bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022‒12‒04
35 papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics
  1. Biological roles of the RNA m6A modification and its implications in cancer.
  2. RNA m6A methyltransferase METTL14 promotes the procession of non-small cell lung cancer by targeted CSF1R.
  3. ELK1-mediated YTHDF1 drives prostate cancer progression by facilitating the translation of Polo-like kinase 1 in an m6A dependent manner.
  4. IGF2BP3 is an essential N6-methyladenosine biotarget for suppressing ferroptosis in lung adenocarcinoma cells.
  5. Comprehensive Analysis of N6-Methyladenosine (m6A) RNA Methylation Regulators and Tumour Microenvironment Cell Infiltration Involving Prognosis and Immunotherapy in Gastroesophageal Adenocarcinomas.
  6. N6-methyladenosine plays a dual role in arsenic carcinogenesis by temporal-specific control of core target AKT1.
  7. m6A demethylase FTO regulate CTNNB1 to promote adipogenesis of chicken preadipocyte.
  8. m6A methyltransferase METTL3 inhibits endometriosis by regulating alternative splicing of MIR17HG.
  9. N6-Methyladenosine Regulator-Mediated RNA Methylation Is Involved in Primary Sjögren's Syndrome Immunoinfiltration.
  10. Analysis of m6A modulator-mediated methylation modification patterns and the tumor microenvironment in lung adenocarcinoma.
  11. Transient regulation of RNA methylation in human hematopoietic stem cells promotes their homing and engraftment.
  12. METTL16 epigenetically enhances GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.
  13. M6A regulator-mediated immune infiltration and methylation modification in hepatocellular carcinoma microenvironment and immunotherapy.
  14. Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
  15. A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells.
  16. Expression of m6A Methylation Regulator in Osteoarthritis and Its Prognostic Markers.
  17. N6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants.
  18. Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs.
  19. METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets.
  20. N6-methyladenosine-associated prognostic pseudogenes contribute to predicting immunotherapy benefits and therapeutic agents in head and neck squamous cell carcinoma.
  21. RNA Modifications Meet Tumors.
  22. m6A reader hnRNPA2B1 drives multiple myeloma osteolytic bone disease.
  23. m(6)A methyltransferase METTL3 relieves cognitive impairment of hyperuricemia mice via inactivating MyD88/NF-κB pathway mediated NLRP3-ASC-Caspase1 inflammasome.
  24. RFWD3 acts as a tumor promotor in the development and progression of bladder cancer.
  25. Interplay between m6 A epitranscriptome and epigenome in cancer: current knowledge and therapeutic perspectives.
  26. FMNL3 is Overexpressed in Tumor Tissues and Predicts an Immuno-Hot Phenotype in Pancreatic Cancer.
  27. Demethylase FTO promotes neuropathic pain development via regulating the m6A methylation levels of CXCR3.
  28. m6A epitranscriptomic modification regulates neural progenitor-to-glial cell transition in the retina.
  29. Bisphenol A exposure induces testicular oxidative damage via FTO/m6A/Nrf2 axis during postnatal development in mice.
  30. m6A-modified circFNDC3B inhibits colorectal cancer stemness and metastasis via RNF41-dependent ASB6 degradation.
  31. The m6A methylation profiles of immune cells in type 1 diabetes mellitus.
  32. IGF2BP2, an RNA-binding protein regulates cell proliferation and osteogenic differentiation by stabilizing SRF mRNA.
  33. Selected ALKBH dioxygenases are overexpressed in salivary gland tumours.
  34. Single-cell analysis in lung adenocarcinoma implicates RNA editing in cancer innate immunity and patient prognosis.
  35. Associations of selenoprotein expression and gene methylation with the outcome of clear cell renal carcinoma.
  1. Exp Mol Med. 2022 Nov 29.
    Biological roles of the RNA m6A modification and its implications in cancer.
    Juyeong Hong, Kexin Xu, Ji Hoon Lee.
      The N6-Methyladenosine (m6A) modification of RNA transcripts is the most prevalent and abundant internal modification in eukaryotic messenger RNAs (mRNAs) and plays diverse and important roles in normal biological processes. Extensive studies have indicated that dysregulated m6A modification and m6A-associated proteins play critical roles in tumorigenesis and cancer progression. However, m6A-mediated physiological consequences often lead to opposite outcomes in a biological context-dependent manner. Therefore, context-related complexity must be meaningfully considered to obtain a comprehensive understanding of RNA methylation. Recently, it has been reported that m6A-modified RNAs are closely related to the regulation of the DNA damage response and genomic integrity maintenance. Here, we present an overview of the current knowledge on the m6A modification and its function in human cancer, particularly in relation to the DNA damage response and genomic instability.
    DOI:  https://doi.org/10.1038/s12276-022-00897-8
  2. Thorac Cancer. 2022 Nov 29.
    RNA m6A methyltransferase METTL14 promotes the procession of non-small cell lung cancer by targeted CSF1R.
    Siying Ren, Ying Xiao, Lulu Yang, Yan Hu.
      BACKGROUND: Non-small cell lung cancer (NSCLC) is one of the most malignant cancer types, characterized by a poor prognosis. N6-methyladenosine (m6A) is a prevalent internal modification of mRNA. METTL14, an RNA methyltransferase that mediates m6A modification, is implicated in mRNA biogenesis. However, the biomechanism of METTL14 in NSCLC is not very clear.METHODS: Here, immunohistochemical (IHC) assay was employed to detect METTL14 in NSCLC tissues. The biological functions of METTL14 were demonstrated using cell transfection, cell proliferation assay, cell clone formation assay, cell cycle analysis, cell death analysis, transwell and wound healing assays. Transcriptome and methylated RNA immunoprecipitation (MERIP)-sequencing were used to explore the pathways and potential mechanism of METTL14 in NSCLC. RNA sequencing, METTL14 rip-sequencing, and METTL14 merip-sequencing were conducted to identify the potential targets of METTL14.
    RESULTS: METTL14 was significantly correlated with clinical pathological parameters of differentiation and M stage. Additionally, METTL14 promotes cell proliferation, induces cell death, and enhances cell migration and invasion in vitro. Transcriptome and MeRIP-sequencing reveal oncogenic mechanism of METTL14. RIP-sequencing highlights CSF1R and AKR1C1 as targets of METTL14. After validation with TCGA dataset, colony stimulating factor 1 receptor (CSF1R) showed significant positive coefficient with METTL14, and was presumed to be one target of METTl14 in lung cancer and verified by the cellular experiments.
    CONCLUSION: In conclusion, our results revealed the clinical significance of m6A RNA modification atlas, the function, and molecular targets CSF1R of METTL14 in NSCLC cell lines. The RNA m6A methyltransferase METTL14 promotes the progression of NSCLC by targeted CSF1R.
    Keywords:  CSF1R; METTL14; N6-methyladenosine; non-small cell lung cancer; profile
    DOI:  https://doi.org/10.1111/1759-7714.14741
  3. Int J Biol Sci. 2022 ;18(16): 6145-6162
    ELK1-mediated YTHDF1 drives prostate cancer progression by facilitating the translation of Polo-like kinase 1 in an m6A dependent manner.
    Peizhang Li, Yuanping Shi, Dajun Gao, Huan Xu, Yun Zou, Zhong Wang, Wenzhi Li.
      Background: N6-methyladenosine (m6A) is one of the most prevalent mRNA modifications in mammals, and it regulates the fate of modified RNA transcripts. In the current study, we aimed to elucidate the role of YTH m6A RNA-binding protein 1 (YTHDF1), a "reader" of m6A modification, in prostate cancer tumorigenesis. Methods: We employed a multi-omics approach to detect the direct target of YTHDF1 upon manipulation of YTHDF1 expression in prostate cancer cells. Expression of YTHDF1 was also evaluated in human prostate tumors and either adjacent or paired normal tissues. Additionally, in vivo tumor growth and metastasis experimental assays were performed to evaluate the role of YTHDF1 in tumorigenesis. Finally, luciferase reporter assays and Chromatin immunoprecipitation (ChIP) were conducted to elucidate the transcriptional regulators of YTHDF1. Results: We demonstrated that polo-like kinase 1 (PLK1) is a direct target of YTHDF1. YTHDF1 facilitated the translation efficiency of PLK1 in an m6A-dependent manner by identifying the m6A-modified PLK1 mRNA and subsequently promoted the hyperactivation of the PI3K/AKT signaling pathway. Moreover, our results indicated that YTHDF1 was upregulated in prostate cancer tissue and that high YTHDF1 expression was associated with adverse prognosis in patients with prostate cancer. Furthermore, upregulation of YTHDF1 promoted prostate cancer tumorigenesis and metastasis in vitro and in vivo. Additionally, dysregulation of ETS transcription factor ELK1 activated the transcription of YTHDF1 by directly binding to its promoter region. Conclusions: Collectively, our findings suggest that the ELK1/YTHDF1/PLK1/PI3K/AKT axis is critical for prostate cancer progression and may serve as a potential therapeutic target for prostate cancer treatment.
