bims-rimeca 2023-12-24 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023–12–24
thirty papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

m6A reader IGF2BP2 promotes lymphatic metastasis by stabilizing DPP4 in papillary thyroid carcinoma.
METTL3/IGF2BP3-regulated m6A modification of HYOU1 confers doxorubicin resistance in breast cancer.
FTO-mediated m6A demethylation regulates GnRH expression in the hypothalamus via the PLCβ3/Ca2+/CAMK signalling pathway.
The m6A Reader YTHDC2 Suppresses Lung Adenocarcinoma Tumorigenesis by Destabilizing MRPL12.
Recent Advances in RNA m6A Modification in Solid Tumors and Tumor Immunity.
A low-cost, low-input method establishment for m6A MeRIP-seq.
Tumor suppressive function of IGF2BP1 in gastric cancer through decreasing MYC.
The RNA m6A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression.
The role of m6A epigenetic modifications in tumor coding and non-coding RNA processing.
METTL3/YTHDC1-mediated upregulation of LINC00294 promotes hepatocellular carcinoma progression.
lncRNA POU6F2-AS1 Regulated by KIAA1429 Contributes to Colorectal Cancer Progression in an m6A Modification Manner.
HIF-1α/METTL1/m7G axis is involved in CRC response to hypoxia.
M6A demethylase ALKBH5 regulates FOXO1 mRNA stability and chemoresistance in triple-negative breast cancer.
Recent Advances of RNA m6A Modifications in Cancer Immunoediting and Immunotherapy.
RNA Modifications in Cancer Stem Cell Biology.
Novel insights into the regulatory role of N6-methyladenosine methylation modified autophagy in sepsis.
The inhibition of FTO attenuates the antifibrotic effect of leonurine in rat cardiac fibroblasts.
Dephosphorylation Switch DNAzyme-RCA Circuit: A Robust Strategy for the Homogeneous and Reliable Detection of FTO Demethylase.
RNA Modifications in Cancer Metabolism and Tumor Microenvironment.
Pancancer analysis uncovers an immunological role and prognostic value of the m6A reader IGF2BP2 in pancreatic cancer.
METTL3 promotes non-small-cell lung cancer growth and metastasis by inhibiting FDX1 through copper death-associated pri-miR-21-5p maturation.
Role of RNA Modifications, Especially m6A, in Aflatoxin Biosynthesis of Aspergillus flavus.
IGF2BP1 facilitates non-small cell lung cancer progression by regulating the KIF2A-mediated Wnt/β-catenin pathway.
RNA m6A modifications regulate crosstalk between tumor metabolism and immunity.
Non-coding RNA methylation modifications in hepatocellular carcinoma: interactions and potential implications.
Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A.
Single-cell profiling reveals transcriptomic signatures of vascular endothelial cells in non-healing diabetic foot ulcers.
Overexpression of MTHFD2 represents an inflamed tumor microenvironment and precisely predicts the molecular subtype and immunotherapy response of bladder cancer.
The impact of LncRNA-SOX2-OT/let-7c-3p/SKP2 Axis on head and neck squamous cell carcinoma progression: Insights from bioinformatics analysis and experimental validation.
Neutrophil extracellular traps promote gastric cancer cell metastasis via the NAT10-mediated N4-acetylcytidine modification of SMYD2.

Cancer Gene Ther. 2023 Dec 15.

m6A reader IGF2BP2 promotes lymphatic metastasis by stabilizing DPP4 in papillary thyroid carcinoma.

Wenlong Wang, Ying Ding, Yunzhe Zhao, Xinying Li.

Lymph node metastasis (LNM) is a major cause of locoregional recurrence of papillary thyroid carcinoma (PTC). However, the mechanisms responsible for LNM are unclear. Aberrant N6-methyladenosine (m6A) RNA modification plays a vital role in cancer progression and metastasis, and whether m6A modification regulates LNM in PTC remains to be determined. This study showed that IGF2BP2 was upregulated in PTC and positively associated with LNM. Functionally, IGF2BP2 knockdown significantly inhibited PTC cell proliferation and invasion in vitro, and vice versa. Moreover, IGF2BP2 knockdown significantly inhibited lymphatic metastasis in vivo. Mechanistically, Human m6A epitranscriptomic microarray, MeRIP, and RIP assays demonstrated that IGF2BP2 activated the NF-KB pathway by enhancing DPP4 stability in an m6A-dependent manner. Furthermore, IGF2BP2 knockdown increased the sensitivity of PTC cells to cisplatin therapy to a certain extent, while its overexpression produced the opposite effects. Overall, this study uncovers that IGF2BP2 promotes lymphatic metastasis via stabilizing DPP4 in an m6A-dependent manner, and provides new insights for understanding the mechanism of lymphatic metastasis in PTC.

DOI: https://doi.org/10.1038/s41417-023-00702-2
Biochim Biophys Acta Gen Subj. 2023 Dec 14. pii: S0304-4165(23)00240-4. [Epub ahead of print] 130542

METTL3/IGF2BP3-regulated m6A modification of HYOU1 confers doxorubicin resistance in breast cancer.

Shaocheng Zhou, Lijuan Sheng, Lin Zhang, Jianan Zhang, Lei Wang.

  Chemoresistance is a main reason for therapeutic failure and poor prognosis for breast cancer (BC) patients, especially for triple-negative BC patients. How the molecular mechanisms underlying the chemoresistance to doxorubicin (Dox) in BC is not well understood. Here, we revealed that METTL3/IGF2BP3-regulated m6A modification of HYOU1 increased Dox resistance in BC cells. CCK-8 and Annexin V-FITC/PI staining assays were employed to measure viability and cell death. Western blotting and qRT-PCR assays were applied to assay the expression of genes. Knockdown and rescue experiments were used to assay the role of METTL3, IGF2BP3 and HYOU1 in regulating BC cell responses to Dox. RIP, MeRIP and dual-luciferase activity assays were applied to examine the function of METTL3/IGF2BP3 in the m6A modification of HYOU1 mRNA. It was found that global mRNA m6A methylation levels were upregulated in Dox-resistant BC cell lines. The methyltransferase METTL3 was upregulated in Dox-resistant BC cell lines, and downregulation of METTL3 could overcome this resistance. Furthermore, HYOU1 was identified as a downstream target of METTL3-mediated m6A modification. Downregulation of HYOU1 could overcome Dox resistance, while forced expression of HYOU1 resulted in Dox resistance in BC cells. METTL3 cooperated with IGF2BP3 to modulate the m6A modification of HYOU1 mRNA and increase its stability. Collectively, our findings unveiled the key roles of the METTL3/IGF2BP3/HYOU1 axis in modulating Dox sensitivity in BC cells; thus, targeting this axis might be a potential strategy to increase Dox efficacy in the treatment of BC.

Keywords:  Breast cancer; Chemoresistance; Doxorubicin; HYOU1; IGF2BP3; METTL3; m6A modification

DOI:  https://doi.org/10.1016/j.bbagen.2023.130542
Commun Biol. 2023 Dec 21. 6(1): 1297

FTO-mediated m6A demethylation regulates GnRH expression in the hypothalamus via the PLCβ3/Ca2+/CAMK signalling pathway.

Shaolian Zang, Xiaoqin Yin, Pin Li.

