bims-rimeca 2021-11-14 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021‒11‒14
sixteen papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

Ginsenoside Rh2 reduces m6A RNA methylation in cancer via the KIF26B-SRF positive feedback loop.
m6A-Mediated Tumor Invasion and Methylation Modification in Breast Cancer Microenvironment.
N6-Methyladenosine Methylation of mRNA in Cell Senescence.
Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection.
Comprehensive Analysis of N6-Methyladenosine-Related lncRNA Signature for Predicting Prognosis and Immune Cell Infiltration in Patients with Colorectal Cancer.
Pan-Cancer Analysis of the N6-Methyladenosine Eraser FTO as a Potential Prognostic and Immunological Biomarker.
RNA demethylase ALKBH5 promotes tumorigenesis in multiple myeloma via TRAF1-mediated activation of NF-κB and MAPK signaling pathways.
m6A mRNA methylation-directed myeloid cell activation controls progression of NAFLD and obesity.
Baicalin suppresses the progression of Type 2 diabetes-induced liver tumor through regulating METTL3/m6A/HKDC1 axis and downstream p-JAK2/STAT1/clevaged Capase3 pathway.
Insulin-like growth factor 2 mRNA binding protein 2 regulates proliferation, migration and angiogenesis of keratinocytes by modulating heparanase stability.
m6A regulators as predictive biomarkers for chemotherapy benefit and potential therapeutic targets for overcoming chemotherapy resistance in small-cell lung cancer.
Characterization of the m6A-related lncRNA signature in predicting prognosis and immune response in patients with colon cancer.
The Role of RNA Methylation in Regulating Stem Cell Fate and Function-Focus on m6A.
The m6A "reader" YTHDF1 promotes osteogenesis of bone marrow mesenchymal stem cells through translational control of ZNF839.
METTL14 gene polymorphisms influence hepatoblastoma predisposition in Chinese children: Evidences from a seven-center case-control study.
N6-methyladenosine reader IMP2 stabilizes the ZFAS1/OLA1 axis and activates the Warburg effect: implication in colorectal cancer.

J Ginseng Res. 2021 Nov;45(6): 734-743

Ginsenoside Rh2 reduces m6A RNA methylation in cancer via the KIF26B-SRF positive feedback loop.

Chunmei Hu, Linhan Yang, Yi Wang, Shijie Zhou, Jing Luo, Yi Gu.

  Background: The underlying mechanisms of the potential tumor-suppressive effects of ginsenoside Rh2 are complex. N6-methyladenosine (m6A) RNA methylation is usually dysregulated in cancer. This study explored the regulatory effect of ginsenoside Rh2 on m6A RNA methylation in cancer.Methods: m6A RNA quantification and gene-specific m6A RIP-qPCR assays were applied to assess total and gene-specific m6A RNA levels. Co-immunoprecipitation, fractionation western blotting, and immunofluorescence staining were performed to detect protein interactions and distribution. QRT-PCR, dual-luciferase, and ChIP-qPCR assays were conducted to check the transcriptional regulation.Results: Ginsenoside Rh2 reduces m6A RNA methylation and KIF26B expression in a dose-dependent manner in some cancers. KIF26B interacts with ZC3H13 and CBLL1 in the cytoplasm of cancer cells and enhances their nuclear distribution. KIF26B inhibition reduces m6A RNA methylation level in cancer cells. SRF bound to the KIF26B promoter and activated its transcription. SRF mRNA m6A abundance significantly decreased upon KIF26B silencing. SRF knockdown suppressed cancer cell proliferation and growth both in vitro and in vivo, the effect of which was partly rescued by KIF26B overexpression.Conclusion: ginsenoside Rh2 reduces m6A RNA methylation via downregulating KIF26B expression in some cancer cells. KIF26B elevates m6A RNA methylation via enhancing ZC3H13/CBLL1 nuclear localization. KIF26B-SRF forms a positive feedback loop facilitating tumor growth.

Keywords:  Cancer; KIF26B; SRF; ginsenoside Rh2; m6A RNA methylation

DOI:  https://doi.org/10.1016/j.jgr.2021.05.004
J Oncol. 2021 ;2021 9987376

m6A-Mediated Tumor Invasion and Methylation Modification in Breast Cancer Microenvironment.

