bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022–09–11
48 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics
  1. 1m6A-modified HOTAIRM1 promotes vasculogenic mimicry formation in glioma.
  2. m1A and m6A modifications function cooperatively to facilitate rapid mRNA degradation.
  3. METTL3-Mediated m6A Modification of lncRNA MALAT1 Facilitates Prostate Cancer Growth by Activation of PI3K/AKT Signaling.
  4. Role of m6A RNA methylation in the development of hepatitis B virus-associated hepatocellular carcinoma.
  5. ALKBH5 inhibits thyroid cancer progression by promoting ferroptosis through TIAM1-Nrf2/HO-1 axis.
  6. Quercetin ameliorated insulin resistance via regulating METTL3-mediated N6-methyladenosine modification of PRKD2 mRNA in skeletal muscle and C2C12 myocyte cell line.
  7. Comprehensive Analysis of N6-Methyladenosine RNA Methylation Regulators in the Diagnosis and Subtype Classification of Acute Myocardial Infarction.
  8. RNA Editing Enzyme ADAR1 Regulates METTL3 in an Editing Dependent Manner to Promote Breast Cancer Progression via METTL3/ARHGAP5/YTHDF1 Axis.
  9. RNA m6A regulates transcription via DNA demethylation and chromatin accessibility.
  10. METTL3 contributes to slow transit constipation by regulating miR-30b-5p/PIK3R2/Akt/mTOR signaling cascade through DGCR8.
  11. METTL3 m6A-dependently promotes miR-21-5p maturation to accelerate choriocarcinoma progression via the HIF1AN-induced inactivation of the HIF1A/VEGF pathway.
  12. FTO/RUNX2 signaling axis promotes cementoblast differentiation under normal and inflammatory condition.
  13. Targeting RNA N6-methyladenosine modification: a precise weapon in overcoming tumor immune escape.
  14. Gene signatures, immune infiltration, and drug sensitivity based on a comprehensive analysis of m6a RNA methylation regulators in cervical cancer.
  15. Interaction between N6-methyladenosine and autophagy in the regulation of bone and tissue degeneration.
  16. The m6A demethylase FTO promotes renal epithelial-mesenchymal transition by reducing the m6A modification of lncRNA GAS5.
  17. METTL3 promotes m6A hypermethylation of RBM14 via YTHDF1 leading to the progression of hepatocellular carcinoma.
  18. Impact of N6-methyladenosine (m6A) modification on immunity.
  19. Differential RNA Methylation Analysis for MeRIP-seq Data under General Experimental Design.
  20. ALKBH5-mediated m6A demethylation of GLUT4 mRNA promotes glycolysis and resistance to HER2-targeted therapy in breast cancer.
  21. Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development.
  22. Comprehensive analysis of m6A circRNAs identified in colorectal cancer by MeRIP sequencing.
  23. Integrated risk scores from N6-methyladenosine-related lncRNAs are potential biomarkers for predicting the overall survival of bladder cancer patients.
  24. METTL1 promotes neuroblastoma development through m7G tRNA modification and selective oncogenic gene translation.
  25. Association of N6-methyladenosine readers' genes variation and expression level with pulmonary tuberculosis.
  26. Critical role of m6A modification in T-helper cell disorders.
  27. TFAP4 activates IGF2BP1 and promotes progression of non-small cell lung cancer by stabilizing TK1 expression through m6A modification.
  28. An m5C methylation regulator-associated signature predicts prognosis and therapy response in pancreatic cancer.
  29. Increased expression of METTL3 in pancreatic cancer tissues associates with poor survival of the patients.
  30. The prognostic value and immune landscapes of m1A/m5C/m6A-associated lncRNA signature in osteosarcoma.
  31. Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System.
  32. Oncogenic signaling pathway dysregulation landscape reveals the role of pathways at multiple omics levels in pan-cancer.
  33. Landscape and Construction of a Novel N6-methyladenosine-related LncRNAs in Cervical Cancer.
  34. Functional Characterization of Two RNA Methyltransferase Genes METTL3 and METTL14 Uncovers the Roles of m6A in Mediating Adaptation of Plutella xylostella to Host Plants.
  35. Hypoxia-induced exosomal circPDK1 promotes pancreatic cancer glycolysis via c-myc activation by modulating miR-628-3p/BPTF axis and degrading BIN1.
  36. Combination of high-fat diet and cadmium impairs testicular spermatogenesis in an m6A-YTHDF2-dependent manner.
  37. E6E7 regulates the HK2 expression in cervical cancer via GSK3β/FTO signal.
  38. DNA 6mA Demethylase ALKBH1 Orchestrates Fatty Acid Metabolism and Suppresses Diet-induced Hepatic Steatosis.
  39. A Comprehensive Bioinformatic Analysis for Identification of Myeloid-Associated Differentiation Marker as a Potential Negative Prognostic Biomarker in Non-Small-Cell Lung Cancer.
  40. Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks.
  41. TRIM46 aggravated high glucose-induced hyper permeability and inflammatory response in human retinal capillary endothelial cells by promoting IκBα ubiquitination.
  42. CircEPSTI1 Promotes the Proliferation of HER2-Positive Breast Cancer Cells via circEPSTI1/miR-145/ERBB3 Axis.
  43. TRIM36 inhibits tumorigenesis through the Wnt/β-catenin pathway and promotes caspase-dependent apoptosis in hepatocellular carcinoma.
  44. circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis.
  45. UBE2C mediated radiotherapy resistance of head and neck squamous cell carcinoma by regulating oxidative-stress-relative apoptosis.
  46. Therapeutic potential of the novel Bcl-2/Bcl-XL dual inhibitor, APG1252, alone or in combination against non-small cell lung cancer.
  47. Identification and Validation of Immune Markers in Coronary Heart Disease.
  48. Integration of Transcriptome and Epigenome to Identify and Develop Prognostic Markers for Ovarian Cancer.
  1. Cancer Sci. 2022 Sep 10.
    1m6A-modified HOTAIRM1 promotes vasculogenic mimicry formation in glioma.
    Zhangyi Wu, Yihai Lin.
      Vasculogenic mimicry (VM) has been demonstrated to accelerate angiogenesis in malignant tumors, yet the mechanism underlying VM has not been fully elucidated. N6-methyladenosine (m6A) mainly modulates mRNA fate and affects multiple tumorigenesis. Here, we aimed to investigate m6A-modified HOTAIRM1 in the regulation of glioma-associated VM formation. Gene expression was analyzed by qRT-PCR. Cell viability, metastases, and VM formation capacity were determined by CCK-8, migration and invasion, as well as tube formation assays, respectively. The function and mechanisms of m6A-modified HOTAIRM1 were defined through LC-MS/MS m6A quantification, methylated RNA immunoprecipitation sequencing (MeRIP), RNA stability assays, and RNA pull-down experiments. A glioma xenograft mouse model was further established for VM evaluation in vivo. The results showed that HOTAIRM1, METTL3, and IGFBP2 were upregulated in glioma tissues and cell lines. HOTAIRM1 functions as an oncogene in glioma progression; however, knockdown of HOTAIRM1 significantly reduced cell viability, migration, invasion, and VM formation. Notably, METTL3-dependent m6A modification enhanced HOTAIRM1 mRNA stability, while knockdown of METTL3 deficiency significantly suppressed VM in glioma. Moreover, HOTAIRM1 was found to bind IGFBP2, and HOTAIRM1 deficiency blocked glioma progression and VM formation in vivo. Our results demonstrated that METTL3-dependent m6A-modified HOTAIRM1 promoted VM formation in glioma.
    Keywords:  Glioma; HOTAIRM1; IGFBP2; METTL3; N6-methyladenosine (m6A); vasculogenic mimicry (VM)
    DOI:  https://doi.org/10.1111/cas.15578
  2. Cell Rep. 2022 Sep 06. pii: S2211-1247(22)01141-X. [Epub ahead of print]40(10): 111317
    m1A and m6A modifications function cooperatively to facilitate rapid mRNA degradation.
    Sung Ho Boo, Hongseok Ha, Yoon Ki Kim.
      N6-Methyladenosine (m6A), the most abundant internal mRNA modification, affects multiple steps in gene expression. Mechanistically, the binding of YTHDF2 to m6A on mRNAs elicits rapid mRNA degradation by recruiting several RNA degrading enzymes. Here, we show that N1-methyladenosine (m1A), another type of RNA modification, accelerates rapid m6A RNA degradation. We identify HRSP12 as an RNA-binding protein that recognizes m1A. The binding of HRSP12 to m1A promotes efficient interaction of YTHDF2 with m6A, consequently facilitating endoribonucleolytic cleavage via the RNase P/MRP complex. Transcriptome-wide analyses also reveal that mRNAs harboring both m1A and m6A are downregulated in an HRSP12-dependent manner compared with mRNAs harboring m6A only. Accordingly, a subset of endogenous circular RNAs that harbor m6A and associate with YTHDF2 in an HRSP12-dependent manner is also subjected to m1A-facilitated rapid degradation. Together, our observations provide compelling evidence for crosstalk between different RNA modifications.
    Keywords:  CP: Molecular biology; HRSP12; N(1)-methyladenosine; N(6)-methyladenosine; RNase P/MRP; YTHDF2; m(1)A; m(6)A; mRNA decay
    DOI:  https://doi.org/10.1016/j.celrep.2022.111317
  3. Cell Transplant. 2022 Jan-Dec;31:31 9636897221122997
    METTL3-Mediated m6A Modification of lncRNA MALAT1 Facilitates Prostate Cancer Growth by Activation of PI3K/AKT Signaling.
    Yuanshen Mao, Wenfeng Li, YiMing Weng, Bao Hua, Xin Gu, Chao Lu, Bin Xu, Huan Xu, Zhong Wang.
      Accumulating data show that N6-methyladenosine (m6A) methyltransferase METTL3 and long noncoding RNA MALAT1 act pivotal roles in multiple malignancies including prostate cancer (PCa). However, the role and molecular mechanism underlying METTL3-mediated m6A modification of MALAT1 in PCa remain undocumented. The association of METTL3 and MALAT1 expression with clinicopathological characteristics and prognosis in patients with PCa was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, and public The Cancer Genome Atlas (TCGA) dataset. The in vitro and in vivo experiments were executed to investigate the role of METTL3 in PCa. m6A dot blot, methylated RNA immunoprecipitation (MeRIP), RIP, and qRT-PCR assays were employed to observe METTL3-mediated m6A modification of MALAT1. The effects of METTL3 on MALAT1-mediated PI3K/AKT pathway were assessed by Western blot analysis. As a result, we found that METTL3 was significantly upregulated in PCa tissues and high expression of METTL3 was associated with Gleason score and tumor recurrence in patients with PCa. Knockdown of METTL3 markedly repressed growth and invasion of PCa cells in vitro and in vivo, whereas ectopic expression of METTL3 showed the opposite effects. Moreover, knockdown of METTL3 decreased the total m6A levels of PCa cells as well as the MALAT1 m6A levels, leading to reduced MALAT1 expression. Overexpression of MALAT1 reversed METTL3 knockdown-induced antitumor effects and PI3K/AKT signaling inactivation. MALAT1 harbored a positive correlation with METTL3 expression and tumor recurrence in PCa. In conclusion, our findings demonstrate that METTL3-mediated m6A modification of lncRNA MALAT1 promotes growth and invasion of PCa cells by activating PI3K/AKT signaling.
    Keywords:  MALAT1; METTL3; growth; m6A; prostate cancer
    DOI:  https://doi.org/10.1177/09636897221122997
  4. J Gastroenterol Hepatol. 2022 Sep 06.
    Role of m6A RNA methylation in the development of hepatitis B virus-associated hepatocellular carcinoma.
    Cheng Zhang, Dongjun Dai, Wangjian Zhang, Wenjun Yang, Yinglu Guo, Qichun Wei.
      Hepatocellular carcinoma (HCC) is the most common liver malignancy which can be developed from hepatitis B and cirrhosis. Many pathophysiological alterations, including HBV DNA integration, oxidative stress, cytokine release, telomerase homeostasis, mitochondrial damage, epigenetic modification and tumor microenvironment, are involved in the biological process from hepatitis B to cirrhosis and HCC. N6-methyladenosine (m6A), as an epitranscriptomic modification of RNAs, can regulate the stability, splicing, degradation, transcription and translation of downstream target RNAs in HBV and liver cancer cells. m6A regulators (writers, erasers and readers) play an important role in the pathogenesis of HBV-associated HCC by regulating cell proliferation, apoptosis, migration, autophagy, differentiation, inflammation, angiogenesis and tumor microenvironment. This review summarizes the current progress of m6A methylation in the molecular mechanisms, biological functions and potential clinical implications of HBV-associated HCC.
