bims-rimeca 2021-08-29 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–08–29
fiveteen papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

The m6A methyltransferase METTL3 controls epithelial-mesenchymal transition, migration and invasion of breast cancer through the MALAT1/miR-26b/HMGA2 axis.
Caspases Switch off the m6A RNA Modification Pathway to Foster the Replication of a Ubiquitous Human Tumor Virus.
METTL14 facilitates global genome repair and suppresses skin tumorigenesis.
Landscape of Prognostic m6A RNA Methylation Regulators in Hepatocellular Carcinoma to Aid Immunotherapy.
METTL3-induced UCK2 m6A hypermethylation promotes melanoma cancer cell metastasis via the WNT/β-catenin pathway.
The functional roles, cross-talk and clinical implications of m6A modification and circRNA in hepatocellular carcinoma.
ALKBH5 promotes cadmium-induced transformation of human bronchial epithelial cells by regulating PTEN expression in an m6A-dependent manner.
m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer.
Loss of m6A methyltransferase METTL3 promotes heart regeneration and repair after myocardial injury.
A Risk Signature Consisting of Eight m6A Methylation Regulators Predicts the Prognosis of Glioma.
N6-Methyladenosine-Regulated mRNAs: Potential Prognostic Biomarkers for Patients With Lung Adenocarcinoma.
Analysis of m6A-Related lncRNAs for Prognosis Value and Response to Immune Checkpoint Inhibitors Therapy in Hepatocellular Carcinoma.
Effects of RNA methylation N6-methyladenosine regulators on malignant progression and prognosis of melanoma.
[Establishment and validation of prognosis predictive model using m6A RNA methylation regulators in children acute myeloid leukemia].
Paraquat-induced oxidative stress regulates N6-methyladenosine (m6A) modification of circular RNAs.

Cancer Cell Int. 2021 Aug 21. 21(1): 441

The m6A methyltransferase METTL3 controls epithelial-mesenchymal transition, migration and invasion of breast cancer through the MALAT1/miR-26b/HMGA2 axis.

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

   BACKGROUND: Previous studies have revealed the key functions of N6-methyladenosine (m6A) modification in breast cancer (BC). MALAT1 as a highly m6A modified lncRNA associated with cancer development and metastasis, but the functional relevance of m6A methyltransferase and MALAT1 in BC is still unknown. Here, our study investigated the effects of the novel m6A methyltransferase METTL3 on epithelial-mesenchymal transition (EMT) in BC via the MALAT1/miR-26b/HMGA2 axis.
METHODS: Firstly, we collected clinical BC samples and cultured BC cells, and detected mRNA and protein levels in the human samples and human cell lines by RT-qPCR and Western blot, respectively. Then, the binding of MALAT1 and miR-26b and the targeting relationship between miR-26b and HMGA2 were examined by dual-luciferase assay. Moreover, the binding of MALAT1 and miR-26b was tested by RNA pull down and RNA immunoprecipitation (RIP) assays. Methylated-RNA immunoprecipitation (Me-RIP) was used to detect the m6A modification level of MALAT1. The interaction of METTL3 and MALAT1 was detected by photoactivatable ribonucleoside-crosslinking immunoprecipitation (PAR-CLIP). Finally, effects on invasion and migration were detected by Transwell.
RESULTS: In BC, the level of miR-26b was consistently low, while the levels of METTL3, MALAT1 and HMGA2 were high. Further experiments showed that METTL3 up-regulated MALAT1 expression by modulating the m6A modification of MALAT1, and that MALAT1 could promote the expression of HMGA2 by sponging miR-26b. In BC cells, we found that silencing METTL3 could inhibit EMT and tumor cell invasion by suppressing MALAT1. Furthermore, MALAT1 mediated miR-26b to target HMGA2 and promote EMT, migration, and invasion. In summary, METTL3 promoted tumorigenesis of BC via the MALAT1/miR-26b/HMGA2 axis.
CONCLUSIONS: Silencing METTL3 down-regulate MALAT1 and HMGA2 by sponging miR-26b, and finally inhibit EMT, migration and invasion in BC, providing a theoretical basis for clinical treatment of BC.

