bims-rimeca 2022-01-16 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022–01–16
27 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

N(6)-adenosine-methyltransferase-14 promotes glioma tumorigenesis by repressing argininosuccinate synthase 1 expression in an m6A-dependent manner.
METTL14 suppresses pyroptosis and diabetic cardiomyopathy by downregulating TINCR lncRNA.
METTL3 Is Suppressed by Circular RNA circMETTL3/miR-34c-3p Signaling and Limits the Tumor Growth and Metastasis in Triple Negative Breast Cancer.
ZC3H13 Inhibits the Progression of Hepatocellular Carcinoma through m6A-PKM2-Mediated Glycolysis and Enhances Chemosensitivity.
METTL3 promotes colorectal carcinoma progression by regulating the m6A-CRB3-Hippo axis.
ALKBH5-mediated N6-methyladenosine modification of TRERNA1 promotes DLBCL proliferation via p21 downregulation.
m6A Modification Patterns With Distinct Immunity, Metabolism, and Stemness Characteristics in Soft Tissue Sarcoma.
WTAP-mediated m6A modification of lncRNA DIAPH1-AS1 enhances its stability to facilitate nasopharyngeal carcinoma growth and metastasis.
Characterization of m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration in acute myeloid leukemia.
m6A demethylation of cytidine deaminase APOBEC3B mRNA orchestrates arsenic-induced mutagenesis.
LncRNA UCA1 promotes SOX12 expression in breast cancer by regulating m6A modification of miR-375 by METTL14 through DNA methylation.
Comprehensive Analysis of N6-methyladenosine Modification Patterns Associated With Multiomic Characteristics of Bladder Cancer.
Mettl5 mediated 18S rRNA N6-methyladenosine (m6A) modification controls stem cell fate determination and neural function.
N6‑methyladenosine upregulates miR‑181d‑5p in exosomes derived from cancer‑associated fibroblasts to inhibit 5‑FU sensitivity by targeting NCALD in colorectal cancer.
Mettl14 Attenuates Cardiac Ischemia/Reperfusion Injury by Regulating Wnt1/β-Catenin Signaling Pathway.
Profiling of N6-Methyladenosine (m6A) Modification Landscape in Response to Drought Stress in Apple (Malus prunifolia (Willd.) Borkh).
Comprehensive Analyses of the Expression, Genetic Alteration, Prognosis Significance, and Interaction Networks of m6A Regulators Across Human Cancers.
The m6A methyltransferase METTL3 regulates muscle maintenance and growth in mice.
METTL14 promotes apoptosis of spinal cord neurons by inducing EEF1A2 m6A methylation in spinal cord injury.
The prognostic value of m6A-related LncRNAs in patients with HNSCC: bioinformatics analysis of TCGA database.
m6A Regulator Expression Segregates Meningiomas Into Biologically Distinct Subtypes.
Non-Coding RNA m6A Modification in Cancer: Mechanisms and Therapeutic Targets.
Modular DNA-Incorporated Aggregation-Induced Emission Probe for Sensitive Detection and Imaging of DNA Methyltransferase.
Alkbh1-mediated DNA N6-methyladenine modification regulates bone marrow mesenchymal stem cell fate during skeletal aging.
Potential Prognostic Value of a Seven m6A-Related LncRNAs Signature and the Correlative Immune Infiltration in Colon Adenocarcinoma.
Demethylase FTO promotes mechanical stress induced osteogenic differentiation of BMSCs with up-regulation of HIF-1α.
Critical roles of FTO-mediated mRNA m6A demethylation in regulating adipogenesis and lipid metabolism: Implications in lipid metabolic disorders.

Bioengineered. 2022 01;13(1): 1858-1871

N(6)-adenosine-methyltransferase-14 promotes glioma tumorigenesis by repressing argininosuccinate synthase 1 expression in an m6A-dependent manner.

You-Qing Miao, Wei Chen, Jianfeng Zhou, Qiyang Shen, Ying Sun, Tao Li, Sheng-Chan Wang.

  Glioma is one of the leading causes of tumor-related deaths worldwide, but its potential mechanism remains unclear. This study aimed to explore the biological role and potential mechanism of argininosuccinate synthase 1 (ASS1) in glioma. The relative expression levels of ASS1 in glioma specimens and cell lines were calculated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western blotting. The biological functions of ASS1 were demonstrated using the 5-ethynyl-2'-deoxyuridine (EdU) assay, transwell assay, and in vivo experiments. In addition, methylated RNA immunoprecipitation (MeRIP), RNA immunoprecipitation (RIP), and luciferase reporter assays were performed to explore the molecular mechanism of ASS1 in glioma. ASS1 expression levels were found to be downregulated in glioma specimens and cell lines. Functionally, we confirmed that ASS1 inhibited glioma cell proliferation, migration, invasion, and growth both. Furthermore, we found that ASS1 was a target of N(6)-adenosine-methyltransferase-14 (METTL14)-mediated N6-methyladenosine (m6A) modification. Overexpression of METTL14 markedly elevated ASS1 mRNA m6A modification and suppressed ASS1 mRNA expression. We also revealed that METTL14-mediated ASS1 mRNA degradation relied on the YTH m6A RNA-binding protein 2 (YTHDF2)-dependent pathway. We confirmed that decreased ASS1 expression promoted the cell proliferation, migration, and invasion in glioma, and that the METTL14/ASS1/YTHDF2 regulatory axis may be an effective therapeutic target for glioma.

Keywords:  ASS1; METTL14; N6-methyladenosine; glioma; malignant progression

DOI:  https://doi.org/10.1080/21655979.2021.2018386
Cell Death Dis. 2022 01 10. 13(1): 38

METTL14 suppresses pyroptosis and diabetic cardiomyopathy by downregulating TINCR lncRNA.

Liping Meng, Hui Lin, Xingxiao Huang, Jingfan Weng, Fang Peng, Shengjie Wu.

N6-methyladenosine (m6A) is one of the most important epigenetic regulation of RNAs, such as lncRNAs. However, the underlying regulatory mechanism of m6A in diabetic cardiomyopathy (DCM) is very limited. In this study, we sought to define the role of METTL14-mediated m6A modification in pyroptosis and DCM progression. DCM rat model was established and qRT-PCR, western blot, and immunohistochemistry (IHC) were used to detect the expression of METTL14 and TINCR. Gain-and-loss functional experiments were performed to define the role of METTL14-TINCR-NLRP3 axis in pyroptosis and DCM. RNA pulldown and RNA immunoprecipitation (RIP) assays were carried out to verify the underlying interaction. Our results showed that pyroptosis was tightly involved in DCM progression. METTL14 was downregulated in cardiomyocytes and hear tissues of DCM rat tissues. Functionally, METTL14 suppressed pyroptosis and DCM via downregulating lncRNA TINCR, which further decreased the expression of key pyroptosis-related protein, NLRP3. Mechanistically, METTL14 increased m6A methylation level of TINCR gene, resulting in its downregulation. Moreover, the m6A reader protein YTHDF2 was essential for m6A methylation and mediated the degradation of TINCR. Finally, TINCR positively regulated NLRP3 by increasing its mRNA stability. To conclude, our work revealed the novel role of METTL14-mediated m6A methylation and lncRNA regulation in pyroptosis and DCM, which could help extend our understanding the epigenetic regulation of pyroptosis in DCM progression.

