bims-rimeca 2022-10-16 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022–10–16
thirty-two papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

Role of m6A RNA Methylation in Thyroid Cancer Cell Lines.
The emerging therapeutic target of dynamic and reversible N6-methyladenosine modification during cancer development.
Integrated Analyses of m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization in Pan-Cancer.
Protein kinase C beta relieves autism-like behavior in EN2 knockout mice via upregulation of the FTO/PGC-1α/UCP1 axis.
Integrative Analysis of N6-Methyladenosine-Related Enhancer RNAs Identifies Distinct Prognosis and Tumor Immune Micro-Environment Patterns in Head and Neck Squamous Cell Carcinoma.
Profiling Analysis of N6-Methyladenosine mRNA Methylation Reveals Differential m6A Patterns during the Embryonic Skeletal Muscle Development of Ducks.
circRERE regulates the expression of GBX2 through miR-1299 and ZC3H13/N6-methyladenosine (m6A) to promote growth and invasion of hepatocellular carcinoma cells.
Construction and validation of prognostic prediction established on N6-methyladenosine related genes in cervical squamous cell carcinoma.
Prognostic N6-methyladenosine (m6A)-related lncRNA patterns to aid therapy in pancreatic ductal adenocarcinoma.
Analysis of the m6A modification regulators in the substantia nigra and striatum of MPTP-induced Parkinson's disease mice.
m6 A demethylase Fto regulates the TNF-α-induced inflammatory response in cementoblasts.
DLGAP1-AS2 promotes human colorectal cancer progression through trans-activation of Myc.
Critical functions of N6-adenosine methylation of mRNAs in T cells.
N6-methyladenosine modification: A potential regulatory mechanism in spinal cord injury.
LncRNA MALAT1 regulates METTL3-mediated PD-L1 expression and immune infiltrates in pancreatic cancer.
Decreased Urine N6-methyladenosine level is closely associated with the presence of diabetic nephropathy in type 2 diabetes mellitus.
Exploration of N6-Methyladenosine Profiles of mRNAs and the Function of METTL3 in Atherosclerosis.
N-acetyltransferase 10 promotes colon cancer progression by inhibiting ferroptosis through N4-acetylation and stabilization of ferroptosis suppressor protein 1 (FSP1) mRNA.
N6-methyladenosine-related microRNAs risk model trumps the isocitrate dehydrogenase mutation status as a predictive biomarker for the prognosis and immunotherapy in lower grade gliomas.
Prediction of prognosis, immune infiltration and immunotherapy response with N6-methyladenosine-related lncRNA clustering patterns in cervical cancer.
Molecular mechanism analysis of m6A modification-related lncRNA-miRNA-mRNA network in regulating autophagy in acute pancreatitis.
Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine.
5-methylcytosine (m5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons.
YTHDF2-mediated FGF14-AS2 decay promotes osteolytic metastasis of breast cancer by enhancing RUNX2 mRNA translation.
m6A Modification of Long Non-Coding RNA HNF1A-AS1 Facilitates Cell Cycle Progression in Colorectal Cancer via IGF2BP2-Mediated CCND1 mRNA Stabilization.
Integrative pan-cancer analysis and clinical characterization of the N7-methylguanosine (m7G) RNA modification regulators in human cancers.
Methylation of N6 adenosine-related long non-coding RNA: effects on prognosis and treatment in "driver-gene-negative" lung adenocarcinoma.
Atranorin driven by nano materials SPION lead to ferroptosis of gastric cancer stem cells by weakening the mRNA 5-hydroxymethylcytidine modification of the Xc-/GPX4 axis and its expression.
Identification of m6A-related long non-coding RNAs for predicting prognosis and immune characterizations in gastric cancer.
MiR-654-3p, reduced by the excessive ALKBH5, Alleviated the Inflammation in OA by targeting TNFRSF9, the trigger of the NF-κB pathway.
Cuproptosis depicts tumor microenvironment phenotypes and predicts precision immunotherapy and prognosis in bladder carcinoma.
Construction and Characterization of n6-Methyladenosine-Related lncRNA Prognostic Signature and Immune Cell Infiltration in Kidney Renal Clear Cell Carcinoma.

Int J Mol Sci. 2022 Sep 29. pii: 11516. [Epub ahead of print]23(19):

Role of m6A RNA Methylation in Thyroid Cancer Cell Lines.

Lorenzo Allegri, Federica Baldan, Elisabetta Molteni, Catia Mio, Giuseppe Damante.

  N6-methyladenosine (m6A) is the most abundant internal modification of RNA in eukaryotic cells, and, in recent years, it has gained increasing attention. A good amount of data support the involvement of m6A modification in tumorigenesis, tumor progression, and metastatic dissemination. However, the role of this RNA modification in thyroid cancer still remains poorly investigated. In this study, m6A-related RNA methylation profiles are compared between a normal thyroid cell line and different thyroid cancer cell lines. With this approach, it was possible to identify the different patterns of m6A modification in different thyroid cancer models. Furthermore, by silencing METTL3, which is the main player in the RNA methylation machinery, it was possible to evaluate the impact of m6A modification on gene expression in an anaplastic thyroid cancer model. This experimental approach allowed us to identify DDI2 as a gene specifically controlled by the m6A modification in anaplastic thyroid cancer cell lines. Altogether, these data are a proof of concept that RNA methylation widely occurs in thyroid cancer cell models and open a way forward in the search for new molecular patterns for diagnostic discrimination between benign and malignant lesions.

Keywords:  METTL3; RNA methylation; epitranscriptome; m6A; thyroid cancer

DOI:  https://doi.org/10.3390/ijms231911516
Front Oncol. 2022 ;12 970833

The emerging therapeutic target of dynamic and reversible N6-methyladenosine modification during cancer development.

Shougeng Liu, Sihong Chen, Chengfang Tang, Yingxi Zhao, Wei Cui, Lina Jia, Lihui Wang.

  As a reversible and dynamic epigenetic modification, N6-methyladenosine (m6A) modification is ubiquitous in eukaryotic cells. m6A methylation is prevalent in almost all RNA metabolism processes that affect the fate of cells, including cancer development. As indicated by the available evidence, targeting m6A regulators may play a crucial role in tumor therapy and multidrug resistance. Currently, many questions remain uncovered. Here, we review recent studies on m6A modification in various aspects of tumor progression, tumor immunity, multidrug resistance, and therapeutic targets to provide new insight into the m6A methylation process.

Keywords:  RNA epigenetics; cancer; cancer immunity; clinical perspectives; m6A modification

DOI:  https://doi.org/10.3389/fonc.2022.970833
Int J Mol Sci. 2022 Sep 23. pii: 11182. [Epub ahead of print]23(19):

Integrated Analyses of m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization in Pan-Cancer.

Qingkang Cao, Yuanyuan Chen.

  The invasion of immune cells in the tumor microenvironment (TME) is closely related to cancer development. Studies have demonstrated that N6-methyladenosine (m6A) can affect the invasion of immune cells in TME as well as cancer development. We comprehensively analyzed the RNA-seq data of 16 different cancer types based on 20 m6A regulators and identified two distinct m6A modification patterns, which were closely associated with TME cell infiltration and overall patient survival. Then, we used principal component analysis (PCA) to construct m6Ascore based on the expression of m6A-related prognostic genes, which can successfully predict patient survival. The low-m6Ascore subtype is characterized by more immune cell infiltration, good prognosis and lower TNM stages, while the high-m6Ascore subtype is characterized by low immune infiltration, stromal activation, and poor prognosis. m6Ascore was also closely associated with immunotherapy response and was significantly higher in complete response/partial response (CR/PR) patients than in stable disease/progressive disease (SD/PD) patients in both immunotherapy cohorts. Therefore, our study indicates that m6A modification plays an important role in the prognosis of pan-cancer and the formation of complex TME in pan-cancer. Our research helps to improve the cognition of m6A modifications at pan-cancer levels and identify more effective strategies for immunotherapy.

Keywords:  N6-methyladenosine; immune infiltration; immunotherapy; pan-cancer; tumor microenvironment

DOI:  https://doi.org/10.3390/ijms231911182
J Biochem Mol Toxicol. 2022 Oct 14. e23236

Protein kinase C beta relieves autism-like behavior in EN2 knockout mice via upregulation of the FTO/PGC-1α/UCP1 axis.

Xingyu Song, Qibo Hu, Xiaoheng Xu, Wei Pan.

