bims-rimeca 2021-02-21 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–02–21
ten papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

Effect of N6-Methyladenosine Regulators on Progression and Prognosis of Triple-Negative Breast Cancer.
The biological function of m6A reader YTHDF2 and its role in human disease.
m6A regulator-mediated methylation modification patterns and characteristics of immunity and stemness in low-grade glioma.
The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance.
RNA m6A Methylation Regulators Subclassify Luminal Subtype in Breast Cancer.
Pan-Cancer Molecular Characterization of m6A Regulators and Immunogenomic Perspective on the Tumor Microenvironment.
Methyladenosine Modification in RNAs: Classification and Roles in Gastrointestinal Cancers.
m6A RNA hypermethylation-induced BACE2 boosts intracellular calcium release and accelerates tumorigenesis of ocular melanoma.
METTL3/IGF2BP1/CD47 contributes to the sublethal heat treatment induced mesenchymal transition in HCC.
Development of a highly sensitive method for the quantitative analysis of modified nucleosides using UHPLC-UniSpray-MS/MS.

Front Genet. 2020 ;11 580036

Effect of N6-Methyladenosine Regulators on Progression and Prognosis of Triple-Negative Breast Cancer.

Shanshan Wang, Xuan Zou, Yajie Chen, William C Cho, Xiang Zhou.

  Background: The N6-methyladenosine (m6A) modification plays a critical role in cancer development. Little is known about the m6A modification in triple-negative breast cancer (TNBC), the most aggressive subtype of breast cancer. Thus, the prognostic value of m6A RNA methylation in TNBC deserves exploration. Methods: The expression levels of the 13 m6A methylation regulators were compared between the 98 TNBC tumor samples and normal tissue samples based on the transcriptome profiles from The Cancer Genome Atlas (TCGA). The association between the m6A regulators and patients' overall survival was assessed by Kaplan-Meier survival analysis and Cox regression analysis. Lasso regression analysis was conducted to construct a prognostic model based on the m6A methylation system. The prognostic performance of the identified model was validated in GSE88847 and GSE135565 datasets. A nomogram combining the TNM stage and the m6A prognostic model was further constructed for the survival prediction of TNBC patients. Results: The m6A regulator genes were remarkably dysregulated in TNBC tumor tissues, with ALKBH5, YTHDF2, HNRNPC, KIAA1429, and RBM15 significantly up-regulated and FTO, YTHDC1, YTHDC2, METTL3, METTL14, and ZC3H13 significantly down-regulated (P < 0.01). The expression level of ALKBH5 was an independent unfavorable prognostic factor (HR = 3.327, P = 0.006), while METTL14 (HR = 0.425, P = 0.009) was an independent favorable prognostic factor for TNBC patients. A prognostic model consisting of ALKBH5 and METTL14 was therefore proposed displaying higher accuracy of risk prediction when combined with TNM stage with an AUC of 0.791. The prognostic value of the identified signature remained consistent within the two external validation datasets. Conclusion: The m6A methylation regulators were significantly dysregulated in TNBC tissues and could constitute a novel prognostic signature for the survival prediction of TNBC patients.

Keywords:  N6-methyladenosine; TNBC; nomogram; prognosis; progression

DOI:  https://doi.org/10.3389/fgene.2020.580036
Cancer Cell Int. 2021 Feb 16. 21(1): 109

The biological function of m6A reader YTHDF2 and its role in human disease.

Jin-Yan Wang, Ai-Qing Lu.

  N6-methyladenosine (m6A) modification is a dynamic and reversible post-transcriptional modification and the most prevalent internal RNA modification in eukaryotic cells. YT521-B homology domain family 2 (YTHDF2) is a member of m6A "readers" and its role in human diseases remains unclear. Accumulating evidence suggests that YTHDF2 is greatly implicated in many aspects of human cancers and non-cancers through various mechanisms. YTHDF2 takes a great part in multiple biological processes, such as migration, invasion, metastasis, proliferation, apoptosis, cell cycle, cell viability, cell adhesion, differentiation and inflammation, in both human cancers and non-cancers. Additionally, YTHDF2 influences various aspects of RNA metabolism, including mRNA decay and pre-ribosomal RNA (pre-rRNA) processing. Moreover, emerging researches indicate that YTHDF2 predicts the prognosis of different cancers. Herein, we focus on concluding YTHDF2-associated mechanisms and potential biological functions in kinds of cancers and non-cancers, and its prospects as a prognostic biomarker.