    Keywords:  ELK1; N6-methyladenosine; PLK1; YTHDF1; prostate cancer
    DOI:  https://doi.org/10.7150/ijbs.75063
  4. Mater Today Bio. 2022 Dec 15. 17 100503
    IGF2BP3 is an essential N6-methyladenosine biotarget for suppressing ferroptosis in lung adenocarcinoma cells.
    Xin Xu, Jiangtao Cui, Hong Wang, Lifang Ma, Xiao Zhang, Wanxin Guo, Xiangfei Xue, Yikun Wang, Shiyu Qiu, Xiaoting Tian, Yayou Miao, Mengyi Wu, Yongchun Yu, Yunhua Xu, Jiayi Wang, Yongxia Qiao.
      A lack of promising targets leads to poor prognosis in patients with lung adenocarcinoma (LUAD). Therefore, it is urgent to identify novel therapeutic targets. The importance of the N6-methyladenosine (m6A) RNA modification has been demonstrated in various types of tumors; however, knowledge of m6A-related proteins in LUAD is still limited. Here, we found that insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), an m6A reader protein, is highly expressed in LUAD and associated with poor prognosis. IGF2BP3 desensitizes ferroptosis (a new form of regulated cell death) in a manner dependent on its m6A reading domain and binding capacity to m6A-methylated mRNAs encoding anti-ferroptotic factors, including but not limited to glutathione peroxidase 4 (GPX4), solute carrier family 3 member 2 (SLC3A2), acyl-CoA synthetase long chain family member 3 (ACSL3), and ferritin heavy chain 1 (FTH1). After IGF2BP3 overexpression, expression levels and mRNA stabilities of these anti-ferroptotic factors were successfully sustained. Notably, significant correlations between SLC3A2, ACSL3, and IGF2BP3 were revealed in clinical LUAD specimens, further establishing the essential role of IGF2BP3 in desensitizing ferroptosis. Inducing ferroptosis has been gradually accepted as an alternative strategy to treat tumors. Thus, IGF2BP3 could be a potential target for the future development of new biomaterial-associated therapeutic anti-tumor drugs.
    Keywords:  ACSL3, acyl-CoA synthetase long chain family member 3; ALKBH5, alkB homolog 5; ELISA, enzyme-linked immunosorbent assay; FTH1, ferritin heavy chain 1; FTO, fat mass-and obesity-associated gene; Ferroptosis; GPX4, glutathione peroxidase 4; HNRNPA2B1, heterogeneous nuclear ribonucleoprotein A2/B1; IB, immunoblotting; IGF2BP3, insulin-like growth factor 2 mRNA binding protein 3; IHC, immunohistochemistry; LUAD, lung adenocarcinoma; Lung adenocarcinoma; MDA, malondialdehyde; METTL14, methyltransferase-like 14; METTL3, methyltransferase-like 3; PKM, pyruvate kinase M1/2; RBM15, RNA binding motif protein 15; ROS, reactive oxygen species; SLC3A2, solute carrier family 3 member 2; TMA, tissue microarray assay; Therapeutic target; VIRMA, vir-like m6A methyltransferase associated; WTAP, Wilms' tumor 1-associating protein; YTHDF2, YTH domain family 2; ZC3H13, zinc finger CCCH-type containing 13; m6A RNA methylation; m6A reader; m6A, N6-methyladenosine; qRT-PCR, quantitative reverse transcription PCR
    DOI:  https://doi.org/10.1016/j.mtbio.2022.100503
  5. Can J Gastroenterol Hepatol. 2022 ;2022 3506518
    Comprehensive Analysis of N6-Methyladenosine (m6A) RNA Methylation Regulators and Tumour Microenvironment Cell Infiltration Involving Prognosis and Immunotherapy in Gastroesophageal Adenocarcinomas.
    Duanrui Liu, Mingjie Yuan, Zongming Wang, Liping Sun, Yusong Fang, Xiaoli Ma, Lulu Zhang, Yuanxin Xing, Jingyu Zhu, Yunyun Liu, Wenshuai Zhu, Shuqin Bao, Yanfei Jia, Yunshan Wang.
      Objective: Gastroesophageal adenocarcinoma (GEA) is a high deadly and heterogeneous cancer. RNA N6-methyladenosine (m6A) modification plays a non-negligible role in shaping individual tumour microenvironment (TME) characterizations. However, the landscape and relationship of m6A modification patterns and TME cell infiltration features remain unknown in GEA.Methods: In this study, we examined the TME of GEA using assessments of the RNA-sequencing data focusing on the distinct m6A modification patterns from the public databases. Intrinsic patterns of m6A modification were evaluated for associations with clinicopathological characteristics, underlying biological pathways, tumour immune cell infiltration, oncological outcomes, and treatment responses. The expression of key m6A regulators and module genes was validated by qRT-PCR analysis.
    Results: We identified two distinct m6A modification patterns of GEA (cluster 1/2 subgroup), and correlated two subgroups with TME cell-infiltrating characteristics. Cluster 2 subgroup correlates with a poorer prognosis, downregulated PD-1 expression, higher risk scores, and distinct immune cell infiltration. In addition, PPI and WGCNA network analysis were integrated to identify key module genes closely related to immune infiltration of GEA to find immunotherapy markers. COL4A1 and COL5A2 in the brown module were significantly correlated to the prognosis, PD-1/L1 and CTLA-4 expression of GEA patients. Finally, a prognostic risk score was constructed using m6A regulator-associated signatures that represented an independent prognosis factor for GEA. Interestingly, COL5A2 expression was linked to the response to anti-PD-1 immunotherapy, m6A regulator expression, and risk score.
    Conclusion: Our work identified m6A RNA methylation regulators as an important class of players in the malignant progression of GEA and were associated with the complexity of the TME. COL5A2 may be the potential biomarker which contributes to predicting the response to anti-PD-1 immunotherapy and patients' prognosis.
    DOI:  https://doi.org/10.1155/2022/3506518
  6. J Hazard Mater. 2022 Nov 24. pii: S0304-3894(22)02262-2. [Epub ahead of print]445 130468
    N6-methyladenosine plays a dual role in arsenic carcinogenesis by temporal-specific control of core target AKT1.
    Tianhe Zhao, Donglei Sun, Wenxiao Xiong, Jin Man, Qian Zhang, Manyu Zhao, Zunzhen Zhang.
      High-profile RNA epigenetic modification N6-methyladenosine (m6A), as a double-edged sword for cancer, can either promote or inhibit arsenic-induced skin carcinogenesis. However, the core m6A-target gene determining the duality of m6A and the regulatory mechanism of m6A on the core gene are still poorly understood. Based on m6A microarray detection, integrated multi-omics analysis, and further experiments in vitro and in vivo, we explored the molecular basis for the dual role of m6A in cancer induced by environmental pollutants using models in different stages of arsenic carcinogenesis, including As-treated, As-transformed, and As-tumorigenic cell models. We found that the key proliferative signaling node AKT1 is in the center of the m6A-regulatory network in arsenic carcinogenicity. The m6A level on AKT1 mRNA (3'UTR, CDS, and 5'UTR) dynamically changed in different stages of arsenic carcinogenesis. The m6A writer METTL3-catalyzed upregulation of m6A promotes AKT1 expression by elevating m6A reader YTHDF1-mediated AKT1 mRNA stability in As-treated and As-transformed cells, while the m6A eraser FTO-catalyzed downregulation of m6A promotes AKT1 expression mainly by inhibiting m6A reader YTHDF2-mediated AKT1 mRNA degradation in As-tumorigenic cells. Furthermore, upregulation of m6A inhibits the expression of AKT1 negative regulator PHLPP2 and promotes the expression of AKT1 positive regulator PDK1. These changes in AKT1 regulators result in AKT1 activation by upregulating AKT1 phosphorylation at S473 and T308. Interestingly, the FTO-catalyzed decrease in m6A prevents AKT upregulation in As-treated cells but promotes AKT upregulation in As-tumorigenic cells. Both inhibitors targeting the m6A writer and eraser can inhibit the AKT1-mediated proliferation of As-tumorigenic cells by breaking the balance of m6A regulators. Our results demonstrated that AKT1 is the core hub determining m6A as a double-edged sword. Changed m6A dynamically upregulates the expression and activity of AKT1 in different stages of arsenic carcinogenesis. This study can advance our understanding of the dual role and precise time-specific mechanism of RNA epigenetics involved in the carcinogenesis of hazardous materials.
    Keywords:  Carcinogen; PDK1; PHLPP2; m(6)A; m(6)A regulators
    DOI:  https://doi.org/10.1016/j.jhazmat.2022.130468
  7. J Anim Sci Biotechnol. 2022 Dec 02. 13(1): 147
    m6A demethylase FTO regulate CTNNB1 to promote adipogenesis of chicken preadipocyte.
    Kan Li, Weichen Huang, Zhijun Wang, Qinghua Nie.
