bims-rimeca 2023-01-29 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023‒01‒29
35 papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

N6-methyladenosine (m6A) reader IGF2BP1 facilitates clear-cell renal cell carcinoma aerobic glycolysis.
The mechanism underlying redundant functions of the YTHDF proteins.
m6A reader HNRNPA2B1 destabilization of ATG4B regulates autophagic activity, proliferation and olaparib sensitivity in breast cancer.
CCL3 secreted by hepatocytes promotes the metastasis of intrahepatic cholangiocarcinoma by VIRMA-mediated N6-methyladenosine (m6A) modification.
METTL3 is essential for normal progesterone signaling during embryo implantation via m6A-mediated translation control of progesterone receptor.
Integrated investigation of the clinical implications and targeted landscape for RNA methylation modifications in hepatocellular carcinoma.
METTL3 knockdown promotes temozolomide sensitivity of glioma stem cells via decreasing MGMT and APNG mRNA stability.
N6-methyladenine- induced LINC00667 promoted breast cancer progression through m6A/KIAA1429 positive feedback loop.
METTL3 potentiates osteogenic differentiation of bone marrow mesenchymal stem cells via IGF2BP1/m6A/RUNX2.
m6A eraser FTO modulates autophagy by targeting SQSTM1/P62 in the prevention of canagliflozin against renal fibrosis.
The potential role of N6-methyladenosine modification of LncRNAs in contributing to the pathogenesis of chronic glomerulonephritis.
The potential role of m6A reader YTHDF1 as diagnostic biomarker and the signaling pathways in tumorigenesis and metastasis in pan-cancer.
N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence.
ALKBH5 inhibits the SIRT3/ACC1 axis to regulate fatty acid metabolism via a m6A-IGF2BP1-dependent manner in cervical squamous cell carcinoma.
Construction of a ferroptosis scoring system and identification of LINC01572 as a novel ferroptosis suppressor in lung adenocarcinoma.
Modification of m5C regulators in sarcoma can guide different immune infiltrations as well as immunotherapy.
m6A modification in inflammatory bowel disease provides new insights into clinical applications.
Identification and validation of signature for prognosis and immune microenvironment in gastric cancer based on m6A demethylase ALKBH5.
Enhancing recombinant protein and viral vector production in mammalian cells by targeting the YTHDF readers of N6-methyladenosine in mRNA.
Genes related to N6-methyladenosine in the diagnosis and prognosis of idiopathic pulmonary fibrosis.
WTAP contributes to the tumorigenesis of osteosarcoma via modulating ALB in an m6A-dependent manner.
RNA N6-methyladenosine methylation and skin diseases.
mRNA m6 A methylation in wood frog brain is maintained during freezing and anoxia.
YTH Domain Family 2 (YTHDF2) Regulates Cell Growth and Cycle by Facilitating KDM1A mRNA Stability.
N6-methylation of RNA-bound adenosine regulator HNRNPC promotes vascular endothelial dysfunction in type 2 diabetes mellitus by activating the PSEN1-mediated Notch pathway.
Identification of cuproptosis related subtypes and construction of prognostic signature in gastric cancer.
Comparative study of the genomic landscape and tumor microenvironment among large cell carcinoma of the lung, large cell neuroendocrine of the lung, and small cell lung cancer.
Single-cell RNA binding protein regulatory network analyses reveal oncogenic HNRNPK-MYC signalling pathway in cancer.
Cancer-associated fibroblast-secreted IGFBP7 promotes gastric cancer by enhancing tumor associated macrophage infiltration via FGF2/FGFR1/PI3K/AKT axis.
METTL3 from Target Validation to the First Small-Molecule Inhibitors: A Medicinal Chemistry Journey.
Angiopoietin-like protein 3 promotes colorectal cancer progression and liver metastasis partly via the mitogen-activated protein kinase 14 pathway.
5-Azacytidine (5-aza) Induces p53-associated Cell Death Through Inhibition of DNA Methyltransferase Activity in Hep3B and HT-29 Cells.
Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.
Insulin-like growth factor-2 mRNA-binding protein 3 promotes cell migration, invasion, and epithelial-mesenchymal transition of esophageal squamous cell carcinoma cells by targeting zinc finger E-box-binding homeobox 1 mRNA.
Obesity promotes radioresistance through SERPINE1-mediated aggressiveness and DNA repair of triple-negative breast cancer.

PeerJ. 2023 ;11 e14591

N6-methyladenosine (m6A) reader IGF2BP1 facilitates clear-cell renal cell carcinoma aerobic glycolysis.

Bao Yuan, Jin Zhou.

  Emerging articles have reported that N6-methyladenosine (m6A) modification is mainly involved in clear-cell renal cell carcinoma (ccRCC) tumorigenesis. However, the regulatory mechanisms of m6A reader IGF2BP1 involved in ccRCC tumor energy metabolism are currently unknown. Results showed that the m6A reader IGF2BP1 exhibited significantly higher expression in ccRCC cells. Functionally, results by gain/loss functional assays indicated that IGF2BP1 promoted the glycolytic characteristics, including glucose uptake, lactate production and extracellular acidification rate (ECAR). Mechanistically, IGF2BP1 recognized the m6A modified sites on LDHA mRNA and enhanced its mRNA stability, thereby accelerating tumor energy metabolism. Thus, our work reveals a novel facet of the m6A that promoted mRNA stability and highlighted the functional importance of IGF2BP1 as m6A readers in post-transcriptional gene regulation.

Keywords:  Aerobic glycolysis; ccRCC; m6A

DOI:  https://doi.org/10.7717/peerj.14591
Genome Biol. 2023 Jan 24. 24(1): 17

The mechanism underlying redundant functions of the YTHDF proteins.

Zhongyu Zou, Caraline Sepich-Poore, Xiaoming Zhou, Jiangbo Wei, Chuan He.

  The YTH N6-methyladenosine RNA binding proteins (YTHDFs) mediate the functional effects of N6-methyladenosine (m6A) on RNA. Recently, a report proposed that all YTHDFs work redundantly to facilitate RNA decay, raising questions about the exact functions of individual YTHDFs, especially YTHDF1 and YTHDF2. We show that YTHDF1 and YTHDF2 differ in their low-complexity domains (LCDs) and exhibit different behaviors in condensate formation and subsequent physiological functions. Biologically, we also find that the global stabilization of RNA after depletion of all YTHDFs is driven by increased P-body formation and is not strictly m6A dependent.

Keywords:  P-body; Translation control; YTHDF1; YTHDF2; YTHDF3; m6A

DOI:  https://doi.org/10.1186/s13059-023-02862-8
Exp Cell Res. 2023 Jan 21. pii: S0014-4827(23)00034-4. [Epub ahead of print] 113487

m6A reader HNRNPA2B1 destabilization of ATG4B regulates autophagic activity, proliferation and olaparib sensitivity in breast cancer.

Renjing Zheng, Yuanhang Yu, Lianqiu Lv, Yue Zhang, Huifang Deng, Jiyong Li, Bo Zhang.

  N6-methyladenosine RNA (m6A) is the most extensive epigenetic modification in mRNA and influences tumor progression. However, the role of m6A regulators and specific mechanisms in breast cancer still need further study. Here, we investigated the significance of the m6A reader HNRNPA2B1 and explored its influence on autophagy and drug sensitivity in breast cancer. HNRNPA2B1 was selected by bioinformatics analysis, and its high expression level was identified in breast cancer tissues and cell lines. HNRNPA2B1 was related to poor prognosis. Downregulation of HNRNPA2B1 reduced proliferation, enhanced autophagic flux, and partially reversed de novo resistance to olaparib in breast cancer. ATG4B was determined by RIP and MeRIP assays as a downstream gene of HNRNPA2B1, by which recognized the m6A site in the 3'UTR. Overexpression of ATG4B rescued the malignancy driven by HNRNPA2B1 in breast cancer cells and increased the olaparib sensitivity. Our study revealed that the m6A reader HNRNPA2B1 mediated proliferation and autophagy in breast cancer cell lines by facilitating ATG4B mRNA decay and targeting HNRNPA2B1/m6A/ATG4B might enhance the olaparib sensitivity of breast cancer cells.

