether m6A modification also plays a role in the maturation process of pre-miRNAs and (if so) whether such a function contributes to tumorigenesis. Here, we found that YTHDF2 is aberrantly overexpressed in acute myeloid leukemia (AML) patients, especially in relapsed patients, and plays an oncogenic role in AML. Moreover, YTHDF2 promotes expression of miR-126-3p (also known as miR-126, as it is the main product of precursor miR-126 (pre-miR-126)), a miRNA that was reported as an oncomiRNA in AML, through facilitating the processing of pre-miR-126 into mature miR-126. Mechanistically, YTHDF2 recognizes m6A modification in pre-miR-126 and recruits AGO2, a regulator of pre-miRNA processing, to promote the maturation of pre-miR-126. YTHDF2 positively and negatively correlates with miR-126 and miR-126's downstream target genes, respectively, in AML patients, and forced expression of miR-126 could largely rescue YTHDF2/Ythdf2 depletion-mediated suppression on AML cell growth/proliferation and leukemogenesis, indicating that miR-126 is a functionally important target of YTHDF2 in AML. Overall, our studies not only reveal a previously unappreciated YTHDF2/miR-126 axis in AML and highlight the therapeutic potential of targeting this axis for AML treatment, but also suggest that m6A plays a role in pre-miRNA processing that contributes to tumorigenesis.

Keywords:  AML; N6-methyladenosine; Pre-miRNA maturation; YTHDF2; miR-126

DOI:  https://doi.org/10.1016/j.gendis.2023.01.016
Int J Immunopathol Pharmacol. 2023 Jan-Dec;37:37 3946320231184997

MiR-183-5p promotes renal cell carcinoma metastasis by targeting TET1.

Shengnan Jin, Lu Chen, Jiayi Wu, Mengjiao Chen, Hua Wang, Haihong Hu, Lushan Yu, Su Zeng.

  Ten-eleven translocation 1 (TET1) is a member of the DNA demethylase family that regulates the methylation level of the genome. Dysregulation of TET1 in renal cell carcinoma (RCC) may be associated with RCC progression, but the mechanism of TET1 down-regulation in RCC is not yet known. MiR-183-5p is up-regulated in various tumor tissues and acts as an oncogene. We used Transwell and wound healing assays to test cell invasion and migration. To investigate DNA methylation, we used dot blot, which indicates TET1 enzyme activity. We verified the binding of miR-183-5p and TET1 3'-UTR (untranslated region) using dual-luciferase reporter assay. Our study demonstrated, for the first time, that miR-183-5p can directly repress TET1 expression in RCC. We observed a significant decrease in TET1 expression in RCC specimens, as reported in the literature, and a significant decrease in the concentration of 5hmC in RCC. By aligning the microRNA with a database and using the luciferase reporter gene method, we found that miR-183-5p can inhibit luciferase activity by binding to 453-459 bp of TET1 3'-UTR, leading to inhibition of TET1 expression. Furthermore, down-regulation of TET1 inhibited miR-200c expression and promoted RCC cell invasion and migration. Our findings suggest that in RCC, increased expression of miR-183-5p inhibits the expression of TET1, which in turn inhibits the expression of miR-200c and E-cadherin, both of which are associated with cell adhesion. This leads to the promotion of cell invasion and migration.

Keywords:  E-cadherin; TET1; invasion and migration; miR-183-5p; miR-200c; renal cell carcinoma

DOI:  https://doi.org/10.1177/03946320231184997
Folia Neuropathol. 2023 ;pii: 50580. [Epub ahead of print]61(2): 168-184

LncRNA FOXD3-AS1/miR-128-3p axis-mediated IGF2BP3 in glioma stimulates cancer angiogenesis and progression.

Hongxin Zhao, Yuyu Wang, Chuandong Liang, Mingxiang Xie.

  INTRODUCTION: The aim of the study was to research the mechanism by which IGF2BP3 regulates glioma progression as well as its upstream regulatory axis.MATERIAL AND METHODS: The researched mRNA was determined using differential expression analysis based on bioinformatics data, and its upstream miRNAs and lncRNAs were predicted. Interaction between genes we researched was identified by dual-luciferase method. The viability, migration, invasion and angiogenesis of glioma were measured with MTT, colony formation, Transwell and Matrigel tube formation experiments, respectively. The mRNA expression of each gene was tested with qRT-PCR. IGF2BP3 level was determined via western blot and immunohistochemistry. Subcellular fractionation of FOXD3-AS1 was tested with fluorescence in situ hybridization. In vivo tumorigenesis assay was conducted on nude mice.
RESULTS: IGF2BP3 high level in glioma cells correlated with patient's prognosis. Downregulation of IGF2BP3 restrained proliferation, migration, invasion and angiogenesis in glioma cells both in vitro and in vivo. There was a binding relationship between IGF2BP3 and miR-128-3p. Besides, FOXD3-AS1 as a sponge of miR-128-3p was located mainly in cytoplasm. Additionally, FOXD3-AS1 facilitated IGF2BP3 level via sponging miR-128-3p to stimulate glioma angiogenesis.
CONCLUSIONS: FOXD3-AS1 was a sponge of miR-128-3p through upregulating IGF2BP3 in glioma. Our findings shed light on diagnosis and treatment of glioma.