Fei Liu, Xiaopeng Yu, Guijin He.

Background: We analyzed the n6-methyladenosine (m6A) modification patterns of immune cells infiltrating the tumor microenvironment of breast cancer (BC) to provide a new perspective for the early diagnosis and treatment of BC.Methods: Based on 23 m6A regulatory factors, we identified m6A-related gene characteristics and m6A modification patterns in BC through unsupervised cluster analysis. To examine the differences in biological processes among various m6A modification modes, we performed genomic variation analysis. We then quantified the relative infiltration levels of different immune cell subpopulations in the tumor microenvironment of BC using the CIBERSORT algorithm and single-sample gene set enrichment analysis. Univariate Cox analysis was used to screen for m6A characteristic genes related to prognosis. Finally, we evaluated the m6A modification pattern of patients with a single BC by constructing the m6Ascore based on principal component analysis.
Results: We identified three different m6A modification patterns in 2128 BC samples. A higher abundance of the immune infiltration of the m6Acluster C was indicated by the results of CIBERSORT and the single-sample gene set enrichment analysis. Based on the m6A characteristic genes obtained through screening, the m6Ascore was determined. The BC patients were segregated into m6Ascore groups of low and high categories, which revealed significant survival benefits among patients with low m6Ascores. Additionally, the high-m6Ascore group had a higher mutation frequency and was associated with low PD-L1 expression, and the m6Ascore and tumor mutation burden showed a positive correlation. In addition, treatment effects were better in patients in the high-m6Ascore group.
Conclusions: In case of a single patient with BC, the immune cell infiltration characteristics of the tumor microenvironment and the m6A methylation modification pattern could be evaluated using the m6Ascore. Our results provide a foundation for improving personalized immunotherapy of BC.

DOI: https://doi.org/10.1155/2021/9987376
Cell Mol Neurobiol. 2021 Nov 12.

N6-Methyladenosine Methylation of mRNA in Cell Senescence.

Lin Zhang, Jian Xia.

  Cell senescence is the growth arrest caused by the accumulation of irreparable cell damage, which is involved in physiological and pathological processes and regulated by the post-transcriptional level. This regulation is performed by transcriptional regulators and driven by aging-related small RNAs, long non-coding RNAs, and RNA-binding proteins. N6-methyladenosine (m6A) is the most common chemical modification in eukaryotic mRNA, which can enhance or reduce the binding of transcriptional regulators. Increasing studies have confirmed the crucial role of m6A in controlling mRNA in various physiological processes. Remarkably, recent reports have indicated that abnormal methylation of m6A-related RNA may affect cell senescence. In this review, we clarified the association between m6A modification and cell senescence and analyzed the limitations of the current research.

Keywords:  Cell senescence; N6-methyladenosine methylation; mRNAs

DOI:  https://doi.org/10.1007/s10571-021-01168-2
BMC Plant Biol. 2021 Nov 08. 21(1): 516

Transcriptome-wide N6-methyladenosine (m6A) methylation in watermelon under CGMMV infection.

Yanjun He, Lili Li, Yixiu Yao, Yulin Li, Huiqing Zhang, Min Fan.

  BACKGROUND: Cucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon.RESULTS: We measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity.
CONCLUSIONS: Our study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.

Keywords:  Cucumber green mottle mosaic virus (CGMMV); RNA-seq; Watermelon; m6A methylation; m6A-seq

DOI:  https://doi.org/10.1186/s12870-021-03289-8
Dis Markers. 2021 ;2021 8686307

Comprehensive Analysis of N6-Methyladenosine-Related lncRNA Signature for Predicting Prognosis and Immune Cell Infiltration in Patients with Colorectal Cancer.

Zhan Zhao, Ya-Bing Yang, Xin-Yuan Li, Xu-Guang Li, Xiao-Dong Chu, Zheng-Bin Lin, Yi-Ran Zhang, Yan-Guan Guo, Hui Ding, Yun-Long Pan, Liang Wang, Jing-Hua Pan.