  Increasing evidence suggests that disruption of neuron activity contributes to the autistic phenotype. Thus, we aimed in this study to explore the role of protein kinase C beta (PKCβ) in the regulation of neuron activity in an autism model. The expression of PKCβ in the microarray data of autism animal models was obtained from the Gene Expression Omnibus database. Then, mice with autism-like behavior were prepared in EN2 knockout (-/- ) mice. The interaction between PKCβ on fat mass and obesity-associated protein (FTO) as well as between PGC-1α and uncoupling protein 1 (UCP1) were characterized. The effect of FTO on the N6 -methyladenosine (m6A) modification level of proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) was assayed. Following transfection of overexpressed PKCβ and/or silenced UCP1, effects of PKCβ and UCP1 in autism-like behaviors in EN2-/- mice were analyzed. Results showed that PKCβ was downregulated in EN2-/- mouse brain tissues or neurons. PKCβ promoted the expression and stability of FTO, which downregulated the m6A modification level of PGC-1α to promote its expression. Moreover, PGC-1α positively targeted the expression of UCP1. PKCβ knockdown enhanced sociability and spatial exploration ability, and reduced neuron apoptosis in EN2-/- mouse models of autism, which was reversed by UCP1 overexpression. Collectively, PKCβ overexpression leads to activation of the FTO/m6A/PGC-1α/UCP1 axis, thus inhibiting neuron apoptosis and providing neuroprotection in mice with autism-like behavior.

Keywords:  EN2 knockout mice; N6-methyladenosine; autism; fat mass and obesity associated protein; peroxisome proliferator-activated receptor gamma coactivator 1-alpha; protein kinase C beta; uncoupling protein 1

DOI:  https://doi.org/10.1002/jbt.23236
Cancers (Basel). 2022 Sep 25. pii: 4657. [Epub ahead of print]14(19):

Integrative Analysis of N6-Methyladenosine-Related Enhancer RNAs Identifies Distinct Prognosis and Tumor Immune Micro-Environment Patterns in Head and Neck Squamous Cell Carcinoma.

Hongshi Cai, Jianfeng Liang, Yaoqi Jiang, Rukeng Tan, Chen Hou, Jinsong Hou.

  At present, the prognostic value of N6-methyladenosine (m6A)-related enhancer RNAs (eRNAs) for head and neck squamous cell carcinoma (HNSCC) still remains unclear. Our study aims to explore the prognostic value of m6A-related eRNAs in HNSCC patients and their potential significance in immune infiltration and immunotherapy. We constructed a 5 m6A-related eRNAs risk model from The Cancer Genome Atlas (TCGA) HNSCC dataset, using univariate and multivariate Cox and least absolute shrinkage and selection operator (LASSO) regression analysis. Based on the SRAMP website and in vitro experiments, it was verified that these 5 m6A-related eRNAs had m6A sites, the expression of which was regulated by corresponding m6A regulators. Moreover, we constructed a nomogram base on 5 m6A-related eRNAs and confirmed the consistency and robustness of an internal TCGA testing set. Further analysis found that the risk score was positively associated with low overall survival (OS), tumor cell metastasis, metabolic reprogramming, low immune surveillance, lower expression of immune-related genes, and higher expression of targeted genes. Finally, we verified that silencing MIR4435-2HG inhibited HNSCC cell migration and invasion. This study contributes to the understanding of the characteristics of m6A-related eRNAs in HNSCC and provides a reference for effective immunotherapy and targeted therapy.

Keywords:  N6-methyladenosine; enhancer RNA; head and neck squamous cell carcinoma; immunity

DOI:  https://doi.org/10.3390/cancers14194657
Animals (Basel). 2022 Sep 28. pii: 2593. [Epub ahead of print]12(19):

Profiling Analysis of N6-Methyladenosine mRNA Methylation Reveals Differential m6A Patterns during the Embryonic Skeletal Muscle Development of Ducks.

Biao Chen, Shuibing Liu, Wentao Zhang, Ting Xiong, Mingfang Zhou, Xiaolong Hu, Huirong Mao, Sanfeng Liu.

  N6-Methyladenosine is a reversible epigenetic modification that influences muscle development. However, the m6A modification profile during poultry skeletal muscle development is poorly understood. Here, we utilized m6A-specific methylated RNA immunoprecipitation sequencing to identify m6A sites during two stages of breast muscle development in ducks: embryonic days 13 (E13) and E19. MeRIP-seq detected 19,024 and 18,081 m6A peaks in the E13 and E19 groups, respectively. Similarly to m6A distribution in mammalian transcripts, our results revealed GGACU as the main m6A motif in duck breast muscle; they also revealed that m6A peaks are mainly enriched near the stop codons. In addition, motif sequence analysis and gene expression analysis demonstrated that m6A modification in duck embryo skeletal muscles may be mediated by the methyltransferase-like 14. GO and KEGG analysis showed that m6A peaks containing genes at E19 were mainly enriched in muscle-differentiation- and muscle-growth-related pathways, whereas m6A peaks containing genes in E13 were mainly enriched in embryonic development and cell proliferation pathways. Combined analysis of MeRIP-seq and RNA-seq showed that the mRNA expression may be affected by m6A modification. Moreover, qRT-PCR analysis of the expression of METTL14 and its cofactors (WTAP, ZC3H13, RBM15 and VIRMA) during duck embryonic skeletal muscle development in breast and leg muscle samples revealed a significant downward trend as the developmental age progressed. Our results demonstrated that m6A mRNA methylation modifications control muscle development in ducks. This is the first study of m6A modification patterns in duck muscle tissue development, and it lays the foundation for the study of the effects of RNA modification on poultry skeletal muscle development.

Keywords:  MeRIP-seq; N6-methyladenosine methylation; breast muscle; duck; embryonic muscle development

DOI:  https://doi.org/10.3390/ani12192593
J Biosci. 2022 ;pii: 52. [Epub ahead of print]47

circRERE regulates the expression of GBX2 through miR-1299 and ZC3H13/N6-methyladenosine (m6A) to promote growth and invasion of hepatocellular carcinoma cells.

Yong-Hua Lin, Bao-Yan Zhang, Zhi-Chao Singh Chen.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumours in the world. Current studies have shown that circular RNAs (circRNAs) and N6-methyladenosine (m6A) methylation play important roles in the progression of HCC, but further studies are needed to confirm the underlying mechanisms. The expression of circRERE was significantly upregulated in HCC cells, and its downregulation reduced HCC cell viability and invasion while increasing apoptosis. Further study showed that circRERE bound directly to miR- 1299. After downregulating the expression of circRERE, miR-1299 expression was significantly enhanced, while the expression of its downstream target gene GBX2 was suppressed, indicating that circRERE promoted the expression of GBX2 through miR-1299. In addition, downregulation of circRERE expression significantly increased the m6A level of GBX2 and promoted the expression of methyltransferase ZC3H13, while overexpression of ZC3H13 significantly inhibited the expression of GBX2 but increased its m6A methylation. circRERE could regulate the m6A modification of GBX2 through ZC3H13, thus promoting the expression of GBX2.GBX2 was upregulated in HCC tissues, while miR-1299 and ZC3H13 were downregulated. MiR-1299 mimics, ZC3H13 overexpression or GBX2 siRNA significantly inhibited HCC cell viability, promoted apoptosis and reduced invasion; GBX2 exerted the opposite effects and could reverse the regulatory effects of miR-1299 or ZC3H13 on HCC cells. Therefore, circRERE promotes the growth and invasion of HCC cells by regulating the expression of GBX2 through miR-1299 and ZC3H13/m6A, indicating that it is a key circRNA in the progression of HCC.
Transl Cancer Res. 2022 Sep;11(9): 3064-3079

Construction and validation of prognostic prediction established on N6-methyladenosine related genes in cervical squamous cell carcinoma.

Danxia Chen, Wenhao Guo, Hailan Yu, Jianhua Yang.

