bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2023–12–31
53 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics
  1. METTL3 suppresses invasion of lung cancer via SH3BP5 m6A modification.
  2. N6-methyladenosine promotes aberrant redox homeostasis required for arsenic carcinogenesis by controlling the adaptation of key antioxidant enzymes.
  3. Potential role of N6-methyladenosine modification in the development of Parkinson's disease.
  4. Aging-Associated ALKBH5-m6A Modification Exacerbates Doxorubicin-Induced Cardiomyocyte Apoptosis Via AT-Rich Interaction Domain 2.
  5. Decoding the role of m6A Regulators in identifying and characterizing molecular subtypes of rosacea.
  6. METTL3/YTHDF1 m6A axis promotes tumorigenesis by enhancing DDR2 expression in ovarian cancer.
  7. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells.
  8. METTL3-mediated m6A RNA methylation was involved in aluminum-induced neurotoxicity.
  9. The PIN1-YTHDF1 axis promotes breast tumorigenesis via the m6A-dependent stabilization of AURKA mRNA.
  10. YTHDF2-mediated regulations bifurcate BHPF-induced programmed cell deaths.
  11. RNA m6A methylation in psychiatric disorders.
  12. Comprehensive analysis of m6A modification patterns and m6A-related lncRNAs as potential biomarkers in lung adenocarcinoma.
  13. The role of N6-methyladenosine methyltransferase RBM15 in non-alcoholic fatty liver disease.
  14. YTHDF2 alleviates microglia activation via promoting circHIPK2 degradation.
  15. Epigenetic targeting of autophagy for cancer: DNA and RNA methylation.
  16. Significance of m6A in subtype identification, immunological evolution, and therapeutic sensitivity of RA.
  17. METTL14 promotes IL-6-induced viability, glycolysis and inflammation in HaCaT cells via the m6A modification of TRIM27.
  18. Identification of a novel signature based on M6a modification regulators related LncRNA for stratification of the prognosis of prostate cancer.
  19. Molecular mechanism of Wilms tumor 1-associated protein in diabetes-related dry eye disease by mediating m6A methylation modification of lncRNA NEAT1.
  20. Exploring urinary modified nucleosides as biomarkers for diabetic retinopathy: Development and validation of a ultra performance liquid chromatography-tandem mass spectrometry method.
  21. ALKHB5-demethylated lncRNA SNHG15 promotes myeloma tumorigenicity by increasing chromatin accessibility and recruiting H3K36me3 modifier SETD2.
  22. Determination of dimethylated nucleosides in serum from colorectal cancer patients by hydrophilic interaction liquid chromatography-tandem mass spectrometry.
  23. dTrmt10A impacts Hsp70 chaperone m6A levels and the stress response in the Drosophila brain.
  24. FTO demethylates regulates cell-cycle progression by controlling CCND1 expression in luteinizing goat granulosa cells.
  25. Demethylase FTO inhibits the occurrence and development of triple-negative breast cancer by blocking m 6A-dependent miR-17-5p maturation-induced ZBTB4 depletion.
  26. Active Fraction of Polyrhachis Vicina Roger (AFPR) Ameliorate Depression Induced Inflammation Response by FTO/miR-221-3p/SOCS1 Axis.
  27. High CTCF expression mediated by FGD5-AS1/miR-19a-3p axis is associated with immunosuppression and pancreatic cancer progression.
  28. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery.
  29. Botrytis cinerea-induced F-box protein 1 enhances disease resistance by inhibiting JAO/JOX-mediated jasmonic acid catabolism in Arabidopsis.
  30. Single-cell Transcriptomic Analysis Reveals an Immunosuppressive Network Between POSTN CAFs and ACKR1 ECs in TKI-resistant Lung Cancer.
  31. TICRR serves as a prognostic biomarker in lung adenocarcinoma with implications in RNA epigenetic modification, DDR pathway, and RNA metabolism.
  32. Ezrin inhibition alleviates oxidative stress and pyroptosis via regulating TRPML1-calcineurin axis mediated enhancement of autophagy in spinal cord injury.
  33. Downregulation of Sirt3 contributes to β-cell dedifferentiation via FoxO1 in type 2 diabetic mellitus.
  34. Hypoxia induced cell dormancy of salivary adenoid cystic carcinoma through miR-922/DEC2 axis.
  35. Ultrasound-responsive spherical nucleic acid against c-Myc/PD-L1 to enhance anti-tumoral macrophages in triple-negative breast cancer progression.
  36. COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes.
  37. GNL3L promotes autophagy via regulating AMPK signaling in esophageal cancer cells.
  38. LncNFYB promotes the proliferation of rheumatoid arthritis fibroblast-like synoviocytes via LncNFYB/ANXA2/ERK1/2 axis.
  39. COX19 is a new target of MACC1 and promotes colorectal cancer progression by regulating copper transport in mitochondria.
  40. Deciphering the Hypoxia-immune interface in esophageal squamous carcinoma: a prognostic network model.
  41. The lncRNA FENDRR inhibits colorectal cancer progression via interacting with and triggering GSTP1 ubiquitination by FBX8.
  42. Demethylation-activated light-up dual-color RNA aptamersensor for label-free detection of multiple demethylases in lung tissues.
  43. Cellular RNA and DNA sensing pathways are essential for the dose-dependent response of human monocytes to ionizing radiation.
  44. Irisin mitigates rheumatoid arthritis by suppressing mitochondrial fission via inhibiting YAP-Drp1 signaling pathway.
  45. Depletion of DNTTIP2 Induces Cell Cycle Arrest in Pancreatic Cancer Cells.
  46. ASCC3 promotes the immunosuppression and progression of non-small cell lung cancer by impairing the type I interferon response via CAND1-mediated ubiquitination inhibition of STAT3.
  47. Assessment of the Response of Human Umbilical Vein Endothelial Cells to Photodynamic Therapy: Highlighting the Role of Il-17 Signaling Pathway.
  48. Parkin enhances sensitivity of paclitaxel to nasopharyngeal carcinoma by activating BNIP3/NIX-mediated mitochondrial autophagy.
  49. MeCP2-Induced Alternations of Transcript Levels and m6A Methylation in Human Retinal Pigment Epithelium Cells.
  50. Prognostic significance of senescence related tumor microenvironment genes in head and neck squamous cell carcinoma.
  51. Association Between Clinicopathological Parameters and S100A8/A9 Expression According to Smoking History in Patients With Non-small Cell Lung Cancer.
  52. Methylation and transcriptomic expression profiles of HUVEC in the oxygen and glucose deprivation model and its clinical implications in AMI patients.
  53. PrLZ regulates EMT and invasion in prostate cancer via the TGF-β1/p-smad2/miR-200 family/ZEB1 axis.
  1. Arch Biochem Biophys. 2023 Dec 21. pii: S0003-9861(23)00375-2. [Epub ahead of print] 109876
    METTL3 suppresses invasion of lung cancer via SH3BP5 m6A modification.
    Binbin Zhang, Rulin Qian, Xiangnan Li.
      The metastasis of lung cancer poses a major clinical challenge, and m6A modification has been implicated in regulating the invasive capabilities of tumor cells. However, the mechanisms underlying m6A modification in lung cancer metastasis are not well understood. This study aims to explore the biological functions and molecular mechanisms of methyltransferase-like 3 (METTL3) in lung cancer. In this study, METTL3 were found to be downregulated in lung cancer tissues. Functionally, METTL3 inhibited the migration and invasion abilities of lung cancer cells in vitro. Furthermore, SH3 domain binding protein 5 (SH3BP5) was identified as a downstream target of METTL3. Overexpression of SH3BP5 suppressed the invasive capacity of lung cancer cells, and this regulation was m6A-dependent. Finally, we discovered that YTH N6-methyladenosine RNA binding protein F1 (YTHDF1) mediated stability is responsible for maintaining the m6A modification of SH3BP5 mRNA. Overall, our study provides insights into the critical role of METTL3-mediated m6A modification and m6A-dependent regulatory mechanisms in the progression of human lung cancer. We demonstrated that METTL3 regulates the mRNA stability of SH3BP5 in a YTHDF1-dependent manner, thereby impacting the invasive capacity of lung cancer cells.
    Keywords:  Cell invasion; Lung cancer; METTL3; SH3BP5; m6A modification
    DOI:  https://doi.org/10.1016/j.abb.2023.109876
  2. J Hazard Mater. 2023 Dec 22. pii: S0304-3894(23)02613-4. [Epub ahead of print]465 133329
    N6-methyladenosine promotes aberrant redox homeostasis required for arsenic carcinogenesis by controlling the adaptation of key antioxidant enzymes.
    Tianhe Zhao, Donglei Sun, Keyan Long, Wenxiao Xiong, Jin Man, Qian Zhang, Zunzhen Zhang.
      N6-methyladenosine (m6A), a high-profile RNA epigenetic modification, responds to oxidative stress and temporal-specifically mediates arsenic carcinogenesis. However, how m6A affects aberrant redox homeostasis required for arsenic carcinogenesis is poorly understood. Here, we established arsenic-carcinogenic models of different stages, including As-treated, As-transformed, and As-tumorigenic cell models. We found that arsenic-induced reactive oxygen species (ROS) elevated m6A levels, thus triggering m6A-dependent antioxidant defenses. During arsenic-induced cell transformation, METTL3-upregulated m6A on the mRNAs of SOD1, SOD2, CAT, TXN, and GPX1 promoted the mRNA translation and protein expressions of these antioxidant enzymes by increasing YTHDF1-mediated mRNA stability. Meanwhile, FTO-downregulated m6A on PRDX5 mRNA increased PRDX5 translation and expression by reducing YTHDF2-mediated mRNA decay. After upregulated antioxidant defenses balanced with high levels of ROS induced by arsenic, the m6A balance formed in mRNAs of six key antioxidant enzymes (SOD1, SOD2, CAT, TXN, GPX1, and PRDX5) and promoted high expressions of these antioxidant enzymes to maintain aberrant redox homeostasis. METTL3 inhibitor STM2457, FTO inhibitor FB23-2, or YTHDF1 knockdown disturbed the aberrant redox homeostasis by breaking the m6A balance, causing cell death in arsenic-induced tumors. Our results demonstrated that m6A promotes the formation and maintenance of aberrant redox homeostasis required for arsenic carcinogenesis by time-dependently orchestrating the adaptive expressions of six key m6A-targeted antioxidant enzymes. This study advances our understanding of arsenic carcinogenicity from the novel aspect of m6A-dependent adaptation to arsenic-induced oxidative stress.
    Keywords:  Antioxidant defenses; Arsenite; Carcinogen; Harmful heavy metal; M(6)A; Oxidative stress
    DOI:  https://doi.org/10.1016/j.jhazmat.2023.133329
  3. Front Cell Dev Biol. 2023 ;11 1321995
    Potential role of N6-methyladenosine modification in the development of Parkinson's disease.
    Jiale Zhou, Yang Han, Ruizhe Hou.
      N6-methyladenosine (m6A) represents the most abundant modification of messenger RNA (mRNA) and is regulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). A dynamic modification process is implicated in nearly every critical stage of RNA metabolism, including mRNA stability, transcription, translation, splicing, nuclear export, and decay. Notably, m6A methylation is significantly enriched in the brain and has recently been shown to be associated with neurodevelopmental disorders and the development of Parkinson's disease (PD). In this review, we summarize the proteins involved in the process of m6A modification and elucidate the emerging role of m6A modification in PD, which could illuminate alternative strategies for the prevention and treatment of PD.
    Keywords:  N6-methylAdenosine (m6A); Neurological disease; RNA methylation; epigenetics; methyltransferase; neurodevelopment
    DOI:  https://doi.org/10.3389/fcell.2023.1321995
  4. J Am Heart Assoc. 2023 Dec 29. e031353
    Aging-Associated ALKBH5-m6A Modification Exacerbates Doxorubicin-Induced Cardiomyocyte Apoptosis Via AT-Rich Interaction Domain 2.
    Runtai Chen, Guogang Zhang, Kun Sun, Alex F Chen.
       BACKGROUND: Chemotherapy-induced cardiovascular disease is a growing concern in the elderly population who have survived cancer, yet the underlying mechanism remains poorly understood. We investigated the role of ALKBH5 (AlkB homolog 5), a primary N6-methyladenosine (m6A) demethylase, and its involvement in m6A methylation-mediated regulation of targets in aging-associated doxorubicin-induced cardiotoxicity.
    METHODS AND RESULTS: To validate the relationship between doxorubicin-induced cardiotoxicity and aging, we established young and old male mouse models. ALKBH5 expression was modulated through adeno-associated virus 9 (in vivo), Lentivirus, and siRNAs (in vitro) to examine its impact on cardiomyocyte m6A modification, doxorubicin-induced cardiac dysfunction, and remodeling. We performed mRNA sequencing, methylated RNA immunoprecipitation sequencing, and molecular assays to unravel the mechanism of ALKBH5-m6A modification in doxorubicin-induced cardiotoxicity. Our data revealed an age-dependent increase in doxorubicin-induced cardiac dysfunction, remodeling, and injury. ALKBH5 expression was elevated in aging mouse hearts, leading to reduced global m6A modification levels. Through mRNA sequencing and methylated RNA immunoprecipitation sequencing analyses, we identified ARID2 (AT-rich interaction domain 2) as the downstream effector of ALKBH5-m6A modulation in cardiomyocytes. Further investigations revealed that ARID2 modulates DNA damage response and enhances doxorubicin-induced cardiomyocyte apoptosis.
