bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2020‒11‒29
fifteen papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

  1. Semin Cancer Biol. 2020 Nov 18. pii: S1044-579X(20)30241-8. [Epub ahead of print]
      RNA methylations, as the prevalent post-transcriptional modifications, are critical in regulating various biological processes, such as RNA transcription, splicing, structure, stability, and translation. Its dysregulation is closely related to the occurrence of human malignancies. The advance of high-throughput sequencing technology facilitates the investigations about how methylation of coding and non-coding RNAs regulates cancer progression through reshaping the transcriptomics. Here, we review the current progress about the regulatory role of several representative RNA modifications in cancers, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A) and 2'-O-methylation (Nm). Meanwhile, we also discuss the potential clinical value of RNA methylation in diagnostic and therapeutic implications of human cancers.
    Keywords:  RNA methylation regulators; RNA modification; human cancer; targeting therapy
  2. Mol Ther Nucleic Acids. 2020 Dec 04. 22 750-765
      Hepatocellular carcinoma (HCC), one of the most aggressive malignancies, ranks as the fourth leading cause of cancer-related deaths worldwide. Emerging evidence indicates that RNA N6-methyladenosine (m6A) plays a critical role in tumor progression. However, the biological function of YTHDF1 in HCC remains unclear. Here, we found that YTHDF1 expression was strikingly elevated in HCC tissues and cell lines and significantly associated with prognosis of HCC patients. Moreover, YTHDF1 expression was transcriptionally regulated by USF1 and c-MYC in HCC. Functional studies showed that YTHDF1 can promote HCC cell proliferation and metastasis both in vitro and in vivo. Multi-omics analysis revealed that YTHDF1 can accelerate the translational output of FZD5 mRNA in an m6A-dependent manner and function as an oncogene through the WNT/β-catenin pathway. Taken together, our study revealed an essential role of YTHDF1 in the progression of HCC cells, which indicated that targeting YTHDF1 may be a potential therapeutic strategy in HCC.
    Keywords:  FZD5; N6-methyladenosine; YTHDF1; growth and metastasis; hepatocellular carcinoma
  3. Mol Cancer. 2020 11 23. 19(1): 163
      BACKGROUND AND AIMS: Accumulating evidence suggests that the primary and acquired resistance of hepatocellular carcinoma (HCC) to sorafenib is mediated by multiple molecular, cellular, and microenvironmental mechanisms. Understanding these mechanisms will enhance the likelihood of effective sorafenib therapy.METHODS: In vitro and in vivo experiments were performed and clinical samples and online databases were acquired for clinical investigation.
    RESULTS: In this study, we found that a circular RNA, circRNA-SORE, which is up-regulated in sorafenib-resistant HCC cells, was necessary for the maintenance of sorafenib resistance, and that silencing circRNA-SORE substantially increased the efficacy of sorafenib-induced apoptosis. Mechanistic studies determined that circRNA-SORE sequestered miR-103a-2-5p and miR-660-3p by acting as a microRNA sponge, thereby competitively activating the Wnt/β-catenin pathway and inducing sorafenib resistance. The increased level of circRNA-SORE in sorafenib-resistant cells resulted from increased RNA stability. This was caused by an increased level of N6-methyladenosine (m6A) at a specific adenosine in circRNA-SORE. In vivo delivery of circRNA-SORE interfering RNA by local short hairpin RNA lentivirus injection substantially enhanced sorafenib efficacy in animal models.
    CONCLUSIONS: This work indicates a novel mechanism for maintaining sorafenib resistance and is a proof-of-concept study for targeting circRNA-SORE in sorafenib-treated HCC patients as a novel pharmaceutical intervention for advanced HCC.
