bims-rimeca 2022-09-04 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022–09–04
thirty-one papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

N6-methyladenosine RNA modification (m6A) is of prognostic value in HPV-dependent vulvar squamous cell carcinoma.
Methyltransferase-like 3 (METTL3) mediated N6-methyladenosine (m6A) modifications facilitate mir-25-3p maturation to promote gastrointestinal stromal tumors (GISTs) progression.
The controversial role and therapeutic development of the m6A demethylase FTO in renal cell carcinoma.
RNA m6A Modification in Liver Biology and Its Implication in Hepatic Diseases and Carcinogenesis.
Determination of adenosine and its modifications in urine and plasma from breast cancer patients by hydrophilic interaction liquid chromatography-tandem mass spectrometry.
The Role of RNA m6A Modification in Cancer Glycolytic Reprogrammingc.
Comprehensive analysis of the m6A-related molecular patterns and diagnostic biomarkers in osteoporosis.
Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine.
Cyclodextrin-Functionalized Gold Nanorods Loaded with Meclofenamic Acid for Improving N6-Methyladenosine-Mediated Second Near-Infrared Photothermal Immunotherapy.
XNA probe and CRISPR/Cas12a-powered flexible fluorescent and electrochemical dual-mode biosensor for sensitive detection of m6A site-specific RNA modification.
Effects of N6-Methyladenosine Regulators on LAG3 and Immune Infiltrates in Lung Adenocarcinoma.
Gene signature of m6A-related targets to predict prognosis and immunotherapy response in ovarian cancer.
Comprehensive analysis of molecular features, prognostic values, and immune landscape association of m6A-regulated immune-related lncRNAs in smoking-associated lung squamous cell carcinoma.
m6A regulator-based methylation modification patterns and characterization of tumor microenvironment in acute myeloid leukemia.
RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs.
Novel insight into m6A regulator-mediated methylation modification patterns and immune characteristics in intracranial aneurysm.
Identification of m6A- and ferroptosis-related lncRNA signature for predicting immune efficacy in hepatocellular carcinoma.
Predictive value of drug efficacy by M6A modification patterns in rheumatoid arthritis patients.
m6A Regulator-Based Exosomal Gene Methylation Modification Patterns Identify Distinct Microenvironment Characterization and Predict Immunotherapeutic Responses in Colon Cancer.
The emerging roles and mechanism of m6a in breast cancer progression.
m6A regulation of cortical and retinal neurogenesis is mediated by the redundant m6A readers YTHDFs.
Identification and Validation of an m6A-Related LncRNA Signature to Predict Progression-Free Survival in Colorectal Cancer.
mRNA-Modified FUS/NRF2 Signalling Inhibits Ferroptosis and Promotes Prostate Cancer Growth.
Wilms tumor 1 associated protein promotes epithelial mesenchymal transition of gastric cancer cells by accelerating TGF-β and enhances chemoradiotherapy resistance.
Long non-coding RNA SNHG16 decreased SMAD4 to induce gemcitabine resistance in pancreatic cancer via EZH2-mediated epigenetic modification.
IGF2BP3-NRF2 axis regulates ferroptosis in hepatocellular carcinoma.
The Relationship between Circulating Irisin and Oxidative Stress in Gastric and Colorectal Cancer Patients.
The m6A demethylase ALKBH5-mediated upregulation of DDIT4-AS1 maintains pancreatic cancer stemness and suppresses chemosensitivity by activating the mTOR pathway.
Identification of PLAUR-related ceRNA and immune prognostic signature for kidney renal clear cell carcinoma.
Allosteric Regulation of IGF2BP1 as a Novel Strategy for the Activation of Tumor Immune Microenvironment.
A peptide translated from circPPP1R12A promotes the malignancy of non-small cell lung cancer cells through AKT signaling pathway.

BMC Cancer. 2022 Sep 01. 22(1): 943

N6-methyladenosine RNA modification (m6A) is of prognostic value in HPV-dependent vulvar squamous cell carcinoma.

Mateja Condic, Thore Thiesler, Christian Staerk, Niklas Klümper, Jörg Ellinger, Eva K Egger, Kirsten Kübler, Glen Kristiansen, Alexander Mustea, Damian J Ralser.

   BACKGROUND: Vulvar squamous cell carcinoma (VSCC) is an uncommon gynecologic malignancy but with an increasing incidence in recent years. Etiologically, VSCC is classified into two subtypes: HPV-dependent and HPV-independent. Localized VSCC is treated surgically and/or with radiation therapy, but for advanced, metastatic or recurrent disease, therapeutic options are still limited. N6-methyladenosine (m6A) is the most prevalent post-transcriptional messenger RNA (mRNA) modification and involved in many physiological processes. The group of m6A proteins can be further divided into: 'writers' (METTL3, METTL4, METTL14, WTAP, KIAA1429), 'erasers' (FTO, ALKBH5), and 'readers' (HNRNPA2B1, HNRNPC, YTHDC1, YTHDF1-3). Dysregulated m6A modification is implicated in carcinogenesis, progression, metastatic spread, and drug resistance across various cancer entities. Up to date, however, only little is known regarding the role of m6A in VSCC.
METHODS: Here, we comprehensively investigated protein expression levels of a diverse set of m6A writers, readers and erasers by applying immunohistochemical staining in 126 patients with primary VSCC.
RESULTS: In the entire study cohort, dominated by HPV-independent tumors, m6A protein expression was not associated with clinical outcome. However, we identified enhanced protein expression levels of the 'writers' METTL3, METTL14 and the 'reader' YTHDC1 as poor prognostic markers in the 23 patients with HPV-dependent VSCC.
CONCLUSION: Our study suggests dysregulated m6A modification in HPV-associated VSCC.

Keywords:  Biomarker; HPV; N6-methyladenosine RNA modification; Vulvar squamous cell carcinoma; m6A

DOI:  https://doi.org/10.1186/s12885-022-10010-x
Genes Genomics. 2022 Aug 30.

Methyltransferase-like 3 (METTL3) mediated N6-methyladenosine (m6A) modifications facilitate mir-25-3p maturation to promote gastrointestinal stromal tumors (GISTs) progression.

Kun Qian, Wei Xu, Xiaoyao Xia, Jinhuo Ding.

   BACKGROUND: Methyltransferase-like 3 (METTL3) is an RNA N6-methyladenosine (m6A) methyltransferase, which plays a critical role in micorRNA (miRNAs) processing and maturation, but it is still unclear whether METTL3 regulated miRNAs participates in the regulation of cancer aggressiveness in gastrointestinal stromal tumors (GISTs).
OBJECTIVES: This study was designed to investigate this issue, and uncover the potential underlying mechanisms.
METHODS: the expression of METTL3 in GISTs tissues and cell lines were determined by RT-qPCR and Western blot. Cell proliferation and migration were assessed by colony formation, CCK-8 and Transwell. The mRNA expression of all proteins was detected by RT-qPCR, and tumor xenograft study was applied to confirm the effect of METTL3 on GISTs development in vivo.
RESULTS: In our study, we showed that METTL3 was significantly upregulated in GISTs tissues and cell lines. Functional experiments demonstrated that overexpression of METTL3 promoted GISTs cell malignant biological behavior and tumor growth in vitro and in vivo, and conversely, silencing of METTL3 had opposite effects and suppressed GISTs progression. Further mechanistical experiments verified that METTL3 promoted the maturation of miR-25-3p in an m6A-dependent manner. Similar to METTL3, miR-25-3p was also validated as an oncogene to promote cancer development in GISTs. Finally, our rescuing experiments hinted that silencing of miR-25-3p abrogated the tumor-initiating effects of METTL3 overexpression on GISTs.
CONCLUSION: Collectively, those results indicated that METTL3 played an oncogenic role in GISTs through positively modulating the miR-25-3p in an m6A-dependent manner, and we firstly discussed how the METTL3/m6A/miR-25-3p axis affected GISTs development.

