bims-rimeca 2023-10-01 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023–10–01
twenty-one papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

ZC3H13 Accelerates Keloid Formation by Mediating N6-methyladenosine Modification of HIPK2.
IGF2BP3 mediates the mRNA degradation of NF1 to promote triple-negative breast cancer progression via an m6A-dependent manner.
METTL3 exerts synergistic effects on m6A methylation and histone modification to regulate the function of VGF in lung adenocarcinoma.
N6-methyladenosine RNA modification in nonalcoholic fatty liver disease.
METTL3 Promotes the Differentiation of Goat Skeletal Muscle Satellite Cells by Regulating MEF2C mRNA Stability in a m6A-Dependent Manner.
Comprehensive analysis of N6-methyladenosine-related RNA methylation in the mouse hippocampus after acquired hearing loss.
N6-methyladenosine (m6A) modification in osteosarcoma: expression, function and interaction with noncoding RNAs - an updated review.
LncRNA TIALD contributes to hepatocellular carcinoma metastasis via inducing AURKA lysosomal degradation.
c-MYC/METTL3/LINC01006 positive feedback loop promotes migration, invasion and proliferation of non-small cell lung cancer.
N6-Methyladenosine Modifications in Pulmonary Hypertension.
Targeting METTL3 reprograms the tumor microenvironment to improve cancer immunotherapy.
ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control.
METTL3 promotes proliferation and migration of colorectal cancer cells by increasing SNHG1 stability.
The Comprehensive Analysis of m6A-Associated Anoikis Genes in Low-Grade Gliomas.
H3K18 lactylation promotes the progression of arsenite-related idiopathic pulmonary fibrosis via YTHDF1/m6A/NREP.
METTL3-induced FGD5-AS1 contributes to the tumorigenesis and PD-1/PD-L1 checkpoint to enhance the resistance to paclitaxel of endometrial carcinoma.
ALKBH5-mediated m6A demethylation of HS3ST3B1-IT1 prevents osteoarthritis progression.
Changes in m6A RNA methylation are associated with male sterility in wolfberry.
Programmed Release METTL3-14 Inhibitor Microneedle Protects Myocardial Function by Reducing Drp1 m6A Modification-Mediated Mitochondrial Fission.
YTHDF1 shapes "cold" tumor and inhibits CD8+ T cells infiltration and function in breast cancer.
NOP2/Sun RNA methyltransferase 2 is a potential pan-cancer prognostic biomarker and is related to immunity.

Biochem Genet. 2023 Sep 26.

ZC3H13 Accelerates Keloid Formation by Mediating N6-methyladenosine Modification of HIPK2.

Manni Fu, Yongjun Chen, Xian Shi.

  Keloids are fibroproliferative skin disorders caused by the improper healing of wounded skin. A growing body of evidence suggests the involvement of N6-Methyladenosine (m6A) modification in various bioprocesses; however, its role in keloid formation has not yet been investigated. The aim of this study was to determine the effect of the m6A regulator zinc finger CCCH domain containing protein 13 (ZC3H13) on the pathogenesis of keloid formation. ZC3H13 and homeodomain-interacting protein kinase 2 (HIPK2) expression was evaluated in healthy skin and keloid tissues, as well as in human dermal fibroblasts and human keloid fibroblasts (HKF), using qRT-PCR and western blotting. The effects of ZC3H13 overexpression and knockdown on the cell function of HKFs were assessed using CCK8, transwell, and flow cytometry. Furthermore, the influence of ZC3H13 on HIPK2 m6A modification was assessed using MeRIP-qPCR and mRNA stability assays. Both ZC3H13 expression and m6A RNA methylation were upregulated in keloid tissues and HKFs. Silencing of ZC3H13 inhibited proliferation and migration, while enhancing apoptosis in HKFs, whereas overexpression had the opposite effect. Furthermore, HIPK2 levels were high in keloid tissues and HKFs, and a positive correlation was observed between ZC3H13 and HIPK2. In HKFs, ZC3H13 overexpression elevated the m6A levels of HIPK2 mRNA and reduced the rate of HIPK2 mRNA degradation. Mechanically, ZC3H13-induced m6A modifications significantly improved HIPK2 mRNA stability. Collectively, ZC3H13 accelerated keloid formation by mediating the m6A modification of HIPK2 mRNA and maintaining its stability.

Keywords:  HIPK2; Keloid; ZC3H13; m6A modification

DOI:  https://doi.org/10.1007/s10528-023-10514-6
Clin Transl Med. 2023 Sep;13(9): e1427

IGF2BP3 mediates the mRNA degradation of NF1 to promote triple-negative breast cancer progression via an m6A-dependent manner.

Xu Zhang, Liang Shi, Han-Dong Sun, Zi-Wen Wang, Feng Xu, Ji-Fu Wei, Qiang Ding.

   BACKGROUND: N6-methyladenosine (m6A) is an abundant reversible modification in eukaryotic mRNAs. Emerging evidences indicate that m6A modification plays a vital role in tumourigenesis. As a crucial reader of m6A, IGF2BP3 usually mediates the stabilisation of mRNAs via an m6A-dependent manner. But the underlying mechanism of IGF2BP3 in the tumourigenesis of triple-negative breast cancer (TNBC) is unclear.
METHODS: TCGA cohorts were analysed for IGF2BP3 expression and IGF2BP3 promoter methylation levels in different breast cancer subtypes. Colony formation, flow cytometry assays and subcutaneous xenograft were performed to identify the phenotype of IGF2BP3 in TNBC. RNA/RNA immunoprecipitation (RIP)/methylated RNA immunoprecipitation (MeRIP) sequencing and luciferase assays were used to certify the target of IGF2BP3 in TNBC cells.
RESULTS: IGF2BP3 was highly expressed in TNBC cell lines and tissues. TET3-mediated IGF2BP3 promoter hypomethylation led to the upregulation of IGF2BP3. Knocking down IGF2BP3 markedly reduced the proliferation of TNBC in vitro and in vivo. Intersection co-assays revealed that IGF2BP3 decreased neurofibromin 1 (NF1) stabilisation via an m6A-dependent manner. NF1 knockdown could rescue the phenotypes of IGF2BP3 knockdown cells partially.
CONCLUSION: TET3-mediated IGF2BP3 accelerated the proliferation of TNBC by destabilising NF1 mRNA via an m6A-dependent manner. This suggests that IGF2BP3 could be a potential therapeutic target for TNBC.