Background: Colorectal cancer (CRC) is the third most common tumor worldwide. Aberrant N6-methyladenosine (m6A) modification can influence the progress of the CRC. Additionally, long noncoding RNA (lncRNA) plays a critical role in CRC and has a close relationship with m6A modification. However, the prognostic potential of m6A-related lncRNAs in CRC patients still remains to be clarified.Methods: We use "limma" R package, "glmnet" R package, and "survival" R package to screen m6A-related-lncRNAs with prognostic potential. Then, we comprehensively analysed and integrated the related lncRNAs in different TNM stages from TCGA database using the LASSO Cox regression. Meanwhile, the relationship between functional enrichment of m6A-related lncRNAs and immune microenvironment in CRC was also investigated using the TCGA database. A prognostic model was constructed and validated to determine the association between m6A-related lncRNAs in different TNM stages and the prognosis of CRC.
Result: We demonstrated that three related m6A lncRNAs in different TNM stages were associated with the prognosis of CRC patients. Patients from the TCGA database were classified into the low-risk and the high-risk groups based on the expression of these lncRNAs. The patients in the low-risk group had longer overall survival than the patients in the high-risk group (P < 0.001). We further constructed and validated a prognostic nomogram based on these genes with a C-index of 0.80. The receiver operating characteristic curves confirmed the predictive capacity of the model. Meanwhile, we also found that the low-risk group has the correlation with the dendritic cell (DC). Finally, we discovered the relationship between the m6A regulators and the three lncRNAs.
Conclusion: The prognostic model based on three m6A-related lncRNAs exhibits superior predictive performance, providing a novel prognostic model for the clinical evaluation of CRC patients.

DOI: https://doi.org/10.1155/2021/8686307
Int J Gen Med. 2021 ;14 7411-7422

Pan-Cancer Analysis of the N6-Methyladenosine Eraser FTO as a Potential Prognostic and Immunological Biomarker.

Chengwen Zhao, Yonghui Liu, Shaoqing Ju, Xudong Wang.

  Background: Fat mass and obesity-associated protein (FTO) is a critical N6-methyladenosine (m6A) demethylase that participates in tumorigenesis and is associated with the prognosis of patients in some cancers. However, the key roles of FTO in pan-cancer are still largely obscure.Methods: FTO expression levels in pan-cancer were estimated via the Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), and The Cancer Genome Atlas (TCGA) databases. Univariate survival analysis was used to estimate the effects of FTO on prognosis. In addition, we used the Tumor Immune Evaluation Resource (TIMER) to assess the immune cell infiltration of FTO gene across cancers. The association of FTO expression with immune checkpoint genes expression, DNA mismatch repair (MMR) gene mutation, DNA methyltransferases, microsatellite instability (MSI), and tumor mutational burden (TMB) was investigated using Spearman's correlation analysis. Moreover, Gene Set Enrichment Analysis (GSEA) was utilized to identify critical pathways in cancers. The STRING website was used to reveal the protein-protein interaction (PPI) network of FTO.
Results: FTO was aberrantly expressed across cancers and survival analysis demonstrated that its expression was associated with clinical prognosis of many cancer patients. Specifically, FTO expression was significantly associated with immune infiltrating cells in colon adenocarcinoma, kidney renal clear cell carcinoma, and liver hepatocellular carcinoma. In addition, FTO expression was significantly associated with immune checkpoint genes expression, MMR, DNA methyltransferases levels, TMB, and MSI in multiple cancers. Moreover, the GSEA unveiled that FTO was involved in the regulation of tumors and immune-related signaling pathways. In addition, several m6A related genes were implicated in the PPI network of FTO.
Conclusion: FTO was related to patients' prognosis and tumor immune infiltrates in various cancers, and may serve as a novel and potential prognostic and immune biomarker in human pan-cancer.

Keywords:  FTO; biomarker; pan-cancer; prognosis; tumor immune

DOI:  https://doi.org/10.2147/IJGM.S331752
Oncogene. 2021 Nov 10.

RNA demethylase ALKBH5 promotes tumorigenesis in multiple myeloma via TRAF1-mediated activation of NF-κB and MAPK signaling pathways.

