bims-rimeca 2023-07-23 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023‒07‒23
eighteen papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

METTL3 promotes hyperoxia-induced pyroptosis in neonatal bronchopulmonary dysplasia by inhibiting ATG8-mediated autophagy.
RNautophagic regulation of DNMT3a-dependent DNA methylation by Linc00942 enhances chemoresistance in gastric cancer.
WTAP-Involved the m6A Modification of lncRNA FAM83H-AS1 Accelerates the Development of Gastric Cancer.
METTL3-dependent m6A modification mediates bladder remodeling after partial bladder outlet obstruction through CCN2 activation.
A lncRNA from the FTO locus acts as a suppressor of the m6A writer complex and p53 tumor suppression signaling.
Knockdown of RBM15 inhibits tumor progression and the JAK-STAT signaling pathway in cervical cancer.
Prognostic signature analysis and survival prediction of esophageal cancer based on N6-methyladenosine associated lncRNAs.
Comprehensive analysis of transcriptome-wide N6-methyladenosine methylomes in the Barrett's esophagus in rats.
FBXO5 acts as a novel prognostic biomarker for patients with cervical cancer.
Protective effects of hsa_circ_0072568 on interleukin‑1β‑stimulated human chondrocytes are mediated via the miR‑382‑5p/TOP1 axis.
Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sugar beet (Beta vulgaris).
MiRNA-338-3p Inhibits Neuroinflammation in the Corpus Callosum of LCV-LPS Rats Via STAT1 Signal Pathway.
Targeting histone deacetylase suppresses tumor growth through eliciting METTL14-modified m6 A RNA methylation in ocular melanoma.
N6-methyladenosine with immune infiltration and PD-L1 in hepatocellular carcinoma: novel perspective to personalized diagnosis and treatment.
N6-methyladenosine-modified circIRF2, identified by YTHDF2, suppresses liver fibrosis via facilitating FOXO3 nuclear translocation.
PSME3 induces radioresistance and enhances aerobic glycolysis in cervical cancer by regulating PARP1.
MTHFD2 promotes PD-L1 expression via activation of the JAK/STAT signalling pathway in bladder cancer.
Lung cancer-derived exosomal miR-132-3p contributed to interstitial lung disease development.

Clinics (Sao Paulo). 2023 Jul 19. pii: S1807-5932(23)00089-3. [Epub ahead of print]78 100253

METTL3 promotes hyperoxia-induced pyroptosis in neonatal bronchopulmonary dysplasia by inhibiting ATG8-mediated autophagy.

Lili Xu, Zhan Shi, Zhaojun Pan, Rong Wu.

  OBJECTIVES: N6-Methyladenosine (m6A) modification plays a vital role in lung disorders. However, the potential of m6A in neonatal Bronchopulmonary Dysplasia (BPD) has not been reported. This study aimed to investigate the roles of METTL3 in BPD.METHODS: BPD models were established by hyperoxia in vivo and in vitro. Histological analysis was determined using HE staining. Gene expression was determined using Western blotting, qRT-PCR, and immunofluorescence. The release of IL-1β and IL-18 was detected using ELISA. The m6A sites of ATG8 were predicted by SCRAPM and verified by MeRIP assay. The location of GSDMD and ATG8 was determined by FISH assay. The interaction between ATG8 and GSDMD was detected using Coimmunoprecipitation (Co-IP). Cell pyroptosis was determined using flow cytometry and TUNEL assays.
RESULTS: METTL3 was overexpressed in BPD, which was accompanied by an increase in m6A levels. Interestingly, METTL3 suppressed hyperoxia-mediated damage and pyroptosis in BEAS-2B cells and promoted cell autophagy. METTL3-mediated m6A modification of ATG8 suppressed its expression and disrupted the interaction between ATG8 and GSDMD. However, autophagy inhibition induced pyroptosis in BEAS-2B cells. In vivo assays showed that METTL3-mediated autophagy inhibition induced a decrease in the radial alveolar count and an increase in the mean linear intercept and promoted cell pyroptosis.
CONCLUSION: In conclusion, METTL3-mediated cell pyroptosis promotes BPD by regulating the m6A modification of ATG8. This may provide new insight into the development of BPD.

Keywords:  Bronchopulmonary Dysplasia; Genetics; N6-methyladenosine; Neonatal

DOI:  https://doi.org/10.1016/j.clinsp.2023.100253
Clin Transl Med. 2023 Jul;13(7): e1337

RNautophagic regulation of DNMT3a-dependent DNA methylation by Linc00942 enhances chemoresistance in gastric cancer.

Liyuan Zhu, Yiran Zhu, Fang Li, Yuan Meng, Hanying Wang, Wenxia Xu, Jingfeng Luo, Xian Wang, Lifeng Feng, Hongchuan Jin.