    Keywords:  Circular RNA; Hepatocellular carcinoma; Sorafenib resistance; m6A
  4. Front Oncol. 2020 ;10 578816
      Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in China. N6-methyladenosine (m6A) plays an important role in posttranscriptional gene regulation. METTL3 and IGF2BP2 are key genes in the m6A signal pathway and have recently been shown to play important roles in cancer development and progression. In our work, higher METTL3 and IGF2BP2 expression were found in HCC tissues and were associated with a poor prognosis. In addition, IGF2BP2 overexpression promoted HCC proliferation in vitro and in vivo. Mechanistically, IGF2BP2 directly recognized and bound to the m6A site on FEN1 mRNA and enhanced FEN1 mRNA stability. Overall, our study revealed that METTL3 and IGF2BP2, acting as an oncogene, maintained FEN1 expression through an m6A-IGF2BP2-dependent mechanism in HCC cells, and indicated a potential biomarker panel for prognostic prediction in liver cancer.
    Keywords:  FEN1; IGF2BP2; METTL3; N6-methyladenosine; liver cancer
  5. Redox Biol. 2020 Nov 18. pii: S2213-2317(20)31006-5. [Epub ahead of print]38 101801
      The biological functions of N6-methyladenosine (m6A) RNA methylation are mainly dependent on the reader; however, its role in lung tumorigenesis remains unclear. Here, we have demonstrated that the m6A reader YT521-B homology domain containing 2 (YTHDC2) is frequently suppressed in lung adenocarcinoma (LUAD). Downregulation of YTHDC2 was associated with poor clinical outcome of LUAD. YTHDC2 decreased tumorigenesis in a spontaneous LUAD mouse model. Moreover, YTHDC2 exhibited antitumor activity in human LUAD cells. Mechanistically, YTHDC2, via its m6A-recognizing YTH domain, suppressed cystine uptake and blocked the downstream antioxidant program. Administration of cystine downstream antioxidants to pulmonary YTHDC2-overexpressing mice rescued lung tumorigenesis. Furthermore, solute carrier 7A11 (SLC7A11), the catalytic subunit of system XC-, was identified to be the direct target of YTHDC2. YTHDC2 destabilized SLC7A11 mRNA in an m6A-dependent manner because YTHDC2 preferentially bound to m6A-modified SLC7A11 mRNA and thereafter promoted its decay. Clinically, a large proportion of acinar LUAD subtype cases exhibited simultaneous YTHDC2 downregulation and SLC7A11 elevation. Patient-derived xenograft (PDX) mouse models generated from acinar LUAD showed sensitivity to system XC- inhibitors. Collectively, the promotion of cystine uptake via the suppression of YTHDC2 is critical for LUAD tumorigenesis, and blocking this process may benefit future treatment.
    Keywords:  Cystine uptake; Lipid peroxidation; METTL3; System X(C)(−); m(6)A RNA methylation
  6. Ann Transl Med. 2020 Sep;8(18): 1130
      Background: Lung adenocarcinoma (LUAD) is still one of the major causes of cancer-related mortality across the globe. Therefore, there is a dire need to identify early specific and sensitive biomarkers or drug targets of LUAD for developing improved diagnosis and clinical management. We aimed to investigate the role of methyltransferase-like 7B (METTL7B) on LUAD tumor development and progression in this study.Methods: METTL7B's expression was confirmed in two independent clinical cohort samples, including LUAD tissues microarray (TMA) via immunohistochemistry (IHC) and serum samples via enzyme-linked immunosorbent assay (ELISA). The correlation between METTL7B expression with clinicopathological features and overall survival rate in LUAD patients was then further analyzed. Meanwhile, the messenger ribonucleic acid (mRNA) and protein levels of METTL7B were verified in cell lines and in vitro experiments, including cell proliferation assay, and migration. Invasion assays were conducted to explore the effects of METTL7B on LUAD by silencing the protein expression.