Jianwei Qu, Yifan Hou, Qingxiao Chen, Jing Chen, Yi Li, Enfan Zhang, Huiyao Gu, Ruyi Xu, Yang Liu, Wen Cao, Jinna Zhang, Liqin Cao, Jingsong He, Zhen Cai.

N6-methyladenosine (m6A), an internal modification in mRNA, plays a critical role in regulating gene expression. Dysregulation of m6A modifiers promotes oncogenesis through enzymatic functions that disrupt the balance between the deposition and removal of m6A modification on critical transcripts. However, the roles of mRNA m6A in multiple myeloma (MM) are poorly understood. The present study showed that RNA demethylase ALKBH5 was overexpressed in MM and associated with a poor prognosis in MM patients. Knocking down ALKBH5 induced apoptosis and inhibited the growth of MM cells in vitro. Xenograft models and gene set enrichment analysis with patient transcriptome datasets also supported the oncogenic role of ALKBH5 in MM. Mechanistic studies showed that ALKBH5 exerted tumorigenic effects in myeloma in an m6A-dependent manner, and TNF receptor-associated factor 1 (TRAF1) was a critical target of ALKBH5. Specifically, ALKBH5 regulated TRAF1 expression via decreasing m6A abundance in the 3'-untranslated region (3'-UTR) of TRAF1 transcripts and enhancing TRAF1 mRNA stability. As a result, ALKBH5 promoted MM cell growth and survival through TRAF1-mediated activation of NF-κB and MAPK signaling pathways. Collectively, our data demonstrated that ALKBH5 played a critical role in MM tumorigenesis and suggested that ALKBH5 could be a novel therapeutic target in MM.

DOI: https://doi.org/10.1038/s41388-021-02095-8
Cell Rep. 2021 Nov 09. pii: S2211-1247(21)01447-9. [Epub ahead of print]37(6): 109968

m6A mRNA methylation-directed myeloid cell activation controls progression of NAFLD and obesity.

Yanqin Qin, Binghua Li, Suyavaran Arumugam, Qiuxia Lu, Salah M Mankash, Junzi Li, Beicheng Sun, Jiansheng Li, Richard A Flavell, Hua-Bing Li, Xinshou Ouyang.

  N6-methyladenosine (m6A) RNA modification is a fundamental determinant of mRNA metabolism, but its role in innate immunity-driven non-alcoholic fatty liver disease (NAFLD) and obesity is not known. Here, we show that myeloid lineage-restricted deletion of the m6A "writer" protein Methyltransferase Like 3 (METTL3) prevents age-related and diet-induced development of NAFLD and obesity in mice with improved inflammatory and metabolic phenotypes. Mechanistically, loss of METTL3 results in the differential expression of multiple mRNA transcripts marked with m6A, with a notable increase of DNA Damage Inducible Transcript 4 (DDIT4) mRNA level. In METTL3-deficient macrophages, there is a significant downregulation of mammalian target of rapamycin (mTOR) and nuclear factor κB (NF-κB) pathway activity in response to cellular stress and cytokine stimulation, which can be restored by knockdown of DDIT4. Taken together, our findings identify the contribution of METTL3-mediated m6A modification of Ddit4 mRNA to macrophage metabolic reprogramming in NAFLD and obesity.

Keywords:  DDIT4; NAFLD; liver inflammation; mRNA m(6)A methylation; myeloid cells; non-alcoholic fatty liver disease

DOI:  https://doi.org/10.1016/j.celrep.2021.109968
Phytomedicine. 2021 Oct 25. pii: S0944-7113(21)00365-2. [Epub ahead of print]94 153823

Baicalin suppresses the progression of Type 2 diabetes-induced liver tumor through regulating METTL3/m6A/HKDC1 axis and downstream p-JAK2/STAT1/clevaged Capase3 pathway.

Hongpeng Jiang, Qianqian Yao, Yongbo An, Linlin Fan, Jing Wang, Huiying Li.