Keywords:  Biological function; Cancers; Non-cancers; Up and downregulation; YTHDF2; m6A; signaling pathways

DOI:  https://doi.org/10.1186/s12935-021-01807-0
Brief Bioinform. 2021 Feb 17. pii: bbab013. [Epub ahead of print]

m6A regulator-mediated methylation modification patterns and characteristics of immunity and stemness in low-grade glioma.

Jianyang Du, Hang Ji, Shuai Ma, Jiaqi Jin, Shan Mi, Kuiyuan Hou, Jiawei Dong, Fang Wang, Chaochao Zhang, Yuan Li, Shaoshan Hu.

  m6A RNA methylation is an emerging epigenetic modification, and its potential role in immunity and stemness remains unknown. Based on 17 widely recognized m6A regulators, the m6A modification patterns and corresponding characteristics of immune infiltration and stemness of 1152 low-grade glioma samples were comprehensively analyzed. Machine-learning strategies for constructing m6AScores were trained to quantify the m6A modification patterns of individual samples. Here, we reveal a significant correlation between the multi-omics data of regulators and clinicopathological parameters. We identified two distinct m6A modification patterns (an immune-activated differentiation pattern and an immune-desert dedifferentiation pattern) and four regulatory patterns of m6A methylation on immunity and stemness. We show that the m6AScores can predict the molecular subtype of low-grade glioma, the abundance of immune infiltration, the enrichment of signaling pathways, gene variation and prognosis. The concentration of high immunogenicity and clinical benefits in the low-m6AScore group confirmed the sensitive response to radio-chemotherapy and immunotherapy in patients with high-m6AScore. The results of the pan-cancer analyses illustrate the significant correlation between m6AScore and clinical outcome, the burden of neoepitope, immune infiltration and stemness. The assessment of individual tumor m6A modification patterns will guide us in improving treatment strategies and developing objective diagnostic tools.

Keywords:  immunotherapy; m6A; machine learning; pan-cancer; stemness; tumor immune microenvironment

DOI:  https://doi.org/10.1093/bib/bbab013
Curr Cancer Drug Targets. 2021 Jan 26.

The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance.

Shaun Wood, Amber Willbanks, Jason X Cheng.

  The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field [1-11]. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C) [12], much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance [13-17]. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.

Keywords:  5'; 5-methylcytosine (m5C); Adenosine-to-inosine editing (A-to-I); Drug resistance; Myc; mTOR; N6-methyladenosine (m6A); Nol1/Nop2/SUN domain (NSUN).; cap

DOI:  https://doi.org/10.2174/1568009621666210127092828
Front Oncol. 2020 ;10 611191

RNA m6A Methylation Regulators Subclassify Luminal Subtype in Breast Cancer.

Lin Yang, Shuangling Wu, Chunhui Ma, Shuhui Song, Feng Jin, Yamei Niu, Wei-Min Tong.