Keywords:  Gastrointestinal stromal tumors; Methyltransferase-like 3; N6-methyladenosine; miR-25-3p

DOI:  https://doi.org/10.1007/s13258-022-01301-5
Transl Oncol. 2022 Aug 27. pii: S1936-5233(22)00177-2. [Epub ahead of print]25 101518

The controversial role and therapeutic development of the m6A demethylase FTO in renal cell carcinoma.

Dalin Zhang, Sarah Wornow, Donna M Peehl, Erinn B Rankin, James D Brooks.

  Fat mass and obesity-associated (FTO) protein, the first m6A demethylase identified in 2011, regulates multiple aspects of RNA biology including splicing, localization, stability, and translation. Accumulating data show that FTO is involved in numerous physiological processes and is implicated in multiple cancers including renal cell carcinoma (RCC). However, the exact role of FTO in RCC remains controversial. Some studies demonstrated that decreased FTO expression was associated with aggressive clinical features and shorter overall survival in clear cell RCC (ccRCC) patients, while others found that FTO inhibition selectively reduced the growth and survival of VHL-deficient ccRCC cells in vitro and in vivo. Here, we review the evidence supporting either a promoting or suppressive role of FTO in kidney cancers, the mechanisms of action of FTO, and recent progress in developing FTO inhibitors.

Keywords:  Cancer progression; FTO; Inhibitors; Prognosis; Renal cell carcinoma; m(6)A RNA demethylase

DOI:  https://doi.org/10.1016/j.tranon.2022.101518
Am J Physiol Cell Physiol. 2022 Aug 29.

RNA m6A Modification in Liver Biology and Its Implication in Hepatic Diseases and Carcinogenesis.

Wenbo Ma, Tong Wu.

  N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic RNAs. This modification is regulated by three different factors (writers, erasers and readers) and influences multiple aspects of RNA metabolism, including RNA splicing, nuclear export, translation, stability and decay. The m6A-mediated modification plays important roles in post-transcriptional regulation of gene expression and mediates a variety of cellular and biological processes. Accordingly, deregulation in m6A modification is closely related to the occurrence and development of human diseases. The liver is the largest digestive and metabolic organ in human and recent studies have shown that m6A modification is importantly implicated in liver cellular and physiological processes and in the pathogenesis of hepatic diseases and cancers. In this review, we summarize the functions of m6A in RNA metabolism and its roles in liver cell biology and discuss its implication in hepatic diseases and carcinogenesis.

Keywords:  METTL3; cholangiocarcinoma; hepatocellular carcinoma; liver cancer; m6A

DOI:  https://doi.org/10.1152/ajpcell.00214.2022
J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Aug 25. pii: S1570-0232(22)00332-4. [Epub ahead of print]1209 123428

Determination of adenosine and its modifications in urine and plasma from breast cancer patients by hydrophilic interaction liquid chromatography-tandem mass spectrometry.

Xiaoxiao Zhang, Yiqiu Hu, Xiujuan Hong, Mingwei Wang, Zhihao Fang, Xiaoji Cao, Kezhi Jiang, Cheng Guo.

  RNA modifications have been revealed to be essential in many biological activities, and their disorders are associated with various human diseases, including cancers. 2'-O-methyladenosine (Am), N1-methyladenosine (m1A), N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am) and N6,N6-dimethyladenosine (m62A) are important adenosine (A) modifications. The noninvasive collection of urine samples and the diverse contents of metabolites in plasma make them favored biofluids for biomarkers discovery. In this work, we established a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method to quantify these six nucleosides in urine and plasma of healthy controls and breast cancer (BC) patients. The limit of detection (LOD) for A, Am, m1A, m6A, m6Am, and m62A were 0.0025, 0.01, 0.05, 0.005, 0.005, and 0.005 nM. The results showed that the concentrations of Am, m6A, and m6Am were increased, whereas m1A was decreased in the urine of BC patients compared with the healthy controls. We also found that the level ratios of m1A/A, m6A/A, and m6Am/A were all reduced in plasma from BC patients, compared with healthy controls. Interestingly, these ratios of methylated adenosine nucleosides to adenosine in plasma could better discriminate BC patients from healthy controls, compared to the levels of these nucleosides. The present study not only suggests these modified adenosines can act as noninvasive biomarkers of BC but also will contribute to investigating the impacts of RNA methylation on the occurrence and development of BC.

Keywords:  Biomarker; Breast cancer; HILIC-MS/MS; Methylated adenosine; Plasma; Urine

DOI:  https://doi.org/10.1016/j.jchromb.2022.123428
Curr Gene Ther. 2022 Aug 30.

The Role of RNA m6A Modification in Cancer Glycolytic Reprogrammingc.

Yuanqi Li, Hao Huang, Shaoxian Wu, You Zhou, Tao Huang, Jingting Jiang.

  As one of the main characteristics of neoplasia, metabolic reprogramming provides nutrition and energy to enhance cell proliferation and maintain environment homeostasis. Glycolysis is one of the most important components of cancer metabolism and Warburg effect contributes to the competitive advantages of cancer cells in the threatened microenvironment. Studies show strong links between N6-methyladenosine (m6A) modification and metabolic recombination of cancer cells. As the most abundant modification in eukaryotic RNA, m6A methylation plays important roles in regulating RNA processing including splicing, stability, transportation, translation and degradation. The aberration of m6A modification can be observed in a variety of diseases such as diabetes, neurological diseases and cancers. This review describes the mechanisms of m6A on cancer glycolysis and their applications in cancer therapy and prognosis evaluation, aiming to emphasize the importance of targeting m6A on modulating cancer metabolism.

Keywords:  Cancer; Glycolysis; N6-methyladenosine; RNA modification

DOI:  https://doi.org/10.2174/1566523222666220830150446
Front Endocrinol (Lausanne). 2022 ;13 957742

Comprehensive analysis of the m6A-related molecular patterns and diagnostic biomarkers in osteoporosis.

Qiong Bai, Min Shi, Xinli Sun, Qiu Lou, Hangya Peng, Zhuan Qu, Jiashuang Fan, Lifen Dai.

   Background: N6-methyladenosine (m6A) modification is a critical epigenetic modification in eukaryotes and involves several biological processes and occurrences of diseases. However, the roles and regulatory mechanisms of m6A regulators in osteoporosis (OP) remain unclear. Thus, the purpose of this study is to explore the roles and mechanisms of m6A regulators in OP.
Methods: The mRNA and microRNA (miRNA) expression profiles were respectively obtained from GSE56815, GSE7158, and GSE93883 datasets in Gene Expression Omnibus (GEO). The differential expression of 21 m6A regulators between high-bone mineral density (BMD) and low-BMD women was identified. Then, a consensus clustering of low-BMD women was performed based on differentially expressed (DE)-m6A regulators. The m6A-related differentially expressed genes (DEGs), the differentially expressed miRNAs (DE-miRNAs), and biological functions were investigated. Moreover, a weighted gene co-expression network analysis (WGCNA) was constructed to identify the OP-related hub modules, hub genes, and the functional pathways. Then, an m6A regulator-target-pathway network and the competing endogenous RNA (ceRNA) network in key modules were constructed. A least absolute shrinkage and selection operation (LASSO) Cox regression model and a Support Vector Machine-Recursive Feature Elimination (SVM-RFE) model were constructed to identify the candidate genes for OP prediction. The receiver operator characteristic (ROC) curves were used to validate the performances of predictive models and candidate genes.
Results: A total of 10,520 DEGs, 13 DE-m6A regulators, and 506 DE-miRNAs between high-BMD and low-BMD women were identified. Two m6A-related subclusters with 13 DE-m6A regulators were classified for OP. There were 5,260 m6A-related DEGs identified between two m6A-related subclusters, the PI3K-Akt, MAPK, and immune-related pathways, and bone metabolism was mainly enriched in cluster 2. Cell cycle-related pathways, RNA methylation, and cell death-related pathways were significantly involved in cluster 1. Five modules were identified as key modules based on WGCNA, and an m6A regulator-target gene-pathway network and the ceRNA network were constructed in module brown. Moreover, three m6A regulators (FTO, YTHDF2, and CBLL1) were selected as the candidate genes for OP.
Conclusion: M6A regulators play an important role in the occurrences and diagnosis of OP.