Keywords:  Breast cancer; Epithelial-mesenchymal transition; MALAT1; METTL3; MiR-26b

DOI:  https://doi.org/10.1186/s12935-021-02113-5
mBio. 2021 Aug 24. e0170621

Caspases Switch off the m6A RNA Modification Pathway to Foster the Replication of a Ubiquitous Human Tumor Virus.

Kun Zhang, Yucheng Zhang, Yunash Maharjan, Febri Gunawan Sugiokto, Jun Wan, Renfeng Li.

  The methylation of RNA at the N6 position of adenosine (m6A) orchestrates multiple biological processes to control development, differentiation, and cell cycle, as well as various aspects of the virus life cycle. How the m6A RNA modification pathway is regulated to finely tune these processes remains poorly understood. Here, we discovered the m6A reader YTHDF2 as a caspase substrate via proteome-wide prediction, followed by in vitro and in vivo validations. We further demonstrated that cleavage-resistant YTHDF2 blocks, while cleavage-mimicking YTHDF2 fragments promote, the replication of a common human oncogenic virus, Epstein-Barr virus (EBV). Intriguingly, our study revealed a feedback regulation between YTHDF2 and caspase-8 via m6A modification of CASP8 mRNA and YTHDF2 cleavage during EBV replication. Further, we discovered that caspases cleave multiple components within the m6A RNA modification pathway to benefit EBV replication. Our study establishes that caspase disarming of the m6A RNA modification machinery fosters EBV replication. IMPORTANCE The discovery of an N6-methyladenosine (m6A) RNA modification pathway has fundamentally altered our understanding of the central dogma of molecular biology. This pathway is controlled by methyltransferases (writers), demethylases (erasers), and specific m6A binding proteins (readers). Emerging studies have linked the m6A RNA modification pathway to the life cycle of various viruses. However, very little is known regarding how this pathway is subverted to benefit viral replication. In this study, we established an unexpected linkage between cellular caspases and the m6A modification pathway, which is critical to drive the reactivation of a common tumor virus, Epstein-Barr virus (EBV).

Keywords:  Epstein-Barr virus; METTL14; METTL3; WTAP; YTHDF2; caspase cleavage; lytic replication; m6A RNA modification; reactivation; restriction factor

DOI:  https://doi.org/10.1128/mBio.01706-21
Proc Natl Acad Sci U S A. 2021 Aug 31. pii: e2025948118. [Epub ahead of print]118(35):

METTL14 facilitates global genome repair and suppresses skin tumorigenesis.

Zizhao Yang, Seungwon Yang, Yan-Hong Cui, Jiangbo Wei, Palak Shah, Gayoung Park, Xiaolong Cui, Chuan He, Yu-Ying He.

  Global genome repair (GGR), a subpathway of nucleotide excision repair, corrects bulky helix-distorting DNA lesions across the whole genome and is essential for preventing mutagenesis and skin cancer. Here, we show that METTL14 (methyltransferase-like 14), a critical component of the N6-methyladenosine (m6A) RNA methyltransferase complex, promotes GGR through regulating m6A mRNA methylation-mediated DDB2 translation and suppresses ultraviolet B (UVB) radiation-induced skin tumorigenesis. UVB irradiation down-regulates METTL14 protein through NBR1-dependent selective autophagy. METTL14 knockdown decreases GGR and DDB2 abundance. Conversely, overexpression of wild-type METTL14 but not its enzymatically inactive mutant increases GGR and DDB2 abundance. METTL14 knockdown decreases m6A methylation and translation of the DDB2 transcripts. Adding DDB2 reverses the GGR repair defect in METTL14 knockdown cells, indicating that METTL14 facilitates GGR through regulating DDB2 m6A methylation and translation. Similarly, knockdown of YTHDF1, an m6A reader promoting translation of m6A-modified transcripts, decreases DDB2 protein levels. Both METTL14 and YTHDF1 bind to the DDB2 transcript. In mice, skin-specific heterozygous METTL14 deletion increases UVB-induced skin tumorigenesis. Furthermore, METTL14 as well as DDB2 is down-regulated in human and mouse skin tumors and by chronic UVB irradiation in mouse skin, and METTL14 level is associated with the DDB2 level, suggesting a tumor-suppressive role of METTL14 in UVB-associated skin tumorigenesis in association with DDB2 regulation. Taken together, these findings demonstrate that METTL14 is a target for selective autophagy and acts as a critical epitranscriptomic mechanism to regulate GGR and suppress UVB-induced skin tumorigenesis.