    CONCLUSIONS: Our findings provide insights into the role of ALKBH5-m6A modification in modulating doxorubicin-induced cardiac dysfunction, remodeling, and cardiomyocyte apoptosis in male mice. These results highlight the potential of ALKBH5-targeted treatments for elderly patients with cancer in clinical settings.
    Keywords:  ALKBH5; aging; cardiotoxicity; doxorubicin; m6A
    DOI:  https://doi.org/10.1161/JAHA.123.031353
  5. Heliyon. 2023 Dec;9(12): e23310
    Decoding the role of m6A Regulators in identifying and characterizing molecular subtypes of rosacea.
    Shuping Zhang, Meng Wu, Wenbo Xue.
      Rosacea is a common skin disease that predominantly affects individuals aged between 30 and 50 years. While the exact cause of the disease remains unclear, various factors have been shown to trigger or exacerbate its symptoms. N6-methyladenosine (m6A) modification is one of the most abundant epigenetic methylation modification in messenger RNA (mRNA) and non-coding RNA (ncRNA), plays a crucial role in RNA splicing, export, stability, and translation. In this study, we aimed to characterize m6A genes in rosacea, identify molecular subtypes based on m6A gene expression, characterize the immune features among subtypes, explore key molecules based on co-expression analysis, and identify potential targets and drugs. To achieve our objectives, we first compared the expression pattern and immune regulation of m6A genes between healthy and diseased groups. Then, we performed clustering to stratify disease samples into different subtypes and analyzed immune regulation and functional enrichment among the subtypes. Then, we conducted differential analysis between subtypes and applied weighted gene co-expression network analysis (WGCNA) in three subtypes. We found hub differential expression analysis (DEG) genes and their potential drug based on the WGCNA results and the drug-gene interaction database (DGIdb). Finally, in vivo and in vitro studies showed significant differences in m6A methyltransferase METTL3 levels in rosacea mice and control mice, as well as in the skin of rosacea patients and healthy people, while reducing METTL3 significantly inhibited the inflammatory response of human fibroblasts (HDFs) stimulated by LL37, suggesting that METTL3 may be associated with changes in overall m6A levels in rosacea. Taken together, our findings provide valuable insights into therapeutic targets and drug predictions for rosacea.
    Keywords:  Rosacea; Subtypes; WGCNA; m6A
    DOI:  https://doi.org/10.1016/j.heliyon.2023.e23310
  6. Pathol Res Pract. 2023 Dec 21. pii: S0344-0338(23)00748-3. [Epub ahead of print]253 155047
    METTL3/YTHDF1 m6A axis promotes tumorigenesis by enhancing DDR2 expression in ovarian cancer.
    Duo Zhi, Kun Zhou, Shuang Liu, Wen Yu, Mei Dong, Caichuan Yan.
      Ovarian cancer has the highest mortality among all gynecological malignancies. Therefore, it is urgent to determine the molecular mechanism of ovarian cancer progression. As the most prevalent modification of messenger RNA (mRNA), N6-Methyladenosine (m6A) modification is recognized as a key regulatory role in the progression of various tumors. However, the specific role of m6A and its related regulatory pathways in ovarian cancer (OV) remains unclear. In this study, we demonstrated that the METTL3/YTHDF1 m6A axis plays an important role in the progression of ovarian cancer. Depletion of METTL3/YTHDF1 impaired cancer proliferation and metastasis in vitro and in vivo. Mechanistically, The METTL3/YTHDF1 m6A axis directly binds to the mRNA of DDR2, thereby promoting the expression levels of the tumor promoter DDR2 and thus contributing to the progression of ovarian cancer. Collectively, our findings on the METTL3/YTHDF1/DDR2 m6A axis provide the insight into the underlying mechanism of ovarian carcinogenesis and highlight potential therapeutic targets for cancer treatment.
    Keywords:  DDR2; METTL3; Ovarian cancer; YTHDF2
    DOI:  https://doi.org/10.1016/j.prp.2023.155047
  7. Epigenetics. 2024 Dec;19(1): 2298058
    N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells.
    Jie Lai, Zhiyong Zhou, Kan Hu, HongLong Yu, Xingyao Su, Xiaoqiang Niu, Huizi Li, Shengxun Mao.
      N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
    Keywords:  M6A methylation; MeRIP-seq; colorectal cancer; drug-resistance
    DOI:  https://doi.org/10.1080/15592294.2023.2298058
  8. Ecotoxicol Environ Saf. 2023 Dec 26. pii: S0147-6513(23)01382-9. [Epub ahead of print]270 115878
    METTL3-mediated m6A RNA methylation was involved in aluminum-induced neurotoxicity.
    Lingling Yang, Liping Chen, Wenxue Li, Yan Zhang, Guangyu Yang, Bing Huang, Yufang Cen, Huiqi Wang, Xueqin Yang, Fangqin Lin, Yaqin Pang, Guangzi Qi.
      Aluminum (Al) exposure has been linked to the development of a variety of neurodegenerative diseases. However, whether m6A RNA methylation participated in Al-induced neurotoxicity remain to be defined. In this study, mice were administrated with aluminum-lactate at dose of 220 mg/kg. bw by gavage for 3 months. Meanwhile, the primary hippocampal neurons were isolated and treated with 0, 50, 100, 150 μM aluminum-lactate, respectively for 7 days. Al exposure caused neuronal shrinkage, decreased Nissl bodies, and increased apoptosis. In accordance, in vitro studies also showed that Al exposure led to neuronal apoptosis in a dose-dependent manner, together with the decline in m6A RNA methylation levels. Moreover, the mRNA expression of Mettl3, Mettl14, Fto, and Ythdf2 were decreased upon Al exposure. Notably, the protein expression of METTL3 was dramatically down-regulated by 42% and 35% in Al-treated mice and neurons, suggesting METTL3 might exert a crucial role in Al-induced neurotoxicity. We next established a mouse model with hippocampus-specific overexpressing of Mettl3 gene to confirm the regulatory role of RNA methylation and found that METTL3 overexpression relieved the neurological injury induced by Al. The integrated MeRIP-seq and RNA-seq analysis elucidated that 631 genes were differentially expressed at both m6A RNA methylation and mRNA expression. Notably, EGFR tyrosine kinase inhibitor resistance, Rap1 signaling pathway, protein digestion and absorption might be involved in Al-induced neurotoxicity. Moreover, VEGFA, Thbs1, and PDGFB might be the central molecules. Collectively, our findings provide the novel sight into the role of m6A RNA methylation in neurodegenerative disease induced by Al.
    Keywords:  Aluminum; M6A RNA methylation; METTL3; Neurotoxicity
    DOI:  https://doi.org/10.1016/j.ecoenv.2023.115878
  9. Arch Pharm Res. 2023 Dec 26.
    The PIN1-YTHDF1 axis promotes breast tumorigenesis via the m6A-dependent stabilization of AURKA mRNA.
    Pratikshya Shrestha, Garam Kim, Hyelim Kang, Poshan Yugal Bhattarai, Hong Seok Choi.
      The post-transcriptional processing of N6-methyladenosine (m6A)-modified mRNA by YTH domain-containing family protein 1 (YTHDF1) plays a crucial role in the regulation of gene expression. Although YTHDF1 expression is frequently upregulated in breast cancer, the regulatory mechanisms for this remain unclear. In this study, we examined the role of peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1) in regulating YTHDF1 stability in breast cancer cells. The WW domain of PIN1 interacted with YTHDF1 in a phosphorylation-dependent manner. Additionally, PIN1 overexpression increased YTHDF1 stability by preventing ubiquitin-dependent proteasomal degradation. Furthermore, using the MS2-tagged RNA pull-down assay, we identified Aurora kinase A (AURKA) mRNA as a bona fide substrate of YTHDF1. PIN1-mediated YTHDF1 stabilization increased the stability of AURKA mRNA in an m6A-dependent manner. Furthermore, YTHDF1 knockout reduced AURKA protein expression levels, resulting in anticancer effects in breast cancer cells, including decreased cell proliferation, cell cycle arrest at the G0/G1 phase, apoptotic cell death, and decreased spheroid formation. The anticancer effects induced by YTHDF1 knockout were reversed by AURKA overexpression. Similarly, the knockout of PIN1 produced comparable anticancer effects to those observed in YTHDF1-knockout cells, and these effects were reversed upon overexpression of YTHDF1. In conclusion, the findings of our study suggest that increased YTHDF1 stability induced by PIN1 promotes breast tumorigenesis via the stabilization of AURKA mRNA. Targeting the PIN1/YTHDF1 axis may represent a novel therapeutic strategy for breast cancer.
    Keywords:  Breast cancer tumorigenesis; Post-transcriptional processing; Protein stability; YTHDF1; mRNA stabilization
    DOI:  https://doi.org/10.1007/s12272-023-01480-z
  10. Natl Sci Rev. 2023 Dec;10(12): nwad227
    YTHDF2-mediated regulations bifurcate BHPF-induced programmed cell deaths.
    Jiebo Lin, Guankai Zhan, Jinfeng Liu, Yasen Maimaitiyiming, Zhiping Deng, Baohua Li, Kunhui Su, Jiafeng Chen, Siqi Sun, Wanlin Zheng, Xianghui Yu, Feng He, Xiaodong Cheng, Lingfang Wang, Bin Shen, Ziqin Yao, Xinquan Yang, Jian Zhang, Wentao He, Hengyu Wu, Hua Naranmandura, Kao-Jung Chang, Junxia Min, Jun Ma, Mikael Björklund, Peng-Fei Xu, Fudi Wang, Chih-Hung Hsu.
      N6-methyladenosine (m6A) is a critical regulator in the fate of RNA, but whether and how m6A executes its functions in different tissues remains largely obscure. Here we report downregulation of a crucial m6A reader, YTHDF2, leading to tissue-specific programmed cell deaths (PCDs) upon fluorene-9-bisphenol (BHPF) exposure. Currently, Bisphenol A (BPA) substitutes are widely used in plastic manufacturing. Interrogating eight common BPA substitutes, we detected BHPF in 14% serum samples of pregnant participants. In a zebrafish model, BHPF caused tissue-specific PCDs triggering cardiac and vascular defects. Mechanistically, BHPF-mediated downregulation of YTHDF2 reduced YTHDF2-facilitated translation of m6A-gch1 for cardiomyocyte ferroptosis, and decreased YTHDF2-mediated m6A-sting1 decay for caudal vein plexus (CVP) apoptosis. The two distinct YTHDF2-mediated m6A regulations and context-dependent co-expression patterns of gch1/ythdf2 and tnfrsf1a/ythdf2 contributed to YTHDF2-mediated tissue-specific PCDs, uncovering a new layer of PCD regulation. Since BHPF/YTHDF2-medaited PCD defects were also observed in mammals, BHPF exposure represents a potential health threat.
    Keywords:  RNA m6A modification; bifurcation role of YTHDF2; environmental stress and m6A regulation; fluorene-9-bisphenol (BHPF); programmed cell deaths
    DOI:  https://doi.org/10.1093/nsr/nwad227
  11. EC Psychol Psychiatr. 2023 ;pii: 01127. [Epub ahead of print]12(11):
    RNA m6A methylation in psychiatric disorders.
    Qiao Mao, Jessica Luo, Xinqun Luo, Xiaoyu Zhu, Kesheng Wang, Lingjun Zuo, Yong Zhang, Xingguang Luo.
      This comprehensive review introduces the features of m6A modification and its role in neuropsychiatric disorders. The research findings suggest that m6A modifications and their regulators play a critical role in the occurrence and development of major psychiatric disorders, especially Alzheimer's disease, affecting synaptic protein synthesis, subtype classification, immune infiltration, pathogenesis, and inflammatory infiltration. These findings highlight m6A regulators as potential new diagnostic and therapeutic targets, with m6A methyltransferase METTL3 being the best-characterized regulator in these diseases. The review concludes that m6A modification is a promising target for the prevention and treatment of major psychiatric disorders.
    Keywords:  Alzheimer’s disease; METTL3; m6A modification; m6A regulator; neuropsychiatric disorders
  12. Environ Toxicol. 2023 Dec 26.
    Comprehensive analysis of m6A modification patterns and m6A-related lncRNAs as potential biomarkers in lung adenocarcinoma.
    Sheng Wang, Xuyu Gu, Duo Xu, Bo Liu, Kai Qin, Xianglin Yuan.
       BACKGROUND: N6-methyladenosine (m6A) methylation is considered to induce tumor cell proliferation, migration, and apoptosis. Understanding the mechanism of m6A-related lncRNAs in the development of lung adenocarcinoma (LUAD) may help predict prognosis.
    METHODS: m6A-related lncRNAs related to lung cancer were identified and combined with the MeRIP-Seq dataset. The consensus clustering method was utilized to divide LUAD patients, and prognostic model was constructed using the Lasso Cox algorithm. The cluster profiler package was used for gene ontology and KEGG enrichment. The proportion of immune infiltration was estimated using the CIBERSORT algorithm. The decision tree was constructed by the rpart package, and nomograms were built by the rms package. The Connectivity Map database was analyzed for the therapeutic effects of small molecule drugs for LUAD. In addition, qPCR, colony formation and transwell assays were performed to validate functions of m6A-associated lncRNAs.