   Background: Cervical cancer (CESC) is the second most common cancer death in middle-aged women. The N6-methyladenosine (m6A) plays an essential role in the epitranscriptomics of cancer and affects immune cell infiltration. Our study used The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data to construct and validate prognostic prediction established on m6A-related genes in CESC.
Methods: We gained gene expression and clinical characteristics from TCGA and GEO. After differentially expression analysis of the m6A-related genes, we identified eight genes of CESC development. Next, we executed consensus clustering to analyze CESC types established on the differential expression of the m6A-related genes and found different subtypes significantly correlate with survival prognosis, immune microenvironment, and PD-L1 expression. Then, based on Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis, a five-gene (IGF2BP1, IGF2BP2, HNRNPA2B1, YTHDF1, RBM15) predictive model was built in the TCGA training cohort. Finally, we checked the predictive model with survival analysis and receiver operating characteristic (ROC) curve both in the training cohort (TCGA) and in the validation cohort (GSE44001). We found the expression and variation of the five genes significantly correlate with immune cell infiltration.
Results: The CESC could be divided into subtypes according to eight expression m6A-related genes. Different subtypes are related to various immune cells, immune scores, and the expression of the PD-L1. We develop a risk prediction model: risk score = (0.023558929) * Exp IGF2BP1 + (0.021148829) * Exp IGF2BP2 + (0.045035491) * Exp HNRNPA2B1 + (-0.106566550) * Exp YTHDF1 + (-0.001037932) * Exp RBM15. Moreover, different m6A-related genes significantly correlated with immune cells.
Conclusions: The m6A-related genes risk prediction model plays an essential role in predicting CESC patients. The m6A-related genes affected the immune cell infiltration in CESC. These results suggest that the expression of m6A-related genes may influence the immune therapy of CESC and be the potential therapeutic target.

Keywords:  Cervical squamous cell carcinoma; immune cell infiltration; m6A RNA methylation; prognostic prediction

DOI:  https://doi.org/10.21037/tcr-22-881
Front Genet. 2022 ;13 866340

Prognostic N6-methyladenosine (m6A)-related lncRNA patterns to aid therapy in pancreatic ductal adenocarcinoma.

Yuxin Wang, Yutian Ji, Qianhui Xu, Wen Huang.

  Background: Mounting research studies have suggested the indispensable roles of N6-methyladenosine (m6A) RNA modification in carcinogenesis. Nevertheless, it was little known about the potential function of m6A-related lncRNAs in sample clustering, underlying mechanism, and anticancer immunity of pancreatic ductal adenocarcinoma (PDAC). Methods: PDAC sample data were obtained from TCGA-PAAD project, and a total of 23 m6A regulators were employed based on published articles. Pearson correlation and univariate Cox regression were analyzed to determine m6A-related lncRNAs with prognostic significance to identify distinct m6A-related lncRNA subtypes by consensus clustering. Next, the least absolute shrinkage and selection operator (LASSO) algorithm was applied for constructing an m6A-related lncRNA scoring system, further quantifying the m6A-related lncRNA patterns in individual samples. Gene set variation analysis (GSVA) was employed to assign pathway activity estimates to individual samples. To decode the comprehensive landscape of TME, the CIBERSORT method and ESTIMATE algorithm were analyzed. The half-maximal inhibitory concentration (IC50) of chemotherapeutic agents was predicted with the R package pRRophetic. Finally, a quantitative real-time polymerase chain reaction was used to determine TRPC7-AS1 mRNA expression in PDAC. Results: Two distinct m6A-related lncRNA patterns with different clinical outcomes, TEM features, and biological enrichment were identified based on 45 prognostic m6A-related lncRNAs. The identification of m6A-related lncRNA patterns within individual samples based on risk scores contributed to revealing biological signatures, clinical outcomes, TEM characterization, and chemotherapeutic effects. A prognostic risk-clinical nomogram was constructed and confirmed to estimate m6A-related lncRNA patterns in individual samples. Finally, the biological roles of TRPC7-AS1 were revealed in PDAC. Conclusion: This work comprehensively elucidated that m6A-related lncRNA patterns served as an indispensable player in prognostic prediction and TEM features. Quantitative identification of m6A-related lncRNA patterns in individual tumors will contribute to sample stratification for further optimizing therapeutic strategies.

Keywords:  m6A-related lncRNA patterns; molecular mechanism; pancreatic ductal adenocarcinoma; prognostic prediction; tumor microenvironment

DOI:  https://doi.org/10.3389/fgene.2022.866340
Neurosci Lett. 2022 Oct 06. pii: S0304-3940(22)00468-2. [Epub ahead of print] 136907

Analysis of the m6A modification regulators in the substantia nigra and striatum of MPTP-induced Parkinson's disease mice.

Ziying Yu, Lishuang Huang, Yinyin Xia, Shuqun Cheng, Cantao Yang, Chengzhi Chen, Zhen Zou, Xiaoliang Wang, Xin Tian, Xuejun Jiang, Lixiao Zhou.

  Parkinson's disease (PD) is one of the most common neurodegenerative disorders of aging that impairs predominately dopaminergic neurons. N6-methyladenosine (m6A) is the most prevalent form of internal RNA modification in eukaryotes and it plays an essential role in normal brain development and neurodegenerative diseases. The m6A status is dynamically modulated by diverse types of genes called "writers", "erasers" and "readers". However, whether these m6A regulators are perturbed in PD remains poorly understood. To clarify this point, we established a PD mouse model using 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). The motor as well as learning and memory ability of mice were evaluated through and rotarod and Y maze spontaneous alternation tests. Morphological characteristics of tyrosine hydroxylase (TH)-positive cells were visualized using immunohistochemistry, while expression of alpha-synuclein (α-syn) and TH were determined by using western blot. Furthermore, the expression of the m6A regulators in the substantia nigra and striatum were evaluated by using qRT-PCR and western blot. As a result, the MPTP-induced PD mice suffered from learning and memory as well as motor defects. Additionally, there were significant TH+ neuron losses in the substantia nigra and striatum of MPTP-injected mice. In the PD mice, proteins including ALKBH5, IGF2BP2 were up-regulated in the substantia nigra, while YTHDF1 and FMR1 were down-regulated. For the striatum, FMR1 and CBLL1were up-regulated, while IGF2BP3, METTL3 and RBM15 were down-regulated. The expressions of genes at the mRNA level were partially in accordance with the protein changes. These findings indicate the m6A regulators may participate in PD pathogenesis.

Keywords:  MPTP; Parkinson’s disease; m6A regulators; striatum; substantia nigra

DOI:  https://doi.org/10.1016/j.neulet.2022.136907
Oral Dis. 2022 Oct 13.

m6 A demethylase Fto regulates the TNF-α-induced inflammatory response in cementoblasts.

Biao Li, Mingyuan Du, Qiao Sun, Zhengguo Cao, Hong He.

   OBJECTIVE: Apical periodontitis is the most frequently occurring pathological lesion. Fat mass and obesity-associated protein (Fto) is the first identified RNA N6-methyladenosine demethylase. However, whether Fto regulates apical periodontitis remains unclear. This study aimed to explore the mechanisms of Fto in the tumor necrosis factor-α (TNF-α)-induced inflammatory response.
MATERIALS AND METHODS: We established an apical periodontitis model. An immortalized cementoblast cell line (OCCM-30) cells were exposed to TNF-α. Fto, Il6, Mcp1, and Mmp9 expressions were assessed by qRT-PCR. We knocked down Fto using lentiviruses and detected TNF-α-induced inflammation-related gene expressions and mRNA stability.
RESULTS: Mice with apical periodontitis showed downregulation of Fto expression. OCCM-30 cells exposed to TNF-α showed an upregulation of inflammation-related genes with a decrease in Fto. Furthermore, knockdown of Fto promoted the expressions of Il6, Mcp1, and Mmp9 in TNF-α-treated OCCM-30 cells as compared with negative control cells, whereas it did not affect the mRNA stability. Interestingly, Fto knockdown activated the p65, p38, and ERK1/2 pathways, and it slightly activated the JNK signaling pathway after TNF-α administration in OCCM-30 cells.
CONCLUSION: A TNF-α-induced decrease in the expression of Fto might play a critical role in the inflammatory response in cementoblasts, and knockdown of Fto might upregulate the inflammatory response.

Keywords:  Fto; MAPK; NF-κB; inflammatory response; mRNA stability

DOI:  https://doi.org/10.1111/odi.14396
Mamm Genome. 2022 Oct 12.

DLGAP1-AS2 promotes human colorectal cancer progression through trans-activation of Myc.

Chunfeng Ren, Hongbin Han, Jingjing Pan, Qian Chang, Wanhai Wang, Xiaobing Guo, Jing Bian.

