bims-rimeca 2022-11-27 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022–11–27
38 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

Novel insights into the N6-methyladenosine RNA modification and phytochemical intervention in lipid metabolism.
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.
RNA N6-Methyladenosine (m6A) Methyltransferase-like 3 Facilitates Tumorigenesis and Cisplatin Resistance of Arecoline-Exposed Oral Carcinoma.
Role of m6A modification in dysregulation of Wnt/β-catenin pathway in cancer.
WTAP dysregulation-mediated HMGN3-m6A modification inhibited trophoblast invasion in early-onset preeclampsia.
N6-Methyladenosine Modification of CIRCKRT17 Initiated by METTL3 Promotes Osimertinib Resistance of Lung Adenocarcinoma by EIF4A3 to Enhance YAP1 Stability.
Systematic analysis of the expression profile and prognostic significance of m6A regulators and PD-L1 in hepatocellular carcinoma.
N6-methyladenosine (m6A) RNA methylation mediated by methyltransferase complex subunit WTAP regulates amelogenesis.
YTHDC1 Promotes Stemness Maintenance and Malignant Progression in Head and Neck Squamous Cell Carcinoma.
m6A-SAC-seq for quantitative whole transcriptome m6A profiling.
Construction and clinical evaluation of N6-methyladenosine risk signature of YTHDC2, IGF2BP2, and HNRNPC in head and neck squamous cell carcinoma.
m6A contributes to a pro-survival state in GC-2 cells by facilitating DNA damage repair: Novel perspectives on the mechanism underlying DEHP genotoxicity in male germ cells.
The landscape of N6-methyladenosine modification patterns and altered transcript profiles in the cardiac-specific deletion of natriuretic peptide receptor A.
ALKBH5 in mouse testicular Sertoli cells regulates Cdh2 mRNA translation to maintain blood-testis barrier integrity.
Implications of m6A-associated snRNAs in the prognosis and immunotherapeutic responses of hepatocellular carcinoma.
KIAA1429 mediates epithelial mesenchymal transition in sorafenib-resistant hepatocellular carcinoma through m6A methylation modification.
Glutamate from nerve cells promotes perineural invasion in pancreatic cancer by regulating tumor glycolysis through HK2 mRNA-m6A modification.
m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site.
Identification and validation of an m6A-related gene signature to predict prognosis and evaluate immune features of breast cancer.
Comparative Genomics and Functional Studies of Putative m6A Methyltransferase (METTL) Genes in Cotton.
Oxidative Phosphorylation-Related Signature Participates in Cancer Development, and PTPRG Overexpression Suppresses the Cancer Progression in Clear Cell Renal Cell Carcinoma.
HDLBP-stabilized lncFAL inhibits ferroptosis vulnerability by diminishing Trim69-dependent FSP1 degradation in hepatocellular carcinoma.
NEAT1 promotes the malignant development of bladder cancer by regulating the miR-101/VEGF-C pathway in vitro and in vivo.
m6A-modified lincRNA Dubr is required for neuronal development by stabilizing YTHDF1/3 and facilitating mRNA translation.
USP10 Alleviates Palmitic Acid-induced Steatosis through Autophagy in HepG2 Cells.
Adenosine deaminase acting on RNA-1 is essential for early B lymphopoiesis.
RRP9 promotes gemcitabine resistance in pancreatic cancer via activating AKT signaling pathway.
DNA5mC Regulator-Mediated Molecular Clusters and Tumor Microenvironment Signatures in Glioblastoma.
Deficiency of carbamoyl phosphate synthetase 1 engenders radioresistance in hepatocellular carcinoma via deubiquitinating c-Myc.
Macrophage membrane-coated nanovesicles for dual-targeted drug delivery to inhibit tumor and induce macrophage polarization.
LncRNA HCG18 promotes M2 macrophage polarization to accelerate cetuximab resistance in colorectal cancer through regulating miR-365a-3p/FOXO1/CSF-1 axis.
LCMT1 indicates poor prognosis and is essential for cell proliferation in hepatocellular carcinoma.
METTL16 regulates m6A methylation on chronic hepatitis B associated gene HLA-DPB1 involved in liver fibrosis.
NSUN5 promotes progression and predicts poor prognosis in hepatocellular carcinoma.
Dynamic regulation of eEF1A1 acetylation affects colorectal carcinogenesis.
Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications.
HDAC1/3-dependent moderate liquid-liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation.
N6-methyladenosine RNA methylation: From regulatory mechanisms to potential clinical applications.

Toxicol Appl Pharmacol. 2022 Nov 22. pii: S0041-008X(22)00468-9. [Epub ahead of print] 116323

Novel insights into the N6-methyladenosine RNA modification and phytochemical intervention in lipid metabolism.

Linghuan Li, Yuanhai Sun, Weiwei Zha, Lingqing Li, Hanbing Li.

  Epitranscriptome (RNA modification) plays a vital role in a variety of biological events. N6-methyladenosine (m6A) modification is the most prevalent mRNA modification in eukaryotic cells. Dynamic and reversible m6A modification affects the plasticity of epitranscriptome, which plays an essential role in lipid metabolism. In this review, we comprehensively delineated the role and mechanism of m6A modification in the regulation of lipid metabolism in adipose tissue and liver, and summarized phytochemicals that improve lipid metabolism disturbance by targeting m6A regulator, providing potential lead candidates for drug therapeutics. Moreover, we discussed the main challenges and possible future directions in this field.

Keywords:  Lipid metabolism; MAFLD; N(6)-methyladenosine; Obesity

DOI:  https://doi.org/10.1016/j.taap.2022.116323
Elife. 2022 Nov 24. pii: e84034. [Epub ahead of print]11

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

Radhika A Varier, Theodora Sideri, Charlotte Capitanchik, Zornitsa Manova, Enrica Calvani, Alice Rossi, Raghu R Edupuganti, Imke Ensinck, Vincent W C Chan, Harshil Patel, Joanna Kirkpatrick, Peter Faull, Ambrosius P Snijders, Michiel Vermeulen, Markus Ralser, Jernej Ule, Nicholas M Luscombe, Folkert Jacobus van Werven.

  N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3'end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.

Keywords:  S. cerevisiae; biochemistry; chemical biology; chromosomes; gene expression

DOI:  https://doi.org/10.7554/eLife.84034
Cells. 2022 Nov 14. pii: 3605. [Epub ahead of print]11(22):

RNA N6-Methyladenosine (m6A) Methyltransferase-like 3 Facilitates Tumorigenesis and Cisplatin Resistance of Arecoline-Exposed Oral Carcinoma.

Chuang Wang, Chamila Kadigamuwa, Songlv Wu, Yijun Gao, Wuya Chen, Yangcong Gu, Shengli Wang, Xia Li.

   BACKGROUND: Arecoline is known as the main active carcinogen found in areca nut extract that drives the pathological progression of oral squamous cell carcinoma (OSCC). Studies have revealed that dysregulation of RNA N6-methyladenosine (m6A) methyltransferase components is intimately linked to cancer initiation and progression, including oral cancer.
METHODS: The arecoline-induced dysregulated methyltransferase-like 3 (METTL3) gene was identified using RNA-seq transcriptome assay. Using in vitro and in vivo models, the biological roles of METTL3 in arecoline-transformed oral cancer were examined.
RESULTS: We found that METTL3 was markedly elevated in arecoline-exposed OSCC cell lines and OSCC tissues of areca nut chewers. We identified that hypoxia-inducible factor 1-alpha (HIF-1α) stimulated METTL3 expression at the transcriptional level and further proved that METTL3-MYC-HIF-1α formed a positive autoregulation loop in arecoline-transformed OSCC cells. Subsequently, we manifested that METTL3 depletion profoundly reduced cell proliferation, cell migration, oncogenicity, and cisplatin resistance of arecoline-exposed OSCC cells.
CONCLUSIONS: Developing novel strategies to target METTL3 may be a potential way to treat OSCC patients, particularly those with areca nut chewing history and receiving cisplatin treatment.

Keywords:  arecoline; cisplatin resistance; methyltransferase-like 3; oral squamous cell carcinoma; tumorigenesis

DOI:  https://doi.org/10.3390/cells11223605
Biomed Pharmacother. 2022 Nov 18. pii: S0753-3322(22)01412-3. [Epub ahead of print]157 114023

Role of m6A modification in dysregulation of Wnt/β-catenin pathway in cancer.

Peyman Tabnak, Yaser Ghasemi, Mohammad Natami, Roya Khorram, Mohammad Ebrahimnezhad.

  N6-methyladenosine (m6A) modification is the most abundant post-transcriptional regulation of RNAs in eukaryotes. Dysregulation of m6A readers, writers, and erasers can significantly promote tumorigenesis by altering the expression of various genes. Wnt/β-catenin is an evolutionarily conserved signaling pathway that has recently been linked to the pathogenesis of many cancers. Given the significance of this pathway in regulating normal tissue homeostasis and stem cell differentiation, a subtle understanding of the molecular mechanism underlying its dysregulation is required for effective targeting. There is mounting evidence that m6A regulators are highly implicated in the dysregulation of the Wnt/β-catenin signaling pathway. Since m6A regulators can affect Wnt pathway components and dysregulation of either leads to carcinogenesis, this study aims to clarify the relationship between m6A regulators and the Wnt/β-catenin signaling pathway to investigate their combined impact on tumorigenesis.

