bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2021‒06‒13
sixteen papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

  1. Stem Cells Int. 2021 ;2021 9955691
      The Pax7+ muscle stem cells (MuSCs) are essential for skeletal muscle homeostasis and muscle regeneration upon injury, while the molecular mechanisms underlying muscle stem cell fate determination and muscle regeneration are still not fully understood. N6-methyladenosine (m6A) RNA modification is catalyzed by METTL3 and plays important functions in posttranscriptional gene expression regulation and various biological processes. Here, we generated muscle stem cell-specific METTL3 conditional knockout mouse model and revealed that METTL3 knockout in muscle stem cells significantly inhibits the proliferation of muscle stem cells and blocks the muscle regeneration after injury. Moreover, knockin of METTL3 in muscle stem cells promotes the muscle stem cell proliferation and muscle regeneration in vivo. Mechanistically, METTL3-m6A-YTHDF1 axis regulates the mRNA translation of Notch signaling pathway. Our data demonstrated the important in vivo physiological function of METTL3-mediated m6A modification in muscle stem cells and muscle regeneration, providing molecular basis for the therapy of stem cell-related muscle diseases.
  2. Front Oncol. 2021 ;11 667451
      Recent studies have identified pleiotropic roles of methyltransferase-like 3 (METTL3) in tumor progression. However, the roles of METTL3 in esophageal squamous cell carcinoma (ESCC) are still unclear. Here, we investigated the function and mechanism of METTL3 in ESCC tumorigenesis. We reported that higher METTL3 expression was found in ESCC tissues and was markedly associated with depth of invasion and poor prognosis. Loss- and gain-of function studies showed that METTL3 promoted the migration and invasion of ESCC cells in vitro. Integrated methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq) analysis first demonstrated that glutaminase 2 (GLS2) was regulated by METTL3 via m6A modification. Our findings identified METTL3/GLS2 signaling as a potential therapeutic target in antimetastatic strategies against ESCC.
    Keywords:  ESCC; GLS2; METTL3; m6A; metastasis
  3. J Cancer. 2021 ;12(13): 3809-3818
      RNA epigenetic modification take part in many biology processes, and the N6-methyladenosine (m6A) methylation of specific mRNAs in endometrial cancer (EC) tissues play a key role in regulating the tumorigenicity of EC, but the specific mechanism still unknown and need to be investigated in the future. Here, we found that m6A reader protein YTHDF2 expression was significantly upregulated in EC compare to tumor adjacent tissues, YTHDF2 was then identified to inhibit the proliferation and invasion of EC cell lines. Mechanistically, the m6A reader YTHDF2 bind the methylation sites of target transcripts IRS1 and promoted IRS1 mRNA degradation, consequently inhibiting the expression of IRS1 and inhibiting IRS1/AKT signaling pathway, finally inhibit the tumorigenicity of EC. Thus, we demonstrated that YTHDF2 inhibited the proliferation and invasion of EC via inhibiting IRS1 expression in m6A epigenetic way, which suggests a potential therapeutic target for EC.
    Keywords:  AKT signaling pathway; IRS1; YTHDF2; endometrial cancer; m6A modification
  4. Cancer Sci. 2021 Jun 07.
      RNA N6 -methyladenosine (m6 A) is an emerging regulatory mechanism for tumor progression in several types of cancer. However, the underlying regulation mechanisms of m6 A methylation in colorectal cancer (CRC) remain unknown. Although the oncogenic function of methyl CpG binding protein 2 (MeCP2) have been reported, it is still unclear whether MeCP2 could alter RNA m6 A methylation state. Here, we systematically identified MeCP2 as a pro-metastasis gene to regulate m6 A methylation in colorectal cancer. Interestingly, MeCP2 could bind to methyltransferase-like 14 (METTL14) to co-regulate tumor suppressor Kruppel like factor 4 (KLF4) expression through changing m6 A methylation modification. Furthermore, Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) recognized the unique modified m6 A methylation sites to enhance KLF4 mRNA stability. Taken together, these findings highlight the novel function of MeCP2 for regulating m6 A methylation and demonstrated the underlying molecular mechanism for the interaction between MeCP2 and METTL14, which offers a better understanding of CRC progression and metastasis.