Keywords:  METTL14; UVB; m6A RNA methylation; nucleotide excision repair; ultraviolet radiation

DOI:  https://doi.org/10.1073/pnas.2025948118
Front Cell Dev Biol. 2021 ;9 669145

Landscape of Prognostic m6A RNA Methylation Regulators in Hepatocellular Carcinoma to Aid Immunotherapy.

Qianhui Xu, Hao Xu, Rongshan Deng, Nanjun Li, Ruiqi Mu, Zhixuan Qi, Yunuo Shen, Zijie Wang, Jingchao Wen, Jiaxin Zhao, Di Weng, Wen Huang.

  Background: Hepatocellular carcinoma (HCC) is the sixth most common malignancy with a high mortality worldwide. N6-methyladenosine (m6A) may participate extensively in tumor progression. Methods: To reveal the landscape of tumor immune microenvironment (TIME), ESTIMATE analysis, ssGSEA algorithm, and the CIBERSORT method were used. Taking advantage of consensus clustering, two different HCC categories were screened. We analyzed the correlation of clustering results with TIME and immunotherapy. Then, we yielded a risk signature by systematical bioinformatics analyses. Immunophenoscore (IPS) was implemented to estimate the immunotherapeutic significance of risk signature. Results: The m6A-based clusters were significantly correlated with overall survival (OS), immune score, immunological signature, immune infiltrating, and ICB-associated genes. Risk signature possessed robust prognostic validity and significantly correlated with TIME context. IPS was employed as a surrogate of immunotherapeutic outcome, and patients with low-risk scores showed significantly higher immunophenoscores. Conclusion: Collectively, m6A-based clustering subtype and signature was a robust prognostic indicator and correlated with TIME and immunotherapy, providing novel insight into antitumor management and prognostic prediction in HCC.

Keywords:  The Cancer Genome Atlas; hepatocellular carcinoma; immune checkpoint blockade; m6A RNA methylation regulators; prognostic value; tumor immune microenvironment

DOI:  https://doi.org/10.3389/fcell.2021.669145
Ann Transl Med. 2021 Jul;9(14): 1155

METTL3-induced UCK2 m6A hypermethylation promotes melanoma cancer cell metastasis via the WNT/β-catenin pathway.

Hao Wu, Haochao Xu, Dongdong Jia, Tao Li, Liming Xia.

   Background: Melanoma is a highly aggressive, malignant skin tumor with a statistically high mortality rate. N6-methyladenosine (m6A) modification is involved in a variety of biological processes, including tumorigenesis. m6A modifications regulate the fate and functions of RNA, such as mRNA stability, nuclear processing, transport, localization, translation, primary microRNA (miRNA) processing, and RNA-protein interactions. Several members (including METTL3, METTL14, FTO, ALKBH5, and YTHDF2) are actively involved in a variety of human cancers. However, the basic mechanism of the involvement of uridine cytidine kinase 2 (UCK2) in melanoma metastasis has not been studied. UCK2 is upregulated in a variety of malignancies. However, the complex molecular mechanisms and therapeutic effects of UCK2 in melanoma remain unclear.
Methods: The expression of UCK2 was evaluated by qRT-PCR. The effects of UCK2 on the biological characteristics of PC cells were investigated on the basis of loss-of-function analyses. Immunoprecipitation-qPCR (MeRIP-qPCR) was performed to identify the m6A targeted effect of UCK2 in melanoma cancer.
Results: Based on the bioinformatics analysis in this study, up-regulation of UCK2 could be essential in melanoma cancer, and associated with poor survival. Furthermore, the m6A modification regulated by METTL3 led to UCK2 increased messenger RNA (mRNA) stability in melanoma cancer. Functional and mechanistic experiments indicated that UCK2 enhanced the metastasis of melanoma cancer cells through the WNT/β-catenin pathway.
Conclusion: In this study, we found that m6A-METTL3 axis induced abnormal UCK2 expression plays a role in melanoma metastasis by enhancing the Wnt/β-catenin pathway, which may provide new clues for melanoma metastasis. It also provides a potential target for the prevention and treatment of melanoma.