Keywords:  Autophagy; Breast cancer; HNRNPA2B1; N(6)-methyladenosine RNA; Olaparib

DOI:  https://doi.org/10.1016/j.yexcr.2023.113487
J Transl Med. 2023 Jan 23. 21(1): 43

CCL3 secreted by hepatocytes promotes the metastasis of intrahepatic cholangiocarcinoma by VIRMA-mediated N6-methyladenosine (m6A) modification.

Shurui Zhou, Kege Yang, Shaojie Chen, Guoda Lian, Yuzhou Huang, Hanming Yao, Yue Zhao, Kaihong Huang, Dong Yin, Haoming Lin, Yaqing Li.

  BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) is a malignant disease characterized by onset occult, rapid progression, high relapse rate, and high mortality. However, data on how the tumor microenvironment (TME) regulates ICC metastasis at the transcriptomic level remains unclear. This study aimed to explore the mechanisms and interactions between hepatocytes and ICC cells.METHODS: We analyzed the interplay between ICC and liver microenvironment through cytokine antibody array analysis. Then we investigated the role of N6-methyladenosine (m6A) modification and the downstream target in vitro, in vivo experiments, and in clinical specimens.
RESULTS: Our study demonstrated that cytokine CCL3, which is secreted by hepatocytes, promotes tumor metastasis by regulating m6A modification via vir-like m6A methyltransferase associated (VIRMA) in ICC cells. Moreover, immunohistochemical analyses showed that VIRMA correlated with poor outcomes in ICC patients. Finally, we confirmed both in vitro and in vivo that CCL3 could activate VIRMA and its critical downstream target SIRT1, which fuels tumor metastasis in ICC.
CONCLUSIONS: In conclusion, our results enhanced our understanding of the interaction between hepatocytes and ICC cells, and revealed the molecular mechanism of the CCL3/VIRMA/SIRT1 pathway via m6A-mediated regulation in ICC metastasis. These studies highlight potential targets for the diagnosis, treatment, and prognosis of ICC.

Keywords:  Intrahepatic cholangiocarcinoma; Metastasis; Tumor microenvironment; Vir-like m6A methyltransferase associated; m6A methylation

DOI:  https://doi.org/10.1186/s12967-023-03897-y
Proc Natl Acad Sci U S A. 2023 Jan 31. 120(5): e2214684120

METTL3 is essential for normal progesterone signaling during embryo implantation via m6A-mediated translation control of progesterone receptor.

Zhan-Hong Zheng, Guo-Le Zhang, Run-Fu Jiang, Yu-Qi Hong, Qing-Yan Zhang, Jia-Peng He, Xin-Ru Liu, Zhen-Shan Yang, Liu Yang, Xing Jiang, Li-Jian Qu, Chen-Hui Ding, Yan-Wen Xu, Shi-Hua Yang, Ji-Long Liu.

  Embryo implantation, a crucial step in human reproduction, is tightly controlled by estrogen and progesterone (P4) via estrogen receptor alpha and progesterone receptor (PGR), respectively. Here, we report that N6-methyladenosine (m6A), the most abundant mRNA modification in eukaryotes, plays an essential role in embryo implantation through the maintenance of P4 signaling. Conditional deletion of methyltransferase-like 3 (Mettl3), encoding the m6A writer METTL3, in the female reproductive tract using a Cre mouse line with Pgr promoter (Pgr-Cre) resulted in complete implantation failure due to pre-implantation embryo loss and defective uterine receptivity. Moreover, the uterus of Mettl3 null mice failed to respond to artificial decidualization. We further found that Mettl3 deletion was accompanied by a marked decrease in PGR protein expression. Mechanistically, we found that Pgr mRNA is a direct target for METTL3-mediated m6A modification. A luciferase assay revealed that the m6A modification in the 5' untranslated region (5'-UTR) of Pgr mRNA enhances PGR protein translation efficiency in a YTHDF1-dependent manner. Finally, we demonstrated that METTL3 is required for human endometrial stromal cell decidualization in vitro and that the METTL3-PGR axis is conserved between mice and humans. In summary, this study provides evidence that METTL3 is essential for normal P4 signaling during embryo implantation via m6A-mediated translation control of Pgr mRNA.

Keywords:  METTL3; embryo implantation; m6A; progesterone receptor

DOI:  https://doi.org/10.1073/pnas.2214684120
Eur J Med Res. 2023 Jan 27. 28(1): 46

Integrated investigation of the clinical implications and targeted landscape for RNA methylation modifications in hepatocellular carcinoma.

Jianping Zhang, Jie Gao, Mingchao Hu, Shiyu Xu, Chun Cheng, Wenjie Zheng, Jie Zhang.

  BACKGROUND: RNA methylation (RM) is a crucial post-translational modification (PTM) that directs epigenetic regulation. It mostly consists of N1-methyladenosine (m1A), 5-methylcytosine (m5C), N3-methylcytidine (m3C), N6-methyladenosine (m6A), and 2'-O-methylation (Nm). The "writers" mainly act as intermediaries between these modifications and associated biological processes. However, little is known about the interactions and potential functions of these RM writers in hepatocellular carcinoma (HCC).METHODS: The expression properties and genetic alterations of 38 RM writers were assessed in HCC samples from five bioinformatic datasets. Two patterns associated with RM writers were identified using consensus clustering. Then, utilizing differentially expressed genes (DEGs) from different RM subtypes, we built a risk model called RM_Score. Additionally, we investigated the correlation of RM_Score with clinical characteristics, tumor microenvironment (TME) infiltration, molecular subtypes, therapeutic response, immunotherapy effectiveness, and competing endogenous RNA (ceRNA) network.
RESULTS: RM writers were correlated with TME cell infiltration and prognosis. Cluster_1/2 and gene.cluster_A/B were shown to be capable of distinguishing the HCC patients with poor prognosis after consensus and unsupervised clustering of RNA methylation writers. Additionally, we constructed RNA modification pattern-specific risk model and subdivided the cases into RM_Score high and RM_Score low subgroups. In individual cohorts or merged datasets, the high RM_Score was related to a worse overall survival of HCC patients. RM_Score also exhibited correlations with immune and proliferation related pathways. In response to anti-cancer treatments, the RM_Score had a negative correlation (drug sensitive) with drugs that focused on the MAPK/ERK and metabolism signaling, and a positive correlation (drug resistant) with compounds targeting RKT and PI3K/mTOR signaling pathway. Notably, the RM_Score was connected to the therapeutic effectiveness of PD-L1 blockage, implying that RM writers may be the target of immunotherapy to optimize clinical outcomes. Additionally, a ceRNA network was generated including 2 lncRNAs, 4 miRNAs, and 7 mRNAs that was connected to RM writers.
CONCLUSIONS: We thoroughly investigated the potential functions of RNA methylation writers and established an RM_patterns-based risk model for HCC patients. This study emphasized the critical functions of RM modification in TME infiltration, targeted therapy, and immunotherapy, providing potential targets for HCC.

Keywords:  Drug sensitivity; Hepatocellular carcinoma; Immunotherapy; RM_Score; RNA methylation; Tumor microenvironment; Writer

DOI:  https://doi.org/10.1186/s40001-023-01016-7
Cell Death Discov. 2023 Jan 23. 9(1): 22

METTL3 knockdown promotes temozolomide sensitivity of glioma stem cells via decreasing MGMT and APNG mRNA stability.

Jia Shi, Peng Zhang, Xuchen Dong, Jiaqi Yuan, Yongdong Li, Suwen Li, Shan Cheng, Yifang Ping, Xingliang Dai, Jun Dong.

Chemo-resistance hinders the therapeutic efficacy of temozolomide (TMZ) in treating glioblastoma multiforme (GBM). Recurrence of GBM even after combination of maximal tumor resection, concurrent radio-chemotherapy, and systemic TMZ applocation is inevitable and attributed to the high therapeutic resistance of glioma stem cells (GSCs), which can survive, evolve, and initiate tumor tissue remodeling, the underlying mechanisms of GSCs chemo-resistance, have not been fully elucidated up-to-now. Emerging evidence showed that METTL3-mediated N6-methyladenosine (m6A) modification contributed to the self-renew and radio-resistance in GSCs, however, its role on maintenance of TMZ resistance of GSCs has not been clarified and need further investigations. We found that the cell viability and half-maximal inhibitory concentration (IC50) of GSCs against TMZ significantly decreased after GSCs underwent serum-induced differentiation to adherent growth of tumor cells. Besides, METTL3 expression and total m6A modification declined dramatically in consistence with GSCs differentiation. Knockdown of METTL3 weakened self-renew, proliferation and TMZ IC50 of GSCs, whereas enhanced TMZ induced γH2AX level, indicating upregulation of double-strand DNA damage. We also found that mRNA stability of two critical DNA repair genes (MGMT and APNG) was regulated by METTL3-mediated m6A modification. In conclusion, we speculated that METTL3-mediated m6A modification of MGMT and APNG mRNAs played crucial roles on suppression of TMZ sensitivity of GSCs, which suggest a potential new therapeutic target of METTL3 against GBM.