    Keywords:  METTL14; MeCP2; colorectal cancer; m6A methylation; metastasis
  5. Front Cell Dev Biol. 2021 ;9 656849
      Dynamic modification of RNA affords proximal regulation of gene expression triggered by non-genomic or environmental changes. One such epitranscriptomic alteration in RNA metabolism is the installation of a methyl group on adenosine [N6-methyladenosine (m6A)] known to be the most prevalent modified state of messenger RNA (mRNA) in the mammalian cell. The methylation machinery responsible for the dynamic deposition and recognition of m6A on mRNA is composed of subunits that play specific roles, including reading, writing, and erasing of m6A marks on mRNA to influence gene expression. As a result, peculiar cellular perturbations have been linked to dysregulation of components of the mRNA methylation machinery or its cofactors. It is increasingly clear that neural tissues/cells, especially in the brain, make the most of m6A modification in maintaining normal morphology and function. Neurons in particular display dynamic distribution of m6A marks during development and in adulthood. Interestingly, such dynamic m6A patterns are responsive to external cues and experience. Specific disturbances in the neural m6A landscape lead to anomalous phenotypes, including aberrant stem/progenitor cell proliferation and differentiation, defective cell fate choices, and abnormal synaptogenesis. Such m6A-linked neural perturbations may singularly or together have implications for syndromic or non-syndromic neurological diseases, given that most RNAs in the brain are enriched with m6A tags. Here, we review the current perspectives on the m6A machinery and function, its role in brain development and possible association with brain disorders, and the prospects of applying the clustered regularly interspaced short palindromic repeats (CRISPR)-dCas13b system to obviate m6A-related neurological anomalies.
    Keywords:  N6-methyladenosine (m6A); clustered regularly interspaced short palindromic repeats (CRISPR)–dCas13b; cortical development; m6A editing; mRNA metabolism; mRNA methylation; neurological disorders
  6. Exp Biol Med (Maywood). 2021 Jun 08. 15353702211019681
      Digestive system tumors, which mainly include esophagus, stomach, colorectum, liver, pancreas, bile duct, and some other tumors, often have a poor prognosis. N6-methyladenosine (m6A) has critical functions in development and tumorigenesis and may help improve the molecular mechanisms of digestive system tumors. However, current understanding of the reconstitution of m6A in digestive system tumors is far from comprehensive. Herein, this study systematically analyzed multi-layered genomic characteristics and clinical relevance of m6A regulators in 1906 patients involving seven digestive system tumor types. We discovered that m6A regulators showed extensive genetic changes and highly consistent expression regulation. The m6A expression was closely related to the activity of cancer pathways. At the same time, we also identified m6A regulators significantly related to the common cancer pathways of digestive system tumors and specific cancer pathways of digestive tract and digestive glands. These cancer pathways may explain the prognostic differences of patients with digestive tract tumors. In addition, m6A regulators demonstrated strong potential in prognostic stratification and drug development, especially in multiple research cohorts on pancreatic cancer, pointing to a strong prognostic stratification capability of m6A regulators. Finally, a m6A scoring model significantly related to highly active ubiquitin-mediated proteolysis, mismatch repair, cell cycle, ebasal transcription factors was constructed and had a strong prognostic stratification ability in digestive gland tumors. The score showed a significant negative correlation with the tumor immune microenvironment. This study demonstrated that the similarities and difference of the action mechanism m6A regulators in the digestive tract and digestive gland tumor progression could guide potential drug development.
    Keywords:  Bioinformatics; N6-methyladenosine; The Cancer Genome Atlas; copy number variation; digestive system pan-cancers
  7. Front Oncol. 2021 ;11 683768
      Osteosarcoma is the most common primary bone malignancy, typically occurring in childhood or adolescence. Unfortunately, the clinical outcomes of patients with osteosarcoma are usually poor because of the aggressive nature of this disease and few treatment advances in the past four decades. N6-methyladenosine (m6A) is one of the most extensive forms of RNA modification in eukaryotes found both in coding and non-coding RNAs. Accumulating evidence suggests that m6A-related factors are dysregulated in multiple osteosarcoma processes. In this review, we highlight m6A modification implicated in osteosarcoma, describing its pathophysiological role and molecular mechanism, as well as future research trends and potential clinical application in osteosarcoma.