    RESULTS: Nineteen m6A-modified lncRNAs in LUAD were identified. LUAD patients were divided into two categories based on the expression of 19 m6A-related lncRNAs. Cluster 2 patients had better antigen production and expression, while naive B cells, plasma cells, and activated NK cells were lower in cluster 1. Nine m6A-related lncRNAs were selected to establish a risk model for evaluating the prognosis of LUAD patients. The high-risk group had higher tumor mutational burden and lower TIDE scores with more gamma delta T cells and neutrophils. Nomograms showed that the prognostic model had predominant predictive ability for LUAD patients based on the risk score analyzed by the decision tree model. Benzo(a)pyrene and neurodazine might improve the prognosis of LUAD patients. The qRT-PCR results confirmed the reliability of the analytical results.
    CONCLUSION: The establishment of a prognostic model of m6A-related lncRNAs can independently predict overall survival in LUAD and may help to develop personalized immunotherapy strategies.
    Keywords:  N6-methyladenosine (m6A); lncRNAs; lung adenocarcinoma; prognostic model
    DOI:  https://doi.org/10.1002/tox.24110
  13. Shock. 2023 Dec 18.
    The role of N6-methyladenosine methyltransferase RBM15 in non-alcoholic fatty liver disease.
    Shiqing Li, Shengyi Lian, Wei Cheng, Tao Zhang, Xiaobing Gong.
       ABSTRACT: Non-alcoholic fatty liver disease (NAFLD) is a prevalent liver disorder with significant health implications. N6-methyladenosine (m6A) methyltransferase is known to exert regulatory functions in liver-related diseases. This study investigates the intricate role of RNA binding motif protein 15 (RBM15) in modulating inflammation and oxidative stress in NAFLD. An NAFLD model was induced in mice (Male, C57BL/6 J, 72 mice in the sham group) through a high-fat diet for 9 weeks, and hepatocytes were exposed to long chain-free fatty acids. The expression levels of RBM15, ring finger protein 5 (RNF5), and rho-kinase 1 (ROCK1) were assessed. RBM15 expression was intervened (injection of AAV9 virus at week 9 and detection at week 11). Liver damage was evaluated using staining assays, along with assessments of weight changes and lipid levels. Notably, RBM15 (decreased about 40%/60%) and RNF5 (decreased about 60%/75%) were poorly expressed while ROCK1 (increased about 2.5-fold) was highly expressed in liver tissues and cells NAFLD. RBM15 overexpression mitigated liver damage, inflammation, and oxidative stress in NAFLD mice, resulting in reduced liver-to-body weight ratio (20%) and decreased levels of alanine aminotransferase (54%), aspartate aminotransferase (36%), total cholesterol (30%), and triglycerides (30%), and inhibited inflammation and oxidative stress level. Mechanistically, RBM15 up-regulated RNF5 expression through m6A methylation modification, and RNF5 suppressed ROCK1 protein levels through ubiquitination modification. RNF5 knockdown or ROCK1 overexpression accelerated inflammation and oxidative stress in NAFLD. Taken together, RBM15 upregulated RNF5 expression through m6A methylation modification. RNF5 inhibited ROCK1 expression through ubiquitination modification to mitigate NAFLD.
    DOI:  https://doi.org/10.1097/SHK.0000000000002294
  14. J Neuroimmunol. 2023 Dec 19. pii: S0165-5728(23)00251-5. [Epub ahead of print]387 578265
    YTHDF2 alleviates microglia activation via promoting circHIPK2 degradation.
    Rongrong Huang, Ming Sun, Weiwei Wang, Xiaoyu Yu, Fan Liu.
      Microglial activation is a common cellular dysfunction in central nervous system inflammation, accompanied by abnormal expression of circular RNAs (circRNAs). YTHDF2, a N6-methyladenosine (m6A) reader, is known as a key element in RNA degradation. Here, lipolysaccharide induced microglia activation in mouse cortex and BV2 cells, accompanied by the decreased YTHDF2 and elevated circHIPK2. YTHDF2 overexpression or circHIPK2 knockdown in BV2 microglia inhibited the expressions of iNOS protein, IL-1β mRNA and IL-6 mRNA. Subsequent experiments revealed that YTHDF2 facilitated circHIPK2 degradation, thereby alleviating microglia activation. These findings suggest that YTHDF2 overexpression could serve as a therapeutic approach for inhibiting microglia activation.
    Keywords:  CircHIPK2; Microglia activation; RNA degradation; YTHDF2
    DOI:  https://doi.org/10.1016/j.jneuroim.2023.578265
  15. Front Oncol. 2023 ;13 1290330
    Epigenetic targeting of autophagy for cancer: DNA and RNA methylation.
    Luobin Lin, Yuntao Zhao, Qinzhou Zheng, Jiayang Zhang, Huaqin Li, Wenmei Wu.
      Autophagy, a crucial cellular mechanism responsible for degradation and recycling of intracellular components, is modulated by an intricate network of molecular signals. Its paradoxical involvement in oncogenesis, acting as both a tumor suppressor and promoter, has been underscored in recent studies. Central to this regulatory network are the epigenetic modifications of DNA and RNA methylation, notably the presence of N6-methyldeoxyadenosine (6mA) in genomic DNA and N6-methyladenosine (m6A) in eukaryotic mRNA. The 6mA modification in genomic DNA adds an extra dimension of epigenetic regulation, potentially impacting the transcriptional dynamics of genes linked to autophagy and, especially, cancer. Conversely, m6A modification, governed by methyltransferases and demethylases, influences mRNA stability, processing, and translation, affecting genes central to autophagic pathways. As we delve deeper into the complexities of autophagy regulation, the importance of these methylation modifications grows more evident. The interplay of 6mA, m6A, and autophagy points to a layered regulatory mechanism, illuminating cellular reactions to a range of conditions. This review delves into the nexus between DNA 6mA and RNA m6A methylation and their influence on autophagy in cancer contexts. By closely examining these epigenetic markers, we underscore their promise as therapeutic avenues, suggesting novel approaches for cancer intervention through autophagy modulation.
    Keywords:  6mA methylation; autophagy; cancers; m6A methylation; therapy
    DOI:  https://doi.org/10.3389/fonc.2023.1290330
  16. Immunobiology. 2023 Dec 21. pii: S0171-2985(23)04583-7. [Epub ahead of print]229(1): 152781
    Significance of m6A in subtype identification, immunological evolution, and therapeutic sensitivity of RA.
    Chenxi Ma, Jiasheng Wu, Hongwei Lei, He Huang, Yingnan Li.
      N6-methyladenosine (m6A) is one kind of important epigenetic modification pattern which is extensively involved in immune regulation. The development and progression of autoimmune diseases are closely related to immune dysregulation. Considering that rheumatoid arthritis (RA) is a typical autoimmune disease, the m6A process might be one of the important regulatory mechanisms in the pathogenesis of RA. In this study, we identified five differentially expressed m6A regulators in normal and RA samples from the GEO database. With these five regulators, we constructed the nomogram, and it could accurately identify the risk of RA morbidity. Next, we identified 121 differentially expressed genes (DEGs) between normal and RA samples, of which 36 DEGs were co-expressed with these five m6A regulators. We noted that these DEGs were highly enriched in multiple immunoregulatory signaling pathways, such as cytokine-mediated immune cell chemotaxis, adhesion, and activation. To further characterize the heterogeneity of immunological features, we clustered the RA samples into two subtypes. The C2 subtype has higher infiltration levels of pro-inflammatory cells and activity of pro-inflammatory signaling pathways. Thus, the inflammatory response might be more vigorous in the C2 subtype. Next, we constructed the m6Asig system with the SVM machine learning algorithms and least absolute shrinkage and selection operator (LASSO) regression. The m6Asig could accurately distinguish the C1 and C2 subtypes, which indicated that the m6Asig could be a potential biomarker for the inflammatory activity of RA. Finally, by comparing the information from the CellMiner, TTD, and DrugBank databases, we determined 25 drugs. The targets of these drugs were positively correlated with m6Asig. To be clarified, the above findings were derived from bioinformatics and statistical analyses, and further experimental validation still requires. In summary, this study further revealed the m6A and immunoregulation mechanisms in RA pathogenesis. Also, the m6Asig could be a novel biomarker with potential applicability in the clinical management of RA.
    Keywords:  Drug therapy; Immune; Multi-omics analysis; N6-methyladenosine; Rheumatoid arthritis; Tissue-specific expressed genes
    DOI:  https://doi.org/10.1016/j.imbio.2023.152781
  17. J Cell Mol Med. 2023 Dec 25.
    METTL14 promotes IL-6-induced viability, glycolysis and inflammation in HaCaT cells via the m6A modification of TRIM27.
    Yiran Chen, Yanwei Xiang, Xiao Miao, Le Kuai, Xiaojie Ding, Tian Ma, Bin Li, Bin Fan.
      Interleukin-6 (IL-6) is a cytokine generated by healthy constituents of the skin, but is also up-regulated by a wide range of skin lesions and inflammatory conditions to trigger cytopathy of skin cells. TRIM27 was identified to contribute to the functional effects of IL-6 on skin cells. However, the underlying mechanism was not clear. Lentivirus infection was used for gene overexpression or silencing. RT-PCR and Western blot were used to respectively assess mRNA and protein levels. Cell viability was assessed by CCK-8 assay. Extracellular flux analysis was used to assess the levels of oxygen consumption rate and extracellular acidification rate. Mouse back skin was treated with imiquimod to produce psoriasis-like inflammation in vivo. Histological assessment and immunohistochemistry staining were respectively applied to analyse lesioned mouse and human skin samples. IL-6-induced increased viability, glycolysis and inflammation in keratinocytes was inhibited both by a chemical methylation inhibitor and by METTL14 knockdown. Further investigation found that METTL14 induces m6A methylation of TRIM27, which is recognized by a m6A reader, IGF2BP2. Elevation of TRIM27 level and activation of IL-6/STAT3 signalling pathway were found in an in vivo psoriasis-like inflammation model, whereas inhibition m6A methylation strongly alleviated the inflammation. Finally, METTL14, TRIM27, STAT3, p-STAT3 and IL-6 expressions were all found to be increased in clinical skin samples of psoriatic patients. Our results unravelled METTL14/TRIM27/IGF2BP2 signalling axis in keratinocyte cytopathy, which plays a critical role in facilitating the activation of IL-6/STAT3 signalling pathway. Our findings should provide inspirations for the design of new therapeutics for skin inflammatory diseases including psoriasis.
    Keywords:  IL-6; METTL14; TRIM27; m6A methylation; psoriasis
    DOI:  https://doi.org/10.1111/jcmm.18085
  18. Environ Toxicol. 2023 Dec 29.
    Identification of a novel signature based on M6a modification regulators related LncRNA for stratification of the prognosis of prostate cancer.
    Sheng-Xiong Wang, Xiang-Hui Xie.
      Prostate cancer emerges as a life-threatening disease that affects approximately 1.3 million patients of male population globally. Various studies established lncRNAs as a critical role in prostate cancer progression by regulating multiple epigenetic pathways. Therefore, it is imperative to disclose the involvement of lncRNAs in prostate cancer and their usability as prognostic markers for the disease. The model was constructed using Cox and LASSO analysis. The accuracy of model was evaluated using various cohorts. Furthermore, the study assessed the correlative relationship of the model with tumor immunity, immunotherapy, SNV mutation, and drug sensitivity, among other factors. We developed an accurate and stable prognostic model for prostate cancer patients by screening out 11 m6A regulators related lncRNAs and integrating pathological features and age through a nomogram model. The model had satisfactory accuracy and stability in stratification of clinical outcomes of prostate cancer patients, as demonstrated by AUC values (higher than 0.7) at 3, 5, and 7 years in both internal and external cohorts. Moreover, we performed PCA analysis to confirm m6A-related lncRNAs as the best modeling strategy. We developed a prognosis predicting model based on 11 selected m6A modification related lncRNA, which displayed satisfactory potency in multiple cohorts.
    Keywords:  immune infiltration; m6A regulator; prognostic model; prostate cancer; tumor mutation
    DOI:  https://doi.org/10.1002/tox.24114
  19. J Drug Target. 2023 Dec 28. 1-34
    Molecular mechanism of Wilms tumor 1-associated protein in diabetes-related dry eye disease by mediating m6A methylation modification of lncRNA NEAT1.
    Chen Guo, Mingyi Yu, Jinghua Liu, Zhe Jia, Hui Liu, Shaozhen Zhao.