DOI: https://doi.org/10.1038/s41419-021-04484-z
Front Oncol. 2021 ;11 778132

METTL3 Is Suppressed by Circular RNA circMETTL3/miR-34c-3p Signaling and Limits the Tumor Growth and Metastasis in Triple Negative Breast Cancer.

Han-Guang Ruan, Wen-Chao Gu, Wen Xia, Yan Gong, Xue-Liang Zhou, Wen-Yan Chen, Juan Xiong.

  Despite N6-methyladenosine (m6A) is functionally important in various biological processes, its role in the underlying regulatory mechanism in TNBC are lacking. In this study, we investigate the pathological role and the underlying mechanism of the m6A methylated RNA level and its major methyltransferase METTL3 in the TNBC progression. We found that the m6A methylated RNA was dramatically decreased in TNBC tissues and cell lines. Functionally, we demonstrated that METTL3 inhibits the proliferation, migration, and invasion ability of TNBC cells. Moreover, we found METTL3 is repressed by miR-34c-3p in TNBC cells. On the mechanism, we found that circMETTL3 could act as a sponge for miR-34c-3p and inhibits cell proliferation, invasion, tumor growth and metastasis by up-regulating the expression of miR-34c-3p target gene METTL3. In conclusion, our study demonstrates the functional importance and regulatory mechanism of METTL3 in suppressing the tumor growth of TNBC.

Keywords:  METTL3; circMETTL3; m6A; miR-34c-3p; triple negative breast cancer

DOI:  https://doi.org/10.3389/fonc.2021.778132
J Oncol. 2021 ;2021 1328444

ZC3H13 Inhibits the Progression of Hepatocellular Carcinoma through m6A-PKM2-Mediated Glycolysis and Enhances Chemosensitivity.

Qibo Wang, Haichuan Xie, Hao Peng, Jianjian Yan, Limin Han, Gang Ye.

Objective: N6-Methyladenosine (m6A) is the most prevalent RNA epigenetic modulation in eukaryotic cells, which serves a critical role in diverse physiological processes. Emerging evidences indicate the prognostic significance of m6A regulator ZC3H13 in hepatocellular carcinoma (HCC). Herein, this study was conducted for revealing biological functions and mechanisms of ZC3H13 in HCC.
Methods: Expression of ZC3H13 was examined in collected HCC and normal tissues, and its prognostic significance was investigated in a public database. Gain/loss of functional assays were presented for defining the roles of ZC3H13 in HCC progression. The specific interactions of ZC3H13 with PKM2 were validated in HCC cells via mRNA stability, RNA immunoprecipitation, and luciferase reporter and MeRIP-qPCR assays. Moreover, rescue experiments were carried out for uncovering the mechanisms.
Results: ZC3H13 expression was downregulated in HCC, and its loss was in relation to dismal survival outcomes. Functionally, overexpressed ZC3H13 suppressed proliferation, migration, and invasion and elevated apoptotic levels of HCC cells. Moreover, ZC3H13 overexpression sensitized to cisplatin and weakened metabolism reprogramming of HCC cells. Mechanically, ZC3H13-induced m6A modified patterns substantially abolished PKM2 mRNA stability. ZC3H13 facilitated malignant behaviors of HCC cells through PKM2-dependent glycolytic signaling.
Conclusion: Collectively, ZC3H13 suppressed the progression of HCC through m6A-PKM2-mediated glycolysis and sensitized HCC cells to cisplatin, which offered a fresh insight into HCC therapy.

DOI: https://doi.org/10.1155/2021/1328444
J Exp Clin Cancer Res. 2022 Jan 10. 41(1): 19

METTL3 promotes colorectal carcinoma progression by regulating the m6A-CRB3-Hippo axis.

Jiashu Pan, Feng Liu, Xiaoli Xiao, Ruohui Xu, Liang Dai, Mingzhe Zhu, Hanchen Xu, Yangxian Xu, Aiguang Zhao, Wenjun Zhou, Yanqi Dang, Guang Ji.

   BACKGROUND: Colorectal carcinoma (CRC) is the third most common cancer and second most common cause of cancer-related deaths worldwide. Ribonucleic acid (RNA) N6-methyladnosine (m6A) and methyltransferase-like 3 (METTL3) play key roles in cancer progression. However, the roles of m6A and METTL3 in CRC progression require further clarification.
METHODS: Adenoma and CRC samples were examined to detect m6A and METTL3 levels, and tissue microarrays were performed to evaluate the association of m6A and METTL3 levels with the survival of patients with CRC. The biological functions of METTL3 were investigated through cell counting kit-8, wound healing, and transwell assays. M6A epitranscriptomic microarray, methylated RNA immunoprecipitation-qPCR, RNA stability, luciferase reporter, and RNA immunoprecipitation assays were performed to explore the mechanism of METTL3 in CRC progression.
RESULTS: M6A and METTL3 levels were substantially elevated in CRC tissues, and patients with CRC with a high m6A or METTL3 levels exhibited shorter overall survival. METTL3 knockdown substantially inhibited the proliferation, migration, and invasion of CRC cells. An m6A epitranscriptomic microarray revealed that the cell polarity regulator Crumbs3 (CRB3) was the downstream target of METTL3. METTL3 knockdown substantially reduced the m6A level of CRB3, and inhibited the degradation of CRB3 mRNA to increase CRB3 expression. Luciferase reporter assays also showed that the transcriptional level of wild-type CRB3 significantly increased after METTL3 knockdown but not its level of variation. Knockdown of YT521-B homology domain-containing family protein 2 (YTHDF2) substantially increased CRB3 expression. RNA immunoprecipitation assays also verified the direct interaction between the YTHDF2 and CRB3 mRNA, and this direct interaction was impaired after METTL3 inhibition. In addition, CRB3 knockdown significantly promoted the proliferation, migration, and invasion of CRC cells. Mechanistically, METTL3 knockdown activated the Hippo pathway and reduced nuclear localization of Yes1-associated transcriptional regulator, and the effects were reversed by CRB3 knockdown.
CONCLUSIONS: M6A and METTL3 levels were substantially elevated in CRC tissues relative to normal tissues. Patients with CRC with high m6A or METTL3 levels exhibited shorter overall survival, and METTL3 promoted CRC progression. Mechanistically, METTL3 regulated the progression of CRC by regulating the m6A-CRB3-Hippo pathway.

Keywords:  Colorectal carcinoma; Crumbs3; Hippo pathway; Methyltransferase-like 3; RNA N6-methyladnosine

DOI:  https://doi.org/10.1186/s13046-021-02227-8
Cell Death Discov. 2022 Jan 14. 8(1): 25

ALKBH5-mediated N6-methyladenosine modification of TRERNA1 promotes DLBCL proliferation via p21 downregulation.

Wei Song, Fei Fei, Fengchang Qiao, Zuyi Weng, Yuanxun Yang, Bei Cao, Jing Yue, Jiaxuan Xu, Meihong Zheng, Juan Li.