Keywords:  Cancer; Epigenetic; N6-methyladenosine; Signaling pathway; Wnt/β-catenin; m6A erasers; m6A readers; m6A writers

DOI:  https://doi.org/10.1016/j.biopha.2022.114023
FASEB J. 2022 Dec;36(12): e22617

WTAP dysregulation-mediated HMGN3-m6A modification inhibited trophoblast invasion in early-onset preeclampsia.

Yue Bian, Jiapo Li, Hongfei Shen, Yuanyuan Li, Yue Hou, Ling Huang, Guiyu Song, Chong Qiao.

  Early-onset preeclampsia (ePE) originates from abnormal implantation and placentation that involves trophoblast invasion, but its pathophysiology is not entirely understood. N6-methyladenosine (m6A) regulators mediate the progression of various cancers. The invasiveness of trophoblast cells is similar to that of tumor cells. However, little is known regarding the potential role of m6A modification in ePE and the underlying mechanism. This study aimed to explore the m6A level in placental tissue samples collected from ePE patients and to investigate whether m6A modification was an essential part of PE pathogenesis. The m6A level in placental tissue samples of 80 PE participants was examined. MeRIP-microarray, RNA-Seq, luciferase reporter assay, and RNA immunoprecipitation chip (RIP) assay were performed. The m6A level in the ePE group was significantly reduced compared with the control group. Wilms' tumor 1-associating protein (WTAP) regulated trophoblast cell migration and invasion. Mechanistically, the high mobility group nucleosomal binding domain 3 (HMGN3) gene was a target gene of WTAP in trophoblast (p < .05). WTAP enhanced the stability of HMGN3 mRNA through binding with its 3'-UTR m6A site(+485A, +522A). HMGN3 was recognized by m6A recognition protein insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), which was inhibited when knocking down WTAP. Both m6A and WTAP levels were downregulated in ePE. The m6A modification mediated by WTAP/IGF2BP1/HMGN3 axis might contribute to abnormal trophoblast invasion. Our work provided a foundation for further exploration of RNA epigenetic regulatory patterns in ePE, and indicated a new treatment strategy for ePE.

Keywords:  N6-methyladenosine; WTAP; early-onset preeclampsia; preeclampsia; trophoblast

DOI:  https://doi.org/10.1096/fj.202200700RR
Cancers (Basel). 2022 Nov 14. pii: 5582. [Epub ahead of print]14(22):

N6-Methyladenosine Modification of CIRCKRT17 Initiated by METTL3 Promotes Osimertinib Resistance of Lung Adenocarcinoma by EIF4A3 to Enhance YAP1 Stability.

Ying Ji, Qing Zhao, Wei Feng, Yue Peng, Bin Hu, Qirui Chen.

   BACKGROUND: Circular RNAs (circRNAs) play a key role in regulating the drug resistance of numerous human tumors. However, whether circKRT17 involves in the osimertinib resistance of lung adenocarcinoma (LUAD) remains undetermined.
METHODS: Relative mRNA/circRNA and protein levels were detected by qRT-PCR and western blotting. Localization of circKRT17 and YAP1 was determined by FISH and immunofluorescence staining. Cell growth and apoptosis were evaluated using colony formation, EdU assays, and flow cytometry. The N6-methyladenosine (m6A) modification was analyzed by MeRIP. The interplay between EIF4A3 and circKRT17 or YAP1 was verified by RNA pull-down or/and RIP assays. Subcutaneous tumor growth was monitored in nude mice, and Ki-67 and TUNEL staining were carried out to evaluate cell proliferation and apoptosis, respectively.
RESULTS: CircKRT17 and METTL3 were elevated in osimertinib-insensitive LUAD tissues and cells. Knockdown of circKRT 17 and METTL3 increased the sensitivity of LUAD cells to osimertinib. Knockdown of METTL3 decreased the expression of circKRT17 by inhibiting m6A modification. CircKRT17 promoted the stability and nuclear transportation of YAP1 by recruiting EIF4A3 in LUAD cells. Overexpression of YAP1 abolished the impacts of circKRT17 knockdown on the osimertinib sensitivity of LUAD cells. CircKRT17 knockdown increased the repressive effects of osimertinib on tumor growth in vivo by inhibiting YAP1 signaling.
CONCLUSION: METTL3 initiated the m6A modification of circKRT17, thus promoting osimertinib resistance of LUAD by enhancing YAP1 stability through EIF4A4 recruitment.

Keywords:  YAP1 signaling; circKRT17; lung adenocarcinoma; m6A modification; osimertinib resistance

DOI:  https://doi.org/10.3390/cancers14225582
Discov Oncol. 2022 Nov 25. 13(1): 131

Systematic analysis of the expression profile and prognostic significance of m6A regulators and PD-L1 in hepatocellular carcinoma.

Fanhua Kong, Kunpeng Wang, Liezhi Wang.

   BACKGROUND: Hepatocellular carcinoma (HCC) is a malignant tumor with poor prognosis. N6-methyladenosine (m6A) modification has dual biological functions in RNA modification and plays an important role in HCC.
METHODS: The GEO, TCGA, ONCOMINE, UALCAN, GEPIA, Kaplan-Meier plotter, cBioPortal for Cancer Genomics, STRING and TIMER2 databases were used for bioinformatic analyses. Quantitative polymerase chain reaction and western blotting were used to detect the expression of m6A regulators in HCC tissues.
RESULTS: The transcription of m6A regulators was upregulated in patients with HCC, and overexpression of YTHDF1/2, YTHDC1, RBM15 and METTL3 was significantly correlated with clinical stages of HCC. In addition, downregulation of ZC3H13 and METTL14 and upregulation of other m6A regulators were associated with a poor prognosis. A high mutation rate (89%) of m6A regulators was also observed in patients with HCC, and mutations in methylation regulators were associated with poor overall survival and disease-free survival. Finally, the expression of the YTHDF family was significantly associated with immune infiltration in the HCC microenvironment.
CONCLUSION: m6A regulators and programmed death-ligand 1 may play an important role in the tumorigenesis and immune invasion and escape of HCC and may be risk factors affecting the survival of patients with HCC.

Keywords:  Bioinformatics analysis; Biomarker; Hepatocellular carcinoma (HCC); Immunology; N6-methyladenosine (m6A); Prognostic value

DOI:  https://doi.org/10.1007/s12672-022-00595-x
J Biol Chem. 2022 Nov 17. pii: S0021-9258(22)01158-9. [Epub ahead of print] 102715

N6-methyladenosine (m6A) RNA methylation mediated by methyltransferase complex subunit WTAP regulates amelogenesis.

Furong Xie, Xueqin Zhu, Xiao Liu, Hui Chen, Jun Wang.

  N6-methyladenosine (m6A) RNA methylation, one of the most widespread posttranscriptional modifications in eukaryotes, plays crucial roles in various developmental processes. The m6A modification process is catalyzed by a methyltransferase complex that includes Wilms tumor 1-associated protein (WTAP) as a key component. Whether the development of dental enamel is regulated by m6A RNA methylation in mammals remains unclear. Here, we reveal that WTAP is widely expressed from the early stage of tooth development. Specific inactivation of Wtap in mouse enamel epithelium by the Cre/loxp system leads to serious developmental defects in amelogenesis. In Wtap conditional knockout (cKO) mice, we determined that the differentiation of enamel epithelial cells into mature ameloblasts at the early stages of enamel development is affected. Mechanistically, loss of Wtap inhibits the expression of Sonic hedgehog (SHH), which plays an important role in the generation of ameloblasts from stem cells. Together, our findings provide new insights into the functional role of WTAP-mediated m6A methylation in amelogenesis in mammals.

Keywords:  WTAP; enamel; m6A methylation; tooth development

DOI:  https://doi.org/10.1016/j.jbc.2022.102715
Stem Cells Int. 2022 ;2022 7494354

YTHDC1 Promotes Stemness Maintenance and Malignant Progression in Head and Neck Squamous Cell Carcinoma.

Junquan Weng, Haidong Fan, Huijuan Liu, Su Tang, Yuyan Zheng.

Background: YTH domain containing 1 (YTHDC1), an N6-methyladenosine (m6A) modification reading protein, plays a key role in regulating RNA translation and degradation. However, the role of YTHDC1 in head and neck squamous cell carcinoma (HNSCC) cancer stem cells remains largely unknown. This study is aimed at investigating the role of YTHDC1 in HNSCC and exploring its role in regulating cancer stem cells.
Methods: RNA sequencing was used to detect differentially expressed genes (DEGs) between SCC9 spheres and SCC9 cells and to uncover molecular pathways and target molecules associated with CSCs. We detected YTHDC1 expression in The Cancer Genome Atlas (TCGA) database data and clinical samples. Subsequently, YTHDC1 gene suppression assays were performed in HNSCC cell lines to investigate the effect of YTHDC1 on tumor cell stemness maintenance, proliferation, and migration capacity. To further confirm the role of YTHDC1 in regulating cancer stem cells in HNSCC, we analyzed online HNSCC single-cell transcriptomic data to investigate YTHDC1 expression patterns at the single-cell level and the correlation of these levels with the expression of stem cell markers.
Results: YTHDC1 expression levels were significantly upregulated in SCC9 spheres, and YTHDC1 was aberrantly expressed in HNSCC tumor tissues. The increased YTHDC1 expression was closely correlated with the clinical characteristics of HNSCC patients. YTHDC1 regulates the malignant phenotype of HNSCC in both in vivo and in vitro studies. Further single-cell transcriptomic data analysis revealed that YTHDC1 positively correlated with malignant epithelial cell stemness capacity at the single-cell level, and that YTHDC1 was involved in regulating stemness maintenance in HNSCC.
Conclusions: These findings suggest that YTHDC1 may serve as a biomarker for stem maintenance and malignant progression in HNSCC, providing new insights into the treatment of cancer.