Substantial evidence suggests that non-coding RNA plays a vital role in human cancer, especially long non-coding RNA (lncRNA) with a length greater than 200nt. Herein, we found a lncRNA facilitating human colorectal cancer (CRC) progression. DLGAP1-AS2 was significantly increased in CRC tissues and cell lines. Knockdown of DLGAP1-AS2 inhibited CRC cell proliferation, migration, invasion in vitro, and tumor growth in vivo. The subcellular localization of DLGAP1-AS2 was translocated from the cytoplasm of normal cells to the nucleus of CRC cells due to reduced levels of N6-methyladenosine (m6A) modification. Further, through the screening of a series of signal pathways, we found that Myc pathway was involved in the effect of DLGAP1-AS2. Silencing of DLGAP1-AS2 markedly reduced Myc mRNA and protein levels. Blockade of Myc effectively abolished the enhanced aggressive behaviors of CRC cells caused by DLGAP1-AS2 overexpression. Mechanistically, DLGAP1-AS2 directly bound CTCF, a well-known transcriptional repressor of Myc, resulting in reduced binding of CTCF on Myc promoter and activating Myc transcription. The second hairpin structure of DLGAP1-AS2 was critical for the interaction between DLGAP1-AS2 and CTCF in the nucleus. Taken together, our study reveals the oncogenic regulatory axis of DLGAP1-AS2/CTCF/Myc in CRC, implying a promising targeted therapy for clinical application.

DOI: https://doi.org/10.1007/s00335-022-09963-y
Biochim Biophys Acta Mol Cell Res. 2022 Oct 10. pii: S0167-4889(22)00172-0. [Epub ahead of print] 119380

Critical functions of N6-adenosine methylation of mRNAs in T cells.

Taku Ito-Kureha, Vigo Heissmeyer.

  The existence of N6-adenosine methylation (m6A) of mRNA has been known for a long time, but only recently its regulatory potential was uncovered. Current research deciphers the molecular determinants leading to the deposition of this modification and consequences for modified mRNAs. It also evaluates the importance of such modifications for specific cell types and programs. In this review, we summarize the current knowledge on m6A modification of mRNAs in conventional and regulatory T cells and T-cell-driven immune responses and pathology. We discuss the impact of m6A modification on T cell activation including cytokine and antigen receptor signaling or sensing of double-stranded RNAs (dsRNA).

Keywords:  Epitranscriptomics; T cell; TCR signaling; m6A

DOI:  https://doi.org/10.1016/j.bbamcr.2022.119380
Front Cell Neurosci. 2022 ;16 989637

N6-methyladenosine modification: A potential regulatory mechanism in spinal cord injury.

Derong Liu, Baoyou Fan, Jinze Li, Tao Sun, Jun Ma, Xianhu Zhou, Shiqing Feng.

  N6-methyladenosine (m6A), an essential post-transcriptional modification in eukaryotes, is closely related to the development of pathological processes in neurological diseases. Notably, spinal cord injury (SCI) is a serious traumatic disease of the central nervous system, with a complex pathological mechanism which is still not completely understood. Recent studies have found that m6A modification levels are changed after SCI, and m6A-related regulators are involved in the changes of the local spinal cord microenvironment after injury. However, research on the role of m6A modification in SCI is still in the early stages. This review discusses the latest progress in the dynamic regulation of m6A modification, including methyltransferases ("writers"), demethylases ("erasers") and m6A -binding proteins ("readers"). And then analyses the pathological mechanism relationship between m6A and the microenvironment after SCI. The biological processes involved included cell death, axon regeneration, and scar formation, which provides new insight for future research on the role of m6A modification in SCI and the clinical transformation of strategies for promoting recovery of spinal cord function.

Keywords:  N6-methyladenosine (m6A); epigenetics; nervous system; post-transcriptional modification; spinal cord injury (SCI)

DOI:  https://doi.org/10.3389/fncel.2022.989637
Front Oncol. 2022 ;12 1004212

LncRNA MALAT1 regulates METTL3-mediated PD-L1 expression and immune infiltrates in pancreatic cancer.

Zhengwei Song, Xiaoguang Wang, Fei Chen, Qiuli Chen, Wenjun Liu, Xiaodan Yang, Xun Zhu, Xiaorong Liu, Peter Wang.

  Pancreatic cancer is the fourth leading cause of cancer death in the United States. The main methods of treating pancreatic cancer are surgery and chemotherapy, but the treatment efficacy is low with a poor prognosis. Immunotherapy represented by PD-1/PD-L1 has brought a milestone progress in the treatment of pancreatic cancer. However, the unique tumor microenvironment of pancreatic cancer presents challenges for immunotherapy. In addition, m6A is a common RNA modification and a potential molecular target in tumor therapy. The expression pattern of m6A in pancreatic cancer is still unclear. LncRNAs also play an essential role in pancreatic cancer development and treatment. In this study, we found that some m6A regulators were significantly elevated in pancreatic cancer and associated with the expression of PD-1/PD-L1. Moreover, we observed that METTL3 can increase the expression of PD-L1. Notably, METTL3 positively regulates the expression of lncRNA MALAT1 in pancreatic cancer cells. Strikingly, lncRNA MALAT1 increased the expression of PD-L1 in pancreatic cancer cells. This finding indicated that METTL3 regulated the expression of PD-L1 possibly via targeting lncRNA MALAT1 in pancreatic cancer cells. Lastly, MALAT1 governed the viability of pancreatic cancer cells. Taken together, lncRNA MALAT1 is involved in METTL3-mediated promotion of PD-L1 expression in pancreatic cancer.

Keywords:  MALAT1; METTL3; PD-L1; TME; lncRNA; pancreatic cancer

DOI:  https://doi.org/10.3389/fonc.2022.1004212
Front Endocrinol (Lausanne). 2022 ;13 986419

Decreased Urine N6-methyladenosine level is closely associated with the presence of diabetic nephropathy in type 2 diabetes mellitus.

Shu-Jun Wan, Qiang Hua, Yu-Jie Xing, Yi Cheng, Si-Min Zhou, Yue Sun, Xin-Ming Yao, Xiang-Jian Meng, Jin-Han Cheng, Han Wu, Qing Zhai, Yan Zhang, Xiang Kong, Kun Lv.

   Background: To investigate the dynamic changes of urine N6-methyladenosine (m6A) levels in patients with type 2 diabetes mellitus (T2DM) and diabetic nephropathy (DN) and evaluate the clinical significance.
Methods: First, the levels of urine m6A were examined and compared among 62 patients with T2DM, 70 patients with DN, and 52 age- and gender-matched normal glucose tolerant subjects (NGT) by using a MethyIFIashTM Urine m6A Quantification Kit. Subsequently, we compared the concentrations of urine m6A between different stages of DN. Moreover, statistical analysis was performed to evaluate the association of urine m6A with DN.
Results: The levels of m6A were significantly decreased in patients with DN [(16.10 ± 6.48) ng/ml], compared with NGT [(23.12 ± 7.52) ng/ml, P < 0.0001] and patients with T2DM [(20.39 ± 7.16) ng/ml, P < 0.0001]. Moreover, the concentrations of urine m6A were obviously reduced with the deterioration of DN. Pearson rank correlation and regression analyses revealed that m6A was significantly associated with DN (P < 0.05). The areas under the receiver operator characteristics curve (AUC) were 0.783 (95% CI, 0.699 - 0.867, P < 0.0001) for the DN and NGT groups, and 0.737 (95% CI, 0.639 - 0.835, P < 0.0001) for the macroalbuminuria and normoalbuminuria groups, and the optimal cutoff value for m6A to distinguish the DN from NGT and the macroalbuminuria from normoalbuminuria cases was 0.4687 (diagnostic sensitivity, 71%; diagnostic specificity, 76%) and 0.4494 (diagnostic sensitivity, 79%; diagnostic specificity, 66%), respectively.
Conclusions: The levels of urine m6A are significantly decreased in patients with DN and change with the deterioration of DN, which could serve as a prospective biomarker for the diagnosis of DN.

Keywords:  N6-methyladenosine; biomarkers; diabetic nephropathy; type 2 diabetes mellitus; urine

DOI:  https://doi.org/10.3389/fendo.2022.986419
Cells. 2022 Sep 24. pii: 2980. [Epub ahead of print]11(19):

Exploration of N6-Methyladenosine Profiles of mRNAs and the Function of METTL3 in Atherosclerosis.

Yaqing Zhou, Rongli Jiang, Yali Jiang, Yahong Fu, Yerbolat Manafhan, Jinfu Zhu, Enzhi Jia.