  BACKGROUND: Epidemiological and clinical evidence suggests that diabetes increases the risk of liver cancer. Although the co-occurrence of type 2 diabetes (T2D) and liver cancer is becoming more frequent, the underlying mechanisms remain unclear. Even though baicalin, extensively used in traditional Chinese medicine (TCM), can control T2D and inhibit liver cancer separately, minimal research is available regarding its possible effect on T2D-induced liver cancer. Thus, in the present study, we aimed to investigate the role of baicalin in T2D-induced hepatocellular cancer, and for the first time, we particularly emphasized the regulation of baicalin in genes RNA m6A in hepatocellular cancer.METHODS: Here, we constructed a cell culture model under a high concentration of glucose and a T2D-induced liver tumor model to evaluate the in vitro and in vivo role of baicalin in T2D-induced liver cancer progression. After confirming the suppressive effect of baicalin and the HKDC1 antibody on T2D-induced liver tumors, the epigenetic alterations (DNA 5mC and RNA m6A) of the baicalin-regulated HKDC1 gene were detected using MS and q-PCR. Next, the METTL3 gene-regulated m6A (2854 site) was investigated using SELECT PCR. Finally, the impact of the other three baicalin analogs (baicalein, wogonoside, and wogonin) on tumor inhibition was tested in vivo while verifying the related RNA m6A mechanism.
RESULTS: The results showed that baicalin and the HKDC1 antibody suppressed T2D-induced liver tumor progression in vitro and in vivo. Furthermore, baicalin significantly inhibited the epigenetic modification (DNA 5mC and RNA m6A) of HKDC1 in HepG2 tumors, mainly targeting the RNA m6A site (2854). The m6A-related gene, METTL3, regulated the RNA m6A site (2854) of HKDC1, which was also restricted by baicalin. Moreover, the study verified that baicalin regulated the METTL3/HKDC1/JAK2/STAT1/caspase-3 pathway in liver cancer cells when exposed to a high glucose concentration. In addition, the three baicalin analogs were proven to regulate the m6A (2854 site) of HKDC1 and suppress T2D-induced liver tumors.
CONCLUSIONS: The findings of this study revealed that baicalin suppressed T2D-induced liver tumor progression by regulating the METTL3/m6A/HKDC1 axis, which might support its potential application for preventing and treating T2D-induced liver cancer.

Keywords:  HKDC1; RNA m(6)A; Type 2 diabetes; baicalin; liver tumor

DOI:  https://doi.org/10.1016/j.phymed.2021.153823
Bioengineered. 2021 Nov 09.

Insulin-like growth factor 2 mRNA binding protein 2 regulates proliferation, migration and angiogenesis of keratinocytes by modulating heparanase stability.

Shaomin Zhi, Jun Li, Xiao Kong, Xuemei Xie, Qiangli Zhang, Guoxiang Fang.

  Wound healing is related to proliferation, migration and angiogenesis of keratinocytes. Insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) is an important N6-methyladenosine (m6A) reader, which is involved in multiple processes, including wound healing. However, the function and mechanism of IGF2BP2 in keratinocyte processes are largely uncertain. In the present study, expression levels of IGF2BP2 and heparanase (HPSE) were detected by quantitative reverse transcription polymerase chain reaction and western blotting assays. Cell proliferation was investigated with cell counting kit-8 analysis. Cell migration was determined through wound healing assay. Angiogenesis was measured by tube formation assay and vascular endothelial growth factor (VEGF) level using enzyme linked immunosorbent assay. The interaction between IGF2BP2 and HPSE was analyzed by RNA immunoprecipitation, pull-down and luciferase reporter analyses. The results showed that IGF2BP2 expression was enhanced in wound healing. IGF2BP2 downregulation constrained HaCaT cell proliferation, migration and angiogenesis. IGF2BP2 knockdown decreased HPSE expression. IGF2BP2 could regulate HPSE stability by binding with 3' untranslated region (UTR) of HPSE. HPSE upregulation attenuated silencing IGF2BP2-mediated suppression of proliferation, migration and angiogenesis. As a conclusion, IGF2BP2 knockdown repressed proliferation, migration and angiogenesis of HaCaT cells by decreasing HPSE stability.

Keywords:  HPSE; IGF2BP2; angiogenesis; keratinocyte; migration; proliferation; wound healing

DOI:  https://doi.org/10.1080/21655979.2021.2002495
J Hematol Oncol. 2021 Nov 10. 14(1): 190

m6A regulators as predictive biomarkers for chemotherapy benefit and potential therapeutic targets for overcoming chemotherapy resistance in small-cell lung cancer.