Keywords:  Uridine-cytidine kinase 2 (UCK2); database; m6A; melanoma cancer; metastasis

DOI:  https://doi.org/10.21037/atm-21-2906
Int J Biol Sci. 2021 ;17(12): 3059-3079

The functional roles, cross-talk and clinical implications of m6A modification and circRNA in hepatocellular carcinoma.

Sha Qin, Yitao Mao, Xue Chen, Juxiong Xiao, Yan Qin, Luqing Zhao.

  Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. HCC has high rates of death and recurrence, as well as very low survival rates. N6-methyladenosine (m6A) is the most abundant modification in eukaryotic RNAs, and circRNAs are a class of circular noncoding RNAs that are generated by back-splicing and they modulate multiple functions in a variety of cellular processes. Although the carcinogenesis of HCC is complex, emerging evidence has indicated that m6A modification and circRNA play vital roles in HCC development and progression. However, the underlying mechanisms governing HCC, their cross-talk, and clinical implications have not been fully elucidated. Therefore, in this paper, we elucidated the biological functions and molecular mechanisms of m6A modification in the carcinogenesis of HCC by illustrating three different regulatory factors ("writer", "eraser", and "reader") of the m6A modification process. Additionally, we dissected the functional roles of circRNAs in various malignant behaviors of HCC, thereby contributing to HCC initiation, progression and relapse. Furthermore, we demonstrated the cross-talk and interplay between m6A modification and circRNA by revealing the effects of the collaboration of circRNA and m6A modification on HCC progression. Finally, we proposed the clinical potential and implications of m6A modifiers and circRNAs as diagnostic biomarkers and therapeutic targets for HCC diagnosis, treatment and prognosis evaluation.

Keywords:  Biomarkers; Hepatocellular carcinoma (HCC); N6-methyladenosine (m6A) modification; Therapeutic targets; circRNA

DOI:  https://doi.org/10.7150/ijbs.62767
Ecotoxicol Environ Saf. 2021 Aug 23. pii: S0147-6513(21)00798-3. [Epub ahead of print]224 112686

ALKBH5 promotes cadmium-induced transformation of human bronchial epithelial cells by regulating PTEN expression in an m6A-dependent manner.

Luyao Li, Mei Zhou, Biyun Chen, Qin Wang, Shuya Pan, Yaxuan Hou, Jiamin Xia, Xue Zhou.

  Cadmium is a carcinogenic heavy metal that poses a severe threat to human beings. The underlying mechanism, however, remains elusive. N6-methyladenosine (m6A) is the most abundant post-transcriptional modification in mRNA that regulates RNA metabolism. Emerging evidence shows that m6A is involved in the pathogenesis of various cancers. In this study, human bronchial epithelial BEAS-2B cells were transformed by exposing to 2 μM of cadmium for 20 weeks to investigate the role of m6A in cadmium carcinogenesis. We found the level of m6A in mRNA was significantly decreased in cadmium-transformed BEAS-2B cells, and this change was regulated by m6A demethylase ALKBH5. ALKBH5 was significantly upregulated in the middle and late stages of cell transformation at week 8, 12, 16 and 20. Knockdown of ALKBH5 in cadmium-transformed cells alleviated cell proliferation, migration, invasion, and anchorage-independent growth, but co-transfection with ALKBH5 siRNA and PTEN siRNA restored the inhibitory effects of ALKBH5 knockdown on those transformation properties. ALKBH5 decreased the m6A level of PTEN mRNA, resulting in its instability and reduction of PTEN protein expression. These results indicate that ALKBH5-mediated demethylation m6A at PTEN mRNA is involved in cadmium-induced cell transformation. Our study provides a new perspective for the involvement of m6A modification in cadmium carcinogenesis.