DOI: https://doi.org/10.1155/2022/7494354
Nat Protoc. 2022 Nov 25.

m6A-SAC-seq for quantitative whole transcriptome m6A profiling.

Ruiqi Ge, Chang Ye, Yong Peng, Qing Dai, Yutao Zhao, Shun Liu, Pingluan Wang, Lulu Hu, Chuan He.

N6-methyladenosine (m6A) is the most abundant mRNA modification in mammalian cells, regulating many physiological processes. Here we describe a method for base-resolution, quantitative m6A sequencing in the whole transcriptome. The enzyme and small-molecule cofactor used in this protocol are prepared by recombinant protein expression and organic synthesis, respectively. Then the library can be prepared from various types of RNA samples using a ligation-based strategy, with m6A modifications being labeled by the enzyme and cofactor. Detailed instructions on ensuing data analysis are also included in this protocol. The method generates highly reproducible results, uncovering 31,233-129,263 sites using as little as 2 ng of poly A+ RNA. These identified sites correspond well with previous m6A profiling results, covering over 65% of peaks detected by the antibody-based approaches. Compared with other currently available methods, this method can be applied to various types of biological samples, including fresh and frozen tissues as well as formalin-fixed paraffin-embedded samples, providing a quantitative method to uncover new insights into m6A biology. The protocol requires basic expertise in molecular biology, recombinant protein expression and organic synthesis. The whole protocol can be done in 15 days, with the library preparation taking 5 days.

DOI: https://doi.org/10.1038/s41596-022-00765-9
Hua Xi Kou Qiang Yi Xue Za Zhi. 2022 Dec 01. pii: 1000-1182(2022)06-0704-06. [Epub ahead of print]40(6): 704-709

Construction and clinical evaluation of N6-methyladenosine risk signature of YTHDC2, IGF2BP2, and HNRNPC in head and neck squamous cell carcinoma.

Qiangwei Yue, Le Xu, Dongsheng Zhang.

   OBJECTIVES: This work aimed to construct N6-methyladenosine (m6A) regulator-based prognostic signature and evaluate the prognostic value and the intervention on tumor immune microenvironment of this m6A risk signature.
METHODS: Using transcriptome and clinical data of head and neck squamous cell carcinoma (HNSCC) from The Cancer Genome Atlas (TCGA), we profiled m6A regulators and constructed an m6A risk signature. The relationship between m6A modulation and immune function was studied by differential gene expression, cell type enrichment, and correlation analyses.
RESULTS: Fifteen m6A regulators had aberrant expression in HNSCC. A three-gene m6A prognostic signature (i.e., YTHDC2, IGF2BP2, and HNRNPC) was constructed and identified as an independent prognostic indicator for HNSCC. The m6A regulator signature-based high-risk group revealed pro-tumoral immune microenvironment due to the dysregulation of immune-related gene expression, abnormal enrichment of multiple immunocytes, and production of immunoregulatory factors.
CONCLUSIONS: This comprehensive analysis of m6A regulators and tumor immune landscape in HNSCC revealed that the m6A signature of YTHDC2, IGF2BP2, and HNRNPC could serve as a promising biomarker for monitoring HNSCC development and may be a potential target for tumor therapy in the future.

Keywords:  N6-methyladenosine; bioinformatic analysis; head and neck squamous cell carcinoma; prognostic risk signature; tumor immune microenvironment

DOI:  https://doi.org/10.7518/hxkq.2022.06.012
Sci Total Environ. 2022 Nov 21. pii: S0048-9697(22)07534-9. [Epub ahead of print] 160432

m6A contributes to a pro-survival state in GC-2 cells by facilitating DNA damage repair: Novel perspectives on the mechanism underlying DEHP genotoxicity in male germ cells.

Haowei Fu, Xiaofang Zhu, Qiannan Di, Jiahui Sun, Qianqian Jiang, Qian Xu.

  Di(2-ethyl-hexyl) phthalate (DEHP), an environmental endocrine disruptor, can destroy the sperm genomic integrity and impairs spermatogenesis. N6-methyladenosine (m6A) is involved in the cellular effects of DEHP. However, the genotoxic effect of DEHP on spermatocytes and the possible role of m6A in this process remain unclear. This study demonstrated that m6A alleviates DEHP genotoxicity in GC-2 cells. In DEHP-treated mice, DNA double-strand breaks (DSBs) were induced in the testis and spermatocytes. To further explore the molecular mechanism of DEHP genotoxicity on spermatocytes, GC-2 cells were exposed to DEHP. DEHP produced distinct genotoxicity and caused DSBs, which led to the inhibition of DNA synthesis and cell cycle arrest. The DNA damage response (DDR) was initiated to repair the DSBs induced by environmentally relevant levels of DEHP (100 μM and 200 μM). During this process, METTL3 upregulated m6A, which facilitated the DDR via stabilizing the DNA damage repair factors (Rad51 and Xrcc5) mRNA to maintain the pro-survival state. Moreover, Mettl3 knockdown partially inhibited DDR. Interestingly, high-dose DEHP (400 μM and 600 μM) directly induced apoptosis rather than the pro-survival state. Altogether: METTL3-mediated m6A participates in maintaining the pro-survival state by upregulating DDR, providing guidance for mitigating the genotoxicity of environment-related level DEHP exposure.

Keywords:  DEHP; DNA damage repair; Genotoxicity; Male germ cells; m6A

DOI:  https://doi.org/10.1016/j.scitotenv.2022.160432
Mol Omics. 2022 Nov 22.

The landscape of N6-methyladenosine modification patterns and altered transcript profiles in the cardiac-specific deletion of natriuretic peptide receptor A.

Xi Shen, Pan Chang, Xiaomeng Zhang, Jing Zhang, Xihui Wang, Zhuo Quan, Pengli Wang, Tian Liu, Yan Niu, Rong Zheng, Baoying Chen, Jun Yu.

The atrial natriuretic peptide (ANP) and the brain natriuretic peptide (BNP) are critical biological makers and regulators of cardiac functions. Our previous results show that NPRA (natriuretic peptide receptor A)-deficient mice have distinct metabolic patterns and expression profiles compared with the control. Still, the molecular mechanism that could account for this observation remains to be elucidated. Here, methylation alterations were detected by mazF-digestion, and differentially expressed genes of transcriptomes were detected by a Genome Oligo Microarray using the myocardium from NPRA-deficient (NPRA-/-) mice and wild-type (NPRA+/+) mice as the control. Comprehensive analysis of m6A methylation data gave an altered landscape of m6A modification patterns and altered transcript profiles in cardiac-specific NPRA-deficient mice. The m6A "reader" igf2bp3 showed a clear trend of increase, suggesting a function in altered methylation and expression in cardiac-specific NPRA-deficient mice. Intriguingly, differentially m6A-methylated genes were enriched in the metabolic process and insulin resistance pathway, suggesting a regulatory role in cardiac metabolism of m6A modification regulated by NPRA. Notably, it was confirmed that the pyruvate dehydrogenase kinase 4 (Pdk4) gene upregulated the gene expression and the hypermethylation level simultaneously, which may be the key factor for the cardiac metabolic imbalance and insulin resistance caused by natriuretic peptide signal resistance. Taken together, cardiac metabolism might be regulated by natriuretic peptide signaling, with decreased m6A methylation and a decrease of Pdk4.

DOI: https://doi.org/10.1039/d2mo00201a
Cell Mol Biol Lett. 2022 Nov 22. 27(1): 101

ALKBH5 in mouse testicular Sertoli cells regulates Cdh2 mRNA translation to maintain blood-testis barrier integrity.

Zhonglin Cai, Yao Zhang, Lin Yang, Chunhui Ma, Yi Fei, Jing Ding, Wei Song, Wei-Min Tong, Yamei Niu, Hongjun Li.

   BACKGROUND: RNA N6-methyladenosine (m6A) is involved in mammalian spermatogenesis. In both germ cells and Leydig cells, ALKBH5 regulates spermatogenesis and androgen synthesis in an m6A-dependent manner. However, it is unclear whether ALKBH5 plays a role in testicular Sertoli cells, which constitute the blood-testis barrier (BTB) through cell junctions between adjacent Sertoli cells.
METHODS: ALKBH5 expression in the testes of humans and mice was detected by immunohistochemical staining and immunofluorescence staining. BTB integrity was evaluated by BTB assay. m6A-seq was performed to screen for BTB-related molecules regulated by ALKBH5. m6A immunoprecipitation-quantitative real-time polymerase chain reaction (qPCR), RNA immunoprecipitation-qPCR, western blot, coimmunoprecipitation, and polysome fractionation-qPCR analyses were performed to explore the mechanisms of ALKBH5 in BTB. Transmission electron microscopy was applied to observe the BTB ultrastructure.
RESULTS: ALKBH5 in Sertoli cells is related to the integrity of the BTB. Subsequently, the m6A level on Cdh2 mRNA, encoding a structural protein N-cadherin in the BTB, was found to be regulated by ALKBH5. IGF2BP1/2/3 complexes and YTHDF1 promoted Cdh2 mRNA translation. In addition, we found that basal endoplasmic specialization, in which N-cadherin is a main structural protein, was severely disordered in the testes of Alkbh5-knockout mice.
CONCLUSIONS: Our study revealed that ALKBH5 regulates BTB integrity via basal endoplasmic specialization by affecting Cdh2 mRNA translation.