N6-methyladenosine (m6A) plays a crucial role in the development and functional homeostasis of the central nervous system. The fat mass and obesity-associated (FTO) gene, which is highly expressed in the hypothalamus, is closely related to female pubertal development. In this study, we found that m6A methylation decreased in the hypothalamus gradually with puberty and decreased in female rats with precocious puberty. FTO expression was increased at the same time. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) showed that the m6A methylation of PLCβ3, a key enzyme of the Ca2+ signalling pathway, was decreased significantly in the hypothalamus in precocious rats. Upregulating FTO increased PLCβ3 expression and activated the Ca2+ signalling pathway, which promoted GnRH expression. Dual-luciferase reporter and MeRIP-qPCR assays confirmed that FTO regulated m6A demethylation of PLCβ3 and promoted PLCβ3 expression. Upon overexpressing FTO in the hypothalamic arcuate nucleus (ARC) in female rats, we observed advanced puberty onset. Meanwhile, PLCβ3 and GnRH expression in the hypothalamus increased significantly, and the Ca2+ signalling pathway was activated. Our study demonstrates that FTO enhances GnRH expression, which promotes puberty onset, by regulating m6A demethylation of PLCβ3 and activating the Ca2+ signalling pathway.

DOI: https://doi.org/10.1038/s42003-023-05677-2
Mol Biotechnol. 2023 Dec 21.

The m6A Reader YTHDC2 Suppresses Lung Adenocarcinoma Tumorigenesis by Destabilizing MRPL12.

Yingchuan Sun, Yanyan Liu, Pengyuan Wang, Lin Chang, Jianmin Huang.

  N6-methyladenosine (m6A) is the most common posttranscriptional RNA modification and plays significant roles in physiological and pathological progression. Here, we probed the functions and mechanism of the m6A reader YTH domain containing 2 (YTHDC2) in Lung Adenocarcinoma (LUAD) tumorigenesis. Levels of genes and proteins of YTHDC2 and Mitochondrial ribosomal protein L7/L12 (MRPL12) were assayed by quantitative real-time polymerase chain reaction, western blotting and Immunohistochemistry (IHC) analyses. In vitro analysis was conducted using 5-ethynyl-2'-deoxyuridine (EdU), colony formation, flow cytometry, and transwell assays, respectively. In vivo assay was performed by using the mouse lung adenocarcinoma model. The methylated RNA immunoprecipitation (MeRIP) assay was used to detect the m6A modification profile of MRPL12 mRNA. YTHDC2 was lowly expressed in lung adenocarcinoma tissues and cells. Overexpression of YTHDC2 suppressed the proliferation, invasion and migration of lung adenocarcinoma cells, but induced cell apoptosis. As expected, forced expression of YTHDC2 hindered lung adenocarcinoma tumor growth in vivo. Mechanistically, YTHDC2 preferentially bound to m6A-modified MRPL12 mRNA and destabilized its expression. MRPL12 was highly expressed in lung adenocarcinoma tissues and cells, and MRPL12 silencing repressed the growth and mobility of lung adenocarcinoma cells. Moreover, MRPL12 upregulation attenuated the anticancer activity of YTHDC2 in lung adenocarcinoma cells. In vivo assay also showed YTHDC2 suppressed tumor growth in the lung adenocarcinoma mouse model via downregulating MRPL12. The m6A reader YTHDC2 repressed lung adenocarcinoma tumorigenesis by destabilizing MRPL12 in an m6A-dependent manner.

Keywords:  Lung adenocarcinoma; MRPL12; YTHDC2; m6A RNA methylation

DOI:  https://doi.org/10.1007/s12033-023-01002-8
Cancer Treat Res. 2023 ;190 95-142

Recent Advances in RNA m6A Modification in Solid Tumors and Tumor Immunity.

Michelle Verghese, Emma Wilkinson, Yu-Ying He.

  An analogous field to epigenetics is referred to as epitranscriptomics, which focuses on the study of post-transcriptional chemical modifications in RNA. RNA molecules, including mRNA, tRNA, rRNA, and other non-coding RNA molecules, can be edited with numerous modifications. The most prevalent modification in eukaryotic mRNA is N6-methyladenosine (m6A), which is a reversible modification found in over 7000 human genes. Recent technological advances have accelerated the characterization of these modifications, and they have been shown to play important roles in many biological processes, including pathogenic processes such as cancer. In this chapter, we discuss the role of m6A mRNA modification in cancer with a focus on solid tumor biology and immunity. m6A RNA methylation and its regulatory proteins can play context-dependent roles in solid tumor development and progression by modulating RNA metabolism to drive oncogenic or tumor-suppressive cellular pathways. m6A RNA methylation also plays dynamic roles within both immune cells and tumor cells to mediate the anti-tumor immune response. Finally, an emerging area of research within epitranscriptomics studies the role of m6A RNA methylation in promoting sensitivity or resistance to cancer therapies, including chemotherapy, targeted therapy, and immunotherapy. Overall, our understanding of m6A RNA methylation in solid tumors has advanced significantly, and continued research is needed both to fill gaps in knowledge and to identify potential areas of focus for therapeutic development.

Keywords:  Epitranscriptomics; anti-tumor immunity.; cancer; chemotherapy; eraser; immunotherapy; m6A RNA methylation; reader; writer

DOI:  https://doi.org/10.1007/978-3-031-45654-1_4
Biosci Rep. 2023 Dec 19. pii: BSR20231430. [Epub ahead of print]

A low-cost, low-input method establishment for m6A MeRIP-seq.

Wenjuan Xia, Ling Guo, Huapeng Su, Jincheng Li, Jiafeng Lu, Hong Li, Boxian Huang.

  N6-methyladenosine (m6A) is a highly prevalent modification found in mammal mRNA molecules that plays a crucial role in the regulation of cellular function. m6A RNA immunoprecipitation sequencing (MeRIP-seq) has been frequently used in transcriptomics research to identify the location of m6A. MABE572 (Millipore) is the most widely utilized and efficient anti-m6A antibody for MeRIP-seq. However, due to the high dose and price of this antibody, which has also been taken off the market, we discovered that CST's anti-m6A antibody can be used instead of MABE572 to map the m6A transcriptome. In this study, we performed different concentrations of the CST anti-m6A antibodies with the corresponding initiation RNA of HEK293T cells, 2.5 μg antibody with 1 μg total RNA, 1.25 μg antibody with 0.5 μg total RNA, 1.25 μg antibody with 0.1 μg total RNA. By comparing the m6A peak calling, enriched motifs, alternative splicing events, and nuclear transcripts modified by m6A between the CST and Millipore libraries, it was found that the CST library presented similar data to Millipore, even at incredibly low doses. The volume and cost of antibodies are significantly reduced by this refined MeRIP-seq using CST antibody, making it convenient to map future large-scale sample m6A methylation.

Keywords:  CST; MeRIP-seq; alternative splicing; anti-m6A antibody; m6A

DOI:  https://doi.org/10.1042/BSR20231430
Cancer Sci. 2023 Dec 19.

Tumor suppressive function of IGF2BP1 in gastric cancer through decreasing MYC.

Ning Ding, Guodong Cao, Zhuo Wang, Shengjun Xu, Wenwen Chen.

