bims-rimeca 2022-12-18 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022–12–18
thirty papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

METTL3 and METTL14-mediated N6-methyladenosine modification promotes cell proliferation and invasion in a model of endometriosis.
Targeting FTO Suppresses Pancreatic Carcinogenesis via Regulating Stem Cell Maintenance and EMT Pathway.
Stage-specific requirement for METTL3-dependent m6A modification during dental pulp stem cell differentiation.
Photoperiod alters testicular methyltransferase complex mRNA expression in Siberian hamsters.
Characterization of immune microenvironment infiltration and m6A regulator-mediated RNA methylation modification patterns in osteoarthritis.
METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner.
Biological and pharmacological roles of m6A modifications in cancer drug resistance.
Use of Novel m6A Regulator-mediated Methylation Modification Patterns in Distinct Tumor Microenvironment Profiles to Identify and Predict Glioma Prognosis and Progression, T-cell Dysfunction, and Clinical Response to ICI Immunotherapy.
Effect of M6A regulators on diagnosis, subtype classification, prognosis and novel therapeutic target development of idiopathic pulmonary fibrosis.
N6-Methyladenosine Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes.
N6-methyladenosine promotes osteogenic differentiation of PDLSCs from periodontitis patients.
An overview of the effects and mechanisms of m6 A methylation on innate immune cells in sepsis.
Prognostic analysis of m6A-related genes as potential biomarkers in idiopathic pulmonary fibrosis.
Long non-coding RNA HOXC-AS1 exerts its oncogenic effects in esophageal squamous cell carcinoma by interaction with IGF2BP2 to stabilize SIRT1 expression.
Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression.
Construction of a m5C-related long non-coding RNA signature for the prognosis of hepatocellular carcinoma.
The alteration of N6-methyladenosine (m6A) modification at the transcriptome-wide level in response of heat stress in bovine mammary epithelial cells.
RNA m6A modification: Mapping methods, roles, and mechanisms in acute myeloid leukemia.
N6-methylandenosine-related immune genes correlate with prognosis and immune landscapes in gastric cancer.
Genomewide m6A Mapping Uncovers Dynamic Changes in the m6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells.
Upregulated YTHDF1 associates with tumor immune microenvironment in head and neck squamous cell carcinomas.
SMOC2 promotes aggressive behavior of fibroblast-like synoviocytes in rheumatoid arthritis through transcriptional and post-transcriptional regulating MYO1C.
Acetyltransferase NAT10 regulates the Wnt/β-catenin signaling pathway to promote colorectal cancer progression via ac4C acetylation of KIF23 mRNA.
The c-MYC-WDR43 signalling axis promotes chemoresistance and tumour growth in colorectal cancer by inhibiting p53 activity.
m6A-related long noncoding RNAs predict prognosis and indicate therapeutic response in endometrial carcinoma.
AKT1 phosphorylates RBM17 to promote Sox2 transcription by modulating alternative splicing of FOXM1 to enhance cancer stem cell properties in colorectal cancer cells.
YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m6A-mediated YWHAZ stability.
Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy.
Prognostic biomarkers of pancreatic cancer identified based on a competing endogenous RNA regulatory network.
IGF2BP2-induced circRUNX1 facilitates the growth and metastasis of esophageal squamous cell carcinoma through miR-449b-5p/FOXP3 axis.

Reprod Biomed Online. 2022 Oct 29. pii: S1472-6483(22)00766-0. [Epub ahead of print]

METTL3 and METTL14-mediated N6-methyladenosine modification promotes cell proliferation and invasion in a model of endometriosis.

Licong Shen, Chun Zhang, Yi Zhang, Yongwen Yang.

   RESEARCH QUESTION: Could METTL3 and METTL14-mediated N6-methyladenosine (m6A) modification play possible cooperative roles in pathogenesis and progression of endometriosis?
DESIGN: An investigation into m6A methylation profiles and the roles of METTL3 and METTL14 in the m6A regulation and pathogenesis of endometriosis. The m6A methylation and mRNA levels in paired ectopic endometrium and eutopic endometrium were measured using m6A-mRNA epitranscriptomic microarrays. The functions of m6A methylation in mRNAs were predicted using bioinformatics analysis. The levels of m6A methyltransferases were detected using quantitative polymerase chain reaction. The role of METTL3 and METTL14 in endometriosis was explored using eutopic endometrium stromal cells.
RESULTS: The m6A methylation levels were decreased in 1312 mRNAs and increased in 518 mRNAs; 1797 mRNAs were increased and 2580 mRNAs were reduced in the ectopic endometrium compared with the eutopic endometrium. Pathway analysis found that the genes with hypo-methylated m6A were significantly associated with important pathways in endometriosis, including oestrogen, Hippo, and PI3K-Akt signalling and cell-cell adhesion. Furthermore, METTL3 and METTL14 were downregulated in the ectopic endometrium compared with the eutopic endometrium (P < 0.001). Simultaneous METTL3 and METTL14 knockdown increased cell proliferation and invasion.
CONCLUSION: Taken together, these data reveal a differential m6A epitranscriptomic pattern in endometriosis. The N6-methyladenosine modification mediated by METTL3 and METTL14 play a cooperative role in promoting cell proliferation and invasion in a model of endometriosis. Therefore, METTL3 and METTL14 may be a novel treatment target of the disease.

Keywords:  Endometriosis; METTL14; METTL3; N6-methyladenosine; mRNAs

DOI:  https://doi.org/10.1016/j.rbmo.2022.10.010
Cancers (Basel). 2022 Nov 30. pii: 5919. [Epub ahead of print]14(23):

Targeting FTO Suppresses Pancreatic Carcinogenesis via Regulating Stem Cell Maintenance and EMT Pathway.

Rachana Garg, Laleh Melstrom, Jianjun Chen, Chuan He, Ajay Goel.

  N6-methyladenosine (m6A) is the most prevalent post-transcriptional RNA modification regulating cancer self-renewal. However, despite its functional importance and prognostic implication in tumorigenesis, the relevance of FTO, an m6A eraser, in pancreatic cancer (PC) remains elusive. Here, we establish the oncogenic role played by FTO overexpression in PC. FTO is upregulated in PC cells compared to normal human pancreatic ductal epithelial (HPDE) cells. Both RNAi depletion and CS1-mediated pharmacological inhibition of FTO caused a diminution of PC cell proliferation via cell cycle arrest in the G1 phase and p21cip1 and p27kip1 induction. While HPDE cells remain insensitive to CS1 treatment, FTO overexpression confers enhancements in growth, motility, and EMT transition, thereby inculcating tumorigenic properties in HPDE cells. Notably, shRNA-mediated FTO depletion in PC cells impairs their mobility and invasiveness, leading to EMT reversal. Mechanistically, this was associated with impaired tumorsphere formation and reduced expression of CSCs markers. Furthermore, FTO depletion in PC cells weakened their tumor-forming capabilities in nude mice; those tumors had increased apoptosis, decreased proliferation markers, and MET conversion. Collectively, our study demonstrates the functional importance of FTO in PC and the maintenance of CSCs via EMT regulation. Thus, FTO may represent an attractive therapeutic target for PC.

Keywords:  EMT; FTO; cancer stem cells; m6A; pancreatic cancer; post-transcriptional modification

DOI:  https://doi.org/10.3390/cancers14235919
J Transl Med. 2022 Dec 16. 20(1): 605

Stage-specific requirement for METTL3-dependent m6A modification during dental pulp stem cell differentiation.

Haiyun Luo, Wenjing Liu, Yachuan Zhou, Yanli Zhang, Junrong Wu, Ruolan Wang, Longquan Shao.