Keywords:  N6-methyladenosine; Osteoporosis; WGCNA; diagnostic markers; molecular patterns

DOI:  https://doi.org/10.3389/fendo.2022.957742
ACS Cent Sci. 2022 Aug 24. 8(8): 1218-1228

Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine.

Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi.

Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field-based classical molecular dynamics simulations are a fundamental tool to characterize biomolecular dynamics, and their application to RNA is flourishing. Here, we show that the set of force-field parameters for N6-methyladenosine (m6A) developed for the commonly used AMBER force field does not reproduce duplex denaturation experiments and, specifically, cannot be used to describe both paired and unpaired states. Then, we use reweighting techniques to derive new parameters matching available experimental data. The resulting force field can be used to properly describe paired and unpaired m6A in both syn and anti conformation, which thus opens the way to the use of molecular simulations to investigate the effects of N6 methylations on RNA structural dynamics.

DOI: https://doi.org/10.1021/acscentsci.2c00565
ACS Appl Mater Interfaces. 2022 Sep 02.

Cyclodextrin-Functionalized Gold Nanorods Loaded with Meclofenamic Acid for Improving N6-Methyladenosine-Mediated Second Near-Infrared Photothermal Immunotherapy.

Jianhua Liu, Yue Song, Yiqiao Wang, Mingda Han, Chunxi Wang, Fei Yan.

  Cancer immunotherapy has achieved considerable clinical progress in recent years on account of its potential to treat metastatic tumors and inhibit recurrence. However, low patient response rates and dose-limiting toxicity are the major limitations of immunotherapy. Nanoparticle-based photothermal immunotherapy can amplify antitumor immune responses, although poor tumor penetration depth of near-infrared radiation (NIR) and the immunosuppressive tumor microenvironment significantly dampen its effects. We designed a nanoplatform based on gold nanorods for NIR-II-mediated photothermal therapy (PTT) combined with N6-methyladenosine (m6A) demethylase inhibition to achieve enhanced photothermal immunotherapy against prostate cancer. The GNRs were assembled layer by layer with polystyrenesulfonate as the interconnecting layer and then coated with a cationic polymer of γ-cyclodextrin (CD)-cross-linked low-molecular-weight polyethylenimine that was conjugated to an 8-mer peptide targeting the prostate tumor-specific gastrin-releasing peptide receptor. The m6A RNA demethylase inhibitor meclofenamic acid (MA) was then loaded into the CD cavity through hydrophobic interactions. GNR-CDP8MA specifically targeted the prostate tumor cells and selectively accumulated at the tumor site in vivo. In addition, GNR-CDP8MA almost completely ablated prostate cancer cell-derived tumors upon 1208 nm laser irradiation. Mechanistically, NIR-II triggered the release of MA from GNR-CDP8MA, which increased global mRNA m6A methylation and decreased the stability of PDL1 transcripts. Furthermore, GNR-CDP8MA-mediated PTT-induced immunogenic cell death in the primary tumor and consequently enhanced antitumor immunity by activating the antigen-presenting dendritic cells and tumor-specific effector T cells in the metastatic tumors. This study offers insights into synergistic m6A RNA methylation and PTT as an effective strategy for cancer immunotherapy.

Keywords:  N6-methyladenosine; RNA methylation; gold nanorods; immunotherapy; photothermal therapy

DOI:  https://doi.org/10.1021/acsami.2c09978
Talanta. 2022 Jul 21. pii: S0039-9140(22)00550-1. [Epub ahead of print]252 123754

XNA probe and CRISPR/Cas12a-powered flexible fluorescent and electrochemical dual-mode biosensor for sensitive detection of m6A site-specific RNA modification.

Qinli Pu, Yuanyuan Ye, Juan Hu, Cong Xie, Xi Zhou, Hongyan Yu, Fangli Liao, Song Jiang, Linshan Jiang, Guoming Xie, Weixian Chen.

  N6-methyladenosine (m6A) in RNAs is closely related to various biological progresses, but the specific regulatory mechanisms are still unclear. The existing m6A single-base resolution analysis techniques have problems of specificity and sensitivity to be improved, which can hardly meet the urgent needs of basic research and clinical applications. This work proposes a new strategy based on xeno nucleic acid (XNA) probe and CRISPR/Cas12a signal amplification for the sensitive detection of site-specific m6A modifications. According to the difference in the thermodynamic stability of hybridization between XNA probe with m6A-RNA and A-RNA, XNA was designed as a block probe to mediate m6A-RNA specific reverse transcription polymerase chain reaction (MsRT-PCR). Therefore, m6A can be specifically distinguished by converting difficult-to-test m6A modifications into easily detectable dsDNA fragments. Integration of CRISPR/Cas12a technology, skilfully designed sequences of crRNAs targeting m6A site-specific amplification dsDNA. The specificity was significantly improved through dual specific recognition of XNA probe and crRNA. Furthermore, the sensitivity of the assay was also greatly increased by the combined signal amplification of PCR and CRISPR/Cas12a. Additionally, we extend the application of CRISPR/Cas12a to flexible fluorescent and electrochemical biosensing system, which can accurately detect m6A modifications with different ranges of methylation fractions. The analysis results of m6A sites in MALAT1, ACTB and TPT1 further demonstrated the feasibility of the constructed biosensor for the accurate detection of hypomethylated samples in cells. The implementation of this work will provide strong technical support to promote the in-depth research on m6A in disease regulation mechanisms and in vitro molecular diagnosis.

Keywords:  CRISPR/Cas12a; Electrochemical biosensor; Fluorescence; N6-methyladenosine; XNA probe

DOI:  https://doi.org/10.1016/j.talanta.2022.123754
Dis Markers. 2022 ;2022 1829528

Effects of N6-Methyladenosine Regulators on LAG3 and Immune Infiltrates in Lung Adenocarcinoma.

Nengchao Wang, Yue Xu, Linzhi Jin, Xiaomin Wang, Shouxin Wu, Yu Wang, Jiangman Zhao, Fuyou Zhou, Hong Ge.

Background: Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer, which is one of the most commonly diagnosed tumors and the leading causes of death from cancer around the world. Since RNA methylation is a posttranscriptional modification and affects so much biological progress, it is urged to explore the role of N6-methyladenosine (m6A) methylation in LUAD.
Methods: We explored the expression of 24 m6A methylation genes, as well as their correlations with LAG3 in 561 LUAD samples from TCGA. Consensus clustering was applied to m6A methylation genes, and two LUAD subgroups were identified. The expression of m6A genes was analyzed by the Wilcoxon test. KEGG and GO enrichment analyses were performed to indicate the pathway affected by differentially expressed genes in the two groups. A prognostic model based on LASSO regression using an eleven-m6A gene signature was constructed according to the expression of these genes. Receiver operating characteristic (ROC) curve was used to confirm the accuracy of the model in the TCGA cohort, as well as in the test cohort from the Gene Expression Omnibus (GEO) database.
Results: Compared to cluster 1, cluster 2 showed poorer overall survival (OS) and higher LAG3 expression. In addition, KEGG and GO enrichment analyses indicated that differentially expressed genes are enriched in the immune response. We also observed that the expression of LAG3 is positively correlated with IGF2BP2, CBLL1, and HNRNPA2B1 and negatively correlated with YTHDF2, YTHDF3, and FTO. For patients in the TCGA cohort, the AUC score is 0.7, and the AUC score for the GSE50081 cohort is 0.675. Patients with lower risk scores exhibited better overall survival and lower expression of LAG3 than patients with higher risk scores.
Conclusions: In brief, our results indicated the important role of m6 methylation in affecting the tumor immune microenvironment and the survival of patients with LUAD. The m6A methylation gene signatures might serve as promising therapeutic targets and help the immunotherapy of LUAD in the future.

