bims-rimeca 2023-05-14 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023–05–14
27 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

RNA N6-methyladenosine reader IGF2BP3 interacts with MYCN and facilitates neuroblastoma cell proliferation.
m6A modification on the fate of colorectal cancer: functions and mechanisms of cell proliferation and tumorigenesis.
METTL3-Mediated m6A Modification of TRIF and MyD88 mRNAs Suppresses Innate Immunity in Teleost Fish, Miichthys miiuy.
Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells.
Deubiquitinase USP13 regulates glycolytic reprogramming and progression in osteosarcoma by stabilizing METTL3/m6A/ATG5 axis.
m6 A-Dependent Modulation via IGF2BP3/MCM5/Notch Axis Promotes Partial EMT and LUAD Metastasis.
m6A methylation regulates hypoxia-induced pancreatic cancer glycolytic metabolism through ALKBH5-HDAC4-HIF1α positive feedback loop.
METTL3 regulates alternative splicing of cell cycle-related genes via crosstalk between mRNA m6A modifications and splicing factors.
The roles and mechanism of m6A RNA methylation regulators in cancer immunity.
ALKBH5 Drives Immune Suppression via targeting AXIN2 to Promote Colorectal Cancer and is a Target for Boosting Immunotherapy.
Crosstalk between N6-methyladenosine (m6A) modification and noncoding RNA in tumor microenvironment.
GPX8 deficiency-induced oxidative stress reprogrammed m6A epitranscriptome of oral cancer cells.
N6-methyladenosine (m6A) in cancer stem cell: From molecular mechanisms to therapeutic implications.
YTHDC2 Retards Cell Proliferation and Triggers Apoptosis in Papillary Thyroid Cancer by Regulating CYLD-Mediated Inactivation of Akt Signaling.
Cigarette smoking, by accelerating the cell cycle, promotes the progression of non-small cell lung cancer through an HIF-1α-METTL3-m6A/CDK2AP2 axis.
Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer.
NAT10-mediated AXL mRNA N4-acetylcytidine modification promotes pancreatic carcinoma progression.
7SK methylation by METTL3 promotes transcriptional activity.
The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma.
m6A-dependent mevalonate kinase in juvenile hormone synthesis pathway regulates the diapause process of bivoltine silkworm (Bombyx mori).
Detailed profiling of m6A modified circRNAs and synergistic effects of circRNA and environmental risk factors for coronary artery disease.
LncRNA LINC00969 promotes acquired gefitinib resistance by epigenetically suppressing of NLRP3 at transcriptional and posttranscriptional levels to inhibit pyroptosis in lung cancer.
N6 -methyladenosine mRNA modification regulates transcripts stability associated with cotton fiber elongation.
Kupffer cell pyroptosis mediated by METTL3 contributes to the progression of alcoholic steatohepatitis.
Epigenetic modification-associated molecular classification of gastric cancer.
N6-methyladenine-mediated aberrant activation of the lncRNA SOX2OT-GLI1 loop promotes non-small-cell lung cancer stemness.
An innovative model based on N7-methylguanosine-related lncRNAs for forecasting prognosis and tumor immune landscape in bladder cancer.

Cell Death Discov. 2023 May 08. 9(1): 151

RNA N6-methyladenosine reader IGF2BP3 interacts with MYCN and facilitates neuroblastoma cell proliferation.

Kai Zhu, Tingting Gao, Zhiru Wang, Liaoran Zhang, Kezhe Tan, Zhibao Lv.

Neuroblastoma (NB) is a kind of typical life-threatening extracranial tumor in children. N6-methyladenosine (m6A) modification is closely related to multiple cancer pathological processes. Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) is a top-ranked prognostic risk gene in NB; however, its function is uncertain. The expression of m6A-associated enzymes in patients with NB was analyzed using the Gene Expression Omnibus (GEO) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. The IGF2BP3 level in NB cell lines and primary samples was tested using quantitative real-time polymerase chain reaction (qRT-PCR), western blot method, and immunohistochemical analysis. The IGF2BP3 function in cell proliferation was clarified based on many functional in vitro and in vivo experiments. The interaction between IGF2BP3 and N-myc was researched via RNA immunoprecipitation (RIP), m6A RNA immunoprecipitation (MeRIP), and chromatin immunoprecipitation (ChIP) assays. The 16 m6A-regulated enzymes in NB were researched, and the result indicated that IGF2BP3 overexpression was related to cancer progression, COG risk, and survival based on the GEO and TARGET databases. Besides, the IGF2BP3 and MYCN levels were positively correlated. IGF2BP3 expression levels increased in MYCN-amplified NB clinical samples and cells. Knockdown of IGF2BP3 inhibited N-myc expression and NB cell proliferation in vitro and in vivo. IGF2BP3 regulates MYCN RNA stability by modifying m6A. In addition, we demonstrated that N-myc is a transcription factor that directly promotes IGF2BP3 expression in NB cells. IGF2BP3 regulates the proliferation of NB cells via m6A modification of MYCN. N-myc also acts as a transcription factor that regulates IGF2BP3 expression. A positive feedback loop between IGF2BP3 and N-myc facilitates NB cell proliferation.

DOI: https://doi.org/10.1038/s41420-023-01449-3
Front Oncol. 2023 ;13 1162300

m6A modification on the fate of colorectal cancer: functions and mechanisms of cell proliferation and tumorigenesis.

Xiaohan Jiang, Ziyao Jin, Yuzhong Yang, Xiang Zheng, Shaohua Chen, Shuaijie Wang, Xuemei Zhang, Nanfang Qu.

  N6-methyladenosine (m6A) is the most pervasive RNA modification in eukaryotic cells. The dynamic and reversible m6A modification of RNA plays a critical role in the occurrence and progression of tumors by regulating RNA metabolism, including translocation, mRNA stability or decay, pre-mRNA splicing, and lncRNA processing. Numerous studies have shown that m6A modification is involved in the development of various cancers. This review aims to summarize the significant role of m6A modification in the proliferation and tumorigenesis of CRC, as well as the potential of modulating m6A modification for tumor treatment. These findings may offer new therapeutic strategies for clinical implementation of m6A modification in CRC in the near future.

Keywords:  N6-methyladenosine; RNA modification; colorectal cancer; proliferation; tumorigenesis

DOI:  https://doi.org/10.3389/fonc.2023.1162300
J Immunol. 2023 May 08. pii: ji2300033. [Epub ahead of print]

METTL3-Mediated m6A Modification of TRIF and MyD88 mRNAs Suppresses Innate Immunity in Teleost Fish, Miichthys miiuy.

Shang Geng, Weiwei Zheng, Yan Zhao, Tianjun Xu.