Keywords:  Alkbh5; Basal endoplasmic specialization; Blood–testis barrier; Cdh2; RNA N 6-methyladenosine

DOI:  https://doi.org/10.1186/s11658-022-00404-x
Front Immunol. 2022 ;13 1001506

Implications of m6A-associated snRNAs in the prognosis and immunotherapeutic responses of hepatocellular carcinoma.

Cheng Zhang, Wangjian Zhang, Yongjie Shui, Ping Li, Zhifeng Tian, Shiwei Duan, Qichun Wei.

   Background: Hepatocellular carcinoma (HCC) is the most prevalent pathological type of liver cancer worldwide with high mortality and poor prognosis. N6-methyladenosine (m6A) can modify RNAs such as mRNA, lncRNA, miRNA, and tRNA, thereby playing a critical role in the pathogenesis of HCC. However, the role of m6A-associated small nuclear RNA (snRNA) in the prognostic value and immunotherapeutic response in HCC remains unclear.
Materials and methods: In this study, snRNA expression data, gene mutation data, and clinical data of HCC patients were acquired from The Cancer Genome Atlas (TCGA) database. We used the least absolute shrinkage and selection operator (LASSO) Cox regression analysis to identify significant prognostic m6A-associated snRNAs, and then developed a multivariate Cox model based on the selected snRNAs. HCC patients were split into low- and high-risk groups based on the median risk score. We subsequently performed Kaplan-Meier curve analysis to estimate overall survival (OS) by clinicopathological characteristics and tumor mutational burden (TMB) status in low- and high-risk HCC patients. Finally, we compared the immunotherapeutic response as represented by tumor immune dysfunction and exclusion (TIDE) scores between the two risk groups.
Results: Eight m6A-associated snRNAs were selected as independent predictors to develop the risk model. Our results revealed that the OS of HCC patients in the high-risk group was significantly worse than that in the low-risk group on clinicopathologic characteristics, including age (≤65 years and >65 years), gender (male), grade (G I-II and G III-IV) and TNM staging (Stage I-II and Stage III-IV). In addition, the OS of low-TMB and low-risk group was longer than that of high-TMB and high-risk group. The TIDE score indicated that HCC patients in the high-risk group were more susceptible to immunotherapy.
Conclusion: Our study suggests that m6A-associated snRNAs may be useful biomarkers for the prognosis of HCC and that m6A-associated snRNA models can predict the effect of immunotherapy in HCC patients.

Keywords:  hepatocellular carcinoma; immunotherapy; m6A; prognosis; snRNA

DOI:  https://doi.org/10.3389/fimmu.2022.1001506
Cancer Med. 2022 Nov 24.

KIAA1429 mediates epithelial mesenchymal transition in sorafenib-resistant hepatocellular carcinoma through m6A methylation modification.

Ye Kuang, Yun Cheng, Jia Wang, Hongyan Li, Xianghong Cao, Yang Wang.

   BACKGROUND: Hepatocellular carcinoma (HCC) is a primary liver cancer with high mortality. The long-term use of sorafenib, a targeted drug for hepatocellular carcinoma, will lead to drug resistance, and patients are prone to cancer metastasis, the molecular mechanism of which is still unclear.
METHODS: In our study, we constructed a sorafenib-resistant hepatocellular carcinoma cell line (HepG2/Sora) and validated the resistance in vivo and in vitro. Transwell assays confirmed the invasion and migration abilities of cells. Colorimetric assays confirmed that the level of m6A methylation modification in cells. RT-qPCR and Western blot assays confirmed that the expression levels of KIAA1429 in HepG2/Sora cells and tissues. The EMT related proteins were detected by Western blot assay.
RESULTS: Transwell and Western blot assays confirmed that HepG2/Sora cells had higher invasion and migration abilities and showed EMT phenomena. Colorimetric assays confirmed that the level of m6A methylation modification was upregulated in HepG2/Sora cells. Transwell and Western blot assays confirmed that inhibiting m6A methylation in HepG2/Sora cells inhibited their invasion, migration ability and EMT phenomenon. RT-qPCR and Western blot assays confirmed that the expression levels of KIAA1429 in HepG2/Sora cells and tissues was increased. Silencing KIAA1429 in HepG2/Sora cells inhibited their invasion, migration ability and EMT phenomenon. Finally, we found that the medium supernatant of sorafenib-resistant HepG2/Sora cells induced vascular production of EA.hy926 cells, and silencing KIAA1429 inhibited this induction effect.
CONCLUSION: We suggest that KIAA1429 promotes sorafenib-resistant hepatocellular carcinoma invasion, migration and EMT by mediating m6A methylation. KIAA1429 with its mediated m6A methylation may be a key factor for sorafenib-resistant patients prone to cancer cell metastasis.

Keywords:  EMT; KIAA1429; hepatocellular carcinoma; m6A methylation; sorafenib resistance

DOI:  https://doi.org/10.1002/cam4.5432
Pharmacol Res. 2022 Nov 17. pii: S1043-6618(22)00501-1. [Epub ahead of print] 106555

Glutamate from nerve cells promotes perineural invasion in pancreatic cancer by regulating tumor glycolysis through HK2 mRNA-m6A modification.

Fengjiao Li, Chong He, Hanming Yao, Yue Zhao, Xijiu Ye, Shurui Zhou, Jinmao Zou, Yaqing Li, Jiajia Li, Shaojie Chen, Fanghai Han, Kaihong Huang, Guoda Lian, Shangxiang Chen.

   BACKGROUND: Perineural invasion (PNI) has a high incidence and poor prognosis in pancreatic ductal adenocarcinoma (PDAC). Our study aimed to identify the underlying molecular mechanism of PNI and propose effective intervention strategies.
METHODS: To observe PNI in vitro and in vivo, a Matrigel/ dorsal root ganglia (DRG) model and a murine sciatic nerve invasion model were respectively used. Magnetic resonance (MR) imaging and positron emission tomography/computed tomography (PET-CT) imaging were also used to evaluate tumor growth. Publicly available datasets and PDAC tissues were used to verify how the nerve cells regulate PDAC cells' PNI.
RESULTS: Our results showed that glutamate from nerve cells could cause calcium influx in PDAC cells via the N-methyl-d-aspartate receptor (NMDAR), subsequently activating the downstream Ca2+ dependent protein kinase CaMKII/ERK-MAPK pathway and promoting the mRNA transcription of gene METTL3. Next, METTL3 upregulates the expression of hexokinase 2 (HK2) through N6-methyladenosine (m6A) modification in mRNA, enhances the PDAC cells' glycolysis, and promotes PNI. Furthermore, the IONPs-PEG-scFvCD44v6-scAbNMDAR2B nanoparticles dual targeting CD44 variant isoform 6 (CD44v6) and t NMDAR subunit 2B (NMDAR2B) on PDAC cells were synthesized and verified showing a satisfactory blocking effect on PNI.
CONCLUSIONS: Here, we firstly provided evidence that glutamate from the nerve cells could upregulate the expression of HK2 through mRNA m6A modification via NMDAR2B and downstream Ca2+ dependent CaMKII/ERK-MAPK pathway, enhance the glycolysis in PDAC cells, and ultimately promote PNI. In addition, the dual targeting nanoparticles we synthesized were verified to block PNI effectively in PDAC.

Keywords:  N6-methyladenosine; Pancreatic ductal adenocarcinoma; glutamate; glycolysis; perineural invasion

DOI:  https://doi.org/10.1016/j.phrs.2022.106555
Elife. 2022 Nov 21. pii: e78808. [Epub ahead of print]11

m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site.

Matthew T Parker, Beth K Soanes, Jelena Kusakina, Antoine Larrieu, Katarzyna Knop, Nisha Joy, Friedrich Breidenbach, Anna V Sherwood, Geoffrey J Barton, Sebastian M Fica, Brendan H Davies, Gordon Grant Simpson.

  Alternative splicing of messenger RNAs is associated with the evolution of developmentally complex eukaryotes. Splicing is mediated by the spliceosome, and docking of the pre-mRNA 5' splice site into the spliceosome active site depends upon pairing with the conserved ACAGA sequence of U6 snRNA. In some species, including humans, the central adenosine of the ACAGA box is modified by N6 methylation, but the role of this m6A modification is poorly understood. Here we show that m6A modified U6 snRNA determines the accuracy and efficiency of splicing. We reveal that the conserved methyltransferase, FIO1, is required for Arabidopsis U6 snRNA m6A modification. Arabidopsis fio1 mutants show disrupted patterns of splicing that can be explained by the sequence composition of 5' splice sites and cooperative roles for U5 and U6 snRNA in splice site selection. U6 snRNA m6A influences 3' splice site usage. We generalise these findings to reveal two major classes of 5' splice site in diverse eukaryotes, which display anti-correlated interaction potential with U5 snRNA loop 1 and the U6 snRNA ACAGA box. We conclude that U6 snRNA m6A modification contributes to the selection of degenerate 5' splice sites crucial to alternative splicing.

Keywords:  A. thaliana; C. elegans; D. melanogaster; chromosomes; gene expression; genetics; genomics; human; zebrafish

DOI:  https://doi.org/10.7554/eLife.78808
Hum Cell. 2022 Nov 20.

Identification and validation of an m6A-related gene signature to predict prognosis and evaluate immune features of breast cancer.

Wenhao Li, Xiaolong Wang, Chen Li, Tong Chen, Xianyong Zhou, Zheng Li, Qifeng Yang.

