bims-rimeca 2023-09-10 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023–09–10
eightteen papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA.
IGF2BP2 promotes ovarian cancer growth and metastasis by upregulating CKAP2L protein expression in an m6 A-dependent manner.
The synergistic effect of EMT regulators and m6A modification on prognosis-related immunological signatures for ovarian cancer.
The m6A reader HNRNPC predicts adverse prognosis and promotes the progression of colorectal cancer.
RNA methylation-driven assembly of fluorescence-encoded nanostructures for sensitive detection of m6A modification writer METTL3/14 complex in human breast tissues.
Branched-chain amino acids prevent obesity by inhibiting the cell cycle in an NADPH-FTO-m6A coordinated manner.
N6 -methyladenosine-modified circFUT8 competitively interacts with YTHDF2 and miR-186-5p to stabilize FUT8 mRNA to promote malignant progression in lung adenocarcinoma.
Dissecting the effects of METTL3 on alternative splicing in prostate cancer.
Emerging role of METTL3 in inflammatory diseases: mechanisms and therapeutic applications.
Hypoxia promotes immune escape of pancreatic cancer cells by lncRNA NNT-AS1/METTL3-HuR-mediated ITGB1 m6A modification.
Distinct N7-methylguanosine profiles of circular RNAs in drug-resistant acute myeloid leukemia.
METTL16 controls Kaposi's sarcoma-associated herpesvirus replication by regulating S-adenosylmethionine cycle.
Ghost authors revealed: The structure and function of human N6 -methyladenosine RNA methyltransferases.
The role of PGRMC2 in the trophoblast invasion.
HNRNPA2B1 is a potential biomarker of breast cancer related to prognosis and immune infiltration.
TET2 inhibits the proliferation and metastasis of lung adenocarcinoma cells via activation of the cGAS-STING signalling pathway.
m1A Regulatory gene signatures are associated with certain immune cell compositions of the tumor microenvironment and predict survival in kidney renal clear cell carcinoma.
Integrative analyses reveal biological function and prognostic role of m7G methylation regulators in high-grade glioma.

PeerJ. 2023 ;11 e15706

RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA.

Jin Fan, Mengqi Zhuang, Wei Fan, Ming Hou.

   Background: N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive.
Methods: Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods.
Results: This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation.
Conclusion: These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.

Keywords:  Acute myeloid leukemia; EPOR; IGF2BP3; JAK/STAT; m6A methylation

DOI:  https://doi.org/10.7717/peerj.15706
FASEB J. 2023 10;37(10): e23183

IGF2BP2 promotes ovarian cancer growth and metastasis by upregulating CKAP2L protein expression in an m6 A-dependent manner.

Yaqian Shi, Xueyou Xiong, Yu Sun, Zhe Geng, Xiyi Chen, Xin Cui, Juan Lv, Lili Ge, Xuemei Jia, Juan Xu.

  Ovarian cancer (OC) is the second leading cause of gynecological cancer-related death in women worldwide. N6-methyladenosine (m6 A) is the most abundant internal modification in eukaryotic RNA. Human insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), an m6 A reader, can enhance mRNA stability and promote translation by recognizing m6 A modifications. Its tumor-promoting effects have been demonstrated in several cancers. However, the roles of m6 A modification and IGF2BP2 in OC remain unclear. Here, by using methylated RNA immunoprecipitation sequencing, we demonstrated that there is widespread dysregulation of m6 A modification in OC tissues. The m6 A modification and the mRNA and protein levels of IGF2BP2 were significantly elevated in OC. Overexpression of IGF2BP2 facilitated OC cell proliferation, migration, and invasion in vitro and accelerated tumor growth and metastasis in vivo. While IGF2BP2-knockdown showed the opposite effect. Mechanistically, we identified cytoskeleton-associated protein 2-like (CKAP2L) as a target of IGF2BP2. IGF2BP2 promoted CKAP2L translation dependent on m6 A modification, rather than affecting mRNA and protein stability. Overexpression of CKAP2L rescued the tumor-suppressive effect of IGF2BP2 knockdown in OC cells. In conclusion, this study revealed the potential role of IGF2BP2 in tumor progression, at least partially via promoting the translation of CKAP2L in an m6 A-dependent manner.

Keywords:  CKAP2L; IGF2BP2; N6-methyladenosine; ovarian cancer; translation

DOI:  https://doi.org/10.1096/fj.202202145RRR
Sci Rep. 2023 Sep 08. 13(1): 14872

The synergistic effect of EMT regulators and m6A modification on prognosis-related immunological signatures for ovarian cancer.