Methyltransferase (METTL3), the most important N6-methyladenosine (m6A) writer, plays a vital role in regulating immune-related signaling pathways. However, the underlying mechanism of METTL3 action remains largely unknown, especially in lower vertebrates. The results of this study show that METTL3 inhibits innate immune response and promotes the infection of miiuy croaker, Miichthys miiuy, by Siniperca chuatsi rhabdovirus and Vibrio anguillarum. Significantly, the function of METTL3 in inhibiting immunity depends on its methylase activity. Mechanistically, METTL3 increases the methylation level of trif and myd88 mRNA, rendering them sensitive to degradation by the YTHDF2/3 reader proteins. By contrast, we found that the YTHDF1 reader protein promotes the translation of myd88 mRNA. In summary, these results indicate that METTL3-mediated m6A modification of trif and myd88 mRNAs suppresses innate immunity by inhibiting the TLR pathway, unveiling a molecular mechanism by which RNA methylation controls innate immunity to pathogens in the teleost fish.

DOI: https://doi.org/10.4049/jimmunol.2300033
Front Genet. 2023 ;14 1121063

Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells.

Yu Lin, Zhifang Zhao, Wenqiang Nie, Manting Huang, Jiazhong Cai, Yadong Wang, Hesong Wang, Yongmei Huang, Yang Bai.

  Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m6A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated. Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts. Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG)pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway. Conclusion: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.

Keywords:  5-methylcytosine; MeRIP-seq; NSun2; RNA methylation; colorectal cancer

DOI:  https://doi.org/10.3389/fgene.2023.1121063
Int J Biol Sci. 2023 ;19(7): 2289-2303

Deubiquitinase USP13 regulates glycolytic reprogramming and progression in osteosarcoma by stabilizing METTL3/m6A/ATG5 axis.

Ce Wang, Yichen Meng, Jianquan Zhao, Jun Ma, Yuechao Zhao, Rui Gao, Wei Liu, Xuhui Zhou.

  Reprogramming metabolism is a hallmark of cancer cells for rapid progression. However, the detailed functional role of deubiquitinating enzymes (DUBs) in tumor glycolytic reprogramming is still unknown and requires further investigation. USP13 was found to upregulate in osteosarcoma (OS) specimens and promote OS progression through regulating aerobic glycolysis. Interestingly, the m6A writer protein, METTL3, has been identified as a novel target of USP13. USP13 interacts with, deubiquitinates, and therefore stabilizes METTL3 at K488 by removing K48-linked ubiquitin chains. Since METTL3 is a well-known m6A writer and USP13 stabilizes METTL3, we further found that USP13 increased global m6A abundance in OS cells. The results of RNA sequencing and methylated RNA immunoprecipitation sequencing indicated METTL3 could bind to m6A-modified ATG5 mRNA, which is crucial for autophagosome formation, and inhibit ATG5 mRNA decay on an IGF2BP3 dependent manner, thereby promoting autophagy and the autophagy-associated malignancy of OS. Using a small-molecule inhibitor named Spautin-1 to pharmacologically inhibit USP13 induced METTL3 degradation and exhibited significant therapeutic efficacy both in vitro and in vivo. Collectively, our study results indicate that USP13 promotes glycolysis and tumor progression in OS by stabilizing METTL3, thereby stabilizing ATG5 mRNA and facilitating autophagy in OS. Our findings demonstrate the role of the USP13-METTL3-ATG5 cascade in OS progression and show that USP13 is a crucial DUB for the stabilization of METTL3 and a promising therapeutic target for treating OS.

Keywords:  ATG5; METTL3; N6-methyladenosine; USP13; glycolytic reprogramming

DOI:  https://doi.org/10.7150/ijbs.82081
Adv Sci (Weinh). 2023 May 12. e2206744

m6 A-Dependent Modulation via IGF2BP3/MCM5/Notch Axis Promotes Partial EMT and LUAD Metastasis.

Xia Yang, Qiaorui Bai, Weizhong Chen, Jiaer Liang, Fang Wang, Weiqi Gu, Lei Liu, Quanfeng Li, Zishuo Chen, Anni Zhou, Jianting Long, Han Tian, Jueheng Wu, Xiaofan Ding, Ningning Zhou, Mengfeng Li, Yi Yang, Junchao Cai.

  The importance of mRNA N6-methyladenosine (m6 A) modification during tumor metastasis is controversial as it plays distinct roles in different biological contexts. Moreover, how cancer cell plasticity is shaped by m6 A modification is interesting but remains uncharacterized. Here, this work shows that m6 A reader insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) is remarkably upregulated in metastatic lung adenocarcinoma (LUAD) and indicates worse prognosis of patients. Interestingly, IGF2BP3 induces partial epithelial-mesenchymal-transition (EMT) and confers LUAD cells plasticity to metastasize through m6 A-dependent overactivation of Notch signaling. Mechanistically, IGF2BP3 recognized m6 A-modified minichromosome maintenance complex component (MCM5) mRNAs to prolong stability of them, subsequently upregulating MCM5 protein, which competitively inhibits SIRT1-mediated deacetylation of Notch1 intracellular domain (NICD1), stabilizes NICD1 protein and contributes to m6 A-dependent IGF2BP3-mediated cellular plasticity. Notably, a tight correlation of the IGF2BP3/MCM5/Notch axis is evidenced in clinical LUAD specimens. Therefore, this study elucidates a critical role of m6 A modification on LUAD cell plasticity in fostering tumor metastasis via the above axis, providing potential targets for metastatic LUAD.

Keywords:  MCM5; Notch signaling; lung adenocarcinoma; m6A modification; partial EMT

DOI:  https://doi.org/10.1002/advs.202206744
Oncogene. 2023 May 06.

m6A methylation regulates hypoxia-induced pancreatic cancer glycolytic metabolism through ALKBH5-HDAC4-HIF1α positive feedback loop.

Xiaoyan Liu, Maoxiao Feng, Xiaodong Hao, Zihan Gao, Zhaoxin Wu, Yuli Wang, Lutao Du, Chuanxin Wang.

Pancreatic cancer (PC) is the most hypoxic cancer type among solid tumors. The dynamic changes of RNA N6-methyl-adenosine (m6A) contribute to tumor cells adaption to hypoxic microenvironmental. However, the regulatory mechanisms of hypoxia response in PC remains elusive. Here, we reported that the m6A demethylase ALKBH5 mediated a decrease of total mRNA m6A modification during hypoxia. Subsequently, methylated RNA immunoprecipitation sequencing (MeRIP-seq) combined with RNA sequencing (RNA-seq) revealed transcriptome-wide gene expression alteration and identified histone deacetylase type 4 (HDAC4) as a key target gene of m6A modification under hypoxic conditionds. Mechanistically, m6A methylation recognized by m6A reader-YTHDF2 enhanced the stability of HDAC4, and then promoted glycolytic metabolism and migration of PC cells. Our assays also demonstrated that hypoxia-induced HDAC4 enhanced HIF1a protein stability, and overexpressed HIF1a promoted transcription of ALKBH5 in hypoxic pancreatic cancer cells. Together, these results found a ALKBH5/HDAC4/HIF1α positive feedback loop for cellular response to hypoxia in pancreatic cancer. Our studies uncover the crosstalk between histone acetylation and RNA methylation modification on layer of epigenetic regulation.