   BACKGROUND: N6-methyladenosine (m6A) is the most prevalent epigenetic modification in eukaryotic messenger RNAs and plays a critical role in cell fate transition. However, it remains to be elucidated how m6A marks functionally impact the transcriptional cascades that orchestrate stem cell differentiation. The present study focuses on the biological function and mechanism of m6A methylation in dental pulp stem cell (DPSC) differentiation.
METHODS: m6A RNA immunoprecipitation sequencing was utilized to assess the m6A-mRNA landscape during DPSC differentiation. Ectopic transplantation of DPSCs in immunodeficient mice was conducted to verify the in vitro findings. RNA sequencing and m6A RNA immunoprecipitation sequencing were combined to identify the candidate targets. RNA immunoprecipitation and RNA/protein stability of Noggin (NOG) were evaluated. The alteration in poly(A) tail was measured by 3'-RACE and poly(A) tail length assays.
RESULTS: We characterized a dynamic m6A-mRNA landscape during DPSC mineralization with increasing enrichment in the 3' untranslated region (UTR). Methyltransferase-like 3 (METTL3) was identified as the key m6A player, and METTL3 knockdown disrupted functional DPSC differentiation. Moreover, METTL3 overexpression enhanced DPSC mineralization. Increasing m6A deposition in the 3' UTR restricted NOG expression, which is required for DPSC mineralization. This stage-specific m6A methylation and destabilization of NOG was suppressed by METTL3 knockdown only in differentiated DPSCs. Furthermore, METTL3 promotes the degradation of m6A-tagged NOG by shortening the poly(A) tail length in the differentiated stage.
CONCLUSIONS: Our results address an essential role of dynamic m6A signaling in the temporal control of DPSC differentiation and provide new insight into epitranscriptomic mechanisms in stem cell-based therapy.

Keywords:  Cell differentiation; Poly(A) tail length; RNA methylation; Stem cell therapy

DOI:  https://doi.org/10.1186/s12967-022-03814-9
Gen Comp Endocrinol. 2022 Dec 12. pii: S0016-6480(22)00211-8. [Epub ahead of print] 114186

Photoperiod alters testicular methyltransferase complex mRNA expression in Siberian hamsters.

Melanie A Rader, Olga G Jaime, Victor O Abarca, Kelly A Young.

  Exposure to long photoperiods stimulates, whereas exposure to short photoperiods transiently inhibit testicular function in Siberian hamsters via well-described neuroendocrine mechanisms. However, less is known about the intra-testicular regulation of these photoperiod-mediated changes. N6-methyladenosine (m6A) is one of the most common mRNA modifications in eukaryotes, with alterations in m6A mRNA methylation affecting testis function and fertility. We hypothesized that genes controlling m6A methylation such as methyltransferase-like-3 (Mettl3) and -14 (Mettl14) and Wilms' tumor-1 associated protein (Wtap), part of an mRNA methylating methyl-transferase complex, or the fat-mass-and-obesity-associated (Fto) and the α-ketoglutarate-dependent dioxygenase alkB homolog-5 (Alkbh5) genes responsible for m6A demethylation, may be differentially regulated by photoperiod in the testis. Male hamsters were exposed to long (LD, control) photoperiod for 14-weeks, short (SD) photoperiod for 2, 5, 8, 11 and 14-weeks to induce regression, or SD for 14-weeks followed by transfer to LD for 1, 2, 4 or 8-weeks to induce recrudescence (post-transfer, PT). SD exposure significantly reduced body, testis, and epididymal masses compared to all other groups. Spermatogenic index, seminiferous tubule diameters and testosterone concentrations significantly decreased in SD as compared to LD, returning to levels no different than LD in post-transfer groups. SD exposure significantly decreased Wtap, Fto, Alkbh5, but increased Mettl14 mRNA expression as compared to LD, with values in PT groups restored to LD levels. Mettl3 mRNA expression did not change. These results suggest that testicular recovery induced by stimulatory photoperiod is relatively rapid, and that methyltransferase complex may play a role during photostimulated testicular recrudescence.

Keywords:  methyltransferase; photoperiod; seasonal breeding; spermatogenesis; testis

DOI:  https://doi.org/10.1016/j.ygcen.2022.114186
Front Immunol. 2022 ;13 1018701

Characterization of immune microenvironment infiltration and m6A regulator-mediated RNA methylation modification patterns in osteoarthritis.

Yulong Ouyang, Yuanqing Tu, Shuilin Chen, Huan Min, Zhexu Wen, Guihao Zheng, Ting Wan, Hao Fan, Wenzhao Yang, Guicai Sun.

   Background: Few studies have been reported the potential role of N6-methyladenosine (m6A) modification in osteoarthritis (OA). We investigated the patterns of m6A modification in the immune microenvironment of OA.
Methods: We evaluated the m6A modification patterns based on 22 m6A regulators in 139 OA samples and systematically associated these modification patterns with immune cell infiltration characteristics. The function of m6A phenotype-related differentially expressed genes (DEGs) was investigated using gene enrichment analysis. An m6A score model was constructed using principal component analysis (PCA), and an OA prediction model was established based on the key m6A regulators. We used real-time PCR analysis to detect the changes of gene expression in the cell model of OA.
Results: Healthy and OA samples showed significant differences in the expression of m6A regulators. Nine key m6A regulators, two m6A modification patterns, m6A-related genes and two gene clusters were identified. Some m6A regulators had a strong correlation with each other. Gene clusters and m6A clusters have high similarity, and cluster A corresponds to a high m6A score. Immunocytes infiltration differed significantly between the two clusters, with the m6A cluster B and gene cluster B having more types of infiltrating immunocytes than cluster A. The predictive model can also predict the progression of OA through m6A regulators expression. The results of real-time PCR analysis showed that the gene expression in the cell model of OA is similar to that of the m6A cluster B.
Conclusions: Our study reveals for the first time the potential regulatory mechanism of m6A modification in the immune microenvironment of OA. This study also sheds new light on the pathogenesis of OA.

Keywords:  RNA methylation; immune microenvironment; immunocytes; m6A regulator; osteoarthritis

DOI:  https://doi.org/10.3389/fimmu.2022.1018701
PeerJ. 2022 ;10 e14379

METTL16-mediated translation of CIDEA promotes non-alcoholic fatty liver disease progression via m6A-dependent manner.

Jinhong Tang, Xiangyun Zhao, Wei Wei, Weiwei Liu, Huining Fan, Xiu Ping Liu, Yungai Li, Long Wang, Jinghui Guo.

   Background: As the most prevalent chemical modifications on eukaryotic mRNAs, N6-methyladenosine (m6A) methylation was reported to participate in the regulation of various metabolic diseases. This study aimed to investigate the roles of m6A methylation and methyltransferase-like16 (METTL16) in non-alcoholic fatty liver disease (NAFLD).
Methods: In this study, we used a model of diet-induced NAFLD, maintaining six male C57BL/6J mice on high-fat diet (HFD) to generate hepatic steatosis. The high-throughput sequencing and RNA sequencing were performed to identify the m6A methylation patterns and differentially expressed mRNAs in HFD mice livers. Furthermore, we detected the expression levels of m6A modify enzymes by qRT-PCR in liver tissues, and further investigated the potential role of METTL16 in NAFLD through constructing overexpression and a knockdown model of METTL16 in HepG2 cells.
Results: In total, we confirmed 15,999 m6A recurrent peaks in HFD mice and 12,322 in the control. Genes with differentially methylated m6A peaks were significantly associated with the dysregulated glucolipid metabolism and aggravated hepatic inflammatory response. In addition, we identified five genes (CIDEA, THRSP, OSBPL3, GDF15 and LGALS1) that played important roles in NAFLD progression after analyzing the differentially expressed genes containing differentially methylated m6A peaks. Intriguingly, we found that the expression levels of METTL16 were substantially increased in the NAFLD model in vivo and in vitro, and further confirmed that METTL16 upregulated the expression level of lipogenic genes CIDEA in HepG2 cells.
Conclusions: These results indicate the critical roles of m6A methylation and METTL16 in HFD-induced mice and cell NAFLD models, which broaden people's perspectives on potential m6A-related treatments and biomarkers for NAFLD.