Zhihui Zhang, Chaoqi Zhang, Zhaoyang Yang, Guochao Zhang, Peng Wu, Yuejun Luo, Qingpeng Zeng, Lide Wang, Qi Xue, Yi Zhang, Nan Sun, Jie He.

  Small-cell lung cancer (SCLC) is a devastating subtype of lung cancer with few therapeutic options. Despite the advent of immunotherapy, platinum-based chemotherapy is still the irreplaceable first-line therapy for SCLCs. However, drug resistance will invariably occur in most patients and the outcomes are heterogeneous. Therefore, clinically feasible classification strategies and potential therapeutic targets for overcoming chemotherapy resistance are urgently needed. N6-methyladenosine (m6A) is a novel epigenetic decisive factor that is involved in tumor progression and drug resistance. However, almost nothing is known about m6A modification in SCLC. Here, we assessed 200 SCLC samples from patients who underwent chemotherapy from three different cohorts, including a validation cohort containing 71 cases with qPCR data and an independent cohort containing 79 cases with immunohistochemistry data (quantified as H-score). We systematically characterized the predictive landscape of m6A regulators in SCLC patients following with chemotherapy. Using the LASSO Cox model, we built a seven-regulator-based (ZCCHC4, IGF2BP3, ALKBH5, YTHDF3, METTL5, G3BP1, and RBMX) chemotherapy benefit predictive classifier (m6A score) and subsequently validated the classifier in two other cohorts. Time-dependent ROC and C-index analyses showed that the m6A score to possessed superior predictive power for chemotherapy benefit in comparison with other clinicopathological parameters. A multicohort multivariate analysis revealed that the m6A score is an independent factor that affects survival benefit across multiple cohorts. Our in vitro experimental results revealed that three regulators-ZCCHC4, G3BP1, and RBMX-may serve as promising novel therapeutic targets for overcoming chemoresistance in SCLCs. Our results, for the first time, demonstrate the predictive significance of m6A regulators for chemotherapy benefit, as well as their potential as therapeutic targets for overcoming chemotherapy resistance in SCLC patients. The m6A score was found to be a reliable prognostic tool that may help guide chemotherapy decisions for patients with SCLC.

Keywords:  Chemotherapy resistance; Epigenetic modification; Individualized medicine; Small-cell lung cancer; m6A regulators

DOI:  https://doi.org/10.1186/s13045-021-01173-4
J BUON. 2021 Sep-Oct;26(5):26(5): 1931-1941

Characterization of the m6A-related lncRNA signature in predicting prognosis and immune response in patients with colon cancer.

Shujia Chen, Xiaofei Li, Lianyi Guo, Jiachen Zhang, Li Li, Xueqiu Wang, Yinghui Zhu, Jiwei Wang.

PURPOSE: Colon adenocarcinoma (COAD) is globally one of the most frequently occurring malignant tumors. The patients' 5-year survival rate with colon cancer was poor. There is a usual form of mRNA modification called N6-methyl adenosine (m6A). It is adjusted by the m6A RNA methylation modulator. Nevertheless, few studies of COAD can fully discuss m6A-related lncRNAs' prognostic function.METHODS: From The Cancer Genome Atlas (TCGA) database, this study of COAD samples discussed 23 m6A regulator-related lncRNAs systemically. 2 m6A patterns with various clinical results were recognized, and a remarkable correlation between various m6A clusters and tumor immune microenvironment was discovered.
RESULTS: According to prognostic analysis, cluster1 had a higher immune checkpoint programmed death-ligand 1 (PD-L1) expression and a better prognosis. A 6 m6A-related lncRNAs model was constructed through least absolute shrinkage and selection operator (LASSO), univariate, multivariate Cox regression and stratified analysis. The outcomes reported that compared with the low-risk group, high-risk groups that were based on model closely were related to poor overall survival (OS). The study ensured a risk model consisting of 6 m6A-related lncRNAs as independent prognosis predictors. For the expression differences between the two groups, Genomes Pathway Analysis, Kyoto Encyclopedia of Genes (KEGG) and Gene Ontology (GO) biological process analyses were conducted. In addition, on the basis of full analysis of OS, a nomogram based on gender, age, lncRNA feature and the stage was constructed. One year, two years, and three years are the periods when the calibration chart performed best.
CONCLUSIONS: The outcomes of the study confirmed the underlying function of m6A-related lncRNAs and offered fresh perspectives to COAD prognosis.
Stem Cells Int. 2021 ;2021 8874360

The Role of RNA Methylation in Regulating Stem Cell Fate and Function-Focus on m6A.