  BACKGROUND: Energy balance has long been known to extend lifespans and inhibit carcinogenesis in multiple species by slowing age-related epigenetic changes while the underlying mechanisms remain largely unknown. Herein, we found that starvation activated autophagy to remodel the DNA methylation profile by inhibiting DNMT3a expression.METHODS: Illumina Infinium MethylationEPIC BeadChip and dot blot assay were performed to quantify the global DNA methylation level. Protein-RNA interactions were validated through RNA immunoprecipitation and RNA pull-down assay. In vitro and in vivo experiments were carried out to testify the effect of DNMT3a on chemoresistance.
RESULTS: Autophagy is impaired in chemoresistance which was associated with differential DNA methylation and could be reversed by DNMT3a inhibition. Autophagy activation decreases the expression of DNMT3a mRNA, accompanied with the downregulation of chemoresistance-related Linc00942. Knockdown of Linc00942 reduces DNMT3a expression and genome-wide DNA methylation while Linc00942 overexpression increased DNMT3a expression and correlated hypermethylation in cancer cells and primary tumour tissues. Mechanistically, Linc00942 recruits RNA methyltransferase METTL3 to stimulate N6-methyladenosine (m6A) deposit on DNMT3a transcripts, triggering IGF2BP3/HuR to recognize modified mRNA for reinforced stability. SQSTM1/p62 recruits Linc00942 for autophagic degradation which can be abrogated after autophagy inhibition by p62 knockdown or chloroquine treatment.
CONCLUSIONS: Inhibition of autophagy increases Linc00942 expression to promote chemoresistance and autophagy activation or hypomethylating agent decitabine restores chemosensitivity by reducing global DNA methylation. Overall, this study identifies a novel methylation cascade linking impaired RNautophagy to global hypermethylation in chemoresistance, and provides a rationale for repurposing decitabine to overcome chemoresistance in cancer treatment.

Keywords:  DNMT3a; Linc00942; N6-methyladenosine; RNautophagy; chemoresistance

DOI:  https://doi.org/10.1002/ctm2.1337
Mol Biotechnol. 2023 Jul 21.

WTAP-Involved the m6A Modification of lncRNA FAM83H-AS1 Accelerates the Development of Gastric Cancer.

Nian Liu, Chao Zhang, Liang Zhang.

  The long noncoding RNA FAM83H-antisense RNA 1 (FAM83H-AS1) is involved in gastric cancer (GC) development. This study determined whether FAM83H-AS1 was regulated by N6-methyladenosine (m6A) modifications in GC. Real-time quantitative polymerase chain reaction was performed to determine the expression levels of FAM83H-AS1 and Wilms' tumor 1 associated protein (WTAP). The protein content of WTAP was evaluated using western blotting. To assess the m6A alterations in FAM83H-AS1, methylated RNA immunoprecipitation was performed to identify interactions between WTAP and FAM83H-AS1. Functionally, the proliferation, migration, and invasion of GC cells were measured using a Cell Counting Kit-8 and transwell assays, respectively. High expression levels of FAM83H-AS1 and WTAP were detected in GC samples and there was a positive correlation between them. In addition, WTAP mediates FAM83H-AS1 expression in an m6A-dependent manner. Further investigations indicated that WTAP silencing reversed the cancer-promoting role of FAM83H-AS1 overexpression in GC cell migration, proliferation, and invasion. Our results suggest that WTAP-mediated FAM83H-AS1 promotes GC development via m6A modification. Our findings provide new biomarkers for GC diagnosis and targeted therapy. Wilms' tumor 1 associated protein (WTAP) promotes gastric cancer (GC) by accelerating cell proliferation, migration, and invasion of GC cells via the N6-methyladenosine(m6A) modification of long non coding RNA FAM83H-AS1.

Keywords:  FAM83H-AS1; Gastric cancer; Wilms’ tumor 1 associated protein; m6A modification

DOI:  https://doi.org/10.1007/s12033-023-00810-2
Neurourol Urodyn. 2023 Jul 16.

METTL3-dependent m6A modification mediates bladder remodeling after partial bladder outlet obstruction through CCN2 activation.

Yafei Yang, Jun Long, Jin Yang, Hanxiong Zheng, Yongchang Lai, Chiheng Chen, Fucai Tang, Yibo Gao, Lin Chen, Zhaohui He.

  AIMS: N6-methyladenosine (m6A) modification is a critical posttranscriptional event in gene regulation. Thus, identifying methyltransferase, demethylase, or m6A binding protein-mediated m6A modifications in cancer or noncancer transcriptomes has become a promising novel strategy for disease therapy development. However, novel insights into m6A modification in partial bladder outlet obstruction (pBOO) and detailed information about the drivers of bladder remodeling remain to be elucidated. Here, we first characterized the m6A modification landscape in pBOO and investigated potential actionable pharmaceutical targets for future therapies.METHODS: We generated an improved animal model of pBOO in SD rats with urethral meatus stricture induced by suturing. Urodynamic investigations and cystometry were carried out to evaluate the physiologic changes elicited by pBOO. Whole-transcriptome sequencing (RNA-seq) and m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq) were subsequently performed to analyze the expression pattern associated with bladder remodeling in pBOO.
RESULTS: The cystometric evaluation of bladder function demonstrated obvious increases in pressure-related parameters in the pBOO group. Hematoxylin and eosin staining and Masson's trichrome staining validated the occurrence of bladder remodeling. A global elevation in m6A RNA methylation levels was observed in parallel to a increased expression of METTL3 in the pBOO group. High-throughput sequencing revealed the differences in expression patterns between the pBOO and sham-operated groups. Furthermore, potential m6A-modified genes, including CCN2, may serve as new pharmaceutical targets to reverse bladder remodeling.
CONCLUSIONS: Exploring the roles of m6A-modified genes identified as associated with bladder remodeling by integrating RNA-seq and MeRIP-seq data can offer new insights for developing promising treatments for pBOO patients.