DOI: https://doi.org/10.1038/s41388-023-02704-8
Am J Cancer Res. 2023 ;13(4): 1443-1456

METTL3 regulates alternative splicing of cell cycle-related genes via crosstalk between mRNA m6A modifications and splicing factors.

Yeongjoo Kim, Seungjae Shin, Sunyoung Kwon, Kisung Moon, Su-Vin Baek, Ahyoung Jo, Hyung-Sik Kim, Gue-Ho Hwang, Sangsu Bae, Yun Hak Kim, Sung-Yup Cho, Jung-Min Oh.

N6-methyladenosine (m6A) modification in RNA affects various aspects of RNA metabolism and regulates gene expression. This modification is modulated by many regulatory proteins, such as m6A methyltransferases (writers), m6A demethylases (erasers), and m6A-binding proteins (readers). Previous studies have suggested that alterations in m6A regulatory proteins induce genome-wide alternative splicing in many cancer cells. However, the functional effects and molecular mechanisms of m6A-mediated alternative splicing have not been fully elucidated. To understand the consequences of this modification on RNA splicing in cancer cells, we performed RNA sequencing and analyzed alternative splicing patterns in METTL3-knockdown osteosarcoma U2OS cells. We detected 1,803 alternatively spliced genes in METTL3-knockdown cells compared to the controls and found that cell cycle-related genes were enriched in differentially spliced genes. A comparison of the published MeRIP-seq data for METTL14 with our RNA sequencing data revealed that 70-87% of alternatively spliced genes had an m6A peak near 1 kb of alternative splicing sites. Among the 19 RNA-binding proteins enriched in alternative splicing sites, as revealed by motif analysis, expression of SFPQ highly correlated with METTL3 expression in 12,839 TCGA pan-cancer patients. We also found that cell cycle-related genes were enriched in alternatively spliced genes of other cell lines with METTL3 knockdown. Taken together, we suggest that METTL3 regulates m6A-dependent alternative splicing, especially in cell cycle-related genes, by regulating the functions of splicing factors such as SFPQ.

Keywords: Alternative splicing; METTL3; cell cycle; m6A modification; splicing factor
Biomed Pharmacother. 2023 May 06. pii: S0753-3322(23)00629-7. [Epub ahead of print]163 114839

The roles and mechanism of m6A RNA methylation regulators in cancer immunity.

Lu Chen, Ying He, Jinyu Zhu, Shujuan Zhao, Shasha Qi, Xudong Chen, Hao Zhang, Ziheng Ni, Yuan Zhou, Gongxing Chen, Shuiping Liu, Tian Xie.

  N6-methyladenosine (m6A), the most common internal modification in RNA, can be regulated by three types of regulators, including methyltransferases (writers), demethylases (erasers), and m6A binding proteins (readers). Recently, immunotherapy represented by immune checkpoint blocking has increasingly become an effective cancer treatment, and increasing shreds of evidence show that m6A RNA methylation affects cancer immunity in various cancers. Until now, there have been few reviews about the role and mechanism of m6A modification in cancer immunity. Here, we first summarized the regulation of m6A regulators on the expression of target messenger RNAs (mRNA) and their corresponding roles in inflammation, immunity response, immune process and immunotherapy in various cancer cells. Meanwhile, we described the roles and mechanisms of m6A RNA modification in tumor microenvironment and immune response by affecting the stability of non-coding RNA (ncRNA). Moreover, we also discussed the m6A regulators or its target RNAs which might be used as predictor of cancer diagnosis and prognosis, and shed light on the potentiality of m6A methylation regulators as therapeutic targets in cancer immunity.

Keywords:  Cancer immunity; Diagnosis; Immunotherapy; Inflammation; M(6)A RNA methylation; Prognosis

DOI:  https://doi.org/10.1016/j.biopha.2023.114839
Gastroenterology. 2023 May 09. pii: S0016-5085(23)00701-1. [Epub ahead of print]

ALKBH5 Drives Immune Suppression via targeting AXIN2 to Promote Colorectal Cancer and is a Target for Boosting Immunotherapy.

Jianning Zhai, Huarong Chen, Chi Chun Wong, Yao Peng, Hongyan Gou, Jingwan Zhang, Yasi Pan, Danyu Chen, Yufeng Lin, Shiyan Wang, Wei Kang, Ka Fai To, Zhiwei Chen, Yuqiang Nie, Housheng Hansen He, Joseph Jao-Yiu Sung, Jun Yu.

   BACKGROUND & AIMS: Immune checkpoint blockade (ICB) therapy only benefits a small subset of colorectal cancer (CRC) patients and identification of CRC-intrinsic events modulating ICB efficacy is an unmet need. Here, we revealed AlkB Homolog 5 (ALKBH5), an RNA N6-methyladenosine (m6A) eraser, drives immunosuppression and is a molecular target to boost ICB therapy in CRC.
METHODS: Clinical significance of ALKBH5 was evaluated in human samples (n=205). Function of ALKBH5 was investigated in allografts, CD34+ humanized mice, and Alkbh5 knockin mice. Immunity change was determined by flow cytometry, immunofluorescence, and functional investigation. MeRIP-seq and RNA-seq were employed to identify ALKBH5 targets. Vesicle-like nanoparticles (VNPs)-encapsulated ALKBH5-siRNA was constructed for targeting ALKBH5 in vivo.
RESULTS: High ALKBH5 expression predicts poor prognosis in CRC. ALKBH5 induced myeloid-derived suppressor cells (MDSCs) accumulation but reduced natural killer cells and cytotoxic CD8+ T cells to induce colorectal tumorigenesis in allografts, CD34+ humanized mice and intestine-specific Alkbh5 knockin mice. Mechanistically, AXIN2, a Wnt suppressor, was identified as a target of ALKBH5. ALKBH5 binds and demethylates AXIN2 mRNA, which caused its dissociation from m6A reader IGF2BP1 and degradation, resulting in hyperactivated Wnt/β-catenin. Subsequently, Wnt/β-catenin targets including Dickkopf-related protein 1 (DKK1) were induced by ALKBH5. ALKBH5-induced DKK1 recruited MDSCs to drive immunosuppression in CRC, and this effect was abolished by anti-DKK1 in vitro and in vivo. Finally, VNPs-encapsulated ALKBH5-siRNA, or anti-DKK1 potentiated anti-PD1 treatment in suppressing CRC growth by enhancing anti-tumor immunity.
CONCLUSIONS: Our study identifies an ALKBH5-m6A-AXIN2-Wnt-DKK1 axis in CRC which drives immune suppression to facilitate tumorigenesis. Targeting of ALKBH5 is a promising strategy for sensitizing CRC to immunotherapy.