DOI: https://doi.org/10.1155/2022/1829528
J Cancer Res Clin Oncol. 2022 Sep 01.

Gene signature of m6A-related targets to predict prognosis and immunotherapy response in ovarian cancer.

Wei Tan, Shiyi Liu, Zhimin Deng, Fangfang Dai, Mengqin Yuan, Wei Hu, Bingshu Li, Yanxiang Cheng.

   PURPOSE: The aim of the study was to construct a risk score model based on m6A-related targets to predict overall survival and immunotherapy response in ovarian cancer.
METHODS: The gene expression profiles of 24 m6A regulators were extracted. Survival analysis screened 9 prognostic m6A regulators. Next, consensus clustering analysis was applied to identify clusters of ovarian cancer patients. Furthermore, 47 phenotype-related differentially expressed genes, strongly correlated with 9 prognostic m6A regulators, were screened and subjected to univariate and the least absolute shrinkage and selection operator (LASSO) Cox regression. Ultimately, a nomogram was constructed which presented a strong ability to predict overall survival in ovarian cancer.
RESULTS: CBLL1, FTO, HNRNPC, METTL3, METTL14, WTAP, ZC3H13, RBM15B and YTHDC2 were associated with worse overall survival (OS) in ovarian cancer. Three m6A clusters were identified, which were highly consistent with the three immune phenotypes. What is more, a risk model based on seven m6A-related targets was constructed with distinct prognosis. In addition, the low-risk group is the best candidate population for immunotherapy.
CONCLUSION: We comprehensively analyzed the m6A modification landscape of ovarian cancer and detected seven m6A-related targets as an independent prognostic biomarker for predicting survival. Furthermore, we divided patients into high- and low-risk groups with distinct prognosis and select the optimum population which may benefit from immunotherapy and constructed a nomogram to precisely predict ovarian cancer patients' survival time and visualize the prediction results.

Keywords:  Immunotherapy; Ovarian cancer; Prognosis; RNA N6-methyladenosine; Tumor mutation burden

DOI:  https://doi.org/10.1007/s00432-022-04162-3
Front Genet. 2022 ;13 887477

Comprehensive analysis of molecular features, prognostic values, and immune landscape association of m6A-regulated immune-related lncRNAs in smoking-associated lung squamous cell carcinoma.

Meng Zhang, Jian Zhang, Yang Liu.

  Lung squamous cell carcinoma (LUSC) is the second most common histopathological subtype of lung cancer, and smoking is the leading cause of this type of cancer. However, the critical factors that directly affect the survival rate and sensitivity to immunotherapy of smoking LUSC patients are still unknown. Previous studies have highlighted the role of N6-methyladenosine (m6A) RNA modification, the most common epigenetic modification in eukaryotic species, together with immune-related long non-coding RNAs (lncRNAs) in promoting the development and progression of tumors. Thus, elucidating m6A-modified immune lncRNAs in LUSC patients with smoking history is vital. In this study, we described the expression and mutation features of the 24 m6A-related regulators in the smoking-associated LUSC cohort from The Cancer Genome Atlas (TCGA) database. Then, two distinct subtypes based on the expression levels of the prognostic m6A-regulated immune lncRNAs were defined, and differentially expressed genes (DEGs) between the subtypes were identified. The distributions of clinical characteristics and the tumor microenvironment (TME) between clusters were analyzed. Finally, we established a lncRNA-associated risk model and exhaustively clarified the clinical features, prognosis, immune landscape, and drug sensitivity on the basis of this scoring system. Our findings give insight into potential mechanisms of LUSC tumorigenesis and development and provide new ideas in offering LUSC patients with individual and effective immunotherapies.

Keywords:  M6A; immune lncRNA; prognosis; smoking; squamous cell lung carcinoma; tumor microenvironment

DOI:  https://doi.org/10.3389/fgene.2022.887477
Front Genet. 2022 ;13 948079

m6A regulator-based methylation modification patterns and characterization of tumor microenvironment in acute myeloid leukemia.

Zi-Jun Xu, Xiang-Mei Wen, Yuan-Cui Zhang, Ye Jin, Ji-Chun Ma, Yu Gu, Xin-Yi Chen, Pei-Hui Xia, Wei Qian, Jiang Lin, Jun Qian.

  RNA N6-methyladenosine (m6A) is the most common and intensively studied RNA modification that critically regulates RNA metabolism, cell signaling, cell survival, and differentiation. However, the overall role of multiple m6A regulators in the tumor microenvironment (TME) has not yet been fully elucidated in acute myeloid leukemia (AML). In our study, we explored the genetic and transcriptional alterations of 23 m6A regulators in AML patients. Three distinct molecular subtypes were identified and associated with prognosis, patient clinicopathological features, as well as TME characteristics. The TME characterization revealed that m6A patterns were highly connected with metabolic pathways such as biosynthesis of unsaturated fatty acids, cysteine and methionine metabolism, and citrate cycle TCA cycle. Then, based on the differentially expressed genes (DEGs) related to m6A molecular subtypes, our study categorized the entire cohort into three m6A gene clusters. Furthermore, we constructed the m6Ascore for quantification of the m6A modification pattern of individual AML patients. It was found that the tumor-infiltrating lymphocyte cells (TILs) closely correlated with the three m6A clusters, three m6A gene clusters, and m6Ascore. And many biological processes were involved, including glycogen degradation, drug metabolism by cytochrome P450, pyruvate metabolism, and so on. Our comprehensive analysis of m6A regulators in AML demonstrated their potential roles in the clinicopathological features, prognosis, tumor microenvironment, and particularly metabolic pathways. These findings may improve our understanding of m6A regulators in AML and offer new perspectives on the assessment of prognosis and the development of anticancer strategy.

Keywords:  acute myeloid leukemia; immune infiltration; m6A; metabolic pathways; tumor microenvironment

DOI:  https://doi.org/10.3389/fgene.2022.948079
Cell Rep. 2022 Aug 30. pii: S2211-1247(22)01113-5. [Epub ahead of print]40(9): 111293

RBM45 is an m6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs.

Seung H Choi, Mathieu N Flamand, Bei Liu, Huanyu Zhu, Meghan Hu, Melanie Wang, Jonathon Sewell, Christopher L Holley, Hashim M Al-Hashimi, Kate D Meyer.

  N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are incompletely understood. RBM45 acts as an m6A-binding protein that is highly expressed during neurodevelopment. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings show a role for RBM45 in controlling mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA.

Keywords:  CP: Developmental biology; CP: Molecular biology; N(6)-methyladenosine; RBM45; RNA splicing; epitranscriptomics; m(6)A; neurobiology; neurodevelopment

DOI:  https://doi.org/10.1016/j.celrep.2022.111293
Front Aging Neurosci. 2022 ;14 973258

Novel insight into m6A regulator-mediated methylation modification patterns and immune characteristics in intracranial aneurysm.