    Keywords:  RNA methylation; clinical implication; hepatitis B virus; hepatocellular carcinoma; m6A
    DOI:  https://doi.org/10.1111/jgh.15999
  5. Mol Cell Biochem. 2022 Sep 07.
    ALKBH5 inhibits thyroid cancer progression by promoting ferroptosis through TIAM1-Nrf2/HO-1 axis.
    Wei Li, Guo Huang, Jinrong Wei, Hong Cao, Guoqin Jiang.
      As a critical catalytic subunit of N6-methyladenosine (m6A) modification in messenger RNA, ALKBH5 has been reported to affect the progression of numerous tumors. However, the functions and mechanisms of ALKBH5 in thyroid cancer remain largely unknown. Relative mRNA and protein levels in thyroid cancer tissues and cells were detected by qRT-PCR and western blot, respectively. The proliferation and viability were evaluated using colony formation and CCK-8 assays. Intracellular iron level was measured by an iron colorimetric assay kit. ROS level was determined using CellRox Green reagent. TIAM1 mRNA m6A level was detected by MeRIP. Xenograft tumor growth was performed to examine the role of ALKBH5 in thyroid tumor growth in vivo. ALKBH5 was decreased in thyroid cancer tissues and cells. ALKBH5 overexpression inhibited thyroid cancer cell proliferation and increased the levels of Fe2+ and ROS and reduced the proteins expression of GPX4 and SLC7A11. Furthermore, overexpression of ALKBH5 inhibited TIAM1 expression by m6A modification, and overexpression of TIAM1 reversed the regulatory of oe-ALKBH5 on cell proliferation and ferroptosis in thyroid cancer. In addition, TIAM1 was elevated in thyroid cancer, and TIAM1 knockdown repressed thyroid cancer cell proliferation and promoted ferroptosis through regulating Nrf2/HO-1 axis. In addition, in vivo evidences also showed that ALKBH5 suppressed thyroid cancer progression by decreasing the m6A level of TIAM1. Our findings suggested that ALKBH5 inhibited thyroid cancer progression by inducing ferroptosis through m6A-TIAM1-Nrf2/HO-1 axis, suggesting ALKBH5 might be a potential target molecule for the treatment and diagnosis of thyroid cancer.
    Keywords:  ALKBH5; Ferroptosis; Nrf2/HO-1 pathway; TIAM1; Thyroid cancer
    DOI:  https://doi.org/10.1007/s11010-022-04541-x
  6. Nutr Metab Cardiovasc Dis. 2022 Jul 02. pii: S0939-4753(22)00284-8. [Epub ahead of print]
    Quercetin ameliorated insulin resistance via regulating METTL3-mediated N6-methyladenosine modification of PRKD2 mRNA in skeletal muscle and C2C12 myocyte cell line.
    Yang Jiao, Albert Williams, Ning Wei.
       BACKGROUND AND AIMS: N6-Methyladenosine (m6A) modification is involved in many pathological processes, including insulin resistance (IR). Quercetin (Que), a bioactive compound with strong antioxidant activity, has potential therapeutic effects on IR-related metabolic diseases. The aim of this study is to investigate the roles of m6A and Que in hyperinsulinemia.
    METHODS AND RESULTS: Male C57Bl/6 mice received a high-fat diet (HFD) for 8 weeks to establish an IR model. Que treatment reduced the body weight, blood glucose, plasma triglycerides (TG) and serum insulin, ameliorated IR, and decreased oxidative stress in HFD-fed mice. Cellular IR model was established in C2C12 cells by palmitic acid (PA) stimulation, and a noncytotoxic dose of Que was found to promote glucose uptake and inhibit oxidative stress. Moreover, methyltransferase-like 3 (METTL3) and serine-threonine kinase protein kinase D2 (PRKD2) was downregulated in skeletal muscle of HFD-fed mouse and in PA-induced C2C12 cells. The online bioinformatic tool SRAMP revealed that there were multiple m6A modification sites in the PRKD2 mRNA sequence. Downregulation of METTL3 enhanced PRKD2 expression by reducing m6A level and promoting mRNA stability in PRKD2 mRNA transcript. Que decreased m6A, METTL3, and phosphorylated insulin receptor substrate 1 (p-IRS1) levels, increased the protein expression of PRKD2, glucose transporter type 4 (GLUT4) and p-AKT, promoted glucose uptake, and reduced oxidative stress in PA-induced C2C12 cells. Moreover, METTL3 overexpression or PRKD2 silence reversed the inhibitory effects of Que on the levels of MDA and p-IRS1 and the promotive effects on glucose uptake, superoxide dismutase (SOD), GSH and GLUT4 and p-AKT levels.
    CONCLUSION: Que promoted glucose uptake, repressed oxidative stress and improved IR through METTL3-mediated m6A of PRKD2 mRNA.
    Keywords:  GLUT4/IRS-1/AKT pathway; Insulin resistance; N6-methyladenosine; Que; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.numecd.2022.06.019
  7. J Immunol Res. 2022 ;2022 5173761
    Comprehensive Analysis of N6-Methyladenosine RNA Methylation Regulators in the Diagnosis and Subtype Classification of Acute Myocardial Infarction.
    Xianpei Wang, Ying Wu, Ruoyao Guo, Linwei Zhao, Juanjuan Yan, Chuanyu Gao.
      Acute myocardial infarction (AMI) is still a huge danger to human health. Sensitive markers are necessary for the prediction of the risk of AMI and would be beneficial for managing the incidence rate. N6-methyladenosine (m6A) RNA methylation regulators have been confirmed to be involved in the development of various diseases. However, their function in AMI has not been fully elucidated. The purpose of this study was to determine the expression of m6A RNA methylation regulators in AMI as well as their possible functions and prognostic values. The GEO database was used to get the gene expression profiles of patients with and without AMI, and bioinformatics assays of genes with differently expressed expression were performed. We establish two separate m6A subtypes, and relationships between subtypes and immunity were studied. In this study, we identified IGF2BP1, FTO, RBM15, METTL3, YTHDC2, FMR1, and HNRNPA2B1 as the seven major m6A regulators. A nomogram model was developed and confirmed. The consensus clustering algorithm was conducted to categorize AMI patients into two m6A subtypes from the identified m6A regulators. Patients who have activated T-cell activities were found to be in clusterA; they may have a better prognosis as a result. Importantly, we found that patients with high METTL3 expressions had an increased level of Activated.CD4.T.cell and Type.2.T.helper.cell, while having a decreased level of CD56bright.natural.killer.cell, Macrophage, Monocyte, Natural.killer.cell, and Type.17.T.helper.cell. Overall, a diagnostic model of AMI was established based on the genes of IGF2BP1, FTO, RBM15, METTL3, YTHDC2, FMR1, and HNRNPA2B1. Our investigation of m6A subtypes may prove useful in the developments of therapy approaches for AMI.
    DOI:  https://doi.org/10.1155/2022/5173761
  8. Int J Mol Sci. 2022 Aug 25. pii: 9656. [Epub ahead of print]23(17):
    RNA Editing Enzyme ADAR1 Regulates METTL3 in an Editing Dependent Manner to Promote Breast Cancer Progression via METTL3/ARHGAP5/YTHDF1 Axis.
    Yi Li, Ning-Xi Wang, Chuan Yin, Shan-Shan Jiang, Jia-Chu Li, Sheng-Yong Yang.
      A-to-I RNA editing and m6A modification are two of the most prevalent types of RNA modifications controlling gene expression in mammals and play very important roles in tumorigenesis and tumor progression. However, the functional roles and correlations of these two RNA modifications remain to be further investigated in cancer. Herein, we show that ADAR1, an A-to-I RNA-editing enzyme, interacts with METTL3 and increases its protein level to promote the proliferation, migration and invasion of breast cancer cells through a mechanism connecting ADAR1, METTL3 and YTHDF1. We show that both ADAR1 and METTL3 are upregulated in breast cancer samples, and ADAR1 positively correlates with METTL3; ADAR1 edits METTL3 mRNA and changes its binding site to miR532-5p, leading to increased METTL3 protein, which further targets ARHGAP5, recognized by YTHDF1. Additionally, we show that loss of ADAR1 significantly inhibits breast cancer growth in vivo. Collectively, our findings identify the ADAR1-METTL3 axis as a novel, important pathway that connects A-to-I editing and m6A RNA modifications during breast cancer progression.
    Keywords:  ADAR1; ARHGAP5; METTL3; YTHDF1; breast cancer
    DOI:  https://doi.org/10.3390/ijms23179656
  9. Nat Genet. 2022 Sep 07.
    RNA m6A regulates transcription via DNA demethylation and chromatin accessibility.
    Shuang Deng, Jialiang Zhang, Jiachun Su, Zhixiang Zuo, Lingxing Zeng, Kaijing Liu, Yanfen Zheng, Xudong Huang, Ruihong Bai, Lisha Zhuang, Ying Ye, Mei Li, Ling Pan, Junge Deng, Guandi Wu, Rui Li, Shaoping Zhang, Chen Wu, Dongxin Lin, Jianjun Chen, Jian Zheng.
      Transcriptional regulation, which integrates chromatin accessibility, transcription factors and epigenetic modifications, is crucial for establishing and maintaining cell identity. The interplay between different epigenetic modifications and its contribution to transcriptional regulation remains elusive. Here, we show that METTL3-mediated RNA N6-methyladenosine (m6A) formation leads to DNA demethylation in nearby genomic loci in normal and cancer cells, which is mediated by the interaction between m6A reader FXR1 and DNA 5-methylcytosine dioxygenase TET1. Upon recognizing RNA m6A, FXR1 recruits TET1 to genomic loci to demethylate DNA, leading to reprogrammed chromatin accessibility and gene transcription. Therefore, we have characterized a regulatory mechanism of chromatin accessibility and gene transcription mediated by RNA m6A formation coupled with DNA demethylation, highlighting the importance of the crosstalk between RNA m6A and DNA modification in physiologic and pathogenic process.
    DOI:  https://doi.org/10.1038/s41588-022-01173-1
  10. J Gastroenterol Hepatol. 2022 Sep 06.
    METTL3 contributes to slow transit constipation by regulating miR-30b-5p/PIK3R2/Akt/mTOR signaling cascade through DGCR8.
    Wen-Jing Gong, Rong Li, Qiao-Qiong Dai, Peng Yu.
       BACKGROUND: N6-methyladenosine (m6A) is the most prevalent methylation modification of eukaryotic RNA, and Methyltransferase-like 3 (METTL3) plays a vital role in multiple cell functions. This study aimed to investigate the role of m6A methylase METTL3 in slow transit constipation (STC).
    MATERIAL AND METHOD: The expression of METTL3 and DGCR8 was measured in STC tissues and glutamic acid-induced interstitial cells of Cajal (ICCs). The effects of METTL3, miR-30b-5p and DGCR8 on the biological characteristics of ICCs were investigated on the basis of loss-of-function analyses. Luciferase reporter assay was used to identify the direct binding sites of miR-30b-5p with PIK3R2.
    RESULTS: The results showed that the METTL3, DGCR8, miR-30b-5p, and the methylation level of m6A were significantly increased in STC tissues and glutamic acid-induced ICCs. Silencing of METTL3, miR-30b-5p inhibited apoptosis, autophagy, and pyroptosis of glutamic acid-induced ICCs. Moreover, overexpression of miR-30b-5p reversed the cytoprotection of METTL3 knock-down in glutamic acid-induced ICCs. Besides, DGCR8 knockdown could facilitate cell growth and decrease apoptotic glutamic acid-induced ICCs. Mechanically, we illustrated that METTL3 in glutamic acid-induced ICCs significantly accelerated the maturation of pri-miR-30b-5p by m6A methylation modification, resulting in the reduction of PIK3R2, which results in the inhibition of PI3K/Akt/mTOR pathway, and ultimately leads to the cell death of STC.
    CONCLUSIONS: Collectively, these data demonstrated that METTL3 promoted the apoptosis, autophagy and pyroptosis of glutamic acid-induced ICCs by interacting with the DGCR8 and successively modulating the miR-30b-5p/PIK3R2 axis in an m6A-dependent manner, and METTL3 may be a potential therapeutic target for STC.