  Breast cancer is the most prevalent cancer, and it is accompanied by high heterogeneity. N6-methyladenosine (m6A) modification significantly contributes to breast cancer tumorigenesis and progression. However, how m6A-related genes affect the clinical outcomes and tumor immune microenvironment (TIME) of breast cancer is largely unknown. Our study developed an m6A-related gene signature on the basis of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The m6A-related gene signature was constructed using univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses. Breast cancer patients were classified into low- and high-risk groups depending on the median risk score. The reliability and efficiency of the signature were validated using Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, and principal component analysis (PCA). The risk score was validated as an independent indicator associated with overall survival, and a nomogram model was created to estimate the overall survival of patients with breast cancer. Functional annotation suggested that the risk score had a strong relationship with immune-related pathways. Different proportions of immune cell infiltration between the two groups were evaluated using various algorithms. The high-risk group had higher immune checkpoint expression levels. We discovered that one of the 6 prognostic genes, TMEM71, was downregulated in breast cancer tissues. In vitro experiments indicated that overexpression of TMEM71 suppressed breast cancer cell proliferation and migration. In conclusion, the m6A-related gene signature may be a sensitive biomarker for overall survival prediction and guide the individualized treatment for breast cancer patients.

Keywords:  Breast cancer; N6-methyladenosine; Prognosis; Signature; Tumor immune microenvironment

DOI:  https://doi.org/10.1007/s13577-022-00826-x
Int J Mol Sci. 2022 Nov 15. pii: 14111. [Epub ahead of print]23(22):

Comparative Genomics and Functional Studies of Putative m6A Methyltransferase (METTL) Genes in Cotton.

Junfeng Cao, Chaochen Huang, Jun'e Liu, Chenyi Li, Xia Liu, Zishou Zheng, Lipan Hou, Jinquan Huang, Lingjian Wang, Yugao Zhang, Xiaoxia Shangguan, Zhiwen Chen.

  N6-methyladenosine (m6A) RNA modification plays important regulatory roles in plant development and adapting to the environment, which requires methyltransferases to achieve the methylation process. However, there has been no research regarding m6A RNA methyltransferases in cotton. Here, a systematic analysis of the m6A methyltransferase (METTL) gene family was performed on twelve cotton species, resulting in six METTLs identified in five allotetraploid cottons, respectively, and three to four METTLs in the seven diploid species. Phylogenetic analysis of protein-coding sequences revealed that METTL genes from cottons, Arabidopsis&nbsp;thaliana, and Homo&nbsp;sapiens could be classified into three clades (METTL3, METTL14, and METTL-like clades). Cis-element analysis predicated the possible functions of METTL genes in G. hirsutum. RNA-seq data revealed that GhMETTL14 (GH_A07G0817/GH_D07G0819) and GhMETTL3 (GH_A12G2586/GH_D12G2605) had high expressions in root, stem, leaf, torus, petal, stamen, pistil, and calycle tissues. GhMETTL14 also had the highest expression in 20 and 25 dpa fiber cells, implying a potential role at the cell wall thickening stage. Suppressing GhMETTL3 and GhMETTL14 by VIGS caused growth arrest and even death in G. hirsutum, along with decreased m6A abundance from the leaf tissues of VIGS plants. Overexpression of GhMETTL3 and GhMETTL14 produced distinct differentially expressed genes (DEGs) in A. thaliana, indicating their possible divergent functions after gene duplication. Overall, GhMETTLs play indispensable but divergent roles during the growth of cotton plants, which provides the basis for the systematic investigation of m6A in subsequent studies to improve the agronomic traits in cotton.

Keywords:  VIGS; cotton; divergent function; m6A methyltransferase; phylogenetics

DOI:  https://doi.org/10.3390/ijms232214111
J Immunol Res. 2022 ;2022 8300187

Oxidative Phosphorylation-Related Signature Participates in Cancer Development, and PTPRG Overexpression Suppresses the Cancer Progression in Clear Cell Renal Cell Carcinoma.

Liang Huang, Yu Xie, Weiqing Han, Shusuan Jiang, Lingfeng Zeng.

Clear cell renal cell carcinoma (ccRCC) was a common cancer type diagnosed with frequent metastases, harboring an unfavorable therapeutic response, and results in a poor prognosis. More promising therapeutic targets are urgently required for treating ccRCC. This study was conducted to explore the role of oxidative phosphorylation in ccRCC development and reveal its clinical potential. We first identified oxidative phosphorylation-related clusters based on consensus clustering and validated their diversity in the genome instability, environmental infiltration, and immunosuppression by Gistic, ESTIMATE, GSVA, and TIDE web tools. We also compared their prognostic and clinical feature differences and predicted the IC50 level between the clusters using pRRophetic. Subsequently, we performed weighted gene coexpression network analysis to select cluster-related genes and performed functional analysis for them. The cluster-related genes were adopted to construct a risk score and nomogram for predicting patient prognosis with predictive accuracy evaluated. Finally, we performed lentivirus to induce ccRCC cell PTPRG overexpression and conducted western blot experiments to detect the critical protein expression of oxidative phosphorylation, apoptosis, cell cycle, and epithelial-mesenchymal transition processes. Also, the cell cycle and apoptosis level were evaluated by flow cytometry. As a result, we discovered that both the C1 cluster and high-risk group predicted patient survival with high accuracy and characterized lower survival rates, lower oxidative phosphorylation levels, higher immune infiltration, and malignant clinical features. Besides, we observed that overexpression of PTPRG activated oxidative phosphorylation and inhibited apoptosis. Its overexpression also depressed the epithelial-mesenchymal transition and promoted G1/S cell cycle arrest. Comprehensively, we confirmed the anticancer role of oxidative phosphorylation in ccRCC cells and discovered its association with immune and immunosuppression. PTPRG was also identified as a potential therapeutic target due to its multiple anticancer effects. We believe this study discovered a novel mechanism of ccRCC pathological progression and will provide promising targets for therapeutic strategy development.

DOI: https://doi.org/10.1155/2022/8300187
Redox Biol. 2022 Nov 19. pii: S2213-2317(22)00318-4. [Epub ahead of print]58 102546

HDLBP-stabilized lncFAL inhibits ferroptosis vulnerability by diminishing Trim69-dependent FSP1 degradation in hepatocellular carcinoma.

Jingsheng Yuan, Tao Lv, Jian Yang, Zhenru Wu, Lvnan Yan, Jiayin Yang, Yujun Shi.

  Recent studies have suggested that exploring the potential mechanisms regulating ferroptosis vulnerability may contribute to improving the systemic therapeutic efficacy in HCC. High-density lipoprotein-binding protein (HDLBP), the largest RNA-binding protein, is an important transporter that protects cells from overaccumulation of cholesterol, but few studies have elucidated the role of HDLBP in the regulation of ferroptosis vulnerability in HCC. Our study suggests that HDLBP was markedly elevated in HCC compared with noncancerous liver tissues and that this elevation inhibited the ferroptosis vulnerability of HCC. Further experiments revealed that HDLBP bound to and stabilized the long noncoding RNA lncFAL (ferroptosis-associated lncRNA), which is derived from the plexin B2 gene. Moreover, our study suggests that the splicing of lncFAL was increased by YTH N6-methyladenosine (m6A) RNA-binding protein 2 (YTHDF2) in a m6A-dependent manner. Although HDLBP or lncFAL could not regulate the GPX4 antioxidant signalling pathway, lncFAL reduced ferroptosis vulnerability by directly binding to ferroptosis suppressor protein 1 (FSP1) and competitively abolishing Trim69-dependent FSP1 polyubiquitination degradation. More importantly, FSP1 inhibition promoted the antitumour activity of ferroptosis inducers both in vitro and in vivo. Collectively, our results provide a clinically promising demonstration that HDLBP stabilizes lncFAL, which mediates a FSP1-dependent anti-ferroptosis mechanism in HCC. These results support the enormous potential of disrupting FSP1 as a promising therapeutic approach for HCC patients with high HDLBP or lncFAL expression.

Keywords:  FSP1; Ferroptosis; HDLBP; Hepatocellular carcinoma; Ubiquitination; lncRNA

DOI:  https://doi.org/10.1016/j.redox.2022.102546
BMC Urol. 2022 Nov 25. 22(1): 193

NEAT1 promotes the malignant development of bladder cancer by regulating the miR-101/VEGF-C pathway in vitro and in vivo.

Huihui Zhang, Shuang Yu, Kuilin Fei, Zhongxin Huang, Shidong Deng, Hanfeng Xu.

   BACKGROUND: NEAT1 has been shown to play an oncogenic role in many kinds of cancers. However, detailed roles of NEAT1 in bladder cancer are largely unknown.
METHODS: In the present study, the expression of NEAT1, miR-101 and VEGF-C was detected in human bladder cancer samples. The relationship between NEAT1 and the prognosis of patients with bladder cancer was analysed. In vitro experiments explored the effects of NEAT1 on biological behaviours of bladder cancer T24 and 5637 cells. Bioinformatics prediction and luciferase assays were used to assay the regulatory mechanism of action of NEAT1 and miR-101. Loss and gain of the expression of miR-101 and VEGF-C were used to explore the effects of the NEAT1/miR-101/VEGF-C pathway on T24 and 5637 cells. The effect of NEAT1 on the growth of bladder cancer in vivo was explored using an orthotopic tumourigenesis model.
RESULTS: NEAT1 and VEGF-C were significantly upregulated in bladder cancer samples, and miR-101 was significantly downregulated. NEAT1 upregulation was associated with poorer recurrence-free survival of patients with bladder cancer. Overexpression of NEAT1 promoted the proliferation, migration and invasion of bladder cancer cells. The results of the luciferase assay indicated that miR-101 was a target of NEAT1. The promoting effects of NEAT1 on bladder cancer cells were reversed by miR-101 upregulation, and inhibition of miR-101 enhanced the effects of NEAT1. Overexpression of VEGF-C had a clear synergistic effect with the action of NEAT1. Overexpression of NEAT1 increased tumour growth and induced the development of liver metastasis.
CONCLUSIONS: In conclusion, our data indicated that NEAT1 was expressed at high levels in bladder cancer patients and correlated with unfavourable prognosis. NEAT1 promoted malignant development of bladder cancer in vitro and in vivo by regulating the miR-101/VEGF-C pathway.