Shifu Li, Qian Zhang, Ling Weng, Ying Han, Jian Li.

   Background: Growing evidence demonstrated that m6A modification in cardiovascular diseases. However, how it is involved in the intracranial aneurysm (IA) is still unclear. This study aimed to identify the role of m6A modification in IA.
Methods: Three datasets downloaded from the Gene Expression Omnibus (GEO) database were used, including GSE122897, GSE15629, and GSE3679. The landscapes of 24 m6A regulators were depicted using the STRING database, Pearson's correlation analysis, and Wilcoxon test. The targets of differentially expressed m6A (DEm6A) were predicted in the m6A2Target database and the modification m6A sites of hub targets were identified in SRAMP online tool. A diagnostic model based on DEm6A was constructed and verified in training and test databases. A consensus clustering algorithm was performed to classify IA patients into distinct m6A-related clusters. Functional analyses including gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set variation analysis, and gene set enrichment analysis analyses were conducted to elucidate the underlying mechanisms. ssGSEA algorithm was performed to uncover the immune characteristics. A PCA method was adopted to quantify the m6A score.
Results: Nine DEm6A (IGF2BP1, IGF2BP3, YTHDF2, ZNF217, RBM15, YTHDF3, YTHDC1, FTO, and LRPPRC) significantly differed between IA and controls. Biological annotations showed that immune-related pathways (such as complement activation, inflammatory response, and interleukin signaling) and apoptosis were more enriched in IAs than in controls. Immune analyses indicate that the abundance of immune cells, immune responses, and HLA gene expression were elevated in IA samples than in controls. PCA results showed that IA has a lower m6A score than controls. An immune/apoptosis-related network modified by DEm6A was constructed. The m6A sites of six hub targets (CDK1, ASPM, AURKB, BUB1B, MKI67, and TPX2) were predicted with very high confidence. A diagnostic model with four genes (LRPPRC, YTHDF3, IGF2BP1, and ZNF217) was constructed and verified. Two m6A modification subtypes were identified with unsupervised cluster analysis. Immune infiltration analysis revealed that cluster 1 had higher immune activation than cluster 2. Further study showed that cluster 1 had a larger proportion of ruptured IAs.
Conclusion: The m6A modification may shape the IAs microenvironment and participates in the formation and rupture of IAs by regulating immune infiltration.

Keywords:  apoptosis; immune infiltrations; intracranial aneurysm; m6A regulators; signature

DOI:  https://doi.org/10.3389/fnagi.2022.973258
Front Immunol. 2022 ;13 914977

Identification of m6A- and ferroptosis-related lncRNA signature for predicting immune efficacy in hepatocellular carcinoma.

Hongjun Xie, Muqi Shi, Yifei Liu, Changhong Cheng, Lining Song, Zihan Ding, Huanzhi Jin, Xiaohong Cui, Yan Wang, Dengfu Yao, Peng Wang, Min Yao, Haijian Zhang.

   Background: N6-methyladenosine (m6A) methylation and ferroptosis assist long noncoding RNAs (lncRNAs) in promoting immune escape in hepatocellular carcinoma (HCC). However, the predictive value of m6A- and ferroptosis-related lncRNAs (mfrlncRNAs) in terms of immune efficacy remains unknown.
Method: A total of 365 HCC patients with complete data from The Cancer Genome Atlas (TCGA) database were used as the training cohort, and half of them were randomly selected as the validation cohort. A total of 161 HCC patients from the International Cancer Genome Consortium (ICGC) database were used as external validation (ICGC cohort).
Results: We first identified a group of specific lncRNAs associated with both m6A regulators and ferroptosis-related genes and then constructed prognosis-related mfrlncRNA pairs. Based on this, the mfrlncRNA signature was constructed using the least absolute shrinkage and selection operator (LASSO) analysis and Cox regression. Notably, the risk score of patients was proven to be an independent prognostic factor and was better than the TNM stage and tumor grade. Moreover, patients with high-risk scores had lower survival rates, higher infiltration of immunosuppressive cells (macrophages and Tregs), lower infiltration of cytotoxic immune cells (natural killer cells), poorer immune efficacy (both immunophenoscore and score of tumor immune dysfunction and exclusion), higher IC50, and enrichment of the induced Treg pathway, which confirmed that the mfrlncRNA signature contributed to survival prediction and risk stratification of patients with HCC.
Conclusions: The mfrlncRNA signature, which has great prognostic value, provides new clues for identifying "cold" and "hot" tumors and might have crucial implications for individualized therapy to improve the survival rate of patients with HCC.

Keywords:  N6-methyladenosine (m6A) methylation; ferroptosis; hepatocellular carcinoma; immune efficacy; long noncoding RNA pairs

DOI:  https://doi.org/10.3389/fimmu.2022.914977
Front Immunol. 2022 ;13 940918

Predictive value of drug efficacy by M6A modification patterns in rheumatoid arthritis patients.

Shan Song, Rong Zhao, Jun Qiao, Jia Liu, Ting Cheng, Sheng-Xiao Zhang, Xiao-Feng Li.

   Background: Rheumatoid arthritis is a highly heterogeneous autoimmune disease characterized by unpredictable disease flares and significant differences in therapeutic response to available treatments. One possible reason for poor efficacy is that it cannot be treated accurately due to no optimal stratification for RA patients.
Objective: This study aims to construct an RA classification model by m6A characters and further predict response to medication.
Methods: Twenty m6A regulators were used to construct a random forest diagnosis model, and RNA-seq analysis was employed for external validation. The RNA modification patterns mediated by 20 m6A regulators were systematically evaluated in 1191 RA samples and explored different molecular clusters associated with other immune microenvironment characteristics and biological pathways. Then, we established an m6A score model to quantify the m6A modification patterns. The model was applied to patients at baseline to test the association between m6Ascore and infliximab responsiveness.
Results: The m6A diagnosis model showed good discriminatory ability in distinguishing RA. Patients with RA were classified into three clusters with distinct molecular and cellular signatures. Cluster A displayed strongly activated inflammatory cells and pathways. Specific innate lymphocytes occupied cluster B. Cluster C was mainly enriched in prominent adaptive lymphocytes and NK-mediated cytotoxicity signatures with the highest m6A score. Patients with a low m6Ascore exhibited significantly infliximab therapeutic benefits compared with those with a high m6Ascore (p< 0.05).
Conclusion: Our study is the first to provide a comprehensive analysis of m6A modifications in RA, which provides an innovative patient stratification framework and potentially enables improved therapeutic decisions.

Keywords:  epigenetic; immune microenvironment; infliximab; m6A RNA modification; rheumatoid arthritis

DOI:  https://doi.org/10.3389/fimmu.2022.940918
Oxid Med Cell Longev. 2022 ;2022 9451480

m6A Regulator-Based Exosomal Gene Methylation Modification Patterns Identify Distinct Microenvironment Characterization and Predict Immunotherapeutic Responses in Colon Cancer.

Junjie Zheng, Panpan Feng, Dawei Chen, Cuiyu Zhang, Yuge Ji, Yanting Liu, Xiaohua Fan, Jingxin Li.

Recent studies have highlighted the biological significance of exosomes and m6A modifications in immunity. Nonetheless, it remains unclear whether the m6A modification gene in exosomes of body fluid has potential roles in the tumor microenvironment (TME). Herein, we identified three different m6A-related exosomal gene modification patterns based on 59 m6A-related exosomal genes, which instructed distinguishing characteristics of TME in colon cancer (CC). We demonstrated that these patterns could predict the stage of tumor inflammation, subtypes, genetic variation, and patient prognosis. Furthermore, we developed a scoring mode-m6A-related exosomal gene score (MREGS)-by detecting the level of m6A modification in exosomes to classify immune phenotypes. Low MREGS, characterized by prominent survival and immune activation, was linked to a better response to anti-PDL1 immunotherapy. In contrast, the higher MREGS group displayed remarkable stromal activation, high activity of innate immunocytes, and a lower survival rate. Hence, this work provides a novel approach for evaluating TME cell infiltration in colon cancer and guiding more effective immunotherapy strategies.