      Dry eye disease (DED) is often secondary to diabetes mellitus (DM). We explored the action of Wilms tumor 1-associated protein (WTAP) in DM-DED via lncRNA NEAT1 m6A methylation. DM-DED mouse models were treated with sh-WTAP/sh-NEAT1 plasmid, followed by assessment of corneal epithelial damage/histopathological changes. HCE-2 cells were exposed to hyperosmotic conditions to establish in vitro DED models and treated with oe-NEAT1/sh-NEAT1/sh-WTAP/nigericin (an NLRP3 inflammasome inducer). Cell viability/apoptosis were evaluated by CCK-8/TUNEL. The levels of WTAP/NEAT1/inflammatory factors/NLRP3 inflammasome- and apoptosis-related markers were determined. m6A modification was examined by MeRIP-qPCR and NEAT1 stability was also detected. DM-DED mice exhibited up-regulated WTAP/NEAT1 expression and severe corneal damage, whereas WTAP/NEAT1 knockdown alleviated inflammation/corneal damage. In hyperosmolarity-induced HCE-2 cells, NEAT1 aggravated inflammation and apoptosis, while NEAT1 knockdown suppressed NLRP3 inflammasome activation and ameliorated cell injury. Hyperosmolarity-induced WTAP expression increased m6A modification and NEAT1 mRNA stability. WTAP mediated m6A methylation of NEAT1 and NLRP3 inflammasome activation in DM-DED mice. Collectively, WTAP upregulates NEAT1 expression and facilitates NLRP3 inflammasome activation by increasing m6A methylation, thereby accelerating DM-DED development. WTAP or lncRNA NEAT1 may become a therapeutic target for DM-DED, which offers a theoretical foundation for the investigation and advancement of nanocarrier-based targeted therapeutic medications for DM-DED.
    Keywords:  Diabetes mellitus; Dry eye disease; Inflammation; LncRNA NEAT1; NLRP3; NLRP6; Wilms tumor 1-associated protein; m6A
    DOI:  https://doi.org/10.1080/1061186X.2023.2300682
  20. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Dec 21. pii: S1570-0232(23)00378-1. [Epub ahead of print]1232 123968
    Exploring urinary modified nucleosides as biomarkers for diabetic retinopathy: Development and validation of a ultra performance liquid chromatography-tandem mass spectrometry method.
    Chen Yao, Daizhu Lv, Xueqing Zhou, Pengcheng Fu, Wen Sun, Jinlian Chen, Huan Lin.
      The dynamic modification of RNA plays a crucial role in biological regulation and is strongly linked to human disease development and progression. Notably, modified nucleosides in urine have shown promising potential as early diagnostic biomarkers for various conditions. In this study, we developed and validated a rapid, sensitive, and accurate UPLC-MS/MS method for quantifying eight types of modified nucleosides (N1-methyladenosine (m1A), N6-methyladenosine (m6A), 5-methyluridine (m5U), 5-taurinomethyl-2-thiouridine (τm5s2U), 5-methylcytidine (m5C), 2'-O-methylcytidine (Cm), N1-methylguanosine (m1G), and N7-methylguanosine (m7G) in human urine. Using the method, we measured the urinary concentrations of m1A, m6A, m5U, τm5s2U, m5C, Cm, m1G, and m7G in a total of 21 control individuals and 23 patients diagnosed with diabetic retinopathy (DR). Cm levels showed promise as a diagnostic marker for diabetic retinopathy (DR), with a significant value (P < 0.01) and an AUC of 0.735. Other modified nucleosides also exhibited significant differences within specific subpopulations. As non-proliferative diabetic retinopathy (NPDR) signifies the latent early stage of diabetic retinopathy, we developed a multivariate linear model that integrates patients' sex, age, height, and urinary concentration of modified nucleosides which aims to predict and differentiate between healthy individuals, NPDR patients, and proliferative diabetic retinopathy (PDR) patients. Encouragingly, the model achieved satisfactory accuracy rates: healthy (81%), NPDR (75%), and PDR (80%). Our findings provide valuable insights into the development of an early, cost-effective, and noninvasive diagnostic approach for diabetic retinopathy.
    Keywords:  Biomarkers; Diabetic retinopathy; Modified nucleosides; UPLC-MS/MS
    DOI:  https://doi.org/10.1016/j.jchromb.2023.123968
  21. Am J Physiol Cell Physiol. 2023 Dec 25.
    ALKHB5-demethylated lncRNA SNHG15 promotes myeloma tumorigenicity by increasing chromatin accessibility and recruiting H3K36me3 modifier SETD2.
    Lan Yao, Tingting Li, Yao Teng, Jingjing Guo, Hongyong Zhang, Linghui Xia, Qiuling Wu.
      Chromatin instability plays a crucial role in multiple myeloma (MM) relapse and progression, but its mechanism remains obscure. Here we uncovered that m6A-demethylase ALKBH5 upregulated and stabilized lncRNA SNHG15, which was elevated in MM and positively correlated with unfavorable clinical prognosis factors. ALKBH5-SNHG15 axis participated in viability, and migration/invasion of myeloma cell lines and MM-xenografted SCID/NOD mice. Mechanically, ALKBH5 promoted the expression of trimethylated histone H3 at lysine 36 (H3K36me3) methyltransferase SETD2 through lncRNA SNHG15-mediated protein stability. ALKBH5-SNHG15 axis increased chromatin accessibility and altered the H3K36me3 enrichment at the gene body, which is responsible for transcription elongation. Our study suggested a novel epigenetically interaction of m6A methylation, lncRNA SNHG15, and histone SETD2/H3K36me3 modifications in myeloma progression, indicating ALKBH5 and lncRNA SNHG15 could serve as potential novel therapeutic targets for MM treatment.
    Keywords:  Chromatin accessibility; Long non-coding RNA; Multiple myeloma; N-6 methyladenosine; Trimethylated histone H3 at lysine 36
    DOI:  https://doi.org/10.1152/ajpcell.00348.2023
  22. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Dec 21. pii: S1570-0232(23)00383-5. [Epub ahead of print]1232 123973
    Determination of dimethylated nucleosides in serum from colorectal cancer patients by hydrophilic interaction liquid chromatography-tandem mass spectrometry.
    Xiaoji Cao, Mingwei Wang, Yanqin Huang, Mengwen Zhang, Fengjin Zheng, Genyin Zhang, Jiaming Su, Ying Yuan, Cheng Guo.
      RNA modifications play a crucial regulatory role in a variety of biological processes and are closely related to numerous diseases, including cancer. The diversity of metabolites in serum makes it a favored biofluid for biomarkers discovery. In this work, a robust and accurate hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) approach was established for simultaneous determination of dimethylated nucleosides in human serum. Using the established method, we were able to accurately quantify the concentrations of N6-2'-O-dimethyladenosine (m6Am), N2,N2-dimethylguanosine (m2,2G), and 5,2'-O-dimethyluridine (m5Um) in serum samples from 53 healthy controls, 57 advanced colorectal adenoma patients, and 39 colorectal cancer (CRC) patients. The results showed that, compared with healthy controls and advanced colorectal adenoma patients, the concentrations of m6Am and m2,2G were increased in CRC patients, while the concentration of m5Um was decreased in CRC patients. These results indicates that these three dimethylated nucleosides could be potential biomarkers for early detection of colorectal cancer. Interestingly, the level of m5Um was gradually decreased from healthy controls to advanced colorectal adenoma patients to CRC patients, indicating m5Um could also be used to evaluate the level of malignancy of colorectal tumor. In addition, this study will contribute to the investigation on the regulatory mechanisms of RNA dimethylation in the onset and development of colorectal cancer.
    Keywords:  Advanced colorectal adenoma; Biomarker; Colorectal cancer; Dimethylated nucleosides; HILIC-MS/MS; Serum
    DOI:  https://doi.org/10.1016/j.jchromb.2023.123973
  23. Sci Rep. 2023 12 28. 13(1): 22999
    dTrmt10A impacts Hsp70 chaperone m6A levels and the stress response in the Drosophila brain.
    Alexandra E Perlegos, Xiuming Quan, Kirby M Donnelly, Hui Shen, Emily J Shields, Heidi Elashal, Kathy Fange Liu, Nancy M Bonini.
      Chronic cellular stress has a profound impact on the brain, leading to degeneration and accelerated aging. Recent work has revealed the vital role of RNA modifications, and the proteins responsible for regulating them, in the stress response. In our study, we defined the role of CG14618/dTrmt10A, the Drosophila counterpart of human TRMT10A a N1-methylguanosine methyltransferase, on m6A regulation and heat stress resilience in the Drosophila brain. By m6A-IP RNA sequencing on Drosophila head tissue, we demonstrated that manipulating dTrmt10A levels indirectly regulates m6A levels on polyA + RNA. dTrmt10A exerted its influence on m6A levels on transcripts enriched for neuronal signaling and heat stress pathways, similar to the m6A methyltransferase Mettl3. Intriguingly, its impact primarily targeted 3' UTR m6A, setting it apart from the majority of Drosophila m6A-modified transcripts which display 5' UTR enrichment. Upregulation of dTrmt10A led to increased resilience to acute heat stress, decreased m6A modification on heat shock chaperones, and coincided with decreased decay of chaperone transcripts and increased translation of chaperone proteins. Overall, these findings establish a potential mechanism by which dTrmt10A regulates the acute brain stress response through m6A modification.
    DOI:  https://doi.org/10.1038/s41598-023-50272-4
  24. Theriogenology. 2023 Dec 23. pii: S0093-691X(23)00506-X. [Epub ahead of print]216 20-29
    FTO demethylates regulates cell-cycle progression by controlling CCND1 expression in luteinizing goat granulosa cells.
    Dongxu Li, Lei Zhou, Zifei Liu, Zhen Zhang, Weijia Mao, Wangwang Shi, Minghui Zhu, Feng Wang, Yongjie Wan.
      In mammals, N6-methyladenosine (m6A) stands out as one of the most abundant internal mRNA modifications and plays a crucial role in follicular development. Nonetheless, the precise mechanism by which the demethylase FTO regulates the progression of the goat luteinizing granulosa cells (LGCs) cycle remains to be elucidated. In our study, we primarily assessed the protein and mRNA expression levels of genes using Western blotting and quantitative real-time polymerase chain reaction (qRT-PCR), cell proliferation via EdU, cell viability with CCK-8, and apoptosis and cell cycle progression through flow cytometry. Here, the results demonstrated that knockdown of FTO significantly enhanced apoptosis, impeded cell proliferation, and increased autophagy levels in goat LGCs. Furthermore, the silencing of FTO substantially reduced cyclin D1 (CCND1) expression through the recognition and degradation of YTHDF2, consequently prolonging the cell cycle progression. This study sheds light on the mechanism by which FTO demethylation governs cell cycle progression by controlling the expression of CCND1 in goat LGCs, underscoring the dynamic role of m6A modification in the regulation of cell cycle progression.
    Keywords:  CCND1; Cell cycle; FTO; Luteinizing granulosa cells; YTHDF2
    DOI:  https://doi.org/10.1016/j.theriogenology.2023.12.029
  25. Acta Biochim Biophys Sin (Shanghai). 2023 Dec 28.
    Demethylase FTO inhibits the occurrence and development of triple-negative breast cancer by blocking m 6A-dependent miR-17-5p maturation-induced ZBTB4 depletion.
    Jingyi Ni, Xiaoyun Lu, Xiangxiang Gao, Conghui Jin, Junfeng Mao.
      Triple-negative breast cancer (TNBC) is a subtype of breast cancer, and its mechanisms of occurrence and development remain unclear. In this study, we aim to investigate the role and molecular mechanisms of the demethylase FTO (fat mass and obesity-associated protein) in TNBC. Through analysis of public databases, we identify that FTO may regulate the maturation of miR-17-5p and subsequently influence the expression of zinc finger and BTB domain-containing protein 4 (ZBTB4), thereby affecting the occurrence and progression of TNBC. We screen for relevant miRNAs and mRNAs from the GEO and TCGA databases and find that the FTO gene may play a crucial role in TNBC. In vitro cell experiments demonstrate that overexpression of FTO can suppress the proliferation, migration, and invasion ability of TNBC cells and can regulate the maturation of miR-17-5p through an m 6A-dependent mechanism. Furthermore, we establish a xenograft nude mouse model and collect clinical samples to further confirm the role and impact of the FTO/miR-17-5p/ZBTB4 regulatory axis in TNBC. Our findings unveil the potential role of FTO and its underlying molecular mechanisms in TNBC, providing new perspectives and strategies for the research and treatment of TNBC.
    Keywords:  FTO demethylase; ZBTB4; mA modification; miR-17-5p; triple-negative breast cancer
    DOI:  https://doi.org/10.3724/abbs.2023267
  26. J Inflamm Res. 2023 ;16 6329-6348
    Active Fraction of Polyrhachis Vicina Roger (AFPR) Ameliorate Depression Induced Inflammation Response by FTO/miR-221-3p/SOCS1 Axis.
    Junhui He, Jiaxiu Xie, Guili Zhou, Chunlian Jia, Dongbo Han, Dongmei Li, Jie Wei, Yi Li, Renshan Huang, Chunlian Li, Bo Wang, Chao Wei, Qibiao Su, Kedao Lai, Guining Wei.
       Purpose: Neuroinflammation is a significant etiological factor in the development of depression. Traditional Chinese medicine (TCM) has demonstrated notable efficacy in the treatment of inflammation. Our previous study surfaces that the active fraction of Polyrhachis vicina Roger (AFPR) has antidepressant and anti-neuroinflammatory effects, but the specific mechanisms remain to be elucidated. The objective of this study was to examine the impact of AFPR on inflammation in depression via the FTO/miR-221-3p/SOCS1 axis.
    Methods: Chronic unpredictable stress (CUMS)-induced rats and LPS-induced BV2 cells were employed to simulate depression models in vivo and in vitro. The levels of inflammatory factors were detected using the ELISA assay. The expression of genes and proteins was detected using qRT-PCR and Western blot. Gene interactions were detected using the dual luciferase reporter gene. Protein-RNA interactions were investigated using RNA methylation immunoprecipitation (MeRIP) and RNA immunoprecipitation (RIP). Neuroinflammation in the brain was examined through H&E staining, while neuronal apoptosis was assessed using TUNEL staining.