    Keywords:  Functional constipation; ICCs; METTL3; PIK3R2; Slow transit constipation; miR-30b-5p
    DOI:  https://doi.org/10.1111/jgh.15994
  11. Genes Genomics. 2022 Sep 08.
    METTL3 m6A-dependently promotes miR-21-5p maturation to accelerate choriocarcinoma progression via the HIF1AN-induced inactivation of the HIF1A/VEGF pathway.
    Kefan Ye, Lingchuan Li, Bao Wu, Dongjie Wang.
       BACKGROUND: Gestational choriocarcinoma is a highly malignant neoplastic disease derived from pathological changes in trophoblastic cells. Recent evidences have shown that N6-methyladenosine (m6A) modifications play important role in modulating the development of multiple cancers, but the detailed mechanisms by which m6A-mediated choriocarcinoma progression have not been fully delineated.
    OBJECTIVES: This study aimed to investigate the role of m6A in choriocarcinoma and reveal its underlying molecular mechanisms.
    METHODS: The expression of METTL3, miR-21-5p and HIF1AN was detected using RT-qPCR in tissues and cells. The protein expression of METTL3, HIF1AN, HIF1A and VEGF were measured by western blot. The luciferase reporter assays and RNA immunoprecipitation (RIP) were used to verify the relationship between miR-21-5p and HIF1AN. The CCK-8, colony formation and transwell assays were used to detected cell proliferation and cell migration, respectively.
    RESULTS: Here, we demonstrated that the m6A methyltransferase-like 3 (METTL3) was aberrantly high-expressed in the clinical choriocarcinoma tissues and choriocarcinoma cell lines compared to the corresponding normal counterparts. The following functional experiments verified that silencing of METTL3 suppressed cell proliferation, migration, epithelial-mesenchymal transition (EMT) and tumorigenesis in vitro and in vivo to hamper the aggressiveness of choriocarcinoma. Next, the mechanical experiments confirmed that METTL3 promoted the maturation of miR-21-5p in an m6A-dependent manner, and elevated miR-21-5p subsequently degraded its downstream hypoxia-inducible factor asparagine hydroxylase (HIF1AN) by targeting its 3' untranslated regions (3'-UTR), resulting in the activation of the tumor-promoting HIF1A/VEGF pathway. Finally, the rescuing experiments verified that METTL3 ablation-induced inhibitory effects on the malignant phenotypes in choriocarcinoma were all abrogated by both miR-21-5p overexpression and HIF1AN downregulation.
    CONCLUSIONS: Collectively, this study firstly reported the involvement of the METTL3/m6A/miR-21-5p/HIF1AN signaling cascade in regulating the progression of choriocarcinoma, which provided novel biomarkers for the diagnosis and treatment of this disease.
    Keywords:  Choriocarcinoma; HIF1A; HIF1AN; METTL3; VEGF; miR-21-5p
    DOI:  https://doi.org/10.1007/s13258-022-01309-x
  12. Biochim Biophys Acta Mol Cell Res. 2022 Sep 06. pii: S0167-4889(22)00150-1. [Epub ahead of print] 119358
    FTO/RUNX2 signaling axis promotes cementoblast differentiation under normal and inflammatory condition.
    Qiao Sun, Tingting Zhao, Biao Li, Mengying Li, Ping Luo, Chen Zhang, Gang Chen, Zhengguo Cao, Yicun Li, Mingyuan Du, Hong He.
      N6-methyladenosine (m6A) is the most prevalent mRNA modification which plays crucial roles in various biological processes, but its role in cementogenesis remains largely unknown. Here, using time-series transcriptomic analysis, we reveal that mRNA m6A demethylase Fat mass and obesity-associated protein (FTO) is involved in cementogenesis. Knocking down FTO decreases cementoblast differentiation and mineralization in both OCCM-30 cellular model and murine ectopic bone formation model. Mechanistically, we find that FTO directly binds Runt-related transcription factor 2 (Runx2) mRNA, an important cementogenesis factor, thus protecting it from YTH domain-containing family protein 2 (YTHDF2) mediated degradation, when cementoblasts are differentiating. Knocking down YTHDF2 restores the expression of Runx2 in FTO-knockdown cells. Moreover, under inflammatory conditions, TNF-α inhibits cementoblast differentiation and mineralization partly through FTO/RUNX2 axis. Collectively, our study reveals an important regulatory role of FTO/RUNX2 axis in normal and pathological cementogenesis.
    Keywords:  Cell differentiation; Cementoblast; Fat mass and obesity-associated protein; Inflammation; N(6)-methyladenosine; Transcription factors
    DOI:  https://doi.org/10.1016/j.bbamcr.2022.119358
  13. Mol Cancer. 2022 Sep 07. 21(1): 176
    Targeting RNA N6-methyladenosine modification: a precise weapon in overcoming tumor immune escape.
    Wei Li, Yi Hao, Xingda Zhang, Shouping Xu, Da Pang.
      Immunotherapy, especially immune checkpoint inhibitors (ICIs), has revolutionized the treatment of many types of cancer, particularly advanced-stage cancers. Nevertheless, although a subset of patients experiences dramatic and long-term disease regression in response to ICIs, most patients do not benefit from these treatments. Some may even experience cancer progression. Immune escape by tumor cells may be a key reason for this low response rate. N6-methyladenosine (m6A) is the most common type of RNA methylation and has been recognized as a critical regulator of tumors and the immune system. Therefore, m6A modification and related regulators are promising targets for improving the efficacy of tumor immunotherapy. However, the association between m6A modification and tumor immune escape (TIE) has not been comprehensively summarized. Therefore, this review summarizes the existing knowledge regarding m6A modifications involved in TIE and their potential mechanisms of action. Moreover, we provide an overview of currently available agents targeting m6A regulators that have been tested for their elevated effects on TIE. This review establishes the association between m6A modifications and TIE and provides new insights and strategies for maximizing the efficacy of immunotherapy by specifically targeting m6A modifications involved in TIE.
    Keywords:  Immunotherapy; N6-methyladenosine (m6A); Tumor; Tumor immune escape (TIE); cancer
    DOI:  https://doi.org/10.1186/s12943-022-01652-3
  14. J Transl Med. 2022 Sep 04. 20(1): 385
    Gene signatures, immune infiltration, and drug sensitivity based on a comprehensive analysis of m6a RNA methylation regulators in cervical cancer.
    Xiaoqin Lu, Rui Li, Yanqi Ying, Wenyi Zhang, Wuliang Wang.
       BACKGROUND: Cervical cancer is the fourth most common cancer in women. N6-dimethyladenosine (m6A) mRNA methylation is closely associated with cervical cancer.
    METHODS: Using TCGA database, we studied the expression and mutation of m6A-related genes in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) and obtained genetic characteristics based on an m6A risk model and prognostic value of m6A. We studied the effects of the m6A risk score on immune features and genomic changes of patients with CESC, evaluated the sensitivity of patients with CESC to different small-molecule drugs based on the m6A risk score, and established a clinical prediction model.
    RESULTS: Ten m6A-related genes were differentially expressed between CESC and normal tissues. High-risk patients had a low overall survival (OS) and significantly low immune scores but showed no significantly altered stromal scores. The tumor mutation burden (TMB) and tumor neoantigen levels significantly differed between the high- and low-risk groups. In the high-risk group, copy number variation (CNV) changes mainly led to gene amplification, while in the low-risk group, CNV changes primarily manifested as gene copy number deletions. ZC3H13 expression was low in CESC tissues. ZC3H13 knockdown promoted CESC cell proliferation, migration, and invasion, reducing the RNA methylation levels. Rapamycin suppressed the CESC cell proliferation, migration, and invasion abilities, increasing the m6A levels.
    CONCLUSION: m6A mRNA methylation is closely related to the occurrence, development, immune invasion, drug sensitivity, and prognosis of cervical cancer. The prognostic m6A feature model of m6A signature genes can accurately predict the OS of patients with CESC. Drugs targeting factors regulating m6A mRNA methylation might offer a good prospect for treating cervical cancer.
    Keywords:  Cervical cancer; Drug sensitivity; Immune infiltration; N6-dimethyladenosine; Rapamycin; ZC3H13
    DOI:  https://doi.org/10.1186/s12967-022-03600-7
  15. Front Bioeng Biotechnol. 2022 ;10 978283
    Interaction between N6-methyladenosine and autophagy in the regulation of bone and tissue degeneration.
    Xiaodong Wen, Junhu Wang, Qiong Wang, Peilong Liu, Hongmou Zhao.
      Bone and tissue degeneration are the most common skeletal disorders that seriously affect people's quality of life. N6-methyladenosine (m6A) is one of the most common RNA modifications in eukaryotic cells, affecting the alternative splicing, translation, stability and degradation of mRNA. Interestingly, increasing number of evidences have indicated that m6A modification could modulate the expression of autophagy-related (ATG) genes and promote autophagy in the cells. Autophagy is an important process regulating intracellular turnover and is evolutionarily conserved in eukaryotes. Abnormal autophagy results in a variety of diseases, including cardiomyopathy, degenerative disorders, and inflammation. Thus, the interaction between m6A modification and autophagy plays a prominent role in the onset and progression of bone and tissue degeneration. In this review, we summarize the current knowledge related to the effect of m6A modification on autophagy, and introduce the role of the crosstalk between m6A modification and autophagy in bone and tissue degeneration. An in-depth knowledge of the above crosstalk may help to improve our understanding of their effects on bone and tissue degeneration and provide novel insights for the future therapeutics.
    Keywords:  M6A; autophagy; degenerative; disease; mRNA; osteoporosis
    DOI:  https://doi.org/10.3389/fbioe.2022.978283
  16. Cytokine. 2022 Sep 01. pii: S1043-4666(22)00209-5. [Epub ahead of print]159 156000
    The m6A demethylase FTO promotes renal epithelial-mesenchymal transition by reducing the m6A modification of lncRNA GAS5.
    Xiaoyan Li, Yongzhen Li, Ying Wang, Xiaojie He.
       BACKGROUND: Renal interstitial fibrosis (RIF) is the main pathological change of a variety of chronic kidney diseases (CKD). Epigenetic modifications of fibrosis-prone genes regulate RIF progression. This study aimed to investigate long non-coding RNA (lncRNA) N6-methyladenosine (m6A) modification and its role in regulating RIF progression.
    METHODS: Unilateral ureteral occlusion (UUO) was employed to construct the RIF in vivo model; and TGF-β1-treated HK-2 and HKC-8 cells were used for in vitro experiments. The mRNA and protein expressions were assessed using qRT-PCR and western blot. The proliferation and migration were evaluated by EdU assay and transwell assay, respectively. In addition, levels of inflammatory cytokines were determined by ELISA assay and qRT-PCR. Moreover, lncRNA GAS5 m6A level was detected using Me-RIP assay. HE and Masson staining were employed to evaluate fibrotic lesions of the kidney.
    RESULTS: FTO expression was elevated in HK-2 and HKC-8 cells after TGF-β1 treatment and mouse kidney tissue following UUO, and lncRNA GAS5 was downregulated. LncRNA GAS5 overexpression or FTO silencing suppressed TGF-β1-induced the increase of EMT-related proteins (Vimentin, Snail and N-cadherin) and inflammatory cytokines (IL-6, IL-1β and TNF-α) levels in HK-2 cells. FTO suppressed lncRNA GAS5 expression by reducing the m6A modification of lncRNA GAS5. Additionally, FTO knockdown could suppress EMT process and inflammation response induced by TGF-β1 and UUO in vitro and in vivo. As expected, FTO knockdown abrogated the promotion effects of lncRNA GAS5 silencing on TGF-β1-induced EMT process and inflammation response in HK-2 and HKC-8 cells.
    CONCLUSION: FTO promoted EMT process and inflammation response through reducing the m6A modification of lncRNA GAS5.
    Keywords:  EMT; FTO; Inflammation; M(6)A modification; Renal interstitial fibrosis; lncRNA GAS5
    DOI:  https://doi.org/10.1016/j.cyto.2022.156000
  17. Hum Cell. 2022 Sep 10.
    METTL3 promotes m6A hypermethylation of RBM14 via YTHDF1 leading to the progression of hepatocellular carcinoma.
    Jingyao Hu, Liang Yang, Xueqiang Peng, Minghuan Mao, Xiaodan Liu, Jianbo Song, Hangyu Li, Fu Chen.