DOI: https://doi.org/10.1155/2022/9451480
Front Genet. 2022 ;13 983564

The emerging roles and mechanism of m6a in breast cancer progression.

Mengying Zhou, Menglu Dong, Xue Yang, Jun Gong, Xinghua Liao, Qi Zhang, Zeming Liu.

  Breast cancer (BC) has continued to be the leading cause of cancer deaths in women, accompanied by highly molecular heterogeneity. N6-methyladenosine (m6A), a methylation that happens on adenosine N6, is the most abundant internal mRNA modification type in eukaryotic cells. Functionally, m6A methylation is a reversible modification process and is regulated by 3 enzymes with different functions, namely "writer", "reader", and "eraser". Abnormal m6A modifications trigger the expression, activation, or inhibition of key signaling molecules in critical signaling pathways and the regulatory factors acting on them in BC. These m6A-related enzymes can not only be used as markers for accurate diagnosis, prediction of prognosis, and risk model construction, but also as effective targets for BC treatment. Here, we have emphasized the roles of different types of m6A-related enzymes reported in BC proliferation, invasion, and metastasis, as well as immune regulation. The comprehensive and in-depth exploration of the molecular mechanisms related to m6A will benefit in finding effective potential targets and effective stratified management of BC.

Keywords:  M6A; breast cancer; gene expression; metastasis; methylation; miRNA

DOI:  https://doi.org/10.3389/fgene.2022.983564
iScience. 2022 Sep 16. 25(9): 104908

m6A regulation of cortical and retinal neurogenesis is mediated by the redundant m6A readers YTHDFs.

Fugui Niu, Pengfei Che, Zhuoxuan Yang, Jian Zhang, Lixin Yang, Mengru Zhuang, Xijun Ou, Sheng-Jian Ji.

  m6A modification plays an important role in regulating mammalian neurogenesis. However, whether and how the major cytoplasmic m6A readers, YTHDF1, YTHDF2, and YTHDF3 mediate this process is still not clear. Here, we demonstrate that Ythdf1 and Ythdf2 double deletion but not individual knockout recapitulates the phenotype of Mettl14 knockout in cortex. In addition, we find that Mettl14 knockout in retina causes protracted proliferation of retinal progenitors, decreased numbers of retinal neurons, and disturbed laminar structure. This phenotype is only reproduced when Ythdf1, Ythdf2, and Ythdf3 are knocked out simultaneously in retina. Analysis of YTHDF target mRNAs in mouse cortex and retina reveals abundant overlapping mRNAs related to neurogenesis that are recognized and regulated by both YTHDF1 and YTHDF2. Together our results demonstrate that the functionally redundant YTHDFs mediate m6A regulation of cortical and retinal neurogenesis.

Keywords:  Molecular Genetics; Molecular biology; Molecular neuroscience; Neuroscience

DOI:  https://doi.org/10.1016/j.isci.2022.104908
Pathol Oncol Res. 2022 ;28 1610536

Identification and Validation of an m6A-Related LncRNA Signature to Predict Progression-Free Survival in Colorectal Cancer.

Yong Zhang, Lu Li, Feifei Chu, Xingguo Xiao, Li Zhang, Kunkun Li, Huili Wu.

  The RNA methylation of N6 adenosine (m6A) plays a crucial role in various biological processes. Strong evidence reveals that the dysregulation of long non-coding RNAs (lncRNA) brings about the abnormality of downstream signaling in multiple ways, thus influencing tumor initiation and progression. Currently, it is essential to discover effective and succinct molecular biomarkers for predicting colorectal cancer (CRC) prognosis. However, the prognostic value of m6A-related lncRNAs for CRC remains unclear, especially for progression-free survival (PFS). Here, we screened 24 m6A-related lncRNAs in 622 CRC patients and identified five lncRNAs (SLCO4A1-AS1, MELTF-AS1, SH3PXD2A-AS1, H19 and PCAT6) associated with patient PFS. Compared to normal samples, their expression was up-regulated in CRC tumors from TCGA dataset, which was validated in 55 CRC patients from our in-house cohort. We established an m6A-Lnc signature for predicting patient PFS, which was an independent prognostic factor by classification analysis of clinicopathologic features. Moreover, the signature was validated in 1,077 patients from six independent datasets (GSE17538, GSE39582, GSE33113, GSE31595, GSE29621, and GSE17536), and it showed better performance than three known lncRNA signatures for predicting PFS. In summary, our study demonstrates that the m6A-Lnc signature is a promising biomarker for forecasting patient PFS in CRC.

Keywords:  colorectal cancer; lncRNA; m6A; progression free survival; signature

DOI:  https://doi.org/10.3389/pore.2022.1610536
Comput Math Methods Med. 2022 ;2022 8509626

mRNA-Modified FUS/NRF2 Signalling Inhibits Ferroptosis and Promotes Prostate Cancer Growth.

Ning Wang, Ying Yu, Rongjiang Wang, Yu Chen, Jianer Tang.

Objective: Regarding the imperfect mechanism of occurrence and development of prostate adenocarcinoma (PRAD), this study investigated mRNA-modified FUS/NRF2 signalling to inhibit ferroptosis and promote prostate adenocarcinoma growth.
Methods: Bioinformatics analysis was used to obtain the expression of FUS and its mRNA modification in PRAD. The expression of FUS in prostate cells (CRPC) and the level of m6A methylation modification, ferroptosis (P53 and GPX4), apoptosis (Caspase3), ferroptosis (P53 and GPX4), and apoptosis (Caspase3) in CRPC after ferroptosis inducer Erastin, ferroptosis inhibitor, and FUS knockdown were detected. Autophagy (LC3B), oxidative stress (GSH and ROS), and expression of NRF2/HO-1 pathway are indicators.
Results: FUS was highly expressed in PRAD and phenomenally reduced the survival rate of patients. After knocking down FUS, the level of m6A methylation was significantly reduced, and the expressions of ferroptosis markers P53 and GPX4 were phenomenally reduced, while the levels of apoptosis and autophagy markers Caspase3 and LC3B remained unchanged. Upregulated and NRF2/HO-1 pathway indicators were upregulated. It shows that m6A methylation modification is reduced when FUS is the low expression, inhibits the expression of P53 and GPX4, downregulates GSH, upregulates ROS, activates the NRF2/HO-1 pathway, and promotes ferroptosis to inhibit the occurrence of RPAD.
Conclusions: The increase of m6A methylation modification can increase the expression of FUS, thereby promoting the expression of P53 and GPX4, upregulating GSH, downregulating ROS, inhibiting the NRF2/HO-1 pathway, inhibiting ferroptosis, and promoting the growth of PRAD.

DOI: https://doi.org/10.1155/2022/8509626
J Cancer Res Clin Oncol. 2022 Aug 28.

Wilms tumor 1 associated protein promotes epithelial mesenchymal transition of gastric cancer cells by accelerating TGF-β and enhances chemoradiotherapy resistance.

Yu Liu, Mingxu Da.