Keywords:  METTL3; bladder outlet obstruction; bladder remodeling; epitranscriptome; m6A modification

DOI:  https://doi.org/10.1002/nau.25233
Mol Cell. 2023 Jul 12. pii: S1097-2765(23)00471-9. [Epub ahead of print]

A lncRNA from the FTO locus acts as a suppressor of the m6A writer complex and p53 tumor suppression signaling.

Jianong Zhang, Jiangbo Wei, Rui Sun, Haoyue Sheng, Kai Yin, Yunqian Pan, Rafael Jimenez, Sujun Chen, Xiao-Long Cui, Zhongyu Zou, Zhiying Yue, Michael J Emch, John R Hawse, Liguo Wang, Housheng Hansen He, Shujie Xia, Bangmin Han, Chuan He, Haojie Huang.

  N6-methyladenosine (m6A) of mRNAs modulated by the METTL3-METTL14-WTAP-RBM15 methyltransferase complex and m6A demethylases such as FTO play important roles in regulating mRNA stability, splicing, and translation. Here, we demonstrate that FTO-IT1 long noncoding RNA (lncRNA) was upregulated and positively correlated with poor survival of patients with wild-type p53-expressing prostate cancer (PCa). m6A RIP-seq analysis revealed that FTO-IT1 knockout increased mRNA m6A methylation of a subset of p53 transcriptional target genes (e.g., FAS, TP53INP1, and SESN2) and induced PCa cell cycle arrest and apoptosis. We further showed that FTO-IT1 directly binds RBM15 and inhibits RBM15 binding, m6A methylation, and stability of p53 target mRNAs. Therapeutic depletion of FTO-IT1 restored mRNA m6A level and expression of p53 target genes and inhibited PCa growth in mice. Our study identifies FTO-IT1 lncRNA as a bona fide suppressor of the m6A methyltransferase complex and p53 tumor suppression signaling and nominates FTO-IT1 as a potential therapeutic target of cancer.

Keywords:  FTO; FTO-IT1; METTL14; METTL3; N(6)-methyladenosine; RBM15; lncRNA; m(6)A; p53; prostate cancer

DOI:  https://doi.org/10.1016/j.molcel.2023.06.024
BMC Cancer. 2023 Jul 20. 23(1): 684

Knockdown of RBM15 inhibits tumor progression and the JAK-STAT signaling pathway in cervical cancer.

Chunnian Zhang, Liqin Gu, Juan Xiao, Feng Jin.

  BACKGROUND: RNA binding motif protein 15 (RBM15), a writer of N6-methyladenosine (m6A) methylation, contributes significantly to the development of various tumors. However, the function of RBM15 in cervical cancer (CC) has not been determined.METHODS: Based on the GSE9750, GSE63514, and m6A datasets, m6A-related differentially expressed genes (DEGs) were screened out. The hub genes were identified by generating a Protein-Protein Interaction (PPI) network. RT-qPCR was conducted to assess the mRNA expression of hub genes. CCK8, scratch wound healing, and transwell assays were utilized to examine the influence of RBM15 on HeLa and SiHa cells. Tumor xenograft models were used to assess the effects of RBM15 on tumorigenesis. A mechanistic analysis of RBM15 in CC tumors was conducted using the GeneCards and Coxpresdb databases, followed by a Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and the pathway-related genes were subsequently validated using Western blotting.
RESULTS: Five DEGs were screened, including WTAP, RBM15, CBLL1, and YTHDC2. Among them, WTAP, RBM15, CBLL1, and YTHDC2 were hub genes and can be used as biomarkers for CC. RBM15 expression was considerably increased, while WTAP, CBLL1, and YTHDC2 were significantly downregulated. Knockdown of RBM15 significantly suppressed the proliferation, invasion, and migration of CC cells and tumorigenesis. Moreover, knockdown of RBM15 significantly reduced the expression levels of proteins related to the JAK-STAT pathway.
CONCLUSIONS: Knockdown of RBM15 inhibited the progression of CC cells, which probably by inhibiting the JAK-STAT pathway pathway.

Keywords:  Cervical cancer; N6-methyladenosine; RBM15; The JAK-STAT signaling pathway

DOI:  https://doi.org/10.1186/s12885-023-11163-z
Brief Funct Genomics. 2023 Jul 18. pii: elad028. [Epub ahead of print]

Prognostic signature analysis and survival prediction of esophageal cancer based on N6-methyladenosine associated lncRNAs.

Ting He, Zhipeng Gao, Ling Lin, Xu Zhang, Quan Zou.