      Liver is a well-known immunological organ with unique microenvironment. In normal conditions, the rich immune-infiltrating cells cooperate with non-parenchymal cells, such as Kupffer cells (KCs). The presence of liver immunosuppressive microenvironment underlines the importance to dissect this interaction to understand how this cross-talk promotes tumor growth in hepatocellular carcinoma (HCC). Therefore, the aim of the study here was to probe the role of methyltransferase-like 3 (METTL3) in the HCC progression and its effect on the polarization of KCs. KCs showed M2 polarization, and METTL3 was overexpressed in our collected HCC tissues relative to adjacent tissues. METTL3 depletion inhibited the M2 polarization of KCs, thereby reverting the malignant phenotype of HCC cells in vitro and growth and metastasis in vivo. Mechanistically, YTH domain-containing family protein 1 (YTHDF1) bound to RNA-binding protein 14 (RBM14), whereas METTL3 knockdown in KCs cells suppressed RBM14 expression by decreasing N-methyladenosine (m6A) methylation. Overexpression of RBM14 mitigated the anti-tumor effects of sh-METTL3 in vitro and in vivo. It is suggested that the mechanism of sh-METTL3 suppressing the polarization of KCs and the progression of HCC is to regulate the RBM14 expression via YTHDF1-dependent m6A modification.
    Keywords:  Hepatocellular carcinoma; Kupffer cells; METTL3; RBM14; m6A modification
    DOI:  https://doi.org/10.1007/s13577-022-00769-3
  18. Cell Commun Signal. 2022 Sep 09. 20(1): 140
    Impact of N6-methyladenosine (m6A) modification on immunity.
    Raghda A Elsabbagh, Mona Rady, Carsten Watzl, Khaled Abou-Aisha, Mohamed Z Gad.
      N6-methyl-adenosine (m6A) is the most prevalent modification on mRNAs and long noncoding RNAs (lnRNAs) in higher eukaryotes. Modulation of m6A relies on m6A writers, erasers and readers. m6A modification contributes to diverse fundamental biological functions at the molecular, cellular, and physiological levels. The dysregulation of m6A modification has been implicated in various human diseases. Thus, m6A modification has now become a research hotspot for its potential therapeutic applications in the treatment of various cancers and diseases. The immune system is essential to provide defense against infections and cancers. This review summarizes the current knowledge about the roles of m6A in regulating immune cell functions and immune responses. Video abstract.
    Keywords:  Adaptive; Immunity; Innate; N6-methyl-adenosine; m6A erasers; m6A readers; m6A writers
    DOI:  https://doi.org/10.1186/s12964-022-00939-8
  19. Bioinformatics. 2022 Sep 05. pii: btac601. [Epub ahead of print]
    Differential RNA Methylation Analysis for MeRIP-seq Data under General Experimental Design.
    Zhenxing Guo, Andrew M Shafik, Peng Jin, Hao Wu.
       MOTIVATION: RNA epigenetics is an emerging field to study the post-transcriptional gene regulation. The dynamics of RNA epigenetic modification have been reported to associate with many human diseases. Recently developed high-throughput technology named Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) enables the transcriptome-wide profiling of N6-methyladenosine (m6A) modification and comparison of RNA epigenetic modifications. There are a few computational methods for the comparison of mRNA modifications under different conditions but they all suffer from serious limitations.
    RESULTS: In this work, we develop a novel statistical method to detect differentially methylated mRNA regions from MeRIP-seq data. We model the sequence count data by a hierarchical negative binomial model that accounts for various sources of variations, and derive parameter estimation and statistical testing procedures for flexible statistical inferences under general experimental designs. Extensive benchmark evaluations in simulation and real data analyses demonstrate that our method is more accurate, robust, and flexible compared to existing methods.
    AVAILABILITY: Our method TRESS is implemented as an R/Bioconductor package and is available at https://bioconductor.org/packages/devel/TRESS.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btac601
  20. Cancer Res. 2022 Sep 07. pii: CAN-22-0800. [Epub ahead of print]
    ALKBH5-mediated m6A demethylation of GLUT4 mRNA promotes glycolysis and resistance to HER2-targeted therapy in breast cancer.
    Hao Liu, Hui Lyu, Guanmin Jiang, Danyang Chen, Sanbao Ruan, Shuang Liu, Lukun Zhou, Mingqiang Yang, Shanshan Zeng, Zhimin He, Hongsheng Wang, Hongsheng Li, Guopei Zheng, Bolin Liu.
      Resistance to HER2-targeted therapy represents a significant challenge for the successful treatment of breast cancer patients with HER2-positive tumors. Through a global mass spectrometry-based proteomics approach, we discovered that the expression of the N6-methyladenosine (m6A) demethylase ALKBH5 was significantly upregulated in HER2-targeted therapy-resistant breast cancer cells. Elevated expression of ALKBH5 was sufficient to confer resistance to HER2-targeted therapy, and specific knockdown of ALKBH5 rescued the efficacy of trastuzumab and lapatinib in resistant breast cancer cells. Mechanistically, ALKBH5 promoted m6A demethylation of GLUT4 mRNA and increased GLUT4 mRNA stability in a YTHDF2-dependent manner, resulting in enhanced glycolysis in resistant breast cancer cells. In breast cancer tissues obtained from patients with poor response to HER2-targeted therapy, increased expression of ALKBH5 or GLUT4 was observed and was significantly associated with poor prognosis in the patients. Moreover, suppression of GLUT4 via genetic knockdown or pharmacological targeting with a specific inhibitor profoundly restored the response of resistant breast cancer cells to trastuzumab and lapatinib both in vitro and in vivo. In conclusion, ALKBH5-mediated m6A demethylation of GLUT4 mRNA promotes resistance to HER2-targeted therapy, and targeting the ALKBH5/GLUT4 axis has therapeutic potential for treating breast cancer patients refractory to HER2-targeted therapies.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0800
  21. Int J Mol Sci. 2022 Aug 31. pii: 9887. [Epub ahead of print]23(17):
    Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development.
    Xiaoyu Huang, Nigara Abuduwaili, Xinting Wang, Miao Tao, Xiaoqian Wang, Gengqing Huang.
      N6-methyladenosine (m6A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m6A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m6A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m6A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways.
    Keywords:  GhVIR; chloroplast biosynthesis; cotton; leaf development; m6A modification
    DOI:  https://doi.org/10.3390/ijms23179887
  22. Front Oncol. 2022 ;12 927810
    Comprehensive analysis of m6A circRNAs identified in colorectal cancer by MeRIP sequencing.
    Feng He, Qin Guo, Guo-Xiu Jiang, Yan Zhou.
       Purpose: To characterize the entire profile of m6A modifications and differential expression patterns for circRNAs in colorectal cancer (CRC).
    Methods: First, High-throughput MeRIP-sequencing and RNA-sequencing was used to determine the difference in m6A methylome and expression of circRNA between CRC tissues and tumor-adjacent normal control (NC) tissues. Then, GO and KEGG analysis detected pathways involved in differentially methylated and differentially expressed circRNAs (DEGs). The correlations between m6A status and expression level were calculated using a Pearson correlation analysis. Next, the networks of circRNA-miRNA-mRNA were visualized using the Target Scan and miRanda software. Finally, We describe the relationship of distance between the m6A peak and internal ribosome entry site (IRES) and protein coding potential of circRNAs.
    Results: A total of 4340 m6A peaks of circRNAs in CRC tissue and 3216 m6A peaks of circRNAs in NC tissues were detected. A total of 2561 m6A circRNAs in CRC tissues and 2129 m6A circRNAs in NC tissues were detected. Pathway analysis detected that differentially methylated and expressed circRNAs were closely related to cancer. The conjoint analysis of MeRIP-seq and RNA-seq data discovered 30 circRNAs with differentially m6A methylated and synchronously differential expression. RT-qPCR showned circRNAs (has_circ_0032821, has_circ_0019079, has_circ_0093688) were upregulated and circRNAs (hsa_circ_0026782, hsa_circ_0108457) were downregulated in CRC. In the ceRNA network, the 10 hyper-up circRNAs were shown to be associated with 19 miRNAs and regulate 16 mRNAs, 14 hypo-down circRNAs were associated with 30 miRNAs and regulated 27 mRNAs. There was no significant correlation between the level of m6A and the expression of circRNAs. The distance between the m6A peak and IRES was not significantly related to the protein coding potential of circRNAs.
    Conclusion: Our study found that there were significant differences in the m6A methylation patterns of circRNAs between CRC and NC tissues. M6A methylation may affect circRNA-miRNA-mRNA co-expression in CRC and further affect the regulation of cancer-related target genes.
    Keywords:  CircRNA; M6A modification; MeRIP sequencing; RNA-Seq; colorectal cancer
    DOI:  https://doi.org/10.3389/fonc.2022.927810
  23. Front Genet. 2022 ;13 906880
    Integrated risk scores from N6-methyladenosine-related lncRNAs are potential biomarkers for predicting the overall survival of bladder cancer patients.
    Xin Huang, Hao-Fei Wang, Shuang Huang.
      Background: N6-methyladenosine (m6A) is the most common form of mRNA- and long noncoding RNA (lncRNA)-specific internal modification encountered in eukaryotes, with important effects on mRNA stability, translation, and splicing. The role of m6A-modified lncRNAs (m6A-lncRNAs) in bladder cancer (BLCA) is rarely reported. This study aimed to evaluate an efficient prognostic model of BLCA in patients, based on m6A-lncRNAs, and to discover potential biological targets. Methods: Differentially expressed lncRNAs were investigated in 433 BLCA samples derived from The Cancer Genome Atlas (TCGA) database. Kaplan-Meier and univariate Cox regression analyses were performed to screen for m6A-lncRNAs with prognostic roles in BLCA. We implemented Pearson correlation analysis to analyze 18 potentially prognostic lncRNAs and 20 known m6A-associated genes. Next, the data were imputed using least absolute shrinkage and selection operator (LASSO) Cox regression to establish an m6A-lncRNA prognostic signature. Results: We established an integrated risk score (RS) containing five m6A-lncRNAs and constructed a nomogram that had the ability to forecast the overall survival (OS) of patients with BLCA. We showed that the predictive accuracy of the RS for BLCA prognosis was high, which was confirmed by the area under the receiver operating characteristic (ROC) curve. We analyzed the correlation between tumor immune infiltrating cells and RS in high- and low-risk patients with BLCA and used tumor immune dysfunction and exclusion to predict the effect of immunotherapy. We screened out the most relevant modules of RS through the weighted gene co-expression network analysis network and explored their potential biological functions using GO and KEGG analyses. Conclusion: Our findings demonstrate that, compared with nomograms constructed using a single prognostic factor, the integrated RS represents a superior model for predicting survival in patients with BLCA, which may improve the clinical management of BLCA.
    Keywords:  N6-methyladenosine; bladder cancer; long noncoding RNA; prognostic signature; risk scores
    DOI:  https://doi.org/10.3389/fgene.2022.906880
  24. Biomark Res. 2022 Sep 07. 10(1): 68
    METTL1 promotes neuroblastoma development through m7G tRNA modification and selective oncogenic gene translation.
    Ying Huang, Jieyi Ma, Cuiyun Yang, Paijia Wei, Minghui Yang, Hui Han, Hua Dong Chen, Tianfang Yue, Shu Xiao, Xuanyu Chen, Zuoqing Li, Yanlai Tang, Jiesi Luo, Shuibin Lin, Libin Huang.
       BACKGROUND: Neuroblastoma (NBL) is the most common extra-cranial solid tumour in childhood, with prognosis ranging from spontaneous remission to high risk for rapid and fatal progression. Despite existing therapy approaches, the 5-year event-free survival (EFS) for patients with advanced NBL remains below 30%, emphasizing urgent necessary for novel therapeutic strategies. Studies have shown that epigenetic disorders play an essential role in the pathogenesis of NBL. However, the function and mechanism of N7-methylguanosine (m7G) methyltransferase in NBL remains unknown.
    METHODS: The expression levels of m7G tRNA methyltransferase Methyltransferase-like 1 (METTL1) were analyzed by querying the Gene Expression Omnibus (GEO) database and further confirmed by immunohistochemistry (IHC) assay. Kaplan-Meier, univariate and multivariate cox hazard analysis were performed to reveal the prognostic role of METTL1. Cell function assays were performed to evaluate how METTL1 works in proliferation, apoptosis and migration in cell lines and xenograft mouse models. The role of METTL1 on mRNA translation activity of NBL cells was measured using puromycin intake assay and polysome profiling assay. The m7G modified tRNAs were identified by tRNA reduction and cleavage sequencing (TRAC-seq). Ribosome nascent-chain complex-bound mRNA sequencing (RNC-seq) was utilized to identify the variation of gene translation efficiency (TE). Analyzed the codon frequency decoded by m7G tRNA to clarify the translation regulation and mechanism of m7G modification in NBL.