Keywords:  Colorectal cancer; DKK1; MDSCs; Wnt/β-catenin signaling; m(6)A modification

DOI:  https://doi.org/10.1053/j.gastro.2023.04.032
Int J Biol Sci. 2023 ;19(7): 2198-2219

Crosstalk between N6-methyladenosine (m6A) modification and noncoding RNA in tumor microenvironment.

Dan Wang, Yingying Han, Lushan Peng, Tao Huang, Xiaoyun He, Junpu Wang, Chunlin Ou.

  N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotes, and it participates in the regulation of pathophysiological processes in various diseases, including malignant tumors, by regulating the expression and function of both coding and non-coding RNAs (ncRNAs). More and more studies demonstrated that m6A modification regulates the production, stability, and degradation of ncRNAs and that ncRNAs also regulate the expression of m6A-related proteins. Tumor microenvironment (TME) refers to the internal and external environment of tumor cells, which is composed of numerous tumor stromal cells, immune cells, immune factors, and inflammatory factors that are closely related to tumors occurrence and development. Recent studies have suggested that crosstalk between m6A modifications and ncRNAs plays an important role in the biological regulation of TME. In this review, we summarized and analyzed the effects of m6A modification-associated ncRNAs on TME from various perspectives, including tumor proliferation, angiogenesis, invasion and metastasis, and immune escape. Herein, we showed that m6A-related ncRNAs can not only be expected to become detection markers of tumor tissue samples, but can also be wrapped into exosomes and secreted into body fluids, thus exhibiting potential as markers for liquid biopsy. This review provides a deeper understanding of the relationship between m6A-related ncRNAs and TME, which is of great significance to the development of a new strategy for precise tumor therapy.

Keywords:  biomarker; exosome; m6A; ncRNA; targeted therapy; tumor metastasis; tumor microenvironment

DOI:  https://doi.org/10.7150/ijbs.79651
Epigenetics. 2023 Dec;18(1): 2208707

GPX8 deficiency-induced oxidative stress reprogrammed m6A epitranscriptome of oral cancer cells.

Xun Chen, Lingyu Yuan, Lejia Zhang, Liutao Chen, Yi He, Chao Wang, Jie Wu, Shangwu Chen, Wei Zhao, Dongsheng Yu.

  Glutathione peroxidase 8 (GPX8) is a key regulator of redox homoeostasis. Whether its antioxidant activity participates in the regulation of m6A modification is a crucial issue, which has important application value in cancer treatment. In this study, MeRIP-seq was used to explore the characteristics of transcriptome-wide m6A modification in GPX8-deficient oral cancer cells. Oxidative stress caused by the lack of GPX8 resulted in 1,279 hyper- and 2,287 hypo-methylated m6A peaks and 2,036 differentially expressed genes in GPX8-KO cells. Twenty-eight differentially expressed genes were related to the cell response to oxidative stress, and half of them changed their m6A modification. In GPX8-KO cells, m6A regulators IGF2BP2 and IGF2BP3 were upregulated, while FTO, RBM15, VIRMA, ZC3H13, and YTHDC2 were downregulated. After H2O2 treatment, the expression changes of RBM15, IGF2BP2, and IGF2BP3 were further enhanced. These data indicated that GPX8-mediated redox homoeostasis regulated m6A modification, thereby affecting the expression and function of downstream genes. This study highlights the possible significance of GPX8 and the corresponding m6A regulatory or regulated genes as novel targets for antioxidant intervention in cancer therapy.

Keywords:  glutathione peroxidase 8 (GPX8); m6A modification; m6A regulatory genes; oxidative stress; reactive oxygen species (ROS)

DOI:  https://doi.org/10.1080/15592294.2023.2208707
Biomed Pharmacother. 2023 May 09. pii: S0753-3322(23)00636-4. [Epub ahead of print]163 114846

N6-methyladenosine (m6A) in cancer stem cell: From molecular mechanisms to therapeutic implications.

Liming Wang, Yuanxin Tang.

  The emergence of drug resistance and metastasis has long been a difficult problem for cancer treatment. Recent studies have shown that cancer stem cell populations are key factors in the regulation of cancer aggressiveness, relapse and drug resistance. Cancer stem cell (CSC) populations are highly plastic and self-renewing, giving them unique metabolic, metastatic, and chemotherapy resistance properties. N6-methyladenosine (m6A) is the most abundant internal modification of mRNA and is involved in a variety of cell growth and development processes, including RNA transcription, alternative splicing, degradation, and translation. It has also been linked to the development of various cancers. At present, the important role of m6A in tumour progression is gradually attracting attention, especially in the tumour stemness regulation process. Abnormal m6A modifications regulate tumour metastasis, recurrence and drug resistance. This paper aims to explore the regulatory mechanism of m6A in CSCs and clinical therapy, clarify its regulatory network, and provide theoretical guidance for the development of clinical targets and improvement of therapeutic effects.

Keywords:  Cancer stem cell; Clinical treatment; FTO; METTL3; N(6)-methyladenosine (m(6)A)

DOI:  https://doi.org/10.1016/j.biopha.2023.114846
Appl Biochem Biotechnol. 2023 May 10.

YTHDC2 Retards Cell Proliferation and Triggers Apoptosis in Papillary Thyroid Cancer by Regulating CYLD-Mediated Inactivation of Akt Signaling.

Guangying Zhou, Shasha Wang.

  N6-Methyladenosine (m6A) mRNA methylation modification is regarded as an important mechanism involved in diverse physiological processes. YT521-B homology (YTH) domain family members are associated with the tumorigenesis of several cancers. However, the role of YTHDC2 in papillary thyroid cancer (PTC) progression remains unknown. Results showed that YTHDC1, YTHDF1, YTHDF2, and YTHDF3 showed no observable difference in thyroid cancer samples. YTHDC2 was significantly downregulated in thyroid cancer samples and cells. YTHDC2 inhibited cell proliferation in PTC cells. YTHDC2 elicited apoptosis in PTC cells, as demonstrated by the elevated expression of pro-apoptotic factors cl-caspase-3/caspase-3 and Bcl-2-associated (Bax), and the reduced anti-apoptotic B cell lymphoma-2 (Bcl-2) expression. There was a positive correlation between YTHDC2 and cylindromatosis (CYLD) expression based on GEPIA database. YTHDC2 increased CYLD expression in PTC cells. CYLD knockdown abolished the effects of YTHDC2 on PTC cell proliferation and apoptosis. Additionally, YTHDC2 inactivated the protein kinase B (Akt) pathway by increasing CYLD in PTC cells. Overall, YTHDC2 inhibited cell proliferation and induced apoptosis in PTC cells by regulating CYLD-mediated inactivation of Akt pathway.