    Results: METTL7B was remarkably overexpressed in clinical LUAD tumor tissues and serum compared to the normal control group and in LUAD cell lines. The expression level of METTL7B was significantly correlated with tumor size, advanced tumor node and metastases (TNM) stages, and lymph node metastasis. The Kaplan-Meier survival curves proved that high METTL7B expression was significantly associated with a reduced survival rate in LUAD patients (P<0.05), and univariate analysis showed that high METTL7B expression was significantly associated with poor overall survival [hazard ratio (HR) =2.220, 95% confidence interval (CI): 1.211-4.086; P=0.010]. In vitro assays showed that METTL7B overexpression augmented cell proliferation, migration, and the invasion in LUAD.
    Conclusions: METTL7B was overexpressed in LUAD and significantly associated with the poor progression, showing that METTL7B may serve as a potential novel biomarker for the diagnosis and prognosis of LUAD. Moreover, METTL7B plays a role in promoting tumor proliferation, migration, and invasion in LUAD.
    Keywords:  Biomarkers; lung adenocarcinoma (LUAD); metastasis; methyltransferase-like 7B (METTL7B)
  7. Onco Targets Ther. 2020 ;13 11913-11921
      Background: N6-methyladenosine (m6A) triggers a new layer of epi-transcription. However, the potential noninvasive screening and diagnostic value of peripheral blood m6A for cancer are still unknown. Here, we intend to investigate whether leukocyte m6A can be a novel biomarker for non-small-cell lung cancer (NSCLC).Materials and Methods: Peripheral blood was collected from 119 NSCLC patients and 74 age-matched healthy controls. Total RNA was isolated from leukocytes for m6A measurement, and clinical information of participants was reviewed. The sensitivity, specificity, and area under the curve (AUC) of m6A for cancer diagnosis were evaluated by the receiver-operating characteristic (ROC) curve analysis. Flow cytometry and the Human Protein Atlas (HPA) database were used to characterize m6A in leukocyte differentials. Pearson's correlation was applied to indicate the relationship between m6A level and hematology variables. qPCR and bioinformatic analysis were used to identity the expression of m6A regulators in leukocyte.
    Results: Leukocyte m6A was significantly elevated in 119 NSCLC patients compared with 74 healthy controls (P<0.001). We did not find significant association between m6A and age or gender. Elevated m6A level in NSCLC was associated with tumor stage (P<0.05) and tumor differentiation (P<0.05), and was significantly reduced after surgery (P<0.01). ROC curve analysis revealed that leukocyte m6A could significantly discriminate patients with lung adenocarcinoma (LUAD) (AUC=0.736, P<0.001) and lung squamous cell carcinoma (LUSC) (AUC=0.963, P<0.001) from healthy individuals. m6A displayed superior sensitivity (100%) and specificity (85.7%) for LUSC than squamous cell carcinoma (SCC) antigen and cytokeratin fragment 211 (Cyfra211). Flow cytometry analysis showed m6A modification was mainly localized on T cells and monocytes among leukocyte differentials. Leukocyte m6A was positively correlated with the number of lymphocytes and negatively correlated with monocytes in NSCLC but not in healthy controls. qPCR and bioinformatic analysis showed that elevated leukocyte m6A in NSCLC was caused by upregulated methyltransferase complex and downregulated FTO and ALKBH5.
    Conclusion: Leukocyte m6A represents a potential noninvasive biomarker for NSCLC screening, monitoring and diagnosis.