   PURPOSE: Wilms tumor 1 associated protein (WTAP) is a key RNA n6-methyladenosine (m6A) methylase, which predicts the occurrence of many diseases, such as liver fibrosis formation, coordinating cancer stem cell function, and promoting tumor development. Gastric cancer (GC) is one of the most common malignant tumors worldwide. However, the role of WTAP in GC development and drug resistance remains unclear.
METHODS: Biological methods and data analysis were used to investigate the expression of WTAP in gastric carcinoma tissue. The expression of transforming growth factor-beta (TGF-β) and epithelial mesenchymal transition (EMT) in GC cells were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and Western blot (WB) with WTAP overexpression cell lines and WTAP knockout cell lines. Gradient concentrations of cisplatin (DDP), gradient cyclophosphamide (CTX), or radiation X-rays were added to WTAP overexpression cell lines and WTAP knockdown cell lines to observe the change of cell viability after radiotherapy and chemotherapy treatment.
RESULTS: The expression of WTAP in gastric carcinoma tissue significantly increased as determined by bioinformatics analysis, and a high expression of WTAP was closely associated with poor prognosis of gastric cancer patients. Overexpression of WTAP promoted migration and EMT of GC cells and promoted the expression of TGF-β and the stability of mRNA. WTAP knockdown inhibited migration of GC cells and decreased TGF-β expression and stability of mRNA. In addition, WTAP promoted multiple chemotherapy resistance and radiotherapy resistance in GC.
CONCLUSIONS: WTAP is a potential predictive biomarker for GC. Our findings revealed a novel mechanism by which WTAP regulates chemoradiotherapy resistance, extending the understanding of the m6A machinery in TGF-β induced EMT and metastasis in GC.

Keywords:  EMT; M6A; TGF-β; Treatment resistance; WTAP

DOI:  https://doi.org/10.1007/s00432-022-04320-7
Kaohsiung J Med Sci. 2022 Sep 02.

Long non-coding RNA SNHG16 decreased SMAD4 to induce gemcitabine resistance in pancreatic cancer via EZH2-mediated epigenetic modification.

Yi Yu, Yu-Feng Zou, Run-Qi Hong, Wen-Jie Chen, Liang Chen, Wen-Qi Chen, Hui-Peng Wang, Yuan Yu.

  Gemcitabine resistance (GR) in pancreatic cancer (PC) results in poor patient outcomes. SMAD family member (Smad4) dysregulation is a significant role of GR in PC, and EZH2 is involved in Smad4 expression in tumor progression. Interestingly, lncRNA small nucleolar RNA host gene 16 (SNHG16) might interact with EZH2, indicating a potential pathway to overcome gemcitabine-resistant PC progression. We investigated the role of the SNHG16/EZH2/Smad4 pathway in gemcitabine-resistant PC cells (PANC-1/GR and SW1990/GR). First, we found that SNHG16 was upregulated both in wild-type PC cells and in gemcitabine-resistant PC cells. SNHG16 overexpression reduced gemcitabine cytotoxicity and apoptosis in PC cells. Meanwhile, SNHG16 upregulation caused p-Akt elevation and Smad4 reduction. However, SNHG16 silencing induced the opposite trend. Then, we found that EZH2 was enriched in SNHG16 based on RIP and RNA pulldown. In particular, SNHG16 overexpression promoted the interaction between EZH2 and the Smad4 promoter according to Chromatin immunoprecipitation-quantitative polymerase chain reaction. Finally, both EZH2 inhibition and Smad4 upregulation increased gemcitabine cytotoxicity and apoptosis in PC cells during SNHG16 overexpression. Moreover, both treatments decreased p-Akt and increased Smad4. Collectively, lncRNA SNHG16 decreased Smad4 to induce GR in PC via EZH2-mediated epigenetic modification.

Keywords:  EZH2; Smad4; gemcitabine resistance; lncRNA SNHG16; pancreatic cancer

DOI:  https://doi.org/10.1002/kjm2.12574
Biochem Biophys Res Commun. 2022 Aug 19. pii: S0006-291X(22)01159-7. [Epub ahead of print]627 103-110

IGF2BP3-NRF2 axis regulates ferroptosis in hepatocellular carcinoma.

Zhihua Lu, Hao Yang, Yuting Shao, Wensheng Sun, Yuanhui Jiang, Jie Li.

  Poor sensitivity to sorafenib has been an important constraint on the efficacy of targeted therapy in advanced hepatocellular carcinoma (HCC). Therefore, it is particularly important to explore effective therapeutic targets to improve the sensitivity of HCC cells to sorafenib. Upregulation of IGF2BP3 is strongly associated with tumor invasion, early recurrence and poor prognosis in various human cancers, including HCC, but its roles in the sorafenib treatment of HCC remain unclear. In our study, IGF2BP3 knock-down significantly promoted ferroptosis in HCC cells through the evaluation of the Reactive Oxygen Species (ROS), Fe2+ and malondialdehyde (MDA) levels after sorafenib administration. In addition, NRF2 mRNA was identified as an important target of IGF2BP3 by bioinformatics analysis, RNA binding protein immunoprecipitation (RIP) and RNA pulldown experiments. More importantly, IGF2BP3, as an m6A (N6-Methyladenosine) reader, was shown to promote the stability of NRF2 mRNA by reading its m6A modification. Similar results were obtained from in vivo experiments. In summary, our study uncovered the role of IGF2BP3-NRF2 axis on ferroptosis in HCC, providing significant evidence for new anti-cancer strategies aimed at improving the efficacy of sorafenib.

Keywords:  Ferroptosis; HCC; IGF2BP3; NRF2; Sorafenib; m6A

DOI:  https://doi.org/10.1016/j.bbrc.2022.08.040
Asian Pac J Cancer Prev. 2022 Aug 01. pii: 90239. [Epub ahead of print]23(8): 2649-2654

The Relationship between Circulating Irisin and Oxidative Stress in Gastric and Colorectal Cancer Patients.

Ahmed Abd Tumer, Farah A Rashid.

   OBJECTIVE: Gastric and colorectal cancers are two obesity-related cancers. Irisin is a dipo-myokine with an important role in the body's energy homeostasis. Oxidative Stress has a crucial role in tumorigenesis. Therefore, this study aims to investigate the association of circulating irisin with oxidative stress in gastric and colorectal cancer patients.
METHODS: A case-control study involving 62 gastric and colorectal cancers and 22 healthy individuals was carried out. Serum irisin and Total Antioxidant Capacity were measured by sandwich enzyme-linked immunosorbed assay (ELIZA) kits. Total Oxidative Stress (TOS) was measured using colorimetric methods and oxidative stress index (OSI) was also calculated.
RESULTS: Serum irisin decreased significantly (p<0.0001) in gastric and colorectal cancer cases compared to healthy individuals. The TOS and OSI levels increased significantly (p<0.0001) in gastric and colorectal cancer cases compared to healthy individuals. No significant correlation was found in terms of irisin, TOS, TAC, and OSI in gastric and colorectal cancer cases and control groups.
CONCLUSION: Circulating irisin decreases and oxidative stress increases in gastric and colorectal cancers. There is no correlation between irisin and oxidative stress. The mechanism by which irisin is associated with oxidative stress is still not clear.

Keywords:  Gastric cancer; colorectal cancer; irisin; oxidative stress

DOI:  https://doi.org/10.31557/APJCP.2022.23.8.2649
Mol Cancer. 2022 Sep 02. 21(1): 174

The m6A demethylase ALKBH5-mediated upregulation of DDIT4-AS1 maintains pancreatic cancer stemness and suppresses chemosensitivity by activating the mTOR pathway.

Yi Zhang, Xiaomeng Liu, Yan Wang, Shihui Lai, Zhiqian Wang, Yudie Yang, Wenhui Liu, Hongquan Wang, Bo Tang.