Keywords:  IGF2BP3; NF1; TET3; TNBC; m6A

DOI:  https://doi.org/10.1002/ctm2.1427
Clin Epigenetics. 2023 09 23. 15(1): 153

METTL3 exerts synergistic effects on m6A methylation and histone modification to regulate the function of VGF in lung adenocarcinoma.

Kesong Shi, Rula Sa, Le Dou, Yuan Wu, Zhiqiang Dong, Xinyao Fu, Haiquan Yu.

   BACKGROUND: Multiple genetic and epigenetic regulatory mechanisms play a vital role in tumorigenesis and development. Understanding the interplay between different epigenetic modifications and its contribution to transcriptional regulation in cancer is essential for precision medicine. Here, we aimed to investigate the interplay between N6-methyladenosine (m6A) modifications and histone modifications in lung adenocarcinoma (LUAD).
RESULTS: Based on the data from public databases, including chromatin property data (ATAC-seq, DNase-seq), methylated RNA immunoprecipitation sequencing (MeRIP-seq), and gene expression data (RNA-seq), a m6A-related differentially expressed gene nerve growth factor inducible (VGF) was identified between LUAD tissues and normal lung tissues. VGF was significantly highly expressed in LUAD tissues and cells, and was associated with a worse prognosis for LUAD, silencing of VGF inhibited the malignant phenotype of LUAD cells by inactivating the PI3K/AKT/mTOR pathway. Through the weighted correlation network analysis (WGCNA) and integration of TCGA-LUAD RNA-seq and m6A methyltransferase METTL3-knockdown RNA-seq data, a significant positive correlation between METTL3 and VGF was observed. By using the MeRIP-qPCR and dual-luciferase reporter assays, we demonstrated that METTL3 knockdown decreased m6A modification level of VGF coding sequences in LUAD cells, the colorimetric m6A quantification assay also showed that METTL3 knockdown significantly decreased global m6A modification level in LUAD cells. Interestingly, we found that METTL3 knockdown also reduced VGF expression by increasing H3K36me3 modification at the VGF promoter. Further research revealed that METTL3 knockdown upregulated the expression of histone methylase SETD2, the major H3K36me3 methyltransferase, by methylating the m6A site in the 3'UTR of SETD2 mRNA in LUAD cells.
CONCLUSIONS: Overall, our results reveal that the expression of VGF in LUAD cells is regulated spatio-temporally by METTL3 through both transcriptional (via histone modifications) and post-transcriptional (via m6A modifications) mechanisms. The synergistic effect of these multiple epigenetic mechanisms provides new opportunities for the diagnosis and precision treatment of tumors.

Keywords:  Histone modification; Lung adenocarcinoma; METTL3; VGF; m6A modification

DOI:  https://doi.org/10.1186/s13148-023-01568-9
Trends Endocrinol Metab. 2023 Sep 25. pii: S1043-2760(23)00191-1. [Epub ahead of print]

N6-methyladenosine RNA modification in nonalcoholic fatty liver disease.

Ping Luo, Shiqi Li, Wei Jing, Jiancheng Tu, Xinghua Long.

  Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease worldwide, influencing numerous regulatory axes and extrahepatic vital organs. The molecular mechanisms that lead to the progression of NAFLD remain unclear and knowledge on the pathways causing hepatocellular damage followed by lipid accumulation is limited. Recently, a number of studies have shown that mRNA N6-methyladenosine (m6A) modification contributes to the progression of NAFLD. In this review, we summarize current knowledge on m6A modification in the metabolic processes associated with NAFLD and discuss the challenges of and prospects for therapeutic avenues based on m6A regulation for the treatment of liver disease.

Keywords:  METTL3; NAFLD; NASH; lipogenesis; m6A methylation

DOI:  https://doi.org/10.1016/j.tem.2023.09.002
Int J Mol Sci. 2023 Sep 14. pii: 14115. [Epub ahead of print]24(18):

METTL3 Promotes the Differentiation of Goat Skeletal Muscle Satellite Cells by Regulating MEF2C mRNA Stability in a m6A-Dependent Manner.

Sen Zhao, Jiaxue Cao, Yanjin Sun, Helin Zhou, Qi Zhu, Dinghui Dai, Siyuan Zhan, Jiazhong Guo, Tao Zhong, Linjie Wang, Li Li, Hongping Zhang.

  The development of mammalian skeletal muscle is a highly complex process involving multiple molecular interactions. As a prevalent RNA modification, N6-methyladenosine (m6A) regulates the expression of target genes to affect mammalian development. Nevertheless, it remains unclear how m6A participates in the development of goat muscle. In this study, methyltransferase 3 (METTL3) was significantly enriched in goat longissimus dorsi (LD) tissue. In addition, the global m6A modification level and differentiation of skeletal muscle satellite cells (MuSCs) were regulated by METTL3. By performing mRNA-seq analysis, 8050 candidate genes exhibited significant changes in expression level after the knockdown of METTL3 in MuSCs. Additionally, methylated RNA immunoprecipitation sequencing (MeRIP-seq) illustrated that myocyte enhancer factor 2c (MEF2C) mRNA contained m6A modification. Further experiments demonstrated that METTL3 enhanced the differentiation of MuSCs by upregulating m6A levels and expression of MEF2C. Moreover, the m6A reader YTH N6-methyladenosine RNA binding protein C1 (YTHDC1) was bound and stabilized to MEF2C mRNA. The present study reveals that METTL3 enhances myogenic differentiation in MuSCs by regulating MEF2C and provides evidence of a post-transcriptional mechanism in the development of goat skeletal muscle.