Keywords:  Akt Pathway; CYLD; Papillary Thyroid Cancer; YTHDC2

DOI:  https://doi.org/10.1007/s12010-023-04540-8
J Hazard Mater. 2023 May 02. pii: S0304-3894(23)00839-7. [Epub ahead of print]455 131556

Cigarette smoking, by accelerating the cell cycle, promotes the progression of non-small cell lung cancer through an HIF-1α-METTL3-m6A/CDK2AP2 axis.

Yi Yang, Cheng Cheng, Bin He, Xuan Du, Jinyuan Liu, Haibo Xia, Peiwen Wang, Meng Wu, Hao Wu, Qizhan Liu.

  Cigarette smoking killed about 8 million people every year and promoted non-small cell lung cancer (NSCLC). We investigated the molecular mechanism of smoking-promoted NSCLC progression. Relative to non-smokers, NSCLC patients who were smokers had a higher tumor malignancy. For NSCLC cells, cigarette smoke extract (CSE) increased levels of HIF-1α, METTL3, Cyclin E1, and CDK2 and promoted the G1/S transition, which promoted cell proliferation. Down-regulation HIF-1α or METTL3 reversed these effects. meRIP-seq and RNA-seq revealed the m6A modification in Cyclin Dependent Kinase 2 Associated Protein 2 (CDK2AP2) mRNA as the key downstream target. Further, for NSCLC cells exposed to CSE, HIF-1α activated METTL3 transcription. Xenografts in nude mice demonstrated that HIF-1α via METTL3 participated in tumor growth. In NSCLC tissues of smokers, protein levels of HIF-1α and METTL3 were higher, and levels of CDK2AP2 were lower. In conclusion, HIF-1α via METTL3 regulation of the m6A modification of CDK2AP2 mRNA drives smoking-induced progression of NSCLC through promoting cell proliferation. This is a previously unknown molecular mechanism for smoking-induced NSCLC progression. The results have potential value for treatment of NSCLC, especially for patients who smoke.

Keywords:  Cell cycle; Cigarette smoking; HIF-1α; M(6)A modification; Non-small cell lung cancer

DOI:  https://doi.org/10.1016/j.jhazmat.2023.131556
Mol Cancer. 2023 May 09. 22(1): 81

Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer.

Yueqin Wang, Jingyao Wei, Luyao Feng, Ouwen Li, Lan Huang, Shaoxuan Zhou, Yingjie Xu, Ke An, Yu Zhang, Ruiying Chen, Lulu He, Qiming Wang, Han Wang, Yue Du, Ruijuan Liu, Chunmin Huang, Xiaojian Zhang, Yun-Gui Yang, Quancheng Kan, Xin Tian.

   BACKGROUND: RNA 5-methylcytosine (m5C) modification plays critical roles in the pathogenesis of various tumors. However, the function and molecular mechanism of RNA m5C modification in tumor drug resistance remain unclear.
METHODS: The correlation between RNA m5C methylation, m5C writer NOP2/Sun RNA methyltransferase family member 2 (NSUN2) and EGFR-TKIs resistance was determined in non-small-cell lung cancer (NSCLC) cell lines and patient samples. The effects of NSUN2 on EGFR-TKIs resistance were investigated by gain- and loss-of-function assays in vitro and in vivo. RNA-sequencing (RNA-seq), RNA bisulfite sequencing (RNA-BisSeq) and m5C methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) were performed to identify the target gene of NSUN2 involved in EGFR-TKIs resistance. Furthermore, the regulatory mechanism of NSUN2 modulating the target gene expression was investigated by functional rescue and puromycin incorporation assays.
RESULTS: RNA m5C hypermethylation and NSUN2 were significantly correlated with intrinsic resistance to EGFR-TKIs. Overexpression of NSUN2 resulted in gefitinib resistance and tumor recurrence, while genetic inhibition of NSUN2 led to tumor regression and overcame intrinsic resistance to gefitinib in vitro and in vivo. Integrated RNA-seq and m5C-BisSeq analyses identified quiescin sulfhydryl oxidase 1 (QSOX1) as a potential target of aberrant m5C modification. NSUN2 methylated QSOX1 coding sequence region, leading to enhanced QSOX1 translation through m5C reader Y-box binding protein 1 (YBX1).
CONCLUSIONS: Our study reveals a critical function of aberrant RNA m5C modification via the NSUN2-YBX1-QSOX1 axis in mediating intrinsic resistance to gefitinib in EGFR-mutant NSCLC.

Keywords:  Gefitinib; Intrinsic resistance; NSUN2; QSOX1; RNA 5-methylcytosinine; YBX1

DOI:  https://doi.org/10.1186/s12943-023-01780-4
Exp Cell Res. 2023 May 06. pii: S0014-4827(23)00167-2. [Epub ahead of print] 113620

NAT10-mediated AXL mRNA N4-acetylcytidine modification promotes pancreatic carcinoma progression.

Guanzhao Zong, Xing Wang, Xingya Guo, Qiuyan Zhao, Chuanyang Wang, Shien Shen, Wenqin Xiao, Qingqing Yang, Weiliang Jiang, Jie Shen, Rong Wan.

  Although the patient's survival time in various cancers has significantly increased in recent decades, the overall 5-year survival rate of pancreatic ductal adenocarcinoma (PDAC) has remained virtually unchanged due to rapid progression and metastasis. While N-acetyltransferase 10 (NAT10) has been identified as a regulator of mRNA acetylation in many malignancies, its role in PDAC remains unclear. Here, we found that NAT10 mRNA and protein levels were upregulated in PDAC tissues. Increased NAT10 protein expression was significantly correlated with poor prognosis in PDAC patients. Through our experiments, we demonstrated that NAT10 acted as an oncogene to promote PDAC tumorigenesis and metastasis in vitro and in vivo. Mechanistically, NAT10 exerts its oncogenic effects by promoting mRNA stability of receptor tyrosine kinase AXL in an ac4C-dependent manner leading to increased AXL expression and further promoting PDAC cell proliferation and metastasis. Together, our findings highlight the critical of NAT10 in PDAC progression and reveal a novel epigenetic mechanism by which modified mRNA acetylation promotes PDAC metastasis.