  RNA N6-methyladenosine (m6A) methylation is the most prevalent epitranscriptomic modification in mammals, with a complex and fine-tuning regulatory system. Recent studies have illuminated the potential of m6A regulators in clinical applications including diagnosis, therapeutics, and prognosis. Based on six datasets of breast cancer in The Cancer Genome Atlas (TCGA) database and two additional proteomic datasets, we provide a comprehensive view of all the known m6A regulators in their gene expression, copy number variations (CNVs), DNA methylation status, and protein levels in breast tumors and their association with prognosis. Among four breast cancer subtypes, basal-like subtype exhibits distinct expression and genomic alteration in m6A regulators from other subtypes. Accordingly, four representative regulators (IGF2BP2, IGF2BP3, YTHDC2, and RBM15) are identified as basal-like subtype-featured genes. Notably, luminal A/B samples are subclassified into two clusters based on the methylation status of those four genes. In line with its similarity to basal-like subtype, cluster1 shows upregulation in immune-related genes and cell adhesion molecules, as well as an increased number of tumor-infiltrating lymphocytes. Besides, cluster1 has worse disease-free and progression-free survival, especially among patients diagnosed with stage II and luminal B subtype. Together, this study highlights the potential functions of m6A regulators in the occurrence and malignancy progression of breast cancer. Given the heterogeneity within luminal subtype and high risk of recurrence and metastasis in a portion of patients, the prognostic stratification of luminal A/B subtypes utilizing basal-featured m6A regulators may help to improve the accuracy of diagnosis and therapeutics of breast cancer.

Keywords:  RNA methylation; breast cancer subtypes; genomic regulation; m6A regulators; subclassification; survival

DOI:  https://doi.org/10.3389/fonc.2020.611191
Front Oncol. 2020 ;10 618374

Pan-Cancer Molecular Characterization of m6A Regulators and Immunogenomic Perspective on the Tumor Microenvironment.

Jie Zhu, Jiani Xiao, Min Wang, Daixing Hu.

   Purpose: N6-methyladenosine (m6A) methylation plays a critical role in diverse biological processes. However, knowledge regarding the constitution of m6A on tumor microenvironment (TME) and tumor-infiltrating lymphocytes (TILs) across cancer types is still lacking. We performed comprehensive immuno-genomic analyses to reveal molecular characterization of the m6A regulators and immune-related genes (IRGs) across TME and TIL heterogeneity.
Methods: We comprehensively analyzed the properties of m6A regulators in genomic profiles from The Cancer Genome Atlas (TCGA) according to expression perturbations of crucial IRGs, CD274, CD8A, GZMA, and PRF1. The four IRGs were proved to be reliable biomarkers of TILs and TME via CIBERSORT and ESTIMATE analyses, and their co-expression relationship was certified by TIMER analysis. Based on their median values, the samples from the pan-cancer tissues (N = 11,057) were classified into eight TME types. The RNA expression levels of 13 m6A regulators were compared across TME subtypes. Single-sample Gene Set Enrichment Analysis (ssGSEA) was also used to classify TME clusters, expression variants of IRGs and m6A regulators were verified among TME clusters. Meanwhile, the correlation between m6A regulators and tumor mutational burden (TMB) were tested. Finally, the impacts of IRGs and TME clusters in clinical characteristics and outcomes were revealed.
Results: CD274, CD8A, GZMA, and PRF1 showed similar TILs' characteristics, of which the level of T cells CD8 and T cells CD4 memory activated are consistent with the expression levels of the four IRGs and higher immune infiltration. Besides, CD274, CD8A, GZMA, and PRF1 were positively correlated with the stromal score or immune score in almost all 33 tumor types. All of four IRGs showed impact between tumor pathological stages or clinical outcomes. Among TME type I to type IV, m6A regulators' expression drift changed from high-level to low-level in ESCA, BLCA, HNSC, CESC, BRCA, and GBM. However among TME type V to type VIII, m6A regulators drew a shift from low-level to high-level expression in CESC, BLCA, ESCA, KIRP, HNSC, BRCA, KIRC, COAD, LAML, GBM, and KICH. In ssGSEA analyses, IRGs' expression levels were elevated with the immune infiltration degree and m6A regulators' expression level varied among three TIL subgroups. With different TMB levels, expression differences of m6A regulators were observed in BLCA, BRCA, COAD, LGG, LUAD, LUSC, STAD, THCA, and UCEC.
Conclusion: We identified four crucial IRGs affecting TILs, TME characteristics and clinical parameters. Expression variants of m6A regulators among the subgroups of TME types and ssGSEA clusters suggested that m6A regulators may be essential factors for phenotypic modifications of IRGs and thus affecting TME characteristics across multiple tumor types.