Keywords:  MEF2C; METTL3; MuSCs; RNA m6A methylation; goat

DOI:  https://doi.org/10.3390/ijms241814115
BMC Genomics. 2023 Sep 27. 24(1): 577

Comprehensive analysis of N6-methyladenosine-related RNA methylation in the mouse hippocampus after acquired hearing loss.

Xuehua Zhou, Lin Jin, Yufeng Li, Yiru Wang, Wen Li, Xia Shen.

   BACKGROUND: The mechanism underlying cognitive impairment after hearing loss (HL) remains unclear. N6-methyladenosine (m6A) is involved in many neurodegenerative diseases; however, its role in cognitive impairment after HL has not yet been investigated. Therefore, we aimed to analyze the m6A modification profile of the mouse hippocampus after HL exposure. A mouse model of neomycin-induced HL was established. An auditory brainstem-response test was utilized for detecting hearing threshold. The passive avoidance test was served as the mean for evaluating cognitive function. The m6A-regulated enzyme expression levels were analyzed by using reverse transcription quantitative real-time polymerase chain reaction and western blot analyses. RNA sequencing (RNA-Seq) and methylated RNA immunoprecipitation sequencing (MeRIP-Seq) were performed with the aim of investigating gene expression differences and m6A modification in the mouse hippocampus.
RESULTS: Neomycin administration induced severe HL in mice. At four months of age, the mice in the HL group showed poorer cognitive performance than the mice in the control group. METTL14, WTAP, and YTHDF2 mRNA levels were downregulated in the hippocampi of HL mice, whereas ALKBH5 and FTO mRNA levels were significantly upregulated. At the protein level, METTL3 and FTO were significantly upregulated. Methylated RNA immunoprecipitation sequencing analysis revealed 387 and 361 m6A hypermethylation and hypomethylation peaks, respectively. Moreover, combined analysis of mRNA expression levels and m6A peaks revealed eight mRNAs with significantly changed expression levels and methylation.
CONCLUSIONS: Our findings revealed the m6A transcriptome-wide profile in the hippocampus of HL mice, which may provide a basis for understanding the association between HL and cognitive impairment from the perspective of epigenetic modifications.

Keywords:  Cognition impairment; Hearing loss; Hippocampus; MeRIP-Seq; RNA-Seq; m6A methylation

DOI:  https://doi.org/10.1186/s12864-023-09697-4
Epigenetics. 2023 Dec;18(1): 2260213

N6-methyladenosine (m6A) modification in osteosarcoma: expression, function and interaction with noncoding RNAs - an updated review.

Yuanzhuang Zhang, Yeqiu Xu, Yuxin Bao, Yinzhou Luo, Guanzhen Qiu, Ming He, Jie Lu, Jian Xu, Bin Chen, Yong Wang.

  Osteosarcoma, originating from primitive bone-forming mesenchymal cells, is the most common malignant bone tumour among children and adolescents. N6-methyladenosine (m6A), the most ubiquitous type of posttranscriptional modification, is a methylation that occurs in the N6-position of adenosine. m6A dramatically affects the splicing, export, translation, and stability of various RNAs, including mRNA and noncoding RNAs (ncRNAs). Increasing evidence suggests that ncRNAs, especially microRNAs (miRNA), long noncoding RNAs (lncRNA), and circular RNAs (circRNAs), regulate the m6A modification process by affecting the expression of m6A-associated enzymes. m6A modification interactions with ncRNAs provide new perspectives for exploring the underlying mechanisms of tumorigenesis and progression. In the current review, we summarized the expression and biological functions of m6A regulators in osteosarcoma. At the same time, the present review systematically elucidated the functional and mechanical interactions between m6A modification and ncRNAs in osteosarcoma. In addition, we discussed the effect of m6A and ncRNAs in the tumour microenvironment and potential clinical applications of osteosarcoma.

Keywords:  N6-methyladenosine; Osteosarcoma; epigenetic regulation; molecular mechanisms; noncoding RNA

DOI:  https://doi.org/10.1080/15592294.2023.2260213
Cell Death Discov. 2023 Aug 26. 9(1): 316

LncRNA TIALD contributes to hepatocellular carcinoma metastasis via inducing AURKA lysosomal degradation.

Yingchao Wang, Yue Zhong, Xiaoyuan Zheng, Niangmei Cheng, Yong Yang, Ye Yang, Fei Wang, Qiuyu Zhuang, Yao Huang, Wuhua Guo, Naishun Liao, Xiaoyu Yang, Bixing Zhao, Xiaolong Liu.