    Keywords:  N6-methyladenosine; biomarker; leukocyte; lung cancer
  8. J Cell Mol Med. 2020 Nov 25.
      Results from various studies reveal that the role of G protein-coupled oestrogen receptor (GPER) is cancer-context dependent, and the function of GPER in non-small-cell lung cancer (NSCLC) is still unclear. The present study demonstrated that neoplasm lung tissues expressed higher level of GPER compared with the normal lung tissues. The clinical data also showed that GPER expression level was positively correlated with the tumour stage of NSCLC. Our experimental data confirmed that GPER played an oncogenic role to promote cell growth of NSCLC cells. Mechanistic dissection revealed that GPER could modulate the NOTCH1 pathway to regulate cell growth in NSCLC cells. Further exploration of the mechanism demonstrated that GPER could up-regulate circNOTCH1, which could compete with NOTCH1 mRNA for METTL14 binding. Because of the lack of m6A modification by METTL14 on the NOTCH1 mRNA, NOTCH1 mRNA was more stable and much easier to undergo protein translation. Subsequently, we found that GPER could prevent YAP1 phosphorylation and promote YAP1-TEAD's transcriptional regulation on QKI, a transacting RNA-binding factor involved in circRNA biogenesis, to facilitate circNOTCH1 generation. Supportively, data from preclinical mice model with implantation of H1299 cells also demonstrated that knock-down of circNOTCH1 could block GPER-induced NOTCH1 to suppress NSCLC tumour growth. Together, our data showed that GPER could promote NSCLC cell growth via regulating the YAP1/QKI/circNOTCH1/m6A methylated NOTCH1 pathway, and targeting our identified molecules may be a potentially therapeutic approach to suppress NSCLC development.
    Keywords:  GPER; NOTCH1; NSCLC; circular RNA
  9. Aging (Albany NY). 2020 Nov 20. 12
      N6-methyladenosine (m6A), internal modification of mRNA, has recently been reported to be an important regulatory mechanism affecting tumor proliferation. However, its role in endocrine system tumors is poorly understood. We obtained datasets for four types tumors from the TCGA database, analyzed the GTEx database as a supplement to the control group, and used "Perl" and "R" softwares to analyze the datasets. Then we differentiated the expression level, used it to cluster consensus. Besides, we established lasso regression model to screen variables, used univariate and multivariate cox analyses to explore the independent risk factors associated with cancer prognosis. The results indicated that except for WTAP, the expression level of METTL3 was negatively correlated with other genes. The expression level of WTAP and METTL16 was positively correlated with overall survival (OS). Moreover, we found that different clinical subtypes of adrenal cortical carcinoma had significant differences in survival status, histologic grading, pathological T grade, and OS. Furthermore, different clinical subtypes of thyroid carcinoma had significant differences in histologic grading and pathological T grade. The differential expression of m6A regulatory genes is closely associated with the presence of endocrine-system-related tumors, and risk scores can be used to assess prognosis.
    Keywords:  endocrine system tumors; m6A methylation regulators; pan-cancer analysis; prognosis; risk score
  10. Front Cell Dev Biol. 2020 ;8 594112
      Background: N6-methyladenosine (m6A) RNA methylation and tumor immune microenvironment played crucial roles in cancer development. However, their association in gliomas remains to be fully elucidated.Methods: A total of 2144 glioma patients from CGGA, TCGA, and Rembrandt databases were extracted in our study, in which 325 were set as the training cohort and 1819 were defined as the validation cohort. Survival differences evaluated by Kaplan-Meier analysis between groups. Patients were clustered into subgroups by consensus clustering. ESTIMATE algorithm was applied to calculate immune and stroma scores. The infiltration of immune cells was characterized by TIMER algorithm. The risk signature was constructed by multivariate Cox regression analysis.
    Results: Nineteen m6A regulators were highly expressed in glioma tissues. The expression of m6A regulators was associated with prognoses, grade, isocitrate dehydrogenase (IDH) status, and 1p19q status of gliomas. Two subgroups were identified by consensus clustering, in which cluster 1 was associated with favorable prognosis, high stroma and immune scores, and high immune infiltration. When the patients were divided into high risk and low risk groups based on their risk scores, we found that patients in the high risk group had poor prognoses. Besides, patients in the high risk group had a higher stroma and immune scores, and higher abundance of immune infiltration. These results were further verified in the validation cohort, which contained three independent datasets. Moreover, patients in the low risk group enjoyed better prognoses without chemoradiotherapy or single chemotherapy.