Long noncoding RNAs (lncRNAs) have crucial functions in the tumorigenesis and metastasis of cancers. N6-methyladenosine (m6A) modification of RNA is an important epigenetic regulatory mechanism in various malignancies. Nevertheless, the mechanism of m6A-modified lncRNA in diffuse large B cell lymphoma (DLBCL) has remained poorly defined. In the present study, we showed that lncRNA TRERNA1 was associated with the poor prognosis of DLBCL patients. TRERNA1 with internal m6A modification was highly correlated with the demethylase ALKBH5 expression. We further demonstrated that TRERNA1 was a potential downstream target of ALKBH5-mediated m6A modification by m6A-RNA sequencing and m6A-RIP assays. Decreased m6A methylation of TRERNA1 regulated by ALKBH5 was shown to regulate cell proliferation in vitro and in vivo. The results of mechanism analyses revealed that TRERNA1 recruited EZH2 to epigenetically silence the expression of the cyclin-dependent kinases inhibitor p21 by H3K27me3 modification of its promoter region. In addition, ALKBH5 further inhibited p21 expression. Taken together, our results elucidate the functional roles and epigenetic alterations of TRERNA1 through m6A modification in DLBCL. TRERNA1, the expression of which is upregulated by ALKBH5, acts as a scaffold that decreases p21 expression. The results of the present study provide novel targets for the diagnosis and treatment of DLBCL.

DOI: https://doi.org/10.1038/s41420-022-00819-7
Front Immunol. 2021 ;12 765723

m6A Modification Patterns With Distinct Immunity, Metabolism, and Stemness Characteristics in Soft Tissue Sarcoma.

Zhen-Dong Huang, Lu-Lu Lin, Zi-Zhen Liu, Chao Hu, Hui-Yun Gu, Ren-Xiong Wei.

  N6-methyladenosine (m6A) RNA methylation has been shown to have prognostic value in cancer. Nonetheless, its potential role regarding immunity, metabolism, and stemness in soft tissue sarcoma (STS) remains unknown. We comprehensively estimated the m6A modification patterns and corresponding immunity, metabolism, and stemness characteristics based on 568 STS samples and 21 m6A regulators. The m6Ascore was constructed to quantify m6A modification patterns in individuals using machine learning algorithms. Two distinct m6A modification patterns among the STS patients were identified, which exhibited differences in prognosis, immune cell infiltration, metabolic pathways, stemness, somatic mutation, and copy number variation. Thereafter, immunity-, metabolism-, and stemness phenotype-related genes associated with m6A modification were identified. Furthermore, patients with lower m6Ascores had increased antitumor immune responses, survival benefit under immunotherapy, tumor mutation burden, immunogenicity, and response to anti-PD-1/L1 immunotherapy. Immunotherapy sensitivity was validated using the IMvigor210 dataset. STS patients with lower m6Ascore might be more sensitive to docetaxel and gemcitabine. Finally, pan-cancer analysis illustrated the significant correlations of m6Ascore with clinical outcomes, immune cell infiltration, metabolism, and stemness. This study revealed that m6A modification plays an important role in immunity, metabolism, and stemness in STS. Evaluating the m6A modification pattern and development of m6Ascore may help to guide more effective immunotherapy and chemotherapy strategies.

Keywords:  cancer molecular subtypes; immunotherapy; m6A methylation; soft tissue sarcoma; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2021.765723
Cell Death Differ. 2022 Jan 08.

WTAP-mediated m6A modification of lncRNA DIAPH1-AS1 enhances its stability to facilitate nasopharyngeal carcinoma growth and metastasis.

Zhi-Xuan Li, Zi-Qi Zheng, Pan-Yang Yang, Li Lin, Guan-Qun Zhou, Jia-Wei Lv, Lu-Lu Zhang, FoPing Chen, Ying-Qin Li, Chen-Fei Wu, Feng Li, Jun Ma, Na Liu, Ying Sun.

As the most predominant RNA epigenetic regulation in eukaryotic cells, N6-methyladenosine (m6A) plays a critical role in human tumorigenesis and cancer progression. However, the biological function and molecular mechanism of m6A regulation in naso-pharyngeal carcinoma (NPC) remain elusive. Here, we showed that Wilms' tumor 1-associating protein (WTAP) expression was apparently upregulated in NPC, and increased WTAP was associated with poor prognosis. WTAP upregulated in NPC was fine-tuned by KAT3A-mediated H3K27 acetylation. Functionally, WTAP was required for the growth and metastasis of NPC. Mechanistically, lncRNA DIAPH1-AS1 was identified as a bona fide m6A target of WTAP. WTAP-mediated m6A modification of DIAPH1-AS1 enhanced its stability relying on the m6A reader IGF2BP2-dependent pathway. Furthermore, DIAPH1-AS1 acted as a molecular adaptor that promoted MTDH-LASP1 complex formation and upregulated LASP1 expression, ultimately facilitating NPC growth and metastasis. Thus, WTAP-mediated DIAPH1-AS1 m6A methylation is required for NPC tumorigenesis and metastasis.

DOI: https://doi.org/10.1038/s41418-021-00905-w
Cancer Med. 2022 Jan 13.

Characterization of m6A regulator-mediated methylation modification patterns and tumor microenvironment infiltration in acute myeloid leukemia.

Shiyu Han, Jiaqian Qi, Kun Fang, Hong Wang, Yaqiong Tang, Depei Wu, Yue Han.

   BACKGROUND: Previous studies have confirmed the existence of epigenetic regulation of immune responses in acute myeloid leukemia. However, the potential role of RNA N6-methyladenosine (m6A) remodeling in tumor microenvironment (TME) infiltration remains unclear.
METHODS AND MATERIALS: m6A patterns of 469 AML patients (420 of which provided survival data) based on 18 m6A regulators were systematically evaluated. Based on the expression of 18 m6A regulators, unsupervised agglomerative cluster analysis was applied to recognize the various m6A modification types and to classify patients. We linked these patterns to TME infiltration characteristics and identified three distinct populations of m6A modifications.
RESULTS: These three TME cell infiltration patterns are characterized by a high degree of concordance with the three tumor immunophenotypes, which include immunoinflammatory, immunorejection, and immune inert patterns. We showed that assessment of m6A modification patterns within individually neoplasms can forecast the stage of neoplasmic inflammation, TME basal activity, subtype, hereditary mutation, and clinical patient prognosis. Limited low m6Ascore, featuring increased mutational load and immune activation, indicates an inflammatory phenotype of TME with a 5-year survival rate at 14.4% compared to the high-m6Ascore group (40.9%).
CONCLUSIONS: Data from two different cohorts demonstrated that a higher m6Ascore showed a marked therapeutic superiority as well as clinical advantage. Assessing m6A modification patterns in AML patients could improve our knowledge of the TME infiltrative profile as well as directing effective immunotherapeutic approaches.

Keywords:  immunotherapy; leukemia; m6A; microenvironment; mutation burden

DOI:  https://doi.org/10.1002/cam4.4531
J Biol Chem. 2022 Jan 05. pii: S0021-9258(22)00003-5. [Epub ahead of print] 101563

m6A demethylation of cytidine deaminase APOBEC3B mRNA orchestrates arsenic-induced mutagenesis.