      BACKGROUND: N6-methyladenosine (m6A) is an abundant post-transcriptional RNA modification that affects various biological processes. The fat mass and obesity-associated (FTO) protein, a demethylase encoded by the FTO gene, has been found to regulate adipocyte development in an m6A-dependent manner in multiple species. However, the effects of the m6A methylation and FTO demethylation functions on chicken adipogenesis remain unclear. This study aims to explore the association between m6A modification and chicken adipogenesis and the underlying mechanism by which FTO affects chicken preadipocyte development.RESULTS: The association between m6A modification and chicken lipogenesis was assessed by treating chicken preadipocytes with different doses of methyl donor betaine and methylation inhibitor cycloleucine. The results showed that betaine significantly increased methylation levels and inhibited lipogenesis, and the inverse effect was found in preadipocytes after cycloleucine treatment. Overexpression of FTO significantly inhibited m6A levels and promoted proliferation and differentiation of chicken preadipocytes. Silencing FTO showed opposite results. Mechanistically, FTO overexpression increased the expression of catenin beta 1 (CTNNB1) by improving RNA stability in an m6A-dependent manner, and we proved that FTO could directly target CTNNB1. Furthermore, CTNNB1 may be a positive regulator of adipogenesis in chicken preadipocytes.
    CONCLUSIONS: m6A methylation of RNA was negatively associated with adipogenesis of chicken preadipocytes. FTO could regulate CTNNB1 expression in a demethylation manner to promote lipogenesis.
    Keywords:  Adipogenesis; CTNNB1; Chicken; FTO; m6A
    DOI:  https://doi.org/10.1186/s40104-022-00795-z
  8. Reproduction. 2022 Nov 01. pii: REP-22-0102. [Epub ahead of print]
    m6A methyltransferase METTL3 inhibits endometriosis by regulating alternative splicing of MIR17HG.
    Qian Li, Li Yang, Feng Zhang, Jiaxi Liu, Min Jiang, Yannan Chen, Chenchen Ren.
      N6-Methyladenosine (m6A) modification is largely involved in the development of different diseases. This study intended to investigate the implication of m6A methylation transferase methyltransferase like 3 (METTL3) in endometriosis (EMs). EMs- and m6A-related mRNAs and lncRNAs were identified through bioinformatics analysis. Next, EMs mouse models established by endometrial autotransplantation and mouse endometrial stromal cell (mESC) were prepared and treated with oe-METTL3 or sh-MIR17HG for pinpointing the in vitro and in vivo effects of METTL3 on EMs in relation to MIR17HG through determination of mESC biological processes as well as estradiol (E2) and related lipoprotein levels. We demonstrated that METTL3 and MIR17HG were downregulated in EMs mouse model. Overexpression of METTL3 suppressed proliferation, migration and invasion of mESCs. In addition, METTL3 enhanced the expression of MIR17HG through m6A modification. Moreover, METTL3 could inhibit the E2 level and alter related lipoprotein levels in EMs mice through upregulation of MIR17HG. The present study highlighted that the m6A methylation transferase METTL3 prevents EMs progression by upregulating MIR17HG expression.
    DOI:  https://doi.org/10.1530/REP-22-0102
  9. Dis Markers. 2022 ;2022 5242287
    N6-Methyladenosine Regulator-Mediated RNA Methylation Is Involved in Primary Sjögren's Syndrome Immunoinfiltration.
    Fang He, Hexu Liu, Changyin Yu.
      The crucial role of epigenetic regulation, especially the modifications of RNA N6-methyladenosine (m6A), in immunity is a current research hotspot. However, the m6A modifications in primary Sjögren's syndrome (pSS) and the immune infiltration pattern they govern remain unknown. Thus, the patterns of 23 m6A regulator-mediated RNA modifications in parotid or blood samples from pSS patients were evaluated by bioinformatics analysis in the current study. Comparing m6A regulators between control and pSS patients showed that m6A regulators are associated with pSS, and regulators also had differential correlations. Further clustering analysis and comparison of gene expression and immune cell infiltration between m6A modification patterns revealed that each modification pattern had its own unique genetic and immune profile. Multiple immune cell infiltrations were differentially expressed between the patterns. The enrichment of gene ontology between the two patterns in parotid was concentrated on RNA metabolism and processing. The KEGG pathway enrichment and weighted correlation network analysis further showed that the autophagy pathway might be involved in the m6A modification patterns in pSS. Together, these findings suggest that m6A regulators play a certain role in the immune cell infiltration of parotid tissue in pSS.
    DOI:  https://doi.org/10.1155/2022/5242287
  10. Sci Rep. 2022 Nov 30. 12(1): 20684
    Analysis of m6A modulator-mediated methylation modification patterns and the tumor microenvironment in lung adenocarcinoma.
    Qing-Cui Zeng, Qin Sun, Wen-Jie Su, Jia-Cen Li, Yi-Sha Liu, Kun Zhang, Li-Qing Yang.
      Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer. In the development and progression of LUAD, epigenetic aberration plays a crucial role. However, the function of RNA N6-methyladenosine (m6A) modifications in the LUAD progression is unknown. The m6A regulator modification patterns in 955 LUAD samples were analyzed comprehensively. Patterns were systematically correlated with the tumor microenvironment (TME) cell-infiltration characteristics. Using principal component analysis algorithms, the m6Ascore was generated to quantify m6A modification patterns in individual tumors. Then, their values for predicting prognoses and therapeutic response in LUAD patients were assessed. Three distinct m6A modification patterns in LUAD were identified. Among them, the prognosis of m6Acluster C was the best, while the prognosis of m6Acluster A was the worst. Interestingly, the characterization of TME cell infiltration and biological behavior differed among the three patterns. To evaluate m6A modification patterns within individual tumors, an m6Ascore signature was constructed. The results showed that the high m6Ascore group was associated with a better prognosis; tumor somatic mutations and tumor microenvironment differed significantly between the high- and low- m6Ascore groups. Furthermore, in the cohort with anti-CTLA-4 treatment alone, patients with a high m6Ascore had higher ICI scores, which indicated significant therapeutic advantage and clinical benefits.
    DOI:  https://doi.org/10.1038/s41598-022-20730-6
  11. Leukemia. 2022 Dec 02.
    Transient regulation of RNA methylation in human hematopoietic stem cells promotes their homing and engraftment.
    Xuepeng Wang, Scott Cooper, Hal E Broxmeyer, Reuben Kapur.
      Enhancing the efficiency of hematopoietic stem cell (HSC) homing and engraftment is critical for cord blood (CB) hematopoietic cell transplantation (HCT). Recent studies indicate that N6-methyladenosine (m6A) modulates the expression of mRNAs that are critical for stem cell function by influencing their stability. Here, we demonstrate that inhibition of RNA decay by regulation of RNA methylation, enhances the expression of the homing receptor chemokine C-X-C receptor-4 (CXCR4) in HSCs. We show that YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), a m6A reader and FTO α-ketoglutarate dependent dioxygenase (FTO), a m6A eraser play an opposite role in this process. Through screening, we identified several FDA-approved compounds that regulate the expression of YTHDF2 and FTO in CB CD34+ cells. We show that transient downregulation of YTHDF2 or activation of FTO by using these compounds inhibits CXCR4 decay in CB HSCs and promotes their homing and engraftment. Our results demonstrate a novel regulation strategy to enhance the function of CB HSCs and provide a translational approach to enhance the clinical efficacy of HCT.
    DOI:  https://doi.org/10.1038/s41375-022-01761-4
  12. Biochem Biophys Res Commun. 2022 Oct 26. pii: S0006-291X(22)01468-1. [Epub ahead of print]638 1-6
    METTL16 epigenetically enhances GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.
    Feng Ye, Jin Wu, Fan Zhang.
      Breast cancer is malignant cancer that severely threatens the life quality of female patients. N6-methyladenosine (m6A) is a prevalent modification of RNA. METTL16 is an important methyltransferase. This work aims to study the role of METTL16 in breast cancer cell death. The expression of METTL16 in clinical breast cancer specimens was analyzed by qPCR assay. The in vitro and in vivo breast cancer cell proliferation was measured by CCK8, colony formation, and xenograft mouse model. Cell ferroptosis was assessed by measuring the accumulation of iron, Fe2+, and lipid ROS. The mechanistic study was performed by RNA degradation, qPCR, and Western blotting assay. METTL16 was overexpressed in tumor tissues from breast cancer patients compared with the para-tumor tissues. Knockdown of METTL16 suppressed in vitro cell proliferation and in vivo tumor growth of breast cancer cells. Meanwhile, METTL16 silencing led to elevated intracellular levels of iron, Fe2+, and lipid ROS, indicating the incidence of ferroptosis. Furthermore, siMETTL16 decreased m6A methylation and enhanced the degradation of GPX4 RNA. METTL16-regulated m6A methylation of GPX4 stimulates proliferation and suppresses ferroptosis of breast cancer cells. Therefore, we concluded that METTL16 epigenetically enhanced GPX4 expression via m6A modification to promote breast cancer progression by inhibiting ferroptosis.