    RESULTS: This study found that METTL1 were significantly up-regulated in advanced NBL, which acted as an independent risk factor and predicted poor prognosis. Further in NBL cell lines and BALB/c-nu female mice, we found METTL1 played a crucial role in promoting NBL progression. Furthermore, m7G profiling and translation analysis revealed downregulation of METTL1 would inhibit puromycin intake efficiency of NBL cells, indicating that METTL1 did count crucially in regulation of NBL cell translation. With all tRNAs with m7G modification identified in NBL cells, knockdown of METTL1 would significantly reduce the levels of both m7G modification and m7G tRNAs expressions. Result of RNC-seq shew there were 339 overlapped genes with impaired translation in NBL cells upon METTL1 knockdown. Further analysis revealed these genes contained higher frequency of codons decoded by m7G-modified tRNAs and were enriched in oncogenic pathways.
    CONCLUSION: This study revealed the critical role and mechanism of METTL1-mediated tRNA m7G modification in regulating NBL progression, providing new insights for developing therapeutic approaches for NBL patients.
    Keywords:  Epigenetics; N7-methylguanosine; Neuroblastoma
    DOI:  https://doi.org/10.1186/s40364-022-00414-z
  25. Front Public Health. 2022 ;10 925303
    Association of N6-methyladenosine readers' genes variation and expression level with pulmonary tuberculosis.
    Hong-Miao Li, Fei Tang, Li-Jun Wang, Qian Huang, Hai-Feng Pan, Tian-Ping Zhang.
      N6-Methyladenosine (m6A) is associated with many biological processes and the development of multiple diseases. The aim of this study was to analyze the association of m6A readers' genes variation, as well as their expression levels, with pulmonary tuberculosis (PTB). A total of 11 single-nucleotide polymorphisms (SNPs) in m6A readers' genes (i.e., YTHDF1 rs6122103, rs6011668, YTHDF2 rs602345, rs3738067, YTHDF3 rs7464, rs12549833, YTHDC1 rs3813832, rs17592288, rs2293596, and YTHDC2 rs6594732, and rs2416282) were genotyped by SNPscan™ technique in 457 patients with PTB and 466 normal controls. The m6A readers' genes expression levels in peripheral blood mononuclear cells (PBMCs) from 78 patients with PTB and 86 normal controls were detected by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). There was no significant association between all SNPs in YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2 genes and PTB susceptibility. The increased frequencies of YTHDF2 rs3738067 GG genotype and YTHDC1 rs3813832 CC genotype, C allele, were, respectively, found in PTB patients with hypoproteinemia and fever. YTHDC2 rs6594732 variant was significantly associated with drug-induced liver damage and sputum smear-positive, and the rs2416282 variant was significantly associated with fever in patients with PTB. Compared with controls, the YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2 mRNA levels were significantly decreased in PTB. Moreover, YTHDF1 level was negatively associated with erythrocyte sedimentation rate (ESR), and YTHDF3 and YTHDC1 levels were negatively related to alanine aminotransferase (ALT) in patients with PTB. Our results demonstrated that YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2 genes SNPs did not contribute to PTB susceptibility, while their decreased levels in patients with PTB suggested that these m6A readers might play significant roles in PTB.
    Keywords:  N6-methyladenosine; epidemiology; infectious diseases; pulmonary tuberculosis; single-nucleotide polymorphisms
    DOI:  https://doi.org/10.3389/fpubh.2022.925303
  26. Mol Immunol. 2022 Sep 01. pii: S0161-5890(22)00411-4. [Epub ahead of print]151 1-10
    Critical role of m6A modification in T-helper cell disorders.
    Xue Chen, Xiaoliang Tong, Lu Zhou, Jian Huang, Lihua Gao, Jinrong Zeng, Lina Tan.
      Diseases with T-helper cell subset imbalance involve multiple systems and organs. In addition to this, the pathogenesis of these diseases is always complex, and involves Th1, Th2, Th9, Th17, Th22, and Tfh cells. T-helper cell subset imbalance mediates immune responses to various pathogenic factors, by secreting specific cytokines. Although several studies have revealed the specific mechanisms of the occurrence and development of these diseases from different aspects, there is still a need for more comprehensive and in-depth studies that can compensate for the corresponding gaps in the diagnosis, targeted therapy, and prognosis of these diseases. N6-methyladenosine(m6A) modification is the most prevalent and abundant post-transcriptional modification in eukaryotic RNAs. In recent years, the critical role of m6A modification has been confirmed in multiple diseases with T-helper cell subset imbalance. m6A modification affects the immune cell development, inflammatory processes, biological behaviour of tumours, and immune response in these diseases. In this review, we focussed on how the enzymes involved in m6A modification, directly or indirectly, influence the pathogenesis and phenotype of various diseases with T-helper cell subset imbalance, and could therefore, serve as potential diagnostic markers and therapeutic targets for these diseases. In addition, this review also discusses the focus of future research in this area. Finally, we summarise the prospects of m6A modification in immunotherapy and chemotherapy.
    Keywords:  Immune; M(6)A modification; T-helper cell; Th1 cells; Th17 cells; Th2 cells
    DOI:  https://doi.org/10.1016/j.molimm.2022.08.015
  27. Mol Cancer Res. 2022 Sep 08. pii: MCR-22-0231. [Epub ahead of print]
    TFAP4 activates IGF2BP1 and promotes progression of non-small cell lung cancer by stabilizing TK1 expression through m6A modification.
    Qiming Shen, Zhe Xu, Guanghao Sun, Haoyou Wang, Lin Zhang.
      Non-small cell lung cancer (NSCLC) is a well-known global health concern. TFAP4 has been reported to function as an oncogene. This study sought to investigate the molecular mechanism of TFAP4 in NSCLC development. Significantly highly-expressed gene IGF2BP1 was screened on online databases and its downstream gene TK1 was predicted. IGF2BP1 promoter sequence was identified. The binding site of TFAP4 and IGF2BP1 was predicted. The expression correlations among TFAP4, IGF2BP1, and TK1 were confirmed. The correlations between TFAP4, IGF2BP1, TK1, and NSCLC prognosis were predicted. NSCLC and paracancerous tissues were collected. The expressions of TFAP4, IGF2BP1, and TK1 were detected. NSCLC cell proliferation, migration, invasion, and apoptosis were detected. The binding of TFAP4 to the IGF2BP1 promoter was verified. m6A modification of TK1 mRNA was detected. The correlation between IGF2BP1 and TK1 was confirmed. A subcutaneous tumor xenograft model was established to validate the effect of TFAP4 in vivo. IGF2BP1 was highly expressed in NSCLC tissues and cells. IGF2BP1 knockdown repressed NSCLC cell proliferation, migration, and invasion and facilitated apoptosis. Mechanically, TFAP4 transcriptionally activated IGF2BP1. IGF2BP1 stabilized TK1 expression via m6A modification and promoted NSCLC cell proliferation, migration, and invasion. In vivo experiments confirmed that TFAP4 knockdown suppressed tumor growth by down-regulating IGF2BP1/TK1. Implications: Our findings revealed that TFAP4 activated IGF2BP1 and facilitated NSCLC progression by stabilizing TK1 expression via m6A modification, which offered new insights into the diagnosis and treatment of NSCLC.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-22-0231
  28. Front Cell Dev Biol. 2022 ;10 975684
    An m5C methylation regulator-associated signature predicts prognosis and therapy response in pancreatic cancer.
    Duo Yun, Zhirong Yang, Shuman Zhang, Hai Yang, Dongxue Liu, Robert Grützmann, Christian Pilarsky, Nathalie Britzen-Laurent.
      Pancreatic ductal adenocarcinoma (PDAC) is the most aggressive digestive malignancy due to frequent late-stage diagnosis, rapid progression and resistance to therapy. With increasing PDAC incidence worldwide, there is an urgent need for new prognostic biomarkers and therapy targets. Recently, RNA methylation has emerged as a new tumorigenic mechanism in different cancers. 5-methylcytosine (m5C) is one of the most frequent RNA modifications and occurs on a variety of RNA species including mRNA, thereby regulating gene expression. Here we investigated the prognostic role of m5C-regulator-associated transcriptional signature in PDAC. We evaluated m5C-regulator status and expression in 239 PDAC samples from publicly available datasets. We used unsupervised consensus clustering analyses to classify PDACs based on m5C-regulator expression. From the resulting signature of differentially expressed genes (DEGs), we selected prognosis-relevant DEGs to stratify patients and build a scoring signature (m5C-score) through LASSO and multivariate Cox regression analyses. The m5C-score represented a highly significant independent prognostic marker. A high m5C-score correlated with poor prognosis in different PDAC cohorts, and was associated with the squamous/basal subtype as well as activated cancer-related pathways including Ras, MAPK and PI3K pathways. Furthermore, the m5C-score correlated with sensitivity to pathway-specific inhibitors of PARP, EGFR, AKT, HER2 and mTOR. Tumors with high m5C-score were characterized by overall immune exclusion, low CD8+ T-cell infiltration, and higher PD-L1 expression. Overall, the m5C-score represented a robust predictor of prognosis and therapy response in PDAC, which was associated with unfavorable molecular subtypes and immune microenvironment.
    Keywords:  5-methylcytosine (m5C); immune cells infiltration; pancreatic cancer; prognosis; targeted drug therapy; tumor microenvironment (TME)
    DOI:  https://doi.org/10.3389/fcell.2022.975684
  29. World J Surg Oncol. 2022 Sep 05. 20(1): 283
    Increased expression of METTL3 in pancreatic cancer tissues associates with poor survival of the patients.
    Yuan Li, Hao Huang, Yulan Zhu, Bin Xu, Junjun Chen, Yingting Liu, Xiao Zheng, Lujun Chen.
       BACKGROUND: Methyltransferase-like 3 (METTL3) expression could be found in various normal and cancerous tissues. As of now, the clinical significance of METTL3 expression in human pancreatic cancer (PC) tissues still remains to be understood. Our present study aims to investigate the prognostic value and clinical implications of METTL3 expression in PC tissues.
    METHODS: The TCGA, GTEx, and GEO public databases were used to study the mRNA expression level of the m6A family members and its relationship among PC tissues and normal pancreatic tissue. The immunohistochemistry was used to analyze the difference of METTL3 expression between cancer tissues and adjacent normal tissues. The prognostic value was evaluated by using the Log-rank survival analysis and Cox model analysis. PAAD samples from TCGA and GEO databases were used to perform the immune infiltration analysis and gene set enrichment analysis based on the genes that were highly correlated with METTL3.
    RESULTS: Based on the analysis of TCGA, GTEx, and GEO public database, we found that the m6A family members showed a higher correlation in PC tissues compared to normal pancreatic tissues, and the mRNA expression level of the m6A family members showed a significant difference between PC tissues and adjacent normal tissues. Moreover, scRNA-seq data indicated that METTL3 showed a higher expression level in malignant epithelial cells. Our immunohistochemistry results also confirmed that the intensity of METTL3 immunostaining in PC tissues was significantly higher than that in adjacent normal tissues (P = 0.015). The overall survival (OS) of PC patients with high expression of METTL3 protein were significantly poorer than those with low expression of METTL3 protein (HR = 1.788, 95% CI 1.071-2.984, P = 0.026). Further analysis of PC data from the database showed that METTL3 expression was associated with a variety of tumor-infiltrating immune cells and was involved in m6A modification and metabolism in PC tissues.
    CONCLUSION: Increased METTL3 expression at the protein level could be found in PC tissues, suggesting that the METTL3 expression was involved in the progression of PC and could serve as an important marker for prognostic prediction of this malignancy.
    Keywords:  Immunohistochemistry; METTL3; Pancreatic cancer; Prognosis
    DOI:  https://doi.org/10.1186/s12957-022-02743-7
  30. Eur Rev Med Pharmacol Sci. 2022 Aug;pii: 29526. [Epub ahead of print]26(16): 5868-5883
    The prognostic value and immune landscapes of m1A/m5C/m6A-associated lncRNA signature in osteosarcoma.
    Z-Y Wu, Z-Y Shi.
       OBJECTIVE: RNA methylation modifications, mainly including N1-methyladenosine (m1A), 5-methylcytosine (m5C), and N6-methyladenosine (m6A), are widely existed in osteosarcoma and involved in the biological processes of cancers. However, there is still no study regarding the relationship between osteosarcoma and m1A/m5C/m6A-associated long non-coding RNAs (lncRNAs).