DOI: https://doi.org/10.1038/s41420-023-01327-y
Bioengineered. 2022 May;13(5): 13462-13473

N6-methyladenine- induced LINC00667 promoted breast cancer progression through m6A/KIAA1429 positive feedback loop.

Saiyu Ren, Yuxing Zhang, Xiaodong Yang, Xue Li, Yuexin Zheng, Yun Liu, Xiliang Zhang.

  Increasing evidence supports that N6-methyladenine (m6A) and long noncoding RNAs (lncRNAs) both act as master regulators involved in breast cancer (BC) tumorigenesis at epigenetic modification level. Here, our research tries to unveil the interaction of m6A and lncRNAs on BC progression and explore the underlying regulatory mechanism. In the current study, we found that LINC00667 was m6A-modified lncRNA, which was up-regulated upon the overexpression of KIAA1429. The high expression of LINC00667 was correlated with the prognosis of BC patients. Bio-functional assays indicated that LINC00667 promoted the proliferation and migration of BC cells. Mechanistic assays illustrated that KIAA1429 targeted the m6A modification site of LINC00667 and enhanced its mRNA stability. Moreover, LINC00667 positively regulated the KIAA1429 via sponging miR-556-5p, forming a KIAA1429/m6A/LINC00667/miR-556-5p feedback loop. Collectively, the central findings of our study suggest that KIAA1429-induced LINC00667 exerted its functions as an oncogene in BC progression through m6A-dependent feedback loop.

Keywords:  LINC00667; METTL3; N6-methyladenosine; breast cancer

DOI:  https://doi.org/10.1080/21655979.2022.2077893
Oral Dis. 2023 Jan 27.

METTL3 potentiates osteogenic differentiation of bone marrow mesenchymal stem cells via IGF2BP1/m6A/RUNX2.

Shuzuo Zhou, Gang Zhang, Kun Wang, Zhong Yang, Yinghui Tan.

  OBJECTIVE: Maxillofacial bone defect is a critical obstacle for maxillofacial tumors and periodontal diseases. The osteogenic differentiation of bone marrow mesenchymal stem cells BMSCs is critical for maxillofacial osteogenesis and functional reconstruction. Here, our study focused on the functions and mechanism of N6 -methyladenosine during BMSCs osteogenic differentiation BMSCs.SUBJECT AND METHODS: Biofunctions of BMSCs were detected using ALP activity and alizarin red S staining assays. The molecular interaction within RNA/protein was identified by RNA immunoprecipitation and/or methylation immunoprecipitation.
RESULTS: Results indicated that m6 A 'writer' METTL3 upregulated during the osteogenic differentiation of BMSCs upon osteogenic induction. Functionally, assays' results revealed that METTL3 overexpression promoted the osteogenic differentiation of BMSC, while METTL3 knockdown repressed the osteogenic differentiation. Mechanistically, results revealed that RUNX2 mRNA was a m6 A-methylated target by METTL3 at its 3'-UTR. Moreover, m6 A reader IGF2BP1 recognized the m6 A site on RUNX2 mRNA to enhance its stability.
CONCLUSION: In conclusion, our findings revealed the novel roles of METTL3 in BMSCs osteogenic differentiation via IGF2BP1/m6 A/RUNX2 signaling axis of m6 A-dependent manner, providing a potential therapeutic target for maxillofacial bone defects treatment.

Keywords:  Bone marrow mesenchymal stem cells; METTL3; N6-methyladenosine; RUNX2

DOI:  https://doi.org/10.1111/odi.14526
Front Immunol. 2022 ;13 1094556

m6A eraser FTO modulates autophagy by targeting SQSTM1/P62 in the prevention of canagliflozin against renal fibrosis.

Youjing Yang, Qianmin Li, Yi Ling, Linxin Leng, Yu Ma, Lian Xue, Guoyuan Lu, Yue Ding, Jianzhong Li, Shasha Tao.

  The dysregulation of autophagy contributes to renal fibrosis. N6-Methyladenosine (m6A) RNA modification is a critical mediator of autophagy. Our previous studies have reported that the disorder of the PPARα/fatty acid oxidation (FAO) axis in renal tubular cells is suppressed by STAT6, which is involved in the regulation of renal fibrotic processes. Here, we found that canagliflozin significantly upregulates SQSTM1/P62, promoting PPARα-mediated FAO by inducing autophagy-dependent STAT6 degradation both in TGF-β1-treated HK2 cells and in unilateral ureteral occlusion (UUO) and ischemia-reperfusion (I/R) renal fibrosis mouse models. Knockdown of P62/SQSTM1 led to the impairment autophagic flux and the dysregulation of the STAT6/PPARα axis, which was confirmed by SQSTM1/P62cKO mice with UUO treatment along with bioinformatics analysis. Furthermore, SQSTM1/P62 deficiency in renal tubular cells inhibited canagliflozin's effects that prevent FAO disorder in renal tubular cells and renal fibrosis. Mechanistically, the level of m6A eraser FTO, which interacted with SQSTM1 mRNA, decreased in the renal tubular cells both in vitro and in vivo after canagliflozin administration. Decrease in FTO stabilized SQSTM1 mRNA, which induced autophagosome formation. Collectively, this study uncovered a previously unrecognized function of canagliflozin in FTO in the autophagy modulation through the regulation of SQSTM1 mRNA stability in the renal tubular STAT6/PPARα/FAO axis and renal fibrosis.

Keywords:  N6-methyladenosine; SQSTM1; STAT6; autophagy; canagliflozin; renal fibrosis

DOI:  https://doi.org/10.3389/fimmu.2022.1094556
Inflamm Res. 2023 Jan 26.

The potential role of N6-methyladenosine modification of LncRNAs in contributing to the pathogenesis of chronic glomerulonephritis.

Tao Liu, Xing Xing Zhuang, Xiu Juan Qin, Liang Bing Wei, Jia Rong Gao.

  BACKGROUND: Increasing evidence indicates that N6-methyladenosine (m6A) modification of mRNAs has been shown to play a critical role in the occurrence and development of many diseases, while little is known about m6A modification in long non-coding RNAs (LncRNAs). Our study aims to investigate the potential functions of LncRNA m6A modifications in lipopolysaccharide (LPS)-induced mouse mesangial cells (MMCs), providing us with a new perspective on the molecular mechanisms of chronic glomerulonephritis (CGN) pathogenesis.METHODS: Differentially methylated LncRNAs were identified by Methylated RNA immunoprecipitation sequencing (MeRIP-seq). LncRNA-mRNA and LncRNA-associated LncRNA-miRNA-mRNA (CeRNA) networks were constructed by bioinformatics analysis. Furthermore, we utilized gene ontology (GO) and pathway enrichment analyses (KEGG) to explore target genes from co-expression networks. In addition, the total level of m6A RNA methylation and expression of methyltransferase and pro-inflammatory cytokines were detected by the colorimetric quantification method and western blot, respectively. Cell viability and cell cycle stage were detected by cell counting kit-8 (CCK-8) and flow cytometry.
RESULTS: In total, 1141 differentially m6A-methylated LncRNAs, including 529 hypermethylated LncRNAs and 612 hypomethylated LncRNAs, were determined by MeRIP-seq. The results of GO and KEGG analysis revealed that the target mRNAs were mainly enriched in signal pathways, such as the NF-kappa B signaling pathway, MAPK signaling pathway, Toll-like receptor signaling pathway, and apoptosis signaling pathway. In addition, higher METTL3 expression was found in CGN kidney tissues using the GEO database. METTL3 knockdown in MMC cells drastically reduced the levels of m6A RNA methylation, pro-inflammatory cytokines IL6 and TNF-α, and inhibited cell proliferation and cycle progression.
CONCLUSIONS: Our findings provide a basis and novel insight for further investigations of m6A modifications in LncRNAs for the pathogenesis of CGN.