Keywords:  N6-methyladenosine methylation; The Cancer Genome Atlas (TCGA); pancancer analysis; tumor microenvironment; tumor-infiltrating lymphocytes

DOI:  https://doi.org/10.3389/fonc.2020.618374
Front Oncol. 2020 ;10 586789

Methyladenosine Modification in RNAs: Classification and Roles in Gastrointestinal Cancers.

Qinghai Li, Weiling He, Guohui Wan.

  Cellular ribonucleic acids (RNAs), including messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs), harbor more than 150 forms of chemical modifications, among which methylation modifications are dynamically regulated and play significant roles in RNA metabolism. Recently, dysregulation of RNA methylation modifications is found to be linked to various physiological bioprocesses and many human diseases. Gastric cancer (GC) and colorectal cancer (CRC) are two main gastrointestinal-related cancers (GIC) and the most leading causes of cancer-related death worldwide. In-depth understanding of molecular mechanisms on GIC can provide important insights in developing novel treatment strategies for GICs. In this review, we focus on the multitude of epigenetic changes of RNA methlyadenosine modifications in gene expression, and their roles in GIC tumorigenesis, progression, and drug resistance, and aim to provide the potential therapeutic regimens for GICs.

Keywords:  RNA; gastrointestinal cancers; m1A; m6A; m6Am; methylation modification

DOI:  https://doi.org/10.3389/fonc.2020.586789
Mol Ther. 2021 Feb 15. pii: S1525-0016(21)00081-2. [Epub ahead of print]

m6A RNA hypermethylation-induced BACE2 boosts intracellular calcium release and accelerates tumorigenesis of ocular melanoma.

Fanglin He, Jie Yu, Jie Yang, Shaoyun Wang, Ai Zhuang, Hanhan Shi, Xiang Gu, Xiaofang Xu, Peiwei Chai, Renbing Jia.

  Ocular melanoma, including uveal melanoma (UM) and conjunctival melanoma (CM), is the most common and deadly eye cancer in adults. Both UM and CM originate from melanocytes and exhibit an aggressive growth pattern with high rates of metastasis and mortality. The integral membrane glycoprotein beta-secretase 2 (BACE2), an enzyme that cleaves amyloid precursor protein into amyloid beta peptide, has been reported to play a vital role in vertebrate pigmentation and metastatic melanoma. However, the role of BACE2 in ocular melanoma remains unclear. Here, we showed that BACE2 was significantly upregulated in ocular melanoma and inhibition of BACE2 significantly impaired tumour progression both in vitro and in vivo. Notably, we identified TMEM38B, whose expression was highly dependent on BACE2, modulated calcium release from endoplasmic reticulum (ER). The inhibition of BACE2/TMEM38B axis could trigger exhaustion of intracellular calcium release and inhibit tumour progression. We further demonstrated that BACE2 presented an increased level of m6A RNA methylation, which led to the upregulation of BACE2 mRNA. To our knowledge, this study provides a novel pattern of BACE2-mediated intracellular calcium release in ocular melanoma progression, and our findings suggest that m6A/BACE2/TMEM38b could be a potential therapeutic axis for ocular melanoma.

Keywords:  BACE2; m(6)A; melanoma

DOI:  https://doi.org/10.1016/j.ymthe.2021.02.014
Biochem Biophys Res Commun. 2021 Feb 11. pii: S0006-291X(21)00150-9. [Epub ahead of print]546 169-177

METTL3/IGF2BP1/CD47 contributes to the sublethal heat treatment induced mesenchymal transition in HCC.

Zhuoyang Fan, Yang Gao, Wei Zhang, Guowei Yang, Pingping Liu, Ligang Xu, Jianhua Wang, Zhiping Yan, Hong Han, Rong Liu, Minfeng Shu.