    PATIENTS AND METHODS: Here, expression data of osteosarcoma from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database were retrieved to identify ER-related lncRNAs associated with the overall survival (OS) of osteosarcoma patients. Then, Lasso penalized Cox regression analysis was applied to construct a lncRNAs risk signature. Meanwhile, patients were stratified into two clusters based on the identified m1A/m5C/m6A-associated lncRNAs. The prognostic value and immune landscape of the identified signature and clusters were further evaluated.
    RESULTS: Two m1A/m5C/m6A-associated lncRNAs were incorporated into our risk signature. The functional analyses indicated that the prognostic model was correlated with patient survival, and cancer metastasis and growth. Meanwhile, the signature model was significantly associated with the infiltration of immune cells, immune microenvironment, as well as several immune checkpoint genes. Similar results were detected for the lncRNAs clusters, which were significantly correlated with immune infiltration, cancer microenvironment, and immune-associated genes, and contributed to predicting the prognosis of patients. Moreover, our risk signature and clusters might help guide the application of immunotherapeutic drugs for osteosarcoma patients. Finally, a nomogram based on the risk score was established.
    CONCLUSIONS: Overall, a risk signature based on two m1A/m5C/m6A-associated lncRNAs was generated and presented predictive value for the prognosis and immune landscapes of osteosarcoma patients. This signature can be further used in the development of novel therapeutic strategies for osteosarcoma.
    DOI:  https://doi.org/10.26355/eurrev_202208_29526
  31. J Immunol Res. 2022 ;2022 7519838
    Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System.
    Chundi Gao, Huayao Li, Wenzhe Ma, Qiming Zhang, Cun Liu, Lijuan Liu, Jing Zhuang, Changgang Sun.
      The recent application of targeted immunotherapy has greatly improved the clinical outcomes of patients with lung adenocarcinoma (LUAD), but drug resistance continues to emerge, and to evaluate and to improve patient prognosis are arduous. The diagnostic and prognostic value of N6-methyladenosine (M6A) in LUAD has attracted increasing attention. We systematically studied correlations among important M6A methylation regulators, tumor mutational burden (TMB), and immune infiltration in clinical and sequencing data from the LUAD cohort of the cancer genome map (TCGA). The molecular subtype clusters 1 and 2 were identified by the consensus clustering of 16 M6A regulatory factors. Clinical prognosis, M6A regulatory factor expression, TMB, pathway enrichment, and immune cell infiltration significantly differed between clusters 1 and 2. Compared with other clinical traits, a prognostic risk score system constructed using the M6A regulatory factors HNRNPA2B1 and HNRNPC can serve as an independent prognostic method for LUAD, with higher predictive sensitivity and specificity. Risk scores were significantly higher for cluster 2 than 1, which was consistent with the trend towards a better prognosis in cluster 1. Overall, our findings revealed an important role of M6A methylation regulators in LUAD, and our risk scoring system involving these regulators might help to screen groups at high risk for LUAD and provide important theoretical bioinformatic support for evaluating the prognosis of such patients.
    DOI:  https://doi.org/10.1155/2022/7519838
  32. Front Genet. 2022 ;13 916400
    Oncogenic signaling pathway dysregulation landscape reveals the role of pathways at multiple omics levels in pan-cancer.
    Na Wang, Dan-Ni He, Zhe-Yu Wu, Xu Zhu, Xiao-Ling Wen, Xu-Hua Li, Yu Guo, Hong-Jiu Wang, Zhen-Zhen Wang.
      Dysregulation of signaling pathways plays an essential role in cancer. However, there is not a comprehensive understanding on how oncogenic signaling pathways affect the occurrence and development with a common molecular mechanism of pan-cancer. Here, we investigated the oncogenic signaling pathway dysregulation by using multi-omics data on patients from TCGA from a pan-cancer perspective to identify commonalities across different cancer types. First, the pathway dysregulation profile was constructed by integrating typical oncogenic signaling pathways and the gene expression of TCGA samples, and four molecular subtypes with significant phenotypic and clinical differences induced by different oncogenic signaling pathways were identified: TGF-β+ subtype; cell cycle, MYC, and NF2- subtype; cell cycle and TP53+ subtype; and TGF-β and TP53- subtype. Patients in the TGF-β+ subtype have the best prognosis; meanwhile, the TGF-β+ subtype is associated with hypomethylation. Moreover, there is a higher level of immune cell infiltration but a slightly worse survival prognosis in the cell cycle, MYC, and NF2- subtype patients due to the effect of T-cell dysfunction. Then, the prognosis and subtype classifiers constructed by differential genes on a multi-omics level show great performance, indicating that these genes can be considered as biomarkers with potential therapeutic and prognostic significance for cancers. In summary, our study identified four oncogenic signaling pathway-driven patterns presented as molecular subtypes and their related potential prognostic biomarkers by integrating multiple omics data. Our discovery provides a perspective for understanding the role of oncogenic signaling pathways in pan-cancer.
    Keywords:  biomarkers; dysregulation landscape; molecular subtypes; multi-omics; pan-cancer; signaling pathways
    DOI:  https://doi.org/10.3389/fgene.2022.916400
  33. Reprod Sci. 2022 Sep 08.
    Landscape and Construction of a Novel N6-methyladenosine-related LncRNAs in Cervical Cancer.
    Xin Liu, Weijie Zhang, Jun Wan, Diming Xiao, Ming Wei.
      Cervical cancer is a crucial clinical problem with high mortality. Despite much research in therapy, the prognosis of patients with cervical cancer is still not ideal. The data on cervical cancer were downloaded from The Cancer Genome Atlas (TCGA) portal. R language was used to screen out the N6-methyladenosine (m6A)-related lncRNAs (long non-coding RNA). A consensus clustering algorithm was performed to identify m6A-related lncRNAs in cervical cancer; 10 m6A-related lncRNAs showing a significant association with survival were filtrated through a gradually univariate Cox regression model, least absolute shrinkage and selection operator (LASSO) algorithm, and multivariate Cox regression preliminarily. Furthermore, we conducted Kaplan-Meier curves, receiver operating curve (ROC) analyses, and proportional hazards model to quantify the underlying character of the m6A-related model in the prevision of cervical cancer patients. Gene set enrichment analysis (GSEA) was used to explore several pathways significantly. Finally, cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) was applied to estimate the immune cell infiltration in the profiling. In the present study, 10 m6A-related lncRNAs make up our prediction model. This prediction model can do duty for an independent predictive biomolecular element. Subsequently, we then found that the model was still valid in further validation of the training group and the test group. Our signature was correlated with immune cell infiltration and partial signaling pathway. These lncRNAs played a no negligible biomolecular role in contributing to the prognosis of cervical cancer.
    Keywords:  Cervical cancer; N6-methyladenosine; Prognosis; The Cancer Genome Atlas; lncRNA
    DOI:  https://doi.org/10.1007/s43032-022-01074-y
  34. Int J Mol Sci. 2022 Sep 02. pii: 10013. [Epub ahead of print]23(17):
    Functional Characterization of Two RNA Methyltransferase Genes METTL3 and METTL14 Uncovers the Roles of m6A in Mediating Adaptation of Plutella xylostella to Host Plants.
    Bei-Bei Wang, Ying-Fang Lai, Fei-Fei Li, Lu Jiao, Qing-Xuan Qiao, Shan-Yu Li, Xiu-Juan Xiang, Huang Liao, Min-Sheng You, Wei-Yi He.
      N6-methyladenosine (m6A) is one of the major epigenetic modifications in eukaryotes. Although increasing functions of m6A have been identified in insects, its role in Plutella xylostella L. for host plant adaptation remains unclear. In the current study, we show that the m6A content of P. xylostella was relatively low in different developmental stages and tissues, with no significant differences. Two RNA methyltransferase genes, PxMETTL3 (methyltransferase-like 3) and PxMETTL14 (methyltransferase-like 14), were identified and characterized. PxMETTL3 could be transcribed into two transcripts, and PxMETTL14 had only one transcript; both of these genes were highly expressed in egg and adult stages and reproductive tissues. The CRISPR/Cas9-mediated knockout of PxMETTL3 (ΔPxMETTL3-2) or PxMETTL14 (ΔPxMETTL14-14) confirmed their function in m6A installation into RNA. Furthermore, upon transfer from an artificial diet to the host plant, the mutant strains were affected in terms of larval and pupal weight or adult emergence rate, while the wildtype (WT) strain did not exhibit any difference. In addition, the fecundity and egg hatching rate of the WT strain decreased significantly, whereas only the ΔPxMETTL14-14 mutant strain displayed significantly decreased fecundity. There seemed to be a tradeoff between the stress adaptation and reproduction in P. xylostella mediated by m6A modification. During host transfer, the expression of PxMETTL14 was consistent with the change in m6A content, which implied that PxMETTL14 could respond to host plant defense effectively, and may regulate m6A content. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the differentially expressed transcripts with changes in m6A levels revealed that the potential functions of m6A-related genes may be involved in steroid biosynthesis for larval performance and metabolic pathways for adult reproduction. Overall, our work reveals an epigenetic regulation mechanism for the rapid adaptation of P. xylostella to variations in the host environment.
    Keywords:  N6-methyladenosine; Plutella xylostella; RNA methyltransferase; host adaptation
    DOI:  https://doi.org/10.3390/ijms231710013
  35. J Hematol Oncol. 2022 Sep 06. 15(1): 128
    Hypoxia-induced exosomal circPDK1 promotes pancreatic cancer glycolysis via c-myc activation by modulating miR-628-3p/BPTF axis and degrading BIN1.
    Jiewei Lin, Xinjing Wang, Shuyu Zhai, Minmin Shi, Chenghong Peng, Xiaxing Deng, Da Fu, Jiancheng Wang, Baiyong Shen.
       BACKGROUND: circRNA has been established to play a pivotal role in tumorigenesis development in a variety of cancers; nevertheless, the biological functions and molecular mechanisms of hypoxia-induced exosomal circRNAs in pancreatic cancer remain largely unknown.
    METHODS: Differentially expressed circRNAs in exosomes between hypoxic exosomes and normoxic exosomes in PC cells were verified by RNA sequencing. The expression of circPDK1 in PC tumors and PC patients was evaluated by qRT-PCR and ISH, and the biological functions of circPDK1 in PC were verified through a series of in vitro and in vivo experiments. Using Western blotting, Co-IP, RNA pull-down, ChIP, RIP, dual-luciferase assays, and rescue experiments, the underlying mechanism of circPDK1 was verified.
    RESULTS: CircPDK1 was highly abundant in PC tumor tissues and serum exosomes and was associated with poor survival. Exosomal circPDK1 significantly promoted PC cell proliferation, migration, and glycolysis both in vitro and in vivo. Mechanistically, circPDK1 could be activated by HIF1A at the transcriptional level and sponges miR-628-3p to activate the BPTF/c-myc axis. In addition, circPDK1 serves as a scaffold that enhances the interaction between UBE2O and BIN1, inducing the UBE2O-mediated degradation of BIN1.
    CONCLUSIONS: We found that circPDK1 was activated by HIF1A at the transcriptional level by modulating the miR-628-3p/BPTF axis and degrading BIN1. Exosomal circPDK1 is a promising biomarker for PC diagnosis and prognosis and represents a potential therapeutic target for PC.
    Keywords:  Exosomes; Hypoxia; Pancreatic cancer; Ubiquitination; ceRNA; circRNA
    DOI:  https://doi.org/10.1186/s13045-022-01348-7
  36. Environ Pollut. 2022 Sep 06. pii: S0269-7491(22)01326-4. [Epub ahead of print] 120112
    Combination of high-fat diet and cadmium impairs testicular spermatogenesis in an m6A-YTHDF2-dependent manner.
    Yong-Wei Xiong, Lu-Lu Tan, Jin Zhang, Hua-Long Zhu, Xin-Mei Zheng, Wei Chang, Lan Gao, Tian Wei, De-Xiang Xu, Hua Wang.