Weiwei Sun, Bin Zhang, Qingli Bie, Na Ma, Na Liu, Zewei Shao.

The biological role of RNA methylation in stem cells has attracted increasing attention. Recent studies have demonstrated that RNA methylation plays a crucial role in self-renewal, differentiation, and tumorigenicity of stem cells. In this review, we focus on the biological role of RNA methylation modifications including N6-methyladenosine, 5-methylcytosine, and uridylation in embryonic stem cells, adult stem cells, induced pluripotent stem cells, and cancer stem cells, so as to provide new insights into the potential innovative treatments of cancer or other complex diseases.

DOI: https://doi.org/10.1155/2021/8874360
Cell Death Dis. 2021 Nov 12. 12(11): 1078

The m6A "reader" YTHDF1 promotes osteogenesis of bone marrow mesenchymal stem cells through translational control of ZNF839.

Tao Liu, Xinfeng Zheng, Chenglong Wang, Chuandong Wang, Shengdan Jiang, Bo Li, Pengbo Chen, Wenning Xu, Huoliang Zheng, Runze Yang, Xingxu Huang, Xiaoling Zhang, Leisheng Jiang.

N6-methyladenosine (m6A) is required for differentiation of human bone marrow mesenchymal stem cells (hBMSCs). However, its intrinsic mechanisms are largely unknown. To identify the possible role of m6A binding protein YTHDF1 in hBMSCs osteogenesis in vivo, we constructed Ythdf1 KO mice and showed that depletion of Ythdf1 would result in decreased bone mass in vivo. Both deletion of Ythdf1 in mouse BMSCs and shRNA-mediated knockdown of YTHDF1 in hBMSCs prevented osteogenic differentiation of cells in vitro. Using methylated RNA immunoprecipitation (Me-RIP) sequencing and RIP-sequencing, we found that ZNF839 (a zinc finger protein) served as a target of YTHDF1. We also verified its mouse homolog, Zfp839, was translationally regulated by Ythdf1 in an m6A-dependent manner. Zfp839 potentiated BMSC osteogenesis by interacting with and further enhancing the transcription activity of Runx2. These findings should improve our understanding of the mechanism of BMSC osteogenesis regulation and provide new ideas for the prevention and treatment of osteoporosis.

DOI: https://doi.org/10.1038/s41419-021-04312-4
Gene. 2021 Oct 29. pii: S0378-1119(21)00645-4. [Epub ahead of print] 146050

METTL14 gene polymorphisms influence hepatoblastoma predisposition in Chinese children: Evidences from a seven-center case-control study.

Huitong Chen, Zhen Chen, Mi Wang, Jiao Zhang, Yong Li, Li Li, Suhong Li, Jiwen Cheng, Xianqiang Wang, Huimin Xia, Zhonghua Yang, Jing He.