Keywords:  AXL; N4-acetylcytidine; NAT10; Pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1016/j.yexcr.2023.113620
Sci Adv. 2023 May 10. 9(19): eade7500

7SK methylation by METTL3 promotes transcriptional activity.

Marcelo Perez-Pepe, Anthony W Desotell, Hengyi Li, Wenxue Li, Bing Han, Qishan Lin, Daryl E Klein, Yansheng Liu, Hani Goodarzi, Claudio R Alarcón.

A fundamental feature of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. The small nuclear RNA 7SK prevents transcriptional elongation by sequestering the cyclin dependent kinase 9/cyclin T1 (CDK9/CCNT1) positive transcription elongation factor (P-TEFb) complex. We found that epidermal growth factor signaling induces phosphorylation of the enzyme methyltransferase 3 (METTL3), leading to METTL3-mediated methylation of 7SK. 7SK methylation enhanced its binding to heterogeneous nuclear ribonucleoproteins, causing the release of the HEXIM1 P-TEFb complex subunit1 (HEXIM1)/P-TEFb complex and inducing transcriptional elongation. Our findings establish the mechanism underlying 7SK activation and uncover a previously unknown function for the m6A modification in converting growth factor signaling events into a regulatory transcriptional response via an RNA methylation-dependent switch.

DOI: https://doi.org/10.1126/sciadv.ade7500
BMC Gastroenterol. 2023 May 11. 23(1): 147

The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma.

Ting Liu, Lei Sun, Zhi-Zhao Li, Kun Yang, Jia-Min Chen, Xiao-Yi Han, Li-Ming Qi, Xin-Gang Zhou, Peng Wang.

   BACKGROUND: RNA methylation is a crucial in many biological functions, and its aberrant regulation is associated with cancer progression. N6-Methyladenosine (m6A), 5-Methylcytosine (m5C), N1-methyladenosine (m1A) are common modifications of RNA methylation. However, the effect of methylation of m6A/m5C/m1A in hepatocellular carcinoma (HCC) remains unclear.
METHOD: The transcriptome datasets, clinic information, and mutational data of 48 m6A/m5C/m1A regulator genes were acquired from the TCGA database, and the prognostic hazard model was established by univariate and Least absolute shrinkage and selection operator (Lasso) regression. The multivariate regression was performed to determine whether the risk score was an independent prognostic indicator. Kaplan-Meier survival analysis and ROC curve analysis were used to evaluate the predictive ability of the risk model. Decision curve analysis（DCA）analysis was conducted to estimate the clinical utility of the risk model. We further analyzed the association between risk score and functional enrichment, tumor immune microenvironment, and somatic mutation.
RESULT: The four-gene (YTHDF1, YBX1, TRMT10C, TRMT61A) risk signature was constructed. The high-risk group had shorter overall survival (OS) than the low-risk group. Univariate and multivariate regression analysis indicated that risk score was an independent prognostic indicator. Risk scores in male group, T3 + T4 group and Stage III + IV group were higher in female group, T1 + T2 group and stage I + II group. The AUC values for 1-, 2-, and 3-year OS in the TCGA dataset were 0.764, 0.693, and 0.689, respectively. DCA analysis showed that the risk score had a higher clinical net benefit in 1- and 2-year OS than other clinical features.The risk score was positively related to some immune cell infiltration and most immune checkpoints.
CONCLUSION: We developed a novel m6A/m5C/m1A regulator genes' prognostic model, which could be applied as a latent prognostic tool for HCC and might guide the choice of immunotherapies.

Keywords:  Hepatocellular carcinoma; Prognostic model; Tumor immune microenvironment; m6A/ m5C/m1A regulatory genes

DOI:  https://doi.org/10.1186/s12876-023-02776-6
Mol Biol Rep. 2023 May 06.

m6A-dependent mevalonate kinase in juvenile hormone synthesis pathway regulates the diapause process of bivoltine silkworm (Bombyx mori).

Yan-Hua Chen, Tao Jiang, Ayinuer Yasen, Bing-Yan Fan, Juan Zhu, Mei-Xian Wang, Ping Qian, Xing-Jia Shen.

   BACKGROUND: Research has shown that epigenetic modification are involved the regulation of diapause in bivoltine silkworms (Bombyx mori), but it remains unclear how epigenetic modification in response to environmental signals precisely to regulate the diapause processing of bivoltine B. mori.
METHODS AND RESULTS: In this study, the diapause terminated eggs of bivoltine B. mori, Qiufeng (QF) were divided into two groups: a QFHT group incubated at 25 °C with a natural day/night cycle to produce diapause eggs, and a QFLT group incubated at 16.5 °C in darkness to produce non-diapause eggs. On the 3rd day of the pupal stage, the total RNAs of the eggs were extracted and their N6-adenosine methylation (m6A) abundances were analyzed to explore the effects of m6A methylation on diapause in the silkworm. The results showed that 1984 m6A peaks are shared, 1563 in QFLT and 659 in QFHT. The m6A methylation level of the QFLT group was higher than that of the QFHT one in various signaling pathways. The m6A methylation rate of mevalonate kinase (MK) in the insect hormone synthesis pathway was significantly different between the two groups. The knockdown of MK by RNA interference in the pupae of QFLT resulted in females laying diapause eggs rather than non-diapause eggs after mating.
CONCLUSIONS: m6A methylation involves in the diapause regulation of bivoltine B. mori by changing the expression levels of MK. This result provides a clearer image of the environmental signals on the regulation of diapause in bivoltine silkworms.

Keywords:  Bombyx mori; Diapause; MeRIP-Seq; Mevalonate kinase; RNA N6-methyladenosine methylation

DOI:  https://doi.org/10.1007/s11033-023-08489-z
Eur J Pharmacol. 2023 May 09. pii: S0014-2999(23)00272-8. [Epub ahead of print] 175761

Detailed profiling of m6A modified circRNAs and synergistic effects of circRNA and environmental risk factors for coronary artery disease.

Yahong Fu, Shu He, Chengcheng Li, Xiongkang Gan, Yanjun Wang, YaQing Zhou, Rongli Jiang, Qian Zhang, Yang Pan, Hanxiao Zhou, Xiumei Chen, Enzhi Jia.