   OBJECTIVES: N6-methylladenosine (m6A) modification has not been fully studied in atherosclerosis. The objectives of this study were to investigate differentially expressed m6A methylated peaks and mRNAs, along with the regulatory role of methyltransferase 3 (METTL3) in pathological processes of atherosclerosis.
METHODS: The pathological models of human coronary artery smooth muscle cells (HCASMCs) were induced in vitro. The differentially expressed mRNAs and m6A peaks were identified by RNA-Seq and meRIP-Seq. The potential mechanisms were analyzed via bioinformatic assays. Methylases expression was tested by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting (WB) in HCASMCs, and by immunohistochemical assays in 40 human coronary arteries. The knockdown of METTL3 expression in cells was performed by siRNA transfection, and cell proliferation and migration were detected after transfection.
RESULTS: We identified 5121 m6A peaks and 883 mRNAs that were expressed differentially in the pathological processes of HCASMCs. Bioinformatic analyses showed that the different m6A peaks were associated with cell growth and cell adhesion, and the 883 genes showed that the extracellular matrix and PI3K/AKT pathway regulate the processes of HCASMCs. Additionally, 10 hub genes and 351 mRNAs with differential methylation and expression levels were found. METTL3 was upregulated in the arteries with atherosclerotic lesions and in the proliferation and migration model of HCASMCs, and pathological processes of HCASMCs could be inhibited by the knockdown of METTL3. The mechanisms behind regulation of migration and proliferation reduced by siMETTL3 are concerned with protein synthesis and energy metabolism.
CONCLUSIONS: These results revealed a new m6A epigenetic method to regulate the progress of atherosclerosis, which suggest approaches for potential therapeutic interventions that target METTL3 for the prevention and treatment of coronary artery diseases.

Keywords:  METTL3; RNA-Seq; atherosclerosis; meRIP-Seq; smooth muscle cell

DOI:  https://doi.org/10.3390/cells11192980
Cancer Commun (Lond). 2022 Oct 08.

N-acetyltransferase 10 promotes colon cancer progression by inhibiting ferroptosis through N4-acetylation and stabilization of ferroptosis suppressor protein 1 (FSP1) mRNA.

Xiao Zheng, Qi Wang, You Zhou, Dachuan Zhang, Yiting Geng, Wenwei Hu, Changping Wu, Yufang Shi, Jingting Jiang.

   BACKGROUND: N-acetyltransferase 10 (NAT10) is the only enzyme known to mediate the N4-acetylcytidine (ac4C) modification of mRNA and is crucial for mRNA stability and translation efficiency. However, its role in cancer development and prognosis has not yet been explored. This study aimed to examine the possible role of NAT10 in colon cancer.
METHODS: The expression levels of NAT10 were evaluated by immunohistochemical analyses with a colon cancer tissue microarray, and its prognostic value in patients was further analyzed. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting were performed to analyze NAT10 expression in harvested colon cancer tissues and cell lines. Stable NAT10-knockdown and NAT10-overexpressing colon cancer cell lines were constructed using lentivirus. The biological functions of NAT10 in colon cancer cell lines were analyzed in vitro by Cell Counting Kit-8 (CCK-8), wound healing, Transwell, cell cycle, and ferroptosis assays. Xenograft models were used to analyze the effect of NAT10 on the tumorigenesis and metastasis of colon cancer cells in vivo. Dot blotting, acetylated RNA immunoprecipitation-qPCR, and RNA stability analyses were performed to explore the mechanism by which NAT10 functions in colon cancer progression.
RESULTS: NAT10 was upregulated in colon cancer tissues and various colon cancer cell lines. This increased NAT10 expression was associated with shorter patient survival. Knockdown of NAT10 in two colon cancer cell lines (HT-29 and LoVo) impaired the proliferation, migration, invasion, tumor formation and metastasis of these cells, whereas overexpression of NAT10 promoted these abilities. Further analysis revealed that NAT10 exerted a strong effect on the mRNA stability and expression of ferroptosis suppressor protein 1 (FSP1) in HT-29 and LoVo cells. In these cells, FSP1 mRNA was found to be modified by ac4C acetylation, and this epigenetic modification was associated with the inhibition of ferroptosis.
CONCLUSIONS: Our study revealed that NAT10 plays a critical role in colon cancer development by affecting FSP1 mRNA stability and ferroptosis, suggesting that NAT10 could be a novel prognostic and therapeutic target in colon cancer.

Keywords:  Colon cancer; Ferroptosis; Ferroptosis suppressor protein 1 (FSP1); N-acetyltransferase 10 (NAT10); N4-acetylcytidine (ac4C); RNA acetylation; mRNA stability

DOI:  https://doi.org/10.1002/cac2.12363
Explor Target Antitumor Ther. 2022 ;3(5): 553-569

N6-methyladenosine-related microRNAs risk model trumps the isocitrate dehydrogenase mutation status as a predictive biomarker for the prognosis and immunotherapy in lower grade gliomas.

Feng Yuan, Yingshuai Wang, Xiangming Cai, Chaonan Du, Junhao Zhu, Chao Tang, Jin Yang, Chiyuan Ma.

   Aim: Lower grade gliomas [LGGs; World Health Organization (WHO) grades 2 and 3], owing to the heterogeneity of their clinical behavior, present a therapeutic challenge to neurosurgeons. The aim of this study was to explore the N6-methyladenosine (m6A) modification landscape in the LGGs and to develop an m6A-related microRNA (miRNA) risk model to provide new perspectives for the treatment and prognostic assessment of LGGs.
Methods: Messenger RNA (mRNA) and miRNA expression data of LGGs were extracted from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. An m6A-related miRNA risk model was constructed via least absolute shrinkage and selection operator (LASSO), univariate, and multivariate Cox regression analysis. Next, Kaplan-Meier analysis, principal-component analysis (PCA), functional enrichment analysis, immune infiltrate analysis, dynamic nomogram, and drug sensitivity prediction were used to evaluate this risk model.
Results: Firstly, six m6A-related miRNAs with independent prognostic value were selected based on clinical information and used to construct a risk model. Subsequently, compared with low-risk group, LGGs in the high-risk group had a higher m6A writer and reader scores, but a lower eraser score. Moreover, LGGs in the high-risk group had a significantly worse clinical prognosis than those in the low-risk group. Simultaneously, this risk model outperformed other clinicopathological variables in the prognosis prediction of LGGs. Immune infiltrate analysis revealed that the proportion of M2 macrophages, regulatory T (Treg) cells, and the expression levels of exhausted immune response markers were significantly higher in the high-risk group than in the low-risk group. Finally, this study constructed an easy-to-use and free dynamic nomogram to help clinicians use this risk model to aid in diagnosis and prognosis assessment.
Conclusions: This study developed a m6A-related risk model and uncovered two different m6A modification landscapes in LGGs. Moreover, this risk model may provide guidance and help in clinical prognosis assessment and immunotherapy response prediction for LGGs.

Keywords:  Lower grade gliomas; N6-methyladenosine; immune infiltrate; microRNAs; nomogram

DOI:  https://doi.org/10.37349/etat.2022.00100
Sci Rep. 2022 Oct 14. 12(1): 17256

Prediction of prognosis, immune infiltration and immunotherapy response with N6-methyladenosine-related lncRNA clustering patterns in cervical cancer.

Haixia Jia, Meiting Cao, Suhua Hao, Jiahao Wang, Jintao Wang.

LncRNAs and tumor microenvironment (TME) exert an important effect in antitumor immunity. Nonetheless, the role of m6A-related lncRNA clustering patterns in prognosis, TME and immunotherapy of cervical cancer (CC) remains unknown. Here, based on 7 m6A-related prognostic lncRNAs obtained from TCGA-CC dataset, two m6AlncRNA clustering patterns were determined. m6AlncRNA clusterA was characterized by immune cell infiltrates and immune activation. m6AlncRNA clusterB was characterized by enrichment of immune evasion and tumorigenic activation pathways as well as survival and clinical stage disadvantage. Then, principal component analysis algorithms were used to construct m6AlncRNAscore based on prognostic differentially expressed genes between two m6AlncRNA clusters to quantify m6AlncRNA clustering patterns. m6AlncRNAscore was an independent prognostic protective factor. Higher Th2 and Treg cells and enrichment of immunosuppressive pathways were observed in the low-m6AlncRNAscore group, with poorer survival. High-m6AlncRNAscore was characterized by increased infiltration of activated CD8 T cell, enrichment of immune activation pathways, lower IL-10 and TGF-beta1 levels, and higher immunophenscore values, indicating inflamed TME and better anti-tumor immunotherapy efficacy. Quantitative Real-Time Polymerase Chain Reaction was used for detection of m6A-related prognostic lncRNAs. Collectively, we identified two m6AlncRNA clustering patterns which play a nonnegligible role in the prognosis, TME heterogeneity and immunotherapy of CC patients.