  Esophageal cancer (ESCA) has a bad prognosis. Long non-coding RNA (lncRNA) impacts on cell proliferation. However, the prognosis function of N6-methyladenosine (m6A)-associated lncRNAs (m6A-lncRNAs) in ESCA remains unknown. Univariate Cox analysis was applied to investigate prognosis related m6A-lncRNAs, based on which the samples were clustered. Wilcoxon rank and Chi-square tests were adopted to compare the clinical traits, survival, pathway activity and immune infiltration in different clusters where overall survival, clinical traits (N stage), tumor-invasive immune cells and pathway activity were found significantly different. Through least absolute shrinkage and selection operator and proportional hazard (Lasso-Cox) model, five m6A-lncRNAs were selected to construct the prognostic signature (m6A-lncSig) and risk score. To investigate the link between risk score and clinical traits or immunological microenvironments, Chi-square test and Spearman correlation analysis were utilized. Risk score was found connected with N stage, tumor stage, different clusters, macrophages M2, B cells naive and T cells CD4 memory resting. Risk score and tumor stage were found as independent prognostic variables. And the constructed nomogram model had high accuracy in predicting prognosis. The obtained m6A-lncSig could be taken as potential prognostic biomarker for ESCA patients. This study offers a theoretical foundation for clinical diagnosis and prognosis of ESCA.

Keywords:  N6-methyladenosine; biomarker; esophageal cancer; long noncoding RNA; prognostic signature

DOI:  https://doi.org/10.1093/bfgp/elad028
Genomics. 2023 Jul 14. pii: S0888-7543(23)00131-3. [Epub ahead of print] 110687

Comprehensive analysis of transcriptome-wide N6-methyladenosine methylomes in the Barrett's esophagus in rats.

Ke Zou, Hui Dong, Mengmeng Li, Ying Zhang, Kai Zhang, Danlin Song, Chuanlian Chu.

  PURPOSE: As the most abundant RNA modification, N6-methyladenosine (m6A) methylation plays crucial roles in various diseases. The aim of this study is to comprehensively map the landscape of the mRNA m6A modification pattern in Barrett's esophagus (BE) in order to find key genes and potential therapy for BE and even esophageal adenocarcinoma (EAC).METHODS: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequencing (RNA-seq) were performed to compare the difference in mRNA m6A methylation and differentially expressed mRNAs between BE and normal control (NC) tissues. Bioinformatics analysis was used to describe the m6A modification pattern and specific genes in BE and NC tissues.
RESULTS: Through MeRIP-seq, we obtained m6A methylation profiling in BE and NC tissues. In total, 11,026 unique peaks were detected in the BE groups, whereas 8564 unique peaks were detected in the NC groups. Peaks were primarily enriched within CDS with GGACU motifs and most of the peaks were within 1000 bp in width. Moreover, functional enrichment analysis demonstrated that hypermethylated and hypomethylated genes were significantly enriched in coronavirus disease pathway, calcium signaling pathway and MAPK signaling pathways. Furthermore, PPI network was conducted and 18 hub genes were identified via STRING database and Cystoscope. Among them, ACTA1, CDC20, CKM, KIF20a, MYH11, TPM2, MYL9, DES, TNNT3 were overexpressed in EAC in the GEPIA gene bank and TPM1, KIF20a impaired patients' survival in the Kaplan-Meier plotter database. Finally, functional enrichment analysis demonstrated that co-expressed genes of TPM1 were significantly enriched in calcium signaling pathway, cGMP-PKG signaling pathway and PI3K-Akt signaling pathway.
CONCLUSION: Our study is the first to perform comprehensive and transcriptome-wide maps to identify the potential roles played by m6A methylation in BE, which widely involved in oxidative stress. This foresees a guiding role in revealing the molecular mechanism of m6A-mediated genes that govern the pathogenesis and progression of BE and EAC.

Keywords:  Barrett's esophagus; Esophageal adenocarcinoma; MeRIP-seq; RNA-seq; m6A

DOI:  https://doi.org/10.1016/j.ygeno.2023.110687
Front Cell Dev Biol. 2023 ;11 1200197

FBXO5 acts as a novel prognostic biomarker for patients with cervical cancer.

Shan Jiang, Jianfeng Zheng, Zhaolei Cui, Yanhong Li, Qiaoling Wu, Xintong Cai, Chaoqiang Zheng, Yang Sun.

  Background: Cervical cancer (CC) remains one of the most common and deadly malignancies in women worldwide. FBXO5, a protein-coding gene, is highly expressed in a variety of primary tumors and promotes tumor progression, however, its role and prognostic value in CC remain largely unknown. Methods: A key differential gene, FBXO5, was screened according to WGCNA based on immunohistochemical assays of clinical samples, multiple analyses of the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, including survival analysis, tumor mutational burden, GO, KEGG, tumor immune infiltration, and chemotherapeutic drug sensitivity, to explore the expression and prognostic value of FBXO5 in CC. The migration and invasiveness of cervical cancer cells following FBXO5 knockdown and overexpression were examined using wound healing and transwell assays, and the viability of cancer cells was assessed using CCK8 and EdU assays. Results: FBXO5 was discovered to be substantially expressed in CC tissues using data from our CC cohort and the TCGA database, and a survival analysis indicated FBXO5 as a predictive factor for poor overall survival in CC patients. In vitro, CC cells were more inclined to proliferate, migrate, and invade when FBXO5 was upregulated as opposed to when it was knocked down.