    Conclusion: Our study revealed that m6A regulators could predict the prognosis and therapeutic efficacy, and were also associated with the immune microenvironment in gliomas.
    Keywords:  N6-methyladenosine methylation; brain tumor; chemoradiotherapy; glioma; immune infiltration; immune microenvironment
  11. Mol Genet Genomic Med. 2020 Nov 22. e1547
      BACKGROUND: N6 -methyladenosine (m6 A) modification is one of the critical gene regulatory mechanisms implicated in cancer biology. However, the roles of m6 A regulators in ovarian cancer are still poorly understood.METHODS: We integrated multiple databases including Gene Expression Omnibus (GEO), ROC Plotter, Kaplan-Meier Plotter, and Tumor Immune Estimation Resource (TIMER) to explore clinicopathological significance of m6 A regulators in ovarian cancer.
    RESULTS: We showed that alterations in the expression of m6 A regulators were related to the malignancy and poor prognosis of ovarian cancer. We found decreased YTHDC1 and increased RBM15 expressions were associated with ovarian cancer cell metastases and HNRNPC was a predictor of paclitaxel resistance. Moreover, dysregulated m6 A regulators were enriched in the activation of cancer-related pathways. Our results further demonstrated that the level of immune cell infiltration and the expression of various immune gene markers were closely associated with the expressions of specific m6 A regulators (RBM15B, ZC3H13, YTHDF1, and IGF2BP1).
    CONCLUSIONS: Our study establishes a new prognostic profile of ovarian cancer patients based on m6 A regulators, and highlights the potential roles of m6 A regulators in ovarian cancer development.
    Keywords:  immune infiltration; m6A regulators; ovarian cancer; survival
  12. Arch Gynecol Obstet. 2020 Nov 22.
      PURPOSE: N6-methyladenosine (m6A) and demethylase fat mass and obesity-associated protein (FTO) were reported to be associated with oocyte development and maturation. But the relationship between FTO and ovarian aging was still unclear. This study was aimed at investigating the FTO expression level and the m6A content during ovarian aging.METHODS: The expression level of FTO and the content of m6A RNA methylation in human follicular fluid (FF), granulosa cells (GCs) and mouse ovary from different age groups were studied by ELISA, WB, qRT-PCR, IHC and m6A Colorimetric.
    RESULTS: Human FF ELISA quantified that the level of FTO protein decreased with age (P = 0.025). QRT-PCR results showed that the relative expression of FTO in human GCs was lower in the elderly group than in the young group (P = 0.012). FTO mRNA and protein expression levels were lower in the ovary of 32-week-old mice than in 3- and 8-week-old mice (P < 0.05). Immunohistochemistry showed FTO was relatively decreased in 32-week-old mice (P < 0.05). The m6A content in total RNA from old human GCs and ovary from 32-week-old mice was significantly higher compared with the younger ones.
    CONCLUSIONS: In human FF, GCs and mouse ovary, the expression of FTO decreased while the content of m6A increased with aging. However, the inner mechanism still needs further investigation.
    Keywords:  Epigenetics; FTO; Ovarian aging; Ovarian reserve; m6A
  13. Onco Targets Ther. 2020 ;13 11795-11806
      Background: Cervical cancer (CC) is the second serious health threat in women worldwide. LncRNA (ZNFX1 antisense RNA 1) ZFAS1 has been observed to abnormally express in human cancers. However, the expression pattern, clinical significance and molecular mechanism of ZFAS1 have not been thoroughly studied in CC.Methods: qRT-PCR was performed to examine the differential expression of ZFAS1 in CC tissues and adjacent normal cervical tissues. Gain- and loss-of-function experiments were constructed to test the functional role of ZFAS1 in CC by CCK-8, colony formation, transwell and xenograft models assays. Luciferase reporter, RNA immunoprecipitation (RIP), methylated RNA immunoprecipitation (MeRIP), RNA pull-down assays were used to reveal the underlying mechanisms.