  Gastric cancer is one of the most common causes of cancer-related death worldwide. The N6 -methyladenosine (m6 A) reader IGF2BP1 (insulin-like growth factor-2 mRNA binding protein 1) has been reported to promote cancer progression by stabilizing oncogenic mRNAs through its m6 A-binding activity in some tumors. However, the role of IGF2BP1 in gastric carcinogenesis remains unclear. In this study, we found that IGF2BP1 is significantly downregulated in tumor tissues from patients with gastric cancer. Lower expression of IGF2BP1 is associated with poor prognosis. Gastric cancer cell proliferation is suppressed by IGF2BP1 in an m6 A-dependent manner. Additionally, IGF2BP1 is able to significantly attenuate tumor growth of gastric cancer cells. Further m6 A sequencing and m6 A-RNA immunoprecipitation assays show that MYC (c-myc proto-oncogene) mRNA is a target transcript of IGF2BP1 in gastric cancer cells. IGF2BP1 inhibits gastric cancer cell proliferation by reducing the mRNA and protein expression of MYC. Mechanistically, IGF2BP1 promotes the degradation of MYC mRNA and inhibits its translation efficiency. Taken together, these data suggest that IGF2BP1 plays a tumor-suppressive role in gastric carcinogenesis by downregulating MYC in an m6 A-dependent manner, thereby making the IGF2BP1-MYC axis a potential target for gastric cancer treatment.

Keywords:  IGF2BP1; MYC; RNA metabolism; gastric cancer; m6A

DOI:  https://doi.org/10.1111/cas.16047
Cell Mol Immunol. 2023 Dec 20.

The RNA m6A demethylase ALKBH5 drives emergency granulopoiesis and neutrophil mobilization by upregulating G-CSFR expression.

Yang Liu, Renjie Song, Zhike Lu, Lu Zhao, Xinyi Zhan, Yini Li, Xuetao Cao.

  Emergency granulopoiesis and neutrophil mobilization that can be triggered by granulocyte colony-stimulating factor (G-CSF) through its receptor G-CSFR are essential for antibacterial innate defense. However, the epigenetic modifiers crucial for intrinsically regulating G-CSFR expression and the antibacterial response of neutrophils remain largely unclear. N6-methyladenosine (m6A) RNA modification and the related demethylase alkB homolog 5 (ALKBH5) are key epigenetic regulators of immunity and inflammation, but their roles in neutrophil production and mobilization are still unknown. We used cecal ligation and puncture (CLP)-induced polymicrobial sepsis to model systemic bacterial infection, and we report that ALKBH5 is required for emergency granulopoiesis and neutrophil mobilization. ALKBH5 depletion significantly impaired the production of immature neutrophils in the bone marrow of septic mice. In addition, Alkbh5-deficient septic mice exhibited higher retention of mature neutrophils in the bone marrow and defective neutrophil release into the circulation, which led to fewer neutrophils at the infection site than in their wild-type littermates. During bacterial infection, ALKBH5 imprinted production- and mobilization-promoting transcriptome signatures in both mouse and human neutrophils. Mechanistically, ALKBH5 erased m6A methylation on the CSF3R mRNA to increase the mRNA stability and protein expression of G-CSFR, consequently upregulating cell surface G-CSFR expression and downstream STAT3 signaling in neutrophils. The RIP-qPCR results confirmed the direct binding of ALKBH5 to the CSF3R mRNA, and the binding strength declined upon bacterial infection, accounting for the decrease in G-CSFR expression on bacteria-infected neutrophils. Considering these results collectively, we define a new role of ALKBH5 in intrinsically driving neutrophil production and mobilization through m6A demethylation-dependent posttranscriptional regulation, indicating that m6A RNA modification in neutrophils is a potential target for treating bacterial infections and neutropenia.

Keywords:  ALKBH5; Emergency granulopoiesis; G-CSF receptor; Neutrophil mobilization; m6A RNA modification

DOI:  https://doi.org/10.1038/s41423-023-01115-9
Cell Commun Signal. 2023 Dec 15. 21(1): 355

The role of m6A epigenetic modifications in tumor coding and non-coding RNA processing.

Tongxuan Wen, Tong Li, Yeqiu Xu, Yuanzhuang Zhang, Hai Pan, Yong Wang.

   BACKGROUND: Epigenetic modifications of RNA significantly contribute to the regulatory processes in tumors and have, thus, received considerable attention. The m6A modification, known as N6-methyladenosine, is the predominant epigenetic alteration found in both eukaryotic mRNAs and ncRNAs.
MAIN BODY: m6A methylation modifications are dynamically reversible and are catalyzed, removed, and recognized by the complex of m6A methyltransferase (MTases), m6A demethylase, and m6A methyl recognition proteins (MRPs). Published evidence suggests that dysregulated m6A modification results in abnormal biological behavior of mature mRNA, leading to a variety of abnormal physiological processes, with profound implications for tumor development in particular.
CONCLUSION: Abnormal RNA processing due to dysregulation of m6A modification plays an important role in tumor pathogenesis and potential mechanisms of action. In this review, we comprehensively explored the mechanisms by which m6A modification regulates mRNA and ncRNA processing, focusing on their roles in tumors, and aiming to understand the important regulatory function of m6A modification, a key RNA epigenetic modification, in tumor cells, with a view to providing theoretical support for tumor diagnosis and treatment. Video Abstract.

Keywords:  Epigenetics; Immunotherapy; Non-coding RNA; RNA methylation; Tumors; m6A modification; mRNA processing

DOI:  https://doi.org/10.1186/s12964-023-01385-w
Heliyon. 2023 Dec;9(12): e22595

METTL3/YTHDC1-mediated upregulation of LINC00294 promotes hepatocellular carcinoma progression.

Rulin Zhang, Rui Yang, Zhuodeng Huang, Xiang Xu, Siang Lv, Xin Guan, Hao Li, Jun Wu.

  Hepatocellular carcinoma (HCC) is a highly prevalent malignancy and the third highest contributor to cancer-associated deaths globally. Research has increasingly demonstrated a strong correlation between long noncoding RNAs (lncRNAs) and the incidence and progression of HCC. Nonetheless, the exact mechanism whereby the function of lncRNAs in HCC has not been elucidated. This study explored the pathological role of LINC00294 in HCC, as well as the modulatory mechanism involved. Based on the "The Cancer Genome Atlas (TCGA)" database and validation in HCC cell lines and tissues, the expression of LINC00294 was discovered to be upregulated in HCC tissues and correlated with tumor grade and the prognosis of patients with HCC. Functionally, LINC00294 stimulated the proliferation of HCC cells as well as the Warburg effect (aerobic glycolysis) to enhance progression of tumor in vivo. Mechanistically, METTL3/YTHDC1-mediated N6-methyladenosine (m6A) modification underwent a significant enrichment within LINC00294 and was shown to enhance its RNA stability. Moreover, LINC00294 promoted the interaction between YTHDC1 and HK2 and GLUT1 mRNA. Overall, our study illustrates the m6A modification-mediated epigenetic mechanism of LINC00294 expression and regulatory role in HK2and GLUT1 mRNA expression and indicate LINC00294 as a potential biomarker panel for prognostic prediction and treatment in HCC.

Keywords:  Hepatocellular carcinoma; LINC00294; METTL3; N6-methyladenosine modification; YTHDC1

DOI:  https://doi.org/10.1016/j.heliyon.2023.e22595
Mol Biotechnol. 2023 Dec 16.

lncRNA POU6F2-AS1 Regulated by KIAA1429 Contributes to Colorectal Cancer Progression in an m6A Modification Manner.

Dunfeng Lu, Aihua Chen.