Yanna Zhang, Xun Wang, Xiaogang Duan, Ting Du, Xiancheng Chen.

Recently, there has been growing interest among researchers in exploring the effects of epithelial-mesenchymal transformation (EMT) or N6-Methyladenosine (m6A) modification regulators on tumor development. However, the synergistic efficiency of these regulators in relation to ovarian cancer development remains unclear. This study aims to explore the transcription patterns of main regulators, including 19 EMT and 22 m6A, in ovarian cancer samples from TCGA datasets and normal samples from GTEx datasets. After conducting a LASSO regression analysis, ten prognostic signatures were identified, namely KIAA1429, WTAP, SNAI1, AXL, IGF2BP1, ELAVL1, CBLL1, CDH2, NANOG and ALKBH5. These signatures were found to have a comprehensive effect on immune infiltrating signatures and the final prognostic outcome. Next, utilizing the ssGSEA algorithm and conducting overall survival analyses, we have identified the key prognosis-related immunological signatures in ovarian cancer to be ALKBH5, WTAP, ELAVL1, and CDH2 as the regulators. The characteristic immune response and related genetic expression have revealed a significant correlation between the alteration of m6A regulators and EMT regulators, indicating a synergistic effect between these two factors in the development of ovarian cancer. In summary, our research offers a novel perspective and strategy to enhance the occurrence, progression, and prognosis of ovarian cancer.

DOI: https://doi.org/10.1038/s41598-023-41554-y
Technol Health Care. 2023 Aug 24.

The m6A reader HNRNPC predicts adverse prognosis and promotes the progression of colorectal cancer.

Yong Ming Yu, Yang Hu.

   BACKGROUND: As a critical m6A RNA methylation regulator, HNRNPC has been revealed to serve as potential biomarkers in various human cancers. The specific expression and significance of HNRNPC in colorectal cancer remain unknown.
OBJECTIVE: This study aimed to confirm HNRNPC expression level and evaluate its function in colorectal cancer progression.
METHODS: 101 paired tissue samples were collected from colorectal cancer patients. HNRNPC levels in colorectal cancer were detected using PCR. CCK8 and transwell assays were conducted to estimate the effect of HNRNPC on cell growth and metastasis with the regulation of HNRNPC by cell transfection.
RESULTS: Upregulated HNRNPC was observed in colorectal cancer compared with normal tissues and cells. The higher HNRNPC levels in tumor tissues were associated with the advanced TNM stage and positive lymph node metastasis. Meanwhile, HNRNPC upregulation could indicate adverse outcomes of colorectal cancer patients. In vitro, the knockdown of HNRNPC significantly suppressed the proliferation, migration, and invasion of colorectal cancer cells.
CONCLUSIONS: Upregulated HNRNPC served as a biomarker for the prognosis and development of colorectal cancer, which provides a novel therapeutic target for colorectal cancer.

Keywords:  HNRNPC; N6-methyladenosine (m6A); colorectal cancer; prognosis; progression

DOI:  https://doi.org/10.3233/THC-230429
Biosens Bioelectron. 2023 Aug 30. pii: S0956-5663(23)00587-0. [Epub ahead of print]240 115645

RNA methylation-driven assembly of fluorescence-encoded nanostructures for sensitive detection of m6A modification writer METTL3/14 complex in human breast tissues.

Wen-Jing Liu, Lu-Yao Wang, Zhimei Sheng, Baogang Zhang, Xiaoran Zou, Chun-Yang Zhang.

  N6-methyladenosine (m6A) is an ubiquitous post-transcriptional modification catalyzed by METTL3/14 complex in eukaryotic mRNAs. The abnormal METTL3/14 complex activity affects multiple steps of RNA metabolism and may induce various diseases. Herein, we demonstrate the RNA methylation-driven assembly of fluorescence-encoded nanostructures for sensitive detection of m6A modification writer METTL3/14 complex in human breast tissues. METTL3/14 complex can catalyze the methylation of RNA probe to prevent it from being cleaved by MazF. The intact RNA probe is recognized by the magnetic bead (MB)-capture probe conjugates to induce duplex-specific nuclease (DSN)-assisted cyclic digestion, exposing numerous shorter ssDNAs with 3'-OH end. The shorter ssDNAs on the MB surface can act as the primers to initiate terminal deoxynucleotidyl transferase (TdT)-enhanced tyramide signal amplification (TSA), forming the Cy5 fluorescence-encoded nanostructures. After magnetic separation, the Cy5 fluorescence-encoded nanostructures are digested by DNase I to release abundant Cy5 ﬂuorophores that can be simply quantified by ﬂuorescence measurement. This assay achieves good specificity and high sensitivity with a detection limit of 58.8 aM, and it can screen METTL3/14 complex inhibitors and quantify METTL3/14 complex activity at the single-cell level. Furthermore, this assay can differentiate the METTL3/14 complex level in breast cancer patient tissues and healthy volunteer tissues.