Keywords:  WGCNA; autophagy; cervical cancer; immunity; prognosis

DOI:  https://doi.org/10.3389/fcell.2023.1200197
Exp Ther Med. 2023 Aug;26(2): 383

Protective effects of hsa_circ_0072568 on interleukin‑1β‑stimulated human chondrocytes are mediated via the miR‑382‑5p/TOP1 axis.

Qing Chang, Chao Li, Junzheng Hu, Rui Geng.

  Circular RNA (circRNA) dysregulation has been linked to osteoarthritis (OA). The present study investigated the involvement of hsa_circ_0072568 (circ0072568) in OA. The expression of circ0072568 was detected in OA tissues and interleukin (IL)-1β-stimulated human chondrocytes. After performing dual-luciferase reporter and RNA immunoprecipitation assays, MTT, enzyme-linked immunosorbent assay and western blot analysis were used to assess the functions of circ0072568 in IL-1β-induced inflammation in chondrocytes in vitro. Circ0072568 was inhibited in OA tissues and the cell model in vitro. Circ0072568 overexpression protected the chondrocytes against IL-1β-induced inflammation and extracellular matrix (ECM) breakdown. Circ0072568 directly attached to microRNA (miR)-382-5p and enhanced the production of topoisomerase 1 (TOP1). Furthermore, miR-382-5p overexpression or TOP1 knockdown attenuated the effects of circ0072568 in IL-1β-stimulated human chondrocytes. On the whole, the present study demonstrates that the Circ0072568/miR-382-5p/TOP1 axis is involved in inflammation and ECM degradation in OA. These findings may contribute to the development of potential therapeutic strategies for OA.

Keywords:  extracellular matrix; hsa_circ_0072568; inflammation; microRNA-382-5p; osteoarthritis; topoisomerase 1

DOI:  https://doi.org/10.3892/etm.2023.12082
Plant Sci. 2023 Jul 15. pii: S0168-9452(23)00211-X. [Epub ahead of print] 111794

Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sugar beet (Beta vulgaris).

Junliang Li, Jiayuan Wang, Qiuying Pang, Xiufeng Yan.

  Salinity is an important environmental factor in crop growth and development. N6-methyladenosine (m6A) is an essential epigenetic modification that regulates plant-environment interaction. Sugar beet is a major sugar-yielding crop that has a certain tolerance to salt, but the dynamic response elicited by the m6A modification of transcripts under salt stress remains unknown. In this study, sugar beet was exposed to 300mM NaCl to investigate its physiological response to high salinity and transcriptome-wide m6A modification profile. After the salt treatment, 7,737 significantly modified m6A sites and 4,981 differentially expressed genes (DEGs) were identified. Among the 312 m6A-modified DEGs, 113 hypomethylated DEGs were up-regulated and 99 hypermethylated DEGs were down-regulated, indicating a negative correlation between m6A modification and gene expression. Well-known salt tolerance genes (e.g., sodium/hydrogen exchanger 1, choline monooxygenase, and nucleoredoxin 2) and phospholipid signaling pathway genes (phosphoinositol-specific phospholipase C, phospholipase D, diacylglycerol kinase 1, etc.) were also among the m6A-modified genes. Further analysis showed that m6A modification may regulate salt-tolerant related gene expression by controlling mRNA stability. Therefore, changes in m6A modification may negatively regulate the expression of the salt-resistant genes in sugar beet, at least in part by modulating the stability of the mRNA via demethylase BvAlkbh10B. These findings could provide a better understanding of the epigenetic mechanisms of salt tolerance in sugar beets and uncover new candidate genes for improving the production of sugar beets planted in high-salinity soil.

Keywords:  Demethylase; M(6)A-seq; RNA methylation; Salt stress; Sugar beet

DOI:  https://doi.org/10.1016/j.plantsci.2023.111794
Cell Mol Neurobiol. 2023 Jul 21.

MiRNA-338-3p Inhibits Neuroinflammation in the Corpus Callosum of LCV-LPS Rats Via STAT1 Signal Pathway.

Nan Liu, Qiuping Zhou, Huifang Wang, Qian Li, Zhuo Chen, Yiyan Lin, Lingling Yi, Shuqi Jiang, Chunbo Chen, Yiyu Deng.