  Long non-coding RNAs (lncRNAs) are participated in tumourigenesis, including colorectal cancer (CRC). However, the effects and mechanisms of lncRNA POU6F2-AS1 in CRC have not been investigated. KIAA1429 act as a member of N6-methyladenosine (m6A) modification, has been knew as an oncogenic factor in various cancer containing CRC. We focus to investigate the regulation effect of lncRNA POU6F2-AS1, and the mechanism among lncRNA POU6F2-AS1 and KIAA1429 in CRC. The lncRNA POU6F2-AS1 and KIAA1429 levels in CRC tissue samples as well as cells were clarified by qRT-PCR, and their relationship was predicted by bioinformatics, MeRIP and Pearson analysis. Cell survival, migration and invasion were analyzed via EdU, wound healing and Transwell assays after lncRNA POU6F2-AS1 was down-regulated and KIAA1429 was up-regulated. LncRNA POU6F2-AS1 and KIAA1429 were enriched in CRC tissue samples. LncRNA POU6F2-AS1 silencing suppressed CRC cell survival, migration, and invasion, and KIAA1429 overexpression facilitated CRC cell malignancy. KIAA1429 promoted lncRNA POU6F2-AS1 expression via m6A modification. Furthermore, KIAA1429 upregulation reversed the inhibitory effect of lncRNA POU6F2-AS1 interference on the malignant behavior of CRC cells. lncRNA POU6F2-AS1 was modulated by KIAA1429 in the form of m6A modification to regulate the malignant phenotype of CRC, which may provide new insights into the potential application of KIAA1429-m6A-lncRNA POU6F2-AS1-based CRC therapy.

Keywords:  Colorectal cancer; KIAA1429; LncRNA POU6F2-AS1; m6A modification

DOI:  https://doi.org/10.1007/s12033-023-00986-7
Biochem Biophys Res Commun. 2023 Dec 13. pii: S0006-291X(23)01479-1. [Epub ahead of print]693 149385

HIF-1α/METTL1/m7G axis is involved in CRC response to hypoxia.

Shuyi Mi, Shangwen Cai, Meng Xue, Weiquan Wu.

   BACKGROUND: In recent years, many studies have confirmed that hypoxia and hypoxia inducible factor (HIF)-1α drive the development of colorectal cancer (CRC). HIF-1α also modulates epitranscriptomic remodeling to regulate cancer development. However, the mechanism by which RNA methylation is altered under hypoxic conditions and the underlying regulatory mechanisms in CRC remain unclear.
METHODS: Here, seven common types of modifications of mRNA and tRNA were quantitated using liquid chromatography-tandem mass spectrometry. To validate the robustness of the profiling data, modifications that were consistently altered across the three CRC cell lines under hypoxia were validated via dot blot analysis. Then, 10 enzymes that could regulate the abundance of three RNA modifications in tRNA were measured in CRC cells after hypoxia treatment using quantitative real-time polymerase chain reaction. Furthermore, the regulatory role of HIF-1α in the expression of methyltransferase 1 (METTL1) under hypoxic conditions was confirmed using METTL1 promoter activity assays and HIF-1α small interfering RNA (siRNA). The binding capacity of HIF-1α to each hypoxia response element (HRE) in the promoter of METTL1 was investigated by performing Chromatin immunoprecipitation assay (ChIP).
RESULTS: Abundance of RNA modifications was altered more consistently and significantly in tRNA than in mRNA under hypoxic conditions. In addition, the abundance of N7-methyleguanosine (m7G) modification in tRNA decreased significantly under hypoxic conditions. As a methyltransferase of the m7G modification in tRNA, the expression of METTL1 mRNA was drastically downregulated under hypoxic conditions. Mechanistically, suppression of HIF-1α by siRNA upregulated the METTL1 promoter activity. Furthermore, ChIP showed that HIF-1α could bind with an HRE in the promoter region of METTL1, indicating that METTL1 is a direct target of HIF-1α in CRC cells under hypoxic conditions.
CONCLUSIONS: Our study revealed that the abundance of the m7G modification in tRNA was drastically reduced in CRC cells dependent on the HIF-1α-mediated inhibition of METTL1 transcription under hypoxic conditions.

Keywords:  Colorectal cancer; HIF-1α; METTL1; RNA modification; m(7)G

DOI:  https://doi.org/10.1016/j.bbrc.2023.149385
Redox Biol. 2023 Dec 12. pii: S2213-2317(23)00394-4. [Epub ahead of print]69 102993

M6A demethylase ALKBH5 regulates FOXO1 mRNA stability and chemoresistance in triple-negative breast cancer.

Xi Liu, Pan Li, Yuanfeng Huang, Hongsheng Li, Xin Liu, Yaxi Du, Xin Lin, Danyang Chen, Hao Liu, Yongchun Zhou.

  Resistance to chemotherapy is the main reason for treatment failure and poor prognosis in patients with triple-negative breast cancer (TNBC). Although the association of RNA N6-methyladenosine (m6A) modifications with therapy resistance is noticed, its role in the development of therapeutic resistance in TNBC is not well documented. This study aimed to investigate the potential mechanisms underlying reactive oxygen species (ROS) regulation in doxorubicin (DOX)-resistant TNBC. Here, we found that DOX-resistant TNBC cells displayed low ROS levels because of increased expression of superoxide dismutase (SOD2), thus maintaining cancer stem cells (CSCs) characteristics and DOX resistance. FOXO1 is a master regulator that reduces cellular ROS in DOX-resistant TNBC cells, and knockdown of FOXO1 significantly increased ROS levels by inhibiting SOD2 expression. Moreover, the m6A demethylase ALKBH5 promoted m6A demethylation of FOXO1 mRNA and increased FOXO1 mRNA stability in DOX-resistant TNBC cells. The analysis of clinical samples revealed that the increased expression levels of ALKBH5, FOXO1, and SOD2 were significantly positively correlated with chemoresistance and poor prognosis in patients with TNBC. To our knowledge, this is the first study to highlight that ALKBH5-mediated FOXO1 mRNA demethylation contributes to CSCs characteristics and DOX resistance in TNBC cells. Furthermore, pharmacological targeting of FOXO1 profoundly restored the response of DOX-resistant TNBC cells, both in vitro and in vivo. In conclusion, we demonstrated a critical function of ALKBH5-mediated m6A demethylation of FOXO1 mRNA in restoring redox balance, which in turn promoting CSCs characteristics and DOX resistance in TNBC, and suggested that targeting the ALKBH5/FOXO1 axis has therapeutic potential for patients with TNBC refractory to chemotherapy.

Keywords:  ALKBH5; Chemoresistance; FOXO1; Reactive oxygen species; Triple-negative breast cancer

DOI:  https://doi.org/10.1016/j.redox.2023.102993
Cancer Treat Res. 2023 ;190 49-94

Recent Advances of RNA m6A Modifications in Cancer Immunoediting and Immunotherapy.

Shoubao Ma, Tasha Barr, Jianhua Yu.

  Cancer immunotherapy, which modulates immune responses against tumors using immune-checkpoint inhibitors or adoptive cell transfer, has emerged as a novel and promising therapy for tumors. However, only a minority of patients demonstrate durable responses, while the majority of patients are resistant to immunotherapy. The immune system can paradoxically constrain and promote tumor development and progression. This process is referred to as cancer immunoediting. The mechanisms of resistance to immunotherapy seem to be that cancer cells undergo immunoediting to evade recognition and elimination by the immune system. RNA modifications, specifically N6-methyladenosine (m6A) methylation, have emerged as a key regulator of various post-transcriptional gene regulatory processes, such as RNA export, splicing, stability, and degradation, which play unappreciated roles in various physiological and pathological processes, including immune system development and cancer pathogenesis. Therefore, a deeper understanding of the mechanisms by which RNA modifications impact the cancer immunoediting process can provide insight into the mechanisms of resistance to immunotherapies and the strategies that can be used to overcome such resistance. In this chapter, we briefly introduce the background of cancer immunoediting and immunotherapy. We also review and discuss the roles and mechanisms of RNA m6A modifications in fine-tuning the innate and adaptive immune responses, as well as in regulating tumor escape from immunosurveillance. Finally, we summarize the current strategies targeting m6A regulators for cancer immunotherapy.