Keywords:  CIDEA; METTL16; N6-methyladenosine (m6A); Non-alcoholic fatty liver disease; m6A sequencing

DOI:  https://doi.org/10.7717/peerj.14379
Mol Cancer. 2022 Dec 14. 21(1): 220

Biological and pharmacological roles of m6A modifications in cancer drug resistance.

Zaoqu Liu, Haijiao Zou, Qin Dang, Hui Xu, Long Liu, Yuyuan Zhang, Jinxiang Lv, Huanyun Li, Zhaokai Zhou, Xinwei Han.

  Cancer drug resistance represents the main obstacle in cancer treatment. Drug-resistant cancers exhibit complex molecular mechanisms to hit back therapy under pharmacological pressure. As a reversible epigenetic modification, N6-methyladenosine (m6A) RNA modification was regarded to be the most common epigenetic RNA modification. RNA methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers) are frequently disordered in several tumors, thus regulating the expression of oncoproteins, enhancing tumorigenesis, cancer proliferation, development, and metastasis. The review elucidated the underlying role of m6A in therapy resistance. Alteration of the m6A modification affected drug efficacy by restructuring multidrug efflux transporters, drug-metabolizing enzymes, and anticancer drug targets. Furthermore, the variation resulted in resistance by regulating DNA damage repair, downstream adaptive response (apoptosis, autophagy, and oncogenic bypass signaling), cell stemness, tumor immune microenvironment, and exosomal non-coding RNA. It is highlighted that several small molecules targeting m6A regulators have shown significant potential for overcoming drug resistance in different cancer categories. Further inhibitors and activators of RNA m6A-modified proteins are expected to provide novel anticancer drugs, delivering the therapeutic potential for addressing the challenge of resistance in clinical resistance.

Keywords:  Cancer drug resistance; Chemotherapy; Immunotherapy; RNA modification; m6A methylation

DOI:  https://doi.org/10.1186/s12943-022-01680-z
Curr Pharm Des. 2022 Dec 07.

Use of Novel m6A Regulator-mediated Methylation Modification Patterns in Distinct Tumor Microenvironment Profiles to Identify and Predict Glioma Prognosis and Progression, T-cell Dysfunction, and Clinical Response to ICI Immunotherapy.

Binghao Zhao, Zhongtian Xiang, Bo Wu, Xiang Zhang, Nan Feng, Yiping Wei, Wenxiong Zhang.

   BACKGROUND: The specific functions of RNA N6-methyladenosine (m6A) modifications in the glioma tumor microenvironment (TME) and glioma patient prognosis and treatment have not been determined to date.
OBJECTIVE: The objective of the study was to determine the role of m6A modifications in glioma TME.
METHODS: Nonnegative matrix factorization (NMF) methods were used to determine m6A clusters and m6A gene signatures based on 21 genes relating to m6A modifications. TME characteristics for each m6A cluster and m6A gene signature were quantified by established m6A score. The utility of m6A score was validated in immunotherapy and other antiangiogenic treatment cohorts.
RESULTS: Three m6A clusters were identified among 3,395 glioma samples, and they were linked to different biological activities and clinical outcomes. The m6A clusters were highly consistent with immune profiles known as immune-inflamed, immune-excluded, and immune-desert phenotypes. Clusters within individual tumors could predict glioma inflammation, molecular subtypes, TME stromal activity, genetic variation, alternative splicing, and prognosis. As for the m6A score and m6A gene signature, patients with low m6A scores exhibited an increased tumor mutation burden, immune activity, neoantigen load, and prolonged survival. A low m6A score indicated the potential for a low level of T-cell dysfunction, a considerably better treatment response, and durable clinical benefits from immunotherapy, bevacizumab and regorafenib.
CONCLUSION: Glioma m6A clusters and gene signatures have distinctive TME features. The m6A gene signature may guide prognostic assessments and promote the use of effective strategies.

Keywords:  Glioma; Immunotherapy; M6A score; Multiomics scale; Tumor microenvironment; m6A modification; targeted therapy

DOI:  https://doi.org/10.2174/1381612829666221207112438
Front Pharmacol. 2022 ;13 993567

Effect of M6A regulators on diagnosis, subtype classification, prognosis and novel therapeutic target development of idiopathic pulmonary fibrosis.

Guirui Huang, Shuaiyang Huang, Hongsheng Cui.

  Molecular biology studies show that RNA N6-methyladenosine (m6A) modifications may take part in the incidence and development of idiopathic pulmonary fibrosis (IPF). Nonetheless, the roles of m6A regulators in IPF are not fully demonstrated. In this study, 12 significant m6A regulators were filtered out between healthy controls and IPF patients using GSE33566 dataset. Random forest algorithm was used to identify 11 candidate m6A regulators to predict the incidence of IPF. The 11 candidate m6A regulators included leucine-rich PPR motif-containing protein (LRPPRC), methyltransferase-like protein 3, FTO alpha-ketoglutarate dependent dioxygenase (FTO), methyltransferase-like 14/16, zinc finger CCCH domain-containing protein 13, protein virilizer homolog, Cbl proto-oncogene like 1, fragile X messenger ribonucleoprotein 1 and YTH domain containing 1/2. A nomogram model was constructed based on 11 candidate m6A regulators and considered beneficial to IPF patients using decision curve analysis. Consensus clustering method was used to distinctly divide IPF patients into two m6A patterns (clusterA and clusterB) based on 12 significant m6A regulators. M6A scores of all IPF patients were obtained using principal component analysis to quantify the m6A patterns. Patients in clusterB had higher m6A scores than those in clusterA. Furthermore, patients in clusterB were correlated with Th17 and Treg cell infiltration, innate immunity and Th1 immunity, while those in clusterA were correlated with adaptive immunity and Th2 immunity. Patients in clusterB also had higher expressions of mesenchymal markers and regulatory factors of fibrosis but lower expressions of epithelial markers. Lastly and interestingly, two m6A regulators, LRPPRC (p = 0.011) and FTO (p = 0.042), were identified as novel prognostic genes in IPF patients for the first time using an external GSE93606 dataset. Both of them had a positive correlation with a better prognosis and may serve as therapy targets. Thus, we conducted virtual screening to discover potential drugs targeting LRPPRC and FTO in the treatment of IPF. In conclusion, m6A regulators are crucial to the onset, development and prognosis of IPF. Our study on m6A patterns may provide clues for clinical diagnosis, prognosis and targeted therapeutic drugs development for IPF.

Keywords:  consensus clustering; diagnostic model; idiopathic pulmonary fibrosis; m6A regulators; novel therapeutic targets; prognostic markers

DOI:  https://doi.org/10.3389/fphar.2022.993567
Genomics Proteomics Bioinformatics. 2022 Dec 07. pii: S1672-0229(22)00151-6. [Epub ahead of print]

N6-Methyladenosine Profile Dynamics Indicates Regulation of Oyster Development by m6A-RNA Epitranscriptomes.

Lorane Le Franc, Bruno Petton, Pascal Favrel, Guillaume Rivière.

  The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the whole development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposon transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with a minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated to transcript levels and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of transposon transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated to gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.

Keywords:  Embryo; Evo-devo; Metamorphosis; RNA methylation; Transcription

DOI:  https://doi.org/10.1016/j.gpb.2022.12.002
Oral Dis. 2022 Dec 14.

N6-methyladenosine promotes osteogenic differentiation of PDLSCs from periodontitis patients.

Xiaochen Zhang, Jia Liu, Jie Gao, Weifu Sun, Xin Chen, Xian Wang, Wen Qin, Zuolin Jin.