  Neuroinflammation is a common characteristic of intracranial infection (ICI), which is associated with the activation of astrocytes and microglia. MiRNAs are involved in the process of neuroinflammation. This study aimed to investigate the potential mechanism by which miR-338-3p negatively modulate the occurrence of neuroinflammation. We here reported that the decreased levels of miR-338-3p were detected using qRT-PCR and the upregulated expression of TNF-α and IL-1β was measured by ELISA in the cerebrospinal fluid (CSF) in patients with ICI. A negative association between miR-338-3p and TNF-α or IL-1β was revealed by Pearson correlation analysis. Sprague-Dawley (SD) rats were injected with LPS (50 μg) into left cerebral ventricule (LCV), following which the increased expression of TNF-α and IL-1β and the reduction of miR-338-3p expression were observed in the corpus callosum (CC). Moreover, the expression of TNF-α and IL-1β in the astrocytes and microglia in the CC of LCV-LPS rats were saliently inhibited by the overexpression of miR-338-3p. In vitro, cultured astrocytes and BV2 cells transfected with mimic-miR-338-3p produced less TNF-α and IL-1β after LPS administration. Direct interaction between miR-338-3p and STAT1 mRNA was validated by biological information analysis and dual luciferase assay. Furthermore, STAT1 pathway was found to be implicated in inhibition of neuroinflammation induced by mimic miR-338-3p in the astrocytes and BV2 cells. Taken together, our results suggest that miR-338-3p suppress the generation of proinflammatory mediators in astrocyte and BV2 cells induced by LPS exposure through the STAT1 signal pathway. MiR-338-3p could act as a potential therapeutic strategy to reduce the neuroinflammatory response. Diagram describing the cellular and molecular mechanisms associated with LPS-induced neuroinflammation via the miR-338-3p/STAT1 pathway. LPS binds to TLRs on astrocytes or microglia to activate the STAT1 pathway and upregulate the production of pro-inflammatory cytokines. However, miR-338-3p inhibits the expression of STAT1 and reduces the production of inflammatory mediators.

Keywords:  Astrocytes; BV2 cells; MiR-338-3p; Neuroinflammation; STAT1

DOI:  https://doi.org/10.1007/s10571-023-01378-w
Cancer Commun (Lond). 2023 Jul 19.

Targeting histone deacetylase suppresses tumor growth through eliciting METTL14-modified m6 A RNA methylation in ocular melanoma.

Ai Zhuang, Xiang Gu, Tongxin Ge, Shaoyun Wang, Shengfang Ge, Peiwei Chai, Renbing Jia, Xianqun Fan.

  BACKGROUND: Diversified histone deacetylation inhibitors (HDACis) have demonstrated encouraging outcomes in multiple malignancies. N6-methyladenine (m6 A) is the most prevalent messenger RNA modification that plays an essential role in the regulation of tumorigenesis. Howbeit, an in-depth understanding of the crosstalk between histone acetylation and m6 A RNA modifications remains enigmatic. This study aimed to explore the role of histone acetylation and m6 A modifications in the regulation of tumorigenesis of ocular melanoma.METHODS: Histone modification inhibitor screening was used to explore the effects of HDACis on ocular melanoma cells. Dot blot assay was used to detect the global m6 A RNA modification level. Multi-omics assays, including RNA-sequencing, cleavage under targets and tagmentation, single-cell sequencing, methylated RNA immunoprecipitation-sequencing (meRIP-seq), and m6 A individual nucleotide resolution cross-linking and immunoprecipitation-sequencing (miCLIP-seq), were performed to reveal the mechanisms of HDACis on methyltransferase-like 14 (METTL14) and FAT tumor suppressor homolog 4 (FAT4) in ocular melanoma. Quantitative real-time polymerase chain reaction (qPCR), western blotting, and immunofluorescent staining were applied to detect the expression of METTL14 and FAT4 in ocular melanoma cells and tissues. Cell models and orthotopic xenograft models were established to determine the roles of METTL14 and FAT4 in the growth of ocular melanoma. RNA-binding protein immunoprecipitation-qPCR, meRIP-seq, miCLIP-seq, and RNA stability assay were adopted to investigate the mechanism by which m6 A levels of FAT4 were affected.
RESULTS: First, we found that ocular melanoma cells presented vulnerability towards HDACis. HDACis triggered the elevation of m6 A RNA modification in ocular melanoma. Further studies revealed that METTL14 served as a downstream candidate for HDACis. METTL14 was silenced by the hypo-histone acetylation status, whereas HDACi restored the normal histone acetylation level of METTL14, thereby inducing its expression. Subsequently, METTL14 served as a tumor suppressor by promoting the expression of FAT4, a tumor suppressor, in a m6 A-YTH N6-methyladenosine RNA-binding protein 1-dependent manner. Taken together, we found that HDACi restored the histone acetylation level of METTL14 and subsequently elicited METTL14-mediated m6 A modification in tumorigenesis.
CONCLUSIONS: These results demonstrate that HDACis exert anti-cancer effects by orchestrating m6 A modification, which unveiling a "histone-RNA crosstalk" of the HDAC/METTL14/FAT4 epigenetic cascade in ocular melanoma.

Keywords:  N6-methyladenine; epigenetics; histone deacetylation inhibitors; histone-RNA crosstalk; melanoma

DOI:  https://doi.org/10.1002/cac2.12471
Front Endocrinol (Lausanne). 2023 ;14 1153802

N6-methyladenosine with immune infiltration and PD-L1 in hepatocellular carcinoma: novel perspective to personalized diagnosis and treatment.

Yanlong Shi, Yizhu Wang, Wenning Zhang, Kaiyi Niu, Xinyu Mao, Kun Feng, Yewei Zhang.