      Environmental cadmium (Cd) or high-fat diet (HFD) exposure alone are risk factors of male infertility. However, the effect and mechanism of co-exposure to HFD and Cd on sperm quality remain unclear. This study was aimed to explore the combined effects of HFD and Cd on spermatogenesis as well as its m6A-dependent mechanism in vivo and in vitro. As a result, co-exposure of HFD and Cd resulted in a significant decrease in the number of mature testicular seminiferous tubules and epididymis sperm quantity in mice, compared with Cd or HFD exposure alone. Correspondingly, the mRNAs expression of Smc3(spermatocytes marker), Acrv1(round spermatids marker) and Lzumo3(elongated spermatids marker) were downregulated in HFD and Cd group. Furthermore, combined exposure downregulated the expression of meiosis-related proteins (STRA8 and SYCP3), increased the m6A level of Stra8, and upregulated the expression of m6A-related proteins (METTL3 and YTHDF2) in mouse spermatocytes. Mechanistically, the above-mentioned impacts caused by co-exposure were markedly restored by Mettl3 siR and Ythdf2 siR. In addition, RNA stability assay showed that Ythdf2 siR obviously reversed co-exposure-increased Stra8 mRNA degradation rate in actinomycin-D-treated mouse spermatocytes. Meanwhile, excess ROS was observed in combined-exposure group, and a free radical scavenger N-tert-Butyl-α-phenylnitrone (PBN) attenuated co-exposure-upregulated expression of METTL3 and YTHDF2 in mouse spermatocytes. These results suggested that combination of HFD and Cd impaired spermatogenesis by degrading Stra8 in an m6A-YTHDF2-dependent manner via ROS activation.
    Keywords:  Cadmium; High-fat diet; Spermatogenesis; YTHDF2; m6A
    DOI:  https://doi.org/10.1016/j.envpol.2022.120112
  37. Arch Biochem Biophys. 2022 Sep 05. pii: S0003-9861(22)00273-9. [Epub ahead of print] 109389
    E6E7 regulates the HK2 expression in cervical cancer via GSK3β/FTO signal.
    Chunyan Liu, Yangyang Li, Changyan Dong, Luyun Qu, Ying Zuo.
       BACKGROUND: Cervical cancer is one of the most common cancers in women worldwide. Hexokinase 2 (HK2) is responsible for phosphorylating glucose into glucose-6-phosphate, which is required for tumorigenesis and metastasis.
    METHODS: E6E7 and FTO were exogenously expressed, and their effects on HK2 mRNA and protein levels were detected by RT-qPCR and Western blot.
    RESULTS: The exogenous expression of E6E7 in SiHa and C33A cells up-regulated the mRNA and protein levels of intracellular HK2, up-regulated the total m6A levels, changed the expression of m6A proteins and activated the GSK3β transcription. The expression levels of METTL3 and WTAP were enhanced, whereas the expression of FTO and ALKBH5 were decreased. In addition, FTO down-regulated the mRNA and protein levels of HK2. FTO overexpression partially inhibited the up-regulated expression of HK2 caused by E6E7. Furthermore, FTO overexpression increased the level of HK2 pre-mRNA in the nucleus and decreased the level of mature HK2 mRNA in the cytoplasm. We also found that GSK3β overexpression enhanced FTO ubiquitination and decreased FTO protein levels.
    CONCLUSION: This study found that E6E7 oncogene activates the transcription of GSK3β; GSK3β can promote the ubiquitination-proteasomal degradation of FTO and reduce the level of FTO protein; FTO inhibits the maturation and translation of HK2 mRNA by retaining HK2 pre-mRNA in the nucleus.
    Keywords:  E6E7 oncogene; Kinase; Nuclear retention; Ubiquitination-proteasomal degradation
    DOI:  https://doi.org/10.1016/j.abb.2022.109389
  38. Cell Mol Gastroenterol Hepatol. 2022 Sep 01. pii: S2352-345X(22)00192-8. [Epub ahead of print]
    DNA 6mA Demethylase ALKBH1 Orchestrates Fatty Acid Metabolism and Suppresses Diet-induced Hepatic Steatosis.
    Liping Luo, Ya Liu, Paul Nizigiyimana, Mingsheng Ye, Ye Xiao, Qi Guo, Tian Su, Xianghang Luo, Yan Huang, Haiyan Zhou.
       BACKGROUND & AIMS: Nonalcoholic fatty liver disease (NAFLD) is a major cause of liver-related morbidity and mortality whereas the pathogenic mechanism remains largely elusive. DNA 6mA modification is recently identified epigenetic mark indicative of transcription in eukaryotic genomes. Here, we aimed to investigate the role and mechanism of DNA 6mA modification in NAFLD progression.
    METHODS: Dot blot and immunohistochemistry were used to detect DNA 6mA levels. Liver-specific ALKBH1 knockout mice and mice with ALKBH1 overexpression in liver were subjected to high-fat diet or methionine choline-deficient diet to evaluate the critical role of ALKBH1-demethylated DNA 6mA modification in the pathogenesis of hepatic steatosis during NAFLD. RNA sequencing and ChIP sequencing were performed to investigate molecular mechanisms underlying this process.
    RESULTS: DNA 6mA level was significantly increased with hepatic steatosis, while ALKBH1 expression was markedly downregulated in both mouse and human fatty liver. Deletion of ALKBH1 in hepatocytes elevated genomic 6mA levels and accelerated diet-induced hepatic steatosis and metabolic dysfunction. Comprehensive analyses of transcriptome and ChIP sequencing data indicated that ALKBH1 directly bound to and exclusively demethylated 6mA levels of genes involved in fatty acid uptake and lipogenesis, leading to reduced hepatic lipid accumulation. Importantly, ALKBH1 overexpression was sufficient to suppressed lipid uptake and synthesis, and alleviated diet-induced hepatic steatosis and insulin resistance.
    CONCLUSIONS: Our findings reveal an indispensable role of ALKBH1 as an epigenetic suppressor of DNA 6mA in hepatic fatty acid metabolism and offer a potential therapeutic target for NAFLD treatment.
    Keywords:  ALKBH1; DNA 6mA; demethylation; fatty liver; lipid metabolism
    DOI:  https://doi.org/10.1016/j.jcmgh.2022.08.011
  39. Pathol Oncol Res. 2022 ;28 1610504
    A Comprehensive Bioinformatic Analysis for Identification of Myeloid-Associated Differentiation Marker as a Potential Negative Prognostic Biomarker in Non-Small-Cell Lung Cancer.
    Min Zhou, Yan Chen, Xuyu Gu, Cailian Wang.
      Objectives: This study aimed to identify a molecular marker associated with the prognosis of non-small-cell lung cancer (NSCLC). Materials and Methods: The RNA sequencing data and clinical information of NSCLC patients were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO). The weighted gene co-expression network analysis (WGCNA) was used to identify the co-expression gene modules and differentially expressed genes (DEGs) by comparing gene expression between NSCLC tumor tissues and normal tissues. Subsequently, the functional enrichment analysis of the DEGs was performed. Kaplan-Meier survival analysis and the GEPIA2 online tool were performed to investigate the relationship between the expression of these genes of interest and the survival of NSCLC patients, and to validate one most survival-relevent hub gene, as well as validated the hub gene using independent datasets from the GEO database. Further analysis was carried out to characterize the relationship between the hub gene and tumor immune cell infiltration, tumor mutation burden (TMB), microsatellite instability (MSI), and other known biomarkers of lung cancer. The related genes were screened by analyzing the protein-protein interaction (PPI) network and the survival model was constructed. GEPIA2 was applied in the potential analysis of pan-cancer biomarker of hub gene. Results: 57 hub genes were found to be involved in intercellular connectivity from the 779 identified differentially co-expressed genes. Myeloid-associated differentiation marker (MYADM) was strongly associated with overall survival (OS) and disease-free survival (DFS) of NSCLC patients, and high MYADM expression was associated with poor prognosis. Thus, MYADM was identified as a risk factor. Additionally, MYADM was validated as a survival risk factor in NSCLC patients in two independent datasets. Further analysis showed that MYADM was nagetively associated with TMB, and was positively correlated with macrophages, neutrophils, and dendritic cells, suggesting its role in regulating tumor immunity. The MYADM expression differed across many types of cancer and had the potential to serve as a pan-cancer marker. Conclusion: MYADM is an independent prognostic factor for NSCLC patients, which can predict the progression of cancer and play a role in the tumor immune cell infiltration in NSCLC.
    Keywords:  MYADM; NSCLC; bioinformatics; biomarker; survival-related gene
    DOI:  https://doi.org/10.3389/pore.2022.1610504
  40. iScience. 2022 Sep 16. 25(9): 104892
    Substrate spectrum of PPM1D in the cellular response to DNA double-strand breaks.
    Justus F Gräf, Ivan Mikicic, Xiaofei Ping, Claudia Scalera, Katharina Mayr, Lukas S Stelzl, Petra Beli, Sebastian A Wagner.
      PPM1D is a p53-regulated protein phosphatase that modulates the DNA damage response (DDR) and is frequently altered in cancer. Here, we employed chemical inhibition of PPM1D and quantitative mass spectrometry-based phosphoproteomics to identify the substrates of PPM1D upon induction of DNA double-strand breaks (DSBs) by etoposide. We identified 73 putative PPM1D substrates that are involved in DNA repair, regulation of transcription, and RNA processing. One-third of DSB-induced S/TQ phosphorylation sites are dephosphorylated by PPM1D, demonstrating that PPM1D only partially counteracts ATM/ATR/DNA-PK signaling. PPM1D-targeted phosphorylation sites are found in a specific amino acid sequence motif that is characterized by glutamic acid residues, high intrinsic disorder, and poor evolutionary conservation. We identified a functionally uncharacterized protein Kanadaptin as ATM and PPM1D substrate upon DSB induction. We propose that PPM1D plays a role during the response to DSBs by regulating the phosphorylation of DNA- and RNA-binding proteins in intrinsically disordered regions.
    Keywords:  Biochemistry; cancer; molecular biology; proteomics
    DOI:  https://doi.org/10.1016/j.isci.2022.104892
  41. Eye Vis (Lond). 2022 Sep 05. 9(1): 35
    TRIM46 aggravated high glucose-induced hyper permeability and inflammatory response in human retinal capillary endothelial cells by promoting IκBα ubiquitination.
    Hangqi Shen, Qiaoyun Gong, Jingting Zhang, Haiyan Wang, Qinghua Qiu, Jingfa Zhang, Dawei Luo.
       BACKGROUND: Diabetic retinopathy (DR) as a severe diabetic complication contributes to blindness. The increased permeability of retinal capillary endothelial cells (RCECs) as well as the production of inflammatory markers are closely related to DR occurrence. We recently revealed that TRIM46 promotes high glucose (HG)-caused ferroptosis in human RCECs (HRCECs). The current study aims to explore the molecular mechanism of how TRIM46 plays its role in DR progression.
    METHODS: Western blot was utilized to determine protein expression. The cell counting kit-8 assay was used to observe cell viability. The permeability of the cell layer was determined by measuring the transepithelial electrical resistance and fluorescein isothiocyanate (FITC)-dextran leak. Enzyme-linked immunosorbent assay was used to quantify the protein level of pro-inflammatory cytokines and co-immunoprecipitation was employed to verify the relationship between TRIM46 and IκBα.
    RESULTS: HG dramatically upregulated TRIM46 protein expression in a dose-dependent way. Silencing TRIM46 effectively reversed HG-induced cell growth inhibition, cell cycle arrest, hyper permeability and pro-inflammatory cytokines secretion in HRCECs, while overexpression of TRIM46 exhibited an opposite effect. Furthermore, TRIM46 was able to interact with IκBα and promote the ubiquitination and degradation of IκBα. IκBα overexpression recovered the effects of TRIM46 overexpression in HRCECs. Furthermore, inhibiting the activation of NF-κB partially recovered HG-induced HRCEC injury, whereas TRIM46 overexpression reversed these effects.
    CONCLUSION: This study demonstrates that TRIM46 interacts with IκBα to activate the NF-κB signaling pathway, thereby enhancing cell proliferation inhibition, hyper permeability and the inflammatory response of HRCECs in a HG state.
    Keywords:  Diabetic retinopathy; IκBα; NF-κB; TRIM46; Ubiquitination
    DOI:  https://doi.org/10.1186/s40662-022-00305-2
  42. J Oncol. 2022 ;2022 1028851
    CircEPSTI1 Promotes the Proliferation of HER2-Positive Breast Cancer Cells via circEPSTI1/miR-145/ERBB3 Axis.
    Yue Zhang, Duxun Tan, Yi Xie, Linyu Wu, Song Wu, Yuhui Tang, Yongzhou Luo, Xiangsheng Xiao, Xing Li.