Keywords:  Fluorescence-encoded nanostructures; METTL3/14 complex; Molecular diagnostics; N(6)-methyladenosine; RNA methylation

DOI:  https://doi.org/10.1016/j.bios.2023.115645
J Nutr Biochem. 2023 Sep 02. pii: S0955-2863(23)00170-5. [Epub ahead of print] 109437

Branched-chain amino acids prevent obesity by inhibiting the cell cycle in an NADPH-FTO-m6A coordinated manner.

Chaoqun Huang, Yaojun Luo, Botao Zeng, Yushi Chen, Youhua Liu, Wei Chen, Xing Liao, Yuxi Liu, Yizhen Wang, Xinxia Wang.

  Obesity has become a major health crisis in the past decades. Branched-chain amino acids (BCAAs), a class of essential amino acids, exerted beneficial health effects with regard to obesity and its related metabolic dysfunction, although the underlying reason is unknown. Here, we show that BCAAs supplementation alleviates high-fat diet (HFD)-induced obesity and insulin resistance in mice and inhibits adipogenesis in 3T3-L1 cells. Further, we find that BCAAs prevent the mitotic clonal expansion (MCE) of preadipocytes by reducing cyclin A2 (CCNA2) and cyclin-dependent kinase 2 (CDK2) expression. Mechanistically, BCAAs decrease the concentration of nicotinamide adenine dinucleotide phosphate (NADPH) in adipose tissue and 3T3-L1 cells by reducing glucose-6-phosphate dehydrogenase (G6PD) expression. The decreased NADPH attenuates the expression of fat mass and obesity-associated (FTO) protein, a well-known m6A demethylase, to increase the N6-methyladenosine (m6A) levels of Ccna2 and Cdk2 mRNA. Meanwhile, the high m6A levels of Ccna2 and Cdk2 mRNA are recognized by YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), which results in mRNA decay and reduction of their protein expressions. Overall, our data demonstrate that BCAAs inhibit obesity and adipogenesis by reducing CDK2 and CCNA2 expression via an NADPH-FTO-m6A coordinated manner in vivo and in vitro, which raises a new perspective on the role of m6A in the BCAAs regulation of obesity and adipogenesis.

Keywords:  Adipogenesis; BCAAs; Cell cycle; FTO; NADPH

DOI:  https://doi.org/10.1016/j.jnutbio.2023.109437
Thorac Cancer. 2023 Sep 05.

N6 -methyladenosine-modified circFUT8 competitively interacts with YTHDF2 and miR-186-5p to stabilize FUT8 mRNA to promote malignant progression in lung adenocarcinoma.

Gaochao Dong, Yingkuan Liang, Bing Chen, Te Zhang, Hui Wang, Yuzhong Chen, Yijian Zhang, Feng Jiang, Yaping Wang.

   BACKGROUND: Lung cancer is the leading cause of cancer related to mortality worldwide, and the main pathological type is lung adenocarcinoma (LUAD). Circular RNAs (circRNAs) have been reported to be modified by N6 -methyladenosine (m6A), which is involved in the progression of diverse tumors. However, the crosstalk between circRNAs and m6A modification has not been well elucidated in LUAD.
METHODS: MeRIP-seq and YTHDF2-RIP-seq datasets were explored to identify candidate circRNAs modified by YTHDF2. Dual-luciferase reporter assay, RIP, and rescue assays were performed to explore the relationship between circFUT8 and its parent mRNA of FUT8. In vitro and in vivo experiments were utilized to uncover the function of circFUT8.
RESULTS: In this study, we identified a novel m6A-modified circFUT8, derived from exon 3 of FUT8, which was elevated in tumor tissues compared with adjacent noncancerous tissues. The m6A reader YTHDF2 recognized and destabilized circFUT8 in an m6A-dependent manner. YTHDF2 also combined with the line form of FUT8 (mFUT8), and circFUT8 competitively interacted with YTHDF2, blunting its binding to mFUT8, to stabilize the mRNA level of FUT8. Additionally, circFUT8 sponged miR-186-5p to elevate the expression of mFUT8. Finally, we revealed that circFUT8 promoted the malignant progression of LUAD dependent on the oncogenic function of FUT8.
CONCLUSIONS: These findings identified a novel m6A-modified circFUT8 recognized and destabilized by YTHDF2, which competitively interacted with YTHDF2 and miR-186-5p to stabilize FUT8 mRNA to promote malignant progression in LUAD.