    Keywords:  N6-methyladenosine (m6A); biomarker; molecular mechanisms; osteosarcoma; therapeutic target
  8. J Transl Med. 2021 Jun 08. 19(1): 251
      N6-methyl-adenosine (m6A) is one of the most common internal modifications on RNA molecules present in mammalian cells. Deregulation of m6A modification has been recently implicated in many types of human diseases. Therefore, m6A modification has become a research hotspot for its potential therapeutic applications in the treatment of various diseases. The immune system mostly involves different types of immune cells to provide the first line of defense against infections. The immunoregulatory network that orchestrate the immune responses to new pathogens plays a pivotal role in the development of the disease. And m6A modification has been demonstrated to be a major post-transcriptional regulator of immune responses in cells. In this review, we summarize the participants involved in m6A regulation and try to reveal how m6A modification affects the immune responses via changing the immunoregulatory networks.
    Keywords:  Immune cells; N6-methyladenosine; RNAs
  9. Adv Sci (Weinh). 2021 06;8(11): e2003902
      Deficiency of the N6 -methyladenosine (m6 A) methyltransferase complex results in global reduction of m6 A abundance and defective cell development in embryonic stem cells (ESCs). However, it's unclear whether regional m6 A methylation affects cell fate decisions due to the inability to modulate individual m6 A modification in ESCs with precise temporal control. Here, a targeted RNA m6 A erasure (TRME) system is developed to achieve site-specific demethylation of RNAs in human ESCs (hESCs). TRME, in which a stably transfected, doxycycline-inducible dCas13a is fused to the catalytic domain of ALKBH5, can precisely and reversibly demethylate the targeted m6 A site of mRNA and increase mRNA stability with limited off-target effects. It is further demonstrated that temporal m6 A erasure on a single site of SOX2 is sufficient to control the differentiation of hESCs. This study provides a versatile toolbox to reveal the function of individual m6 A modification in hESCs, enabling cell fate control studies at the epitranscriptional level.
    Keywords:  ALKBH5; CRISPR; differentiation; m6A RNA modification; pluripotent stem cells
  10. Bioengineered. 2021 Dec;12(1): 2649-2663
      In recent years, genes associated with N6-methyladenosine (m6A) modification were found to participate in modulation of multiple tumor biological processes. Concomitantly, the significantly complicated dual effects of tumor microenvironment have been observed on cancer progression. The present study aims to investigate m6A-related immune genes (m6AIGs) for their signatures and prognostic values in bladder cancer (BC). Out of 2856 differentially expressed genes (DEGs) of BC, a total of 85 genes were obtained following intersection of DEGs, immune genes and m6A-related genes. The results of multivariate Cox regression analysis illustrated four genes (BGN, GRK5, IL32, and SREBF1) were significantly associated with the prognosis of BC patients. The BC samples were divided into two types based on the consensus clustering, and the principal component analysis demonstrated a separation between them. It was found that high expression of BGN and GRK5 were linked with advanced T and N stage, and the expression of SREBF1 in early T stage was higher than that in advanced T stage. Subsequently, the nomogram to predict 3- and 5-year survival probability of BC patients was developed and calibrated. GSEA analysis for risk subgroups showed WNT and TGF-beta signaling pathways were involved in regulation of BC progression in high risk level group. In the low risk level group, cytosolic DNA-Sensing cGAS-STING and RIG-I-like receptors signaling pathways were found to be correlated with BC development. These findings provide a novel insight on studies for BC progression.
    Keywords:  Bladder cancer; m6A modification; prognostic prediction; tumor microenvironment
  11. Front Oncol. 2021 ;11 630417
      Background: NAT10 (also known as human N-acetyltransferase-like protein) is a critical gene that regulates N4-acetylcytidine formation in RNA, similar to the multiple regulators of N6-methyladenosine. However, the underlying functions and mechanisms of NAT10 in tumor progression and immunology are unclear.Methods: In this study, we systematically analyzed the pan-cancer expression and correlations of NAT10, using databases including Oncomine, PrognoScan, GEPIA2, and Kaplan-Meier Plotter. The potential correlations of NAT10 with immune infiltration stages and gene marker sets were analyzed using the Tumor Immune Estimation Resource and GEPIA2.
    Results: Compared with normal tissues, NAT10 showed higher expression in most cancers based on combined data from TCGA and GTEx. In different datasets, high NAT10 expression was significantly correlated with poor prognosis in adrenocortical carcinoma, head and neck squamous cell carcinoma, liver hepatocellular carcinoma, kidney renal papillary cell carcinoma, and pheochromocytoma and paraganglioma. Moreover, there were significant positive correlations between NAT10 expression and immune infiltrates, including B cells, CD8+ T cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, endothelial cells, and fibroblasts in LIHC. NAT10 expression showed strong correlations with diverse immune marker gene sets in LIHC.