Keywords:  ALKBH5; Cadmium; Cell transformation; M6A modification; PTEN

DOI:  https://doi.org/10.1016/j.ecoenv.2021.112686
Front Med (Lausanne). 2021 ;8 667543

m6A RNA Methylation Regulator YTHDF1 Correlated With Immune Microenvironment Predicts Clinical Outcomes and Therapeutic Efficacy in Breast Cancer.

Ying Hu, Qinwen Pan, Minghao Wang, Xiang Ai, Yuzhao Yan, Yuan Tian, Yuting Jing, Peng Tang, Jun Jiang.

  Objective: Increasing evidence highlights the roles of N6-methyladenosine (m6A) and its regulators in oncogenesis. Herein, this study observed the associations of m6A regulators with breast cancer. Methods: RNA-seq profiles of breast cancer were retrieved from the Cancer Genome Atlas (TCGA) database. The expression of m6A regulators was analyzed in tumor and normal tissues. Their expression correlations were analyzed by Spearson test. Overall survival (OS) analysis of these regulators was then presented. Gene set enrichment analysis (GSEA) was performed in high and low YTHDF1 expression groups. The correlations of YTHDF1 expression with immune cells and tumor mutation burden (TMB) were calculated in breast cancer samples. Somatic variation was assessed in high and low YTHDF1 expression groups. Results: Most of m6A regulators were abnormally expressed in breast cancer compared to normal tissues. At the mRNA levels, there were closely relationships between them. Among them, YTHDF1 up-regulation was significantly related to undesirable prognosis (p = 0.025). GSEA results showed that high YTHDF1 expression was associated with cancer-related pathways. Furthermore, YTHDF1 expression was significantly correlated with T cells CD4 memory activated, NK cells activated, monocytes, and macrophages. There were higher TMB scores in YTHDF1 up-regulation group than its down-regulation group. Missense mutation and non-sense mutation were the most frequent mutation types. Conclusion: Our findings suggested that dysregulated m6A regulator YTHDF1 was predictive of survival outcomes as well as response to immunotherapy of breast cancer, and were closely related to immune microenvironment.

Keywords:  N6-methyladenosine; breast cancer; immune microenvironment; immunotherapy; regulators; somatic mutation

DOI:  https://doi.org/10.3389/fmed.2021.667543
Pharmacol Res. 2021 Aug 21. pii: S1043-6618(21)00429-1. [Epub ahead of print] 105845

Loss of m6A methyltransferase METTL3 promotes heart regeneration and repair after myocardial injury.

Rui Gong, Xiuxiu Wang, Hanjing Li, Shenzhen Liu, Zuke Jiang, Yiming Zhao, Yang Yu, Zhenbo Han, Ying Yu, Chaorun Dong, Shuainan Li, Binbin Xu, Wenwen Zhang, Ning Wang, Xingda Li, Xinlu Gao, Fan Yang, Djibril Bamba, Wenya Ma, Yu Liu, Benzhi Cai.

   AIMS: N6-Methyladenosine (m6A) is the most commonly chemical modification of messenger RNAs (mRNAs) in eukaryotes, and has been involved in various diseases. However, the role of m6A modification in heart regeneration after injury remains unclear. The study was conducted to investigate whether targeting methyltransferase-like 3 (METTL3) could replenish the loss of cardiomyocytes and improve cardiac function after myocardial infarction (MI).
METHODS AND RESULTS: METTL3 knockout mouse line was generated. A series of functional experiments were carried out and the molecular mechanism was further explored. We identified that METL3, a methyltransferase of m6A methylation, is upregulated after birth in mice, which is exactly the opposite of the changes in cardiomyocytes (CMs) proliferation. Notably, METTL3 knockout mice or administration of METTL3 shRNA adenovirus exhibited that the pre-existing CMs cell cycle re-entered, infract size decreased and cardiac function improved after MI. Mechanically, the silence of METTL3 reduced primary miR-143 (pri-miR-143) purified by m6A, thereby inhibiting the cleavage of pri-miR-143 into mature miR-143-3p. Moreover, it was found that miR-143-3p, Yap and Ctnnd1 have targeting effects to regulate CMs proliferation.
CONCLUSION: METTL3-mediated m6A modification contributes to heart regeneration after MI via the METTL3-pri-miR-143-(miR-143)-Yap/Ctnnd1 axis. This study provides new insights into the significance of RNA m6A modification in heart regeneration.