Keywords:  N6-methyladenosine; YTHDF2; circFUT8; lung adenocarcinoma; miR-186-5p

DOI:  https://doi.org/10.1111/1759-7714.15086
Front Oncol. 2023 ;13 1227016

Dissecting the effects of METTL3 on alternative splicing in prostate cancer.

Lin Wang, Ling Shi, Yonghao Liang, Judy Kin-Wing Ng, Chan Hoi Yin, Lingyi Wang, Jinpao Hou, Yiwei Wang, Cathy Sin-Hang Fung, Peter Ka-Fung Chiu, Chi-Fai Ng, Stephen Kwok-Wing Tsui.

  Although the role of METTL3 has been extensively studied in many cancers, its role in isoform switching in prostate cancer (PCa) has been poorly explored. To investigate its role, we applied standard RNA-sequencing and long-read direct RNA-sequencing from Oxford Nanopore to examine how METTL3 affects alternative splicing (AS) in two PCa cell lines. By dissecting genome-wide METTL3-regulated AS events, we noted that two PCa cell lines (representing two different PCa subtypes, androgen-sensitive or resistant) behave differently in exon skipping and intron retention events following METTL3 depletion, suggesting AS heterogeneity in PCa. Moreover, we revealed that METTL3-regulated AS is dependent on N6-methyladenosine (m6A) and distinct splicing factors. Analysis of the AS landscape also revealed cell type specific AS signatures for some genes (e.g., MKNK2) involved in key functions in PCa tumorigenesis. Finally, we also validated the clinical relevance of MKNK2 AS events in PCa patients and pointed to the possible regulatory mechanism related to m6A in the exon14a/b region and SRSF1. Overall, we characterize the role of METTL3 in regulating PCa-associated AS programs, expand the role of METTL3 in tumorigenesis, and suggest that MKNK2 AS events may serve as a new potential prognostic biomarker.

Keywords:  METTL3; MKNK2; N 6 -methyladenosine; RNA splicing; nanopore direct RNA sequencing; prostate cancer

DOI:  https://doi.org/10.3389/fonc.2023.1227016
Front Immunol. 2023 ;14 1221609

Emerging role of METTL3 in inflammatory diseases: mechanisms and therapeutic applications.

Bimei Song, Yue Zeng, Yanqing Cao, Jiamin Zhang, Chao Xu, Yaping Pan, Xida Zhao, Jingbo Liu.

  Despite improvements in modern medical therapies, inflammatory diseases, such as atherosclerosis, diabetes, non-alcoholic fatty liver, chronic kidney diseases, and autoimmune diseases have high incidence rates, still threaten human health, and represent a huge financial burden. N6-methyladenosine (m6A) modification of RNA contributes to the pathogenesis of various diseases. As the most widely discussed m6A methyltransferase, the pathogenic role of METTL3 in inflammatory diseases has become a research hotspot, but there has been no comprehensive review of the topic. Here, we summarize the expression changes, modified target genes, and pathogenesis related to METTL3 in cardiovascular, metabolic, degenerative, immune, and infectious diseases, as well as tumors. In addition to epithelial cells, endothelial cells, and fibroblasts, METTL3 also regulates the function of inflammation-related immune cells, including macrophages, neutrophils, dendritic cells, Th17 cells, and NK cells. Regarding therapeutic applications, METTL3 serves as a target for the treatment of inflammatory diseases with natural plant drug components, such as emodin, cinnamaldehyde, total flavonoids of Abelmoschus manihot, and resveratrol. This review focuses on recent advances in the initiation, development, and therapeutic application of METTL3 in inflammatory diseases. Knowledge of the specific regulatory mechanisms involving METTL3 can help to deepen understanding of inflammatory diseases and lay the foundation for the development of precisely targeted drugs to address inflammatory processes.