DOI: https://doi.org/10.1038/s41598-022-20162-2
Islets. 2022 Dec 31. 14(1): 184-199

Molecular mechanism analysis of m6A modification-related lncRNA-miRNA-mRNA network in regulating autophagy in acute pancreatitis.

Xiang Li, Hong Qin, Ali Anwar, Xingwen Zhang, Fang Yu, Zheng Tan, Zhanhong Tang.

  This study aims to explore the molecular mechanism of N6-methyladenosine (m6A) modification-related long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network in regulating autophagy and affecting the occurrence and development of acute pancreatitis (AP). RNA-seq datasets related to AP were obtained from Gene Expression Omnibus (GEO) database and merged after batch effect removal. lncRNAs significantly related to m6A in AP, namely candidate lncRNA, were screened by correlation analysis and differential expression analysis. In addition, candidate autophagy genes were screened through the multiple databases. Furthermore, the key pathways for autophagy to play a role in AP were determined by functional enrichment analysis. Finally, we predicted the miRNAs binding to genes and lncRNAs through TargetScan, miRDB and DIANA TOOLS databases and constructed two types of lncRNA-miRNA-mRNA regulatory networks mediated by upregulated and downregulated lncRNAs in AP. Nine lncRNAs related to m6A were differentially expressed in AP, and 21 candidate autophagy genes were obtained. Phosphoinositide 3-kinase (PI3K)-Akt signaling pathway and Forkhead box O (FoxO) signaling pathway might be the key pathways for autophagy to play a role in AP. Finally, we constructed a lncRNA-miRNA-mRNA regulatory network. An upregulated lncRNA competitively binds to 13 miRNAs to regulate 6 autophagy genes, and a lncRNA-miRNA-mRNA regulatory network in which 2 downregulated lncRNAs competitively bind to 7 miRNAs to regulate 2 autophagy genes. m6A modification-related lncRNA Pvt1, lncRNA Meg3 and lncRNA AW112010 may mediate the lncRNA-miRNA-mRNA network, thereby regulating autophagy to affect the development of AP.

Keywords:  AP; autophagy; bioinformatics analysis; ceRNA; lncRNA; m6A modification

DOI:  https://doi.org/10.1080/19382014.2022.2132099
Nat Commun. 2022 Oct 11. 13(1): 5994

Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine.

Satoshi Kimura, Veerasak Srisuknimit, Kacie L McCarty, Peter C Dedon, Philip J Kranzusch, Matthew K Waldor.

Post-transcriptional RNA editing modulates gene expression in a condition-dependent fashion. We recently discovered C-to-Ψ editing in Vibrio cholerae tRNA. Here, we characterize the biogenesis, regulation, and functions of this previously undescribed RNA editing process. We show that an enzyme, TrcP, mediates the editing of C-to-U followed by the conversion of U to Ψ, consecutively. AlphaFold-2 predicts that TrcP consists of two globular domains (cytidine deaminase and pseudouridylase) and a long helical domain. The latter domain tethers tRNA substrates during both the C-to-U editing and pseudouridylation, likely enabling a substrate channeling mechanism for efficient catalysis all the way to the terminal product. C-to-Ψ editing both requires and suppresses other modifications, creating an interdependent network of modifications in the tRNA anticodon loop that facilitates coupling of tRNA modification states to iron availability. Our findings provide mechanistic insights into an RNA editing process that likely promotes environmental adaptation.

DOI: https://doi.org/10.1038/s41467-022-33714-x
Proc Natl Acad Sci U S A. 2022 Oct 18. 119(42): e2123338119

5-methylcytosine (m5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons.

Yuexiu Zhang, Li-Sheng Zhang, Qing Dai, Phylip Chen, Mijia Lu, Elizabeth L Kairis, Valarmathy Murugaiah, Jiayu Xu, Rajni Kant Shukla, Xueya Liang, Zhongyu Zou, Estelle Cormet-Boyaka, Jianming Qiu, Mark E Peeples, Amit Sharma, Chuan He, Jianrong Li.

  5-methylcytosine (m5C) is one of the most prevalent modifications of RNA, playing important roles in RNA metabolism, nuclear export, and translation. However, the potential role of RNA m5C methylation in innate immunity remains elusive. Here, we show that depletion of NSUN2, an m5C methyltransferase, significantly inhibits the replication and gene expression of a wide range of RNA and DNA viruses. Notably, we found that this antiviral effect is largely driven by an enhanced type I interferon (IFN) response. The antiviral signaling pathway is dependent on the cytosolic RNA sensor RIG-I but not MDA5. Transcriptome-wide mapping of m5C following NSUN2 depletion in human A549 cells revealed a marked reduction in the m5C methylation of several abundant noncoding RNAs (ncRNAs). However, m5C methylation of viral RNA was not noticeably altered by NSUN2 depletion. In NSUN2-depleted cells, the host RNA polymerase (Pol) III transcribed ncRNAs, in particular RPPH1 and 7SL RNAs, were substantially up-regulated, leading to an increase of unshielded 7SL RNA in cytoplasm, which served as a direct ligand for the RIG-I-mediated IFN response. In NSUN2-depleted cells, inhibition of Pol III transcription or silencing of RPPH1 and 7SL RNA dampened IFN signaling, partially rescuing viral replication and gene expression. Finally, depletion of NSUN2 in an ex vivo human lung model and a mouse model inhibits viral replication and reduces pathogenesis, which is accompanied by enhanced type I IFN responses. Collectively, our data demonstrate that RNA m5C methylation controls antiviral innate immunity through modulating the m5C methylome of ncRNAs and their expression.

Keywords:  5-methylcytosine; innate immune response; interferon; virus infection

DOI:  https://doi.org/10.1073/pnas.2123338119
Br J Cancer. 2022 Oct 10.

YTHDF2-mediated FGF14-AS2 decay promotes osteolytic metastasis of breast cancer by enhancing RUNX2 mRNA translation.

Ming Zhang, Jue Wang, Yucui Jin, Que Zheng, Mengying Xing, Yuting Tang, Yunfei Ma, Lingyun Li, Bing Yao, Hao Wu, Changyan Ma.

BACKGROUND: LncRNA FGF14-AS2 is a critical suppressor in breast cancer (BCa) metastasis. However, whether FGF14-AS2 plays a role in the bone metastasis of BCa remains unknown.
METHODS: TRAP assay and intratibial injection were carried out to evaluate the role of FGF14-AS2 in BCa bone metastasis in vitro and in vivo. Polyribosome profiling was done to examine the translation level. RNA pulldown combined with LC/MS was performed to identify the lncRNA-binding partner, RIP, dual-luciferase assay, and Co-IP assays as well to testify these physical interactions. The prognostic value of FGF14-AS2 expression level in BCa patients was analysed using Kaplan-Meier Plotter.
RESULTS: We found that FGF14-AS2 suppresses osteoclast differentiation and osteolytic metastasis of BCa. Mechanistically, FGF14-AS2 suppresses the translation of RUNX2 by inhibiting the assembly of eIF4E/eIF4G complex and the phosphorylation of eIF4E, thereby reducing the transcription of RANKL, an essential regulator of osteoclast differentiation. Moreover, FGF14-AS2 is downregulated by YTHDF2-mediated RNA degradation in an m6A-dependent manner. Clinically, patients with high YTHDF2 and low FGF14-AS2 expression levels showed worse distant metastasis-free survival (DMFS).
CONCLUSIONS: FGF14-AS2 plays a crucial role in osteolytic metastasis, and may serve as a promising prognostic biomarker and therapeutic target for BCa bone metastasis.

DOI: https://doi.org/10.1038/s41416-022-02006-y
Cells. 2022 Sep 27. pii: 3008. [Epub ahead of print]11(19):

m6A Modification of Long Non-Coding RNA HNF1A-AS1 Facilitates Cell Cycle Progression in Colorectal Cancer via IGF2BP2-Mediated CCND1 mRNA Stabilization.

Yibo Bian, Yang Wang, Shufen Xu, Zhishuang Gao, Chao Li, Zongyao Fan, Jie Ding, Keming Wang.