Keywords:  Bladder cancer; NEAT1; VEGF-C; miR-101

DOI:  https://doi.org/10.1186/s12894-022-01151-z
Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01567-4. [Epub ahead of print]41(8): 111693

m6A-modified lincRNA Dubr is required for neuronal development by stabilizing YTHDF1/3 and facilitating mRNA translation.

Jiansong Huang, Bowen Jiang, Guo-Wei Li, Dandan Zheng, Mingyi Li, Xuan Xie, Yuxiang Pan, Manyi Wei, Xiaoyan Liu, Xingyu Jiang, Xu Zhang, Li Yang, Lan Bao, Bin Wang.

  Long intergenic noncoding RNAs (lincRNAs) are crucial regulators in numerous biological processes. However, the functions and mechanisms of m6A-modified lincRNAs in neuronal development remain unclear. Here, we report an m6A-modified lincRNA, Dppa2 upstream binding RNA (Dubr), abundantly expressed at the early developmental stage of dorsal root ganglion (DRG) and cerebral cortex. Silencing Dubr impairs axon elongation of DRG neurons and axon projection and migration of cortical neurons, whereas lacking m6A modification of Dubr fully loses its functions. Mechanically, Dubr interacts with m6A-binding proteins, the YTHDF1/3 complex, through its m6A motifs to protect YTHDF1/3 from degradation via the proteasome pathway. Furthermore, Tau and Calmodulin are regulated by YTHDF1/3 and m6A-modified Dubr. Overexpression of YTHDF1/3 not only rescues the reduced Tau and Calmodulin but also restores axon elongation of DRG neurons by Dubr knockdown. This study uncovers a critical role of m6A-modified lincRNA in neuronal development by regulating the degradation of RNA-binding protein.

Keywords:  CP: Molecular biology; CP: Neuroscience; Dubr; Neuronal development; YTHDF1; YTHDF3; m(6)A-modified lincRNA; mRNA translation

DOI:  https://doi.org/10.1016/j.celrep.2022.111693
J Clin Transl Hepatol. 2023 Feb 28. 11(1): 45-57

USP10 Alleviates Palmitic Acid-induced Steatosis through Autophagy in HepG2 Cells.

Sheng-Liang Xin, Xiao-Li Pan, Xiao-Yuan Xu, Yan-Yan Yu.

   Background and Aims: Nonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease caused by over-nutrition. Impaired autophagy is closely related to NAFLD progression. Recently, ubiquitin-specific peptidase-10 (USP10) was reported to ameliorate hepatic steatosis, but the underlying mechanism is still unclear. In view of the potential effects of USP10 on autophagy, we investigated whether USP10 alleviated steatosis through autophagy.
Methods: HepG2 cells were treated with palmitic acid (PA) to model NAFLD in vitro. Lentivirus was used to regulate USP10 level in cells. Autophagic regulators were used to autophagic progression in cells. Western blotting, real-time fluorescence quantitative polymerase chain reaction, lipid drop staining and immunofluorescent staining were performed to determine the effect of USP10 on lipid autophagy. Student's t-test and Tukey's post hoc test were used to compare the means among groups.
Results: PA induced cellular steatosis with dependance on autophagy. USP10 overexpression alleviated PA-induced steatosis, restored autophagic activity, promoted autophagic flux, including synthesis and degradation of autophagosomes, and lipid-targeted autophagy. In the presence of autophagy inhibitors, the protective effectiveness of USP10 on steatosis decreased. Furthermore, the specific inhibitor to C-jun N-terminal protein kinase-1 (JNK1), DB07268, abolished USP10-induced autophagy. However, during early stage inhibition of JNK1, compensatory expression of tuberous sclerosis complex-2 (TSC2) maintained autophagy. The degree of TSC2-to-JNK1 compensation was positively associated with USP10 level. Functionally, JNK1 and TSC2 were involved in the lipid-lowering effect of USP10.
Conclusions: USP10 alleviated hepatocellular steatosis in autophagy-dependent manner. JNK1/TSC2 signaling pathways were required for USP10-induced autophagy.

Keywords:  Autophagy; C-jun N-terminal protein kinase-1; Nonalcoholic fatty liver disease; Steatosis; Tuberous sclerosis complex-2; Ubiquitin-specific peptidase-10

DOI:  https://doi.org/10.14218/JCTH.2022.00060
Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01561-3. [Epub ahead of print]41(8): 111687

Adenosine deaminase acting on RNA-1 is essential for early B lymphopoiesis.

Wenjing Chen, Yuxing Li, Gui-Xin Ruan, Hengjun Huang, Rui Zhang, Jing Wang, Yu Ouyang, Yan Li, Shengli Xu, Xijun Ou.

  Adenosine deaminase acting on RNA-1 (ADAR1) is a ubiquitously expressed RNA deaminase catalyzing adenosine-to-inosine editing to prevent hyperactivated cytosolic double-stranded RNA (dsRNA) response mediated by MDA5. Here, we demonstrate that ADAR1 is essential for early B lymphopoiesis from late pro-B and large pre-B cell stages onward. ADAR1 exerts its requisite role via both MDA5-dependent and -independent pathways. Interestingly, the MDA5-dependent mechanisms regulate early pro-B to large pre-B cell transition by promoting early B cell survival. In contrast, the MDA5-independent mechanisms control large pre-B to small pre-B cell transition by regulating pre-B cell receptor (pre-BCR) expression. Moreover, we show that protein kinase R (PKR) and oligoadenylate synthetase/ribonuclease (OAS/RNase) L pathways are dispensable for ADAR1's role in early B lymphopoiesis. Importantly, we demonstrate that p150 isoform of ADAR1 exclusively accounts for ADAR1's function in early B lymphopoiesis, and its conventional dsRNA-binding, but not the Z-DNA/RNA-binding or the RNA-editing, activity is required for ADAR1's function in B cell development. Thus, our findings suggest that ADAR1 regulates early B lymphopoiesis through various mechanisms.

Keywords:  ADAR1; B cell development; CP: Immunology; MDA5; RNA editing; dsRNA binding; pre-BCR

DOI:  https://doi.org/10.1016/j.celrep.2022.111687
Cell Commun Signal. 2022 Nov 24. 20(1): 188

RRP9 promotes gemcitabine resistance in pancreatic cancer via activating AKT signaling pathway.

Zhiqi Zhang, Haitao Yu, Wenyan Yao, Na Zhu, Ran Miao, Zhiquan Liu, Xuwei Song, Chunhua Xue, Cheng Cai, Ming Cheng, Ke Lin, Dachuan Qi.

   BACKGROUND: Pancreatic cancer (PC) is a highly lethal malignancy regarding digestive system, which is the fourth leading factor of cancer-related mortalities in the globe. Prognosis is poor due to diagnosis at advanced disease stage, low rates of surgical resection, and resistance to traditional radiotherapy and chemotherapy. In order to develop novel therapeutic strategies, further elucidation of the molecular mechanisms underlying PC chemoresistance is required. Ribosomal RNA biogenesis has been implicated in tumorigenesis. Small nucleolar RNAs (snoRNAs) is responsible for post-transcriptional modifications of ribosomal RNAs during biogenesis, which have been identified as potential markers of various cancers. Here, we investigate the U3 snoRNA-associated protein RRP9/U3-55 K along with its role in the development of PC and gemcitabine resistance.
METHODS: qRT-PCR, western blot and immunohistochemical staining assays were employed to detect RRP9 expression in human PC tissue samples and cell lines. RRP9-overexpression and siRNA-RRP9 plasmids were constructed to test the effects of RRP9 overexpression and knockdown on cell viability investigated by MTT assay, colony formation, and apoptosis measured by FACS and western blot assays. Immunoprecipitation and immunofluorescence staining were utilized to demonstrate a relationship between RRP9 and IGF2BP1. A subcutaneous xenograft tumor model was elucidated in BALB/c nude mice to examine the RRP9 role in PC in vivo.
RESULTS: Significantly elevated RRP9 expression was observed in PC tissues than normal tissues, which was negatively correlated with patient prognosis. We found that RRP9 promoted gemcitabine resistance in PC in vivo and in vitro. Mechanistically, RRP9 activated AKT signaling pathway through interacting with DNA binding region of IGF2BP1 in PC cells, thereby promoting PC progression, and inducing gemcitabine resistance through a reduction in DNA damage and inhibition of apoptosis. Treatment with a combination of the AKT inhibitor MK-2206 and gemcitabine significantly inhibited tumor proliferation induced by overexpression of RRP9 in vitro and in vivo.
CONCLUSIONS: Our data reveal that RRP9 has a critical function to induce gemcitabine chemoresistance in PC through the IGF2BP1/AKT signaling pathway activation, which might be a candidate to sensitize PC cells to gemcitabine. Video abstract.

Keywords:  AKT; Apoptosis; DNA damage; Gemcitabine resistance; IGF2BP1; RRP9

DOI:  https://doi.org/10.1186/s12964-022-00974-5
Front Cell Dev Biol. 2022 ;10 1055567

DNA5mC Regulator-Mediated Molecular Clusters and Tumor Microenvironment Signatures in Glioblastoma.