Keywords:  METTL3; immune cell; inflammation; inflammatory diseases; m6A modification; therapy

DOI:  https://doi.org/10.3389/fimmu.2023.1221609
Exp Cell Res. 2023 Aug 31. pii: S0014-4827(23)00312-9. [Epub ahead of print] 113764

Hypoxia promotes immune escape of pancreatic cancer cells by lncRNA NNT-AS1/METTL3-HuR-mediated ITGB1 m6A modification.

Yebin Lu, Qizhen Chen, Shuai Zhu, Xuejun Gong.

  Pancreatic cancer (PC) cell immune escape is a crucial element in PC malignant development. Some previous studies have reported that LncRNA NNT-AS1 played a carcinogenic role in various tumors. However, the effect of lncRNA NNT-AS1 in PC cell immune escape remains unclear. To evaluate PC cell immune escape, PC cells were co-cultured with CD8+ T cells under a hypoxic condition. PC cell proliferation and migration were evaluated using the colony formation assay and transwell assay. CD8+ T cell proliferation and apoptosis were measured using the carboxy fluorescein diacetate succinimidyl ester (CFSE) assay and flow cytometry. The secretion of antitumor cytokines was assessed using enzyme-linked immunosorbent assay (ELISA). The molecular interactions were analyzed using chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP), or dual-luciferase reporter gene assays. A tumor xenograft model was established to evaluate the effects of lncRNA NNT-AS1 on PC in vivo. It was found that lncRNA NNT-AS1 was highly expressed in PC, and its silencing inhibited hypoxia-induced PC cell growth and immune escape in vivo and in vitro. Mechanically, HIF-1α transcriptionally activated NNT-AS1 expression and NNT-AS1 increased ITGB1 stability and expression in a METTL3-HuR dependent manner. ITGB1 overexpression reversed the inhibitory effects of NNT-AS1 knockdown on hypoxia-induced PC cell immune escape. In conclusion, Hypoxia promoted PC cell immune escape through lncRNA NNT-AS1/METTL3-HuR-mediated m6A modification to increase ITGB1 expression, which provided a theoretical foundation and a potential therapeutic target for PC.

Keywords:  Hypoxia; Immune escape; Pancreatic cancer; lncRNA NNT-AS1; m(6)A

DOI:  https://doi.org/10.1016/j.yexcr.2023.113764
Sci Rep. 2023 Sep 07. 13(1): 14704

Distinct N7-methylguanosine profiles of circular RNAs in drug-resistant acute myeloid leukemia.

Jinqiu Fu, Libo Si, Yao Zhou, Dong Li, Ran Wang.

Post-transcriptional methylation modifications, such as the N7-methylguanosine (m7G) modification, are increasingly acknowledged for their role in the development and resistance to chemotherapy in acute myeloid leukemia (AML). This study employed MeRIP-seq technology to investigate the m7G sites within circular RNAs (circRNAs) derived from human AML cells and drug-resistant AML cells, in order to identify these sites more comprehensively. In addition, a detailed analysis of the relationship between m7G and drug-resistant AML was conducted. The bioinformatics analysis was utilized to predict the functions of specific methylated transcripts. The findings revealed a significant difference in m7G level between AML cells and drug-resistant AML cells, suggesting a potentially critical role of m7G in circRNAs in drug-resistant AML development. The methylation of M7G could affect the circRNA-miRNA-mRNA co-expression during the development of AML resistance, which could further influence the regulation of resistance-associated target genes in AML. Furthermore, gene ontology analysis indicated that the distinct distribution pattern of circRNAs with m7G methylation in drug-resistant AML cells was correlated with metabolism-related pathways. These results suggested a potential association between drug-resistant AML and m7G methylation of circRNAs. Moreover, the results revealed a novel role of m7G RNA methylation in circRNAs in the progression of AML chemoresistance.

DOI: https://doi.org/10.1038/s41598-023-41974-w
Cell Death Dis. 2023 09 06. 14(9): 591

METTL16 controls Kaposi's sarcoma-associated herpesvirus replication by regulating S-adenosylmethionine cycle.

Xinquan Zhang, Wen Meng, Jian Feng, Xinghong Gao, Chao Qin, Pinghui Feng, Yufei Huang, Shou-Jiang Gao.

Oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) consists of latent and lytic replication phases, both of which are important for the development of KSHV-related cancers. As one of the most abundant RNA modifications, N6-methyladenosine (m6A) and its related complexes regulate KSHV life cycle. However, the role of METTL16, a newly discovered RNA methyltransferase, in KSHV life cycle remains unknown. In this study, we have identified a suppressive role of METTL16 in KSHV lytic replication. METTL16 knockdown increased while METTL16 overexpression reduced KSHV lytic replication. METTL16 binding to and writing of m6A on MAT2A transcript are essential for its splicing, maturation and expression. As a rate-limiting enzyme in the methionine-S-adenosylmethionine (SAM) cycle, MAT2A catalyzes the conversion of L-methionine to SAM required for the transmethylation of protein, DNA and RNA, transamination of polyamines, and transsulfuration of cystathionine. Consequently, knockdown or chemical inhibition of MAT2A reduced intracellular SAM level and enhanced KSHV lytic replication. In contrast, SAM treatment was sufficient to inhibit KSHV lytic replication and reverse the effect of the enhanced KSHV lytic program caused by METTL16 or MAT2A knockdown. Mechanistically, METTL16 or MAT2A knockdown increased while SAM treatment decreased the intracellular reactive oxygen species level by altering glutathione level, which is essential for efficient KSHV lytic replication. These findings demonstrate that METTL16 suppresses KSHV lytic replication by modulating the SAM cycle to maintain intracellular SAM level and redox homeostasis, thus illustrating the linkage of KSHV life cycle with specific m6A modifications, and cellular metabolic and oxidative conditions.

DOI: https://doi.org/10.1038/s41419-023-06121-3
Wiley Interdiscip Rev RNA. 2023 Sep 06. e1810

Ghost authors revealed: The structure and function of human N6 -methyladenosine RNA methyltransferases.

Kurtis Breger, Charlotte N Kunkler, Nathan J O'Leary, Jacob P Hulewicz, Jessica A Brown.

  Despite the discovery of modified nucleic acids nearly 75 years ago, their biological functions are still being elucidated. N6 -methyladenosine (m6 A) is the most abundant modification in eukaryotic messenger RNA (mRNA) and has also been detected in non-coding RNAs, including long non-coding RNA, ribosomal RNA, and small nuclear RNA. In general, m6 A marks can alter RNA secondary structure and initiate unique RNA-protein interactions that can alter splicing, mRNA turnover, and translation, just to name a few. Although m6 A marks in human RNAs have been known to exist since 1974, the structures and functions of methyltransferases responsible for writing m6 A marks have been established only recently. Thus far, there are four confirmed human methyltransferases that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM) to the N6 position of adenosine, producing m6 A: methyltransferase-like protein (METTL) 3/METTL14 complex, METTL16, METTL5, and zinc-finger CCHC-domain-containing protein 4. Though the methyltransferases have unique RNA targets, all human m6 A RNA methyltransferases contain a Rossmann fold with a conserved SAM-binding pocket, suggesting that they utilize a similar catalytic mechanism for methyl transfer. For each of the human m6 A RNA methyltransferases, we present the biological functions and links to human disease, RNA targets, catalytic and kinetic mechanisms, and macromolecular structures. We also discuss m6 A marks in human viruses and parasites, assigning m6 A marks in the transcriptome to specific methyltransferases, small molecules targeting m6 A methyltransferases, and the enzymes responsible for hypermodified m6 A marks and their biological functions in humans. Understanding m6 A methyltransferases is a critical steppingstone toward establishing the m6 A epitranscriptome and more broadly the RNome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Keywords:  N6-methyladenosine; RNA methyltransferase; RNA modification

DOI:  https://doi.org/10.1002/wrna.1810
Biol Reprod. 2023 Sep 04. pii: ioad109. [Epub ahead of print]

The role of PGRMC2 in the trophoblast invasion.

Tae Yokouchi-Konishi, Yongjie Liu, Liping Feng.