The N6-methyladenosine (m6A) RNA methyltransferase METTL16 is an emerging player in RNA modification landscape and responsible for the deposition of m6A in a few transcripts. AURKA (aurora kinase A) has been confirmed as an oncogene in cancer development including hepatocellular carcinoma (HCC). Nevertheless, it remains unclear whether METTL16 mediated m6A modification of lncRNAs can regulate AURKA activation in cancer progression. Here we aimed to investigate the functional links between lncRNAs and the m6A modification in AURKA signaling and HCC progression. Here we show that LncRNA TIALD (transcript that induced AURKA Lysosomal degradation) was down-regulated in HCC tissues by METTL16 mediated m6A methylation to facilitate its RNA degradation, and correlates with poor prognosis. Functional assays reveal that TIALD inhibits HCC metastasis both in vitro and in vivo. Mechanistically, TIALD directly interacts with AURKA and facilitate its degradation through the lysosomal pathway to inhibited EMT and metastasis of HCC. AURKA's specific inhibitor alisertib exerts effective therapeutic effect on liver cancer with low TIALD expression, which might provide a new insight into HCC therapy. Our study uncovers a negative functional loop of METTL16-TIALD-AURKA axis, and identifies a new mechanism for METTL16 mediated m6A-induced decay of TIALD on AURKA signaling in HCC progression, which may provide potential prognostic and therapeutic targets for HCC.

DOI: https://doi.org/10.1038/s41420-023-01620-w
Biomed J. 2023 Sep 27. pii: S2319-4170(23)00101-4. [Epub ahead of print] 100664

c-MYC/METTL3/LINC01006 positive feedback loop promotes migration, invasion and proliferation of non-small cell lung cancer.

Chunfeng Liu, Qiang Ren, Jun Deng, Songping Wang, Lei Ren.

   BACKGROUND: This study aims to clarify the N6-methyladenosine (m6A) modification of LINC01006, which is involved in migration, invasion and proliferation of non-small cell lung cancer (NSCLC).
MATERIALS AND METHODS: LINC01006 and METTL3 expressions were analyzed in TCGA-LUAD cohort. Colony formation assay, wound-healing assay and transwell assay were performed to evaluate the ability of colony formation, migration and invasion. Q-PCR and western blot analysis determined gene expressions. M6A-RNA immunoprecipitation and m6A quantification assay were used to evaluate m6A modification. qChIP assay was used to validate transcriptional target. Luciferase assay validated the miRNA targets and transcriptional targets. In-situ xenograft model were included to evaluate tumor proliferation in vivo.
RESULTS: LINC01006 and METTL3 expressions were elevated in NSCLC cells and tissues. LINC01006 promoted the migration and invasion of NSCLC via epithelial - mesenchymal transition (EMT). The expression of LINC01006 was positively correlated to the expression of METTL3. METTL3 promoted tumor formation and proliferation in the in-situ xenograft model of NSCLC. The expression of LINC01006 was increased by METTL3 via m6A modification. c-MYC directly induced METTL3. Both c-MYC and LINC01006 were commonly targeted by miR-34a/b/c and miR-2682, and thereby c-MYC/METTL3/LINC01006 formed a positive feedback loop through miRNA targets in NSCLC.
CONCLUSIONS: LINC01006 is an oncogenic lncRNA, which induces migration, invasion and proliferation of NSCLC. METTL3 increases LINC01006 expression through stabilizing LINC01006 mRNA. c-MYC, as a transcription factor, activates METTL3, which results in an elevated level of LINC01006. c-MYC, METTL3 and LINC01006 form a positive feedback loop through multiple miRNA targets in NSCLC.

Keywords:  LINC01006; METTL3; N6-methyladenosine; NSCLC; c-MYC

DOI:  https://doi.org/10.1016/j.bj.2023.100664
Pharmacology. 2023 Sep 22. 1-7

N6-Methyladenosine Modifications in Pulmonary Hypertension.

Yu Xia, Yanyan Zhang, Jie Huang, Bing Chen, YanJiao Jiang, Zengxian Sun, Yun Liu.

   BACKGROUND: The most prevalent kind of RNA methylation modification existing in eukaryotes is N6-methyladenosine (m6A), which is a reversible type of posttranscriptional modification.
SUMMARY: Many studies have reported that m6A participates in cell differentiation, self-renewal, invasion, and apoptosis by modifying protein synthesis. Furthermore, m6A modification is also involved in disease progression and pulmonary vascular remodeling in pulmonary hypertension. However, very few researchers have investigated the effect of m6A modifications on pulmonary hypertension.
KEY MESSAGES: Here, we have reviewed the latest research advances in the field of m6A RNA methylation in pulmonary hypertension and explored its regulatory role in pulmonary hypertension development and progression.

Keywords:  N6-methyladenosine demethylase; N6-methyladenosine methyltransferase; N6-methyladenosine modification; Pulmonary hypertension

DOI:  https://doi.org/10.1159/000533588
Cell Chem Biol. 2023 Sep 21. pii: S2451-9456(23)00291-X. [Epub ahead of print]

Targeting METTL3 reprograms the tumor microenvironment to improve cancer immunotherapy.

Haisheng Yu, Jing Liu, Xia Bu, Zhiqiang Ma, Yingmeng Yao, Jinfeng Li, Tiantian Zhang, Wenjing Song, Xiangling Xiao, Yishuang Sun, Wenjun Xiong, Jie Shi, Panpan Dai, Bolin Xiang, Hongtao Duan, Xiaolong Yan, Fei Wu, Wen Cai Zhang, Dandan Lin, Hankun Hu, Haojian Zhang, Frank J Slack, Housheng Hansen He, Gordon J Freeman, Wenyi Wei, Jinfang Zhang.