Keywords:  Chronic glomerulonephritis; LncRNA; METTL3; MMCs; N6-methyladenosine

DOI:  https://doi.org/10.1007/s00011-023-01695-2
Cell Death Discov. 2023 Jan 28. 9(1): 34

The potential role of m6A reader YTHDF1 as diagnostic biomarker and the signaling pathways in tumorigenesis and metastasis in pan-cancer.

Yanan Zhu, Jing Li, Hang Yang, Xinyi Yang, Ya Zhang, Xinchao Yu, Ying Li, Gangxian Chen, Zuozhang Yang.

m6A is an important RNA methylation in progression of various human cancers. As the m6A reader protein, YTHDF1 is reported to accelerate m6A-modified mRNAs translation in cytoplasm. It is highly expressed in various human cancers and contributes to the progression and metastasis of cancers. YTHDF1 was closely associated with poor prognosis and also used as a molecular marker for clinical diagnosis or therapy in human cancers. It has been reported to promote chemoresistance to Adriamycin, Cisplatin and Olaparib by increasing mRNA stability of its target molecule. Moreover, it contributes to CSC-like characteristic of tumor cells and inducing the antitumor immune microenvironment. Here, we reviewed the clinical diagnostic and prognostic values of YTHDF1, as well as the molecular mechanisms of YTHDF1 in progression and metastasis of human cancers.

DOI: https://doi.org/10.1038/s41420-023-01321-4
Front Plant Sci. 2022 ;13 1064131

N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence.

Elżbieta Rudy, Magda Grabsztunowicz, Magdalena Arasimowicz-Jelonek, Umesh Kumar Tanwar, Julia Maciorowska, Ewa Sobieszczuk-Nowicka.

  Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.

Keywords:  RNA modifications; abiotic stress; barley; crop improvement; epitranscriptomics; leaf senescence; m6A

DOI:  https://doi.org/10.3389/fpls.2022.1064131
Clin Exp Pharmacol Physiol. 2023 Jan 27.

ALKBH5 inhibits the SIRT3/ACC1 axis to regulate fatty acid metabolism via a m6A-IGF2BP1-dependent manner in cervical squamous cell carcinoma.

Lan Zhen, Wuyuan Pan.

  Cervical cancer (CC) is the most common malignancy of the female reproductive system, among which cervical squamous cell carcinoma (CESC) is the most common type. The demethylase ALKBH5 has been previously revealed to be downregulated in CC tissue. N6 methyladenine (m6A) is the most common modification in eukaryotic RNAs and is involved in modulating tumor progression. Thus, we attempted to clarify the ALKBH5 role and mechanism underlying CESC progression. In CESC patient tissue and control tissue m6A levels were measured. RT-qPCR, western blotting and IHC were used to measure ALKBH5 levels. A correlation between CESC patient survival and ALKBH5 levels was evaluated. Wound healing, transwell and colony formation assays were used to detect CESC cellular behaviors. Corresponding kits and BODIPY staining were used to detect CESC lipid metabolism. Bioinformatics, IP, RNA pulldown and RIP assays as well as half-life measurements were used to assess the association and mechanism of ALKBH5 with SIRT3, ACC1 and IGF2BP1. The m6A demethylase ALKBH5 was depleted in CESC tissue and cells, and a low level of ALKBH5 predicted an unfavorable prognosis in CESC patients. ALKBH5 overexpression suppressed CESC growth and lipid metabolism in vitro and CESC tumor growth in vivo, and ACC1 overexpression rescued these changes. ALKBH5 downregulated ACC1 levels in CESC cells by facilitating SIRT3 methylation to repress ACC1 deacetylation. ALKBH5 destabilized SIRT3 to downregulate SIRT3 levels in CESCs in a m6A-IGF2BP1-dependent manner. ALKBH5 demethylates and destabilizes SIRT3 in a m6A-IGF2BP1-dependent manner, repressing CESC growth, lipid metabolism, and tumorigenesis by downregulating ACC1. This article is protected by copyright. All rights reserved.

Keywords:  ALKBH5; Cervical squamous cell carcinoma; N6-methyladenosine; fatty acid metabolism

DOI:  https://doi.org/10.1111/1440-1681.13754
Front Pharmacol. 2022 ;13 1098136

Construction of a ferroptosis scoring system and identification of LINC01572 as a novel ferroptosis suppressor in lung adenocarcinoma.

Lingling Hong, Xuehai Wang, Weiming Cui, Fengxu Wang, Weiwei Shi, Shali Yu, Yonghua Luo, Lixin Zhong, Xinyuan Zhao.

  Background: Ferroptosis is a novel process of programmed cell death driven by excessive lipid peroxidation that is associated with the development of lung adenocarcinoma. N6-methyladenosine (m6a) modification of multiple genes is involved in regulating the ferroptosis process, while the predictive value of N6-methyladenosine- and ferroptosis-associated lncRNA (FMRlncRNA) in the prognosis of patients remains with LUAD remains unknown. Methods: Unsupervised cluster algorithm was applied to generate subcluster in LUAD according to ferroptosis-associated lncRNA. Stepwise Cox analysis and LASSO algorithm were applied to develop a prognostic model. Cellular location was detected by single-cell analysis. Also, we conducted Gene set enrichment analysis (GSEA) enrichment, immune microenvironment and drug sensitivity analysis. In addition, the expression and function of the LINC01572 were investigated by several in vitro experiments including qRT-PCR, cell viability assays and ferroptosis assays. Results: A novel ferroptosis-associated lncRNAs-based molecular subtype containing two subclusters were determined in LUAD. Then, we successfully created a risk model according to five ferroptosis-associated lncRNAs (LINC00472, MBNL1-AS1, LINC01572, ZFPM2-AS1, and TMPO-AS1). Our nominated model had good stability and predictive function. The expression patterns of five ferroptosis-associated lncRNAs were confirmed by polymerase chain reaction (PCR) in LUAD cell lines. Knockdown of LINC01572 significantly inhibited cell viability and induced ferroptosis in LUAD cell lines. Conclusion: Our data provided a risk score system based on ferroptosis-associated lncRNAs with prognostic value in LUAD. Moreover, LINC01572 may serve as a novel ferroptosis suppressor in LUAD.

Keywords:  LINC01572; N6-methyladenosine (m6A) methylation; ferroptosis; long non-coding RNA; lung adenocarcinoma; signature

DOI:  https://doi.org/10.3389/fphar.2022.1098136
Front Surg. 2022 ;9 948371

Modification of m5C regulators in sarcoma can guide different immune infiltrations as well as immunotherapy.

Shusheng Wu, Mengge Li, Rixin Su, Hao Shen, Yifu He, Yangfan Zhou.

  Background: Recent studies have found that 5-methylcytosine (m5C) modulators are associated with the prognosis and treatment of cancer. However, the relevance of m5C modulators in sarcoma prognosis and the tumour microenvironment is unclear.Methods: We selected 15 m5C regulators and performed unsupervised clustering to identify m5C modification patterns and differentially expressed genes associated with the m5C phenotype in The Cancer Genome Atlas (TCGA) sarcomas. The extent of immune cell infiltration in different clustering groups was explored using single-sample gene set enrichment analysis and estimation algorithms. A principal component analysis algorithm-based m5C scoring protocol was performed to assess the m5C modification patterns of individual tumors.
Results: We identified two distinct m5C modification patterns in the TCGA sarcoma cohort, which possess different clinical outcomes and biological processes. Tumour microenvironment analysis revealed two groups of immune infiltration patterns highly consistent with m5C modification patterns, classified as immune inflammatory and immune desert types. We constructed m5C scores and found that high m5C scores were closely associated with leiomyosarcoma and other subtypes, and were associated with poorer prognosis, lower PD-L1 expression, and poorer immunotherapy outcomes. The best application was validated against the m5C database.
Conclusion: We constructed an m5C score for sarcoma based on the TCGA database and identified a poorer prognosis in the high m5c score group. The stability and good prognostic predictive power of the m5C score was verified by an external database. We found that sarcomas in the low m5C score group may have a better response to immunotherapy.

Keywords:  immunotherapy; m5C; prognosis; sarcoma; tumour microenvironment

DOI:  https://doi.org/10.3389/fsurg.2022.948371
Biomed Pharmacother. 2023 Jan 25. pii: S0753-3322(23)00086-0. [Epub ahead of print]159 114298

m6A modification in inflammatory bowel disease provides new insights into clinical applications.