  Proper extravillous trophoblasts (EVTs) invasion is essential for normal placentation and pregnancy. However, the molecular mechanisms by which cytotrophoblasts (CTBs) differentiate into EVTs are unclear. We discovered that in the first trimester placentae, PGRMC2 was highly expressed in syncytiotrophoblast (STB) but significantly lower in EVTs and CTBs, indicating a divergent role for PGRMC2 in trophoblast functions. We aim to examine the role of PGRMC2 in EVTs invasion mediated by both intracellular and extracellular signals. PGRMC2 knockdown and overexpression cells were established in HTR8/SVneo cells, a first-trimester EVTs-derived cell model, by transfection with siRNA or PGRMC2 plasmids, respectively. We studied cell morphology through microscope observation and immunofluorescent staining for an epithelial biomarker, cytokeratin, and a mesenchymal biomarker, vimentin. The proliferation, invasiveness, and angiogenesis of HTR8/SVneo cells were assessed using an MTS assay, a 24-well Matrigel invasion chamber plates, and a tube formation assay, respectively. The expression of Hypoxia-Inducible Factor 1 α (HIF1α) was examined by Western blot and RT-qPCR. The methylation and translocation of HIF1α mRNA were examined by RNA immunoprecipitation and cellular fraction followed by RT-qPCR. Culture supernatants were assessed for mediating the invasiveness of these cells. PGRMC2 knockdown led to cellular morphological changes, specifically, an epithelial-mesenchymal cell transition, enhanced trophoblast proliferation, and invasion, and promoted tube formation. These effects were mediated by the activation of HIF1α and an increased expression of vascular endothelial growth factor A, a HIF1α target gene in PGRMC2 knockdown cells. The inhibition of HIF1α protein degradation through downregulation of HIF1AN and enhanced HIF1α mRNA stability through reduced HIF1A-AS2 and methylation (m6A levels) in HIF1α mRNA were attributed to the sustained activation of HIF1α in PGRMC2 knockdown EVTs. The dysregulation of methyltransferases by PGRMC2 pointed to the decreased mRNA methylation including downregulation of METTL3, METTL14, YTHDC2, and upregulated IGF2BP3. The culture supernatant collected from PGRMC2 knockdown cells did not significantly affect EVT invasion compared to the controls, indicating that extracellular signaling did not robustly regulate EVT invasion in this study. In conclusion, PGRMC2 plays a role in placentation by promoting cell proliferation, invasion, and angiogenesis in EVTs via activation of HIF1α signaling. We thus identified a new function of PGRMC2 and provide insights on understanding the mechanisms of trophoblast invasion.

Keywords:  HIF1α; PGRMC2; Trophoblasts invasion; m6A

DOI:  https://doi.org/10.1093/biolre/ioad109
Aging (Albany NY). 2023 Sep 05. 15

HNRNPA2B1 is a potential biomarker of breast cancer related to prognosis and immune infiltration.

Aisikeer Ayoufu, Lina Yi, Muhairemu Tuersuntuoheti, Yongtao Li.

   OBJECTIVE: HNRNPA2B1, one of the regulator of m6A methylation, is involved in a wide range of physiological processes. However, the aberrant expression of HNRNPA2B1 in Breast Cancer (BC) and its clinical significance still need to be further studied.
METHODS: We used related databases to analyze the relationship between HNRNPA2B1 and BC by bioinformatics. Then, we further detected the expression of HNRNPA2B1 by immunohistochemical method, and analyzed the relationship between it and the prognosis of breast cancer by COX regression method.
RESULTS: In the study, we found that the expression level of HNRNPA2B1 in breast cancer (BC) was significantly higher than that in normal breast tissues. In addition, the expression level of HNRNPA2B1 in BC samples was significantly correlated with clinical indexes such as TNM stage. The Cox analysis revealed that the expression of HNRNPA2B1 in BC had significant clinical prognostic value. The results of immune infiltration of HNRNPA2B1 showed that there was a significant correlation between HNRNPA2B1 and immune cell subsets.
CONCLUSION: Our results show that the expression of HNRNPA2B1 in BC has important clinical diagnostic significance and high expression may be related with poor clinical outcome of BC. This helps to provide us with a new direction of BC targeted therapy.

Keywords:  HNRNPA2B1; breast cancer; immune infiltration; m6A; prognosis

DOI:  https://doi.org/10.18632/aging.204992
BMC Cancer. 2023 Sep 04. 23(1): 825

TET2 inhibits the proliferation and metastasis of lung adenocarcinoma cells via activation of the cGAS-STING signalling pathway.

Gui Cheng, Jun Wu, Mei Ji, Wenwei Hu, Changping Wu, Jingting Jiang.