    Results: The results showed that AFPR ameliorated depression induced inflammation by increasing SOCS1 expression. However, SOCS1 was identified as a target of miR-221-3p. Overexpression of miR-221-3p decreased the expression of SOCS1 and increased the levels of NF-κB, IL-7, and IL-6. In addition, we found that miR-221-3p was regulated by FTO-mediated m6A modification through MeRIP and RIP experiments. Interference with miR-221-3p and overexpression of FTO resulted in increased SOCS1 gene expression and decreased levels of NF-κB, IL-7, and IL-6, which were reversed by AFPR.
    Conclusion: AFPR inhibits the maturation of pri-miR-221-3p through FTO-mediated m6A modification, reduces the production of miR-221-3p, increases the expression of SOCS1, and reduces the level of inflammation, thereby improving depressive symptoms.
    Keywords:  FTO; Polyrhachis vicina Roger; SOCS1; depression; inflammation
    DOI:  https://doi.org/10.2147/JIR.S439912
  27. Heliyon. 2023 Dec;9(12): e22584
    High CTCF expression mediated by FGD5-AS1/miR-19a-3p axis is associated with immunosuppression and pancreatic cancer progression.
    Yihao Liu, Wenxin Qi, Jingxin Yin, Xirui He, Songqi Duan, Haili Bao, Chen Li, Minmin Shi, Jiao Wang, Shaohua Song.
      The most common reason for cancer-related death globally is predicted to be pancreatic cancer (PC), one of the deadliest cancers. The CCCTC-binding factor (CTCF) regulates the three-dimensional structure of chromatin, was reported to be highly regulated in various malignancies. However, the underlying biological functions and possible pathways via which CTCF promotes PC progression remain unclear. Herein, we examined the CTCF function in PC and discovered that CTCF expression in PC tissues was significantly raised compared to neighboring healthy tissues. Additionally, Kaplan-Meier survival analysis demonstrated a strong connection between elevated CTCF expression and poor patient prognosis. A study of the ROC curve (receiver operating characteristic) revealed an AUC value for CTCF of 0.968. Subsequent correlation analysis exhibited a strong relationship between immunosuppression and CTCF expression in PC. CTCF knockdown significantly inhibited the malignant biological process of PC in vitro and in vivo, suggesting that CTCF may be a potential PC treatment target. We also identified the FGD5 antisense RNA 1 (FGD5-AS1)/miR-19a-3p axis as a possible upstream mechanism for CTCF overexpression. In conclusion, our data suggest that ceRNA-mediated CTCF overexpression contributes to the suppression of anti-tumor immune responses in PC and could be a predictive biomarker and potential PC treatment target.
    Keywords:  CTCF; FGD5-AS1; PC; TME; miR-19a-3p
    DOI:  https://doi.org/10.1016/j.heliyon.2023.e22584
  28. Nucleic Acids Res. 2023 Dec 24. pii: gkad1211. [Epub ahead of print]
    Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery.
    Josh McQuail, Gianluca Matera, Tom Gräfenhan, Thorsten Bischler, Per Haberkant, Frank Stein, Jörg Vogel, Sivaramesh Wigneshweraraj.
      The RNA binding protein Hfq has a central role in the post-transcription control of gene expression in many bacteria. Numerous studies have mapped the transcriptome-wide Hfq-mediated RNA-RNA interactions in growing bacteria or bacteria that have entered short-term growth-arrest. To what extent post-transcriptional regulation underpins gene expression in growth-arrested bacteria remains unknown. Here, we used nitrogen (N) starvation as a model to study the Hfq-mediated RNA interactome as Escherichia coli enter, experience, and exit long-term growth arrest. We observe that the Hfq-mediated RNA interactome undergoes extensive changes during N starvation, with the conserved SdsR sRNA making the most interactions with different mRNA targets exclusively in long-term N-starved E. coli. Taking a proteomics approach, we reveal that in growth-arrested cells SdsR influences gene expression far beyond its direct mRNA targets. We demonstrate that the absence of SdsR significantly compromises the ability of the mutant bacteria to recover growth competitively from the long-term N-starved state and uncover a conserved post-transcriptional regulatory axis which underpins this process.
    DOI:  https://doi.org/10.1093/nar/gkad1211
  29. Mol Plant. 2023 Dec 27. pii: S1674-2052(23)00414-8. [Epub ahead of print]
    Botrytis cinerea-induced F-box protein 1 enhances disease resistance by inhibiting JAO/JOX-mediated jasmonic acid catabolism in Arabidopsis.
    Min Zhang, Weiwei Li, Tingyu Zhang, Yueyan Liu, Lijing Liu.
      Jasmonic acid (JA) is a crucial phytohormone that regulates plant immunity. The endogenous JA level is determined by the rates of its biosynthesis and catabolism in plants. To date, the activation of JA biosynthesis has been well documented; however, how plants repress JA catabolism upon pathogen infection remains elusive. Here, we identified Botrytis cinerea-induced F-box protein 1 (BFP1) in Arabidopsis. The expression of BFP1 was induced by B. cinerea in a JA signaling dependent manner, and BFP1 protein was critical for plant defense against B. cinerea and plant response to JA. Additionally, BFP1 overexpression increased plant defenses against broad-spectrum pathogens without fitness costs. Further experiments demonstrated that BFP1 interacts with and mediates the ubiquitination and degradation of jasmonic acid oxidases (JAOs, also known as jasmonate-induced oxygenases, JOXs), the enzymes that hydroxylate JA to 12OH-JA. Consistently, the accumulation of JA and 12OH-JA was regulated by BFP1 during B. cinerea infection. Moreover, mutation of JAO2 complemented the phenotypic effects of the bfp1 mutant. Collectively, our results unveil an undiscovered strategy to enhance plant immunity by suppressing the catabolism of immune-related hormone.
    Keywords:  BFP1; JA catabolism; JAO/JOXs; Plant immunity; Ubiquitination-mediated degradation
    DOI:  https://doi.org/10.1016/j.molp.2023.12.020
  30. Cancer Genomics Proteomics. 2024 Jan-Feb;21(1):21(1): 65-78
    Single-cell Transcriptomic Analysis Reveals an Immunosuppressive Network Between POSTN CAFs and ACKR1 ECs in TKI-resistant Lung Cancer.
    Zhiyi Wang, Ning Yan, Hailong Sheng, Yazhi Xiao, Jingyuan Sun, Chuanhui Cao.
       BACKGROUND/AIM: Tyrosine kinase inhibitor (TKI) therapy, a principal treatment for advanced non-small cell lung cancer (NSCLC), frequently encounters the development of drug resistance. The tumor microenvironment (TME) plays a critical role in the progression of NSCLC, yet the relationship between endothelial cells (ECs) and cancer-associated fibroblasts (CAFs) subpopulations in TKI treatment resistance remains largely unexplored.
    MATERIALS AND METHODS: The BioProject database PRJNA591860 project was used to analyze scRNA-seq data including 49 advanced-stage NSCLC samples across three different time points: pre-targeted therapy (naïve), post-partial response (PR) to targeted therapy, and post-progressive disease (PD) stage. The data involved clustering stromal cells into multiple CAFs and ECs subpopulations. The abundance changes and functions of each cluster during TKI treatment were investigated by KEGG and GO analysis. Additionally, we identified specific transcription factors and metabolic pathways via DoRothEA and scMetabolism. Moreover, cell-cell communications between PD and PR stages were compared by CellChat.
    RESULTS: ECs and CAFs were clustered and annotated using 49 scRNA-seq samples. We identified seven ECs subpopulations, with OIT3 ECs showing enrichment in the PR phase with a drug-resistance phenotype, and ACKR1 ECs being prevalent in the PD phase with enhanced cell adhesion. Similarly, CAFs were clustered into 7 subpopulations. PLA2G2A CAFs were predominant in PR, whereas POSTN CAFs were prevalent in PD, characterized by an immunomodulatory phenotype and increased collagen secretion. CellChat analysis showed that ACKR1 ECs strongly interacted with macrophage through the CD39 pathway and POSTN CAFs secreted Tenascin-C (TNC) to promote the progression of epithelial cells, primarily malignant ones, in PD.
    CONCLUSION: This study reveals that POSTN CAFs and ACKR1 ECs are associated with resistance to TKI treatment, based on single-cell sequencing.
    Keywords:  ACKR1 ECs; NSCLC; POSTN CAFs; TKI treatment; single cell analysis
    DOI:  https://doi.org/10.21873/cgp.20430
  31. Front Oncol. 2023 ;13 1274439
    TICRR serves as a prognostic biomarker in lung adenocarcinoma with implications in RNA epigenetic modification, DDR pathway, and RNA metabolism.
    Xunbo Zheng, Li Han, Jun Guan, Chenteng Chen, Yue Zhang, Jiali Zhang, Yiran Zhang, Siyao Liu, Junyan Su, Mengyuan Liu, Hanxing Huang.
       Purpose: TOPBP1 interacting checkpoint and replication regulator (TICRR), a hub gene of the Cdk2-mediated initiation step of DNA replication, has been shown an essential role in tumorigenesis by accelerating the DNA replication of tumor cells.
    Methods: RT-qPCR was used to detect the mRNA expression of TICRR in LUAD tumors and adjacent normal tissues. The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database of LUAD were acquired to analyze the critical role of TICRR expression in survival prognosis and clinicopathology characters in LUAD. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed using the R package. The correlation of TICRR expression with immune cell infiltration, RNA epigenetic modification, DNA damage repair (DDR) pathway, and cell metabolism of LUAD was further explored to verify significant conclusions.
    Results: TICRR was significantly upregulated in most cancer types, including LUAD, lung squamous cell carcinoma (LUSC), and others. Cox regression analysis indicated the overexpression of TICRR was associated with poor survival in several cancers. In LUAD, TICRR expression was positively correlated with tumor stage and was increased in smoking, male, and high tumor mutational burden (TMB) patients. Enrichment analysis revealed that TICRR could influence tumor proliferation and prognosis via activating pathways involving cell cycle, DNA repair, DNA replication, cysteine metabolism, oxidative phosphorylation, and ubiquitin-mediated proteolysis pathways. Interestingly, high TICRR expression correlated with DDR pathway signature (34 genes), 37 m6A/m5C regulated genes, and some metabolism-regulated genes. Silencing the TICRR gene affects cysteine metabolism and modifies cancer-related pathways, with decreased cell cycle and increased B/T cell receptor signaling. Our TICRR risk model accurately predicts LUAD patient prognosis, validated across GEO datasets, and is integrated with clinical characteristics via a nomogram, facilitating personalized treatment strategies and enhancing patient management.
    Conclusions: Taken together, TICRR has emerged as a promising prognostic biomarker in lung adenocarcinoma (LUAD), with implications in immune activation, cell cycle regulation, RNA modification, and tumor energy metabolism. These findings suggest that TICRR could serve as a viable therapeutic target and a reliable prognostic indicator for LUAD.
    Keywords:  RNA metabolism; TICRR; cell cycle; immune feature; lung adenocarcinoma; nomogram
    DOI:  https://doi.org/10.3389/fonc.2023.1274439
  32. Free Radic Biol Med. 2023 Dec 22. pii: S0891-5849(23)01176-0. [Epub ahead of print]
    Ezrin inhibition alleviates oxidative stress and pyroptosis via regulating TRPML1-calcineurin axis mediated enhancement of autophagy in spinal cord injury.
    Junsheng Lou, Mengran Jin, Conghui Zhou, Yunpeng Fan, Libin Ni, Yiting Mao, Honghao Shen, Jiafeng Li, Haojie Zhang, Chunyan Fu, Xingjia Mao, Yingying Chen, Jinjie Zhong, Kailiang Zhou, Linlin Wang, Junsong Wu.
      Spinal cord injury (SCI) presents profound ramifications for patients, leading to diminished motor and sensory capabilities distal to the lesion site. Once SCI occurs, it not only causes great physical and psychological problems for patients but also imposes a heavy economic burden. Ezrin is involved in various cellular processes, including signal transduction, cell death, inflammation, chemotherapy resistance and the stress response. However, whether Ezrin regulates functional repair after SCI and its underlying mechanism has not been elucidated. Here, our results showed that there is a marked augmentation of Ezrin levels within neurons and Ezrin inhibition markedly diminished glial scarring and bolstered functional recuperation after SCI. RNA sequencing indicated the potential involvement of pyroptosis, oxidative stress and autophagy in the enhancement of functional recovery upon reduced Ezrin expression. Moreover, the inhibition of Ezrin expression curtailed pyroptosis and oxidative stress by amplifying autophagy. Our studies further demonstrated that Ezrin inhibition promoted autophagy by increasing TFEB activity via the Akt-TRPML1-calcineurin pathway. Finally, we concluded that inhibiting Ezrin expression alleviates pyroptosis and oxidative stress by enhancing TFEB-driven autophagy, thereby promoting functional recovery after SCI, which may be a promising therapeutic target for SCI treatment.