Jiamin Zhang, Bimei Song, Yue Zeng, Chao Xu, Liang Gao, Yan Guo, Jingbo Liu.

  Inflammatory bowel disease (IBD) results from a complex interplay between genetic predisposition, environmental factors, and gut microbes. The role of N6-methyladenosine (m6A) methylation in the pathogenesis of IBD has attracted increasing attention. m6A modification not only regulates intestinal mucosal immunity and intestinal barrier function, but also affects apoptosis and autophagy in intestinal epithelial cells. Additionally, m6A modification participated in the interaction between gut microbes and the host, providing a novel direction to explore the molecular mechanisms of IBD and the theoretical basis for specific microorganism-oriented prevention and treatment measures. m6A regulators are expected to be biomarkers for predicting the prognosis of IBD patients. m6A methylation may be utilized as a novel target in the management of IBD. This review focused on the recent advances in how m6A modification causes the initiation and development of IBD, and provided new insights into optimal prevention and treatment measures for IBD.

Keywords:  IBD therapy; Inflammatory bowel disease; Intestinal barrier; Intestinal immunity; M6A modification

DOI:  https://doi.org/10.1016/j.biopha.2023.114298
Front Oncol. 2022 ;12 1079402

Identification and validation of signature for prognosis and immune microenvironment in gastric cancer based on m6A demethylase ALKBH5.

Tiannan Ji, Xiaohui Gao, Dan Li, Siyuan Huai, Yajing Chi, Xian An, Wenyu Ji, Siming Yang, Jianxiong Li.

  Background: N6-methyladenosine (m6A) RNA regulators play important roles in cancers, but their functions and mechanism have not been demonstrated clearly in gastric cancer (GC).Methods: In this study, the GC samples with clinical information and RNA transcriptome were downloaded from The Cancer Genome Atlas database. The different expression genes were compared by the absolute value and median ± standard deviation. Samples with complete information were randomly divided into a training dataset and a test dataset. The differential expression genes (DEGs) between ALKBH5-low and ALKBH5-high subgroups were identified in the training dataset and constructed a risk model by Cox and least absolute shrinkage and selection operator regression. The model was testified in test datasets, overall survival (OS) was compared with the Kaplan-Meier method, and immune cell infiltration was calculated by the CIBERSORT algorithm in the low-risk and high-risk subgroups based on the model. The protein levels of ALKBH5 were detected with immunohistochemistry. The relative expression of messenger-ribonucleic acid (mRNA) was detected with quantitative polymerase chain reaction.
Results: ALKBH5 was the only regulator whose expression was lower in tumor samples than that in normal samples. The low expression of ALKBH5 led to the poor OS of GC patients and seemed to be an independent protective factor. The model based on ALKBH5-regulated genes was validated in both datasets (training/test) and displayed a potential capacity to predict a clinical prognosis. Gene Ontology analysis implied that the DEGs were involved in the immune response; CIBERSORT results indicated that ALKBH5 and its related genes could alter the immune microenvironment of GC. The protein levels of ALKBH5 were verified as lowly expressed in GC tissues. SLC7A2 and CGB3 were downregulated with ALKBH5 knockdown.
Conclusions: In this study, we found that ALKBH5 might be a suppressor of GC; ALKBH5 and its related genes were latent biomarkers and immunotherapy targets.

Keywords:  ALKBH5; gastric cancer; immune cell infiltration; m6A; prognosis

DOI:  https://doi.org/10.3389/fonc.2022.1079402
Biotechnol J. 2023 Jan 24. e2200451

Enhancing recombinant protein and viral vector production in mammalian cells by targeting the YTHDF readers of N6-methyladenosine in mRNA.

Nga Lao, Niall Barron.

  N6 -methyl adenosine (m6A) is the most abundant internal modification on eukaryotic mRNA and has been implicated in a wide range of fundamental cellular processes. This modification is regulated and interpreted by a set of writer, eraser, and reader proteins. To date, there have been no reports on the potential of mRNA epigenetic regulators to influence recombinant protein expression in mammalian cells. In this study we evaluated the potential of manipulating the expression of the m6A YTH domain-containing readers, YTHDF1, 2, and 3 to improve recombinant protein yield based on their role in regulating mRNA stability and promoting translation. Using siRNA-mediated gene depletion, cDNA over-expression and methylation-specific RNA immunoprecipitation, we demonstrate that (i) knock-down of YTHDF2 enhances (∼2-fold) the levels of recombinant protein derived from GFP and EPO transgenes in CHO cells; (ii) the effects of YTHDF2 depletion on transgene expression is m6A-mediated and (iii) YTHDF2 depletion or over-expression of YTHDF1 increases viral protein expression and yield of infectious lentiviral particles (∼2-3 fold) in HEK293 cells. We conclude that various transgenes can be subjected to regulation by m6A regulators in mammalian cell lines and that these findings demonstrate the utility of epi-transcriptomic-based approaches to host cell line engineering for improved recombinant protein and viral vector production. This article is protected by copyright. All rights reserved.

Keywords:  XXX

DOI:  https://doi.org/10.1002/biot.202200451
Front Genet. 2022 ;13 1102422

Genes related to N6-methyladenosine in the diagnosis and prognosis of idiopathic pulmonary fibrosis.

Jingcheng Zhang, Ying Zhang, Ziyuan Wang, Jiachao Zhao, Zhenyu Li, Keju Wang, Lin Tian, Baojin Yao, Qibiao Wu, Tan Wang, Jing Wang.

  Introduction: Idiopathic pulmonary fibrosis (IPF) is a chronic progressive pulmonary fibrotic disease with unknown etiology and poor outcomes. It severely affects the quality of life. In this study, we comprehensively analyzed the expression of N6-methyladenosine (m6A) RNA methylation regulators using gene expression data from various tissue sources in IPF patients and healthy volunteers. Methods: The gene expression matrix and clinical characteristics of IPF patients were retrieved from the Gene Expression Omnibus database. A random forest model was used to construct diagnosis signature m6A regulators. Regression analysis and correlation analysis were used to identify prognosis m6A regulators. Consensus cluster analysis was used to construct different m6A prognosis risk groups, then functional enrichment, immune infiltration and drug sensitivity analysis were performed. Result: Five candidate m6A genes from lung tissue were used to predict the incidence, and the incidence was validated using datasets from bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells. Subsequently, the BALF dataset containing outcomes data was used for the prognosis analysis of m6A regulators. METTL14, G3BP2, and ZC3H13 were independent protective factors. Using correlation analysis with lung function in the lung tissue-derived dataset, METTL14 was a protective factor in IPF. Based on METTL14 and G3BP2, a consensus cluster analysis was applied to distinguish the prognostic m6A regulation patterns. The low-risk group's prognosis was significantly better than the high-risk group. Biological processes regulated by various risk groups included fibrogenesis and cell adhesion. Analysis of immune cell infiltration showed upregulation of neutrophils in the m6A high-risk group. Subsequently, five m6A high-risk group sensitive drugs and one m6A low-risk group sensitive drug were identified. Discussion: These findings suggest that m6A regulators are involved in the diagnosis and prognosis of IPF, and m6A patterns are a method to identify IPF outcomes.

Keywords:  METTL14; N6-methyladenosine; diagnosis; idiopathic pulmonary fibrosis; prognosis

DOI:  https://doi.org/10.3389/fgene.2022.1102422
Genomics. 2023 Jan 20. pii: S0888-7543(23)00010-1. [Epub ahead of print] 110566

WTAP contributes to the tumorigenesis of osteosarcoma via modulating ALB in an m6A-dependent manner.

Qiyong Pan, Jigang Lou, Penghui Yan, Xiaobiao Kang, Pengfei Li, Zongqiang Huang.