    Keywords:  Breast cancer; Ferroptosis; METTL16; m6A methylation
    DOI:  https://doi.org/10.1016/j.bbrc.2022.10.065
  13. Front Pharmacol. 2022 ;13 1052177
    M6A regulator-mediated immune infiltration and methylation modification in hepatocellular carcinoma microenvironment and immunotherapy.
    Kun Zhao, Bing Wei, Yingxuan Zhang, Wenkai Shi, Guokun Zhang, Zhengfeng Wang.
      Introduction: Tremendous evidence indicates that N6-methyladenosine (m6A) epigenetic modification and m6A-related enzymes constitute a complex network, which jointly regulates prevailing pathological processes and various signaling pathways in humankind. Currently, the role of the m6A-mediated molecular regulatory network in hepatocellular carcinoma (HCC) remains elusive. Methods: We recruited expression and pathological files of 368 HCC patients from The Cancer Genome Atlas cohort. Four public datasets serve as external authentication sets for nearest template prediction (NTP) validation. The correlation between 35 regulators and their prognostic value was compared. Gene set variation analysis (GSVA) was used to explore the latent mechanism. Four independent algorithms (ssGSEA, xCell, MCP-counter, and TIMER) were used to calculate the ratio of tumor cells and non-tumor cells to evaluate the tumor immune microenvironment. The m6Ascore model was established by principal component analysis (PCA). Prediction of immunotherapy and potential drugs was performed using TIDE and SubMap. Results: A total of 35 m6A regulators were widely associated, most of which were risk factors for HCC patients. The m6A phenotypic-cluster revealed differences in regulator transcriptional level, gene mutation frequency, functional pathways, and immune cell infiltration abundance under distinct m6A patterns. As expected, the m6A gene cluster confirmed the aforementioned results. The m6Ascore model further found that patients in the high-m6Ascore group were associated with lower tumor purity, higher enrichment of immune and stromal cells, upregulation of metabolic pathways, lower expression of m6A regulators, and favorable outcomes. Low-m6Ascore patients were associated with adverse outcomes. Notably, low-m6Ascore patients might be more sensitive to anti-PD-L1 therapy. Conclusion: This study found that a classification model based on the m6A manner could predict HCC prognosis and response to immunotherapy for HCC patients, which might improve prognosis and contribute to clinical individualized decision-making.
    Keywords:  hepatocellular carcinoma; immunotherapy; m6A regulators; prognosis; tumor microenvironment
    DOI:  https://doi.org/10.3389/fphar.2022.1052177
  14. Mol Pain. 2022 Nov 28. 17448069221144540
    Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
    Wei Lin, Yuan Liu, Yifei Zhou, Mengying Lin, Congxu Liu, Ying Tang, Bin Wu, Chun Lin.
      BACKGROUND: Accumulating evidence shows that N6-methyladenosine (m6A) modulators contribute to the process of chronic pain. However, the exact mechanisms of m6A writers involved in visceral hypersensitivity of IBS remain unclear. This article aimed to reveal a new mechanism for the progression of IBS.METHODS: The IBS-like model was established by neonatal colorectal distention (CRD). The relationship between m6A and circKcnk9 was analyzed by bioinformatics, immunofluorescence and RNA fluorescent in situ hybridization (FISH) assays. Visceral hypersensitivity was assessed based on the electromyography (EMG) response of the abdominal external oblique muscle to CRD. In vivo and in vitro studies (including EMG, stereotactic infusion, Western blot and qRT-PCR) were utilized to explore the biological functions of related indicators. The bioinformatics, RIP experiments and RNA pull-down assays were used to explore the potential molecular mechanisms.
    RESULTS: We identified that neonatal CRD increased the level of the m6A via methyltransferase-like 3 (METTL3) in the hippocampal neurons. Subsequently, knockdown of METTL3 could alleviate visceral hypersensitivity in IBS-like rats. By contrast, overexpression of METTL3 could induce visceral hypersensitivity and activate hippocampal neurons in control rats. Moreover, YTHDC1, the only m6A-associated protein predicted by bioinformatics to bind to circKcnk9, modulated visceral hypersensitivity through regulating the nuclear export of circKcnk9 in an m6A-dependent manner. Notably, FISH data suggested that the increased nuclear staining of circKcnk9 caused by siYTHDC1 could be recovered by overexpression of YTHDC1 wild type (WT) but not YTHDC1 negative control (NC) in PC12 cells.
    CONCLUSIONS: Our findings reveal a new regulatory mechanism in progress of IBS, that is, METTL3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
    Keywords:  IBS; METTL3; YTHDC1; hippocampus; visceral hypersensitivity
    DOI:  https://doi.org/10.1177/17448069221144540
  15. PLoS Biol. 2022 Nov 28. 20(11): e3001885
    A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells.
    Allison M Porman, Justin T Roberts, Emily D Duncan, Madeline L Chrupcala, Ariel A Levine, Michelle A Kennedy, Michelle M Williams, Jennifer K Richer, Aaron M Johnson.
      N6-methyladenosine (m6A) modification of RNA regulates normal and cancer biology, but knowledge of its function on long noncoding RNAs (lncRNAs) remains limited. Here, we reveal that m6A regulates the breast cancer-associated human lncRNA HOTAIR. Mapping m6A in breast cancer cell lines, we identify multiple m6A sites on HOTAIR, with 1 single consistently methylated site (A783) that is critical for HOTAIR-driven proliferation and invasion of triple-negative breast cancer (TNBC) cells. Methylated A783 interacts with the m6A "reader" YTHDC1, promoting chromatin association of HOTAIR, proliferation and invasion of TNBC cells, and gene repression. A783U mutant HOTAIR induces a unique antitumor gene expression profile and displays loss-of-function and antimorph behaviors by impairing and, in some cases, causing opposite gene expression changes induced by wild-type (WT) HOTAIR. Our work demonstrates how modification of 1 base in an lncRNA can elicit a distinct gene regulation mechanism and drive cancer-associated phenotypes.
    DOI:  https://doi.org/10.1371/journal.pbio.3001885
  16. Cartilage. 2022 Nov 28. 19476035221137722
    Expression of m6A Methylation Regulator in Osteoarthritis and Its Prognostic Markers.
    Di Zhang, DanDan Zhang, XiaoLi Yang, Qiang Li, RongQiang Zhang, YongMin Xiong.
      OBJECTIVE: Osteoarthritis (OA) is a multifactorial disorder, in which genetic factors are strongly associated with its development. However, the pathogenesis of OA is still unclear, and recently it has been observed that epigenetic modifications are also involved in the pathogenesis of OA. This study aims to study the potential role of m6A-related genes in the occurrence and development of OA.DESIGN: We downloaded the OA expression profile data (GSE55235) from the Gene Expression Omnibus database. First, function enrichment analysis of 17 representative m6A methylation regulatory factors was performed using the DAVID database and Metascape online tool. Then, we analyzed the expression of 17 m6A methylation regulatory factors in OA and the correlation between regulatory factors using Perl software. Finally, receiver operating characteristic (ROC) curve analysis and the area under the ROC curve were used to evaluate the diagnostic effectiveness of m6A-related genes for discriminating patients with OA and healthy.
    RESULTS: We first identified that 12 of the 17 genes were differentially expressed in OA. ALKBH1, EIF3, IGF2BP3, WTAP, and YTHDC1 were associated with early diagnosis and prognosis of OA.
    CONCLUSIONS: m6A RNA methylation regulator factors are key players in the progression of OA and have potential role in the stratification of prognosis and the formulation of treatment strategies.
    Keywords:  N6-methyladenosine (m6A) modification; biomarkers; gene expression; osteoarthritis (OA)
    DOI:  https://doi.org/10.1177/19476035221137722
  17. Nat Commun. 2022 Dec 02. 13(1): 7441
    N6-methyladenosine RNA modification regulates photosynthesis during photodamage in plants.
    Man Zhang, Yunping Zeng, Rong Peng, Jie Dong, Yelin Lan, Sujuan Duan, Zhenyi Chang, Jian Ren, Guanzheng Luo, Bing Liu, Kamil Růžička, Kewei Zhao, Hong-Bin Wang, Hong-Lei Jin.
      N6-methyladenosine (m6A) modification of mRNAs affects many biological processes. However, the function of m6A in plant photosynthesis remains unknown. Here, we demonstrate that m6A modification is crucial for photosynthesis during photodamage caused by high light stress in plants. The m6A modification levels of numerous photosynthesis-related transcripts are changed after high light stress. We determine that the Arabidopsis m6A writer VIRILIZER (VIR) positively regulates photosynthesis, as its genetic inactivation drastically lowers photosynthetic activity and photosystem protein abundance under high light conditions. The m6A levels of numerous photosynthesis-related transcripts decrease in vir mutants, extensively reducing their transcript and translation levels, as revealed by multi-omics analyses. We demonstrate that VIR associates with the transcripts of genes encoding proteins with functions related to photoprotection (such as HHL1, MPH1, and STN8) and their regulatory proteins (such as regulators of transcript stability and translation), promoting their m6A modification and maintaining their stability and translation efficiency. This study thus reveals an important mechanism for m6A-dependent maintenance of photosynthetic efficiency in plants under high light stress conditions.