  The tumor microenvironment (TME) is a heterogeneous ecosystem containing cancer cells, immune cells, stromal cells, cytokines, and chemokines which together govern tumor progression and response to immunotherapies. Methyltransferase-like 3 (METTL3), a core catalytic subunit for RNA N6-methyladenosine (m6A) modification, plays a crucial role in regulating various physiological and pathological processes. Whether and how METTL3 regulates the TME and anti-tumor immunity in non-small-cell lung cancer (NSCLC) remain poorly understood. Here, we report that METTL3 elevates expression of pro-tumorigenic chemokines including CXCL1, CXCL5, and CCL20, and destabilizes PD-L1 mRNA in an m6A-dependent manner, thereby shaping a non-inflamed TME. Thus, inhibiting METTL3 reprograms a more inflamed TME that renders anti-PD-1 therapy more effective in several murine lung tumor models. Clinically, NSCLC patients who exhibit low-METTL3 expression have a better prognosis when receiving anti-PD-1 therapy. Collectively, our study highlights targeting METTL3 as a promising strategy to improve immunotherapy in NSCLC patients.

Keywords:  METTL3; PD-L1; cancer immunotherapy; chemokines; tumor microenvironment

DOI:  https://doi.org/10.1016/j.chembiol.2023.09.001
Cell Rep. 2023 Sep 23. pii: S2211-1247(23)01175-0. [Epub ahead of print]42(10): 113163

ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control.

Yimeng Gao, Joshua T Zimmer, Radovan Vasic, Chengyang Liu, Rana Gbyli, Shu-Jian Zheng, Amisha Patel, Wei Liu, Zhihong Qi, Yaping Li, Raman Nelakanti, Yuanbin Song, Giulia Biancon, Andrew Z Xiao, Sarah Slavoff, Richard G Kibbey, Richard A Flavell, Matthew D Simon, Toma Tebaldi, Hua-Bing Li, Stephanie Halene.

  N6-methyladenosine (m6A) RNA modification controls numerous cellular processes. To what extent these post-transcriptional regulatory mechanisms play a role in hematopoiesis has not been fully elucidated. We here show that the m6A demethylase alkB homolog 5 (ALKBH5) controls mitochondrial ATP production and modulates hematopoietic stem and progenitor cell (HSPC) fitness in an m6A-dependent manner. Loss of ALKBH5 results in increased RNA methylation and instability of oxoglutarate-dehydrogenase (Ogdh) messenger RNA and reduction of OGDH protein levels. Limited OGDH availability slows the tricarboxylic acid (TCA) cycle with accumulation of α-ketoglutarate (α-KG) and conversion of α-KG into L-2-hydroxyglutarate (L-2-HG). L-2-HG inhibits energy production in both murine and human hematopoietic cells in vitro. Impaired mitochondrial energy production confers competitive disadvantage to HSPCs and limits clonogenicity of Mll-AF9-induced leukemia. Our study uncovers a mechanism whereby the RNA m6A demethylase ALKBH5 regulates the stability of metabolic enzyme transcripts, thereby controlling energy metabolism in hematopoiesis and leukemia.

Keywords:  ALKBH5; ATP production; CP: Molecular biology; CP: Stem cell research; OXPHOS; RNA stability; energy metabolism; hematopoietic stem and progenitor cells; leukemia; m(6)A modification; oxidative phosphorylation; stress hematopoiesis

DOI:  https://doi.org/10.1016/j.celrep.2023.113163
Mol Med Rep. 2023 Nov;pii: 217. [Epub ahead of print]28(5):

METTL3 promotes proliferation and migration of colorectal cancer cells by increasing SNHG1 stability.

Yeqiu Xu, Yuxin Bao, Guanzhen Qiu, Huinan Ye, Ming He, Xilin Wei.

  N6‑methyladenosine (m6A) serves an essential role in RNA modulation and is implicated in multiple malignancies, including colorectal cancer (CRC). Methyltransferase‑like 3 (METTL3) is an important writer in m6A modification, however its role in CRC in modifying small nucleolar RNA host gene 1 (SNHG1), an oncogenic long noncoding RNA, remains unclear. In the present study, METTL3 expression in CRC was assessed using online bioinformatics analysis, immunohistochemistry staining, western blotting, reverse transcription (RT)‑quantitative PCR (qPCR) and cell transfections. Cell proliferation, migration and invasion were determined using functional Cell Counting Kit‑8 (CCK‑8) and Transwell assays. SNHG1 expression in CRC was evaluated using online bioinformatics analysis and RT‑qPCR. Methylated RNA immunoprecipitation qPCR was performed to assess m6A modification changes of SNHG1 mRNA. The present study demonstrated that METTL3 is upregulated in CRC tissues and cell lines. Moreover, METTL3 expression was associated with several unfavourable clinical features in patients with CRC, including the stage of lymph node metastases and overall survival. Functional Transwell and CCK‑8 assays demonstrated that knockdown of METTL3 suppressed CRC cell proliferation and migration. Furthermore, METTL3 was positively correlated with SNHG1 in CRC tissue, as indicated by analysis of data from The Cancer Genome Atlas. Mechanistically, SNHG1 contains 18 m6A modification sites. Through cell transfections and actinomycin D assays, the present study found that METTL3‑mediated m6A modification at these sites enhances the stability of SNHG1 in CRC cells. Finally, it was demonstrated that SNHG1 knockdown partially diminished the facilitative effect of METTL3 on CRC cell migration and proliferation. The present study concluded that METTL3, a potential biomarker for assessing overall survival and metastasis in CRC, may serve as an oncogene, promote SNHG1 m6A modification, improve the stability of SNHG1 and enhance SNHG1‑mediated oncogenic function in CRC.

Keywords:  N6‑methyladenosine; SNHG1; colorectal cancer; methyltransferase‑like 3; migration; proliferation

DOI:  https://doi.org/10.3892/mmr.2023.13104
Brain Sci. 2023 Sep 12. pii: 1311. [Epub ahead of print]13(9):

The Comprehensive Analysis of m6A-Associated Anoikis Genes in Low-Grade Gliomas.

Hui Zheng, Yutong Zhao, Hai Zhou, Yuguang Tang, Zongyi Xie.