Ming Gao, Zijuan Qi, Wenya Feng, Hongyang Huang, Zhijie Xu, Zheng Dong, Ming Xu, Jinxiang Han, Jake A Kloeber, Jinzhou Huang, Zhenkun Lou, Sijin Liu.

  The cytidine deaminase APOBEC3B is an endogenous inducer of somatic mutations and causes chromosomal instability by converting cytosine to uracil in single-stranded DNA. Therefore, identification of factors and mechanisms that mediate APOBEC3B expression will be helpful for developing therapeutic approaches to decrease DNA mutagenesis. Arsenic is one well-known mutagen and carcinogen, but the mechanisms by which it induces mutations have not been fully elucidated. Herein we show that APOBEC3B is upregulated and required for arsenic-induced DNA damage and mutagenesis. We found that arsenic treatment causes a decrease of N6-methyladenosine (m6A) modification near the stop codon of APOBEC3B, consequently increasing the stability of APOBEC3B mRNA. We further reveal that the demethylase FTO is responsible for arsenic-reduced m6A modification of APOBEC3B, leading to increased APOBEC3B expression and DNA mutation rates in a manner dependent on the m6A reader YTHDF2. Our in vivo data also confirm that APOBEC3B is a downstream target of FTO in arsenic-exposed lung tissues. In addition, FTO protein is highly expressed and positively correlates with the protein levels of APOBEC3B in tumor samples from human non-small cell lung cancer (NSCLC) patients. These findings indicate a previously unrecognized role of APOBEC3B in arsenic-triggered somatic mutation, and might open new avenues to reduce DNA mutagenesis by targeting the FTO/m6A axis.

Keywords:  APOBEC3B; Arsenic; FTO; m6A modification; mutagenesis

DOI:  https://doi.org/10.1016/j.jbc.2022.101563
Cancer Gene Ther. 2022 Jan 13.

LncRNA UCA1 promotes SOX12 expression in breast cancer by regulating m6A modification of miR-375 by METTL14 through DNA methylation.

Chengpeng Zhao, Xiaoling Ling, Yunxia Xia, Bingxue Yan, Quanlin Guan.

Breast cancer, a multifactorial disease, represents one of the leading causes of cancer-related morbidity and mortality in women. This study set out to elucidate the underlying mechanism by which lncRNA UCA1 affects the m6A modification of miR-375 by mediating the DNA methylation of METTL14 and then altering SOX12 expression in breast cancer. First, the expression patterns of lncRNA UCA1, miR-375, and apoptosis-related factors were quantitated by means of RT-qPCR and western blot analysis. In addition, the proliferation, invasion, and apoptosis of cells were detected using CCK-8, Transwell, and flow cytometry, respectively. RIP was performed to further uncover the interaction of lncRNA UCA1 and DNA methyltransferases, and MSP was employed for METTL14 promoter region methylation. The DNA methyltransferase enrichment in the METTL14 promoter region was measured by ChIP. The targeting relationship between miR-375 and SOX12 was confirmed by bioinformatics analysis and dual-luciferase report assay. Lastly, the aforementioned mechanism was also verified using tumor xenograft in vivo. It was found the elevated lncRNA UCA1 expression levels serve as a risk factor of poor prognosis in breast cancer. Meanwhile, silencing lncRNA UCA1 could inhibit the proliferation and invasion, but promote apoptosis of breast cancer cells by reducing the DNA methylation of METTL14 and augmenting its expression. Furthermore, METTL14 was observed to mediate the low miR-375 expression through m6A modification, leading to increased SOX12 expression levels in breast cancer. Altogether, findings obtained in our study indicated that silencing lncRNA UCA1 curbed the progression of breast cancer through the METTL14-miR-375-SOX12 axis.

DOI: https://doi.org/10.1038/s41417-021-00390-w
Front Med (Lausanne). 2021 ;8 757432

Comprehensive Analysis of N6-methyladenosine Modification Patterns Associated With Multiomic Characteristics of Bladder Cancer.

Jingchao Liu, Jianlong Wang, Meng Wu, Wei Zhang, Lingfeng Meng, Jiawen Wang, Zhengtong Lv, Haoran Xia, Yaoguang Zhang, Jianye Wang.

  Purpose: To comprehensively analyze N6-methyladenosine modification patterns in bladder tumors and to further systematically explore the inherent relationships between these modification patterns and multiomic tumor characteristics. Materials and Methods: A total of 901 bladder tumor samples, including 405 samples from TCGA database, 188 samples from GSE13507 and 308 samples from GSE32894, were included in this systematic analysis. The N6-methyladenosine modification patterns were identified utilizing unsupervised clustering analysis. To quantify N6-methyladenosine modification patterns, the m6Ascore of individual sample was developed using principal component analysis algorithms. Relationships among immune infiltration, tumor mutation burden, various clinical characteristics, molecular subtypes, and the m6Ascore were systematically analyzed. The guiding value of m6Ascore in immunotherapy was further validated in an external trial cohort. Genomics of Drug Sensitivity in Cancer expression references were also utilized to perform drug sensitivity analysis for patients with distinct m6A modification patterns. Results: We determined three different N6-methyladenosine modification patterns for 901 bladder tumors. The quantitative m6Ascore of individual sample derived from N6-methyladenosine modification patterns could play a significant role in predicting overall survival, immune cell infiltration, and classic oncogene mutations. A low m6Ascore combined with high tumor mutation burden indicated better survival outcomes (p < 0.001). A higher m6Ascore also indicated a higher grade, higher T and N stage, elder ages, higher death rate, and higher PD1/PDL1/CTLA4 expressions (p < 0.01). The Basal type tended to exhibit significantly higher m6Ascores than the Luminal and Neuronal subtypes. External immunotherapy cohorts demonstrated that no difference in therapeutic effects was noted between the high and low m6Ascore groups when anti-PD1 immunotherapy was exclusively administered. When anti-PD1 and anti-CTLA4 immunotherapy were simultaneously administered, the high m6Ascore group had a significantly better prognosis than the low m6Ascore group (p < 0.001). High m6A groups were potentially sensitive to various medical treatments including Bleomycin, Bortezomib, Cisplatin, Cyclopamine, Dasatinib, Docetaxe, Rapamycin, and Vinblastine in this study. Conclusions: This study systematically revealed the important roles of m6A methylation modification patterns in bladder tumors. Detailed quantification of m6A modification patterns could improve our understanding of the bladder tumor microenvironments and could provide guidance for future immunotherapy strategies.

Keywords:  N6-methyladenosine; bladder tumor; immunotherapy; m6A; tumor mutation burden

DOI:  https://doi.org/10.3389/fmed.2021.757432
Genes Dis. 2022 Jan;9(1): 268-274

Mettl5 mediated 18S rRNA N6-methyladenosine (m6A) modification controls stem cell fate determination and neural function.

Lu Wang, Yu Liang, Rongzhi Lin, Qiuchan Xiong, Peng Yu, Jieyi Ma, Maosheng Cheng, Hui Han, Xiaochen Wang, Ganping Wang, Fengyin Liang, Zhong Pei, Demeng Chen, Quan Yuan, Yi-Zhou Jiang, Shuibin Lin.