    DOI:  https://doi.org/10.1038/s41467-022-35146-z
  18. J Anim Sci Biotechnol. 2022 Dec 01. 13(1): 146
    Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs.
    Du Zhang, Shumei Wu, Xinxin Zhang, Shuqiang Ren, Zhonglin Tang, Fei Gao.
      BACKGROUND: N6-methyladenosine (m6A) and DNA 5-methylcytosine (5mC) methylation plays crucial roles in diverse biological processes, including skeletal muscle development and growth. Recent studies unveiled a potential link between these two systems, implicating the potential mechanism of coordinated transcriptional and post-transcriptional regulation in porcine prenatal myogenesis and postnatal skeletal muscle growth.METHODS: Immunofluorescence and co-IP assays were carried out between the 5mC writers and m6A writers to investigate the molecular basis underneath. Large-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis (WGCNA) to identify the co-expression patterns of m6A and 5mC regulators and their potential role in pig myogenesis. Whole-genome bisulfite sequencing (WGBS) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages (days 30, 60, 120 and 180).
    RESULTS: Significantly correlated expression between 5mC writers and m6A writers and co-occurrence of 5mC and m6A modification were revealed from public datasets of C2C12 myoblasts. The protein-protein interactions between the DNA methylase and the m6A methylase were observed in mouse myoblast cells. Further, by analyzing transcriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages, we identified a 5mC/m6A epigenetic module eigengene and decoded its potential functions in pre- or post-transcriptional regulation in postnatal skeletal muscle development and growth of pigs. Following integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m6A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m6A modifications as a consequence of 5mC/m6A crosstalk in the postnatal myogenesis progress of pigs. Last, we identified a group of myogenesis-related genes collaboratively regulated by both 5mC and m6A modifications in postnatal skeletal muscle growth in pigs.
    CONCLUSIONS: Our study discloses a potential epigenetic mechanism in skeletal muscle development and provides a novel direction for animal breeding and drug development of related human muscle-related diseases.
    Keywords:  5mC regulators; DNA methylation; Epigenetic modification; Epigenomic analysis; Myogenesis; m6A methylation; m6A regulators
    DOI:  https://doi.org/10.1186/s40104-022-00791-3
  19. Genome Biol. 2022 Dec 02. 23(1): 249
    METTL4-mediated nuclear N6-deoxyadenosine methylation promotes metastasis through activating multiple metastasis-inducing targets.
    Kai-Wen Hsu, Joseph Chieh-Yu Lai, Jeng-Shou Chang, Pei-Hua Peng, Ching-Hui Huang, Der-Yen Lee, Yu-Cheng Tsai, Chi-Jung Chung, Han Chang, Chao-Hsiang Chang, Ji-Lin Chen, See-Tong Pang, Ziyang Hao, Xiao-Long Cui, Chuan He, Kou-Juey Wu.
      BACKGROUND: DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive.RESULTS: Here we show that hypoxia induces nuclear 6mA modification through a DNA methyltransferase, METTL4, in hypoxia-induced epithelial-mesenchymal transition (EMT) and tumor metastasis. Co-expression of METTL4 and 6mA represents a prognosis marker for upper tract urothelial cancer patients. By RNA sequencing and 6mA chromatin immunoprecipitation-exonuclease digestion followed by sequencing, we identify lncRNA RP11-390F4.3 and one novel HIF-1α co-activator, ZMIZ1, that are co-regulated by hypoxia and METTL4. Other genes involved in hypoxia-mediated phenotypes are also regulated by 6mA modification. Quantitative chromatin isolation by RNA purification assay shows the occupancy of lncRNA RP11-390F4.3 on the promoters of multiple EMT regulators, indicating lncRNA-chromatin interaction. Knockdown of lncRNA RP11-390F4.3 abolishes METTL4-mediated tumor metastasis. We demonstrate that ZMIZ1 is an essential co-activator of HIF-1α.
    CONCLUSIONS: We show that hypoxia results in enriched 6mA levels in mammalian tumor cells through METTL4. This METTL4-mediated nuclear 6mA deposition induces tumor metastasis through activating multiple metastasis-inducing genes. METTL4 is characterized as a potential therapeutic target in hypoxic tumors.
    Keywords:  6mA; Hypoxia; METTL4; Metastasis; ZMIZ1; lncRNA
    DOI:  https://doi.org/10.1186/s13059-022-02819-3
  20. Theranostics. 2022 ;12(17): 7267-7288
    N6-methyladenosine-associated prognostic pseudogenes contribute to predicting immunotherapy benefits and therapeutic agents in head and neck squamous cell carcinoma.
    Liqiang Tan, Yali Qin, Ruiling Xie, Tianliang Xia, Xiaotong Duan, Lan Peng, Rui You, Youping Liu, Xiong Zou, Mengxia Zhang, Mei Lin, Mingyuan Chen.
      Rationale: N6-methyladenosine (m6A) is involved in critical cancerous processes. Pseudogenes play various roles in carcinogenesis and progression. However, the functional roles of m6A-associated pseudogenes in head and neck squamous cell carcinoma (HNSCC) are largely unknown. Methods: We systematically analyzed the mRNA profile of 24 m6A regulators and 13931 pseudogenes from The Cancer Genome Atlas HNSCC dataset and ultimately identified 10 m6A-associated prognostic pseudogenes, which were validated in the Gene Expression Omnibus and our hospital datasets. Based on the risk score of m6A-associated pseudogenes, comprehensive analytical frameworks and experimental validation were implemented among pseudogene-defined low-/high-risk subtypes. Results: Here, we found expression pattern of m6A-associated pseudogenes was significantly associated with infiltrating immune cell compositions, and the expression of antitumor immune response markers, including T cell exhaustion, antigen presentation, interferon, and kinase genes. The m6A-associated pseudogenes, which had dramatic m6A peaks and higher m6A levels, could regulate the expression of targeted immune-involved genes through miRNAs. We experimentally validate the oncogene PDIA3P1, and tumor-suppressor RRN3P3, which promote the RNA and protein expression of their targeted immune-involved genes AKT1 and EZH2 via miR-34a-5p and miR-26b-5p, respectively. Moreover, HNSCC patients in the high-risk subtype could benefit more from immune checkpoint inhibitors therapy. Furthermore, doxorubicin and topotecan were considered to hold the most promising therapeutic potential robustly in silico evidence and in vitro experiments for HNSCC patients in the high-risk subtype. Conclusions: Our discovery revealed that the 10 m6A-associated prognostic pseudogenes significantly contribute to predicting immunotherapy benefits and therapeutic agents, which might bring some potential implications for both immunotherapy and chemotherapy in HNSCC.
    Keywords:  Head and neck squamous cell carcinoma; Immunotherapy benefits; N6-methyladenosine; Pseudogene; Therapeutic agents
    DOI:  https://doi.org/10.7150/thno.76689
  21. Cancer Manag Res. 2022 ;14 3223-3243
    RNA Modifications Meet Tumors.
    Zhiyuan Yang, Siyu Zhang, Tian Xia, Yue Fan, Ying Shan, Kaiwen Zhang, Jiayan Xiong, Miao Gu, Bo You.
      RNA modifications occur through the whole process of gene expression regulation, including transcription, translation, and post-translational processes. They are closely associated with gene expression, RNA stability, and cell cycle. RNA modifications in tumor cells play a vital role in tumor development and metastasis, changes in the tumor microenvironment, drug resistance in tumors, construction of tumor cell-cell "internet", etc. Several types of RNA modifications have been identified to date and have various effects on the biological characteristics of different tumors. In this review, we discussed the function of RNA modifications, including N 6-methyladenine (m6A), 5-methylcytosine (m5C), N 7-methyladenosine (m7G), N 1-methyladenosine (m1A), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I), in the microenvironment and therapy of solid and liquid tumors.
    Keywords:  RNA modification; non-coding RNA; tumor; tumor microenvironment; tumor therapy
    DOI:  https://doi.org/10.2147/CMAR.S391067
  22. Theranostics. 2022 ;12(18): 7760-7774
    m6A reader hnRNPA2B1 drives multiple myeloma osteolytic bone disease.
    Rui Liu, Yuping Zhong, Rui Chen, Chengchao Chu, Gang Liu, Yong Zhou, Yazhu Huang, Zhihong Fang, Huan Liu.