  Background: Increasing evidence elucidated N6-methyladenosine (m6A) dysregulation participated in regulating RNA maturation, stability, and translation. This study aimed to demystify the crosstalk between m6A regulators and the immune microenvironment, providing a potential therapeutic target for patients with hepatocellular carcinoma (HCC).Methods: Totals of 371 HCC and 50 normal patients were included in this study. GSE121248 and GSE40367 datasets were used to validate the expression of HNRNPC. The R package "ConsensusClusterPlus" was performed to screen consensus clustering types based on the expression of m6A regulators in HCC. The R package "pheatmap", "immunedeconv", "survival", "survminer" and "RMS" were applied to investigate the expression, immunity, overall survival, and clinical application in different clusters and expression groups. Comprehensive analysis of HNRNPC in pan-cancer was conducted by TIMER2 database. Besides, HNRNPC mRNA and protein expression were verified by qRT-PCR and immunohistochemistry analysis.
Results: Most of m6A regulators were over-expressed excerpt for ZC3H13 in HCC. Three independent clusters were screened based on m6A regulators expression, and the cluster 2 had a favorable prognosis in HCC. Then, the cluster 2 was positively expression in macrophage, hematopoietic stem cell, endothelial cell, and stroma score, while negatively in T cell CD4+ memory and mast cell. We identified HNRNPC was an independent prognostic factor in HCC, and nomogram performed superior application value for clinical decision making. Moreover, PD-L1 was significantly up-regulated in HCC tissues, cluster 1, and cluster 3, and we found PD-L1 expression was positively correlated with HNRNPC. Patients with HCC in high-expression groups was associated with tumor-promoting cells. Besides, HNRNPC was correlated with prognosis, TMB, and immune checkpoints in cancers. Particularly, the experiments confirmed that HNRNPC was positively expression in HCC cells and tissues.
Conclusion: The m6A regulators play irreplaceable roles in prognosis and immune infiltration in HCC, and the relationship of HNRNPC and PD-L1 possesses a promising direction for therapeutic targets of immunotherapy response. Exploration of m6A regulators pattern could be build the prognostic stratification of individual patients and move toward to personalized treatment.

Keywords:  N6-methyladenosine; PD-L1; hepatocellular carcinoma; hnRNPC; immune infiltration; immunotherapy; prognosis

DOI:  https://doi.org/10.3389/fendo.2023.1153802
Int J Biol Macromol. 2023 Jul 17. pii: S0141-8130(23)02706-X. [Epub ahead of print] 125811

N6-methyladenosine-modified circIRF2, identified by YTHDF2, suppresses liver fibrosis via facilitating FOXO3 nuclear translocation.

Xin Chen, Sai Zhu, Hai-Di Li, Jia-Nan Wang, Li-Jiao Sun, Jin-Jin Xu, Ya-Ru Hui, Xiao-Feng Li, Liang-Yun Li, Yu-Xin Zhao, Xiao-Guo Suo, Chuan-Hui Xu, Ming-Lu Ji, Ying-Yin Sun, Cheng Huang, Xiao-Ming Meng, Lei Zhang, Xiong-Wen Lv, Dong-Qing Ye, Jun Li.

  Circular RNA (circRNA) has been implicated in liver fibrosis and modulated by multiple elusive molecular mechanisms, while the effects of N6-methyladenosine (m6A) modification on circRNA are still elusive. Herein, we identify circIRF2 from our circRNA sequencing data, which decreased in liver fibrogenesis stage and restored in resolution stage, indicating that dysregulated circIRF2 may be closely associated with liver fibrosis. Gain/loss-of-function analysis was performed to evaluate the effects of circIRF2 on liver fibrosis at both the fibrogenesis and resolution in vivo. Ectopic expression of circIRF2 attenuated liver fibrogenesis and HSCs activation at the fibrogenesis stage, whereas downregulation of circIRF2 impaired mouse liver injury repair and inflammation resolution. Mechanistically, YTHDF2 recognized m6A-modified circIRF2 and diminished circIRF2 stability, partly accounting for the decreased circIRF2 in liver fibrosis. Microarray was applied to investigate miRNAs regulated by circIRF2, our data elucidate cytoplasmic circIRF2 may directly harbor miR-29b-1-5p and competitively relieve its inhibitory effect on FOXO3, inducing FOXO3 nuclear translocation and accumulation. Clinically, circIRF2 downregulation was prevalent in liver fibrosis patients compared with healthy individuals. In summary, our findings offer a novel insight into m6A modification-mediated regulation of circRNA and suggest that circIRF2 may be an exploitable prognostic marker and/or therapeutic target for liver fibrosis.

Keywords:  FOXO3; Liver fibrosis; YTHDF2; circIRF2; circRNAs; m(6)A

DOI:  https://doi.org/10.1016/j.ijbiomac.2023.125811
Tissue Cell. 2023 Jun 29. pii: S0040-8166(23)00139-8. [Epub ahead of print]83 102151

PSME3 induces radioresistance and enhances aerobic glycolysis in cervical cancer by regulating PARP1.

Xing Wei, Ke Sun, Shubo Li, Cheng Lin, Zhongheng Wei.