Keywords:  Ctnnd1; Heart regeneration; METTL3; MiR-143; Yap; m(6)A

DOI:  https://doi.org/10.1016/j.phrs.2021.105845
Cell Mol Neurobiol. 2021 Aug 25.

A Risk Signature Consisting of Eight m6A Methylation Regulators Predicts the Prognosis of Glioma.

Sizhong Guan, Ye He, Yanna Su, Liping Zhou.

  Glioma progression seriously correlates to the epigenetic context. This study aims to identify glioma subtypes by clustering analysis of patients using the multi-omics data of N6-methyladenosine (m6A) methylation regulators and to construct a risk signature for investigating the role of m6A methylation regulators in the prognosis of glioma. Multi-omics data of glioma and normal control tissues were obtained through The Cancer Genome Atlas (TCGA) database. The clustering analysis of multi-omics data of patients was conducted using the R package iClusterPlus software. The risk model was constructed by univariate and multivariate Cox analysis, and the glioma expression data and related clinical data were obtained by Chinese Glioma Genome Atlas (CGGA) datasets to verify the risk model. By analyzing the glioma data in TCGA, we found that the risk signature could be constructed according to the eight genes with m6A methylation modification function, including ALKBH5, HNRNPA2B1, IGF2BP2, IGF2BP3, RBM15, WTAP, YTHDF1, and YTHDF2. Meanwhile, we found that IGF2BP2 and IGF2BP3 were highly expressed in glioma subtypes with high-risk scores and closely related to the prognosis of glioma patients. m6A methylation regulators, especially IGF2BP2 and IGF2BP3, play important roles in the malignant progression of glioma. The risk signature constructed by eight m6A methylation regulators can predict the prognosis of glioma. IGF2BP2 and IGF2BP3 may be the key regulatory factors of m6A methylation regulators involved in the occurrence and development of glioma, and can serve as molecular markers for the prognosis of glioma.

Keywords:  Cox regression analysis; Glioma; Multi-omics clustering; N6-methyladenosine; The cancer genome atlas

DOI:  https://doi.org/10.1007/s10571-021-01135-x
Front Cell Dev Biol. 2021 ;9 705962

N6-Methyladenosine-Regulated mRNAs: Potential Prognostic Biomarkers for Patients With Lung Adenocarcinoma.

Junjun Sun, Yili Ping, Jingjuan Huang, Bingjie Zeng, Ping Ji, Dong Li.

  Aberrant regulation of m6A mRNA modification can lead to changes in gene expression, thus contributing to tumorigenesis in several types of solid tumors. In this study, by integrating analyses of m6A methylation and mRNA expression, we identified 84 m6A-regulated mRNAs in lung adenocarcinoma (LUAD). Although the m6A methylation levels of total RNA in LUAD patient tumor tissue were reduced, the majority (75.2%) of m6A-regulated mRNAs were hypermethylated. The m6A-hypermethylated mRNAs were mainly enriched in terms related to transcription factor activity. We established a 10-m6A-regulated-mRNA signature score system through least absolute shrinkage and selection operator Cox regression analysis, with its predictive value validated by Kaplan-Meier curve and time-dependent receiver operating characteristic curves. RFXAP and KHDRBS2 from the signature also exhibited an independent prognostic value. The co-expression and interaction network analyses demonstrated the strong correlation between m6A regulators and the genes in the signature, further supporting the results of the m6A methylation modification patterns. These findings highlight the potential utility of integrating multi-omics data (m6A methylation level and mRNA expression) to accurately obtain potential prognostic biomarkers, which may provide important insights into developing novel and effective therapies for LUAD.

Keywords:  N6-methyladenosine; biomarkers; lung adenocarcinoma; multi-omics; prognostic signature

DOI:  https://doi.org/10.3389/fcell.2021.705962
Cancer Manag Res. 2021 ;13 6451-6471

Analysis of m6A-Related lncRNAs for Prognosis Value and Response to Immune Checkpoint Inhibitors Therapy in Hepatocellular Carcinoma.

Yi Wang, Na Li, Di Tian, Chang-Wu Zhou, You-Hua Wang, Chun Yang, Meng-Su Zeng.