   BACKGROUND: Effective identification and development of new molecular methods for the diagnosis, treatment and prognosis of lung adenocarcinoma (LUAD) remains an urgent clinical need. DNA methylation patterns at cytosine bases in the genome are closely related to gene expression, and abnormal DNA methylation is frequently observed in various cancers. The ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) and promote locus-specific DNA methylation reversal. This study aimed to explore the role of the TET2 protein and its downstream effector, 5-hmC/5-mC DNA modification, in LUAD progression.
METHODS: The expression of TET2 was analysed by real-time PCR, Western blotting and immunohistochemistry. The 5-hmC DNA content was determined by a colorimetric kit. Activation of the cGAS-STING signalling pathway was evaluated by Western blotting. CCK-8, wound healing and Transwell assays were performed to evaluate the effect of TET2 on cell proliferation, migration and invasion abilities. A xenograft model was used to analyse the effect of TET2 on the tumorigenic ability of A549 cells.
RESULTS: TET2 overexpression decreased proliferation and metastasis of A549 and H1975 cells in vitro and in vivo. However, TET2 knockdown dramatically enhanced the proliferation, migration and invasion of A549 and H1975 cells. Mechanistically, activation of the cGAS-STING signalling pathway is critical for the TET2-mediated suppression of LUAD cell tumorigenesis and metastasis.
CONCLUSION: In this study, we demonstrate a tumour suppressor role of TET2 in LUAD, providing new potential molecular therapeutic targets and clinical therapies for patients with non-small cell lung cancer.

Keywords:  5hmC; DNA hydroxymethylation; Non-Small Cell Lung Cancer; TET2; cGAS-STING signaling

DOI:  https://doi.org/10.1186/s12885-023-11343-x
Eur J Med Res. 2023 Sep 07. 28(1): 321

m1A Regulatory gene signatures are associated with certain immune cell compositions of the tumor microenvironment and predict survival in kidney renal clear cell carcinoma.

Linjun Zhou, Weidong Zhou, Yuan Li, Ruifang Hua.

Adenosine N1 methylation (m1A) of RNA, a type of post-transcriptional modification, has been shown to play a significant role in the progression of cancer. The objective of the current research was to analyze the genetic alteration and prognostic significance of m1A regulators in kidney renal clear cell carcinoma (KIRC). Genomic and clinicopathological characteristics were obtained from 558 KIRC patients in the Cancer Genome Atlas (TCGA) and Gene Omnibus Expression (GEO) databases. Alterations in the gene expression of ten m1A-regulators were analyzed and survival analysis was performed using the Cox regression method. We also identified three clusters of patients based on their distinct m1A alteration patterns, using integrated analysis of the ten m1A-related regulators, which were significantly related to overall survival (OS), disease-free survival (DFS) and tumor microenvironment (TME) immune cell infiltration cells in KIRC. Our findings showed that m1A alteration patterns have critical roles in determining TME complexity and its immune cell composition. Furthermore, different m1A expression patterns were significantly associated with DFS and OS rates in KIRC patients. In conclusion, the identified m1A RNA modification patterns offer a potentially effective way to classify KIRC patients based on their TME immune cell infiltration, enabling the development of more personalized and successful treatment strategies for these patients.

DOI: https://doi.org/10.1186/s40001-023-01292-3
Aging (Albany NY). 2023 Sep 06. 15

Integrative analyses reveal biological function and prognostic role of m7G methylation regulators in high-grade glioma.

Xiaoli Li, Yanyan Li, Na Li, Liangfang Shen, Zhanzhan Li.

  Based on 29 m7G regulators, glioma patients were categorized into three groups using data from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets. Distinct characteristics were observed in immune cell infiltration, functional enrichment, and clinical prognosis for every glioma subtype. Analyzing the differentially expressed genes (DEGs) confirmed the distinction among the three m7G clusters. A predictive tool for overall survival (OS) in high-grade glioma patients was developed and confirmed, consisting of 13 m7G regulators forming a prognostic signature. Elevated m7G levels were found to be associated with increased tumor mutation burden and immune activation, indicating a tumor microenvironment characterized by inflammation and a lower overall survival rate. In contrast, reduced m7G scores were linked to a deficiency in immune infiltration, a low burden of mutations, and a non-inflamed phenotype, suggesting a more positive clinical outlook. Additionally, the m7G risk scores were found to impact chemotherapy sensitivity. The m7G predictive pattern shows potential as a marker for the overall survival of patients with high-grade glioma. By significantly improving our comprehension of the functional role of m7G regulators in the advancement of glioma and their impact on clinical results, this study offers valuable perspectives for precision therapy in the management of high-grade glioma.

Keywords:  high-grade glioma; immune infiltration; m7G methylation; prognosis

DOI:  https://doi.org/10.18632/aging.204999