  PURPOSE: Osteosarcoma (OS) is a prevalent bone malignancy mainly occurred in adolescents. WTAP/N6-methyladenosine (m6A) modification is confirmed to be involved in OS progression. This study is conducted to bring some novel insights to the action mechanism of WTAP/m6A under the hidden pathogenesis of OS.METHODS: qRT-PCR was executed to evaluate the expression levels of WTAP and ALB. ALB protein level in OS cells was measured by western blotting. The content of m6A in total RNA was assessed by m6A quantification assay. Me-RIP and dual luciferase reporter assays confirmed the target relationship of WTAP with ALB. With the use of the wound healing, CCK-8, and transwell invasion assays, the functional relationship between WTAP and ALB in OS cells was confirmed. The influences of WTAP on tumor growth in vivo were performed in the xenograft model of mouse.
RESULTS: WTAP was increased but ALB was diminished in OS tissues and/or cell lines. WTAP modulated ALB expression in an m6A-dependent manner. Silencing of WTAP retarded the development of OS via inhibiting cell viability, migration, invasion, and tumor growth. Knockdown of ALB exerted the opposite effects on OS progression. Additionally, ALB deficiency partially eliminated the inhibiting effects of WTAP silencing on cellular processes in OS.
CONCLUSIONS: This is the first report to clarify the interaction of WTAP/m6A with ALB in OS progression. These experimental data to some extent broadened the horizons of WTAP/m6A in the development of OS.

Keywords:  ALB; N6-methyladenosine; Osteosarcoma; WTAP

DOI:  https://doi.org/10.1016/j.ygeno.2023.110566
Autoimmunity. 2023 Dec;56(1): 2167983

RNA N6-methyladenosine methylation and skin diseases.

Yaqin Yu, Shuang Lu, Hui Jin, Huan Zhu, Xingyu Wei, Tian Zhou, Ming Zhao.

  Skin diseases are global health issues caused by multiple pathogenic factors, in which epigenetics plays an invaluable role. Post-transcriptional RNA modifications are important epigenetic mechanism that regulate gene expression at the genome-wide level. N6-methyladenosine (m6A) is the most prevalent modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, which is installed by methyltransferases called "writers", removed by demethylases called "erasers", and recognised by RNA-binding proteins called "readers". To date, m6A is emerging to play essential part in both physiological processes and pathological progression, including skin diseases. However, a systematic summary of m6A in skin disease has not yet been reported. This review starts by illustrating each m6A-related modifier specifically and their roles in RNA processing, and then focus on the existing research advances of m6A in immune homeostasis and skin diseases.

Keywords:  N6-methyladenosine (m6A); RNA methylation; skin cancers; skin diseases

DOI:  https://doi.org/10.1080/08916934.2023.2167983
J Exp Zool A Ecol Integr Physiol. 2023 Jan 26.

mRNA m6 A methylation in wood frog brain is maintained during freezing and anoxia.

Steven Wade, Hanane Hadj-Moussa, Kenneth B Storey.

  Freeze tolerance is an adaptive strategy that wood frogs (Rana sylvatica) use to survive the subzero temperatures of winter. It is characterized by a variety of metabolic and physiological changes that facilitate successful freezing and anoxia. As both mRNA regulation and posttranslation protein modification have been implicated in freeze tolerance, we hypothesized that posttranslational RNA regulation is also involved in coordinating freeze-thaw cycles and metabolic rate depression. As such, we investigated the most abundant RNA modification, adenosine methylation (N6 -methyladenosine; m6 A) in wood frog brains during 24 h periods of freezing and anoxia. This was followed by an examination of levels of RNA methyltransferases, demethyltransferases, and the readers of RNA methylation. Despite relative levels of methylation on mRNA remaining constant throughout freezing and anoxia, a significant increase in relative abundance of m6 A methyltransferases METTL3 and METTL14 was observed. In addition, we investigated the effect of m6 A RNA methylation on mRNA triaging to stress granules and report a significant increase in stress granule markers TIAR and TIA-1 in both freezing and anoxia. Our findings are the first report of RNA posttranslational regulation during metabolic rate depression in the wood frog brain and suggest that the dynamic RNA methylation observed is not directly linked to mRNA regulation during periods of extreme metabolic reorganization, warranting future investigations.

Keywords:  RNA methylation; Rana sylvatica; freeze tolerance; metabolic rate depression

DOI:  https://doi.org/10.1002/jez.2681
Am J Pathol. 2023 Jan 18. pii: S0002-9440(23)00026-3. [Epub ahead of print]

YTH Domain Family 2 (YTHDF2) Regulates Cell Growth and Cycle by Facilitating KDM1A mRNA Stability.

Xin Li, KeJing Zhang, Yu Hu, Na Luo.

Breast cancer is the leading cause of cancer death in women. More than one million women worldwide are diagnosed with breast cancer each year, and the incidence rates are increasing. The physiological functions of N6-methyladenosine methylation in cancer have been appreciated in recent years. Herein, four data sets (GSE70947, GSE45827, GSE42586, and The Cancer Genome Atlas Breast Cancer) were analyzed to confirm the differentially expressed N6-methyladenosine genes. YTHDF2 was found to be highly expressed in breast cancer tissues and cells. In vitro, YTHDF2 affects cell proliferation, the cell cycle, and invasive ability. Tumorigenesis in xenograft nude mice confirmed that YTHDF2 interference reduced the tumor formation ability of cancer cells. Pearson correlation analysis demonstrated a positive correlation between YTHDF2 and KDM1A. An online tool (SRAMP) predicted that there are eight methylation sites in the KDM1A mRNA sequence. The expression of KDM1A was dramatically increased in breast cancer tissues and cells. Down-regulation of YTHDF2 reduced KDM1A expression and the methylation level of KDM1A mRNA. YTHDF2 interference promoted the degradation of KDM1A mRNA, which suggested an interaction between YTHDF2 and KDM1A. KDM1A interference altered cell proliferation, cell cycle, and invasive ability, whereas YTHDF2 overexpression rescued KDM1A interference-induced cell phenotypic changes. In conclusion, YTHDF2 promotes breast cancer cell growth and cell cycle progression by facilitating KDM1A mRNA stability. This study provides new therapeutic targets for breast cancer treatment in the future.

DOI: https://doi.org/10.1016/j.ajpath.2022.12.010
Diabetes Res Clin Pract. 2023 Jan 18. pii: S0168-8227(23)00026-8. [Epub ahead of print] 110261

N6-methylation of RNA-bound adenosine regulator HNRNPC promotes vascular endothelial dysfunction in type 2 diabetes mellitus by activating the PSEN1-mediated Notch pathway.

Ying Cai, Tao Chen, Mingzhu Wang, Lihua Deng, Cui Li, Siqian Fu, Kangling Xie.

  AIM: The regulatory mechanism of m6A regulators in vascular endothelial function of type 2 diabetes mellitus (T2DM) remains largely unknown. We addressed this issue based on the data retrieved Gene Expression Omnibus (GEO) database and experimental validations.METHODS: Expression of m6A methylation regulators was evaluated in T2DM samples of GSE76894 dataset and GSE156341 dataset. Further analysis of candidate m6A methylation regulators was conducted in the thoracic aorta of db/db mice and high glucose (HG)-induced human umbilical vein endothelial cells (HUVECs). Ectopic expression and depletion experiments were conducted to detect effects of m6A methylation regulators on vascular endothelial function in T2DM.
RESULTS: It emerged that three m6A methylation regulators (HNRNPC, RBM15B, and ZC3H13) were highly expressed in T2DM, which were related to vascular EC function, showing diagnostic values for T2DM. HNRNPC expression in the thoracic aorta of db/db mice was higher than that in heterozygous db mice, and HNRNPC expression in HG-induced HUVECs was upregulated when compared with normal glucose-exposed HUVECs. Furthermore, HNRNPC activated PSEN1-dependent Notch pathway to induce eNOS inactivation and NO production decrease, thereby causing vascular endothelial dysfunction in T2DM.
CONCLUSIONS: HNRNPC impaired vascular endothelial function to enhance the development of vascular complications in T2DM through PSEN1-mediated Notch signaling pathway.

Keywords:  HNRNPC; Notch pathway; PSEN1; Type 2 diabetes mellitus; Vascular endothelial dysfunction; m6A regulators

DOI:  https://doi.org/10.1016/j.diabres.2023.110261
Front Surg. 2022 ;9 991624

Identification of cuproptosis related subtypes and construction of prognostic signature in gastric cancer.

Hao Dong, Shutao Zhao, Chao Zhang, Xudong Wang.