  Microwave ablation is a first-line treatment of small hepatocellular carcinoma (HCC), while incomplete ablation induces recurrence and metastasis. However, its underlying mechanism remains largely unexplored. Here we reported that sublethal heat treatment (46 °C) strongly promoted migration and EMT transition in HCC cells. Mechanistic investigation revealed that compared with 37 °C, HCC cells treated with 46 °C expressed higher level of CD47. Knockdown of CD47 significantly attenuated sublethal heat treatment stimulated migration and EMT transition. In addition, METTL3 which is the key enzyme of m6A modification was also induced by 46 °C treatment and triggered CD47 expression in HCC cells. Moreover, CD47 mRNA degradation was further proved to be stabled in the IGF2BP1-dependent manner. Importantly, sublethal heat treatment stimulated CD47 expression and EMT transition were also confirmed in patient-derived organoid. Taken together, our study suggests that METTL3/IGF2BP1/CD47 mediated EMT transition contributes to the incomplete ablation induced metastasis in HCC cells. Moreover, these findings identify the METTL3/IGF2BP1/CD47 axis as a potential therapeutic target for the microwave ablation and shed new lights on the crosstalk between incomplete heat ablation and RNA methylation.

Keywords:  CD47; Hepatocellular carcinoma; IGF2BP1; METTL3; Patient-derived organoid

DOI:  https://doi.org/10.1016/j.bbrc.2021.01.085
J Pharm Biomed Anal. 2021 Feb 02. pii: S0731-7085(21)00055-8. [Epub ahead of print]197 113943

Development of a highly sensitive method for the quantitative analysis of modified nucleosides using UHPLC-UniSpray-MS/MS.

Takahiro Kogaki, Ikumi Ohshio, Hasumi Ura, Souta Iyama, Kaori Kitae, Toshiya Morie, Shintarou Fujii, Shohei Sato, Toshiyuki Nagata, Aya Harada Takeda, Masaya Aoki, Kazuhiro Ueda, Kentaro Minami, Masatatsu Yamamoto, Kohichi Kawahara, Tatsuhiko Furukawa, Masami Sato, Yuko Ueda, Kentaro Jingushi, Zenzaburo Tozuka, Daisuke Saigusa, Hiroaki Hase, Kazutake Tsujikawa.

  There are more than 150 types of naturally occurring modified nucleosides, which are believed to be involved in various biological processes. Recently, an ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) technique has been developed to measure low levels of modified nucleosides. A comprehensive analysis of modified nucleosides will lead to a better understanding of intracellular ribonucleic acid modification, but this analysis requires high-sensitivity measurements. In this perspective, we established a highly sensitive and quantitative method using the newly developed ion source, UniSpray. A mass spectrometer was used with a UniSpray source in positive ion mode. Our UHPLC-UniSpray-MS/MS methodology separated and detected the four major nucleosides, 42 modified nucleosides, and dG15N5 (internal standard) in 15 min. The UniSpray method provided good correlation coefficients (>0.99) for all analyzed nucleosides, and a wide range of linearity for 35 of the 46 nucleosides. Additionally, the accuracy and precision values satisfied the criteria of <15% for higher concentrations and <20% for the lowest concentrations of all nucleosides. We also investigated whether this method could measure nucleosides in biological samples using mouse tissues and non-small cell lung cancer clinical specimens. We were able to detect 43 and 31 different modified nucleosides from mouse and clinical tissues, respectively. We also found significant differences in the levels of N6-methyl-N6-threonylcarbamoyladenosine (m6t6A), 1-methylinosine (m1I), 2'-O-methylcytidine (Cm), 5-carbamoylmethyluridine (ncm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5S2U), and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) between cancerous and noncancerous tissues. In conclusion, we developed a highly sensitive methodology using UHPLC-UniSpray-MS/MS to simultaneously detect and quantify modified nucleosides, which can be used for analysis of biological samples.

Keywords:  Modified nucleosides; Non-small cell lung cancer; Ribonucleic acid; UHPLC-MS/MS; UniSpray

DOI:  https://doi.org/10.1016/j.jpba.2021.113943