   Introduction: N6-methyladenosine (m6A) modification and long non-coding RNAs (lncRNAs) play pivotal roles in the progression of hepatocellular carcinoma (HCC). However, how their interaction is involved in the prognostic value of HCC and immune checkpoint inhibitors (ICIs) therapy remains unclear.
Methods: The RNA sequencing and clinical data of HCC patients were collected from TCGA database. The prognostic m6A-related lncRNAs were screened out with Pearson correlation test, univariate Cox analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. Patients with HCC were classified into 2 subtypes by consensus clustering. Survival analyses were performed to assess the prognostic value of different clusters and risk models. Potential tumor correlated biological pathways correlated with different clusters were explored through gene set enrichment analysis. We also identified the relationship of the risk model and clusters with response to immune checkpoint inhibitors (ICIs) therapy and tumor microenvironment (TME). Furthermore, the prognostic value of the 9 m6A-related lncRNAs was validated in the external cohort. Finally, the role of SNHG4 was explored by silencing and overexpression of SNHG4 through conducting proliferation, migration and invasion experiments.
Results: Patients from 2 clusters and different risk groups based on m6A-related lncRNAs had significantly different clinicopathological characteristics and overall survival outcomes. Tumor-correlated biological pathways were found to be correlated with Cluster 2 through GSEA. Moreover, we found that patients from different clusters and risk groups expressed higher levels of immune checkpoint genes and had distinct TME and different responses for ICIs therapy. Prognostic value of this risk model was further confirmed in the external cohort. Finally, consistent with the discovery, SNHG4 played an oncogenic role in vitro.
Conclusion: Our study demonstrated that the 9 m6A-related lncRNA signature may serve as a novel predictor in the prognosis of HCC and optimize (ICIs) therapy. SNHG4 plays an oncogenic role in HCC.

Keywords:  N6-methyladenosine; hepatocellular carcinoma; immune checkpoints inhibitors therapy; long non-coding RNAs; prognosis

DOI:  https://doi.org/10.2147/CMAR.S322179
Cancer Cell Int. 2021 Aug 26. 21(1): 453

Effects of RNA methylation N6-methyladenosine regulators on malignant progression and prognosis of melanoma.

Jinfang Liu, Zijian Zhou, Ling Ma, Chujun Li, Yu Lin, Ting Yu, Ji-Fu Wei, Lingjun Zhu, Gang Yao.

   BACKGROUND: Melanoma is an extremely aggressive type of skin cancer and experiencing a expeditiously rising mortality in a current year. Exploring new potential prognostic biomarkers and therapeutic targets of melanoma are urgently needed. The ambition of this research was to identify genetic markers and assess prognostic performance of N6-methyladenosine (m6A) regulators in melanoma.
METHODS: Gene expression data and corresponding clinical informations of melanoma patients as well as sequence data of normal controls are collected from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Quantitative real-time PCR (qRT-PCR) analysis was carried out to detect the RNA expression of IGF2BP3 in A375 cell line, melanoma tissues, and normal tissues. Western blot, cell proliferation, and migration assays were performed to assess the ability of IGF2BP3 in A375 cell line.
RESULTS: Differently expressed m6A regulators between tumor samples and normal samples were analyzed. A three-gene prognostic signature including IGF2BP3, RBM15B, and METTL16 was constructed, and the risk score of this signature was identified to be an independent prognostic indicator for melanoma. In addition, IGF2BP3 was verified to promote melanoma cell proliferation and migration in vitro and associate with lymph node metastasis in clinical samples. Moreover, risk score and the expression of IGF2BP3 were positively associated with the infiltrating immune cells and these hub genes made excellent potential drug targets in melanoma.
CONCLUSION: We identified the genetic changes in m6A regulatory genes and constructed a three-gene risk signature with distinct prognostic value in melanoma. This research provided new insights into the epigenetic understanding of m6A regulators and novel therapeutic strategies in melanoma.

Keywords:  IGF2BP35; Melanoma1; Prognostic signature3; TCGA4; m6A RNA methylation2

DOI:  https://doi.org/10.1186/s12935-021-02163-9
Zhonghua Yu Fang Yi Xue Za Zhi. 2021 Aug 06. 55(8): 983-989

[Establishment and validation of prognosis predictive model using m6A RNA methylation regulators in children acute myeloid leukemia].