  Cuprotosis is a novel mechanism of cell death that differs from known mechanisms, which depends on mitochondrial respiration and is closely related to lipoylated components of the tricarboxylic acid (TCA) cycle. However, it is unclear whether cuprotosis-related genes (CRGs) affect the tumor microenvironment (TME) and prognosis of patients with gastric cancer. In this study, the genetic and transcriptional characteristics of CRGs in gastric cancer (GC) were analyzed, and five CRGs that were differentially expressed and correlated with the survival of patients were obtained. Two different molecular subtypes were identified according to the five CRGs. Then, we constructed a CRG_score applied to patients of any age, gender, and stage. Subsequently, we found that cluster B and a high CRG_score had a worse prognosis, fewer immune checkpoints, and higher tumor immune dysfunction and exclusion (TIDE) compared to cluster A and a low CRG_score. In addition, two subtypes and the CRG_score were closely associated with clinicopathological characteristics, human leukocyte antigens (HLAs) and TME cell infiltration. A high CRG_score was featured with decreased microsatellite instability-high (MSI-H) and mutational burden. Meanwhile, the CRG_score was significantly related to the cancer stem cell (CSC) index and chemotherapeutic response. Moreover, we developed a nomogram to predict the survival probability of patients. Our study explained the role of CRGs in GC, and the prognostic signature could potentially provide an approach for personalized tumor therapy.

Keywords:  cuproptosis; gastric cancer; immunotherapy; molecule subtypes; tumor microenvironment

DOI:  https://doi.org/10.3389/fsurg.2022.991624
Medicine (Baltimore). 2023 Jan 27. 102(4): e32781

Comparative study of the genomic landscape and tumor microenvironment among large cell carcinoma of the lung, large cell neuroendocrine of the lung, and small cell lung cancer.

Fanghua Li, Yue Yang, Ying Xu, Ke Li, Linhong Song, Yang Xue, Dandan Dong.

Deciphering the genomic profiles and tumor microenvironment (TME) in large cell carcinomas of the lung (LCC), large cell neuroendocrine of the lung (LCNEC), and small cell lung cancer (SCLC) might contribute to a better understanding of lung cancer and then improve outcomes. Ten LCC patients, 12 LCNEC patients, and 18 SCLC patients were enrolled. Targeted next-generation sequencing was used to investigate the genomic profiles of LCC, LCNEC, and SCLC. Tumor-infiltrating lymphocytes (TILs) within cancer cell nests and in cancer stroma were counted separately. Precise 60% of LCNEC patients harbored classical non-small cell lung cancer driver alterations, occurring in BRAF, KRAS, ROS1, and RET. More than 70% of SCLC patients harbored TP53-RB1 co-alterations. Moreover, 88.9%, 40%, and 77.8% of LCC, LCNEC, and SCLC cases had a high tumor mutation burden level with more than 7 mutations/Mb. Furthermore, high index of CD68+ CD163+ (TILs within cancer cell nests/ TILs within cancer cell nests and in cancer stroma, P = .041, 548 days vs not reached) and CD163+ TILs (P = .041, 548 days vs not reached) predicted a shorter OS in SCLC. Our findings revealed the distinct genomic profiles and TME contexture among LCC, LCNEC, and SCLC. Our findings suggest that stratifying LCNEC/SCLC patients based on TME contexture might help clinical disease management.

DOI: https://doi.org/10.1097/MD.0000000000032781
Commun Biol. 2023 Jan 21. 6(1): 82

Single-cell RNA binding protein regulatory network analyses reveal oncogenic HNRNPK-MYC signalling pathway in cancer.

Weiwei Zhou, Qiuling Jie, Tao Pan, Jingyi Shi, Tiantongfei Jiang, Ya Zhang, Na Ding, Juan Xu, Yanlin Ma, Yongsheng Li.

RNA-binding proteins (RBPs) are key players of gene expression and perturbations of RBP-RNA regulatory network have been observed in various cancer types. Here, we propose a computational method, RBPreg, to identify the RBP regulators by integration of single cell RNA-Seq (N = 233,591) and RBP binding data. Pan-cancer analyses suggest that RBP regulators exhibit cancer and cell specificity and perturbations of RBP regulatory network are involved in cancer hallmark-related functions. We prioritize an oncogenic RBP-HNRNPK, which is highly expressed in tumors and associated with poor prognosis of patients. Functional assays performed in cancer cells reveal that HNRNPK promotes cancer cell proliferation, migration, and invasion in vitro and in vivo. Mechanistic investigations further demonstrate that HNRNPK promotes tumorigenesis and progression by directly binding to MYC and perturbed the MYC targets pathway in lung cancer. Our results provide a valuable resource for characterizing RBP regulatory networks in cancer, yielding potential biomarkers for precision medicine.

DOI: https://doi.org/10.1038/s42003-023-04457-2
Cell Death Discov. 2023 Jan 21. 9(1): 17

Cancer-associated fibroblast-secreted IGFBP7 promotes gastric cancer by enhancing tumor associated macrophage infiltration via FGF2/FGFR1/PI3K/AKT axis.

Dandan Li, Lingyun Xia, Pan Huang, Zidi Wang, Qiwei Guo, Congcong Huang, Weidong Leng, Shanshan Qin.

We previously reported that IGFBP7 plays a role in maintaining mRNA stability of oncogenic lncRNA UBE2CP3 by RNA-RNA interaction in gastric cancer (GC). Clinical cohort studies had implied an oncogenic role of IGFBP7 in GC. However, the molecular mechanism of IGFBP7 in GC progression remains unknown. In this study, clinical analysis based on two independent cohorts showed that IGFBP7 was positively associated with poor prognosis and macrophage infiltration in GC. Loss-of-function studies confirmed the oncogenic properties of IGFBP7 in regulating GC cell proliferation and invasion. Mechanismly, IGFBP7 was highly expressed in cancer-associated fibroblasts (CAF) and mesenchymal cells, and was induced by epithelial-to-mesenchymal transition (EMT) signaling, since its expression was increased by TGF-beta treatment and reduced by overexpression of OVOL2 in GC. RNA sequencing, qRT-PCR, ELISA assay showed that IGFBP7 positively regulated FGF2 expression and secretion in GC. Transcriptome analysis revealed that FGFR1 was downregulated in M1 polarization but upregulated in M2 polarization. Exogenous recombinant IGFBP7 treatment in macrophages and GC cells further identified that IGFBP7 promotes tumor associated macrophage (TAM) polarization via FGF2/FGFR1/PI3K/AKT axis. Our finding here represented the first evidence that IGFBP7 promotes GC by enhancing TAM/M2 macrophage polarization through FGF2/FGFR1/PI3K/AKT axis.

DOI: https://doi.org/10.1038/s41420-023-01336-x
J Med Chem. 2023 Jan 24.

METTL3 from Target Validation to the First Small-Molecule Inhibitors: A Medicinal Chemistry Journey.

Francesco Fiorentino, Martina Menna, Dante Rotili, Sergio Valente, Antonello Mai.

RNA methylation is a critical mechanism for regulating the transcription and translation of specific sequences or for eliminating unnecessary sequences during RNA maturation. METTL3, an RNA methyltransferase that catalyzes the transfer of a methyl group to the N6-adenosine of RNA, is one of the key mediators of this process. METTL3 dysregulation may result in the emergence of a variety of diseases ranging from cancer to cardiovascular and neurological disorders beyond contributing to viral infections. Hence, the discovery of METTL3 inhibitors may assist in furthering the understanding of the biological roles of this enzyme, in addition to contributing to the development of novel therapeutics. Through this work, we will examine the existing correlations between METTL3 and diseases. We will also analyze the development, mode of action, pharmacology, and structure-activity relationships of the currently known METTL3 inhibitors. They include both nucleoside and non-nucleoside compounds, with the latter comprising both competitive and allosteric inhibitors.

DOI: https://doi.org/10.1021/acs.jmedchem.2c01601
Mol Carcinog. 2023 Jan 24.

Angiopoietin-like protein 3 promotes colorectal cancer progression and liver metastasis partly via the mitogen-activated protein kinase 14 pathway.

Yuexia Wang, Yi Yi, Shengli Pan, Yuhao Zhang, Jun Fu, Xiaolin Wu, Xianju Qin.