  Ribosome RNA (rRNA) accounts for more than 80% of the cell's total RNA, while the physiological functions of rRNA modifications are poorly understood. Mutations of 18S rRNA m6A methyltransferase METTL5 cause intellectual disability, microcephaly, and facial dysmorphisms in patients, however, little is known about the underlying mechanisms. In this study, we identified METTL5 protein complex and revealed that METTL5 mainly interacts with RNA binding proteins and ribosome proteins. Functionally, we found that Mettl5 knockout in mESCs leads to the abnormal craniofacial and nervous development. Moreover, using Mettl5 knockout mouse model, we further demonstrated that Mettl5 knockout mice exhibit intellectual disability, recapitulating the human phenotype. Mechanistically, we found that Mettl5 maintains brain function and intelligence by regulating the myelination process. Our study uncovered the causal correlation between mis-regulated 18S rRNA m6A modification and neural function defects, supporting the important physiological functions of rRNA modifications in human diseases.

Keywords:  18S rRNA; Intellectual disability; METTL5; N6-methyladenosine (m6A); Neural development

DOI:  https://doi.org/10.1016/j.gendis.2020.07.004
Int J Oncol. 2022 Feb;pii: 14. [Epub ahead of print]60(2):

N6‑methyladenosine upregulates miR‑181d‑5p in exosomes derived from cancer‑associated fibroblasts to inhibit 5‑FU sensitivity by targeting NCALD in colorectal cancer.

Shengli Pan, Yingying Deng, Jun Fu, Yuhao Zhang, Zhijin Zhang, Xianju Qin.

  Resistance to 5‑Fluorouracil (5‑FU) is a frequent occurrence in patients with colorectal cancer (CRC). MicroRNAs (miRNAs) from cancer‑associated fibroblasts (CAFs)‑secreted exosomes have been associated with 5‑FU sensitivity. The potential molecular mechanism of CAFs‑exosomal miRNAs in CRC remains unclear. The aim of the present study was to elucidate the role of exosomal miRNAs in 5‑FU sensitivity in CRC. Exosomes derived from CAFs were extracted. Exosomal miR‑181d‑5p was identified as a miRNA associated with 5‑FU sensitivity. The putative function of exosomal miR‑181d‑5p was evaluated by ethynyl‑2‑deoxyuridine staining, flow cytometry, RNA immunoprecipitation, luciferase reporter assay, tumor xenograft formation, reverse transcription‑quantitative PCR and western blot analysis. Modification of miR‑181d‑5p by the RNA N6‑methyladenosine (m6A) methyltransferase like (METTL)3 was examined by m6A methylation analysis. The results indicated that m6A modification and METTL3 expression were upregulated in CRC patients. METTL3‑dependent m6A methylation promoted the miR‑181b‑5p process by DiGeorge Syndrome Critical Region 8 (DGCR8) in CAFs. CAFs‑derived exosomes inhibited 5‑FU sensitivity in CRC cells through the METTL3/miR‑181d‑5p axis. A mechanistic study revealed that miR‑181d‑5p directly targeted neurocalcin δ (NCALD) to inhibit the 5‑FU sensitivity of CRC cells. Patients with higher NCALD levels exhibited a higher survival rate. Taken together, METTL3‑dependent m6A methylation was upregulated in CRC to promote the processing of miR‑181d‑5p by DGCR8. This led to increased miR‑181d‑5p expression, which inhibited the 5‑FU sensitivity of CRC cells by targeting NCALD. The results of the present study provided novel insight into exosomal microRNAs in 5‑FU sensitivity in CRC cells. Furthermore, exosomal miR‑181d‑5p may represent a potential prognostic marker for CRC.

Keywords:  cancer‑associated fibroblast; chemosensitivity; colorectal cancer; exosome; microRNA

DOI:  https://doi.org/10.3892/ijo.2022.5304
Front Cell Dev Biol. 2021 ;9 762853

Mettl14 Attenuates Cardiac Ischemia/Reperfusion Injury by Regulating Wnt1/β-Catenin Signaling Pathway.

Ping Pang, Zhezhe Qu, Shuting Yu, Xiaochen Pang, Xin Li, Yuelin Gao, Kuiwu Liu, Qian Liu, Xiuzhu Wang, Yu Bian, Yingqi Liu, Yingqiong Jia, Zhiyong Sun, Hanif Khan, Zhongting Mei, Xiaoqian Bi, Changhao Wang, Xinda Yin, Zhimin Du, Weijie Du.

  N6-methyladenosine (m6A) methylation in RNA is a dynamic and reversible modification regulated by methyltransferases and demethylases, which has been reported to participate in many pathological processes of various diseases, including cardiac disorders. This study was designed to investigate an m6A writer Mettl14 on cardiac ischemia-reperfusion (I/R) injury and uncover the underlying mechanism. The m6A and Mettl14 protein levels were increased in I/R hearts and neonatal mouse cardiomyocytes upon oxidative stress. Mettl14 knockout (Mettl14+/-) mice showed pronounced increases in cardiac infarct size and LDH release and aggravation in cardiac dysfunction post-I/R. Conversely, adenovirus-mediated overexpression of Mettl14 markedly reduced infarct size and apoptosis and improved cardiac function during I/R injury. Silencing of Mettl14 alone significantly caused a decrease in cell viability and an increase in LDH release and further exacerbated these effects in the presence of H2O2, while overexpression of Mettl14 ameliorated cardiomyocyte injury in vitro. Mettl14 resulted in enhanced levels of Wnt1 m6A modification and Wnt1 protein but not its transcript level. Furthermore, Mettl14 overexpression blocked I/R-induced downregulation of Wnt1 and β-catenin proteins, whereas Mettl14+/- hearts exhibited the opposite results. Knockdown of Wnt1 abrogated Mettl14-mediated upregulation of β-catenin and protection against injury upon H2O2. Our study demonstrates that Mettl14 attenuates cardiac I/R injury by activating Wnt/β-catenin in an m6A-dependent manner, providing a novel therapeutic target for ischemic heart disease.

Keywords:  Mettl14; Wnt/β-catenin; cardiomyocyte; ischemia–reperfusion injury; m6A modification

DOI:  https://doi.org/10.3389/fcell.2021.762853
Plants (Basel). 2021 Dec 30. pii: 103. [Epub ahead of print]11(1):

Profiling of N6-Methyladenosine (m6A) Modification Landscape in Response to Drought Stress in Apple (Malus prunifolia (Willd.) Borkh).

Xiushan Mao, Nan Hou, Zhenzhong Liu, Jieqiang He.