  The modification of N6-methyladenosine (m6A) modification is implicated in human diseases. However, considerable uncertainty is associated with the regulatory mechanisms of m6A circRNAs in coronary artery disease (CAD), which require further clarification. In this study, m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq) was conducted to investigate m6A-modified circRNAs in human coronary artery smooth muscle cells (HCASMCs) and to identify potential biomarkers for CAD. A total of 830 and 331 up- and down-regulated m6A peaks, (corresponding to 463 and 243 up- and down-regulated circRNAs, respectively), were identified in HCASMCs in a pathological condition. Functional analysis suggested that these circRNAs appeared to participate in intracellular protein, histone deacetylase complex, ATP-dependent activity, autophagy, and AMPK signaling pathway. Four candidate circRNAs were selected for further evaluation in HCASMCs and human samples. The results suggested that hsa_circHECTD1 and hsa_circZBTB46 were significantly increased in patients with CAD (p-value = 0.039 and p-value = 0.014) and may act as potential diagnostic biomarkers of CAD. Furthermore, statistical results showed that hsa_circHECTD1 and hsa_circSEC62 were positively correlated with triglyceride (TG) (r = 0.213, p-value = 0.014) and Gensini Score (used to quantify the severity of CAD) (r = 0.349, p-value <0.001), respectively. Logistic regression revealed that hsa_circZBTB46 was strongly correlated with the incidence of CAD, and the synergistic effects of circRNAs and hypertension enhanced the risk of CAD. These results show that hsa_circHECTD1 and hsa_circZBTB46 may be new targets for further studies, and this study enhances our understanding of the effects of m6A-circRNAs on the pathogenesis of CAD.

Keywords:  Biomarker; Circular RNA; Coronary artery disease; N6-methyladenosine; Synergistic effects

DOI:  https://doi.org/10.1016/j.ejphar.2023.175761
Cell Death Dis. 2023 05 08. 14(5): 312

LncRNA LINC00969 promotes acquired gefitinib resistance by epigenetically suppressing of NLRP3 at transcriptional and posttranscriptional levels to inhibit pyroptosis in lung cancer.

Jiali Dai, Tianyu Qu, Dandan Yin, Yanan Cui, Chen Zhang, Erbao Zhang, Renhua Guo.

Epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) treatment prolongs the survival of lung cancer patients harbouring activating EGFR mutations. However, resistance to EGFR-TKIs is inevitable after long-term treatment. Molecular mechanistic research is of great importance in combatting resistance. A comprehensive investigation of the molecular mechanisms underlying resistance has important implications for overcoming resistance. An accumulating body of evidence shows that lncRNAs can contribute to tumorigenesis and treatment resistance. By bioinformatics analysis, we found that LINC00969 expression was elevated in lung cancer cells with acquired gefitinib resistance. LINC00969 regulated resistance to gefitinib in vitro and in vivo. Mechanistically, gain of H3K4me1 and H3K27Ac led to the activation of LINC00969 expression. LINC00969 interacts with EZH2 and METTL3, transcriptionally regulates the level of H3K27me3 in the NLRP3 promoter region, and posttranscriptionally modifies the m6A level of NLRP3 in an m6A-YTHDF2-dependent manner, thus epigenetically repressing NLRP3 expression to suppress the activation of the NLRP3/caspase-1/GSDMD-related classical pyroptosis signalling pathways, thereby endowing an antipyroptotic phenotype and promoting TKI resistance in lung cancer. Our findings provide a new mechanism for lncRNA-mediated TKI resistance from the new perspective of pyroptosis via simultaneous regulation of histone methylation and RNA methylation. The pivotal role of LINC00969 gives it the potential to be a novel biomarker and therapeutic target for overcoming EGFR-TKI resistance in lung cancer.

DOI: https://doi.org/10.1038/s41419-023-05840-x
Plant J. 2023 May 09.

N6 -methyladenosine mRNA modification regulates transcripts stability associated with cotton fiber elongation.

Kun Xing, Zhao Liu, Le Liu, Jie Zhang, Ghulam Qanmber, Ye Wang, Lisen Liu, Yu Gu, Changsheng Zhang, Shuaijie Li, Yan Zhang, Zuoren Yang.

  N6 -methyladenosine (m6 A) is the most abundant methylation modification in eukaryotic mRNA. The discovery of the dynamic and reversible regulatory mechanism of m6 A has greatly promoted the development of m6 A-led epitranscriptomics. However, the characterization of m6 A in cotton fiber is still unknown. Here, we reveal the potential link between m6 A modification and cotton fiber elongation by parallel m6 A-immunoprecipitation-sequencing (m6 A-seq) and RNA-seq analysis of fibers from the short fiber mutants Ligonliness-2 (Li2 ) and wild-type (WT). This study demonstrated a higher level of m6 A in the Li2 mutant, with the enrichment of m6 A modifications in the stop codon, 3' untranslated region, and coding sequence regions than in WT cotton. In the correlation analysis between genes containing differential m6 A modifications and differentially expressed genes, we identified several genes that could potentially regulate fiber elongation, including cytoskeleton, microtubule binding, cell wall and transcription factors. We further confirmed that the methylation of m6 A affected the mRNA stability of these fiber elongation-related genes including the transcription factor GhMYB44 which showed the highest expression level in the RNA-seq data and m6 A methylation in the m6 A-seq data. Next, the overexpression of GhMYB44 reduces fiber elongation, whereas the silencing of GhMYB44 produces longer fibers. In summary, these results uncover that m6 A methylation regulated the expression of genes related to fiber development by affecting mRNA's stability, ultimately affecting cotton fiber elongation.

Keywords:  GhMYB44; Ligon lintless-2; fiber elongation; gene expression; m6A methylation

DOI:  https://doi.org/10.1111/tpj.16274
FASEB J. 2023 Jun;37(6): e22965

Kupffer cell pyroptosis mediated by METTL3 contributes to the progression of alcoholic steatohepatitis.

Xue-Sheng Pan, Bo-Wen Li, Li-Li Wang, Ning Li, Hui-Min Lin, Jin Zhang, Na Du, Yue-Qin Zhu, Xian Wu, Cheng-Mu Hu, Wen-Yong Wu, Hui Hou, Hong-Chuan Zhao, Song-Yan Liao, Ya-Nan Yang, Yan Huang.

  Chronic alcohol consumption is a major risk factor for alcoholic steatohepatitis (ASH). Previous studies have shown that direct injury of hepatocytes is the key factor in its occurrence and development. However, our study shows that the role of Kupffer cells in ASH cannot be ignored. We isolated Kupffer cells from the livers of ASH mice and found that alcohol consumption induced Kupffer cell pyroptosis and increased the release of interleukin-1β (IL-1β). Furthermore, we screened the related m6A enzyme methyltransferase-like 3 (METTL3) from liver Kupffer cells, and found that silencing METTL3 alleviated inflammatory cytokine eruption by Kupffer cell pyroptosis in ASH mice. In vitro, we silenced METTL3 with lentivirus in BMDMs and RAW264.7 cells and confirmed that METTL3 could reduce pyroptosis by influencing the splicing of pri-miR-34A. Together, our results revealed a critical role of KC pyroptosis in ASH and highlighted the mechanism by which METLL3 relieves cell pyroptosis, which could be a promising therapeutic strategy for ASH.