  Colorectal cancer (CRC) remains one of the most common malignancies worldwide, and liver metastasis represents a considerable challenge during CRC treatment. Aberrant expression of angiopoietin-like protein 3 (ANGPTL3) has been reported in several human cancer types. However, the function and mechanism of ANGPTL3 in CRC remain unclear. In this study, we first explored ANGPTL3 expression profiles in CRC datasets from ONCOMINE and in local samples from patients with CRC. We then elucidated the function of ANGPTL3 via knockdown and overexpression experiments. Bioinformatic analyses were performed to investigate the biological function and associated molecular mechanisms of ANGPTL3 in CRC oncogenesis and development. Finally, a xenograft model of liver metastasis was used to determine the role of ANGPTL3 in CRC metastasis. Our findings indicated that ANGPTL3 expression was upregulated in human CRC tissues, with high ANGPTL3 expression significantly correlated with poor survival of patients with CRC. ANGPTL3 overexpression promoted the proliferation and migration of CRC cells partially through mitogen-activated protein kinase 14 (MAPK14), while ANGPTL3 silencing had the opposite effect. Moreover, ANGPTL3 downregulation suppressed tumor growth and liver metastasis in xenograft mice. Collectively, the results presented here indicate that ANGPTL3 promotes cell proliferation and liver metastasis partly via MAPK14, suggesting that ANGPTL3 plays a tumor-promoting role in CRC progression and thus may represent a therapeutic target for CRC treatment.

Keywords:  ANGPTL3; MAPK14; colorectal cancer; liver metastasis; migration

DOI:  https://doi.org/10.1002/mc.23506
Anticancer Res. 2023 Feb;43(2): 639-644

5-Azacytidine (5-aza) Induces p53-associated Cell Death Through Inhibition of DNA Methyltransferase Activity in Hep3B and HT-29 Cells.

Dae-Yeon Kim, Rangyeon Lee, Hee-Tae Cheong, Chang-Six Ra, Ki-Jong Rhee, Jeongho Park, Bae Dong Jung.

  BACKGROUND/AIM: DNA methylation regulates the expression of genes that control mechanisms of cell death. TP53 gene expression inhibits tumorigenesis, and its action is closely associated with cell death. 5-Azacytidine (5-aza), increases the expression of the TP53 gene by inhibiting DNA methyltransferase.MATERIALS AND METHODS: Using 5-aza, we induced DNA hypomethylation in p53-null and p53-expressing cancer cell lines and investigated potential mechanisms of cancer cell death.
RESULTS: TP53 expression promoted cell death. Notably, methylation-specific PCR (MSP) and bisulfite sequencing revealed more methylation sites at the TP53 promoter region in p53-null cells than in p53-expressing cells.
CONCLUSION: This study suggests a novel mechanism of tumorigenesis regulated by p53 expression.

Keywords:  5-azacytidine; Cancer; Cell death; DNA methylation; p53

DOI:  https://doi.org/10.21873/anticanres.16200
Elife. 2023 Jan 24. pii: e69521. [Epub ahead of print]12

Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms.

Gary K L Chan, Samantha Maisel, Yeonjoo C Hwang, Bryan C Pascual, Rebecca R B Wolber, Phuong Vu, Krushna C Patra, Mehdi Bouhaddou, Heidi L Kenerson, Huat C Lim, Donald Long, Raymond S Yeung, Praveen Sethupathy, Danielle L Swaney, Nevan J Krogan, Rigney E Turnham, Kimberly J Riehle, John D Scott, Nabeel Bardeesy, John D Gordan.

  Genetic alterations that activate protein kinase A (PKA) are found in many tumor types. Yet, their downstream oncogenic signaling mechanisms are poorly understood. We used global phosphoproteomics and kinase activity profiling to map conserved signaling outputs driven by a range of genetic changes that activate PKA in human cancer. Two signaling networks were identified downstream of PKA: RAS/MAPK components, and an Aurora Kinase A (AURKA) /glycogen synthase kinase (GSK3) sub-network with activity toward MYC oncoproteins. Findings were validated in two PKA-dependent cancer models: a novel, patient-derived fibrolamellar liver cancer (FLC) line that expresses a DNAJ-PKAc fusion, and a PKA-addicted melanoma model with a mutant Type I PKA regulatory subunit. We identify PKA signals that can influence both de novo translation and stability of the proto-oncogene c-MYC. However, the primary mechanism of PKA effects on MYC in our cell models was translation and could be blocked with the eIF4A inhibitor zotatifin. This compound dramatically reduced c-MYC expression and inhibited FLC cell line growth in vitro. Thus, targeting PKA effects on translation is a potential treatment strategy for FLC and other PKA-driven cancers.

Keywords:  cancer biology; human

DOI:  https://doi.org/10.7554/eLife.69521
Mol Carcinog. 2023 Jan 23.

Insulin-like growth factor-2 mRNA-binding protein 3 promotes cell migration, invasion, and epithelial-mesenchymal transition of esophageal squamous cell carcinoma cells by targeting zinc finger E-box-binding homeobox 1 mRNA.

Yadong Feng, Yanbing Lin, Zhaoyan Jiang, Lei Wu, Youyu Zhang, Hailu Wu, Xiaoqin Yuan.

  The role and mechanism of insulin-like growth factor-2 mRNA-binding protein 3 (IGF2BP3) in the metastasis of esophageal squamous cell carcinoma (ESCC) remain unclear. In this study, IGF2BP3 mRNA and protein expression levels were evaluated in ESCC tissues. Small interfering RNAs (siRNAs), plasmid overexpression, and stable lentivirus transfection were used to manipulate intracellular IGF2BP3 expression levels. The role of IGF2BP3 in ESCC tumorigenesis was investigated in vitro and in vivo. IGF2BP3 target transcripts were detected, and the acetylation effect ratios of the IGF2BP3 promoter region by H3K27ac were determined. IGF2BP3 mRNA expression levels were significantly higher in ESCC tissues than in normal esophageal tissues. Increased IGF2BP3 expression levels were detected in node-negative ESCC tissues and correlated with greater lesion depth in ESCC. Overexpression of IGF2BP3 promoted ESCC development in vitro and in vivo, and IGF2BP3 knockdown caused an opposite effect. IGF2BP3 was found to directly bind to the zinc finger E-box-binding homeobox 1 (Zeb1) mRNA, and the downregulation of IGF2BP3 reduced the stability of Zeb1 mRNA. IGF2BP3 induced epithelial-mesenchymal transition in ESCC cells in a Zeb1-dependent manner. IGF2BP3 was transcriptionally activated in ESCC cell lines via H3K27 acetylation. Our results demonstrate that IGF2BP3 plays a vital role in ESCC cell proliferation, invasion, and metastasis and is a potential therapeutic target for treating ESCC.

Keywords:  ESCC; IGF2BP3; metastasis; signaling pathway; therapeutic target

DOI:  https://doi.org/10.1002/mc.23502
Cell Death Dis. 2023 Jan 21. 14(1): 53

Obesity promotes radioresistance through SERPINE1-mediated aggressiveness and DNA repair of triple-negative breast cancer.

Yong-Han Su, Yi-Zhen Wu, David K Ann, Jenny Ling-Yu Chen, Ching-Ying Kuo.

Obesity is a risk factor in various types of cancer, including breast cancer. The disturbance of adipose tissue in obesity highly correlates with cancer progression and resistance to standard treatments such as chemo- and radio-therapies. In this study, in a syngeneic mouse model of triple-negative breast cancer (TNBC), diet-induced obesity (DIO) not only promoted tumor growth, but also reduced tumor response to radiotherapy. Serpine1 (Pai-1) was elevated in the circulation of obese mice and was enriched within tumor microenvironment. In vitro co-culture of human white adipocytes-conditioned medium (hAd-CM) with TNBC cells potentiated the aggressive phenotypes and radioresistance of TNBC cells. Moreover, inhibition of both cancer cell autonomous and non-autonomous SERPINE1 by either genetic or pharmacological strategy markedly dampened the aggressive phenotypes and radioresistance of TNBC cells. Mechanistically, we uncovered a previously unrecognized role of SERPINE1 in DNA damage response. Ionizing radiation-induced DNA double-strand breaks (DSBs) increased the expression of SERPINE1 in cancer cells in an ATM/ATR-dependent manner, and promoted nuclear localization of SERPINE1 to facilitate DSB repair. By analyzing public clinical datasets, higher SERPINE1 expression in TNBC correlated with patients' BMI as well as poor outcomes. Elevated SERPINE1 expression and nuclear localization were also observed in radioresistant breast cancer cells. Collectively, we reveal a link between obesity and radioresistance in TNBC and identify SERPINE1 to be a crucial factor mediating obesity-associated tumor radioresistance.

DOI: https://doi.org/10.1038/s41419-023-05576-8