      Rationale: Bone destruction is a hallmark of multiple myeloma (MM) and affects more than 80% of patients. Although previous works revealed the roles of N6-methyladenosine (m6A) reader hnRNPA2B1 in the development of tumors, whether hnRNPA2B1 regulates bone destruction in MM is still unknown. Methods: Alizarin red S staining, TRAP staining, ELISA and quantitative real-time PCR assays were used to evaluate osteogenesis and osteoclastogenesis in vitro. X ray and bone histomorphometric analysis were preformed to identify bone resorption and bone formation in vivo. Exosome isolation and characterization were demonstrated by transmission electron microscopy, dynamic light scattering, immunofluorescence and flow cytometry assays. The interactions between hnRNPA2B1 and primary microRNAs were examined using RNA pull-down and RIP assays. Coimmunoprecipitation assay was used to test the interaction between hnRNPA2B1 and DGCR8 proteins. Luciferase assay was established to assess miRNAs target genes. Results: Here we show that myeloma cells hnRNPA2B1 mediates microRNAs processing and upregulates miR-92a-2-5p and miR-373-3p expression. These two microRNAs are transported to recipient monocytes or mesenchymal stem cells (MSCs) through exosomes, leading to activation of osteoclastogenesis and suppression of osteoblastogenesis by inhibiting IRF8 or RUNX2. Furthermore, clinical studies revealed a highly positive correlation between the level of myeloma cells hnRNPA2B1 and the number of osteolytic bone lesions in myeloma patients. Conclusions: This study elucidates an important mechanism by which myeloma-induced bone lesions, suggesting that hnRNPA2B1 may be targeted to prevent myeloma-associated bone disease.
    Keywords:  Multiple myeloma; bone lesion; exosome; hnRNPA2B1; microRNA
    DOI:  https://doi.org/10.7150/thno.76852
  23. Int Immunopharmacol. 2022 Dec;pii: S1567-5769(22)00859-1. [Epub ahead of print]113(Pt A): 109375
    m(6)A methyltransferase METTL3 relieves cognitive impairment of hyperuricemia mice via inactivating MyD88/NF-κB pathway mediated NLRP3-ASC-Caspase1 inflammasome.
    Yanfang Chen, Peng Cao, Zijian Xiao, Zhongfan Ruan.
      BACKGROUND: Recent studies have uncovered that hyperuricemia (HUA) leads to cognitive deficits, which are accompanied by neuronal damage and neuroinflammation. Here, we aim to explore the role of methyltransferase-like 3 (METTL3) in HUA-mediated neuronal apoptosis and microglial inflammation.METHODS: A HUA mouse model was constructed. The spatial memory ability of the mice was assessed by the Morris water maze experiment (MWM), and neuronal apoptosis was analyzed by the TdT-mediated dUTP nick end labeling (TUNEL) assay. Besides, enzyme-linked immunosorbent assay (ELISA) was utilized to measure the contents of inflammatory factors (IL-1β, IL-6, and TNF-α) and oxidative stress markers (MDA, SOD, and CAT) in the serum of mice. In vitro, the mouse hippocampal neuron (HT22) and microglia (BV2) were treated with uric acid (UA). Flow cytometry was applied to analyze HT22 and BV2 cell apoptosis, and ELISA was conducted to observe neuroinflammation and oxidative stress. In addition, the expression of MyD88, p-NF-κB, NF-κB, NLRP3, ASC and Caspase1 was determined by Western blot.
    RESULTS: METTL3 and miR-124-3p were down-regulated, while the MyD88-NF-κB pathway was activated in the HUA mouse model. UA treatment induced neuronal apoptosis in HT22 and stimulated microglial activation in BV2. Overexpressing METTL3 alleviated HT22 neuronal apoptosis and resisted the release of inflammatory cytokines and oxidative stress mediators in BV2 cells. METTL3 repressed MyD88-NF-κB and NLRP3-ASC-Caspase1 inflammasome. In addition, METTL3 overexpression enhanced miR-124-3p expression, while METTL3 knockdown aggravated HT22 cell apoptosis and BV2 cell overactivation.
    CONCLUSION: METTL3 improves neuronal apoptosis and microglial activation in the HUA model by choking the MyD88/NF-κB pathway and up-regulating miR-124-3p.
    Keywords:  Hyperuricemia; METTL3; NLRP3-ASC-Caspase1 inflammasome; The MyD88/NF-κB pathway; miR-124-3p
    DOI:  https://doi.org/10.1016/j.intimp.2022.109375
  24. Histol Histopathol. 2022 Dec 02. 18558
    RFWD3 acts as a tumor promotor in the development and progression of bladder cancer.
    Peng Jiang, Zhijie Xu, Shan Wu, Junjie Sun, Junjie Tian, Xiaoyi Chen.
      BACKGROUND: Bladder cancer is one of the most commonly diagnosed malignancies of the urinary system with relatively poor prognosis and insufficient treatment strategies. RFWD3 is an E3 ligase whose function is rarely investigated in malignant tumors.METHODS: A tissue microarray was used for evaluating RFWD3 expression in clinical samples and its correlation with tumor characteristics and patients' prognosis. RFWD3 knockdown and overexpression cell models were constructed for conducting loss-of-function and gain-of-function assays. qPCR and western blotting were used for detecting mRNA and protein levels of RFWD3, respectively. MTT assay, colony formation assay, flow cytometry, wound-healing assay and transwell assay were carried out to demonstrate the change of cell phenotypes upon RFWD3 knockdown.
    RESULTS: RFWD3 expression was relatively higher in bladder cancer tissues than in normal tissues, which is correlated with higher N stage and poorer prognosis of patients. Knockdown of RFWD3 in bladder cancer cells significantly inhibited cell proliferation, colony formation, promote cell apoptosis and restrained cell migration. Overexpression of RFWD3 induced the opposite effects.
    CONCLUSIONS: It was illustrated that RFWD3 possesses excellent tumor-promoting ability in bladder cancer. Accordingly, RFWD3 may be a promising therapeutic target in the targeted therapy of bladder cancer, which is worth further research.
    DOI:  https://doi.org/10.14670/HH-18-558
  25. Int J Cancer. 2022 Nov 28.
    Interplay between m6 A epitranscriptome and epigenome in cancer: current knowledge and therapeutic perspectives.
    Guglielmo Bove, Sajid Amin, Mehrad Babaei, Rosaria Benedetti, Angela Nebbioso, Lucia Altucci, Nunzio Del Gaudio.
      Chromatin has an extremely flexible structure that allows the fine regulation of gene expression. To orchestrate this process, small chemical modifications are dynamically added or removed on DNA, RNA and histone substrates. Epigenetic modifications govern a plethora of key cellular functions, whose dysregulation contributes to oncogenesis. The interrelationship between (irreversible) genetic mutations and (reversible) epigenetic alterations and how this crosstalk regulates gene expression has long been a major area of interest. Marks modulating the RNA code (epitranscriptome), such as the well-studied N6 -methyladenosine (m6 A), are known to influence stability, metabolism and life cycle of many mRNAs, including cancer-associated transcripts. Together, epigenetic and epitranscriptomic pathways therefore control the entire cellular expression profile and, eventually, cell fate. Recently, previously undescribed crosstalk between these two pathways has started to be unrevealed. For example, m6 A and its effectors cooperate with histone modifications to localize chromatin-modifying complexes to their target regions. Epigenetic marks governing the expression of m6 A factors can also be found at specific genetic loci. m6 A itself can mark noncoding RNAs (including lncRNAs, circRNAs and miRNAs), influencing their structure, maturation and function. These interactions affect both cell physiology and pathology. Clear evidence that dysregulation of this network plays a role in cancer has emerged, suggesting a new layer of complexity in the landscape of gene expression. Here, we summarize current knowledge on the interplay between m6 A epitranscriptome and epigenome, focusing on cancer processes. We also discuss strategies to target m6 A machinery for future therapeutic intervention.
    Keywords:  RNA modifications; cancer; epigenetics; epitranscriptomics; m6A
    DOI:  https://doi.org/10.1002/ijc.34378
  26. Int J Gen Med. 2022 ;15 8285-8298
    FMNL3 is Overexpressed in Tumor Tissues and Predicts an Immuno-Hot Phenotype in Pancreatic Cancer.
    Qinglin Zhang, He Nie, Jiadong Pan, Haoran Xu, Qiang Zhan.
      Background: FMNL3 (Formin-like protein 3) is involved in the tumorigenesis of multiple cancers. The critical role of FMNL3 in malignancies has been preliminarily explored, but its immunological correlation is not clear.Methods: A pan-cancer analysis was performed to investigate the expressions, prognostic values, and immunological roles of FMNL3 across cancer types in The Cancer Genome Atlas (TCGA) database. Next, the correlations between FMNL3 and immunological features in the tumor microenvironment (TME) of pancreatic cancer (PAAD) were assessed. Besides, the role of FMNL3 in predicting the clinical characteristics and the responses to various therapies in PAAD was evaluated as well. Besides, the correlations between FMNL3 and the emerging immune-related biomarkers were also evaluated.