   OBJECTIVES: This study aimed to investigate the mechanism of N6-methyladenosine (m6A) in the osteogenic differentiation of periodontal ligament stem cells (PDLSCs) from periodontitis patients.
METHODS: Differentially m6A-methylated lncRNA/mRNA profiles were detected by a m6A epitranscriptomic microarray. Bioinformatics analysis was performed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The transfection efficiency of the lentivirus was detected. The osteogenic activity of PDLSCs from periodontitis patients (PPDLSCs) was assessed.
RESULTS: The microarray results showed that 275 lncRNAs and 1292 mRNAs were significantly differentially methylated between PPDLSCs and PDLSCs from healthy people. Among those lncRNAs, lncRNA4114 (transcript_ID: ENST00000444114) showed both reduced m6A methylation levels and expression levels in PPDLSCs. Further bioinformatics analysis predicted that the differentially methylated mRNAs were mainly involved in cell interaction, stem cell pluripotency, and osteogenic differentiation signals. Then, overexpression of methyltransferase like 3 (METTL3) promoted the osteogenic differentiation of PPDLSCs, while knocking down METTL3 showed an inhibitory effect. Furthermore, METTL3 overexpression promotes the stability of lncRNA4114 to upregulate the expression level. Moreover, lncRNA4114 overexpression promoted the osteogenic differentiation of PPDLSCs.
CONCLUSION: METTL3 promotes the osteogenic differentiation of PPDLSCs by regulating the stability of lncRNA4114.

Keywords:  lncRNAs; m6A; microarray; osteogenesis; periodontitis

DOI:  https://doi.org/10.1111/odi.14467
Front Immunol. 2022 ;13 1041990

An overview of the effects and mechanisms of m6 A methylation on innate immune cells in sepsis.

Weiwei Qian, Yu Cao.

   Introduction: Sepsis is a severe clinical syndrome caused by dysregulated systemic inflammatory responses to infection. Methylation modification, as a crucial mechanism of RNA functional modification, can manipulate the immunophenotype and functional activity of immune cells to participate in sepsis progression. This study aims to explore the mechanism of N6-methyladenosine (m6A) methylation modification in immune cell-mediated sepsis through keyword search.
Methods: Literature retrieval.
Results and Discussion: Literature retrieval reveals that m6A methylation is implicated in sepsis-induced lung injury and myocardial injury,as well as sepsis-related encephalopathy. Furthermore, it is found that m6A methylation can regulate sepsis by inhibiting the chemotaxis of neutrophils and the formation of neutrophil extracellular traps and suppressing macrophage phagocytosis, thereby playing a role in sepsis.

Keywords:  immune cells; inflammation; m6A methylation; oxidative stress; sepsis

DOI:  https://doi.org/10.3389/fimmu.2022.1041990
Front Genet. 2022 ;13 1059325

Prognostic analysis of m6A-related genes as potential biomarkers in idiopathic pulmonary fibrosis.

Zhiqiang Wang, Lanyu Shen, Junjie Wang, Jiaqian Huang, Huimin Tao, Xiumin Zhou.

  Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options. N6-methyladenosine (m6A) is a reversible RNA modification and has been implicated in various biological processes. However, there are few studies on m6A in IPF. This project mainly explores the prognostic value of m6A-related genes as potential biomarkers in IPF, in order to establish a set of accurate prognostic prediction model. In this study, we used GSE28042 dataset in GEO database to screen out 218 m6A-related candidate genes with high IPF correlation and high differential expression through differentially expressed gene analysis, WGCNA and m6A correlation analysis. The genes associated with the prognosis of IPF were screened out by univariate Cox regression analysis, LASSO analysis, and multivariate Cox regression analysis, and the multivariate Cox model of prognostic risk of related genes was constructed. We found that RBM11, RBM47, RIC3, TRAF5 and ZNF14 were key genes in our model. Finally, the prognostic prediction ability and independent prognostic characteristics of the risk model were evaluated by survival analysis and independent prognostic analysis, and verified by the GSE93606 dataset, which proved that the prognostic risk model we constructed has a strong and stable prediction efficiency.

Keywords:  IPF; N6-methyladenosine (m6A); WGCNA; m6A-related genes; prognosis risk model

DOI:  https://doi.org/10.3389/fgene.2022.1059325
J Clin Lab Anal. 2022 Dec 12. e24801

Long non-coding RNA HOXC-AS1 exerts its oncogenic effects in esophageal squamous cell carcinoma by interaction with IGF2BP2 to stabilize SIRT1 expression.

Zhengwu Yang, Junhu Wan, Liwei Ma, Zhuofang Li, Ruotong Yang, Haijun Yang, Junkuo Li, Fuyou Zhou, Liang Ming.

   BACKGROUND: Long non-coding RNA HOXC cluster antisense RNA 1 (HOXC-AS1) is a novel lncRNA whose cancer-promoting effect in gastric cancer and nasopharyngeal carcinoma has already been demonstrated. However, its functions in esophageal squamous cell carcinoma (ESCC) remains unknown. LncRNAs can interact with RNA-binding proteins (RBPs) and affect gene expression levels through post-transcriptional regulation. Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is a widely studied RBP, and sirtuin 1 also known as SIRT1 has been reported to be involved in cancer progression.
METHODS: Establishment of in vivo models, HE and immunohistochemistry staining verified the oncogenic effect of HOXC-AS1. The interaction relationship between HOXC-AS1, IGF2BP2 and SIRT1 was verified by RNA pulldown and RNA immunoprecipitation (RIP) assay. Relative expression and stability changes of genes were detected by qPCR and actinomycin D experiments. Finally, the effect of HOXC-AS1-IGF2BP2-SIRT1 axis on ESCC was verified by rescue experiments.
RESULTS: HOXC-AS1 is highly expressed in ESCC cells and plays oncogenic effects in vivo. qPCR showed the positive relationship between HOXC-AS1 and SIRT1 following HOXC-AS1 knockdown or overexpression. RNA-pulldown, mass spectrometry and RIP assay demonstrated that IGF2BP2 is an RBP downstream of HOXC-AS1. Then, RIP and qPCR showed that IGF2BP2 could bind to SIRT1 mRNA and knockdown IGF2BP2 resulted in decreased SIRT1 mRNA level. Finally, a series of rescue assay showed that the HOXC-AS1-IGF2BP2-SIRT1 axis can affect the function of ESCC.
CONCLUSION: LncRNA HOXC-AS1 acts as an oncogenic role in ESCC, which impacts ESCC progression by interaction with IGF2BP2 to stabilize SIRT1 expression.

Keywords:  ESCC; HOXC-AS1; IGF2BP2; RNA binding protein; SIRT1

DOI:  https://doi.org/10.1002/jcla.24801
Cell Rep. 2022 Dec 13. pii: S2211-1247(22)01672-2. [Epub ahead of print]41(11): 111784

Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression.

Kalina Timcheva, Solenne Dufour, Leila Touat-Todeschini, Callum Burnard, Marie-Christine Carpentier, Florent Chuffart, Rémy Merret, Marion Helsmoortel, Sabrina Ferré, Aude Grézy, Yohann Couté, Sophie Rousseaux, Saadi Khochbin, Claire Vourc'h, Cécile Bousquet-Antonelli, Rosemary Kiernan, Daphné Seigneurin-Berny, André Verdel.

  Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.

Keywords:  CP: Molecular biology; HSF1; HSP; HSPs; N(6)-methyladenosine; RNA; YTH; chromatin; heat shock proteins; heat stress; intron retention; m(6)A; m6A; nSBs; ncRNA; ncRNAs; non-coding RNAs; nuclear stress bodies; nuclear stress body; satellite RNA

DOI:  https://doi.org/10.1016/j.celrep.2022.111784
Hum Cell. 2022 Dec 15.