  Hepatoblastoma as the most prevalent hepatic malignancy in children, its etiology remains unclear. N6-Methyladenosine (m6A) modification which can modify various physiological processes, plays a critical role in tumorigenesis. Methyltransferase-like 14 (METTL14), an important component of the m6A methyltransferase complex, remains elusive during hepatoblastoma occurrence and development. We explored the relationship between METTL14 gene polymorphisms (rs1064034 T > A, rs298982 G > A, rs62328061 A > G, rs9884978 G > A, and rs4834698 T > C) and hepatoblastoma susceptibility from 313 patients and 1446 controls. The role of METTL14 polymorphisms in hepatoblastoma was evaluated by odds ratios (ORs) and 95% confidence intervals (CIs). Of the included subjects, 308 patients and 1444 controls were successfully genotyped. We did not find any significant correlation between the risk of hepatoblastoma and the five potentially functional METTL14 polymorphisms individually. However, the presence of 4-5 risk genotypes exhibited a significant increased hepatoblastoma risk (adjusted OR = 1.32, 95% CI = 1.03-1.69, P = 0.031) compared to those carriers with 0-3 risk genotypes. Furthermore, the stratified analysis demonstrated that the rs1064034 AA genotype, rs62328061 AG/GG genotypes, rs4834698 TC/CC genotypes, and 4-5 risk genotypes were related to hepatoblastoma susceptibility in certain subgroups. The expression quantitative trait loci (eQTL) analysis revealed that rs1064034 T > A and rs4834698 T > C were correlated with the expression levels of METTL14 and its surrounding genes. Prospectively, these findings suggested that METTL14 polymorphisms may correlation with hepatoblastoma susceptibility and provide a fresh insight into the genetic underpinnings of m6A modification in hepatoblastoma.

Keywords:  Hepatoblastoma; M(6)A; METTL14; Polymorphism; Susceptibility

DOI:  https://doi.org/10.1016/j.gene.2021.146050
J Hematol Oncol. 2021 Nov 07. 14(1): 188

N6-methyladenosine reader IMP2 stabilizes the ZFAS1/OLA1 axis and activates the Warburg effect: implication in colorectal cancer.

Senxu Lu, Li Han, Xiaoyun Hu, Tong Sun, Dongping Xu, Yalun Li, Qiuchen Chen, Weifan Yao, Miao He, Zhenning Wang, Huizhe Wu, Minjie Wei.

  BACKGROUND: Accumulating evidence shows that N6-methyladenine (m6A) modulators contribute to the etiology and progression of colorectal cancer (CRC). However, the exact mechanisms of m6A reader involved in glycolytic metabolism remain vague. This article aimed to crosstalk the m6A reader with glycolytic metabolism and reveal a new mechanism for the progression of CRC.METHODS: The relationship between candidate lncRNA and m6A reader was analyzed by bioinformatics, ISH and IHC assays. In vivo and in vitro studies (including MTT, CFA, trans-well, apoptosis, western blot, qRT-PCR and xenograft mouse models) were utilized to explore the biological functions of these indicators. Lactate detection, ATP activity detection and ECAR assays were used to verify the biological function of the downstream target. The bioinformatics, RNA stability, RIP experiments and RNA pull-down assays were used to explore the potential molecular mechanisms.
RESULTS: We identified that the crosstalk of the m6A reader IMP2 with long-noncoding RNA (lncRNA) ZFAS1 in an m6A modulation-dependent manner, subsequently augmented the recruitment of Obg-like ATPase 1 (OLA1) and adenosine triphosphate (ATP) hydrolysis and glycolysis during CRC proliferation and progression. Specifically, IMP2 and ZFAS1 are significantly overexpressed with elevated m6A levels in CRC cells and paired CRC cohorts (n = 144). These indicators could be independent biomarkers for CRC prognostic prediction. Notably, IMP2 regulated ZFAS1 expression and enhanced CRC cell proliferation, colony formation, and apoptosis inhibition; thus, it was oncogenic. Mechanistically, ZFAS1 is modified at adenosine +843 within the RGGAC/RRACH element in an m6A-dependent manner. Thus, direct interaction between the KH3-4 domain of IMP2 and ZFAS1 where IMP2 serves as a reader for m6A-modified ZFAS1 and promotes the RNA stability of ZFAS1 is critical for CRC development. More importantly, stabilized ZFAS1 recognizes the OBG-type functional domain of OLA1, which facilitated the exposure of ATP-binding sites (NVGKST, 32-37), enhanced its protein activity, and ultimately accelerated ATP hydrolysis and the Warburg effect.
CONCLUSIONS: Our findings reveal a new cancer-promoting mechanism, that is, the critical modulation network underlying m6A readers stabilizes lncRNAs, and they jointly promote mitochondrial energy metabolism in the pathogenesis of CRC.

Keywords:  ATP-hydrolyzing and glycolysis; Colorectal cancer; IMP2; OLA1; ZFAS1; m6A methylation

DOI:  https://doi.org/10.1186/s13045-021-01204-0