J R Xu, D H Yang, G F Long, H Sun, H B Chen.

Objective: To figure out the association between the expression of m6A RNA methylation regulators and the prognosis of children AML, and provide genetic markers for monitoring the progression and recurrence of AML. Methods: Twenty two m6A RNA methylation regulators were firstly analyzed using the data from Therapeutically Applicable Research To Generate Effective Treatments(TARGET) database and The Genotype-Tissue Expression(GTEx) database, Wilcoxon rank test was performed to analyze the differentially expression of m6A RNA methylation regulators between the AML and normal tissue, 296 AML children were divided into training cohort and validation cohort by simple random sampling method, Lasso regression was used to screen out the risk factors and the multivariate Cox regression was applied for establishing prognosis predicting model in training cohort. Kaplan-Meier survival curve, time-dependent ROC curve and multivariate Cox regression were used to estimate the efficiency of risk score calculated by predictive model in validation cohort. Results: Twenty one m6A genes were up regulated in AML compared to Normal patients. Five m6A RNA methylation regulators(ZC3H13, YTHDC2, HNRNPA2B1, METTL3, METTL5) were included in final predicting model. Risk score could independently predict the survival of AML patients in training cohort(HR:2.72, 95%CI: 1.54-4.81, P=0.000 6) and validation cohort(HR:2.01, 95%CI:1.14-3.50, P=0.016). Low-risk patients had better prognoses than high-risk patients both in training cohort(P=0.001 9) and validation cohort(P=0.023). Conclusion: This prognosis predicting model constructed by m6A RNA methylation regulators could independently predict the survival prognosis in AML children, and should be helpful for clinical therapy.

DOI: https://doi.org/10.3760/cma.j.cn112150-20210303-00212
Environ Pollut. 2021 Jul 20. pii: S0269-7491(21)01398-1. [Epub ahead of print]290 117816

Paraquat-induced oxidative stress regulates N6-methyladenosine (m6A) modification of circular RNAs.

Nengzhou Chen, Jianping Tang, Qianqian Su, Wei-Chun Chou, Fuli Zheng, Zhenkun Guo, Guangxia Yu, Wenya Shao, Huangyuan Li, Siying Wu.

  Paraquat (PQ), a widely used herbicide and well-known oxidative stress inducer, has been linked to numerous neurodegenerative diseases, but the underlying mechanism(s) remains unknown. Circular RNAs (circRNAs) have recently been reported to be associated with oxidative stress in Parkinson's disease. Herein, we performed methylated RNA immunoprecipitation and RNA sequencing assays for mouse neuroblastoma (Neuro-2a) cells and successfully established a positive link between the alteration of circRNAs driven by m6A modification and PQ-induced oxidative stress. We observed oxidative stress and antioxidative stress present distinct m6A modification pattern of circRNAs as well as biological effect. Gene ontology and pathway analysis predicted that differentially m6A-methylated and expressed circRNAs are highly clustered in pathways associated with function and development of nervous system, including axon cargo transport, nervous system development, long-term potentiation, and neurotrophic signaling pathways. Moreover, we demonstrated that the alteration of m6A-methylated circRNAs upon PQ exposure could be partially reversed by N-acetylcysteine pretreatment. The mechanistic analysis further demonstrated that N-acetylcysteine pretreatment attenuated the decreased expression of target genes (UBC and PPP2CA) induced by PQ. These findings revealed distinct patterns of differentially m6A-modified circRNAs, indicating that m6A could participate in a specific regulatory network of circRNAs to modulate the expression of downstream genes in response to PQ-induced oxidative stress. In conclusion, our work established a link between m6A modification of circRNAs and PQ-induced oxidative stress, and further studies are required to explore the underlying molecular mechanisms associated with PQ-induced neurotoxicity.

Keywords:  CircRNA; N(6)-methyladenosine (m(6)A); Neurotoxicity; Oxidative stress; Paraquat

DOI:  https://doi.org/10.1016/j.envpol.2021.117816