   BACKGROUND: Long non-coding RNAs modulate tumor occurrence through different molecular mechanisms. It had been reported that HNF1A-AS1 (HNF1A Antisense RNA 1) was differently expressed in multiple tumors. The role of HNF1A-AS1 in colorectal cancer was less analyzed, and the mechanism of regulating the cell cycle has not been completely elucidated.
METHODS: Differentially expressed lncRNAs were screened out from the TCGA database. HNF1A-AS1 was examined in CRC clinical samples and cell lines by RT-qPCR. CCK8 assay, colony formation assay, flow cytometry, transwell assays, tube forming assay and vivo experiments were performed to study the function of HNF1A-AS1 in CRC tumor progression. Bioinformatic analysis, luciferase report assay, RNA pull-down and RIP assays were carried out to explore proteins binding HNF1A-AS1 and the potential downstream targets.
RESULTS: Our results showed that HNF1A-AS1 was upregulated in CRC and associated with unfavorable prognosis. HNF1A-AS1 promoted proliferation, migration and angiogenesis, accelerated cell cycle and reduced cell apoptosis in CRC. Bioinformatics prediction and further experiments proved that HNF1A-AS1 could promote CCND1 expression by suppressing PDCD4 or competitively sponging miR-93-5p. Meanwhile, METTL3 mediated HNF1A-AS1 m6A modification and affected its RNA stability. HNF1A-AS1/IGF2BP2/CCND1 may act as a complex to regulate the stability of CCND1.
CONCLUSION: In summary, our result reveals the novel mechanism in which m6A-mediated HNF1A-AS1/IGF2BP2/CCND1 axis promotes CRC cell cycle progression, along with competitively sponging miR-93-5p to upregulate CCND1, demonstrating its significant role in cell cycle regulation and suggesting that HNF1A-AS1 may act as a potential prognostic marker of colorectal cancer in the future.

Keywords:  CCND1; HNF1A-AS1; IGF2BP2; colorectal cancer; m6A

DOI:  https://doi.org/10.3390/cells11193008
Front Genet. 2022 ;13 998147

Integrative pan-cancer analysis and clinical characterization of the N7-methylguanosine (m7G) RNA modification regulators in human cancers.

Chun-Ming He, Xin-Di Zhang, Song-Xin Zhu, Jia-Jie Zheng, Yu-Ming Wang, Qing Wang, Hang Yin, Yu-Jie Fu, Song Xue, Jian Tang, Xiao-Jing Zhao.

  Background: RNA modification is one of the epigenetic mechanisms that regulates post-transcriptional gene expression, and abnormal RNA modifications have been reported to play important roles in tumorigenesis. N7-methylguanosine (m7G) is an essential modification at the 5' cap of human mRNA. However, a systematic and pan-cancer analysis of the clinical relevance of m7G related regulatory genes is still lacking. Methods: We used univariate Cox model and Kaplan-Meier analysis to generate the forest plot of OS, PFI, DSS and identified the correlation between the altered expression of m7G regulators and patient survival in 33 cancer types from the TCGA and GTEx databases. Then, the "estimate" R-package, ssGSEA and CIBERSORT were used to depict the pan-cancer immune landscape. Through Spearman's correlation test, we analyzed the correlation between m7G regulators and the tumor microenvironment (TME), immune subtype, and drug sensitivity of the tumors, which was further validated in NSCLC. We also assessed the changes in the expression of m7G related regulatory genes in NSCLC with regards to the genetic and transcriptional aspects and evaluated the correlation of METTL1 and WDR4 expression with TMB, MSI and immunotherapy in pan-cancer. Results: High expression of most of the m7G regulators was significantly associated with worse prognosis. Correlation analyses revealed that the expression of majority of the m7G regulators was correlated with tumor immune infiltration and tumor stem cell scores. Drug sensitivity analysis showed that the expression of CYFP1,2 was closely related to drug sensitivity for various anticancer agents (p < 0.001). Analysis of the pan-cancer immune subtype revealed significant differences in the expression of m7G regulators between different immune subtypes (p < 0.001). Additionally, the types and proportions of mutations in METTL1 and WDR4 and their relevance to immunotherapy were further described. Conclusion: Our study is the first to evaluate the correlation between the altered expression of m7G regulators and patient survival, the degree of immune infiltration, TME and drug sensitivity in pan-cancer datasets.

Keywords:  drug sensitivity; immune score; m7G regulators; pan-cancer analysis; survival; tumor microenevironment

DOI:  https://doi.org/10.3389/fgene.2022.998147
Mol Oncol. 2022 Oct 11.

Methylation of N6 adenosine-related long non-coding RNA: effects on prognosis and treatment in "driver-gene-negative" lung adenocarcinoma.

Hao-Shuai Yang, He-Yuan Cai, Shi-Chao Shan, Ting-Fei Chen, Jian-Yong Zou, Maimaiti Abudurufu, Hong-He Luo, Yi-Yan Lei, Zun-Fu Ke, Ying Zhu.

  The improvement of treatment for patients with "driver-gene-negative" lung adenocarcinoma (LUAD) remains a critical problem to be solved. We aimed to explore the role of methylation of N6 adenosine (m6A)-related long non-coding RNA (lncRNA) in stratifying "driver-gene-negative" LUAD risk. Patients negative for mutations in EGFR, KRAS, BRAF, HER2, MET, ALK, RET and ROS1 were identified as "driver-gene-negative" cases. RNA sequencing was performed in 46 paired tumors and adjacent normal tissues from patients with "driver-gene-negative" LUAD. Twenty-three m6A regulators and relevant lncRNAs were identified using Pearson's correlation analysis. K-means cluster analysis was used to stratify patients, and a prognostic nomogram was developed. The CIBERSORT and pRRophetic algorithms were employed to quantify the immune microenvironment and chemosensitivity. We identified two clusters highly consistent with the prognosis based on their unique expression profiles for 46 m6AlncRNAs. A risk model constructed from nine m6A lncRNAs could stratify patients into high- and low-risk groups with promising predictive power (C-index=0.824), and the risk score was an independent prognostic factor. The clusters and risk models were closely related to immune characteristics and chemosensitivity. Additional pan-cancer analysis using the nine m6AlncRNAs showed that the expression of DIO3 opposite strand upstream RNA (DIO3OS) is closely related to the immune/stromal score and tumor stemness in a variety of cancers. Our results show that m6AlncRNAs are a reliable prognostic tool and can aid treatment decision-making in "driver-gene-negative" LUAD. DIO3OS is associated with the development of various cancers and has potential clinical applications.

Keywords:  N6 adenosine methylation; driver-gene-negative; long non-coding RNA; lung adenocarcinoma; nomogram

DOI:  https://doi.org/10.1002/1878-0261.13323
Int J Med Sci. 2022 ;19(11): 1680-1694

Atranorin driven by nano materials SPION lead to ferroptosis of gastric cancer stem cells by weakening the mRNA 5-hydroxymethylcytidine modification of the Xc-/GPX4 axis and its expression.

Zhentian Ni, Xiaoli Nie, Hairong Zhang, Lingquan Wang, Zixiang Geng, Xiling Du, Haiyang Qian, Wentao Liu, Te Liu.

  Gastric cancer is a highly malignant tumor. Gastric cancer stem cells (GCSCs) are the main causes of drug resistance, metastasis, recurrence, and poor prognosis. As a secondary metabolite of lichen, Atranorin has a variety of biological effects, such as antibacterial, anti-inflammatory, analgesic, and wound healing; however, its killing effect on GCSCs has not been reported. In this study, we constructed Atranorin complexes comprising superparamagnetic iron oxide nanoparticles (SPION) (Atranorin@SPION). In vitro and in vivo experiments confirmed that Atranorin@SPION could significantly inhibit the proliferation, invasion, angiogenesis, and tumorigenicity of CD44+/ CD24+ GCSCs, and induce oxidative stress injury, Fe2+ accumulation, and ferroptosis. Quantitative real-time reverse transcription PCR and western blotting results showed that Atranorin@SPION not only reduced the expression levels of GCSC stem cell markers and cell proliferation and division markers, but also significantly inhibited the expression levels of key molecules in the cystine/glutamate transporter (Xc-)/glutathione peroxidase 4 (GPX4) and Tet methylcytosine dioxygenase (TET) family proteins. The results of high performance liquid chromatography-mass spectrometry and Dot blotting showed that Atranorin@SPION significantly inhibited the mRNA 5‑hydroxymethylcytidine modification of GCSCs. Meanwhile, the results of RNA immunoprecipitation-PCR also indicated that Atranorin@SPIONs significantly reduced the 5-hydroxymethylcytidine modification level of GPX4 and SLC7A11 mRNA 3' untranslated region in GCSCs, resulting in a decrease in their stability, shortening their half-lives and reducing translation activity. Therefore, this study revealed that Atranorin@SPIONs induced ferroptosis of GCSCs by weakening the expression of the Xc-/GPX4 axis and the 5-hydroxymethylcytidine modification of mRNAs in the pathway, thereby achieving their therapeutic effect on gastric cancer.