  The relationship between N6-methyladenosine (m6A) regulators and anoikis and their effects on low-grade glioma (LGG) is not clear yet. The TCGA-LGG cohort, mRNAseq 325 dataset, and GSE16011 validation set were separately obtained via the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Altas (CGGA), and Gene Expression Omnibus (GEO) databases. In total, 27 m6A-related genes (m6A-RGs) and 508 anoikis-related genes (ANRGs) were extracted from published articles individually. First, differentially expressed genes (DEGs) between LGG and normal samples were sifted out by differential expression analysis. DEGs were respectively intersected with m6A-RGs and ANRGs to acquire differentially expressed m6A-RGs (DE-m6A-RGs) and differentially expressed ANRGs (DE-ANRGs). A correlation analysis of DE-m6A-RGs and DE-ANRGs was performed to obtain DE-m6A-ANRGs. Next, univariate Cox and least absolute shrinkage and selection operator (LASSO) were performed on DE-m6A-ANRGs to sift out risk model genes, and a risk score was gained according to them. Then, gene set enrichment analysis (GSEA) was implemented based on risk model genes. After that, we constructed an independent prognostic model and performed immune infiltration analysis and drug sensitivity analysis. Finally, an mRNA-miRNA-lncRNA regulatory network was constructed. There were 6901 DEGs between LGG and normal samples. Six DE-m6A-RGs and 214 DE-ANRGs were gained through intersecting DEGs with m6A-RGs and ANRGs, respectively. A total of 149 DE-m6A-ANRGs were derived after correlation analysis. Four genes, namely ANXA5, KIF18A, BRCA1, and HOXA10, composed the risk model, and they were involved in apoptosis, fatty acid metabolism, and glycolysis. The age and risk scores were finally sifted out to construct an independent prognostic model. Activated CD4 T cells, gamma delta T cells, and natural killer T cells had the largest positive correlations with risk model genes, while activated B cells were significantly negatively correlated with KIF18A and BRCA1. AT.9283, EXEL.2280, Gilteritinib, and Pracinostat had the largest correlation (absolute value) with a risk score. Four risk model genes (mRNAs), 12 miRNAs, and 21 lncRNAs formed an mRNA-miRNA-lncRNA network, containing HOXA10-hsa-miR-129-5p-LINC00689 and KIF18A-hsa-miR-221-3p-DANCR. Through bioinformatics, we constructed a prognostic model of m6A-associated anoikis genes in LGG, providing new ideas for research related to the prognosis and treatment of LGG.

Keywords:  N6-methyladenosine; anoikis; low-grade glioma

DOI:  https://doi.org/10.3390/brainsci13091311
J Hazard Mater. 2023 Sep 19. pii: S0304-3894(23)01865-4. [Epub ahead of print]461 132582

H3K18 lactylation promotes the progression of arsenite-related idiopathic pulmonary fibrosis via YTHDF1/m6A/NREP.

Peiwen Wang, Daxiao Xie, Tian Xiao, Cheng Cheng, Dapeng Wang, Jing Sun, Meng Wu, Yi Yang, Aihua Zhang, Qizhan Liu.

  As epigenetic modifications, lactylation and N6-methyladenosine (m6A) have attracted wide attention. Arsenite is an environmental pollutant that has been proven to induce idiopathic pulmonary fibrosis (IPF). However, the molecular mechanisms of lactylation and m6A methylation are unclear in arsenite-related IPF (As-IPF). In view of the limited understanding of molecular mechanism of m6A and lactylation in As-IPF, MeRIP-seq, RNA-seq and ChIP-seq were analyzed to verify the target gene regulated by m6A and H3K18 lactylation (H3K18la). We found that, for As-IPF, the global levels of m6A, levels of YTHDF1 and m6A-modified neuronal protein 3.1 (NREP) were elevated in alveolar epithelial cells (AECs). The secretion levels of TGF-β1 were increased via YTHDF1/m6A/NREP, which promoted the fibroblast-to-myofibroblast transition (FMT). Further, extracellular lactate from myofibroblasts elevated levels of the global lactylation (Kla) and H3K18la via the lactate monocarboxylate transporter 1 (MCT1), and, in AECs, H3K18la facilitated the transcription of Ythdf1. This report highlights the role of crosstalk between AECs and myofibroblasts via lactylation and m6A and the significance of H3K18la regulation of YTHDF1 in the progression of As-IPF, which may be useful for finding effective therapeutic targets.

Keywords:  Chronic exposure of arsenite; Fibroblast-to-myofibroblast transition; Idiopathic pulmonary fibrosis; Lactylation; M6A modification

DOI:  https://doi.org/10.1016/j.jhazmat.2023.132582
J Cell Mol Med. 2023 Sep 27.

METTL3-induced FGD5-AS1 contributes to the tumorigenesis and PD-1/PD-L1 checkpoint to enhance the resistance to paclitaxel of endometrial carcinoma.

Min Hao, Tianjie Li, Ling Xiao, Yun Liu.

  Endometrial cancer (EC), a widely occurring cancer in the uterus, is among the top four most frequent malignancies in women. To improve approaches for combating this disease, it is essential to gain a more comprehensive comprehension of the intricate causes of EC. Accumulating evidence highlight the essential role of long non-coding RNA (LncRNA) in EC progression, while its biological and mechanical function has not been fully revealed. In this study, a LncRNA microarray analysis was performed using four pairs of paclitaxel (PTX) resistant EC cells, FGD5-AS1 was identified as a significantly upregulated gene. Biologically, it was found that FGD5-AS1 enhances chemoresistance of EC cells to PTX treatment and blocking immune escape via PD-1/PD-L1 checkpoint. Furthermore, FGD5-AS1 exerted an oncogene role in EC cells via promoting cell proliferation and migration. Mechanically, METTL3 could upregulate FGD5-AS1 expression via N6-methyladenosine (m6A) modification. The biological roles of METTL3 were exerted via modulating FGD5-AS1 expression in EC. Collectively, our research has shed light on the involvement of the METTL3/FGD5-AS1 axis in the development of PTX resistance in EC. This finding offers a new avenue for further exploration of the underlying mechanisms of chemoresistance in EC and provides valuable insights for the development of potential therapeutic targets in the treatment of EC.