    Keywords:  Autophagy; Ezrin; Oxidative stress; Pyroptosis; Spinal cord injury; TFEB
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.12.020
  33. Acta Diabetol. 2023 Dec 27.
    Downregulation of Sirt3 contributes to β-cell dedifferentiation via FoxO1 in type 2 diabetic mellitus.
    Yaxing Nie, Yunye Zhang, Shuqing Liu, Zhi Xu, Chunya Xia, Lei Du, Xiaoxing Yin, Jianyun Wang.
       AIMS: FoxO1 is an important factor in the β-cell differentiation in type 2 diabetes mellitus (T2DM). Sirt3 is found to be involved in FoxO1 function. This study investigated the role of Sirt3 in the β-cell dedifferentiation and its mechanism.
    METHODS: Twelve-week-old db/db mice and INS1 cells transfected with Sirt3-specific short hairpin RNA (shSirt3) were used to evaluate the dedifferentiation of β-cell. Insulin levels were measured by enzyme linked immunosorbent assay. The proteins of Sirt3, T-FoxO1, Ac-FoxO1 and differentiation indexes such as NGN3, OCT4, MAFA were determined by western blot or immunofluorescence staining. The combination of Sirt3 and FoxO1 was determined by the co-immunoprecipitation assay. The transcriptional activity of FoxO1 was detected by dual luciferase reporter assay.
    RESULTS: Both the in vivo and in vitro results showed that Sirt3 was decreased along with β-cell dedifferentiation and decreased function of insulin secretion under high glucose conditions. When Sirt3 was knocked down in INS1 cells, increased β-cell dedifferentiation and lowered insulin secretion were observed. This effect was closely related to the amount loss and the decreased deacetylation of FoxO1, which resulted in a reduction in transcriptional activity.
    CONCLUSION: Downregulation of Sirt3 contributes to β-cell dedifferentiation in high glucose via FoxO1. Intervention of Sirt3 may be an effective approach to prevent β-cell failure in T2DM.
    Keywords:  Dedifferentiation; FoxO1; High glucose; Sirt3; T2DM; β-Cell
    DOI:  https://doi.org/10.1007/s00592-023-02221-w
  34. Transl Oncol. 2023 Dec 22. pii: S1936-5233(23)00254-1. [Epub ahead of print]40 101868
    Hypoxia induced cell dormancy of salivary adenoid cystic carcinoma through miR-922/DEC2 axis.
    Li Dai, Hongchun Xian, Haofan Wang, Mao Li, Mei Zhang, Xin-Hua Liang, Ya-Ling Tang.
       BACKGROUND: Hypoxia has been shown to induce cancer cells to become dormant meanwhile these cells inclined to disseminate and eventually cause metastasis. However, the molecular mechanism is still elusive. The purpose is to explore whether dormancy-associated microRNAs (DmiRs) get involved in hypoxia-induced cell dormancy of salivary adenoid cystic carcinoma (SACC).
    MATERIAL AND METHODS: This study performed multi-perspective investigation of the biological effects of miR-922/DEC2 on SACC based on clinical samples, 2D and 3D in vitro model and nude mice in vivo model, based on our previous study of overexpression of DEC2 inducing SACC cellular dormancy.
    RESULTS: According to the existing microRNA array of SACC tissue, we found that miR-922 was upregulated in SACC tissue and was inversely correlated with DEC2, suggesting that miR-922 might participate in the activation of SACC cell dormancy as a DmiR. Then, we found miR-922 low SACC cells exhibited cell dormancy and a low level of fatty acid oxidation with propensity for lipid droplets accumulation through DEC2. Moreover, HIF1a downregulated the level of miR-922 to induce SACC cell dormancy. In addition, in xenografts of nude mice the inhibition of miR-922 attenuated the growth of primary tumor and the lung metastasis of SACC.
    CONCLUSIONS: miR-922/DEC2 axis was necessary to hypoxia-induced cell dormancy and played an important role in the lipid metabolism reprogramming of SACC.
    Keywords:  Cancer cell dormancy; Dormancy-associated microrna; Hypoxia; Salivary adenoid cystic carcinoma
    DOI:  https://doi.org/10.1016/j.tranon.2023.101868
  35. Sci China Life Sci. 2023 Nov 30.
    Ultrasound-responsive spherical nucleic acid against c-Myc/PD-L1 to enhance anti-tumoral macrophages in triple-negative breast cancer progression.
    Runtian Wang, Gaigai Li, Fangyan Gao, Feng Xu, Xintong Li, Jian Zhang, Jinbo Li, Xiaoxiang Guan.
      Triple-negative breast cancer (TNBC) is the most challenging breast cancer subtype because of its aggressive behavior and limited therapeutic targets. c-Myc is hyperactivated in the majority of TNBC tissues, however, it has been considered an "undruggable" target due to its disordered structure. Herein, we developed an ultrasound-responsive spherical nucleic acid (SNA) against c-Myc and PD-L1 in TNBC. It is a self-assembled and carrier-free system composed of a hydrophilic small-interfering RNA (siRNA) shell and a hydrophobic core made of a peptide nucleic acid (PNA)-based antisense oligonucleotide (ASO) and a sonosensitizer. We accomplished significant enrichment in the tumor by enhanced permeability and retention (EPR) effect, the controllable release of effective elements by ultrasound activation, and the combination of targeted therapy, immunotherapy and physiotherapy. Our study demonstrated significant anti-tumoral effects in vitro and in vivo. Mass cytometry showed an invigorated tumor microenvironment (TME) characterized by a significant alteration in the composition of tumor-associated macrophages (TAM) and decreased proportion of PD-1-positive (PD-1+) T effector cells after appropriate treatment of the ultrasound-responsive SNA (USNA). Further experiments verified that tumor-conditioned macrophages residing in the TME were transformed into the anti-tumoral population. Our finding offers a novel therapeutic strategy against the "undruggable" c-Myc, develops a new targeted therapy for c-Myc/PD-L1 and provides a treatment option for the TNBC.
    Keywords:  c-Myc; self-assembly; spherical nucleic acid; triple-negative breast cancer
    DOI:  https://doi.org/10.1007/s11427-023-2433-y
  36. Int Immunopharmacol. 2023 Dec 24. pii: S1567-5769(23)01743-5. [Epub ahead of print]127 111416
    COL3A1 is a potential diagnostic biomarker for synovial chondromatosis and affects the cell cycle and migration of chondrocytes.
    Wen-Kang Chen, Han-Jing Zhang, Jianghua Liu, Zhu Dai, Xin-Li Zhan.
       BACKGROUND: Synovial chondromatosis (SC) primarily affects the major joints and is characterized by the formation of benign cartilaginous nodules. In the present study, we evaluated the differences in the histology and gene expression of SC and normal cartilages and further elucidated the function of hub genes in SC.
    METHODS: Histological staining and biochemical analysis were performed to measure collagen and glycosaminoglycan (GAG) contents in SC and normal cartilage samples. Then, microarray analysis was performed using knee joint samples (three normal and three SC samples) to identify the differentially expressed genes (DEGs). Subsequently, bioinformatics analysis was performed to identify the hub genes and explore the mechanisms underlying SC. The intersection of the top 10 upregulated DEGs, top 10 downregulated DEGs, and hub genes was validated in SC tissues. Lastly, in vitro experiments and our clinical cohort were used to determine the potential biological functions and diagnostic value, respectively, of the most significant gene.
    RESULTS: The GAG and collagen contents were comparable to or higher in SC tissues than in normal tissues. Microarray analysis revealed 143 upregulated and 107 downregulated DEGs in SC. Furthermore, functional enrichment analysis revealed an association between immunity and metabolism-related pathways and SC development. Among 20 hub genes, two intersection genes, namely, collagen type III alpha 1 chain (COL3A1) and HSPA8, were notably expressed in SC tissues, with COL3A1 exhibiting a more significant difference in mRNA expression. Furthermore, COL3A1 can promote chondrocyte migration and cell cycle progression. Additionally, clinical data revealed COL3A1 can be a diagnostic marker for primary SC (AUC = 0.82) and be a positive correlation with neutrophil-to-lymphocyte ratio.
    CONCLUSIONS: These results suggest that SC tissues contained the abundant GAG and collagen. COL3A1 can affect the function of chondrocytes and be a diagnostic marker of primary SC patients. These findings provide a novel approach and a fundamental contribution for diagnosis and treatment in SC.
    Keywords:  COL3A1; Chondrocytes migration; Diagnostic biomarker; Synovial chondromatosis
    DOI:  https://doi.org/10.1016/j.intimp.2023.111416
  37. Med Oncol. 2023 Dec 26. 41(1): 29
    GNL3L promotes autophagy via regulating AMPK signaling in esophageal cancer cells.
    Weiting He, Fengyao Sun, Wen Li, Ruihang Du, Siyuan Yan, Changqing Liu.
      Guanine nucleotide-binding protein-like 3-like (GNL3L), a conserved GTP-binding nucleolar protein, participates in regulating cell proliferation, and associates with tumorigenesis and poor prognosis in several kind of cancers. However, the role of GNL3L in modulating autophagy remains unclear. Here, we verified that GNL3L was higher expressed in esophageal cancer (ESCA) biopsies than that in the corresponding normal biopsies by a human ESCA tissue array. Utilizing immunoblotting and real-time PCR assays, we analyzed the expression of GNL3L in several ESCA cell lines, and it was highly expressed in KYSE410 cells and rarely expressed in KYSE150 cells, respectively. GNL3L overexpression promoted cell viability and cell proliferation in KYSE150 cells. On the contrary, silencing of GNL3L resulted in opposite phenotypes in KYSE410 cells. Furthermore, GNL3L level correlated with autophagic flux and influenced the levels of autophagy core proteins. Meanwhile, GNL3L also affected the AMPK signaling pathway, which is a pivotal signaling pathway for autophagy regulation. In the GNL3L-silenced cells, the AMPK agonist AICAR partly rescued the autophagic flux. Inversely, both pharmacologically and genetically deprivation of AMPK attenuated the autophagic flux induced by GNL3L overexpression. Moreover, AMPK activity alteration influenced the effect of GNL3L in regulating cell proliferation. Collectively, these findings suggest that GNL3L positively regulates cell proliferation and autophagy in ESCA cells via regulating the AMPK signaling, making itself a promising therapeutic target for ESCA.
    Keywords:  AMPK signaling; Autophagy; Esophageal cancer; GNL3L; Proliferation
    DOI:  https://doi.org/10.1007/s12032-023-02270-9
  38. J Biol Chem. 2023 Dec 21. pii: S0021-9258(23)02619-4. [Epub ahead of print] 105591
    LncNFYB promotes the proliferation of rheumatoid arthritis fibroblast-like synoviocytes via LncNFYB/ANXA2/ERK1/2 axis.
    Shibai Xiao, Qingqing Ouyang, Yi Feng, Xiaoxi Lu, Yipeng Han, Hao Ren, Qin Huang, Jinjun Zhao, Changhong Xiao, Min Yang.
      Long noncoding RNAs (lncRNAs) are specifically expressed in different diseases and regulate disease progression. To explore the functions of rheumatoid arthritis (RA)- specific lncRNA, we determined the lncRNA expression profile of fibroblast-like synoviocytes (FLS) obtained from patients with RA and osteoarthritis (OA) using an LncRNA microarray and identified up-regulated LncNFYB in RA as a potential therapeutic target. Using gain- and loss-of-function studies, LncNFYB was proved promoting FLS proliferation and cell cycle progress, but not affecting their invasion, migration, and apoptotic abilities. Further investigation discovered that LncRNA could combine with annexin A2 (ANXA2) and enhanced the level of phospho-ANXA2 (Tyr24) in the plasma membrane area, which induced the activation of ERK1/2 to promoting proliferation. These findings provide new insights into the biological functions of LncNFYB on modification of FLS, which may be exploited for the therapy of RA.
    Keywords:  ANXA2; ERK1/2; fibroblast-like synoviocytes; lncRNA; rheumatoid arthritis
    DOI:  https://doi.org/10.1016/j.jbc.2023.105591
  39. J Nutr. 2023 Dec 21. pii: S0022-3166(23)72821-6. [Epub ahead of print]
    COX19 is a new target of MACC1 and promotes colorectal cancer progression by regulating copper transport in mitochondria.
    Sheng Gao, Xiaodong Zhang, Jian Wang, Wenqi Bai, Bo Jiang.
       BACKGROUND: Recent studies have demonstrated that Cu plays an important role in the progression of tumor diseases. Metastasis associated with colon cancer protein 1 (MACC1) promotes the transcription and expression of various tumor-related genes. Cytochrome c oxidase (COX) 19, present in the cytoplasm and intermembrane space of mitochondria, may transport Cu within the mitochondria. However, the mechanism through which MACC1 regulates the Cu homeostasis mediated by COX19 remains unclear.
    OBJECTIVES: The aim of this study was to elucidate the mechanism through which MACC1 initiates the transcription and expression of COX19, and promotes malignant behavior in tumor cells.
    METHODS: Immunohistochemistry, western blotting, and real-time PCR analyses were conducted to analyze the expression of MACC1 and COX19 proteins and genes in tumor and normal tissues. RNA-CHIP was used to detect the transcriptional initiation of COX19 by MACC1. The effects of MACC1 and COX19 on mitochondrial activity were determined using an ATP assay kit and Cytochrome c Oxidase Assay Kit. A CCK-8 kit was used to detect the effect of high-dose Cu or overexpression of MACC1 and COX19 on tumor cell proliferation. A xenograft mouse model was used to analyze the effect of COX19 overexpression on the malignant behavior of the tumors.