Keywords:   IGF2BP3; MiR-128-3p; biofunction; glioma; FOXD3-AS1

DOI:  https://doi.org/10.5114/fn.2023.126862
Elife. 2023 Aug 17. pii: RP87283. [Epub ahead of print]12

A cleaved METTL3 potentiates the METTL3-WTAP interaction and breast cancer progression.

Chaojun Yan, Jingjing Xiong, Zirui Zhou, Qifang Li, Chuan Gao, Mengyao Zhang, Liya Yu, Jinpeng Li, Ming-Ming Hu, Chen-Song Zhang, Cheguo Cai, Haojian Zhang, Jing Zhang.

  N6-methyladenosine (m6A) methylation of RNA by the methyltransferase complex (MTC), with core components including METTL3-METTL14 heterodimers and Wilms' tumor 1-associated protein (WTAP), contributes to breast tumorigenesis, but the underlying regulatory mechanisms remain elusive. Here, we identify a novel cleaved form METTL3a (residues 239-580 of METTL3). We find that METTL3a is required for the METTL3-WTAP interaction, RNA m6A deposition, as well as cancer cell proliferation. Mechanistically, we find that METTL3a is essential for the METTL3-METTL3 interaction, which is a prerequisite step for recruitment of WTAP in MTC. Analysis of m6A sequencing data shows that depletion of METTL3a globally disrupts m6A deposition, and METTL3a mediates mammalian target of rapamycin (mTOR) activation via m6A-mediated suppression of TMEM127 expression. Moreover, we find that METTL3 cleavage is mediated by proteasome in an mTOR-dependent manner, revealing positive regulatory feedback between METTL3a and mTOR signaling. Our findings reveal METTL3a as an important component of MTC, and suggest the METTL3a-mTOR axis as a potential therapeutic target for breast cancer.

Keywords:  METTL3; MTC; breast tumorigenesis; cell biology; human; m6A methylation; methyltransferase complex

DOI:  https://doi.org/10.7554/eLife.87283
RNA Biol. 2023 Jan;20(1): 603-613

RNA modification-mediated translational control in immune cells.

Yujuan Zhang, Weiguo Hu, Hua-Bing Li.

  RNA modifications play a vital role in multiple pathways of mRNA metabolism, and translational regulation is essential for immune cells to promptly respond to stimuli and adapt to the microenvironment. N6-methyladenosine (m6A) methylation, which is the most abundant mRNA modification in eukaryotes, primarily functions in the regulation of RNA splicing and degradation. However, the role of m6Amethylation in translational control and its underlying mechanism remain controversial. The role of m6A methylation in translation regulation in immune cells has received relatively limited attention. In this review, we aim to provide a comprehensive summary of current studies on the translational regulation of m6A modifications and recent advances in understanding the translational control regulated by RNA modifications during the immune response. Furthermore, we envision the possible pathways through which m6A modifications may be involved in the regulation of immune cell function via translational control.

Keywords:  RNA modification; RNA regulators; immune cell; m6A; translation

DOI:  https://doi.org/10.1080/15476286.2023.2246256
J Clin Transl Hepatol. 2023 Oct 28. 11(5): 1130-1142

IL-33 Downregulates Hepatic Carboxylesterase 1 in Acute Liver Injury via Macrophage-derived Exosomal miR-27b-3p.

Ping Gao, Min Li, Jingli Lu, Daochun Xiang, Ximin Wang, Yanjiao Xu, Yue Zu, Xinlei Guan, Guodong Li, Chengliang Zhang.