Keywords:  FGD5-AS1; METTL3; endometrial carcinoma; immune checkpoint; paclitaxel

DOI:  https://doi.org/10.1111/jcmm.17971
iScience. 2023 Oct 20. 26(10): 107838

ALKBH5-mediated m6A demethylation of HS3ST3B1-IT1 prevents osteoarthritis progression.

Yuting Tang, Yang Liu, Xiaoshu Zhu, Yanlin Chen, Xinluan Jiang, Siyang Ding, Que Zheng, Ming Zhang, Jiashu Yang, Yunfei Ma, Mengying Xing, Zongyu Zhang, Huimin Ding, Yucui Jin, Changyan Ma.

  HS3ST3B1-IT1 was identified as a downregulated long noncoding RNA in osteoarthritic cartilage. However, its roles and mechanisms in the pathogenesis of osteoarthritis (OA) are unclear. In this study, we demonstrated that the expressions of HS3ST3B1-IT1 and its maternal gene HS3ST3B1 were downregulated and positively correlated in osteoarthritic cartilage. Overexpression of HS3ST3B1-IT1 significantly increased chondrocyte viability, inhibited chondrocyte apoptosis, and upregulated extracellular matrix (ECM) proteins, whereas HS3ST3B1-IT1 knockdown had the opposite effects. In addition, HS3ST3B1-IT1 significantly ameliorated monosodium-iodoacetate-induced OA in vivo. Mechanistically, HS3ST3B1-IT1 upregulated HS3ST3B1 expression by blocking its ubiquitination-mediated degradation. Knockdown of HS3ST3B1 reversed the effects of HS3ST3B1-IT1 on chondrocyte viability, apoptosis, and ECM metabolism. AlkB homolog 5 (ALKBH5)-mediated N6-methyladenosine (m6A) demethylation stabilized HS3ST3B1-IT1 RNA. Together, our data revealed that ALKBH5-mediated upregulation of HS3ST3B1-IT1 suppressed OA progression by elevating HS3ST3B1 expression, suggesting that HS3ST3B1-IT1/HS3ST3B1 may serve as potential therapeutic targets for OA treatment.

Keywords:  Biological sciences; Molecular biology; Molecular mechanism of gene regulation; Orthopedics

DOI:  https://doi.org/10.1016/j.isci.2023.107838
BMC Plant Biol. 2023 Sep 29. 23(1): 456

Changes in m6A RNA methylation are associated with male sterility in wolfberry.

Jiawen Zhao, Chujun Zhang, Sifan Li, Mengmeng Yuan, Wenlan Mu, Jing Yang, Yutong Ma, Cuiping Guan, Chuang Ma.

   BACKGROUND: N6-methyladenosine (m6A) modification is the most abundant type of RNA modification in eukaryotic cells, playing pivotal roles in multiple plant growth and development processes. Yet the potential role of m6A in conferring the trait of male sterility in plants remains unknown.
RESULTS: In this study, we performed RNA-sequencing (RNA-Seq) and m6A-sequencing (m6A-Seq) of RNAs obtained from the anther tissue of two wolfberry lines: 'Ningqi No.1' (LB1) and its natural male sterile mutant 'Ningqi No.5' (LB5). Based on the newly assembled transcriptome, we established transcriptome-wide m6A maps for LB1 and LB5 at the single nucleus pollen stage. We found that the gene XLOC_021201, a homolog of m6A eraser-related gene ALKBH10 in Arabidopsis thaliana, was significantly differentially expressed between LB1 and LB5. We also identified 1642 and 563 m6A-modified genes with hypermethylated and hypomethylated patterns, respectively, in LB1 compared with LB5. We found the hypermethylated genes significantly enriched in biological processes related to energy metabolism and lipid metabolism, while hypomethylation genes were mainly linked to cell cycle process, gametophyte development, and reproductive process. Among these 2205 differentially m6A methylated genes, 13.74% (303 of 2205) were differentially expressed in LB1 vis-à-vis LB5.
CONCLUSIONS: This study constructs the first m6A transcriptome map of wolfberry and establishes an association between m6A and the trait of male sterility in wolfberry.

Keywords:  Differential methylation; Male sterility; N 6-methyladenosine; Wolfberry; m6A regulators

DOI:  https://doi.org/10.1186/s12870-023-04458-7
ACS Appl Mater Interfaces. 2023 Sep 26.

Programmed Release METTL3-14 Inhibitor Microneedle Protects Myocardial Function by Reducing Drp1 m6A Modification-Mediated Mitochondrial Fission.

Boyue Huang, Liu Xie, Ming Ke, Yonghong Fan, Ju Tan, Jianhua Ran, Chuhong Zhu.