    RESULTS: Cu enhanced the proliferation, invasion, and migration and inhibited apoptosis of SW480 cells. MACC1 was highly expressed in colorectal cancer tissues and activated the expression of COX19 by binding to its promoter region of COX19. The overexpression of COX19 increased mitochondrial Cu content and enhanced the activity of mitochondrial COX and ATP content, and inhibited apoptosis, promoted tumor growth of mice.
    CONCLUSIONS: Our results indicate that COX19 functions as a target gene of MACC1 and regulates mitochondrial activity and promotes the progression of colorectal cancer. MACC1/COX19 may provide a novel therapeutic target for colorectal cancer.
    Keywords:  COX19; Colorectal cancer; Copper metabolic; MACC1
    DOI:  https://doi.org/10.1016/j.tjnut.2023.12.032
  40. Front Oncol. 2023 ;13 1296814
    Deciphering the Hypoxia-immune interface in esophageal squamous carcinoma: a prognostic network model.
    Jie Hu, Qilong Liu, Bi Feng, Yanling Lu, Kai Chen.
       Introduction: The rapid progress and poor prognosis of the exercise of esophageal squamous cell carcinoma (ESCA) bring great challenges to the treatment. Hypoxia in the tumor microenvironment has become a key factor in the pathogenesis of tumors. However, due to the lack of clear therapeutic targets, hypoxia targeted therapy of ESCA is still in the exploratory stage.
    Methods: To bridge this critical gap, we mined a large number of gene expression profiles and clinical data on ESCA from public databases. First, weighted gene co-expression network analysis (WGCNA) and functional enrichment analysis were performed. We next delved into the relationship between hypoxia and apoptotic cell interactions. Meanwhile, using LASAS-Cox regression, we designed a robust prognostic risk score, which was subsequently validated in the GSE53625 cohort. In addition, we performed a comprehensive analysis of immune cell infiltration and tumor microenvironment using cutting-edge computational tools.
    Results: Hypoxia-related genes were identified and classified by WGCNA. Functional enrichment analysis further elucidated the mechanism by which hypoxia affected the ESCA landscape. The results of the interaction analysis of hypoxia and apoptotic cells revealed their important roles in driving tumor progression. The validation results of the prognostic risk score model in the GSE53625 cohort obtained a good area under the receiver operating characteristic (ROC) curve, and the risk score was independently verified as a significant predictor of ESCA outcome. The results of immune cell infiltration and tumor microenvironment analysis reveal the profound impact of immune cell dynamics on tumor evolution.
    Conclusion: Overall, our study presents a pioneering hypoxiacentered gene signature for prognostication in ESCA, providing valuable prognostic insights that could potentially revolutionize patient stratification and therapeutic management in clinical practice.
    Keywords:  esophageal squamous cell carcinoma (ESCA); hypoxia; immune infiltration; prognostic biomarkers; weighted gene co-expression network analysis (WGCNA)
    DOI:  https://doi.org/10.3389/fonc.2023.1296814
  41. Heliyon. 2023 Dec;9(12): e23161
    The lncRNA FENDRR inhibits colorectal cancer progression via interacting with and triggering GSTP1 ubiquitination by FBX8.
    Jing Yang, Yuemei Hu, Zhenyu Tan, Feng Zhang, Wentao Huang, Kai Chen.
       Background: Colorectal cancer (CRC) is characterized by its aggressiveness and high fatality rate. Long noncoding RNAs (lncRNAs) as molecular scaffolding in CRC have received little attention.
    Methods: The TCGA database was used to find putative anti-oncogenic lncRNAs in CRC. The effect of FENDRR on CRC was evaluated using the colony formation assay, transwell assays, and wound healing assays, and FENDRR expression was validated by qRT-PCR. The location of the FENDRR binding proteins was determined by an RNA pull-down experiment, and the retrieved proteins were recognized by mass spectrometry. RNA immunoprecipitation (RIP) studies were used to demonstrate the interaction of GSTP1, FBX8, and FENDRR. Co-IP and immunofluorescence were utilized to confirm the connection between GSTP1 and FBX8. To determine the precise signaling pathways implicated in the action of FENDRR in CRC, we performed next-generation sequencing (NGS) on CRC cells transfected with a vector overexpressing FENDRR.
    Results: The expression of FENDRR was significantly downregulated in CRC tissue and cells. The results of the function experiments showed that overexpression of FENDRR reduced CRC cells' ability to proliferation, invasion, migration and tube formation. In terms of mechanism, FENDRR could bind both GSTP1 and FBX8, act as a molecular scaffold, and utilize FBX8 to regulate the stability of GSTP1's protein. Additionally, the outcomes of NGS and qRT-PCR demonstrated that the expression of genes linked to the HIF-1 pathway was down-regulated following FENDRR overexpression. Lastly, rescue tests demonstrated that overexpression of GSTP1 in CRC cells could completely restore the inhibition induced by FENDRR.
    Conclusion: In this study, we found that the molecular scaffolding protein FENDRR regulates the ubiquitination of GSTP1 and the suppression of the HIF-1 signaling pathway in the development of CRC. Our research provides more evidence of FENDRR's crucial role in the emergence of CRC and identifies it as a potential therapeutic target for CRC patients.
    Keywords:  CRC; FBX8; FENDRR; GSTP1; HIF-1 signaling pathway; Ubiquitination
    DOI:  https://doi.org/10.1016/j.heliyon.2023.e23161
  42. Biosens Bioelectron. 2023 Dec 21. pii: S0956-5663(23)00908-9. [Epub ahead of print]247 115966
    Demethylation-activated light-up dual-color RNA aptamersensor for label-free detection of multiple demethylases in lung tissues.
    Xiao-Wen Liu, Ning-Ning Zhao, Hui-Min Yuan, Dong-Ling Li, Meng Liu, Chun-Yang Zhang.
      Methylation is one of the most prevalent epigenetic modifications in natural organisms, and the processes of methylation and demethylation are closely associated with cell growth, differentiation, gene transcription and expression. Abnormal methylation may lead to various human diseases including cancers. Simultaneous analysis of multiple DNA demethylases remains a huge challenge due to the requirement of diverse substrate probes and scarcity of proper signal transduction strategies. Herein, we propose a sensitive and label-free method for simultaneous monitoring of multiple DNA demethylases on the basis of demethylation-activated light-up dual-color RNA aptamers. The presence of targets AlkB homologue-3 (ALKBH3) and fat mass and obesity-associated enzyme (FTO) erases the methyl group in DNA substrate probes, activating the ligation-mediate bidirectional transcription amplification reaction to produce enormous Spinach and Mango aptamers. The resulting RNA aptamers (i.e., Spinach and Mango aptamers) can bind with their cognate nonfluorescent fluorogens (DFHBI and TO1-biotin) to significantly improve the fluorescence signals. This aptamersensor shows high specificity and sensitivity with a limit of detection (LOD) of 8.50 × 10-14 M for ALKBH3 and 6.80 × 10-14 M for FTO, and it can apply to screen DNA demethylase inhibitors, evaluate DNA demethylase kinetic parameters, and simultaneously measure multiple endogenous DNA demethylases in a single cell. Importantly, this aptamersensor can accurately discriminate the expressions of ALKBH3 and FTO between healthy tissues and non-small cell lung cancer (NSCLC) patient tissues, offering a powerful platform for clinical diagnosis and drug discovery.
    Keywords:  DNA demethylases; Dual-color RNA aptamersensor; Label-free detection; Lung cancer; Transcription amplification
    DOI:  https://doi.org/10.1016/j.bios.2023.115966
  43. Front Immunol. 2023 ;14 1235936
    Cellular RNA and DNA sensing pathways are essential for the dose-dependent response of human monocytes to ionizing radiation.
    Natallia Mikhalkevich, Eric Russ, Sergey Iordanskiy.
      Circulating monocytes are important players of the inflammatory response to ionizing radiation (IR). These IR-resistant immune cells migrate to radiation-damaged tissues and differentiate into macrophages that phagocytize dying cells, but also facilitate inflammation. Besides the effect of damage-associated molecular patterns, released from irradiated tissues, the inflammatory activation of monocytes and macrophages is largely dependent on IR-induced DNA damage and aberrant transcriptional activity, which may facilitate expression of type I interferons (IFN-I) and numerous inflammation-related genes. We analyzed the accumulation of dsRNA, dsDNA fragments, and RNA:DNA hybrids in the context of induction of RNA-triggered MAVS-mediated and DNA-triggered STING-mediated signaling pathways, in primary human monocytes and a monocytic cell line, THP1, in response to various doses of gamma IR. We found that exposure to lower doses (<7.5 Gy) led to the accumulation of dsRNA, along with dsDNA and RNA:DNA hybrids and activated both MAVS and STING pathway-induced gene expression and signaling activity of IFN-I. Higher doses of IR resulted in the reduced dsRNA level, degradation of RNA-sensing mediators involved in MAVS signaling and coincided with an increased accumulation of dsDNA and RNA:DNA hybrids that correlated with elevated STING signaling and NF-κB-dependent gene expression. While both pathways activate IFN-I expression, using MAVS- and STING-knockout THP1 cells, we identified differences in the spectra of interferon-stimulated genes (ISGs) that are associated with each specific signaling pathway and outlined a large group of STING signaling-associated genes. Using the RNAi technique, we found that increasing the dose of IR activates STING signaling through the DNA sensor cGAS, along with suppression of the DDX41 helicase, which is known to reduce the accumulation of RNA:DNA hybrids and thereby limit cGAS/STING signaling activity. Together, these results indicate that depending on the applied dose, IR leads to the activation of either dsRNA-induced MAVS signaling, which predominantly leads to the expression of both pro- and anti-inflammatory markers, or dsDNA-induced STING signaling that contributes to pro-inflammatory activation of the cells. While RNA:DNA hybrids boost both MAVS- and STING-mediated signaling pathways, these structures being accumulated upon high IR doses promote type I interferon expression and appear to be potent enhancers of radiation dose-dependent pro-inflammatory activation of monocytes.
    Keywords:  MAVS; RIG-I-like receptors (RLRs); RNA:DNA hybrids; gamma radiation; macrophages; melanoma differentiation-associated protein 5 (MDA-5); monocytes; stimulator of interferon genes (STING)
    DOI:  https://doi.org/10.3389/fimmu.2023.1235936
  44. Int Immunopharmacol. 2023 Dec 27. pii: S1567-5769(23)01770-8. [Epub ahead of print]127 111443
    Irisin mitigates rheumatoid arthritis by suppressing mitochondrial fission via inhibiting YAP-Drp1 signaling pathway.
    Yongmei Yu, Meican Ma, Chunyan Li, Qiujie Dang, Hongwei Lei, Gang Wang, Jianling Su, Yang Li.
       BACKGROUND: Irisin is a hormone-like factor secreted by muscle cells and produced by cleavage of the membrane protein fibronectin type III domain protein 5 (FNDC5), which exerts anti-inflammatory and anti-proliferative effects. However, the effects and the underlying mechanisms of irisin in rheumatoid arthritis (RA) are still unclear.
    METHOD: Collagen-induced arthritis (CIA) model was induced in DBA/1 mice and then treated with irisin. Arthritis index, paw thickness, weight, number of affected paws, serum inflammatory factors and related pathological tests were measured. RA fibroblast-like synoviocytes (RA-FLSs) were pretreated with IL-1β and irisin, and the migration, proliferation, invasion, oxidative stress and mitochondrial related function of RA-FLSs were detected.
    RESULTS: Irisin significantly improved arthritis symptoms in CIA mice, as indicated by reduced arthritis index, alleviated paw thickness, decreased the number of affected paws and inhibited release of inflammatory factors. Irisin alleviated joint destruction, FLSs proliferation and the expression of YES-associated protein (YAP) and mitochondrial dynamic related protein 1 (Drp1) in the FLSs of CIA mice. In vitro experiment, irisin inhibited the proliferation, migration and invasion of RA-FLSs and improved oxidative stress induced by IL-1β, thereby restraining the pathogenic transformation of RA-FLSs. Mechanically, irisin suppressed the nuclear translocation of YAP, in turn, could reduce the synthesis of Drp1 protein and inhibit the mitochondrial fission of RA-FLSs, which was reversed by YAP agonists. Therefore, irisin has a protective effect on RA.
    CONCLUSION: Irisin inhibits the proliferation, migration, invasion and inflammatory response of RA-FLSs by inhibiting the YAP-Drp1 signaling pathway, which implies a potential therapeutic effect on RA.
    Keywords:  Fibroblast-like synoviocytes; Irisin; Mitochondrial fission; Rheumatoid arthritis; YAP/Drp1
    DOI:  https://doi.org/10.1016/j.intimp.2023.111443
  45. Cancer Genomics Proteomics. 2024 Jan-Feb;21(1):21(1): 18-29
    Depletion of DNTTIP2 Induces Cell Cycle Arrest in Pancreatic Cancer Cells.
    Masato Yoshizawa, Atsushi Shiozaki, Eishi Ashihara.