      Breast cancer is the most common type of cancer worldwide. There are great challenges in the prevention and treatment of breast cancer. In this study, we explored the molecular and biological mechanisms of circular RNA circEPSTI1 (has_circ_0000479) in the regulation of HER2-positive breast cancer cells. The expression of CircEPSTI1, microRNA miR-145, and ERBB3 in HER2-positive breast cancer cells was evaluated by qRT-PCR and western blot assays. Cell proliferation was assessed by CCK-8. Wound-healing and transwell migration assays were performed to evaluate cell migration. A transwell invasion assay was performed to detect cell invasion. The interaction of miR-145, circEPSTI1, and ERBB3 was confirmed bydual-luciferase reporter and RIP assays. CircEPSTI1 was upregulated in the HER2-positive breast cancer tissues and cells. Knockdown of circEPSTI1 inhibited SKBR3 and BT474 cell proliferation, migration, and invasion. Mechanistically, circEPSTI1 directly targeted miR-145, and miR-145 was a downstream mediator of circEPSTI1 in modulating the proliferation, migration, and invasion of SKBR3 and BT474 cells. ERBB3 was identified as a direct and functional target of miR-145 in HER2-positive breast cancer cells. Our findings demonstrate that circEPSTI1, an overexpressed circRNA in HER2-positive breast cancer, promotes the proliferation, migration, and invasion of SKBR3 and BT474 cells through the miR-145/ERBB3 axis.
    DOI:  https://doi.org/10.1155/2022/1028851
  43. Cancer Cell Int. 2022 Sep 06. 22(1): 278
    TRIM36 inhibits tumorigenesis through the Wnt/β-catenin pathway and promotes caspase-dependent apoptosis in hepatocellular carcinoma.
    Qing Tong, Mingyu Yi, Panpan Kong, Lin Xu, Wukui Huang, Yue Niu, Xiaojing Gan, Huan Zhan, Rui Tian, Dong Yan.
       BACKGROUND: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and has an extremely poor prognosis. We aimed to determine the latent relationships between TRIM36 regulation of apoptosis and the Wnt/β-catenin pathway in HCC.
    METHODS: Immunohistochemistry and western blotting were used to characterize the aberrant expression of TRIM36 in HCC and adjacent tissues. Clinical information was analyzed using Kaplan-Meier and Cox methods. RNA-seq of potential targets was conducted to detect the regulation of TRIM36. Apoptosis assays and cellular proliferation, invasion and migration were conducted in a loss- and gain-of-function manner in cultured cells to determine the biological functions of TRIM36. A rescue experiment was conducted to confirm the role of Wnt/β-catenin signaling in TRIM36 regulation. Finally, in vivo experiments were conducted using cell line-derived xenografts in nude mice to validate the central role of TRIM36 in HCC.
    RESULTS: TRIM36 expression was significantly downregulated in HCC tissues compared to adjacent non-tumor tissues. TRIM36 repressed the proliferation, migration, and invasion of Huh7 and HCCLM3 cells, whereas it stimulated apoptosis. Wnt/β-catenin signaling was inhibited by TRIM36, and rescue experiments highlighted its importance in HCC proliferation, migration, and invasion. In vivo experiments further confirmed the effects of sh-TRIM36 on HCC tumorigenesis, inhibition of apoptosis, and promotion of Wnt/β-catenin signaling.
    CONCLUSION: Our study is the first to indicate that TRIM36 acts as a tumor suppressor in HCC. TRIM36 activates apoptosis and inhibits cellular proliferation, invasion, and migration via the Wnt/β-catenin pathway, which may serve as an important biomarker and promising therapeutic target for HCC.
    Keywords:  Apoptosis; Caspase-3; Caspase-7; RNA-seq; TRIM36; Wnt/β-catenin pathway
    DOI:  https://doi.org/10.1186/s12935-022-02692-x
  44. Cell Cycle. 2022 Sep 07. 1-15
    circRNA PLOD2 promotes tumorigenesis and Warburg effect in colon cancer by the miR-513a-5p/SIX1/LDHA axis.
    Yingjia Li, Hongbing Ma.
      Increasing evidence has proved that circRNAs might act as potential biomarkers for tumor diagnosis and prognosis. However, the functions and mechanisms of multiple circRNAs in colon cancer remains unclear. Here, we found circPLOD2 was dramatically upregulated in colon cancer tissue and cell lines. In vitro CCK-8, colony formation and transwell assays, and in vivo tumor transplantation assay were performed and explored that circPLOD2 might promote tumor proliferation, migration and invasion in vitro and in vivo. Moreover, based on the analysis of RNA pull-down, RNA immunoprecipitation, luciferase and rescued assays, we confirmed that the interactions between circPLOD2, miR-513a-5p and SIX1. It suggested that circPLOD2 acted as a sponge of miR-513a-5p to regulate the activation of the target gene SIX1. In addition, as a key transcription factor of Warburg effect related genes, SIX1 was proved to enhance the transcriptional expression of LDHA by chromatin immunoprecipitation assay, thereby regulating glycolysis in colon cancer cells. Therefore, we identified that circPLOD2 promoted colon cancer progression through miR-513a-5p/SIX1/LDHA axis, and acted as a new biomarker for colon cancer prognosis and treatment.
    Keywords:  SIX1; Warburg effect; circPLOD2; colon cancer; miR-513a-5p
    DOI:  https://doi.org/10.1080/15384101.2022.2103339
  45. Aging (Albany NY). 2022 Sep 05. 14(undefined):
    UBE2C mediated radiotherapy resistance of head and neck squamous cell carcinoma by regulating oxidative-stress-relative apoptosis.
    Yingchun Zhou, Junbin Zhang, Jinglin Gong, Xi Tang, Chengyao Zhang.
       PURPOSE: Radiotherapy resistance is the main obstacle in the effective treatment of advanced head and neck squamous cell carcinoma (HNSCC). Increasing scientific opinions present that ubiquitin-conjugating enzyme E2C (UBE2C) might be a target gene acting as an oncogene.
    METHOD: TCGA database was used to analyze the expression of UBE2C in HNSCC patients, and the relationship between UBE2C expression and prognosis. Western blot and RT-PCR were used to assess UBE2C expression before and after radiation. Then, cell viability experiment and colony formation were used to evaluate proliferation after 2 Gy radiation. Cell viability experiment, migration, and invasion were evaluated in the condition of UBE2C knock-down. Western blot and RT-PCR were used to assess the expression of apoptosis and ROS relative gene expression. Then, the xenograft model was used to evaluate the efficacy of radiation combined with UBE2C suppression.
    RESULT: The expression of UBE2C was high in tumors of patients with HNSCC and relatives with poor prognoses. Si-UBE2C cells showed proliferation inhibited and apoptosis enhanced after radiation. Furthermore, the mechanism of UBE2C in HNSCC radioresistance was explored. We performed RT-PCR to find the 4-HNE, which increases oxidative-stress-relative apoptosis in Si-UBE2C cells after radiation.
    CONCLUSIONS: Through the RT-PCR, WB, cell viability experiment, migration, invasion, and in vivo experiment, UBE2C was confirmed to downregulate oxidative-stress-relative apoptosis induced by radiation and promote the development of malignant tumor cells.
    Keywords:  HNSCC; UBE2C; oxidative stress; radiotherapy resistance
    DOI:  https://doi.org/10.18632/aging.204265
  46. Mol Carcinog. 2022 Sep 06.
    Therapeutic potential of the novel Bcl-2/Bcl-XL dual inhibitor, APG1252, alone or in combination against non-small cell lung cancer.
    Luxi Qian, Karin A Vallega, Weilong Yao, Dongsheng Wang, Yifan Zhai, Xia He, Shi-Yong Sun.
      Targeting the induction of apoptosis is a promising cancer therapeutic strategy with some clinical success. This study focused on evaluating the therapeutic efficacy of the novel Bcl-2/Bcl-XL dual inhibitor, APG1252-M1 (also named APG-1244; an in vivo active metabolite of APG1252 or pelcitoclax), as a single agent or in combination, against non-small cell lung cancer (NSCLC) cells. APG1252-M1 effectively decreased the survival of some NSCLC cell lines expressing low levels of Mcl-1 and induced apoptosis. Overexpression of ectopic Mcl-1 in the sensitive cells substantially compromised APG1252-M1's cell-killing effects, whereas inhibition of Mcl-1 greatly sensitized insensitive cell lines to APG1252-M1, indicating the critical role of Mcl-1 levels in impacting cell response to APG1252-M1. Moreover, APG1252-M1, when combined with the third generation epidermal growth factor receptor (EGFR) inhibitor, osimertinib, synergistically decreased the survival of EGFR-mutant NSCLC cell lines including those resistant to osimertinib with enhanced induction of apoptosis and abrogated emergence of acquired resistance to osimertinib. Importantly, the combination was effective in inhibiting the growth of osimertinib-resistant tumors in vivo. Collectively, these results demonstrate the efficacy of APG1252 alone or in combination against human NSCLC cells.
    Keywords:  APG121252-M1 (APG1252 or pelcitoclax); Bcl-2; Bcl-XL; Mcl-1; apoptosis; lung cancer; osimertinib
    DOI:  https://doi.org/10.1002/mc.23458
  47. Comput Math Methods Med. 2022 ;2022 2877679
    Identification and Validation of Immune Markers in Coronary Heart Disease.
    Yuxiong Pan, Jian Zhang, Jin Li, Wei Zhao.
       Background: Coronary heart disease (CHD) is an ischemic heart disease involving a variety of immune factors. This study was aimed at investigating unique immune and m6A patterns in patients with CHD by gene expression in peripheral blood mononuclear cells (PBMCs) and at identifying novel immune biomarkers.
    Methods: The CIBERSORT algorithm and single-sample gene set enrichment analysis (ssGSEA) were applied to assess the population of specific infiltrating immunocytes. Weighted Gene Coexpression Network Analysis (WGCNA) was utilized on immune genes matching CHD. A prediction model based on core immune genes was constructed and verified by a machine learning model. Unsupervised cluster analysis identified various immune patterns in the CHD group according to the abundance of immune cells. Methylation of N6 adenosine- (m6A-) related gene was identified from the literature, and t-distributed stochastic neighbor embedding (t-SNE) analysis was used to determine the rationality of the m6A classification. The association between m6A-related genes and various immune cells was estimated using heat maps.
    Results: 22/28 immune-associated cells differed between the CHD and normal groups, and a significant difference was detected in the expression of 21 m6A-related genes. The proportion of immune-related cells (activated CD4+ T cells and CD8+ T cells) in the peripheral blood of the CHD group was lower than that of the normal group. The immune genes were divided into four modules, of which the turquoise modules showed a significant association with coronary heart disease. Eight hub immune genes (PDGFRA, GNLY, OSMR, NUDT6, FGFR2, IL2RB, TPM2, and S100A1) can well distinguish the CHD group from the normal group. Two different immune patterns were identified in the CHD group. Interestingly, a significant association was detected between the m6A-related genes and immune cell abundance.
    Conclusion: In conclusion, we identified different immune and m6A patterns in CHD. Thus, it could be speculated that the immune system plays a crucial role in CHD, and m6A is correlated with immune genes.
    DOI:  https://doi.org/10.1155/2022/2877679
  48. J Oncol. 2022 ;2022 3744466
    Integration of Transcriptome and Epigenome to Identify and Develop Prognostic Markers for Ovarian Cancer.
    Can Xu, Wei Cao.
      DNA methylation is a widely researched epigenetic modification. It is associated with the occurrence and development of cancer and has helped evaluate patients' prognoses. However, most existing DNA methylation prognosis models have not simultaneously considered the changes of the downstream transcriptome. Methods. The RNA-Sequencing data and DNA methylation omics data of ovarian cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database. The Consensus Cluster Plus algorithm was used to construct the methylated molecular subtypes of the ovary. Lasso regression was employed to build a multi-gene signature. An independent data set was applied to verify the prognostic value of the signature. The Gene Set Variation Analysis (GSVA) was used to carry out the enrichment analysis of the pathways linked to the gene signature. The IMvigor 210 cohort was used to explore the predictive efficacy of the gene signature for immunotherapy response. Results. We distinguished ovarian cancer samples into two subtypes with different prognosis, based on the omics data of DNA methylation. Differentially expressed genes and enrichment analysis among subtypes indicated that DNA methylation was related to fatty acid metabolism and the extracellular matrix (ECM)-receptor. Furthermore, we constructed an 8-gene signature, which proved to be efficient and stable in predicting prognostics in ovarian cancer patients with different data sets and distinctive pathological characteristics. Finally, the 8-gene signature could predict patients' responses to immunotherapy. The polymerase chain reaction experiment was further used to verify the expression of 8 genes. Conclusion. We analyzed the prognostic value of the related genes of methylation in ovarian cancer. The 8-gene signature predicted the prognosis and immunotherapy response of ovarian cancer patients well and is expected to be valuable in clinical application.
    DOI:  https://doi.org/10.1155/2022/3744466
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:28.