  Drought stress is a significant environmental factor limiting crop growth worldwide. Malus prunifolia is an important apple species endemic to China and is used for apple cultivars and rootstocks with great drought tolerance. N6-methyladenosine (m6A) is a common epigenetic modification on messenger RNAs (mRNAs) in eukaryotes which is critical for various biological processes. However, there are no reports on m6A methylation in apple response to drought stress. Here, we assessed the m6A landscape of M. prunifolia seedlings in response to drought and analyzed the association between m6A modification and transcript expression. In total, we found 19,783 and 19,609 significant m6A peaks in the control and drought treatment groups, respectively, and discovered a UGUAH (H: A/U/C) motif. In M. prunifolia, under both control and drought conditions, peaks were highly enriched in the 3' untranslated region (UTR) and coding sequence (CDS). Among 4204 significant differential m6A peaks in drought-treated M. prunifolia compared to control-treated M. prunifolia, 4158 genes with m6A modification were identified. Interestingly, a large number of hypermethylated peaks (4069) were stimulated by drought treatment compared to hypomethylation. Among the hypermethylated peak-related genes, 972 and 1238 differentially expressed genes (DEGs) were up- and down-regulated in response to drought, respectively. Gene ontology (GO) analyses of differential m6A-modified genes revealed that GO slims related to RNA processing, epigenetic regulation, and stress tolerance were significantly enriched. The m6A modification landscape depicted in this study sheds light on the epigenetic regulation of M. prunifolia in response to drought stress and indicates new directions for the breeding of drought-tolerant apple trees.

Keywords:  apple; drought stress; epitranscriptome; gene expression; m6A methylation

DOI:  https://doi.org/10.3390/plants11010103
Front Genet. 2021 ;12 771853

Comprehensive Analyses of the Expression, Genetic Alteration, Prognosis Significance, and Interaction Networks of m6A Regulators Across Human Cancers.

Xiujuan Shi, Jieping Zhang, Yuxiong Jiang, Chen Zhang, Xiaoli Luo, Jiawen Wu, Jue Li.

  Accumulating lines of evidence indicate that the deregulation of m6A is involved in various cancer types. The m6A RNA methylation is modulated by m6A methyltransferases, demethylases, and reader proteins. Although the aberrant expression of m6A RNA methylation contributes to the development and progression of multiple cancer types, the roles of m6A regulators across numerous types of cancers remain largely unknown. Here, we comprehensively investigated the expression, genetic alteration, and prognosis significance of 20 commonly studied m6A regulators across diverse cancer types using TCGA datasets via bioinformatic analyses. The results revealed that the m6A regulators exhibited widespread dysregulation, genetic alteration, and the modulation of oncogenic pathways across TCGA cancer types. In addition, most of the m6A regulators were closely relevant with significant prognosis in many cancer types. Furthermore, we also constructed the protein-protein interacting network of the 20 m6A regulators, and a more complex interacting regulatory network including m6A regulators and their corresponding interacting factors. Besides, the networks between m6A regulators and their upstream regulators such as miRNAs or transcriptional factors were further constructed in this study. Finally, the possible chemicals targeting each m6A regulator were obtained by bioinformatics analysis and the m6A regulators-potential drugs network was further constructed. Taken together, the comprehensive analyses of m6A regulators might provide novel insights into the m6A regulators' roles across cancer types and shed light on their potential molecular mechanisms as well as help develop new therapy approaches for cancers.

Keywords:  TCGA; bioinformatics; cancer; comprehensive analyses; m6A methylation

DOI:  https://doi.org/10.3389/fgene.2021.771853
Nat Commun. 2022 Jan 10. 13(1): 168

The m6A methyltransferase METTL3 regulates muscle maintenance and growth in mice.

Jennifer M Petrosino, Scott A Hinger, Volha A Golubeva, Juan M Barajas, Lisa E Dorn, Chitra C Iyer, Hui-Lung Sun, W David Arnold, Chuan He, Federica Accornero.

Skeletal muscle serves fundamental roles in organismal health. Gene expression fluctuations are critical for muscle homeostasis and the response to environmental insults. Yet, little is known about post-transcriptional mechanisms regulating such fluctuations while impacting muscle proteome. Here we report genome-wide analysis of mRNA methyladenosine (m6A) dynamics of skeletal muscle hypertrophic growth following overload-induced stress. We show that increases in METTL3 (the m6A enzyme), and concomitantly m6A, control skeletal muscle size during hypertrophy; exogenous delivery of METTL3 induces skeletal muscle growth, even without external triggers. We also show that METTL3 represses activin type 2 A receptors (ACVR2A) synthesis, blunting activation of anti-hypertrophic signaling. Notably, myofiber-specific conditional genetic deletion of METTL3 caused spontaneous muscle wasting over time and abrogated overload-induced hypertrophy; a phenotype reverted by co-administration of a myostatin inhibitor. These studies identify a previously unrecognized post-transcriptional mechanism promoting the hypertrophic response of skeletal muscle via control of myostatin signaling.

DOI: https://doi.org/10.1038/s41467-021-27848-7
Cell Death Discov. 2022 Jan 10. 8(1): 15

METTL14 promotes apoptosis of spinal cord neurons by inducing EEF1A2 m6A methylation in spinal cord injury.

Gang Gao, Yufen Duan, Feng Chang, Ting Zhang, Xinhu Huang, Chen Yu.

Spinal cord injury (SCI) is a devastating traumatic condition. METTL14-mediated m6A modification is associated with SCI. This study was intended to investigate the functional mechanism of RNA methyltransferase METTL14 in spinal cord neuron apoptosis during SCI. The SCI rat model was established, followed by evaluation of pathological conditions, apoptosis, and viability of spinal cord neurons. The neuronal function of primary cultured spinal motoneurons of rats was assessed after hypoxia/reoxygenation treatment. Expressions of EEF1A2, Akt/mTOR pathway-related proteins, inflammatory cytokines, and apoptosis-related proteins were detected. EEF1A2 was weakly expressed and Akt/mTOR pathway was inhibited in SCI rat models. Hypoxia/Reoxygenation decreased the viability of spinal cord neurons, promoted LDH release and neuronal apoptosis. EEF1A2 overexpression promoted the viability of spinal cord neurons, inhibited neuronal apoptosis, and decreased inflammatory cytokine levels. Silencing METTL14 inhibited m6A modification of EEF1A2 and increased EEF1A2 expression while METTL14 overexpression showed reverse results. EEF1A2 overexpression promoted viability and inhibited apoptosis of spinal cord neurons and inflammation by activating the Akt/mTOR pathway. In conclusion, silencing METTL14 repressed apoptosis of spinal cord neurons and attenuated SCI by inhibiting m6A modification of EEF1A2 and activating the Akt/mTOR pathway.

DOI: https://doi.org/10.1038/s41420-021-00808-2
Sci Rep. 2022 Jan 12. 12(1): 579

The prognostic value of m6A-related LncRNAs in patients with HNSCC: bioinformatics analysis of TCGA database.

Liu-Qing Zhou, Jin-Xiong Shen, Jie-Yu Zhou, Yao Hu, Hong-Jun Xiao.

N6-methyladenosine (m6A) modifications play an essential role in tumorigenesis. These modifications modulate RNAs, including mRNAs and lncRNAs. However, the prognostic role of m6A-related lncRNAs in head and neck squamous cell carcinoma (HNSCC) is poorly understood. Based on LASSO Cox regression, enrichment analysis, univariate and multivariate Cox regression analysis, a prognostic risk model, and consensus clustering analysis, we analyzed 12 m6A-related lncRNAs in HNSCC sample data from The Cancer Genome Atlas (TCGA) database. We found 12 m6A-related lncRNAs in the training cohort and validated them in all cohorts by Kaplan-Meier and Cox regression analyses, revealing their independent prognostic value in HNSCC. Moreover, ROC analysis was conducted, confirming the strong predictive ability of this signature for HNSCC survival. GSEA and detailed immune infiltration analyses revealed specific pathways associated with m6A-related lncRNAs. In this study, a novel risk model including twelve genes (SAP30L-AS1, AC022098.1, LINC01475, AC090587.2, AC008115.3, AC015911.3, AL122035.2, AC010226.1, AL513190.1, ZNF32-AS1, AL035587.1 and AL031716.1) was built. It could accurately predict HNSCC outcomes and could provide new therapeutic targets for HNSCC patients.