   BACKGROUND: Chemoresistance is a major factor contributing to the poor prognosis of patients with pancreatic cancer, and cancer stemness is one of the most crucial factors associated with chemoresistance and a very promising direction for cancer treatment. However, the exact molecular mechanisms of cancer stemness have not been completely elucidated.
METHODS: m6A-RNA immunoprecipitation and sequencing were used to screen m6A-related mRNAs and lncRNAs. qRT-PCR and FISH were utilized to analyse DDIT4-AS1 expression. Spheroid formation, colony formation, Western blot and flow cytometry assays were performed to analyse the cancer stemness and chemosensitivity of PDAC cells. Xenograft experiments were conducted to analyse the tumour formation ratio and growth in vivo. RNA sequencing, Western blot and bioinformatics analyses were used to identify the downstream pathway of DDIT4-AS1. IP, RIP and RNA pulldown assays were performed to test the interaction between DDIT4-AS1, DDIT4 and UPF1. Patient-derived xenograft (PDX) mouse models were generated to evaluate chemosensitivities to GEM.
RESULTS: DDIT4-AS1 was identified as one of the downstream targets of ALKBH5, and recruitment of HuR onto m6A-modified sites is essential for DDIT4-AS1 stabilization. DDIT4-AS1 was upregulated in PDAC and positively correlated with a poor prognosis. DDIT4-AS1 silencing inhibited stemness and enhanced chemosensitivity to GEM (Gemcitabine). Mechanistically, DDIT4-AS1 promoted the phosphorylation of UPF1 by preventing the binding of SMG5 and PP2A to UPF1, which decreased the stability of the DDIT4 mRNA and activated the mTOR pathway. Furthermore, suppression of DDIT4-AS1 in a PDX-derived model enhanced the antitumour effects of GEM on PDAC.
CONCLUSIONS: The ALKBH5-mediated m6A modification led to DDIT4-AS1 overexpression in PDAC, and DDIT-AS1 increased cancer stemness and suppressed chemosensitivity to GEM by destabilizing DDIT4 and activating the mTOR pathway. Approaches targeting DDIT4-AS1 and its pathway may be an effective strategy for the treatment of chemoresistance in PDAC.

Keywords:  ALKBH5; Chemosensitivity; DDIT4-AS1; Stemness; UPF1

DOI:  https://doi.org/10.1186/s12943-022-01647-0
Front Oncol. 2022 ;12 834524

Identification of PLAUR-related ceRNA and immune prognostic signature for kidney renal clear cell carcinoma.

Yu Wang, Zhuolun Sun, Shuo Lu, Xu Zhang, Chutian Xiao, Tengcheng Li, Jieying Wu.

  Kidney renal clear cell carcinoma (KIRC) represents one of the most fatal cancers, usually showing malignant progression and a high tumor recurrence rate. The urokinase-type plasminogen activator receptor (PLAUR) plays a critical role in the initiation and progression of several cancers, including KIRC. However, the function and mechanism of PLAUR in patients with KIRC are still unclear and require further investigation. In the present study, we first explored the expression profile and prognostic values of PLAUR in pan-cancer based on The Cancer Genome Atlas and Genotype-Tissue Expression databases. PLAUR was upregulated in multiple cancers and was significantly associated with poor overall survival and disease-free survival only in patients with KIRC. Subsequently, the PVT1/SNHG15-hsa-miR-532-3p axis was identified as the most potential upstream regulatory network of PLAUR in KIRC. In addition, PLAUR expression was closely associated with tumor-infiltrating immune cells, tumor immunity biomarkers, and immunomodulator expression. Furthermore, we constructed a multiple-gene risk prediction signature according to the PLAUR-related immunomodulators (PRIs). A prognostic nomogram was then developed to predict the 1-, 3-, and 5-year survival probabilities of individuals. In conclusion, our study identified the PVT1/SNHG15-hsa-miR-532-3p-PLAUR axis and a prognostic signature of PRIs, which could be a reference for future clinical research.

Keywords:  PLAUR; ceRNA; immunomodulators; kidney renal clear cell carcinoma; prognostic signature

DOI:  https://doi.org/10.3389/fonc.2022.834524
ACS Cent Sci. 2022 Aug 24. 8(8): 1102-1115

Allosteric Regulation of IGF2BP1 as a Novel Strategy for the Activation of Tumor Immune Microenvironment.

Yang Liu, Qiang Guo, Heng Yang, Xiao-Wen Zhang, Na Feng, Jing-Kang Wang, Ting-Ting Liu, Ke-Wu Zeng, Peng-Fei Tu.

Tumor immune microenvironment (TIME) regulators are promising cancer immunotherapeutic targets. IGF2BP1, as a crucial N 6-methyladenosine (m6A) reader protein, recognizes m6A target transcripts, ultimately leading to cancer development. However, currently, the biological function of IGF2BP1 in regulating the TIME is not well-understood. In this study, we report that IGF2BP1 knockdown induces cancer cell apoptosis, thereby significantly not only activating immune cell infiltration including CD4+, CD8+ T cells, CD56+ NK cells, and F4/80+ macrophage but also decreasing PD-L1 expression in hepatocellular carcinoma (HCC). Then, chemical genetics identifies a small-molecule cucurbitacin B (CuB), which directly targets IGF2BP1 at a unique site (Cys253) in the KH1-2 domains. This leads to a pharmacological allosteric effect to block IGF2BP1 recognition of m6A mRNA targets such as c-MYC, which is highly associated with cell apoptosis and immune response. In vivo, CuB exhibits an obvious anti-HCC effect through inducing apoptosis and subsequently recruits immune cells to tumor microenvironment as well as blocking PD-L1 expression. Collectively, IGF2BP1 may serve as a novel pharmacological allosteric target for anticancer therapeutics via mediating TIME.

DOI: https://doi.org/10.1021/acscentsci.2c00107
J Clin Lab Anal. 2022 Aug 21. e24644

A peptide translated from circPPP1R12A promotes the malignancy of non-small cell lung cancer cells through AKT signaling pathway.

Weijun Zhao, Yibo Xue, Yandan Zhang, Yonggang Zhu, Zixuan Chen, Xiaodong Zhao.

   BACKGROUND: Recent literature have indicated that the malignancy of cancer cells is modulated by hsa_circ_0000423 (named circPPP1R12A) through the way of translating protein. Herein, we investigated the role and latent mechanisms of circPPP1R12A in Non-Small Cell Lung Cancer (NSCLC).
METHODS: CircPPP1R12A expression was measured by qRT-PCR. The malignancy of NSCLC was determined by CCK-8, TUNEL assay, Wound healing, Transwell and Western blotting assays. The underlying mechanisms of circPPP1R12A were confirmed by Western blotting and qRT-PCR assays.
RESULTS: CircPPP1R12A expression in NSCLC tissues was higher than that of neighboring normal tissues. CircPPP1R12A showed an upregulated expression in NSCLC cells. Upregulation of circPPP1R12A could promote the cell viability of NSCLC cells and reduce the apoptosis of NSCLC cells, while it could not promote cell invasion and migration. The reduction of cell viability and apoptosis was discovered in NSCLC cells with the silencing of circPPP1R12A, but circPPP1R12A knockdown does not inhibit cell invasion and migration. There was something interesting that circPPP1R12A encoding protein circPPP1R12A-73aa was found in NSCLC cells. Mutations in circPPP1R12a-73AA might disrupt the function of circPPP1ra-73AA in A549 and H1299 cells. Next, we found that circPPP1R12A caused the increased growth of NSCLC cells by activating AKT signaling pathway.
CONCLUSION: In summary, our study proved that NSCLC cell proliferation was promoted by circPPP1R12A-73aa translated from circPPP1R12A through the AKT pathway, which could throw some light on the understanding of the mechanism of NSCLC.

Keywords:  AKT pathway; Hsa_circ_0000423; non-small cell lung cancer; proliferation

DOI:  https://doi.org/10.1002/jcla.24644