    Conclusion: NAT10 expression affects the prognosis of pan-cancer patients and is significantly correlated with tumor immune infiltration. Furthermore, it represents a potential target for cancer therapy.
    Keywords:  N4-acetylcytidine; NAT10; pan-cancer; prognosis; tumor infiltration
  12. FEBS Lett. 2021 Jun 09.
      AlkB homolog 5 (ALKBH5) has been reported as a key m6A demethylase that is involved in development and diseases; however, the function of ALKBH5 in osteogenesis remains unknown. In this study, we report that ALKBH5 mRNA and protein expression were upregulated during osteoblast differentiation, and that ALKBH5 knockdown suppressed osteoblast differentiation, mineralization, and the expression of osteogenic biomarkers. Conversely, ALKBH5 overexpression promoted osteogenesis. Moreover, the expression of wild type ALKBH5, but not the m6A-modified active site mutant ALKBH5, could rescue ALKBH5 knockdown-induced osteogenesis inhibition. Furthermore, knockdown of ALKBH5 significantly impaired the mRNA stability of the transcription factor Runx2, which plays a key role in osteoblast differentiation. Taken together, our results suggest that ALKBH5 promotes osteogenesis through modulating Runx2 mRNA stability.
    Keywords:  ALKBH5; N6-methyladenosine; mRNA stability; osteoblast differentiation
  13. Front Cell Dev Biol. 2021 ;9 679662
      N 6-methyladenosine (m6A) modification, as the most prevalent internal modification on mRNA, has been implicated in many biological processes through regulating mRNA metabolism. Given that m6A modification is highly enriched in the mammalian brain, this dynamic modification provides a crucial new layer of epitranscriptomic regulation of the nervous system. Here, in this review, we summarize the recent progress on studies of m6A modification in the mammalian nervous system ranging from neuronal development to basic and advanced brain functions. We also highlight the detailed underlying mechanisms in each process mediated by m6A writers, erasers, and readers. Besides, the involvement of dysregulated m6A modification in neurological disorders and injuries is discussed as well.
    Keywords:  development; learning and memory; m6A modification; nervous system; neurological disorders
  14. Cell Cycle. 2021 Jun 07. 1-16
      RNA pumilio RNA binding family member 1 (circPUM1) has been reported to play important roles in the tumorigenesis of several cancers. However, the underlying molecular role of circPUM1 in non-small cell lung cancer (NSCLC) progression remains unknown. The qRT-PCR and western blot were used to evaluate the expression of RNAs and proteins. In vitro cell proliferation assays, flow cytometric and glucose metabolism analyses were performed to test the effects of circPUM1 and its target on NSCLC cell growth and glycolysis. The interaction between microRNA (miR)-590-5p and circPUM1 or methyltransferase like 3 (METTL3) was analyzed by using dual-luciferase reporter, pull-down or RNA immunoprecipitation (RIP) assays. Murine xenograft model was established to conduct in vivo experiments. CircPUM1 was highly expressed in NSCLC tissues and cell lines. CircPUM1 knockdown suppressed cell proliferation, cell cycle and glycolysis in vitro. Moreover, circPUM1 directly bound to miR-590-5p, and miR-590-5p inhibitor reversed the inhibitory effects of circPUM1 knockdown on NSCLC carcinogenesis. Additionally, miR-590-5p suppressed NSCLC progression by directly targeting and regulating METTL3. Importantly, circPUM1 could regulate METTL3 in NSCLC cells through miR-590-5p. In addition, it was also proved circPUM1 silencing impeded tumor growth and glycolysis in the murine xenograft model by regulating miR-590-5p/METTL3 axis. CircPUM1 promoted NSCLC tumor growth and glycolysis through sequestering miR-590-5p and up-regulating METTL3, providing an improved understanding of NSCLC tumorigenesis and a potential therapeutic target for NSCLC therapy.