DOI: https://doi.org/10.1038/s41598-021-04591-z
Front Oncol. 2021 ;11 760892

m6A Regulator Expression Segregates Meningiomas Into Biologically Distinct Subtypes.

Jiawei Chen, Shuchen Sun, Leihao Ren, Lingyang Hua, Daijun Wang, Qing Xie, Hans-Georg Wirsching, Jiaojiao Deng, Michael Weller, Ye Gong.

   Background: Meningiomas are the most common primary intracranial tumors in adults. According to the 2021 World Health Organization (WHO) classification of central nervous system tumors, approximately 80% of meningiomas are WHO grade 1, that is, histopathologically benign, whereas about 20% are WHO grade 2 or grade 3, showing signs of atypia or malignancy. The dysregulation of N6-methylation (m6A) regulators is associated with disorders of diverse critical biological processes in human cancer. This study aimed to explore whether m6A regulator expression was associated with meningioma molecular subtypes and immune infiltration.
Methods: We evaluated the m6A modification patterns of 160 meningioma samples based on 19 m6A regulators and correlated them with immune infiltration characteristics. Novel molecular subtypes were defined based on prognostic hub gene expression.
Results: Two meningioma clusters were identified based on the expression of 19 m6A regulators. In cluster 1, 607 differentially expressed genes (DEGs) were upregulated and 519 were downregulated. A total of 1,126 DEGs comprised three gene expression modules characterized by turquoise, blue, and gray. Functional annotation suggested that the turquoise module was involved in Wnt-related and other important cancer-related pathways. We identified 32 hub genes in this module by constructing a protein-protein interaction network. The meningioma samples were divided into two molecular subtypes. EPN1, EXOSC4, H2AX, and MZT2B not only showed significant differences between meningioma molecular subtypes but also had the potential to be the marker genes of specific meningioma subtypes.
Conclusion: m6A regulator gene expression may be a novel prognostic marker in meningioma.

Keywords:  WGCNA; immune infiltration; m6A; meningioma; molecular subtype

DOI:  https://doi.org/10.3389/fonc.2021.760892
Front Cell Dev Biol. 2021 ;9 778582

Non-Coding RNA m6A Modification in Cancer: Mechanisms and Therapeutic Targets.

Da-Hong Chen, Ji-Gang Zhang, Chuan-Xing Wu, Qin Li.

  Recently, N6-methyl-adenosine (m6A) ribonucleic acid (RNA) modification, a critical and common internal RNA modification in higher eukaryotes, has generated considerable research interests. Extensive studies have revealed that non-coding RNA m6A modifications (e.g. microRNAs, long non-coding RNAs, and circular RNAs) are associated with tumorigenesis, metastasis, and other tumour characteristics; in addition, they are crucial molecular regulators of cancer progression. In this review, we discuss the relationship between non-coding RNA m6A modification and cancer progression from the perspective of various cancers. In particular, we focus on important mechanisms in tumour progression such as proliferation, apoptosis, invasion and metastasis, tumour angiogenesis. In addition, we introduce clinical applications to illustrate more vividly that non-coding RNA m6A modification has broad research prospects. With this review, we aim to summarize the latest insights and ideas into non-coding RNA m6A modification in cancer progression and targeted therapy, facilitating further research.

Keywords:  cancer therapy; epigenetics; m6A RNA modification; non-coding RNA; tumorigenesis mechanism

DOI:  https://doi.org/10.3389/fcell.2021.778582
ACS Appl Bio Mater. 2020 Dec 21. 3(12): 9002-9011

Modular DNA-Incorporated Aggregation-Induced Emission Probe for Sensitive Detection and Imaging of DNA Methyltransferase.

Jun Wu, Qinyu Hu, Qing Chen, Jun Dai, Xia Wu, Shixuan Wang, Xiaoding Lou, Fan Xia.

  DNA adenine methylation (Dam) MTase serves a very important epigenetic process that transfers a methyl group on an adenine residue including N6-methyladenosine (m6A). A variety of evidence have demonstrated that m6A methylation plays a significant role in modulating genes in human disease and development. Hence, a modular DNA-incorporated AIEgen probe (TPE-Py-DNA) was specifically developed for detection and imaging of Dam MTase. TPE-Py-DNA consisted of two modules: a "turn-on" fluorescent AIEgen (TPE-Py) and a DNA sequence (Alk-DNA) involved in specific recognition of the targeted strand. The TPE-Py-DNA probe was dispersed and almost nonfluorescent in an aqueous environment. On the contrary, the TPE-Py-DNA molecule was digested based on the target-recycling strategy in assistance with exonuclease III (Exo III) when Dam MTase was presented, finally releasing aggregated AIEgens to produce a remarkably increased fluorescence signal. Therefore, the detection limit toward Dam MTase was as low as 3.1 × 10-5 U mL-1, and the fluorescent signal could be used to detect Dam MTase activities in real samples and screen its inhibitors. More importantly, the Dam MTase expression was visualized in E. coli cells via CLMS imaging and confirmed in E. coli cell-bearing tissues. In this vein, our results demonstrated that the TPE-Py-DNA probe is a potent tool for the Dam MTase detection and imaging as well as offers an efficient biosensing platform for further investigation of disease pathway and carcinogenesis.

Keywords:  AIEgen; DNA methyltransferase; modular DNA-incorporated probe; real-time visualization; tissue diagnosis

DOI:  https://doi.org/10.1021/acsabm.0c01249
Cell Prolif. 2022 Jan 11. e13178

Alkbh1-mediated DNA N6-methyladenine modification regulates bone marrow mesenchymal stem cell fate during skeletal aging.

Guang-Ping Cai, Ya-Lin Liu, Li-Ping Luo, Ye Xiao, Tie-Jian Jiang, Jian Yuan, Min Wang.