  M6A modification is an RNA-important processing event mediated by methyltransferases METTL3 and METTL14 and the demethylases. M6A dynamic changes after myocardial infarction (MI), involved in the massive loss of cardiomyocytes due to hypoxia, as well as the recruitment and activation of myofibroblasts. Balanced mitochondrial fusion and fission are essential to maintain intracardiac homeostasis and reduce poststress myocardial remodeling. Double-layer programmed drug release microneedle (DPDMN) breaks the limitations of existing therapeutic interventions in one period or one type of cells, and multitargeted cellular combination has more potential in MI therapy. By employing hypoxia-ischemic and TGF-β1-induced fibrosis cell models, we found that METTL3-14 inhibition effectively decreased cardiomyocyte death through the reduction of mitochondrial fragmentation and inhibiting myofibrillar transformation. DPDMN treatment of MI in rat models showed improved cardiac function and decreased infarct size and fibrosis level, demonstrating its superior effectiveness. The DPDMN delivers METTL3 inhibitor swiftly in the early phase to rescue dying cardiomyocytes and slowly in the late phase to achieve long-term suppression of fibroblast over proliferation, collagen synthesis, and deposition. RIP assay and mechanistic investigation confirmed that METTL3 inhibition reduced the translation efficiency of Drp1 mRNA by 5'UTR m6A modification, thus decreasing the Drp1 protein level and mitochondrial fragment after hypoxic-ischemic injury. This project investigated the efficacy of DPDMNs-loaded METTL3 inhibitor in MI treatment and the downstream signaling pathway proteins, providing an experimental foundation for the translation of the utility, safety, and versatility of microneedle drug delivery for MI into clinical applications.

Keywords:  Drp1; METTL3; microneedle; mitochondrial fission; myocardial infarction

DOI:  https://doi.org/10.1021/acsami.3c06318
Exp Cell Res. 2023 Sep 22. pii: S0014-4827(23)00326-9. [Epub ahead of print]432(2): 113778

YTHDF1 shapes "cold" tumor and inhibits CD8+ T cells infiltration and function in breast cancer.

Lanyu Jing, Kaiwen Zhou, Zilin Wang, Yuying Li, Yuanjian Fan, Ting Liu, Zhen Shan, Ying Lin.

While YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) was recognized as a crucial contributor in the development and immune-related regulation of various types of tumors, its function in the immune response of breast cancer has largely remained uninvestigated. Through analysis of public databases, we found YTHDF1 as a highly expressed gene in breast cancers and confirmed this finding in breast cancer cells and clinical specimens from our center. Subsequently, we examined the link between YTHDF1 expression and immune cells and molecules by utilizing immune-related public databases and algorithm. We further validated our findings through cellular and animal experiments, as well as RNA sequencing. YTHDF1 was found highly expressed in tumor tissues of breast cancer, which negatively correlated with patient survival. The downregulation of YTHDF1 promoted the expression of pro-inflammatory markers and improved the anti-cancer ability of immune cells in breast cancer. RNA sequencing analysis revealed that YTHDF1 knockdown resulted in enrichment of differential genes in signal transduction pathways. Additionally, in vitro experiments showed that immune cells had higher cytotoxicity against breast cancer cells with decreased YTHDF1 expression. Moreover, in vivo studies indicated that YTHDF1 promoted breast cancer growth while inhibiting CD8+ T cell infiltration and function. Our study demonstrates that YTHDF1 plays a crucial role in establishing a "cold" tumor microenvironment in breast cancer by inhibiting the release of pro-inflammatory cytokines from cancer cells. As a result, the infiltration and functional differentiation of anti-tumor CD8+ T cells are hindered, ultimately resulting in the immune evasion of breast cancer.

DOI: https://doi.org/10.1016/j.yexcr.2023.113778
PLoS One. 2023 ;18(9): e0292212

NOP2/Sun RNA methyltransferase 2 is a potential pan-cancer prognostic biomarker and is related to immunity.

Lemei Zheng, Mengna Li, Jianxia Wei, Shipeng Chen, Changning Xue, Yumei Duan, Faqing Tang, Guiyuan Li, Wei Xiong, Kelin She, Hongyu Deng, Ming Zhou.

BACKGROUND: NOP2/Sun RNA methyltransferase 2 (NSUN2), an important methyltransferase of m5C, has been poorly studied in cancers, and the relationship between NSUN2 and immunity remains largely unclear. Therefore, the purpose of this study was to explore the expression and prognostic value of NSUN2 and the role of NSUN2 in immunity in cancers.
METHODS: The TIMER, CPTAC and other databases were used to analyze the expression of NSUN2, its correlation with clinical stage and its prognostic value across cancers. Moreover, the TISIDB, TIMER2.0 and Sangerbox platform were used to depict the relationships between NSUN2 and immune molecular subtypes, tumor-infiltrating lymphocytes (TILs), immune checkpoints (ICPs) and immunoregulatory genes. Furthermore, the NSUN2-interacting proteins and related genes as well as the coexpression networks of NSUN2 in LIHC, LUAD and HNSC were explored with the STRING, DAVID, GEPIA2 and LinkedOmics databases. Finally, the subcellular location and function of NSUN2 in HepG2, A549 and 5-8F cells were investigated by performing immunofluorescence, CCK-8 and wound healing assays.
RESULTS: Overall, NSUN2 was highly expressed and related to a poor prognosis in most types of cancers and was also significantly associated with immune molecular subtypes in some cancer types. Furthermore, NSUN2 was significantly associated with the levels of ICPs and immunoregulatory genes. In addition, NSUN2 was found to be involved in a series of immune-related biological processes, such as the humoral immune response in LIHC and LUAD and T-cell activation and B-cell activation in HNSC. Immunofluorescence and CCK-8 assays also confirmed that NSUN2 was widely expressed in the nucleus and cytoplasm, and overexpression of NSUN2 promoted the proliferation and migration of HepG2, A549 and 5-8F cells. NSUN2 was also confirmed to positively regulate the expression of PD-L1.
CONCLUSION: NSUN2 serves as a pan-cancer prognostic biomarker and is correlated with the immune infiltration of tumors.

DOI: https://doi.org/10.1371/journal.pone.0292212