    Results: The pan-cancer analysis uncovered inconsistent expression status and prognostic values in several cancers. Besides, FMNL3 exhibited positive correlations with a majority of immunomodulators and tumor-infiltrating immune cells (TIICs) in several cancer types, including PAAD. In addition, FMNL3 was associated with an inflamed phenotype in the TME and predicted significantly higher responses to multiple anti-cancer therapies. In addition, FMNL3 was notably correlated with immune-related microbiota and N6-methyladenosine (m6A) genes.
    Conclusion: In summary, FMNL3 predicts an immuno-hot phenotype, which could be a promising indicator for identifying high immunogenicity in PAAD.
    Keywords:  FMNL3; PAAD; bioinformatics analysis; formin; tumor microenvironment
    DOI:  https://doi.org/10.2147/IJGM.S384195
  27. Acta Biochim Pol. 2022 Dec 02.
    Demethylase FTO promotes neuropathic pain development via regulating the m6A methylation levels of CXCR3.
    Song Fei Wu, Yang Wang, Qiu Cheng Zhao.
      OBJECTIVE: Neuropathic pain (NPP) is an indirect or direct pain caused by somatic sensory nervous system dysfunction or primary injury, which is considered to be one of the most serious public health problems. This study aimed to investigate the role of adiposity-associated protein (FTO) in NPP.MATERIALS AND METHODS: Sciatic nerve injury (SNI) treatment was performed to establish an NPP model in vivo. The qRT-PCR and western blot assays were conducted to measure the relative mRNA and protein expressions. Additionally, the paw withdrawal threshold (PWT) and paw withdrawal latency (PWL) of the mice were measured on days 0, 1, 3, 5, 7, and 14. The m6A level of CXCR3 was determined with Methylated RNA immunoprecipitation (MeRIP) assay and the inflammatory factor expressions were determined with Elisa kits.
    RESULTS AND DISCUSSION: The FTO and CXCR3 expressions were up-regulated and the METTL14 expression was down-regulated in SNI mice. FTO-silenced increased the m6A and decreased the mRNA levels of CXCR3 in SNI mice. Furthermore, FTO-silenced decreased the mRNA stability of the CXCR3. Besides, in the SNI mice, FTO-silenced increased the PWL and PWT, and decreased the TNF-α, IL-1β, and IL-6 levels. While over-expressed CXCR3 inverted the FTO-silenced effects.
    CONCLUSIONS: Knockdown of FTO relieved the NPP progression via triggering the demethylation of CXCR3, thereby down-regulating the CXCR3expression.
    DOI:  https://doi.org/10.18388/abp.2020_6185
  28. Elife. 2022 Dec 02. pii: e79994. [Epub ahead of print]11
    m6A epitranscriptomic modification regulates neural progenitor-to-glial cell transition in the retina.
    Yanling Xin, Qinghai He, Huilin Liang, Ke Zhang, Jingyi Guo, Qi Zhong, Dan Chen, Jinyan Li, Yizhi Liu, Shuyi Chen.
      N 6-methyladenosine (m6A) is the most prevalent mRNA internal modification and has been shown to regulate the development, physiology, and pathology of various tissues. However, the functions of the m6A epitranscriptome in the visual system remain unclear. In this study, using a retina-specific conditional knockout mouse model, we show that retinas deficient in Mettl3, the core component of the m6A methyltransferase complex, exhibit structural and functional abnormalities beginning at the end of retinogenesis. Immunohistological and single-cell RNA sequencing (scRNA-seq) analyses of retinogenesis processes reveal that retinal progenitor cells (RPCs) and Müller glial cells are the two cell types primarily affected by Mettl3 deficiency. Integrative analyses of scRNA-seq and MeRIP-seq data suggest that m6A fine-tunes the transcriptomic transition from RPCs to Müller cells by promoting the degradation of RPC transcripts, the disruption of which leads to abnormalities in late retinogenesis and likely compromises the glial functions of Müller cells. Overexpression of m6A-regulated RPC transcripts in late RPCs partially recapitulates the Mettl3-deficient retinal phenotype. Collectively, our study reveals an epitranscriptomic mechanism governing progenitor-to-glial cell transition during late retinogenesis, which is essential for the homeostasis of the mature retina. The mechanism revealed in this study might also apply to other nervous systems.
    Keywords:  developmental biology; glial cell; m6A; mouse; retinal development
    DOI:  https://doi.org/10.7554/eLife.79994
  29. J Appl Toxicol. 2022 Nov 30.
    Bisphenol A exposure induces testicular oxidative damage via FTO/m6A/Nrf2 axis during postnatal development in mice.
    Yuanchao Ling, Xiaodi Huang, Anlong Li, Jinzhi Zhang, Jianmei Chen, Jiale Ren, Yanan Liu, Meina Xie.
      Bisphenol A (BPA), a commonly used plasticizer in the production of polycarbonate plastics and epoxy resins, has been shown male reproductive toxicity. However, the effects of BPA exposure on early testicular development have not been thoroughly studied and the underlying mechanism is yet to be elucidated. In the current study, neonatal male mice were exposed to BPA at 0, 0.1, and 5 mg/kg, respectively, by daily subcutaneous injection during postnatal day (PND) 1-35 to explore its effects on testicular development at PND 36 (the end of the first round of spermatogenesis). Morphological analyses showed that BPA exposure significantly induced apoptosis of testicular cells (P < 0.01 and P < 0.001) and reduced the thickness of seminiferous epithelium (P < 0.01). In addition, BPA exposure significantly decreased the total antioxidant capacity of testes and levels of transcription factor Nrf2 as well as its downstream antioxidant molecules of NQO1 and GPx-1 (P < 0.05 and P < 0.01). Furthermore, global m6A modifications of mRNAs were up-regulated accompanied by declined m6A demethylase (FTO) in the testes of BPA groups (P < 0.05 and P < 0.01). MeRIP-qPCR demonstrated that BPA exposure markedly increased the m6A modification of Nrf2 mRNA (P < 0.05 and P < 0.01). These findings suggest that up-regulation of m6A induced by inhibited FTO may be involved in BPA-induced testicular oxidative stress and developmental injury during postnatal development, which provides a new idea to reveal the mechanism underlying BPA interfering with testicular development.
    Keywords:  Bisphenol A; FTO; Nrf2; m6A modification; testis
    DOI:  https://doi.org/10.1002/jat.4417
  30. Cell Death Dis. 2022 Nov 29. 13(11): 1008
    m6A-modified circFNDC3B inhibits colorectal cancer stemness and metastasis via RNF41-dependent ASB6 degradation.
    Wei Zeng, Jin-Feng Zhu, Jian Guo, Gen-Jie Huang, Li-Sha Ai, Yu Zeng, Wang-Jun Liao.
      Colorectal cancer (CRC) is the third most frequently diagnosed cancer with unfavorable clinical outcomes worldwide. circFNDC3B plays as a tumor suppressor in CRC, however, the mechanism of circFNDC3B in CRC remains ambiguous. The stem-like properties of CRC cells were detected by the evaluation of stemness markers, sphere formation assay and flow cytometry. qRT-PCR, FISH, IHC, and western blotting assessed the expression and localization of circFNDC3B, RNF41, ASB6, and stemness markers in CRC. The metastatic capabilities of CRC cells were examined by wound healing and Transwell assays, as well as in vivo liver metastasis model. Bioinformatics analysis, RNA immunoprecipitation (RIP), RNA pull-down assay and co-IP were used to detect the associations among circFNDC3B, FXR2, RNF41, and ASB6. Downregulated circFNDC3B was associated with unfavorite survival in CRC patients, and circFNDC3B overexpression suppressed CRC stemness and metastasis. Mechanistically, studies revealed that YTHDC1 facilitated cytoplasmic translocation of m6A-modified circFNDC3B, and circFNDC3B enhanced RNF41 mRNA stability and expression via binding to FXR2. circFNDC3B promoted ASB6 degradation through RNF41-mediated ubiquitination. Functional studies showed that silencing of RNF41 counteracted circFNDC3B-suppressed CRC stemness and metastasis, and ASB6 overexpression reversed circFNDC3B- or RNF41-mediated regulation of CRC stemness and metastasis. Elevated ASB6 was positively correlated with unfavorite survival in CRC patients. In vivo experiments further showed that circFNDC3B or RNF41 overexpression repressed tumor growth, stemness and liver metastasis via modulating ASB6. Taken together, m6A-modified circFNDC3B inhibited CRC stemness and metastasis via RNF41-dependent ASB6 degradation. These findings provide novel insights and important clues for targeted therapeutic strategies of CRC.
    DOI:  https://doi.org/10.1038/s41419-022-05451-y
  31. Front Immunol. 2022 ;13 1030728
    The m6A methylation profiles of immune cells in type 1 diabetes mellitus.
    Yimeng Wang, Linling Xu, Shuoming Luo, Xiaoxiao Sun, Jiaqi Li, Haipeng Pang, Jun Zhou, Yuemin Zhou, Xiajie Shi, Xia Li, Gan Huang, Zhiguo Xie, Zhiguang Zhou.