Keywords:  5-hydroxymethylcytidine; Atranorin; Ferroptosis; Xc-/GPX4 axis; gastric cancer stem cell (GCSCs); superparamagnetic iron oxide nanoparticle (SPION)

DOI:  https://doi.org/10.7150/ijms.73701
Front Genet. 2022 ;13 1011716

Identification of m6A-related long non-coding RNAs for predicting prognosis and immune characterizations in gastric cancer.

Xianhui Zhang, Changjing Wang, Zhongxin Liu, Yuan Si.

  Background: N6-methyladenosine (m6A) mRNA modification triggers malignant behavior in tumor cells, which promotes malignant progression and migration of gastric cancer (GC). Nevertheless, studies on the prognostic value of m6A-related long non-coding RNA (MRlncRNA) in GC remain quite restricted. The study aimed to develop a reasonable predictive model to explore the prognostic potential of MRlncRNAs in predicting the prognosis of GC patients and monitoring the efficacy of immunotherapy. Methods: Transcriptomic and clinical data for GC were derived from TCGA. Next, univariate Cox, LASSO and multivariate Cox regression analyses were next used to identify prognostic MRlncRNAs, calculate risk scores and build risk assessment models. The predictive power of the risk models was then validated by Kaplan-Meier analysis, ROC curves, DCA, C-index, and nomogram. We attempted to effectively differentiate between groups in terms of immune cell infiltration status, ICI-related genes, immunotherapy responses, and common anti-tumor drug sensitivity. Results: A risk model based on 11 MRlncRNAs was developed with an AUC of 0.850, and the sensitivity and specificity of this model in predicting survival probability is satisfactory. The Kaplan-Meier analysis revealed that the low-risk group in the model had a significantly higher survival rate, and the model was highly associated with survival status, clinical features, and clinical stage. Furthermore, the model was verified to be an independent prognostic risk factor, and the low-risk group in the model had a remarkable positive correlation with a variety of immune cell infiltrates. The expression levels of ICI-related genes differed significantly between the different groups. Lastly, immunotherapy responses and common anti-tumor drug sensitivity also differed significantly between different groups. Conclusion: The risk model on the basis of 11-MRlncRNAs can serve as independent predictors of GC prognosis and may be useful in developing personalized treatment strategies for patients.

Keywords:  gastric cancer; immune; immunotherapy; long non-coding RNA; m6A; prognostic model

DOI:  https://doi.org/10.3389/fgene.2022.1011716
Biochem Biophys Res Commun. 2022 Oct 04. pii: S0006-291X(22)01365-1. [Epub ahead of print]634 30-39

MiR-654-3p, reduced by the excessive ALKBH5, Alleviated the Inflammation in OA by targeting TNFRSF9, the trigger of the NF-κB pathway.

Baoxi Yu, Anyu Zeng, Hailong Liu, Zhijian Yang, Ming Fu.

  MicroRNA (miRNA) is one of the most potent therapeutic targets for osteoarthritis (OA). We identified that miR-654-3p protected the phenotype of chondrocytes. We demonstrated that TNF receptor superfamily member 9 (TNFRSF9) was the target of miR-654-3p by binding to its 3'UTR regions, based on a dual-luciferase reporter assay and an RNA binding protein immunoprecipitation (RIP) assay. In addition, further experiments proved that TNFRSF9, as a trigger of the NF-κB pathway, correlated with the inflammation in chondrocytes. MiR-654-3p overexpressed in the knee of mice alleviated the OA in vivo. Moreover, we examined the m6A enzyme level in OA, proving that the abnormal expression of α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) contributed to the miR-654-3p decrease. Our research illustrated the significant role of miR-654-3p in OA, including its maturation and the mechanism in protecting the phenotype of chondrocytes, which could be a new treatment target for OA.

Keywords:  NF-κB; Osteoarthritis; TNF receptor Superfamily member 9; miR-654-3p; α-Ketoglutarate-dependent dioxygenase alkB homolog 5

DOI:  https://doi.org/10.1016/j.bbrc.2022.09.103
Front Immunol. 2022 ;13 964393

Cuproptosis depicts tumor microenvironment phenotypes and predicts precision immunotherapy and prognosis in bladder carcinoma.

Huihuang Li, Xiongbing Zu, Jiao Hu, Zicheng Xiao, Zhiyong Cai, Ning Gao, Jinbo Chen.

   Background: Though immune checkpoint inhibitors (ICIs) exhibit durable efficacy in bladder carcinomas (BLCAs), there are still a large portion of patients insensitive to ICIs treatment.
Methods: We systematically evaluated the cuproptosis patterns in BLCA patients based on 46 cuproptosis related genes and correlated these cuproptosis patterns with tumor microenvironment (TME) phenotypes and immunotherapy efficacies. Then, for individual patient's evaluation, we constructed a cuproptosis risk score (CRS) for prognosis and a cuproptosis signature for precise TME phenotypes and immunotherapy efficacies predicting.
Results: Two distinct cuproptosis patterns were generated. These two patterns were consistent with inflamed and noninflamed TME phenotypes and had potential role for predicting immunotherapy efficacies. We constructed a CRS for predicting individual patient's prognosis with high accuracy in TCGA-BLCA. Importantly, this CRS could be well validated in external cohorts including GSE32894 and GSE13507. Then, we developed a cuproptosis signature and found it was significantly negative correlated with tumor-infiltrating lymphocytes (TILs) both in TCGA-BLCA and Xiangya cohorts. Moreover, we revealed that patients in the high cuproptosis signature group represented a noninflamed TME phenotype on the single cell level. As expected, patients in the high cuproptosis signature group showed less sensitive to immunotherapy. Finally, we found that the high and low cuproptosis signature groups were consistent with luminal and basal subtypes of BLCA respectively, which validated the role of signature in TME in terms of molecular subtypes.
Conclusions: Cuproptosis patterns depict different TME phenotypes in BLCA. Our CRS and cuproptosis signature have potential role for predicting prognosis and immunotherapy efficacy, which might guide precise medicine.

Keywords:  bladder carcinoma; cuproptosis; immunotherapy; prognosis; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2022.964393
J Oncol. 2022 ;2022 7495183

Construction and Characterization of n6-Methyladenosine-Related lncRNA Prognostic Signature and Immune Cell Infiltration in Kidney Renal Clear Cell Carcinoma.

Zerong Chen, Zehai Huang, Jialiang Hui, Zhuangfei Chen, Haibo Zhang, Yaodong Jiang, Weisen Zeng.

Background: Kidney renal clear cell carcinoma (KIRC) lacks effective prognostic biomarkers and the role and mechanism of N6-methyladenosine (m6A) modification of long noncoding RNAs (lncRNAs) in KIRC remain unclear.
Methods: We extracted standard mRNA-sequencing and clinical data from the TCGA database. The prognostic risk model was obtained by Lasso regression and Cox regression. We randomly divided the samples into training and test sets, each taking half of the cases. Based on Lasso regression and Cox regression for training set, the prognostic risk signature was constructed; risk scores were calculated with the R package "glmnet." Based on the median value of the prognostic risk score, risk scores were calculated for each patient and we divided all KIRC samples into high-risk and low-risk groups. Then, high- and low-risk subtypes were established and their prognosis, clinical features, and immune infiltration microenvironment were evaluated in test set and the entire sampled data set. The reliability of the prognostic model was confirmed by receiver operating characteristic curve analysis.
Results: We found 28 prognostic m6A-related lncRNAs and established a m6A-related lncRNAs prognostic signature. Risk score=AC015813.1∗(0.0086)+EMX2OS∗(-0.0101)+LINC00173∗(0.0309)+PWAR5∗(-0.0146)+SNHG1∗(0.0043). The signature showed a better predictive ability than other clinical indicators, including tumor node metastasis classification (TNM), histological, and pathological stages. In the high-risk group, M0 macrophages, CD8+ T cells, and regulatory T cells had significantly higher scores. Contrarily, in the low-risk group, activated dendritic cells, M1 macrophages, mast resting cells, and monocytes had significantly higher scores. In the high-risk group, LSECtin was overexpressed. In the low-risk group, PD-L1 was overexpressed. Moreover, high-risk patients may benefit more from AZ628.
Conclusions: In conclusion, prognosis prediction of patients with KIRC and new insights for immunotherapy are provided by the m6A-related lncRNA prognostic signature.

DOI: https://doi.org/10.1155/2022/7495183