Construction of a m5C-related long non-coding RNA signature for the prognosis of hepatocellular carcinoma.

Jing Lu, Haoyu Wang, Wanyue Cao, Desheng Chen, Zeping He, Junming Xu.

  RNA modification serves as a kind of posttranscriptional modification. Besides N6-methyladenosine (m6A), 5-methylcytosine(m5C) is also an important RNA modification. Long non-coding RNAs (lncRNAs) play an important role in tumor progression. Thus, we performed bioinformatic analysis to establish a m5C-related lncRNA signature(m5ClncSig) for hepatocellular carcinoma (HCC). The RNA sequencing data and clinical data were obtained from The Cancer Genome Atlas (TCGA) database. Pearson correlation coefficient analysis was applied to conduct m5C-related genes and m5C-related lncRNAs co-expressing network. Univariate Cox regression was used to screen the m5C-related lncRNAs with prognosis value. LASSO regression was applied to establish m5ClncSig. Functional analysis including KEGG and GO were performed. The relation between m5ClncSig and immunity was assessed by CIBERSORT and ESTIMATE. RP11-498C9.15 was selected for in vitro validation. A m5ClncSig was established containing 8 lncRNAs with significantly prognosis value. According to risk score calculated by m5ClncSig, high-risk group had worse clinical outcomes than low-risk group. The risk score was validated as an independent prognosis factor. Moreover, the abundances of 11 types of immune cells were significantly different between high-risk group and low-risk group while 8 immune-related genes expressed differently between these two groups. RP11-498C9.15 was validated as a risk factor in HCC progression.

Keywords:  HCC; Immunity; Prognosis; lncRNA; m5C DNA methylation

DOI:  https://doi.org/10.1007/s13577-022-00845-8
BMC Genomics. 2022 Dec 14. 23(1): 829

The alteration of N6-methyladenosine (m6A) modification at the transcriptome-wide level in response of heat stress in bovine mammary epithelial cells.

Ying Qi, Yiming Zhang, Jing Zhang, Jing Wang, Qiuling Li.

   BACKGROUND: Heat stress has a substantial negative economic impact on the dairy industry. N6-methyladenosine (m6A) is the most common internal RNA modification in eukaryotes and plays a key role in regulating heat stress response in animals. In dairy cows, however, this modification remains largely unexplored. Therefore, we examined the effects of heat stress on the m6A modification and gene expression in bovine mammary epithelial cells to elucidate the mechanism of heat stress response. In this study, Mammary alveolar cells-large T antigen (MAC-T) cells were incubated at 37 °C (non-heat stress group, NH) and 40 °C (heat stress group, H) for 2 hours, respectively. HSP70, HSF1, BAX and CASP3 were up regulated in H group compared with those in the NH group.
RESULTS: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were conducted to identify m6A peaks and to produce gene expression data of MAC-T cells in the H and NH groups. In total, we identified 17,927 m6A peaks within 9355 genes in the H group, and 18,974 peaks within 9660 genes in the NH groups using MeRIP-seq. Compared with the NH group, 3005 significantly differentially enriched m6A peaks were identified, among which 1131 were up-regulated and 1874 were down-regulated. In addition, 1502 significantly differentially expressed genes were identified using RNA-seq, among which 796 were up-regulated and 706 were down-regulated in the H group compared to the NH group. Furthermore, 199 differentially expressed and synchronously differentially methylated genes were identified by conjoint analysis of the MeRIP-seq and RNA-seq data, which were subsequently divided into four groups: 47 hyper-up, 53 hyper-down, 59 hypo-up and 40 hypo-down genes. In addition, GO enrichment and KEGG analyses were used to analyzed the potential functions of the genes in each section.
CONCLUSION: The comparisons of m6A modification patterns and conjoint analyses of m6A modification and gene expression profiles suggest that m6A modification plays a critical role in the heat stress response by regulating gene expression.

Keywords:  Heat stress; MAC-T; MeRIP-seq; N6-methyladenosine; m6A

DOI:  https://doi.org/10.1186/s12864-022-09067-6
Blood Sci. 2022 Jul;4(3): 116-124

RNA m6A modification: Mapping methods, roles, and mechanisms in acute myeloid leukemia.

Rong Yin, Yashu Li, Wen Tian, Fuling Zhou, Haojian Zhang.

  N6-Methyladenosine (m6A) is the most abundant modification in eukaryotic mRNA, and plays important biological functions via regulating RNA fate determination. Recent studies have shown that m6A modification plays a key role in hematologic malignancies, including acute myeloid leukemia. The current growth of epitranscriptomic research mainly benefits from technological progress in detecting RNA m6A modification in a transcriptome-wide manner. In this review, we first briefly summarize the latest advances in RNA m6A biology by focusing on writers, readers, and erasers of m6A modification, and describe the development of high-throughput methods for RNA m6A mapping. We further discuss the important roles of m6A modifiers in acute myeloid leukemia, and highlight the identification of potential inhibitors for AML treatment by targeting of m6A modifiers. Overall, this review provides a comprehensive summary of RNA m6A biology in acute myeloid leukemia.

Keywords:  Acute myeloid leukemia; Mapping; RNA m6A modification

DOI:  https://doi.org/10.1097/BS9.0000000000000131
Front Oncol. 2022 ;12 1009881

N6-methylandenosine-related immune genes correlate with prognosis and immune landscapes in gastric cancer.

Yuancheng Huang, Yushan Zou, Yanhua Tian, Zehong Yang, Zhengkun Hou, Peiwu Li, Fengbin Liu, Jiasheng Ling, Yi Wen.

   Objectives: This study aimed to probe into the significance of N6-methyladenosine (m6A)-related immune genes (m6AIGs) in predicting prognoses and immune landscapes of patients with gastric cancer (GC).
Methods: The clinical data and transcriptomic matrix of GC patients were acquired from The Cancer Genome Atlas database. The clinically meaningful m6AIGs were acquired by univariate Cox regression analysis. GC patients were stratified into different clusters via consensus clustering analysis and different risk subgroups via m6AIGs prognostic signature. The clinicopathological features and tumor microenvironment (TME) in the different clusters and different risk subgroups were explored. The predictive performance was evaluated using the KM method, ROC curves, and univariate and multivariate regression analyses. Moreover, we fabricated a nomogram based on risk scores and clinical risk characteristics. Biological functional analysis was performed based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The connectivity map was used to screen out potential small molecule drugs for GC patients.
Results: A total of 14 prognostic m6AIGs and two clusters based on 14 prognostic m6AIGs were identified. A prognostic signature based on 4 m6AIGs and a nomogram based on independent prognostic factors was constructed and validated. Different clusters and different risk subgroups were significantly correlated with TME scores, the distribution of immune cells, and the expression of immune checkpoint genes. Some malignant and immune biological processes and pathways were correlated with the patients with poor prognosis. Ten small molecular drugs with potential therapeutic effect were screened out.
Conclusions: This study revealed the prognostic role and significant values of m6AIGs in GC, which enhanced the understanding of m6AIGs and paved the way for developing predictive biomarkers and therapeutic targets for GC.

Keywords:  N6-methyladenosine; gastric cancer; immune genes; prognostic signature; tumor microenvironment

DOI:  https://doi.org/10.3389/fonc.2022.1009881
Cells. 2022 Dec 02. pii: 3905. [Epub ahead of print]11(23):

Genomewide m6A Mapping Uncovers Dynamic Changes in the m6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells.

Azime Akçaöz Alasar, Özge Tüncel, Ayşe Bengisu Gelmez, Buket Sağlam, İpek Erdoğan Vatansever, Bünyamin Akgül.