   OBJECTIVES: DNA N6-methyladenine (N6-mA) demethylase Alkbh1 participates in regulating osteogenic differentiation of mesenchymal stem cell (MSCs) and vascular calcification. However, the role of Alkbh1 in bone metabolism remains unclear.
MATERIALS AND METHODS: Bone marrow mesenchymal stem cells (BMSCs)-specific Alkbh1 knockout mice were used to investigate the role of Alkbh1 in bone metabolism. Western blot, qRT-PCR, and immunofluorescent staining were used to evaluate the expression of Alkbh1 or optineurin (optn). Micro-CT, histomorphometric analysis, and calcein double-labeling assay were used to evaluate bone phenotypes. Cell staining and qRT-PCR were used to evaluate the osteogenic or adipogenic differentiation of BMSCs. Dot blotting was used to detect the level of N6-mA in genomic DNA. Chromatin immunoprecipitation (Chip) assays were used to identify critical targets of Alkbh1. Alkbh1 adeno-associated virus was used to overexpress Alkbh1 in aged mice.
RESULTS: Alkbh1 expression in BMSCs declined during aging. Knockout of Alkbh1 promoted adipogenic differentiation of BMSCs while inhibited osteogenic differentiation. BMSC-specific Alkbh1 knockout mice exhibited reduced bone mass and increased marrow adiposity. Mechanistically, we identified optn as the downstream target through which Alkbh1-mediated DNA m6A modification regulated BMSCs fate. Overexpression of Alkbh1 attenuated bone loss and marrow fat accumulation in aged mice.
CONCLUSIONS: Our findings demonstrated that Alkbh1 regulated BMSCs fate and bone-fat balance during skeletal aging and provided a potential target for the treatment of osteoporosis.

Keywords:  Alkbh1; BMSCs; aging; epigenetic; osteoporosis

DOI:  https://doi.org/10.1111/cpr.13178
Front Genet. 2021 ;12 774010

Potential Prognostic Value of a Seven m6A-Related LncRNAs Signature and the Correlative Immune Infiltration in Colon Adenocarcinoma.

Xiu-Kun Chai, Wei Qi, Chun-Yan Zou, Chen-Xi He, Miao Su, Dong-Qiang Zhao.

  Long non-coding RNAs (lncRNAs) and their N6-methyladenosine (m6A) modifications play an essential role in tumorigenesis and cancer progression. This study was designed to explore the value of m6A-related lncRNAs in prognosis and therapeutic applications of immune infiltration of colon adenocarcinoma (COAD). We downloaded the COAD gene expression and clinical data from The Cancer Genome Atlas project. By co-expression analysis, Lasso Cox regression analysis, and univariate and multivariate Cox regression, we constructed an independent prognostic signature of seven m6A-related lncRNAs. The prognostic lncRNAs were divided into two clusters by consistent clustering analysis, as well as into two groups of low-high risk based on the signature. Then we identified the relationship between the different groups with clinical features and immune cell infiltration. Cluster 2 had a higher risk score with a lower survival rate. The risk score was higher in groups with advanced clinical features, such as stage III-IV, N1-3, and M1. The expression of AC156455.1 was increased in tumor tissues and cluster 2, and the lncRNA ZEB1-AS1 was notably higher in the high-risk group. Five types of immune cells showed differences in two clusters, and most were upregulated in type 2. The expression of memory B cells was positively correlated with the risk score. The prognostic model was verified by the Gene Expression Omnibus (GEO) dataset. Besides, we found that the expression of these seven lncRNAs in tumor tissues was significantly higher than that in normal tissues, which verified the feasibility of the model. Thus, the signature of seven m6A-related lncRNAs can independently predict the prognosis of COAD. This signature is also closely associated with immune cell infiltration, and new therapeutic targets can be explored from this field.

Keywords:  COAD; bioinformatics analysis; immune cell infiltration; lncRNA; m6A

DOI:  https://doi.org/10.3389/fgene.2021.774010
Mol Biol Rep. 2022 Jan 10.

Demethylase FTO promotes mechanical stress induced osteogenic differentiation of BMSCs with up-regulation of HIF-1α.

Renhao Sun, Chunxi Zhang, Yicong Liu, Zhenggang Chen, Wen Liu, Fang Yang, Fei Zeng, Qingyuan Guo.

   BACKGROUND: In orthodontics, mechanical stress plays an important role in the process of bone remodeling. Mechanical stress has an effect on osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs). However, the mechanism remains to be studied. The aim of this study is to investigate the effects of demethyltransferase fat mass and obesity-associated (FTO) on osteogenic differentiation of BMSCs under mechanical stress condition.
METHODS AND RESULTS: The rat BMSCs were cultured in vitro, followed by flow cytometry to identify the cell surface antigens. Osteogenic differentiation of BMSCs was induced by mechanical stress by using the flexcell tension system for 6 h every day and 3 days in total. BMSCs were transfected by using plasmid for FTO knockdown. The expression level of FTO, hypoxia-inducible factor (HIF)-1α, runt-related transcription factor 2 (RUNX2), bone morphogenetic proteins (BMPs) and alkaline phosphatase (ALP) were measured by real-time qPCR, western blotting. ALP activity were determined by ALP staining assays. The expression of FTO and HIF-1α in BMSCs with mechanical stress were significantly higher than BMSCs without mechanical stress, also, the expression of osteogenic differentiation markers were higher in BMSCs with mechanical stress. Knockdown of FTO decreased expression of osteogenic differentiation marker and ALP activity in stretched BMSCs. In addition, the expression of HIF-1α was decreased after knocking down FTO.
CONCLUSIONS: FTO promotes the expression of HIF-1α and osteogenic differentiation under the condition of mechanical stress. This finding may facilitate the clinical application of orthodontics and the mechanism research of mechanical stress-induced osteogenesis.

Keywords:  Bone marrow-derived mesenchymal stem cells; Hypoxia-inducible factor; Mechanical stress; N6-methyladenosine; Osteogenic differentiation

DOI:  https://doi.org/10.1007/s11033-021-07089-z
Genes Dis. 2022 Jan;9(1): 51-61

Critical roles of FTO-mediated mRNA m6A demethylation in regulating adipogenesis and lipid metabolism: Implications in lipid metabolic disorders.

Zhou Yang, Guang-Li Yu, Xiao Zhu, Tian-Hong Peng, Yun-Cheng Lv.

  The goal this review is to clarify the effects of the fat mass and obesity-associated protein (FTO) in lipid metabolism regulation and related underlying mechanisms through the FTO-mediated demethylation of m6A modification. FTO catalyzes the demethylation of m6A to alter the processing, maturation and translation of the mRNAs of lipid-related genes. FTO overexpression in the liver promotes lipogenesis and lipid droplet (LD) enlargement and suppresses CPT-1-mediated fatty acid oxidation via the SREBP1c pathway, promoting excessive lipid storage and nonalcoholic fatty liver diseases (NAFLD). FTO enhances preadipocyte differentiation through the C/EBPβ pathway, and facilitates adipogenesis and fat deposition by altering the alternative splicing of RUNX1T1, the expression of PPARγ and ANGPTL4, and the phosphorylation of PLIN1, whereas it inhibits lipolysis by inhibiting IRX3 expression and the leptin pathway, causing the occurrence and development of obesity. Suppression of the PPARβ/δ and AMPK pathways by FTO-mediated m6A demethylation damages lipid utilization in skeletal muscles, leading to the occurrence of diabetic hyperlipidemia. m6A demethylation by FTO inhibits macrophage lipid influx by downregulating PPARγ protein expression and accelerates cholesterol efflux by phosphorylating AMPK, thereby impeding foam cell formation and atherosclerosis development. In summary, FTO-mediated m6A demethylation modulates the expression of lipid-related genes to regulate lipid metabolism and lipid disorder diseases.

Keywords:  Adipose tissue; FTO; Lipid disorder diseases; Lipid metabolism; Liver; Skeletal muscle

DOI:  https://doi.org/10.1016/j.gendis.2021.01.005