Keywords:  METTL3; SIRT1; alcoholic steatohepatitis; miR-34a-5p; pyroptosis

DOI:  https://doi.org/10.1096/fj.202300059RR
Lab Invest. 2023 May 05. pii: S0023-6837(23)00113-7. [Epub ahead of print] 100170

Epigenetic modification-associated molecular classification of gastric cancer.

Wei Zeng, Jinfeng Zhu, Dongqiang Zeng, Jian Guo, Genjie Huang, Yu Zeng, Ling Wang, Jianping Bin, Yulin Liao, Min Shi, Wangjun Liao.

  Epigenetic modification is involved in tumorigenesis and cancer progression. We developed an epigenetic modification-associated molecular classification of gastric cancer (GC) to identify signature genes that accurately predict prognosis and the efficacy of immunotherapy. Last absolute shrinkage and selection operator and multivariate Cox regression analysis were conducted to develop an epigenetic modification-associated molecular classification. We investigated the significance of PIP4P2, an independent prognostic factor of the classification system, in predicting the prognosis and immunotherapy efficacy of GC patients. Epigenetic modification-associated molecular classification was highly associated with the clinicopathological characteristics of patients and the existing classification of GC. PIP4P2 was highly expressed in GC tissue and tumor-associated macrophages. High PIP4P2 expression in GC tissue induced tumor progression by activating PI3K/AKT signal transduction and had a negative impact on immunotherapy efficacy. High expression of PIP4P2 in macrophages was correlated with poor prognosis in GC patients. PIP4P2, as an independent unfavorable prognostic factor of epigenetic modification-associated molecular classification, is involved in tumorigenic progression and is essential for assessing the prognosis and immunotherapy efficacy of GC.

Keywords:  PIP4P2 1; epigenetic modification 2; gastric cancer 3; immunotherapy efficacy 5; prognosis 4

DOI:  https://doi.org/10.1016/j.labinv.2023.100170
Cell Death Discov. 2023 May 06. 9(1): 149

N6-methyladenine-mediated aberrant activation of the lncRNA SOX2OT-GLI1 loop promotes non-small-cell lung cancer stemness.

Hongliang Dong, Lili Zeng, Weiwei Chen, Qian Zhang, Fei Wang, Yan Wu, Bingjie Cui, Jingjing Qi, Xin Zhang, Cuilan Liu, Jiong Deng, Yong Yu, Clemens A Schmitt, Jing Du.

Despite the advent of precision medicine and immunotherapy, mortality due to lung cancer remains high. The sonic hedgehog (SHH) cascade and its key terminal factor, glioma-associated oncogene homolog 1 (GLI1), play a pivotal role in the stemness and drug resistance of lung cancer. Here, we investigated the molecular mechanism of non-canonical aberrant GLI1 upregulation. The SHH cascade was upregulated in stem spheres and chemo-resistant lung cancer cells and was accountable for drug resistance against multiple chemotherapy regimens. GLI1 and the long non-coding RNA SOX2OT were positively regulated, and the GLI1-SOX2OT loop mediated the proliferation of parental and stem-like lung cancer cells. Further mechanistic investigation revealed that SOX2OT facilitated METTL3/14/IGF2BP2-mediated m6A modification and stabilization of the GLI1 mRNA. Additionally, SOX2OT upregulated METTL3/14/IGF2BP2 by sponging miR-186-5p. Functional analysis corroborated that GLI1 acted as a downstream target of METTL3/14/IGF2BP2, and GLI1 silencing could block the oncogenicity of lung cancer stem-like cells. Pharmacological inhibition of the loop remarkably inhibited the oncogenesis of lung cancer cells in vivo. Compared with paired adjacent normal tissues, lung cancer specimens exhibited consistently upregulated GLI1/SOX2OT/METTL3/14/IGF2BP2. The m6A-modified GLI1-SOX2OT loop may serve as a potential therapeutic target and prognostic predictor for lung cancer therapy and diagnosis in the clinic.

DOI: https://doi.org/10.1038/s41420-023-01442-w
Cancer Cell Int. 2023 May 08. 23(1): 85

An innovative model based on N7-methylguanosine-related lncRNAs for forecasting prognosis and tumor immune landscape in bladder cancer.

Lei Ren, Xu Yang, Jinwen Liu, Weifeng Wang, Zixiong Liu, Qingyuan Lin, Bin Huang, Jincheng Pan, Xiaopeng Mao.

   BACKGROUND: As a novel type of the prevalent post-transcriptional modifications, N7-methylguanosine (m7G) modification is essential in the tumorigenesis, progression, and invasion of many cancers, including bladder cancer (BCa). However, the integrated roles of m7G-related lncRNAs in BCa remain undiscovered. This study aims to develop a prognostic model based on the m7G-related lncRNAs and explore its predictive value of the prognosis and anti-cancer treatment sensitivity.
METHODS: We obtained RNA-seq data and corresponding clinicopathological information from the TCGA database and collected m7G-related genes from previous studies and GSEA. Based on LASSO and Cox regression analysis, we developed a m7G prognostic model. The Kaplan-Meier (K-M) survival analysis and ROC curves were performed to evaluate the predictive power of the model. Gene set enrichment analysis (GSEA) was conducted to explore the molecular mechanisms behind apparent discrepancies between the low- and high-risk groups. We also investigated immune cell infiltration, TIDE score, TMB, the sensitivity of common chemotherapy drugs, and the response to immunotherapy between the two risk groups. Finally, we validated the expression levels of these ten m7G-related lncRNAs in BCa cell lines by qRT-PCR.
RESULTS: We developed a m7G prognostic model (risk score) composed of 10 m7G-related lncRNAs that are significantly associated with the OS of BCa patients. The K-M survival curves revealed that the high-risk group patients had significantly worse OS than those in the low-risk group. The Cox regression analysis confirmed that the risk score was a significant independent prognostic factor for BCa patients. We found that the high-risk group had higher the immune scores and immune cell infiltration. Furthermore, the results of the sensitivity of common anti-BCa drugs showed that the high-risk group was more sensitive to neoadjuvant cisplatin-based chemotherapy and anti-PD1 immunotherapy. Finally, qRT-PCR revealed that AC006058.1, AC073133.2, LINC00677, and LINC01338 were significantly downregulated in BCa cell lines, while the expression levels of AC124312.2 and AL158209.1 were significantly upregulated in BCa cell lines compared with normal cell lines.
CONCLUSION: The m7G prognostic model can be applied to accurately predict the prognosis and provide robust directions for clinicians to develop better individual-based and precise treatment strategies for BCa patients.

Keywords:  Bladder cancer (BCa); Immunotherapy; N7-methylguanosine; Prognostic model; Tumor microenvironment; lncRNA

DOI:  https://doi.org/10.1186/s12935-023-02933-7