Keywords:  Cancer immunoediting; Cancer immunotherapy; Chimeric antigen receptor cell therapy; Epigenetic regulation; Immune checkpoint inhibitors; Immunosurveillance; RNA modification; m6A modification

DOI:  https://doi.org/10.1007/978-3-031-45654-1_3
Cancer Treat Res. 2023 ;190 25-47

RNA Modifications in Cancer Stem Cell Biology.

Jonas Cerneckis, Qi Cui, Wei Liu, Yanhong Shi.

  Post-transcriptional regulation of gene expression shapes the cell state both in health and disease. RNA modifications-especially N6-methyladenosine (m6A)-have recently emerged as key players in RNA processing that depends on a sophisticated interplay between proteins of the RNA modification machinery. Importantly, the RNA epitranscriptome becomes dysregulated in cancer and promotes cancer-associated gene expression programs as well as cancer cell adaptation to the tumor microenvironment. At the top of the tumor hierarchy, cancer stem cells (CSCs) are master regulators of tumorigenesis and resistance to therapeutic intervention. Therefore, defining how RNA modifications influence the CSC state is of great importance for cancer drug development. In this chapter, we summarize the current knowledge of the roles of RNA modifications in shaping the CSC state and driving gene expression programs that confer stem-like properties to CSCs, promote CSC adaptation to the local microenvironment, and endow CSCs with metastatic potential and drug resistance.

Keywords:  Cancer stem cells; Cancer therapy; N6-methyladenosine; Pseudouridine; RNA modifications

DOI:  https://doi.org/10.1007/978-3-031-45654-1_2
Aging (Albany NY). 2023 Dec 18. 15

Novel insights into the regulatory role of N6-methyladenosine methylation modified autophagy in sepsis.

Cheng-Fei Bi, Jia Liu, Xiao-Dong Hu, Li-Shan Yang, Jun-Fei Zhang.

  Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. It is characterized by high morbidity and mortality and one of the major diseases that seriously hang over global human health. Autophagy is a crucial regulator in the complicated pathophysiological processes of sepsis. The activation of autophagy is known to be of great significance for protecting sepsis induced organ dysfunction. Recent research has demonstrated that N6-methyladenosine (m6A) methylation is a well-known post-transcriptional RNA modification that controls epigenetic and gene expression as well as a number of biological processes in sepsis. In addition, m6A affects the stability, export, splicing and translation of transcripts involved in the autophagic process. Although it has been suggested that m6A methylation regulates the biological metabolic processes of autophagy and is more frequently seen in the progression of sepsis pathogenesis, the underlying molecular mechanisms of m6A-modified autophagy in sepsis have not been thoroughly elucidated. The present article fills this gap by providing an epigenetic review of the processes of m6A-modified autophagy in sepsis and its potential role in the development of novel therapeutics.

Keywords:  autophagy; m6A methylation; sepsis

DOI:  https://doi.org/10.18632/aging.205312
Biochem Biophys Res Commun. 2023 Dec 12. pii: S0006-291X(23)01469-9. [Epub ahead of print]693 149375

The inhibition of FTO attenuates the antifibrotic effect of leonurine in rat cardiac fibroblasts.

Yuwei Meng, Tianlan Xi, Jun Fan, Qiyu Yang, Jing Ouyang, Jiadan Yang.

   BACKGROUND: Myocardial fibrosis (MF) is a common pathological condition in cardiovascular diseases that often causes severe cardiac dysfunction. MF is characterized by changes in cardiomyocytes, cardiac fibroblasts (CFs), levels of collagen (Col) -1, -3, and overdeposition of the extracellular matrix. Our previous research showed that leonurine (LE) effectively inhibits collagen synthesis and differentiation of CFs, but the mechanism is not fully elucidated. Recent evidence indicates that fat mass and obesity-associated proteins (FTO) regulates the occurrence and development of MF. This study aimed to explore the role of FTO in the antifibrotic effects of LE.
METHODS: Neonatal rat CFs were isolated, and induced using angiotensin II (Ang II) to establish a cell model of MF. Cell viability, wound healing and transwell assays were used to detect cell activity and migration ability. The protein and mRNA levels of MF-related factors were measured following stimulation with Ang II and LE under normal conditions or after FTO knockdown. The RNA methylation level was measured by dot blot assay.
RESULTS: The results showed that LE (20, 40 μM) was not toxic to normal CFs. LE reduced the proliferation, migration and collagen synthesis of Ang II-induced CFs. Further investigation showed that FTO was downregulated by Ang II stimulation, whereas LE reversed this effect. FTO knockdown facilitated the migration of CFs, upregulated the protein levels of Col-3, α-SMA and Col-1 in Ang II and LE-stimulated CFs, and enhanced the fluorescence intensity of α-SMA. Furthermore, LE reduced N6-methyladenosine (m6A) RNA methylation, which was partially blocked by FTO knockdown. FTO knockdown also reduced the expression levels of p53 protein in Ang II and LE-stimulated CFs.
CONCLUSIONS: Our findings suggest that the inhibition of FTO may attenuate the antifibrotic effect of LE in CFs, suggesting that FTO may serve as a key protein for anti-MF of LE.

Keywords:  FTO; Leonurine; Myocardial fibrosis

DOI:  https://doi.org/10.1016/j.bbrc.2023.149375
Anal Chem. 2023 Dec 20.

Dephosphorylation Switch DNAzyme-RCA Circuit: A Robust Strategy for the Homogeneous and Reliable Detection of FTO Demethylase.

Taorong Shen, Xing Huang, Yanfei Zhang, Yanli Tong, Yakun Shi, Jianhe Guo, Xiaoyong Zou, Yuzhi Xu, Zong Dai.

Fat mass and obesity-associated protein (FTO) plays a crucial role in regulating the dynamic modification of N6-methyladenosine (m6A) in eukaryotic mRNA. Sensitive detection of the FTO level and efficient evaluation of the FTO demethylase activity are of great importance to early cancer diagnosis and anticancer drug discovery, which are currently challenged by limited sensitivity/precision and low throughput. Herein, a robust strategy based on the dephosphorylation switch DNAzyme-rolling circle amplification (RCA) circuit, termed DSD-RCA, is developed for highly sensitive detection of FTO and inhibitor screening. Initially, the catalytic activity of DNAzyme is silenced by engineering with an m6A modification in its catalytic core. Only in the presence of target FTO can the methyl group on DNAzyme be eliminated, resulting in the activation of the catalytic activity of DNAzyme and thus cleaving the hairpin substrate to release numerous primers. Different from the conventional methods that use the downstream cleavage primer with the original 3'-hydroxyl end directly as the RCA primer with the problem of high background signal, which should be compensated by additional separation and wash steps in heterogeneous format, our DSD-RCA assay uses the upstream cleavage primer with a 2',3'-cyclic phosphate terminus at the 3'-end serving as an intrinsically blocked 3' end. Only after a dephosphorylation reaction mediated by T4 polynucleotide kinase can the upstream cleavage primers with a resultant 3'-hydroxyl end be extended by RCA. With the high signal-to-noise ratio and homogeneous property, the proposed platform can sensitively detect FTO with a limit of detection of 31.4 pM, and the relative standard deviations (RSDs %) ranging from 0.8 to 2.0% were much lower than the heterogeneous methods. The DSD-RCA method was applied for analyzing FTO in cytoplasmic lysates from different cell lines and tissues of breast cancer patients and further used for screening FTO inhibitors without the need for separation or cleaning, providing an opportunity for achieving high throughput and demonstrating the potential applications of this strategy in disease diagnostics, drug discovery, and biological applications.