  Cervical cancer (CC) ranks the fourth in gynecologic cancers. The incidence and mortality of CC has been decreased due to the cancer screening and early treatments in recent years, but the prognosis of CC patients at advanced stage is still sorrowful. Whether PSME3 exerted a role in the radioresistance of CC cells remains to be investigated. In this study, the expression of PSME3 in mRNA and protein levels was measured by RT-qPCR and western blot analysis, and increased expression of PSME3 in CC tissues and cells was observed. CCK-8 and colony formation assay revealed that the cell viability and proliferation of Hela and CaSki cells treated with different doses of X-ray was reduced due to the depletion of PSME3, indicating that silencing of PSME3 enhanced the radiosensitivity of CC cells. In addition, repair on DNA damage in CC cells was enhanced by PSME3 and the damage was attenuated by PSME3. Besides, the expression of glycolysis-related proteins (GLUT1, PGC-1α, LDHA and HK2) were enhanced by PSME3 but reduced by silencing PSME3 in CC cells. PSME3 restraint attenuated the levels of glucose consumption and lactate production, suggesting PSME3 depletion suppressed abnormal glycolysis of CC cells. Mechanically, PSME3 increased the PARP1 expression via elevating c-myc. Finally, we observed PSME3 attenuation inhibited CC growth in vivo. In conclusion, PSME3 enhanced radioresistance and aerobic glycolysis in CC by regulating PARP1, which might shed a light into the function of PSME3 in CC treatment.

Keywords:  Aerobic glycolysis; Cervical cancer; PARP1; PSME3; Radioresistance

DOI:  https://doi.org/10.1016/j.tice.2023.102151
J Cell Mol Med. 2023 Jul 21.

MTHFD2 promotes PD-L1 expression via activation of the JAK/STAT signalling pathway in bladder cancer.

Linzhi Li, Yunlong Zhang, Weimin Hu, Fan Zou, Jinzhuo Ning, Ting Rao, Yuan Ruan, Weimin Yu, Fan Cheng.

  Although combination chemotherapy is widely used for bladder cancer (BC) treatment, the recurrence and progression rates remain high. Therefore, novel therapeutic targets are required. Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) contributes to tumourigenesis and immune evasion in several cancers; however, its biological function in BC remains unknown. This study aimed to investigate the expression, prognostic value and protumoural function of MTHFD2 in BC and elucidate the mechanism of programmed death-ligand 1 (PD-L1) upregulation by MTHFD2. An analysis using publicly available databases revealed that a high MTHFD2 expression was correlated with clinical features and a poor prognosis in BC. Furthermore, MTHFD2 promoted the growth, migration, invasion and tumourigenicity and decreased the apoptosis of BC cells in vivo and in vitro. The results obtained from databases showed that MTHFD2 expression was correlated with immune infiltration levels, PD-L1 expression, and the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway. The expression of MTHFD2, PD-L1 and JAK/STAT signalling pathway-related proteins increased after interferon gamma treatment and decreased after MTHFD2 knockdown. Moreover, addition of a JAK/STAT pathway activator partially reduced the effect of MTHFD2 knockdown on BC cells. Collectively, our findings suggest that MTHFD2 promotes the expression of PD-L1 through the JAK/STAT signalling pathway in BC.

Keywords:  MTHFD2; PD-L1; bladder cancer (BC); malignant phenotype; poor prognosis

DOI:  https://doi.org/10.1111/jcmm.17863
World J Surg Oncol. 2023 Jul 15. 21(1): 205

Lung cancer-derived exosomal miR-132-3p contributed to interstitial lung disease development.

Sufang Fang, Ting Wang, Ling Weng, Ximei Han, Rongshan Zheng, Hongying Zhang.

  PURPOSE: Interstitial lung diseases (ILDs) have high morbidity and mortality and poor prognosis. The significance of microRNAs (miRNAs) was highlighted in ILDs development. Currently, we attempted to confirm the functions of lung cancer-derived exosomal miR-132-3p and reveal the underlying mechanism.METHOD: Characteristics of exosomes were verified by transmission electron microscope (TEM), nanoparticle tracking analysis, and Western blot assay. Exosome uptake for the normal human lung fibroblasts (NHLF) was assessed using a PKH67 staining assay. MTT and colony formation assays were applied to examine the proliferation abilities of NHLF. The interaction between miR-132-3p and sprouty1 (SPRY1) was confirmed by a luciferase reporter assay.
RESULTS: Lung cancer-derived exosomes promoted normal human lung fibroblast activation. Exosome inhibitor GW4869 reversed the effects of Exo on NHLF. Subsequently, miR-132-3p in lung cancer-derived exosomes activated the normal human lung fibroblast and promoted interstitial lung disease development ex vivo. Next, SPRY1 was verified to be the binding protein of miR-132-3p, and sh-SPRY1 abrogated the effects of the miR-132-3p inhibitor on NHLF.
CONCLUSION: Exosomal miR-132-3p from A549 cells accelerated the development of interstitial lung disease through binding to SPRY1, which might serve as an important target for ILDs.

Keywords:  Exosome; Interstitial lung diseases; NHLF; SPRY1; miR-132-3p

DOI:  https://doi.org/10.1186/s12957-023-03095-6