  Cisplatin (CP), which is a conventional cancer chemotherapeutic drug, induces apoptosis by modulating a diverse array of gene regulatory mechanisms. However, cisplatin-mediated changes in the m6A methylome are unknown. We employed an m6A miCLIP-seq approach to investigate the effect of m6A methylation marks under cisplatin-mediated apoptotic conditions on HeLa cells. Our high-resolution approach revealed numerous m6A marks on 972 target mRNAs with an enrichment on 132 apoptotic mRNAs. We tracked the fate of differentially methylated candidate mRNAs under METTL3 knockdown and cisplatin treatment conditions. Polysome profile analyses revealed perturbations in the translational efficiency of PMAIP1 and PHLDA1 transcripts. Congruently, PMAIP1 amounts were dependent on METTL3. Additionally, cisplatin-mediated apoptosis was sensitized by METTL3 knockdown. These results suggest that apoptotic pathways are modulated by m6A methylation events and that the METTL3-PMAIP1 axis modulates cisplatin-mediated apoptosis in HeLa cells.

Keywords:  HeLa; apoptosis; cisplatin; epitranscriptomics; m6A

DOI:  https://doi.org/10.3390/cells11233905
Transl Cancer Res. 2022 Nov;11(11): 3986-3999

Upregulated YTHDF1 associates with tumor immune microenvironment in head and neck squamous cell carcinomas.

Yongsheng Huang, Jianwei Liao, Sangqing Wu, Yuchu Ye, Haicang Zeng, Faya Liang, Xinke Yin, Yuanling Jiang, Nengtai Ouyang, Ping Han, Xiaoming Huang.

   Background: The nature of the tumor immune microenvironment (TME) is essential for the head and neck squamous cell carcinomas (HNSCC) initiation, prognosis, and response to immunotherapy. However, its gene regulatory network remains to be elucidated.
Methods: To identify N6-methyladenosine (m6A) regulators that are involved in regulating the HNSCC TME, a computational screen was applied to The Cancer Genome Atlas (TCGA) HNSCC patient samples. The effects of mutation, copy number variation (CNV), and transcriptional regulation on YTHDF1 expression were analyzed. We analyzed the TME infiltration, cancer-immunity cycle activities, and YTHDF1-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
Results: Among the 24 m6A regulators, 3 factors (YTHDF1, ELAVL1, and METTL3) were highly correlated with TME infiltration. As the top candidate, YTHDF1 was up-regulated and amplified in HNSCC. YTHDF1 promoter gains active histone marks and high chromatin accessibility, which might be transcriptionally activated by SOX2 and TP63. Moreover, YTHDF1 expression significantly associates with tumor malignant phenotype in HNSCC, which has a positive correlation with CD4+ T cells and a negative correlation with CD8+ T cells infiltration. Specifically, YTHDF1 expression is negatively associated with the cancer-immunity cycle and immune checkpoint inhibitors. In terms of the underlying biological mechanisms, YTHDF1 may interact with YTHDF2/3 to regulate several vital immune-related pathways.
Conclusions: We identify YTHDF1 associated with TME and elucidate an underlying mechanism of immune escape in HNSCC, which might be used as a predictive marker in guiding immunotherapy.

Keywords:  YTHDF1; head and neck squamous cell carcinomas (HNSCC); tumor immune microenvironment (TME)

DOI:  https://doi.org/10.21037/tcr-22-503
Cell Death Dis. 2022 Dec 13. 13(12): 1035

SMOC2 promotes aggressive behavior of fibroblast-like synoviocytes in rheumatoid arthritis through transcriptional and post-transcriptional regulating MYO1C.

Di Liu, Ruiru Li, Siqi Xu, Maohua Shi, Yu Kuang, Jingnan Wang, Chuyu Shen, Qian Qiu, Liuqin Liang, Youjun Xiao, Hanshi Xu.

Fibroblast-like synoviocytes (FLSs), play a key role in perpetuating synovial inflammation and bone erosion in rheumatoid arthritis (RA), however, the underlying mechanism(s) of RA FLSs activation and aggression remain unclear. Identifying endogenous proteins that selectively target FLSs is urgently needed. Here, we systematically identified that secreted modular calcium-binding protein 2 (SMOC2), was significantly increased in RA FLSs and synovial tissues. SMOC2 knockdown specifically regulated cytoskeleton remodeling and decreased the migration and invasion of RA FLSs. Mechanistically, cytoskeleton-related genes were significantly downregulated in RA FLSs with reduced SMOC2 expression, especially the motor protein myosin1c (MYO1C). SMOC2 controlled MYO1C expression by SRY-related high-mobility group box 4 (SOX4) and AlkB homolog 5 (ALKHB5) mediated-m6A modification through transcriptional and post-transcriptional regulation. Furthermore, intra-articular Ad-shRNA-SMOC2 treatment attenuated synovial inflammation as well as bone and cartilage erosion in rats with collagen-induced arthritis (CIA). Our findings suggest that increased SMOC2 expression in FLSs may contribute to synovial aggression and joint destruction in RA. SMOC2 may serve as a potential target against RA. SMOC2-mediated regulation of the synovial migration and invasion in RA FLSs. In RA FLSs, SMOC2 is significantly increased, leading to the increased level of MYO1C via SOX4-mediated transcriptional regulation and ALKBH5-mediated m6A modification, thereby causing cytoskeleton remodeling and promoting RA FLSs migration and invasion. The Figure was drawn by Figdraw.

DOI: https://doi.org/10.1038/s41419-022-05479-0
J Exp Clin Cancer Res. 2022 Dec 15. 41(1): 345

Acetyltransferase NAT10 regulates the Wnt/β-catenin signaling pathway to promote colorectal cancer progression via ac4C acetylation of KIF23 mRNA.

Chi Jin, Tuo Wang, Dongsheng Zhang, Peng Yang, Chuan Zhang, Wen Peng, Kangpeng Jin, Lu Wang, Jiahui Zhou, Chaofan Peng, Yuqian Tan, Jiangzhou Ji, Zhihao Chen, Qingyang Sun, Sheng Yang, Junwei Tang, Yifei Feng, Yueming Sun.

   BACKGROUND: N4-acetylcytidine (ac4C) as a significant RNA modification has been reported to maintain the stability of mRNA and to regulate the translation process. However, the roles of both ac4C and its 'writer' protein N-acetyltransferase 10 (NAT10) played in the disease especially colorectal cancer (CRC) are unclear. At this point, we discover the underlying mechanism of NAT10 modulating the progression of CRC via mRNA ac4C modification.
METHODS: The clinical significance of NAT10 was explored based on the TCGA and GEO data sets and the 80 CRC patients cohort of our hospital. qRT-PCR, dot blot, WB, and IHC were performed to detect the level of NAT10 and ac4C modification in CRC tissues and matched adjacent tissues. CCK-8, colony formation, transwell assay, mouse xenograft, and other in vivo and in vitro experiments were conducted to probe the biological functions of NAT10. The potential mechanisms of NAT10 in CRC were clarified by RNA-seq, RIP-seq, acRIP-seq, luciferase reporter assays, etc. RESULTS: The levels of NAT10 and ac4C modification were significantly upregulated. Also, the high expression of NAT10 had important clinical values like poor prognosis, lymph node metastasis, distant metastasis, etc. Furthermore, the in vitro experiments showed that NAT10 could inhibit apoptosis and enhance the proliferation, migration, and invasion of CRC cells and also arrest them in the G2/M phase. The in vivo experiments discovered that NAT10 could promote tumor growth and liver/lung metastasis. In terms of mechanism, NAT10 could mediate the stability of KIF23 mRNA by binding to its mRNA 3'UTR region and up-regulating its mRNA ac4c modification. And then the protein level of KIF23 was elevated to activate the Wnt/β-catenin pathway and more β-catenin was transported into the nucleus which led to the CRC progression. Besides, the inhibitor of NAT10, remodelin, was applied in vitro and vivo which showed an inhibitory effect on the CRC cells.
CONCLUSIONS: NAT10 promotes the CRC progression through the NAT10/KIF23/GSK-3β/β-catenin axis and its expression is mediated by GSK-3β which forms a feedback loop. Our findings provide a potential prognosis or therapeutic target for CRC and remodelin deserves more attention.