  Background and Aims: We previously reported that carboxylesterase 1 (CES1) expression was suppressed following liver injury. The study aimed to explore the role of interleukin (IL)-33 in liver injury and examine the mechanism by which IL-33 regulates CES1.Methods: IL-33 and CES1 levels were determined in the livers of patients and lipopolysaccharide (LPS)-, acetaminophen (APAP)-treated mice. We constructed IL-33 and ST2 knockout (KO) mice. ST2-enriched immune cells in livers were screened to identify the responsible cells. Macrophage-derived exosome (MDE) activity was tested by adding exosome inhibitors. Micro-RNAs (miRs) were extracted from control and IL-33-stimulated MDEs (IL-33-MDEs) and subjected miR sequencing (miR-Seq). Candidate miR was tested in vitro and in vivo and its binding of a target gene was assessed by luciferase reporter assays. Lentivirus-vector cellular transfection and transcript silencing were used to examine pathways mediating IL-33 suppression of miR-27b-3p.
Results: Patient liver IL-33 and CES1 expression levels were inversely correlated. CES1 downregulation in liver injury was rescued in both IL-33-deficient and ST2 KO mice. Macrophages were shown to be responsible for IL-33 effects. IL-33-MDEs reduced CES1 levels in hepatocytes. Exosomal miR-Seq and qRT-PCR demonstrated increased miR-27b-3p levels in IL-33-MDEs; miR-27b-3p was implicated in Nrf2 targeting. IL-33 inhibition of miR-27b-3p was found to be GATA3-dependent.
Conclusions: IL-33-ST2-GATA3 pathway signaling increases miR-27b-3p content in MDEs, which upon being internalized by hepatocytes reduce CES1 expression by inhibiting Nrf2. The elucidation of this mechanism in this study contributes to a better understanding of CES1 dysregulation in liver injury.

Keywords:  Carboxylesterase 1; IL-33; Liver injury; miR-27b-3p

DOI:  https://doi.org/10.14218/JCTH.2022.00144
Neurochem Res. 2023 Aug 12.

The m6A Reader YTHDF1 Improves Sevoflurane-Induced Neuronal Pyroptosis and Cognitive Dysfunction Through Augmenting CREB-BDNF Signaling.

Yuanlu Huang, Yuxuan Yang, Changsheng Ye, Ziye Liu, Fusheng Wei.

  Sevoflurane is one of the most widely used anesthetics in surgery which is the main cause of postoperative cognitive dysfunction (POCD). Previous reports confirmed that YTHDF1 is differently expressed in sevoflurane-induced POCD, while the roles and mechanistic details remain unclear. The molecular expressions were assessed using qRT-PCR, western blot, immunofluorescence and immunohistochemistry. Pathological change in the hippocampus tissues was analyzed using HE staining. Cognitive ability in rats was measured using MWM test. Hippocampal neuronal viability and apoptosis were measured by MTT assay and flow cytometry, respectively. The levels of pro-inflammatory cytokines were assessed using ELISA. The interaction between YTHDF1 and CREB was analyzed by RNA immunoprecipitation assay. YTHDF1 was significantly decreased in hippocampus tissues by sevoflurane exposure, and its overexpression could improve sevoflurane-induced neuron damage and cognitive dysfunction. Meanwhile, YTHDF1 upregulation repressed sevoflurane-induced activation of NLRP3 inflammation and pyroptosis in hippocampus tissues. Subsequently, YTHDF1 directly interacted to CREB mRNA to augment its stability and translation via a m6A-dependent manner, thus activating CREB/BDNF pathway. In addition, the inactivation of CREB/BDNF pathway could reverse the protective effects of YTHDF1 overexpression on sevoflurane-mediated neuronal damage and pyroptosis. These findings revealed that YTHDF1 improved sevoflurane-induced neuronal pyroptosis and cognitive dysfunction through activating CREB-BDNF signaling.

Keywords:  CREB/BDNF/ NLRP3; Postoperative cognitive dysfunction; Sevoflurane; YTHDF1

DOI:  https://doi.org/10.1007/s11064-023-04007-6
Environ Pollut. 2023 Aug 11. pii: S0269-7491(23)01369-6. [Epub ahead of print] 122367

Benzo[a]pyrene-induced up-regulation of circ_0003552 via ALKBH5-mediated m6A modification promotes DNA damage in human bronchial epithelial cells.

Shuwei Yao, Xintong Chen, Ningdong Hu, Nan Zhang, Miaoyun Qiu, Yangyang Jia, Han Zhang, Jihuan Liang, Zehao Chen, Liting Zheng, Jialu Zhu, Rulin Mao, Yiguo Jiang.

  Benzo [a]pyrene (B [a]P) is a widespread environmental chemical pollutant that has been linked to the development of various diseases. However, the specific mechanism of action remains unclear. In this study, human bronchial epithelial 16HBE and BEAS-2B cells were exposed to B [a]P at 0-32 μM to assess the DNA-damaging effects. B [a]P exposure resulted in elevated expression of γ-H2AX, a marker of DNA damage. The m6A RNA methylation assay showed that B [a]P exposure increased the extent of m6A modification and the demethylase ALKBH5 played an integral role in this process. Moreover, the results of the comet assay and Western blot analysis showed an increase in m6A modification mediated by ALKBH5 that promoted DNA damage. Furthermore, the participation of a novel circular RNA, circ_0003552, was assessed by high-throughput sequencing under the condition of high m6A modification induced by B [a]P exposure. In subsequent functional studies, an interference/overexpression system was created to confirm that circ_0003552 participated in regulation of DNA damage. Mechanistically, circ_0003552 had an m6A binding site that could regulate its generation. This study is the first to report that B [a]P upregulated circ_0003552 through m6A modification, thereby promoting DNA damage. These findings revealed that epigenetics played a key role in environmental carcinogen-induced DNA damage, and the quantitative changes it brought might provide an early biomarker for future medical studies of genetic-related diseases and a new platform for investigations of the interaction between epigenetics and genetics.