Xinyu Yu, Yijun Che, Weiyang Li, Peng Zhang, Yunhu Yu, Jialin Chen, Ting Gong, Fang Cao.

  Growing evidence links DNA methylation to tumor immunity. The impact of DNA methylation (5 mC) on the microenvironment surrounding tumors and immunotherapy remains to be clarified. Through clustering gene expression of 20 DNA methylation regulators, this study aimed at systematically analyzing DNA methylation regulator patterns and tumor microenvironment characteristics of TCGA-GBM patients. Various subtypes of glioblastoma exhibit different tumor microenvironments and DNA methylation patterns. Each DNA methylation modification was then assigned a DNA methylation score (DMS). High DMS was associated with a good prognosis. In contrast, the low DMS group had a relatively low survival rate. A correlation was also found between high DMS and enhanced immunotherapy efficacy in two immune checkpoint blocking treatment cohorts. To conclude, identifying DNA methylation regulation patterns may prove critical to understanding glioblastoma progression and differentiation, as well as future therapeutic targets.

Keywords:  DNA5mC; glioblastoma; molecular clusters; signatures; tumor microenvironment

DOI:  https://doi.org/10.3389/fcell.2022.1055567
Int J Radiat Oncol Biol Phys. 2022 Nov 21. pii: S0360-3016(22)03549-0. [Epub ahead of print]

Deficiency of carbamoyl phosphate synthetase 1 engenders radioresistance in hepatocellular carcinoma via deubiquitinating c-Myc.

Sisi Zhang, Yue Hu, Zilong Wu, Xiaoshu Zhou, Tong Wu, Pindong Li, Qiuyu Lian, Shuangbing Xu, Jin Gu, Lei Chen, Gang Wu, Tao Zhang, Jing Tang, Jun Xue.

PURPOSE: Tumor radiation resistance is the main obstacle to effective radiotherapy of hepatocellular carcinoma (HCC) patients. we identified the role of urea cycle key enzyme carbamoyl phosphate synthetase 1 (CPS1) in radioresistance of HCC and explored its mechanism, aiming to provide a novel radiosensitization strategy for the CPS1-deficiency HCC subtype.
METHODS AND MATERIALS: The expression of CPS1 was measured by western blot and immunohistochemistry; Cell growth assay, EdU assay, cell apoptosis assay, cell cycle assay, clone formation assay, and subcutaneous tumor assay were performed to explore the relationship between CPS1 and radioresistance of HCC cells; lipid metabonomic analysis was used for investigating the effects of CPS1 on lipid synthesis of HCC cells; RNA-sequencing and co-immunoprecipitation assay were carried out to reveal the mechanism of CPS1 participating in the regulation of HCC radiotherapy resistance; Furthermore, 10074-G5, the specific inhibitor of c-Myc, was administered to HCC cells for investigating the role of c-Myc in CPS1-deficiency HCC cells.
RESULTS: We found that urea cycle key enzyme CPS1 was frequently lower in human HCC samples and positively associated with the patient's prognosis. Functionally, the present study proved that CPS1 depletion could accelerate the development of HCC and induce radiation resistance of HCC in vitro and in vivo, and deficiency of CPS1 promoted the synthesis of some lipid molecules. Mechanismly, we uncovered that inhibition of CPS1 upregulated CyclinA2 and CyclinD1 by stabilizing oncoprotein c-Myc at the post-transcriptional level and generated radioresistance of HCC cells. Moreover, inactivation of c-Myc using 10074-G5, a specific c-Myc inhibitor, could partially attenuate the proliferation and radioresistance induced by depletion of CPS1.
CONCLUSIONS: Our results recapitulated that silencing CPS1 could promote HCC progression and radioresistance via c-Myc stability mediated by the ubiquitin-proteasome system, suggesting that targeting c-Myc in CPS1-deficiency HCC subtype may be a valuable radiosensitization strategy in the treatment of HCC.

DOI: https://doi.org/10.1016/j.ijrobp.2022.11.022
Bioact Mater. 2023 May;23 69-79

Macrophage membrane-coated nanovesicles for dual-targeted drug delivery to inhibit tumor and induce macrophage polarization.

Xin Huang, Lutong Wang, Haoyu Guo, Weiyue Zhang.

   Background: Immunosuppressive M2 macrophages in the tumor microenvironment (TME) can mediate the therapeutic resistance of tumors, and seriously affect the clinical efficacy and prognosis of tumor patients. This study aims to develop a novel drug delivery system for dual-targeting tumor and macrophages to inhibit tumor and induce macrophage polarization.
Methods: The anti-tumor effects of methyltransferase like 14 (METTL14) were investigated both in vitro and in vivo. The underlying mechanisms of METTL14 regulating macrophages were also explored in this study. We further constructed the cyclic (Arg-Gly-Asp) (cRGD) peptide modified macrophage membrane-coated nanovesicles to co-deliver METTL14 and the TLR4 agonist.
Results: We found that METTL14 significantly inhibits the growth of tumor in vitro. METTL14 might downregulate TICAM2 and inhibit the Toll-like receptor 4 (TLR4) pathway of macrophages, meanwhile, the combination of METTL14 and the TLR4 agonist could induce M1 polarization of macrophages. Macrophage membrane-coated nanovesicles are characterized by easy modification, drug loading, and dual-targeting tumor and macrophages, and cRGD modification can further enhance its targeting ability. It showed that the nanovesicles could improve the in vivo stability of METTL14, and dual-target tumor and macrophages to inhibit tumor and induce M1 polarization of macrophages.
Conclusions: This study anticipates achieving the dual purposes of tumor inhibition and macrophage polarization, and providing a new therapeutic strategy for tumors.

Keywords:  Cell membrane-coated nanovesicles; Macrophage polarization; Osteosarcoma; Targeted drug delivery system; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.bioactmat.2022.09.027
Pathol Res Pract. 2022 Nov 15. pii: S0344-0338(22)00471-X. [Epub ahead of print]240 154227

LncRNA HCG18 promotes M2 macrophage polarization to accelerate cetuximab resistance in colorectal cancer through regulating miR-365a-3p/FOXO1/CSF-1 axis.

Cao Gao, Wenwei Hu, Jiemin Zhao, Xuefeng Ni, Yanjie Xu.

   BACKGROUND: Cetuximab (CET) resistance in colorectal cancer (CRC) is responsible to poor prognosis to some extent. M2 macrophage polarization is closely correlated with drug resistance to cancers. Therefore, this study aims to investigate whether the mechanism of HCG18 on CET resistance to CRC involving in M2 macrophage polarization.
METHODS: Clinic samples and SW620 cells with/without M0 macrophage co-culture served as experimental subjects. CET treatment was performed to induce SW620 cell resistant to CET. qRT-PCR and western blot were employed to evaluate the mRNA and protein expression of genes. The capabilities of cell viability, proliferation, migration and invasion were examined using CCK-8, clone formation assay and transwell. ELISA was employed to examine the protein concentrations of IL-10 and TGF-β1. StarBase and luciferase activity assay were conducted to consolidate the interactions among HCG18, miR-365a-3p and FOXO1.
RESULTS: In clinical samples and CRC cells, the abundance of HCG18 was enhanced whereas miR-365a-3p was reduced. Besides, HCG18 expression in CET-resistant tumor tissues was higher than that in CET-sensitive tumor tissues and the trend of miR-365a-3p was opposite to that of HCG18. HCG18 knockdown attenuated macrophage-induced CET resistance in SW620 cells and suppressed M2 polarization of THP-1 cells. Mechanistically, HCG18 interacted with miR-365a-3p and miR-365a-3p targeted FOXO1. MiR-365a-3p inhibitor abolished HCG18 knockdown-mediated inhibition of CET resistance, while FOXO1 knockdown compromised the influences of miR-365a-3p inhibitor. FOXO1 could positively regulate CSF-1 expression to promote M2 macrophage polarization and macrophage-induced CET resistance.
CONCLUSION: Our results revealed that HCG18 promoted M2 macrophage polarization to facilitate CET resistance to CRC cells through modulating miR-365a-3p/FOXO1/CSF-1 axis.

Keywords:  Cetuximab resistance; Colorectal cancer; FOXO1; HCG18; MiR-365a-3p

DOI:  https://doi.org/10.1016/j.prp.2022.154227
Transl Oncol. 2022 Nov 16. pii: S1936-5233(22)00231-5. [Epub ahead of print]27 101572

LCMT1 indicates poor prognosis and is essential for cell proliferation in hepatocellular carcinoma.

Ning Zhang, Cailing Lu, Jiao Mo, Xinhang Wang, Simi Liao, Ningjing Liang, Mei Feng, Tingting Tang, Yijie Wu, Yunqing Li, Chunhua Lan, Chengying Chen, Qianqian Shi, Lancheng Wei, Zhijian Zheng, Yu Lei, Zhiming Zhang, Shen Tang, Xiyi Li.

   BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most malignant type of cancers. Leuci carboxyl methyltransferase 1 (LCMT1) is a protein methyltransferase that plays an improtant regulatory role in both normal and cancer cells. The aim of this study is to evaluate the expression pattern and clinical significance of LCMT1 in HCC.
METHODS: The expression pattern and clinical relevance of LCMT1 were determined using the Gene Expression Omnibus (GEO) database, the Cancer Genome Atlas (TCGA) program, and our datasets. Gain-of-function and loss-of-function studies were employed to investigate the cellular functions of LCMT1 in vitro and in vivo. Quantitative real-time polymerase chain reaction (RT-PCR) analysis, western blotting, enzymatic assay, and high-performance liquid chromatography were applied to reveal the underlying molecular functions of LCMT1.
RESULTS: LCMT1 was upregulated in human HCC tissues, which correlated with a "poor" prognosis. The siRNA-mediated knockdown of LCMT1 inhibited glycolysis, promoted mitochondrial dysfunction, and increased intracellular pyruvate levels by upregulating the expression of alani-neglyoxylate and serine-pyruvate aminotransferase (AGXT). The overexpression of LCMT1 showed the opposite results. Silencing LCMT1 inhibited the proliferation of HCC cells in vitro and reduced the growth of tumor xenografts in mice. Mechanistically, the effect of LCMT1 on the proliferation of HCC cells was partially dependent on PP2A.
CONCLUSIONS: Our data revealed a novel role of LCMT1 in the proliferation of HCC cells. In addition, we provided novel insights into the effects of glycolysis-related pathways on the LCMT1regulated progression of HCC, suggesting LCMT1 as a novel therapeutic target for HCC therapy.

Keywords:  Cell proliferation; Hepatocellular carcinoma (HCC); Leucine carboxyl methyltransferase 1 (LCMT1); Prognosis

DOI:  https://doi.org/10.1016/j.tranon.2022.101572
Front Genet. 2022 ;13 996245

METTL16 regulates m6A methylation on chronic hepatitis B associated gene HLA-DPB1 involved in liver fibrosis.

Haibing Gao, Xiangmei Wang, Huaxi Ma, Shenglong Lin, Dongqing Zhang, Wenjun Wu, Ziyuan Liao, Mengyun Chen, Qin Li, Minghua Lin, Dongliang Li.

  The role of genetic factors in the occurrence and progression of CHB (CHB) is still not fully explored. In recent years, genome-wide association studies on CHB patients have demonstrated that a large number of CHB-associated single nucleotide polymorphisms exist in the gene intron, which may regulate expression at the transcriptional level. Modification of RNA m6A methylation is one of the key mechanisms regulating gene expression. Here we show that METTL16, an m6A regulator involved in mRNA intron splicing, is differentially expressed in CHB the tissue of patients who has definite diagnosis of mild and severe fibrosis. At the same time, there are also significant differences in the expression of CHB-associated genes such as HLA-DPA1 and HLA-DPB1. The expression of HLA-DPB1 is related to METTL16. Furthermore, analyses of RNA binding of METTL16 and HLA-DPB1 show that the silencing of METTL16 in astrocytes downregulates m6A and expression of HLA-DPB1. In conclusion, METTL16 participates in the progression of CHB fibrosis by regulating the m6A level and expression of HLA-DPB1.

Keywords:  CHB (chronic hepatitis B); GWAS; HBV-hepatitis B virus; M6A; METTL16

DOI:  https://doi.org/10.3389/fgene.2022.996245
Oncol Lett. 2022 Dec;24(6): 439

NSUN5 promotes progression and predicts poor prognosis in hepatocellular carcinoma.

Xiao-Wen Zhang, Lu-Yi Wu, Hui-Rong Liu, Yan Huang, Qin Qi, Rui Zhong, Lu Zhu, Chun-Fang Gao, Lin Zhou, Jian Yu, Huan-Gan Wu.

  The 5-methylcytosine (m5C) RNA methyltransferase NOP2/Sun RNA methyltransferase 5 (NSUN5) has been reported to serve important roles in numerous diseases. However, the functions and clinical significance of NSUN5 in hepatocellular carcinoma (HCC) remain unknown. Clinical information and NSUN5 mRNA sequencing data for 374 patients with HCC were downloaded from The Cancer Genome Atlas (TCGA) database, and NSUN5 mRNA and protein expression levels in 120 patients with HCC (present study cohorts) were assessed using reverse transcription-quantitative PCR, western blotting or immunohistochemistry. The association between NSUN5 mRNA and protein expression levels and the clinical characteristics (or prognosis) of patients with HCC was analyzed using the χ2 or log-rank test. The functions of NSUN5 in HCC were evaluated using in vitro and in vivo experiments, and the mechanism by which NSUN5 affected the progression of HCC was assessed using bioinformatics analysis using LinkedOmics. NSUN5 was significantly upregulated and predicted poor prognosis in HCC according to data from both TCGA database and present study cohorts. NSUN5 significantly promoted HCC proliferation and migration in vitro and significantly induced HCC tumor growth in vivo. Bioinformatics analysis demonstrated that NSUN5 was positively correlated with genes associated with translation in HCC. It was hypothesized that overexpression of NSUN5 strengthened ribosome functions and global protein translation, which may promote the proliferation and migration of HCC. In conclusion, NSUN5 may promote the progression of HCC by enhancing translation, thus making it a potential target for HCC treatment.

Keywords:  NSUN5; RNA methyltransferase; hepatocellular carcinoma; m5C

DOI:  https://doi.org/10.3892/ol.2022.13559
Biol Chem. 2022 Nov 25.

Dynamic regulation of eEF1A1 acetylation affects colorectal carcinogenesis.

Hongpeng Jiang, Yu Zhang, Boya Liu, Xin Yang, Zhe Wang, Meng Han, Huiying Li, Jianyuan Luo, Hongwei Yao.

  The dysregulation of the translation elongation factor families which are responsible for reprogramming of mRNA translation has been shown to contribute to tumor progression. Here, we report that the acetylation of eukaryotic Elongation Factor 1 Alpha 1 (eEF1A1/EF1A1) is required for genotoxic stress response and maintaining the malignancy of colorectal cancer (CRC) cells. The evolutionarily conserved site K439 is identified as the key acetylation site. Tissue expression analysis demonstrates that the acetylation level of eEF1A1 K439 is higher than paired normal tissues. Most importantly, hyperacetylation of eEF1A1 at K439 negatively correlates with CRC patient survival. Mechanistically, CBP and SIRT1 are the major acetyltransferase and deacetylase of eEF1A1. Hyperacetylation of eEF1A1 at K439 shows a significant tumor-promoting effect by increasing the capacity of proliferation, migration, and invasion of CRC cells. Our findings identify the altered post-translational modification at the translation machines as a critical factor in stress response and susceptibility to colorectal carcinogenesis.

Keywords:  acetylation; colorectal cancer; eEF1A1; genotoxic stress; translation elongation

DOI:  https://doi.org/10.1515/hsz-2022-0180
Int J Mol Sci. 2022 Nov 10. pii: 13851. [Epub ahead of print]23(22):

Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications.

Viktoriia A Arzumanian, Georgii V Dolgalev, Ilya Y Kurbatov, Olga I Kiseleva, Ekaterina V Poverennaya.

  The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.

Keywords:  RNA; RNA modifications; epitranscriptome

DOI:  https://doi.org/10.3390/ijms232213851
Cell Death Dis. 2022 Nov 24. 13(11): 992

HDAC1/3-dependent moderate liquid-liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation.

Meng Li, Mingying Li, Yuan Xia, Guosheng Li, Xiuhua Su, Dongmei Wang, Jingjing Ye, Fei Lu, Tao Sun, Chunyan Ji.

Methyltransferase-like protein 3 (METTL3) plays critical roles in acute myeloid leukemia (AML) progression, however, the mechanism of abnormal overexpression of METTL3 in AML remain elusive. In the current study, we uncovered that Yin Yang 1 (YY1) binds to the promoter region of METTL3 as a transcription factor and promotes its expression, which in turn enhances the proliferation of AML cells. Mechanistically, YY1 binds to HDAC1/3 and regulates METTL3 expression in a moderate liquid-liquid phase separation (LLPS) manner. After mutation of the HDAC-binding site of YY1 or HDAC inhibitor (HDACi) treatment, YY1 was separated from HDAC1/3, which resulted in an excessive LLPS state, thereby inhibiting the expression of METTL3 and the proliferation of AML cells. In conclusion, our study clarified the regulatory mechanism of the abnormal expression of METTL3 in AML, revealed the precise "Yin-Yang" regulatory mechanism of YY1 from the perspective of LLPS degree, and provided new ideas for the precise diagnosis and treatment of AML.

DOI: https://doi.org/10.1038/s41419-022-05435-y
Front Cell Dev Biol. 2022 ;10 1055808

N6-methyladenosine RNA methylation: From regulatory mechanisms to potential clinical applications.

Peipei Li, Yuntao Wang, Yiwen Sun, Sanjie Jiang, Jingjing Li.

  Epitranscriptomics has emerged as another level of epigenetic regulation similar to DNA and histone modifications. N 6-methyladenosine (m6A) is one of the most prevalent and abundant posttranscriptional modifications, widely distributed in many biological species. The level of N 6-methyladenosine RNA methylation is dynamically and reversibly regulated by distinct effectors including methyltransferases, demethylases, histone modification and metabolites. In addition, N 6-methyladenosine RNA methylation is involved in multiple RNA metabolism pathways, such as splicing, localization, translation efficiency, stability and degradation, ultimately affecting various pathological processes, especially the oncogenic and tumor-suppressing activities. Recent studies also reveal that N 6-methyladenosine modification exerts the function in immune cells and tumor immunity. In this review, we mainly focus on the regulatory mechanisms of N 6-methyladenosine RNA methylation, the techniques for detecting N 6-methyladenosine methylation, the role of N 6-methyladenosine modification in cancer and other diseases, and the potential clinical applications.

Keywords:  N6-methyladenosine; RNA methylation; cancer; regulatory mechanisms; tumor therapy

DOI:  https://doi.org/10.3389/fcell.2022.1055808