DOI: https://doi.org/10.1021/acs.analchem.3c04762
Cancer Treat Res. 2023 ;190 3-24

RNA Modifications in Cancer Metabolism and Tumor Microenvironment.

Ying Qing, Dong Wu, Xiaolan Deng, Jianjun Chen, Rui Su.

  RNA modifications have recently been recognized as essential posttranscriptional regulators of gene expression in eukaryotes. Investigations over the past decade have revealed that RNA chemical modifications have profound effects on tumor initiation, progression, refractory, and recurrence. Tumor cells are notorious for their robust plasticity in response to the stressful microenvironment and undergo metabolic adaptations to sustain rapid cell proliferation, which is termed as metabolic reprogramming. Meanwhile, cancer-associated metabolic reprogramming leads to substantial alterations of intracellular and extracellular metabolites, which further reshapes the tumor microenvironment (TME). Moreover, cancer cells compete with tumor-infiltrating immune cells for the limited nutrients to maintain their proliferation and function in the TME. In this chapter, we review recent interesting findings on the engagement of epitranscriptomic pathways, especially the ones associated with N6-methyladenosine (m6A), in the regulation of cancer metabolism and the surrounding microenvironment. We also discuss the promising therapeutic approaches targeting RNA modifications for anti-tumor therapy.

Keywords:  Aerobic glycolysis; Amino acid metabolism; Cancer metabolism; Immune cells; Immunotherapy; Lipid metabolism; RNA modification; Tumor microenvironment; m6A

DOI:  https://doi.org/10.1007/978-3-031-45654-1_1
Mol Cell Probes. 2023 Dec 18. pii: S0890-8508(23)00057-9. [Epub ahead of print] 101948

Pancancer analysis uncovers an immunological role and prognostic value of the m6A reader IGF2BP2 in pancreatic cancer.

Hui Deng, Hanming Yao, Shurui Zhou, Chong He, Yuzhou Huang, Yunlong Li, Hanwei Chen, Jianchang Shu.

   INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant gastrointestinal tumors worldwide with a dismal prognosis and high relapse rate. PDAC is considered a "cold cancer" for which immunotherapy is not effective. Therefore, to improve the prognosis for PDAC patients, it is urgent to explore the mechanism driving its insensitivity to immunotherapy.
MATERIALS AND METHODS: We conducted pancancer analyses to test IGF2BP family expression and survival in patients with different cancers via TCGA and GETx databases. Then, we determined the immunological role and prognostic value of IGF2BP2 in vitro, in vivo and in clinical specimens.
RESULTS: In the present study, we found that the m6A reader IGF2BP2 was the most clinically relevant member of the IGF2BP family for pancreatic cancer. High expression of IGF2BP2 was most associated with poor prognosis and an immunosuppressive microenvironment in PDAC. By IGF2BP2 knockdown, we found that tumor cell proliferation and invasive ability were significantly diminished. Importantly, we found that IGF2BP2 expression was closely associated with high expression of immunosuppressive molecules such as PD-L1. IGF2BP2 modulated downstream PD-L1 expression by regulating its mRNA stability via m6A methylation control, and we obtained the same verification in animal experiments and human tissue specimens.
CONCLUSION: Our study contributes to existing knowledge regarding the IGF2BP2-regulated PD-L1 signaling pathway as a potential prognostic and immune biomarker in pancreatic cancer.

Keywords:  IGF2BP2; PD-L1; Pan-cancer analysis; Pancreatic cancer; Tumor immunity

DOI:  https://doi.org/10.1016/j.mcp.2023.101948
Epigenomics. 2023 Dec 21.

METTL3 promotes non-small-cell lung cancer growth and metastasis by inhibiting FDX1 through copper death-associated pri-miR-21-5p maturation.

Shuai Qian, Jun Liu, Wenliang Liao, Fengping Wang.

  Objective: We probed into the significance of METTL3 in the maturation process of pri-miR-21-5p. We specifically investigated its impact on the regulation of FDX1 and its involvement in the progression of non-small-cell lung cancer (NSCLC). Methods: The Cancer Genome Atlas (TCGA) identified NSCLC factors. Methylation-specific PCR (MSP), clonogenic tests and flow cytometry analyzed cells. Methylated RNA immunoprecipitation (Me-RIP) and dual-luciferase studied miR-21-5p/FDX1. Mice xenografts showed METTL3's tumorigenic effect. Results: METTL3, with high expression but low methylation in NSCLC, influenced cell behaviors. Its suppression reduced oncogenic properties. METTL3 enhanced miR-21-5p maturation, targeting FDX1 and boosting NSCLC tumorigenicity in mice. Conclusion: METTL3 may promote NSCLC development by facilitating pri-miR-21-5p maturation, upregulating miR-21-5p and targeting inhibition of FDX1.

Keywords:  DNA methylation; FDX1; METTL3; NSCLC; m6A methylation transferase; m6A modification; miR-21-5p; pri-miR-21-5p

DOI:  https://doi.org/10.2217/epi-2023-0230
J Agric Food Chem. 2023 Dec 19.

Role of RNA Modifications, Especially m6A, in Aflatoxin Biosynthesis of Aspergillus flavus.

Chi Yang, Dandan Wu, Hong Lin, Dongmei Ma, Wangzhuo Fu, Yanfang Yao, Xiaohua Pan, Shihua Wang, Zhenhong Zhuang.

  RNA modifications play key roles in eukaryotes, but the functions in Aspergillus flavus are still unknown. Temperature has been reported previously to be a critical environmental factor that regulates the aflatoxin production of A. flavus, but much remains to be learned about the molecular networks. Here, we demonstrated that 12 kinds of RNA modifications in A. flavus were significantly changed under 29 °C compared to 37 °C incubation; among them, m6A was further verified by a colorimetric method. Then, the transcriptome-wide m6A methylome and m6A-altered genes were comprehensively illuminated through methylated RNA immunoprecipitation sequencing and RNA sequencing, from which 22 differentially methylated and expressed transcripts under 29 °C were screened out. It is especially notable that AFCA_009549, an aflatoxin biosynthetic pathway gene (aflQ), and the m6A methylation of its 332nd adenine in the mRNA significantly affect aflatoxin biosynthesis in A. flavus both on media and crop kernels. The content of sterigmatocystin in both ΔaflQ and aflQA332C strains was significantly higher than that in the WT strain. Together, these findings reveal that RNA modifications are associated with secondary metabolite biosynthesis of A. flavus.

Keywords:  Aspergillus flavus; RNA modifications; aflQ; aflatoxin; m6A; temperature

DOI:  https://doi.org/10.1021/acs.jafc.3c05926
Funct Integr Genomics. 2023 Dec 15. 24(1): 4

IGF2BP1 facilitates non-small cell lung cancer progression by regulating the KIF2A-mediated Wnt/β-catenin pathway.

Ming Sun, Ling Wang, Lei Ge, Daojun Xu, Renquan Zhang.

  Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are crucially implicated in the cancer progression. The current study intends to excavate and clarify the mechanisms of the key IGF2BPs in non-small cell lung cancer (NSCLC). The expression of IGF2BPs and kinesin family member 2A (KIF2A) was examined using immunohistochemistry, real-time quantitative polymerase chain reaction, and western blot in NSCLC tissue samples or cell lines. NSCLC cell viability was examined using a cell counting kit-8 assay. Cell apoptotic rate was assessed using flow cytometry analysis. The migration and invasion of H1299 cells were subject to scratch test and Transwell assays, respectively. Starbase 2.0 was used to detect the downstream factors of the IGF2BP1 protein. The binding of IGF2BP with KIF2A was detected using RNA binding protein immunoprecipitation assays. Ki-67 immunohistochemistry assay and TUNEL assays were applied for the evaluation of proliferation and apoptosis in vivo, respectively. IGF2BP1 was upregulated in NSCLC tissue samples and cells. Functionally, IGF2BP1 overexpression promoted the proliferative ability, migration, and invasiveness of H1299 cells, while inhibiting cell apoptosis in vitro. In vivo studies revealed that overexpression of IGF2BP1 promoted tumor growth of NSCLC. Mechanistically, IGF2BP1 was involved in KIF2A mRNA stabilization. KIF2A exerted the same functions as IGF2BP1 via the Wnt/β-catenin signaling. In conclusion, IGF2BP1 enhances NSCLC malignant progression by stabilizing KIF2A to modulate the Wnt/β-catenin pathway.

Keywords:  Gene regulation; IGF2BP; Non-small cell lung cancer; Wnt/β-catenin signaling pathway

DOI:  https://doi.org/10.1007/s10142-023-01275-x
Wiley Interdiscip Rev RNA. 2023 Dec 19. e1829

RNA m6A modifications regulate crosstalk between tumor metabolism and immunity.

Jinghua Gu, Huake Cao, Xiaoli Chen, Xu Dong Zhang, Rick F Thorne, Xiaoying Liu.

  In recent years, m6A modifications in RNA transcripts have arisen as a hot topic in cancer research. Indeed, a number of independent studies have elaborated that the m6A modification impacts the behavior of tumor cells and tumor-infiltrating immune cells, altering tumor cell metabolism along with the differentiation and functional activity of immune cells. This review elaborates on the links between RNA m6A modifications, tumor cell metabolism, and immune cell behavior, discussing this topic from the viewpoint of reciprocal regulation through "RNA m6A-tumor cell metabolism-immune cell behavior" and "RNA m6A-immune cell behavior-tumor cell metabolism" axes. In addition, we discuss the various factors affecting RNA m6A modifications in the tumor microenvironment, particularly the effects of hypoxia associated with cancer cell metabolism along with immune cell-secreted cytokines. Our analysis proposes the conclusion that RNA m6A modifications support widespread interactions between tumor metabolism and tumor immunity. With the current viewpoint that long-term cancer control must tackle cancer cell malignant behavior while strengthening anti-tumor immunity, the recognition of RNA m6A modifications as a key factor provides a new direction for the targeted therapy of tumors. This article is categorized under: RNA Processing > RNA Editing and Modification RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Keywords:  RNA; immunity; m6A; metabolism; tumor microenvironment

DOI:  https://doi.org/10.1002/wrna.1829
Cell Commun Signal. 2023 Dec 18. 21(1): 359

Non-coding RNA methylation modifications in hepatocellular carcinoma: interactions and potential implications.

Qingmiao Shi, Qingfei Chu, Yifan Zeng, Xin Yuan, Jinzhi Wang, Yaqi Zhang, Chen Xue, Lanjuan Li.

  RNA methylation modification plays a crucial role as an epigenetic regulator in the oncogenesis of hepatocellular carcinoma (HCC). Numerous studies have investigated the molecular mechanisms underlying the methylation of protein-coding RNAs in the progression of HCC. Beyond their impact on mRNA, methylation modifications also influence the biological functions of non-coding RNAs (ncRNAs). Here, we present an advanced and comprehensive overview of the interplay between methylation modifications and ncRNAs in HCC, with a specific focus on their potential implications for the tumor immune microenvironment. Moreover, we summarize promising therapeutic targets for HCC based on methylation-related proteins. In the future, a more profound investigation is warranted to elucidate the effects of ncRNA methylation modifications on HCC pathogenesis and devise valuable intervention strategies. Video Abstract.

Keywords:  HCC; m1A; m5C; m6A; ncRNA

DOI:  https://doi.org/10.1186/s12964-023-01357-0
Nucleic Acids Res. 2023 Dec 20. pii: gkad1193. [Epub ahead of print]

Histone lactylation-boosted ALKBH3 potentiates tumor progression and diminished promyelocytic leukemia protein nuclear condensates by m1A demethylation of SP100A.

Xiang Gu, Ai Zhuang, Jie Yu, Ludi Yang, Shengfang Ge, Jing Ruan, Renbing Jia, Xianqun Fan, Peiwei Chai.

Albeit N1-Methyladenosine (m1A) RNA modification represents an important regulator of RNA metabolism, the role of m1A modification in carcinogenesis remains enigmatic. Herein, we found that histone lactylation enhances ALKBH3 expression and simultaneously attenuates the formation of tumor-suppressive promyelocytic leukemia protein (PML) condensates by removing the m1A methylation of SP100A, promoting the malignant transformation of cancers. First, ALKBH3 is specifically upregulated in high-risk ocular melanoma due to excessive histone lactylation levels, referring to m1A hypomethylation status. Moreover, the multiomics analysis subsequently identified that SP100A, a core component for PML bodies, serves as a downstream candidate target for ALKBH3. Therapeutically, the silencing of ALKBH3 exhibits efficient therapeutic efficacy in melanoma both in vitro and in vivo, which could be reversed by the depletion of SP100A. Mechanistically, we found that YTHDF1 is responsible for recognition of the m1A methylated SP100A transcript, which increases its RNA stability and translational efficacy. Conclusively, we initially demonstrated that m1A modification is necessary for tumor suppressor gene expression, expanding the current understandings of dynamic m1A function during tumor progression. In addition, our results indicate that lactylation-driven ALKBH3 is essential for the formation of PML nuclear condensates, which bridges our knowledge of m1A modification, metabolic reprogramming, and phase-separation events.

DOI: https://doi.org/10.1093/nar/gkad1193
Front Endocrinol (Lausanne). 2023 ;14 1275612

Single-cell profiling reveals transcriptomic signatures of vascular endothelial cells in non-healing diabetic foot ulcers.

Yangzhou Lu, Xiaogang Liu, Jingling Zhao, Fan Bie, Yiling Liu, Julin Xie, Peng Wang, Junyou Zhu, Yahui Xiong, Shitian Qin, Fan Yang, Lei Chen, Yingbin Xu.

   Background: The treatment of diabetic foot ulcers (DFUs) poses a challenging medical problem that has long plagued individuals with diabetes. Clinically, wounds that fail to heal for more than 12 weeks after the formation of DFUs are referred to as non-healing/chronic wounds. Among various factors contributing to the non-healing of DFUs, the impairment of skin microvascular endothelial cell function caused by high glucose plays a crucial role. Our study aimed to reveal the transcriptomic signatures of non-healing DFUs endothelial cells, providing novel intervention targets for treatment strategies.
Methods: Based on the GEO dataset (GSE165816), we selected DFU-Healer, DFU-Non-healer, and healthy non-diabetic controls as research subjects. Single-cell RNA transcriptomic sequencing technology was employed to analyze the heterogeneity of endothelial cells in different skin tissue samples and identify healing-related endothelial cell subpopulations. Immunofluorescence was applied to validate the sequencing results on clinical specimens.
Results: The number of endothelial cells and vascular density showed no significant differences among the three groups of skin specimens. However, endothelial cells from non-healing DFUs exhibited apparent inhibition of angiogenesis, inflammation, and immune-related signaling pathways. The expression of CCND1, ENO1, HIF1α, and SERPINE1 was significantly downregulated at the transcriptomic and histological levels. Further analysis demonstrated that healing-related endothelial cell subpopulations in non-healing DFUs has limited connection with other cell types and weaker differentiation ability.
Conclusion: At the single-cell level, we uncovered the molecular and functional specificity of endothelial cells in non-healing DFUs and highlighted the importance of endothelial cell immune-mediated capability in angiogenesis and wound healing. This provides new insights for the treatment of DFUs.