Keywords:  Ac4C; Colorectal cancer; KIF23; NAT10; RNA modification; Remodelin; Wnt/β-catenin pathway

DOI:  https://doi.org/10.1186/s13046-022-02551-7
Drug Resist Updat. 2022 Dec 13. pii: S1368-7646(22)00108-X. [Epub ahead of print]66 100909

The c-MYC-WDR43 signalling axis promotes chemoresistance and tumour growth in colorectal cancer by inhibiting p53 activity.

Yuqin Di, Xiaoqian Jing, Kunhua Hu, Xiangqiong Wen, Lvlan Ye, Xiang Zhang, Jiale Qin, Jinning Ye, Run Lin, Ziyang Wang, Weiling He.

  Oxaliplatin chemoresistance is a major challenge in the clinical treatment of colorectal cancer (CRC), which is one of the most common malignancies worldwide. In this study, we identified the tryptophan-aspartate repeat domain 43 (WDR43) as a potentially critical oncogenic factor in CRC pathogenesis through bioinformatics analysis. It was found that WDR43 is highly expressed in CRC tissues, and WDR43 overexpression is associated with poor prognosis of CRC patients. WDR43 knockdown significantly inhibits cell growth by arresting cell cycle and enhancing the effect of oxaliplatin chemotherapy both in vitro and in vivo. Mechanistically, upon oxaliplatin stimulation, c-MYC promotes the transcriptional regulation and expression of WDR43. WDR43 enhances the ubiquitination of p53 by MDM2 through binding to RPL11, thereby reducing the stability of the p53 protein, which induces proliferation and chemoresistance of CRC cells. Thus, the overexpression of WDR43 promotes CRC progression, and could be a potential therapeutic target of chemoresistance in CRC.

Keywords:  C-MYC; Chemoresistance; Colorectal cancer; P53; WD repeat domain 43 (WDR43)

DOI:  https://doi.org/10.1016/j.drup.2022.100909
J Clin Lab Anal. 2022 Dec 16. e24813

m6A-related long noncoding RNAs predict prognosis and indicate therapeutic response in endometrial carcinoma.

Xinying Zhou, Hu Zhang, Yingchun Duan, Jianlong Zhu, Haiyan Dai.

   BACKGROUND: N6-methyladenosine (m6A) has been identified as the most common, abundant, and conserved internal transcriptional modification. Long noncoding RNAs (lncRNAs) are noncoding RNAs consisting of more than 200 nucleotides, and the expression of various lncRNAs may affect cancer prognosis. The impact of m6A-associated lncRNAs on uterine corpus endometrial carcinoma (UCEC) prognosis is unknown.
METHODS: In this study, UCEC prognosis-related m6A lncRNAs were screened, bioinformatics analysis was performed, and experimental validation was conducted. Endometrial carcinoma (EC) and normal tissue samples were obtained from The Cancer Genome Atlas. The prognosis-related m6A lncRNAs screened by the least absolute shrinkage and selection operator method were used for multivariate Cox proportional risk regression modeling. Principal component analysis and Gene Ontology, immune function difference, and drug sensitivity analyses of the prognostic models were performed. Prognostic analysis was conducted for m6A-associated lncRNAs. The immune infiltration relationship of m6A-associated lncRNAs in EC was identified using the ssGSEA immune infiltration algorithm. A competing endogenouse RNA network was constructed using the LncACTdb database. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays were used to validate the differences in m6A-related lncRNA expression in normal and EC cells.
RESULTS: CDKN2B-AS1 and MIR924HG were found to be risk factors for EC. RAB11B-AS1 was a protective factor in EC patients. MIR924HG expression was upregulated in KLE and RL95-2 endometrial cancer cell lines. Prognostic models involved RAB11B-AS1, LINC01812, HM13-IT1, TPM1-AS, SLC16A1-AS1, LINC01936, and CDKN2B-AS1. The high-risk group was more sensitive to five compounds (ABT.263, ABT.888, AP.24534, ATRA, and AZD.0530) than the low-risk group.
CONCLUSION: These findings contribute to understanding of the function of m6A-related lncRNAs in UCEC and provide promising therapeutic strategies for UCEC.

Keywords:  bioinformatics analysis; endometrial cancer; immune infiltration; m6A-associated lncRNA; prognosis

DOI:  https://doi.org/10.1002/jcla.24813
FASEB J. 2023 Jan;37(1): e22707

AKT1 phosphorylates RBM17 to promote Sox2 transcription by modulating alternative splicing of FOXM1 to enhance cancer stem cell properties in colorectal cancer cells.

Yan Fu, Chen Bai, Shengsheng Wang, Denggang Chen, Peng Zhang, Hailang Wei, Fan Rong, Chao Zhang, Shaojuan Chen, Zhenjun Wang.

  Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. The existence of cancer stem cells (CSC) causes tumor relapses, metastasis, and resistance to conventional therapy. Alternative splicing has been shown to affect physiological and pathological processes. Accumulating evidence has confirmed that targeting alternative splicing could be an effective strategy to treat CRC. Currently, the role of alternative splicing in the regulation of CSC properties in CRC has not been elucidated. Here, we show that RBM17 displays oncogenic roles in CRC cells. RBM17 enhances cell proliferation and reduces chemotherapeutic-induced apoptosis in CRC cells. Besides, RBM17 increases CD133 positive and ALDEFLUOR positive populations and promotes sphere formation in CRC cells. In mechanism studies, we found that FOXM1 is critical for RBM17 enhanced CSC properties. Moreover, FOXM1 alternative splicing is essential for RBM17 enhanced CSC properties in CRC cells. Additionally, RBM17 enhances CSC characteristics by controlling FOXM1 expression to promote Sox2 expression. Furthermore, AKT1 works as an upstream kinase to control RBM17-mediated FOXM1 alternative splicing and enhancement of CSC properties in CRC cells. Our study reveals that AKT1-RBM17-FOXM1-Sox2 axis could be a potential target for modulating alternative splicing to reduce CSC properties in CRC cells.

Keywords:  RBM17; alternative splicing; cancer stem cells; colorectal cancer

DOI:  https://doi.org/10.1096/fj.202201255R
Cell Oncol (Dordr). 2022 Dec 13.

YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m6A-mediated YWHAZ stability.

Jihua Chai, Qifan Wang, Qiang Qiu, Guoqiang Han, Yilin Chen, Weiming Li, Haojian Zhang.

   PURPOSE: Chronic myeloid leukemia (CML) is a myeloproliferative disease derived from hematopoietic stem cells (HSCs) that harbor Philadelphia chromosome (Ph chromosome). In clinic, leukemia stem cells (LSCs) in CML are insensitive to the treatment with tyrosine kinase inhibitors, and are responsible for disease relapse. However, the molecular mechanisms for maintaining LSCs survival remain elusive.
METHODS: CML patient-derived cell lines and BCR-ABL-induced CML mouse model were used to explore the role of YBX1 in regulating the survival of CML LSCs. Bone marrow transduction and transplantation, and colony-forming unit assay were used to investigate LSC function. The underlying mechanism of how YBX1 regulates LSCs survival were assessed using flow cytometry, RNA sequencing, western blot, RNA decay assay, co-immunoprecipitation and RNA immunoprecipitation.
RESULTS: Here we show that RNA-binding protein YBX1 plays an important role in regulating survival of CML LSCs. We find that YBX1 expression is significantly increased in CML cells, and confirm that YBX1 is required for maintaining survival of LSCs. Deletion of YBX1 impairs the propagation of CML through blocking cell proliferation and inducing apoptosis of LSCs. Mechanistically, we find that YBX1 regulates expression of apoptotic associated genes. YBX1 cooperates with RNA m6A reader IGF2BPs to stabilize YWHAZ transcript in an m6A-dependent manner, and loss of YBX1 decreases YWHAZ expression by accelerating mRNA decay. Restoration of YWHAZ efficiently rescues the defects of YBX1-deficient CML cells.
CONCLUSION: Our findings reveal a critical role of YBX1 in maintaining survival of CML LSCs, which provides a rationale for targeting YBX1 in CML treatment.