    Results: We found that ZFAS1 was significantly upregulated in CC tissues. Elevation of ZFAS1 correlated with advanced FIGO stage, lymph node and distant metastasis, and also indicated poor overall survival in patients with CC. Functional experiments demonstrated that ZFAS1 promoted CC cell proliferation, migration and invasion in vitro, and facilitated tumor growth and metastasis in vivo. Mechanistic investigation revealed that ZAFS1 sequestered miR-647, and this RNA-RNA interaction is regulated by METLL3-mediated m6A modification.
    Conclusion: Our findings elucidate the functional roles of ZFAS1 and its m6A modification in CC cells and indicate that ZFAS1 may be a promising target for CC treatment.
    Keywords:  ceRNA; growth; m6A modification; metastasis
  14. Cancer Manag Res. 2020 ;12 11953-11964
      Purpose: Gastric cancer (GC) is aggressive cancer with a high mortality rate worldwide. N6-methyladenosine (m6A) RNA methylation is related to tumorigenesis, which is dynamically regulated by m6A modulators ("writer," "eraser," and "reader"). We conducted a comprehensive analysis of the m6A genes of GC patients in TCGA datasets to identify the potential diagnostic biomarkers.Materials and Methods: We analyzed the expression profile of m6A genes in the TCGA cohort and constructed a diagnostic-m6A-score (DMS) by the LASSO-logistic model. In addition, by consensus cluster analysis, we identified two different subgroups of GC risk individuals by the expression profile of m6A modulators, revealing that YTHDF1's expression variation profile in GC diagnosis. We also performed RT-qPCR and WB verification in 17 pairs of GC specimens and paired adjacent non-tumor tissues and GC cell lines, and verified the expression trend of YTHDF1 in five GEO GC datasets. YTHDF1 expression and clinical features of GC patients were assessed by the UALCAN.
    Results: The DMS with high specificity and sensitivity (AUC = 0.986) is proven to distinguish cancer from normal controls better. Moreover, we found that the expression profile variation of YTHDF1 was significantly associated with the high-risk subtype of GC patients. RT-qPCR and Western blot results are consistent with silicon analysis, revealing that YTHDF1's potential oncogene role in GC tumor.
    Conclusion: In conclusion, we developed the m6A gene-based diagnostic signature for GC and found that YTHDF1 was significantly correlated with the high-risk subtype of GC patients, suggesting that YTHDF1 might be a potential target in GC early diagnosis.
    Keywords:  RNA methylation; YTHDF1; diagnostic signature; gastric cancer; m6A
  15. Hum Cell. 2020 Nov 24.
      Esophageal squamous cell carcinoma (ESCC) is one of the most frequent malignancies worldwide. miR-193a-3p acts as an oncogene or tumor suppressor in different cancers. However, the functional role and regulatory mechanism of miR-193a-3p in ESCC remain to be elucidated. Our results demonstrated that miR-193a-3p expression was significantly upregulated and associated with advanced TNM stage, recurrence, and poor prognosis in ESCC patients. miR-193-3p targeted ALKBH5 and suppressed its expression. ALKBH5 inhibited miR-193a-3p expression in turn. ALKBH5 affected the primary miR-193a-3p processing by negatively regulating its m6A modification. These findings suggested a positive feedback regulation between miR-193a-3p and ALKBH5 in ESCC cells. Moreover, the functional assays indicated that the miR-193-3p-ALKBH5 feedback loop promoted the proliferation, migration and invasion ability of ESCC cells in vitro, and facilitated tumor growth and metastasis in vivo. Collectively, our current study identified a novel positive feedback regulation between miR-193a-3p and ALKBH5 in ESCC, which may be helpful to gain insight into ESCC pathogenesis and provide novel therapeutic target for ESCC.
    Keywords:  Positive feedback loop; RNA methylation; m6A modification; microRNA processing