    Keywords:  Circpum1; METTL3; NSCLC; glycolysis; miR-590-5p
  15. Stroke. 2021 Jun 09. STROKEAHA121034173
      BACKGROUND AND PURPOSE: Hemorrhage-caused gene changes in the thalamus likely contribute to thalamic pain genesis. RNA N6-methyladenosine modification is an additional layer of gene regulation. Whether FTO (fat-mass and obesity-associated protein), an N6-methyladenosine demethylase, participates in hemorrhage-induced thalamic pain is unknown.METHODS: Expression of Fto mRNA and protein was assessed in mouse thalamus after hemorrhage caused by microinjection of Coll IV (type IV collagenase) into unilateral thalamus. Effect of intraperitoneal administration of meclofenamic acid (a FTO inhibitor) or microinjection of adeno-associated virus 5 (AAV5) expressing Cre into the thalamus of Ftofl/fl mice on the Coll IV microinjection-induced TLR4 (Toll-like receptor 4) upregulation and nociceptive hypersensitivity was examined. Effect of thalamic microinjection of AAV5 expressing Fto (AAV5-Fto) on basal thalamic TLR4 expression and nociceptive thresholds was also analyzed. Additionally, level of N6-methyladenosine in Tlr4 mRNA and its binding to FTO or YTHDF2 (YTH N6-methyladenosine RNA binding protein 2) were observed.
    RESULTS: FTO was detected in neuronal nuclei of thalamus. Level of FTO protein, but not mRNA, was time-dependently increased in the ipsilateral thalamus on days 1 to 14 after Coll IV microinjection. Intraperitoneal injection of meclofenamic acid or adeno-associated virus-5 expressing Cre microinjection into Ftofl/fl mouse thalamus attenuated the Coll IV microinjection-induced TLR4 upregulation and tissue damage in the ipsilateral thalamus and development and maintenance of nociceptive hypersensitivities on the contralateral side. Thalamic microinjection of AAV5-Fto increased TLR4 expression and elicited hypersensitivities to mechanical, heat and cold stimuli. Mechanistically, Coll IV microinjection produced an increase in FTO binding to Tlr4 mRNA, an FTO-dependent loss of N6-methyladenosine sites in Tlr4 mRNA and a reduction in the binding of YTHDF2 to Tlr4 mRNA in the ipsilateral thalamus.
    CONCLUSIONS: Our findings suggest that FTO participates in hemorrhage-induced thalamic pain by stabilizing TLR4 upregulation in thalamic neurons. FTO may be a potential target for the treatment of this disorder.
    Keywords:  FTO protein; hemorrhagic stroke; meclofenamic acid; microinjections; neurons; thalamus
  16. J Clin Lab Anal. 2021 Jun;35(6): e23779
      BACKGROUND: Patients with triple-negative breast cancer (TNBC) face a major challenge of the poor prognosis, and N6-methyladenosine-(m6A) mediated regulation in cancer has been proposed. Therefore, this study aimed to explore the prognostic roles of m6A-related long non-coding RNAs (LncRNAs) in TNBC.METHODS: Clinical information and expression data of TNBC samples were collected from TCGA and GEO databases. Pearson correlation, univariate, and multivariate Cox regression analysis were employed to identify independent prognostic m6A-related LncRNAs to construct the prognostic score (PS) risk model. Receiver operating characteristic (ROC) curve was used to evaluate the performance of PS risk model. A competing endogenous RNA (ceRNA) network was established for the functional analysis on targeted mRNAs.
    RESULTS: We identified 10 independent prognostic m6A-related LncRNAs (SAMD12-AS1, BVES-AS1, LINC00593, MIR205HG, LINC00571, ANKRD10-IT1, CIRBP-AS1, SUCLG2-AS1, BLACAT1, and HOXB-AS1) and established a PS risk model accordingly. Relevant results suggested that TNBC patients with lower PS had better overall survival status, and ROC curves proved that the PS model had better prognostic abilities with the AUC of 0.997 and 0.864 in TCGA and GSE76250 datasets, respectively. Recurrence and PS model status were defined as independent prognostic factors of TNBC. These ten LncRNAs were all differentially expressed in high-risk TNBC compared with controls. The ceRNA network revealed the regulatory axes for nine key LncRNAs, and mRNAs in the network were identified to function in pathways of cell communication, signaling transduction and cancer.
    CONCLUSION: Our findings proposed a ten-m6A-related LncRNAs as potential biomarkers to predict the prognostic risk of TNBC.
    Keywords:  N6-methyladenosine; ceRNA network; long non-coding RNA; prognostic signature; triple-negative breast cancer