Keywords:  angiogenesis; diabetic foot ulcers; immune; inflammation; non-healing wounds; single-cell RNA sequencing; vascular endothelial cell

DOI:  https://doi.org/10.3389/fendo.2023.1275612
Front Immunol. 2023 ;14 1326509

Overexpression of MTHFD2 represents an inflamed tumor microenvironment and precisely predicts the molecular subtype and immunotherapy response of bladder cancer.

Xiaokai Shi, Xiangrong Peng, Yin Chen, Zebin Shi, Chuang Yue, Li Zuo, Lifeng Zhang, Shenglin Gao.

   Introduction: Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), whose aberrant expression is common in cancers, has recently been identified as a potential regulator of immune response. However, its immune-related role in bladder cancer (BLCA) and its association with immunotherapy efficacy remain unclear.
Methods: RNA sequencing data from The Cancer Genome Atlas (TCGA) was applied to analyze the immunological roles and prognostic value of MTHFD2 in pan-cancers. The association of MTHFD2 with several immunological features of tumor microenvironment (TME), including cancer-immunity cycle, immune cells infiltration, immune checkpoints expression, and T cell inflamed score was analyzed in TCGA-BLCA cohort. The predictors of cancer treatments effectiveness, including the expression and mutation of certain genes, molecular subtypes, and several signatures were evaluated as well. These results were validated by another independent cohort (GSE48075). Finally, the predictive value of MTHFD2 for TME and immunotherapy efficacy were validated using immunohistochemistry assay and RNA sequencing data from IMvigor210 cohort, respectively.
Results: MTHFD2 was found to be positively associated with several immunological features of an inflamed tumor microenvironment (TME) in various cancers and could predict BLCA patients' prognosis. In BLCA, high expression of MTHFD2 was observed to be positively related with the cancer-immunity cycle, the infiltration of several immune cells, and the expression of immunoregulators and T-cell inflamed scores, indicating a positive correlation with the inflamed TME. Moreover, patients with high MTHFD2 expression were more likely to be basal-like subtypes and respond to BLCA treatments, including immunotherapy, chemotherapy, and target therapy. The clinical data of the IMvigor210 cohort confirmed the higher response rates and better survival benefits of immunotherapy in high-MTHFD2-expression patients.
Conclusion: Collectively, high MTHFD2 predicts an inflamed TME, a basal-like subtype, and a better response to various therapeutic strategies, especially the ICB therapy, in bladder cancer.

Keywords:  MTHFD2; bladder cancer; immunotherapy; inflamed tumor microenvironment; molecular subtype

DOI:  https://doi.org/10.3389/fimmu.2023.1326509
Cell Signal. 2023 Dec 16. pii: S0898-6568(23)00433-3. [Epub ahead of print] 111018

The impact of LncRNA-SOX2-OT/let-7c-3p/SKP2 Axis on head and neck squamous cell carcinoma progression: Insights from bioinformatics analysis and experimental validation.

Di Wang, Xue Zhao, Shuang Li, Haixian Guo, Shaonan Li, Dan Yu.

   BACKGROUND: LncRNA SRY-box transcription factor 2 overlapping transcript (SOX2-OT) is linked to multiple cancers, but its specific role and mechanism in head and neck squamous cell carcinoma (HNSCC) remain poorly understood.
METHODS: We harnessed clinical data and HNSCC transcriptome profiles from UCSC Xena, TCGA, and GEO databases. Employing various algorithms, we assessed the correlation between SOX2-OT expression and the HNSCC immune microenvironment. Differential expression analysis identified immune-enriched miRNAs (DEmiRNAs) and mRNAs (DEmRNAs). Utilizing miRanda, miRWalk, and Cytoscape, we constructed a ceRNA network encompassing SOX2-OT, DEmiRNAs, and DEmRNAs. A Sankey diagram visualized pivotal SOX2-OT-miRNA-mRNA-pathways. Functional assays validated SOX2-OT silencing effects in HNSCC cells. Luciferase reporter assays verified SOX2-OT/let-7c-3p/SKP2 relationships. Additionally, a xenograft mouse model revealed SOX2-OT's impact on xenograft growth and lung metastasis.
RESULTS: SOX2-OT expression demonstrated a predominantly positive correlation with B lineage and VTCN1, while manifesting a negative correlation with Neutrophil and CD47 in HNSCC tissues. We discerned a ceRNA network comprising 65 DEmiRNAs and 116 DEmRNAs, while a protein-protein interaction (PPI) network revealed 97 protein nodes among DEmRNAs. Notably, the Sankey diagram spotlighted six key DEmRNAs intricately linked to the SOX2-OT-regulated DEmiRNAs immune-related pathway. Experimental assays established that SOX2-OT silencing exerted inhibitory effects on cell proliferation, migration, tumor growth, and lung metastasis within HNSCC cells, both in vitro and in vivo. We identified let-7c-3p as a target miRNA of SOX2-OT and SKP2 as a target mRNA of let-7c-3p.
CONCLUSIONS: Our study establishes the critical SOX2-OT/let-7c-3p/SKP2 axis as a pivotal regulator of HNSCC tumorigenesis and metastasis.

Keywords:  Head and neck squamous cell carcinoma; Immune; Informatics analysis; Prognosis; SOX2-OT; ceRNA

DOI:  https://doi.org/10.1016/j.cellsig.2023.111018
Cell Signal. 2023 Dec 16. pii: S0898-6568(23)00429-1. [Epub ahead of print] 111014

Neutrophil extracellular traps promote gastric cancer cell metastasis via the NAT10-mediated N4-acetylcytidine modification of SMYD2.

Donghui Liu, Xiaoyao Yang, Xuyao Wang.

  It has been reported that the formation of neutrophil extracellular traps (NETs) is associated with cancer metastasis. The current study aimed to explore the effects of NETs on gastric cancer (GC) cell metastasis and uncover their underlying mechanism. NETs were measured in the plasma of patients with GC. Then, GC cells were treated with NETs to assess cell viability, migration, and invasion using cell counting kit 8 and Transwell assay, The liver metastasis and xenograft tumor mouse models were established to assess tumor growth and metastasis. The N4-acetylcytidine (ac4C) modification of SET and MYND domain containing 2 (SMYD2) mediated by NAT10 was evaluated using acetylated RNA immunoprecipitation. The results showed that the level of NETs was increased in the plasma of patients with GC, particularly in those with metastatic GC. In addition, GC cell co-treatment with NETs promoted cell viability, migration and invasion, while NAT10 or SMYD2 knockdown abrogated this effect. NAT10 also promoted the ac4C modification of SMYD2, thus increasing SMYD2 stability. Furthermore, NETs promoted the metastasis of GC cells in the liver in vivo. Overall, the results of the present study demonstrated that NETs promoted GC cell metastasis via the NAT10-mediated ac4C modification of SMYD2. These findings suggested that inhibiting the formation of NETs could be an effective approach for attenuating GC progression.

Keywords:  Gastric cancer; Metastasis; NAT10; Neutrophil extracellular traps; SMYD2; ac(4)C acetylation

DOI:  https://doi.org/10.1016/j.cellsig.2023.111014