Keywords:  Benzo[a]pyrene; DNA damage; circRNA; m(6)A modification

DOI:  https://doi.org/10.1016/j.envpol.2023.122367
Genes Genomics. 2023 Aug 18.

METTL14 drives growth and metastasis of non-small cell lung cancer by regulating pri-miR-93-5p maturation and TXNIP expression.

Shuai Qian, Jun Liu, Wenliang Liao, Fengping Wang.

  BACKGROUND: Non-small cell lung cancer (NSCLC) is a prevalent and aggressive malignancy responsible for a significant number of cancer-related deaths worldwide. Unraveling the molecular mechanisms governing NSCLC growth and metastasis is crucial for the identification of novel therapeutic targets and the development of effective anti-cancer strategies. One such mechanism of interest is the involvement of METTL14, an RNA methyltransferase implicated in various cellular processes, in NSCLC progression.OBJECTIVE: The objective of this study was to investigate the role of METTL14 in NSCLC development and metastasis and to elucidate the underlying molecular mechanisms. By understanding the impact of METTL14 on NSCLC pathogenesis, the study aimed to identify potential avenues for targeted therapies in NSCLC treatment.
METHODS: We used bioinformatics and high-throughput transcriptome sequencing analyses to screen regulatory mechanisms affecting NSCLC. The Kaplan-Meier method assessed the correlation between METTL14 expression and the prognosis of NSCLC patients. The effects of manipulated METTL14 on malignant phenotypes of NSCLC cells were examined by colony formation assay, flow cytometry, scratch assay, and Transwell assay. The tumorigenic capacity and metastatic potential of NSCLC cells in vivo were evaluated in nude mice.
RESULTS: METTL14 was overexpressed in NSCLC tissues and cell lines. Its high expression indicated a poor prognosis for NSCLC patients. METTL14 silencing promoted apoptosis and repressed proliferation, migration, and invasion of NSCLC cells. miR-93-5p targeted and inhibited TXNIP. METTL14 increased miR-93-5p expression and matured pri-miR-93-5p through m6A alteration to inhibit TXNIP, thereby inhibiting NSCLC cell apoptosis. By controlling the miR-93-5p/TXNIP axis, METTL14 increased the tumorigenic potential and lung metastasis of NSCLC cells in nude mice.
CONCLUSION: This study revealed a role for METTL14 in the contribution to NSCLC development and metastasis and identified METTL14 as a potential target for NSCLC treatment.

Keywords:  METTL14; Non-small cell lung cancer; Pri-miR-93-5p; TXNIP; m6A methyltransferase; m6A modification; miR-93-5p

DOI:  https://doi.org/10.1007/s13258-023-01436-z
Int Immunopharmacol. 2023 Aug 15. pii: S1567-5769(23)01020-2. [Epub ahead of print]123 110695

Malat1 promotes macrophage-associated inflammation by increasing PPAR-γ methylation through binding to EZH2 in acute myocardial infarction.

Fangyuan Chang, Chunxiao Wang, Ping Zheng, Zhen Liu, Hua Wang, Lei Gong, Haibin Dong, Yanyan Jing, Shaohua Mi, Zan Xie, Peipei Ge, Jun Yang, Lin Zhong.

  The inflammatory microenvironment of macrophage plays an important role in acute myocardial infarction (AMI), but the regulatory mechanism is unknown. Here, we aimed to investigate the role of Malat1 on inflammation microenvironment of macrophage in AMI. Our study found that Malat1 expression was increased in AMI, which mainly expressed in macrophages. Malat1 inhibition improved collagen deposition and inflammation in infarcted heart. In vitro, Malat1 inhibition evidently reduced macrophage-associated inflammation. The results from ribonucleic acid pull-down (RNA pull-down) and RNA Immunoprecipitation (RIP) assay demonstrated that Malat1 directly binds to EZH2. Malat1 and EZH2 complex could increase histone H3K27me3 expression and further inhibit the production of PPAR-γ. In vivo, inhibition of Malat1 also leaded to the down-regulation of both EZH2 and H3K27me3, as well as up-regulation of PPAR-γ in infarcted heart. Therefore, these findings demonstrate a novel mechanism of Malat1 on inflammation microenvironment of macrophage in AMI, which provide a new target for its treatment.

Keywords:  Acute myocardial infarction; Epigenetic modification; Inflammatory microenvironment; Long non-coding RNA; Macrophages

DOI:  https://doi.org/10.1016/j.intimp.2023.110695