      Background: Type 1 diabetes mellitus (T1DM) is caused by immune cell-mediated β-cell dysfunction. In recent decades, N6-methyladenosine (m6A) has attracted widespread attention in the scientific research field because it plays vital roles in the pathogenesis of immunity-related diseases, including autoimmune diseases. However, neither the m6A modification profile nor the potential role it plays in T1DM pathogenesis has been investigated to date.Materials and Methods: An m6A mRNA epitranscriptomic microarray analysis was performed to analyze m6A regulator expression patterns and m6A methylation patterns in immune cells of T1DM patients (n=6) and healthy individuals (n=6). A bioinformatics analysis was subsequently performed to explore the potential biological functions and signaling pathways underlying T1DM pathogenesis. Furthermore, mRNA expression and m6A methylation levels were subsequently verified by qRT-PCR and methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR), respectively, in the T1DM and healthy groups (n=6 per group).
    Results: Among the multiple m6A regulators, METTL3 and IGF2BP2 had significantly downregulated expression, and YTHDC1 and HNRNPA2B1 had significantly upregulated expression in the T1DM group relative to the healthy group. The microarray analysis revealed 4247 differentially methylated transcripts, including 932 hypermethylated and 3315 hypomethylated transcripts, and 4264 differentially expressed transcripts, including 1818 upregulated transcripts and 2446 downregulated transcripts in the T1DM group relative to the healthy group. An association analysis between methylation and gene expression demonstrated that the expression of 590 hypermethylated transcripts was upregulated, and that of 1890 hypomethylated transcripts was downregulated. Pearson correlation analysis showed significant correlations between the expression levels of differentially expressed m6A regulators and the methylation levels of differentially methylated transcripts and significant correlations between the expression levels of differentially expressed m6A regulators and that of differentially expressed transcripts. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that differentially methylated transcripts were involved in pathways related to immunity, including some closely associated with T1DM.
    Conclusions: Our study presents m6A regulator expression patterns and m6A methylation patterns of immune cells in T1DM, showing that the m6A mark and m6A regulators are promising targets for T1DM diagnosis and treatment.
    Keywords:  N6-methyladenosine; autoimmune diseases; epigenetic regulation; immunity; type 1 diabetes mellitus
    DOI:  https://doi.org/10.3389/fimmu.2022.1030728
  32. J Cell Physiol. 2022 Nov 27.
    IGF2BP2, an RNA-binding protein regulates cell proliferation and osteogenic differentiation by stabilizing SRF mRNA.
    Zimo Zhou, Senxiang Chen, Tong Wu, Yifeng Chen, Yuxiao Cao, Ying Huang, Da Liu.
      Osteoblast proliferation and osteogenic differentiation (OGD) are regulated by complex mechanisms. The roles in cell proliferation and OGD of RNA-binding proteins in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family remain unclear. To elucidate this, we examined the differential expression of IGF2BP2 in OGD and osteoporosis, and the expression profile of IGF2BP2-binding RNA in vitro. We screened the GEO database for differential expression of IGF2BP in OGD and osteoporosis, and verified the RNAs interacting with IGF2BP2 via RNA immunoprecipitation sequencing assays. The proliferation and OGD of IGF2BP2- and serum response factor (SRF)-treated cells, and their regulatory mechanisms, were examined. IGF2BP2 was differentially expressed in OGD and osteoporosis. The RNA immunoprecipitation sequencing assay identified all of the RNAs that bind with IGF2BP2, and revealed SRF as a target of IGF2BP2. IGF2BP2 and SRF inhibition impaired MC3T3-E1 cell growth but promoted OGD. The mRNA stability analysis revealed that IGF2BP2 enhanced SRF mRNA stability against degradation. In summary, IGF2BP2 is a potential biomarker and therapeutic target for osteoporosis and OGD.
    Keywords:  IGF2BP2; RNA-binding protein; cell proliferation; osteogenic differentiation; serum response factor
    DOI:  https://doi.org/10.1002/jcp.30919
  33. Acta Biochim Pol. 2022 Dec 02.
    Selected ALKBH dioxygenases are overexpressed in salivary gland tumours.
    Michał Marcinkowski, Damian Garbicz, Tomaš Pilžys, Wojciech Kukwa, Elżbieta Grzesiuk.
      Salivary gland tumours (SGTs) are a heterogeneous group of benign tumours of various origins and pathologies, showing a number of DNA modifications. Previously, in malignant head and neck cancer (HNSCC), we found overexpression of ALKBH proteins, the homologs of Escherichia coli AlkB 2-oxoglutarate and Fe(II) dependent dioxygenase. Moreover, we proved the connection of some of these dioxygenases with cancer development. Here, we studied the expression of five of these ALKBH dioxygenases: 1, 3, 4, 5, and FTO in benign SGTs. Using Western blot analysis, we found overexpression of three proteins: ALKBH1, 4, and FTO in SGT as compared to the surrounding, unaffected tissue. ALKBH4 was overexpressed in 76% of patient samples, whereas ALKBH1 and FTO in 65% of the samples. These results differ from those obtained in HNSCC, where FTO overexpression has been observed in 90% of patient samples. We also investigated the relationships between ALKBHs' expression levels in normal and SGT tissues and identified two correlated pairs: ALKBH1-ALKBH3 and ALKBH1-ALKBH5. Additionally, in tumour tissue ALKBHs: ALKBH1, ALKBH3, ALKBH4, and ALKBH5 levels were correlated with each other. Together, these findings show that the ALKBH proteins exhibit pro cancerogenic action in SGT, even though the levels ALKBHs are generally lower in benign SGT than in malignant HNSCC. We suggest that the overexpression of the ALKBHs, especially FTO, may be used as a cancer marker and for its grading.
    DOI:  https://doi.org/10.18388/abp.2020_6486
  34. Cancer Res. 2022 Nov 30. pii: CAN-22-1062. [Epub ahead of print]
    Single-cell analysis in lung adenocarcinoma implicates RNA editing in cancer innate immunity and patient prognosis.
    Tracey W Chan, Jack P Dodson, Jaron Arbet, Paul C Boutros, Xinshu Xiao.
      RNA editing modifies single nucleotides of RNAs, regulating primary protein structure and protein abundance. In recent years, the diversity of proteins and complexity of gene regulation associated with RNA editing dysregulation has been increasingly appreciated in oncology. Large-scale shifts in editing have been observed in bulk tumors across various cancer types. However, RNA editing in single cells and individual cell types within tumors has not been explored. By profiling editing in single cells from lung adenocarcinoma biopsies, we found that the increased editing trend of bulk lung tumors was unique to cancer cells. Elevated editing levels were observed in cancer cells resistant to targeted therapy, and editing sites associated with drug response were enriched. Consistent with the regulation of antiviral pathways by RNA editing, higher editing levels in cancer cells were associated with reduced anti-tumor innate immune response, especially levels of natural killer cell infiltration. In addition, the level of RNA editing in cancer cells was positively associated with somatic point mutation burden. This observation motivated the definition of a new metric, RNA editing load, reflecting the amount of RNA mutations created by RNA editing. Importantly, in lung cancer, RNA editing load was a stronger predictor of patient survival than DNA mutations. This study provides the first single cell dissection of editing in cancer and highlights the significance of RNA editing load in cancer prognosis.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-1062
  35. Arch Biochem Biophys. 2022 Nov 25. pii: S0003-9861(22)00356-3. [Epub ahead of print] 109470
    Associations of selenoprotein expression and gene methylation with the outcome of clear cell renal carcinoma.
    Waleed Ali, Daniel Jacobs, Simon Zhen, Alan M Diamond, André Kajdacsy-Balla.
      Selenoproteins are a ubiquitous class of proteins defined by having a selenocysteine amino acid residue. While many of the selenoproteins have been well characterized with important roles in oxidation-reduction reactions and hormone synthesis among others, there exist some whose biological roles are not as well understood as denoted by the "SELENO" root. In this study, we explored associations between the reported RNA levels of "SELENO" proteins and clear cell renal cell carcinoma (ccRCC), the most common subtype of renal carcinoma in the US. Utilizing The Cancer Genome Atlas (TCGA) alongside other in silico tools, we discovered higher mRNA expression of Selenoprotein I, T, and P was associated with better overall survival outcomes and differential expression of other selenoproteins based on tumor stage. Additionally, we uncovered relative hypomethylation among selenoproteins in primary ccRCC tumor samples compared to normal tissue. Network and enrichment analysis showed numerous genes through which selenoproteins may modulate cancer progression and outcomes such as DERL1, PNPLA2/3, MIEN1, and FOXO1 which have been well-described in other cancers. In light of our findings highlighting an association of selenoprotein methylation and expression patterns with ccRCC outcome, further wet lab research is warranted.
    Keywords:  In silico; Methylation; Renal cell carcinoma; Selenoproteins
    DOI:  https://doi.org/10.1016/j.abb.2022.109470
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