Keywords:  Chronic myeloid leukemia; Leukemia stem cells; RNA m6A; YBX1; YWHAZ

DOI:  https://doi.org/10.1007/s13402-022-00762-w
EMBO J. 2022 Dec 14. e111673

Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy.

Lingling Wang, Lujing Wu, Zhouting Zhu, Qiong Zhang, Wanyu Li, Gwendolyn Michelle Gonzalez, Yinsheng Wang, Tariq M Rana.

  Adenosine N6-methylation (m6A) and N6,2'-O-dimethylation (m6Am) are regulatory modifications of eukaryotic mRNAs. m6Am formation is catalyzed by the methyl transferase phosphorylated CTD-interacting factor 1 (PCIF1); however, the pathophysiological functions of this RNA modification and PCIF1 in cancers are unclear. Here, we show that PCIF1 expression is upregulated in colorectal cancer (CRC) and negatively correlates with patient survival. CRISPR/Cas9-mediated depletion of PCIF1 in human CRC cells leads to loss of cell migration, invasion, and colony formation in vitro and loss of tumor growth in athymic mice. Pcif1 knockout in murine CRC cells inhibits tumor growth in immunocompetent mice and enhances the effects of anti-PD-1 antibody treatment by decreasing intratumoral TGF-β levels and increasing intratumoral IFN-γ, TNF-α levels, and tumor-infiltrating natural killer cells. We further show that PCIF1 modulates CRC growth and response to anti-PD-1 in a context-dependent mechanism with PCIF1 directly targeting FOS, IFITM3, and STAT1 via m6Am modifications. PCIF1 stabilizes FOS mRNA, which in turn leads to FOS-dependent TGF-β regulation and tumor growth. While during immunotherapy, Pcif1-Fos-TGF-β, as well as Pcif1-Stat1/Ifitm3-IFN-γ axes, contributes to the resistance of anti-PD-1 therapy. Collectively, our findings reveal a role of PCIF1 in promoting CRC tumorigenesis and resistance to anti-PD-1 therapy, supporting that the combination of PCIF1 inhibition with anti-PD-1 treatment is a potential therapeutic strategy to enhance CRC response to immunotherapy. Finally, we developed a lipid nanoparticles (LNPs) and chemically modified small interfering RNAs (CMsiRNAs)-based strategy to silence PCIF1 in vivo and found that this treatment significantly reduced tumor growth in mice. Our results therefore provide a proof-of-concept for tumor growth suppression using LNP-CMsiRNA to silence target genes in cancer.

Keywords:  NK cells; PCIF1; anti-PD-1 treatment; colorectal carcinoma; m6Am methylation

DOI:  https://doi.org/10.15252/embj.2022111673
Transl Cancer Res. 2022 Nov;11(11): 4019-4036

Prognostic biomarkers of pancreatic cancer identified based on a competing endogenous RNA regulatory network.

Yuanxu Qu, Jiongdi Lu, Wentong Mei, Yuchen Jia, Chunjing Bian, Yixuan Ding, Yulin Guo, Feng Cao, Fei Li.

   Background: Pancreatic cancer is an insidious and heterogeneous malignancy with poor prognosis that is often locally unresectable. Therefore, determining the underlying mechanisms and effective prognostic indicators of pancreatic cancer may help optimize clinical management. This study was conducted to develop a prognostic model for pancreatic cancer based on a competing endogenous RNA (ceRNA) network.
Methods: We obtained transcriptomic data and corresponding clinicopathological information of pancreatic cancer samples from The Cancer Genome Atlas (TCGA) database (training set). Based on the ceRNA interaction network, we screened candidate genes to build prediction models. Univariate Cox regression analysis was performed to screen for genes associated with prognosis, and least absolute shrinkage and selection operator (LASSO) regression analysis was conducted to construct a predictive model. A receiver operating characteristic (ROC) curve was drawn, and the C-index was calculated to evaluate the accuracy of the prediction model. Furthermore, we downloaded transcriptomic data and related clinical information of pancreatic cancer samples from the Gene Expression Omnibus database (validation set) to evaluate the robustness of our prediction model.
Results: Eight genes (ANLN, FHDC1, LY6D, SMAD6, ACKR4, RAB27B, AUNIP, and GPRIN3) were used to construct the prediction model, which was confirmed as an independent predictor for evaluating the prognosis of patients with pancreatic cancer through univariate and multivariate Cox regression analysis. By plotting the decision curve, we found that the risk score model is an independent predictor has the greatest impact on survival compared to pathological stage and targeted molecular therapy.
Conclusions: An eight-gene prediction model was constructed for effectively and independently predicting the prognosis of patients with pancreatic cancer. These eight genes identified show potential as diagnostic and therapeutic targets.

Keywords:  Pancreatic cancer; competing endogenous RNA network (ceRNA network); computational biology; prognosis; survival analysis

DOI:  https://doi.org/10.21037/tcr-22-709
J Exp Clin Cancer Res. 2022 Dec 15. 41(1): 347

IGF2BP2-induced circRUNX1 facilitates the growth and metastasis of esophageal squamous cell carcinoma through miR-449b-5p/FOXP3 axis.

Chang Wang, Mingxia Zhou, Peiyu Zhu, Chenxi Ju, Jinxiu Sheng, Dan Du, Junhu Wan, Huiqing Yin, Yurong Xing, Hongle Li, Jing He, Fucheng He.

   BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the most common digestive malignancies with relatively high morbidity and mortality. Emerging evidence suggests circular RNAs (circRNAs) play critical roles in tumor cell malignancy. However, the biological function and clinical significance of many circRNAs in ESCC remain elusive.
METHODS: The expression level and clinical implication of circRUNX1 in ESCC tissues were evaluated using qRT-PCR. In vitro and in vivo functional studies were conducted to investigate the underlying biological effects of circRUNX1 on ESCC cell growth and metastasis. Moreover, bioinformatics analysis, RNA sequencing (RNA-seq), RNA immunoprecipitation (RIP) assays, dual-luciferase reporter assays, and rescue experiments were performed to explore the relationships between circRUNX1, miR-449b-5p, Forkhead box protein P3 (FOXP3), and insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2).
RESULTS: CircRUNX1 was found to be significantly up-regulated in ESCC tissues and associated with TNM stage and differentiation grade. Functionally, circRUNX1 promoted ESCC cell proliferation and metastasis in vitro and in vivo. CircRUNX1 enhanced FOXP3 expression by competitively sponging miR-449b-5p. Notably, both miR-449b-5p mimics and FOXP3 knockdown restored the effects of circRUNX1 overexpression on cell proliferation and metastasis. Furthermore, IGF2BP2 binding to circRUNX1 prevented its degradation.
CONCLUSIONS: IGF2BP2 mediated circRUNX1 functions as an oncogenic factor to facilitate ESCC progression through the miR-449b-5p/FOXP3 axis, implying that circRUNX1 has the potential to be a promising diagnostic marker and therapeutic target for ESCC patients.

Keywords:  Biomarker; CircRUNX1; Esophageal squamous cell carcinoma (ESCC); FOXP3; IGF2BP2

DOI:  https://doi.org/10.1186/s13046-022-02550-8