       BACKGROUND/AIM: Pancreatic cancer is one of the most lethal malignant cancers worldwide and the seventh most common cause of cancer-related death in both sexes. Herein, we analyzed open access data and discovered that expression of a gene called deoxynucleotidyltransferase terminal-interacting protein 2 (DNTTIP2) is linked to prognosis of pancreatic ductal adenocarcinoma (PDAC). We then elucidated the role of DNTTIP2 in the proliferation of pancreatic cancer cells in vitro.
    MATERIALS AND METHODS: A WST-8 assay, cell cycle analysis, Annexin-V staining, quantitative reverse transcription-PCR, and western blot analysis were conducted to assess cell proliferation, cell cycle, apoptosis, and expression of DNTTIP2 mRNA and protein, respectively, in DNTTIP2-depleteted MIA-PaCa-2 and PK-1 cells.
    RESULTS: Depletion of DNTTIP2 induced G1 arrest in MIA-PaCa-2 cells by decreasing expression of special AT-rich sequence binding protein 1 (SATB1) and cyclin-dependent kinase 6 (CDK6). In addition, depletion of DNTTIP2 induced G2 arrest in PK-1 cells by decreasing expression of CDK1. Depletion of DNTTIP2 did not induce apoptosis in MIA-PaCa-2 or PK-1 cells.
    CONCLUSION: DNTTIP2 is involved in proliferation of pancreatic cancer cells. Thus, DNTTIP2 is a potential target for inhibiting progression of pancreatic cancers.
    Keywords:  CDK1; CDK6; DNTTIP2; Pancreatic cancer; SATB1; cells
    DOI:  https://doi.org/10.21873/cgp.20426
  46. J Immunother Cancer. 2023 Dec 26. pii: e007766. [Epub ahead of print]11(12):
    ASCC3 promotes the immunosuppression and progression of non-small cell lung cancer by impairing the type I interferon response via CAND1-mediated ubiquitination inhibition of STAT3.
    Yong-Qiang Ao, Jian Gao, Chun Jin, Shuai Wang, Li-Cheng Zhang, Jie Deng, Zong-Wei Chen, Hai-Kun Wang, Jia-Hao Jiang, Jian-Yong Ding.
       BACKGROUND: Activating signal cointegrator 3 (ASCC3) has been identified as an oncogenic factor that impairs host immune defense. However, the underlying mechanisms of carcinogenesis and its impact on the antitumor immune response remain unclear. In this study, we aimed to investigate the molecular mechanisms of ASCC3 in the progression of non-small cell lung cancer (NSCLC).
    METHODS: Single-cell sequencing data from the Gene Expression Omnibus and gene expression profiles from The Cancer Genome Atlas database were analyzed. The expression, clinical relevance and biological functions of ASCC3 in NSCLC were explored. Then, RNA sequencing, immunoprecipitation, mass spectrometry, immunofluorescence, and flow cytometry analyses were conducted to explore the underlying molecular mechanisms. In addition, in vivo experiments in mouse models were conducted to explore the probability of ASCC3 knockdown to improve the efficacy of anti-Programmed Death-1 (PD-1) therapy in NSCLC.
    RESULTS: ASCC3 was significantly upregulated in NSCLC and correlated with poor pathological characteristics and prognosis in patients with NSCLC. Overexpression of ASCC3 promoted malignant phenotypes of NSCLC cells and induced an immunosuppressive tumor microenvironment, which was characterized by a decrease in CD8+ T cells, natural killer cells and dendritic cells but an increase in regulatory T(Treg) cells. Mechanistically, ASCC3 stabilized signal transducer and activator of transcription (STAT)3 signaling by recruiting Cullin-associated and neddylation dissociated 1 (CAND1), which inhibited ubiquitin-mediated degradation of STAT3, thereby impairing the type I interferon response of tumor cells and promoting the immunosuppression and progression of NSCLC. Furthermore, high expression of ASCC3 impaired the efficacy of anti-PD-1 therapy, and an anti-PD-1 antibody combined with ASCC3 knockdown exerted promising synergistic efficacy in a preclinical mouse model.
    CONCLUSION: ASCC3 could stabilize the STAT3 pathway via CAND1, reshaping the tumor microenvironment and inducing resistance to anti-PD-1 therapy, which promotes the progression of NSCLC. It is a reliable prognostic indicator and can be a target in combination therapy for NSCLC.
    Keywords:  Immunotherapy; Lung Neoplasms; Tumor Microenvironment
    DOI:  https://doi.org/10.1136/jitc-2023-007766
  47. J Lasers Med Sci. 2023 ;14 e59
    Assessment of the Response of Human Umbilical Vein Endothelial Cells to Photodynamic Therapy: Highlighting the Role of Il-17 Signaling Pathway.
    Mona Zamanian Azodi, Babak Arjmand, Maryam Hamzeloo-Moghadam, Mostafa Rezaei Tavirani, Zahra Razzaghi, Alireza Ahmadzadeh, Reza M Robati, Majid Rezaei Tavirani.
      Introduction: Photodynamic therapy (PDT) is a method based on the application of a photosensitive agent and the administration of light irradiation on the treated samples. PDT is applied as an effective tool with minimal side effects against tumor tissues. This study aimed to assess the targets of critical genes by PDT at the cellular level of cancer to provide a new perspective on its molecular mechanism. Methods: To assess the effect of PDT, we extracted the differentially expressed genes (DEGs) from the gene expression profiles of human umbilical vein endothelial cells (HUVECs) treated with PDT from Gene Expression Omnibus (GEO) databases. The queried DEGs were evaluated via a regulatory network and gene ontology enrichment to find the critical targets. Results: Among 76 queried significant DEGs, 27 individuals were interacted by activation, inhibition, and co-expression actions. Thirty DEGs were related to the five classes of biological terms. The IL-17 signaling pathway and PTGS2, CXCL8, FOS, JUN, CXCL1, ZFP36, and FOSB were identified as the crucial targets of PDT. Conclusion: PDT as a stimulator of gene expression and an activator of gene activity overexpressed and hyper-activated many genes. It seems that PDT introduces a number of genes and pathways that can be regulated by anticancer drugs to fight against cancers.
    Keywords:  Cell; Gene; Human; Pathway; Photodynamic therapy
    DOI:  https://doi.org/10.34172/jlms.2023.59
  48. Chin J Physiol. 2023 Nov-Dec;66(6):66(6): 503-515
    Parkin enhances sensitivity of paclitaxel to nasopharyngeal carcinoma by activating BNIP3/NIX-mediated mitochondrial autophagy.
    Haifeng Ni, Renhui Liu, Zhen Zhou, Bo Jiang, Bin Wang.
      As a malignant head and neck cancer, nasopharyngeal carcinoma (NPC) has high morbidity. Parkin expression has been reported to be reduced in NPC tissues and its upregulation could enhance paclitaxel-resistant cell cycle arrest. This study was performed to explore the possible mechanism of Parkin related to B-cell lymphoma-2 (Bcl-2)/adenovirus E1B 19 kDa interacting protein 3 (BNIP3)/BNIP3-like (NIX)-mediated mitochondrial autophagy in NPC cells. Initially, after Parkin overexpression or silencing, cell viability and proliferation were evaluated by lactate dehydrogenase and colony formation assays. JC-1 staining was used to assess the mitochondrial membrane potential. In addition, the levels of cellular reactive oxygen species (ROS) and mitochondrial ROS were detected using DCFH-DA staining and mitochondrial ROS (MitoSOX) red staining. The expression of proteins was measured using Western blot. Results showed that Parkin overexpression inhibited, whereas Parkin knockdown promoted the proliferation of paclitaxel-treated NPC cells. Besides, Parkin overexpression induced, whereas Parkin knockdown inhibited mitochondrial apoptosis in paclitaxel-treated NPC cells, as evidenced by the changes of Cytochrome C (mitochondria), Cytochrome C (cytoplasm), BAK, and Bcl-2 expression. Moreover, the levels of ROS, mitochondrial membrane potential, and LC3II/LC3I in paclitaxel-treated C666-1 cells were hugely elevated by Parkin overexpression and were all declined by Parkin knockdown in CNE-3 cells. Furthermore, Parkin upregulation activated, whereas Parkin downregulation inactivated BNIP3/NIX signaling. Further, BNIP3 silencing or overexpression reversed the impacts of Parkin upregulation or downregulation on the proliferation and mitochondrial apoptosis of paclitaxel-treated NPC cells. Particularly, Mdivi-1 (mitophagy inhibitor) or rapamycin (an activator of autophagy) exerted the same effects on NPC cells as BNIP3 silencing or overexpression, respectively. Collectively, Parkin overexpression activated BNIP3/NIX-mediated mitochondrial autophagy to enhance sensitivity to paclitaxel in NPC.
    Keywords:  BNIP3/NIX; Parkin; mitochondrial autophagy; nasopharyngeal carcinoma; paclitaxel
    DOI:  https://doi.org/10.4103/cjop.CJOP-D-23-00076
  49. ACS Omega. 2023 Dec 19. 8(50): 47964-47973
    MeCP2-Induced Alternations of Transcript Levels and m6A Methylation in Human Retinal Pigment Epithelium Cells.
    Xueru Zhao, Yongya Zhang, Fei Wu, Xue Li, Sibei Guo, Xiaohua Li.
      MeCP2 is a transcriptional regulator that is involved in epithelial-mesenchymal transition (EMT) and is highly expressed in proliferative vitreoretinopathy. m6A methylation is a critical post-transcriptional regulation in eukaryotic cells. However, the connection between MeCP2 and m6A methylation has not been revealed in retinal pigment epithelium (RPE), and the regulatory role of MeCP2 at the post-transcriptional level in an m6A-dependent manner is rarely investigated. In this study, we used sequencing to reveal differences in transcript levels and m6A abundance of individual genes in RPE cells after treatment with human recombinant protein MeCP2. The biological functions and processes of differential genes were further analyzed by bioinformatics. The results exhibited that after MeCP2 treatment, 65 genes were up-regulated and 43 genes were down-regulated at the transcription level, and 4 peaks were hypermethylated and 9,041 peaks were hypomethylated at the m6A modification level. Enrichment analysis found that differentially expressed genes were associated with organic acid metabolism, melanogenesis, and vascular smooth muscle contraction. In addition, differentially methylated genes were related to cell junction, RNA processing and metabolism, cell activity, actin cytoskeleton, and several signaling pathways associated with EMT. Further conjoint analysis indicated that the transcription and m6A levels of the EGR1, ELOVL2, and SFR1 genes were altered, and EGR1 is an essential transcription factor in the EMT process. The RNA levels and m6A levels of the three genes were verified by qPCR and m6A-IP-qPCR, respectively. Overall, this study preliminarily revealed the differential mapping of MeCP2-induced m6A modifications, which contributes to the study of the epigenetic and EMT mechanism in RPE cells.
    DOI:  https://doi.org/10.1021/acsomega.3c06610
  50. Aging (Albany NY). 2023 Dec 21. 15
    Prognostic significance of senescence related tumor microenvironment genes in head and neck squamous cell carcinoma.
    Young Chan Lee, Yonghyun Nam, Minjeong Kim, Su Il Kim, Jung-Woo Lee, Young-Gyu Eun, Dokyoon Kim.
      The impact of the senescence related microenvironment on cancer prognosis and therapeutic response remains poorly understood. In this study, we investigated the prognostic significance of senescence related tumor microenvironment genes (PSTGs) and their potential implications for immunotherapy response. Using the Cancer Genome Atlas- head and neck squamous cell carcinoma (HNSC) data, we identified two subtypes based on the expression of PSTGs, acquired from tumor-associated senescence genes, tumor microenvironment (TME)-related genes, and immune-related genes, using consensus clustering. Using the LASSO, we constructed a risk model consisting of senescence related TME core genes (STCGs). The two subtypes exhibited significant differences in prognosis, genetic alterations, methylation patterns, and enriched pathways, and immune infiltration. Our risk model stratified patients into high-risk and low-risk groups and validated in independent cohorts. The high-risk group showed poorer prognosis and immune inactivation, suggesting reduced responsiveness to immunotherapy. Additionally, we observed a significant enrichment of STCGs in stromal cells using single-cell RNA transcriptome data. Our findings highlight the importance of the senescence related TME in HNSC prognosis and response to immunotherapy. This study contributes to a deeper understanding of the complex interplay between senescence and the TME, with potential implications for precision medicine and personalized treatment approaches in HNSC.
    Keywords:  cellular senescence; head and neck cancer; immunotherapy; microenvironment; single cell
    DOI:  https://doi.org/10.18632/aging.205346
  51. In Vivo. 2024 Jan-Feb;38(1):38(1): 474-481
    Association Between Clinicopathological Parameters and S100A8/A9 Expression According to Smoking History in Patients With Non-small Cell Lung Cancer.
    Sung Bae Cho, In Kyoung Kim, Chang Dong Yeo, Sang Haak Lee.
       BACKGROUND/AIM: Lung cancer is a major cause of cancer-related deaths worldwide, and chronic inflammation caused by cigarette smoke plays a crucial role in the development and progression of this disease. S100A8/9 and RAGE are associated with chronic inflammatory diseases and cancer. This study aimed to investigate the expression of S100A8/9, HMBG1, and other related pro-inflammatory molecules and clinical characteristics in patients with non-small cell lung cancer (NSCLC).
    PATIENTS AND METHODS: We obtained serum and bronchoalveolar lavage (BAL) fluid samples from 107 patients and categorized them as never or ever-smokers. We measured the levels of S100A8/9, RAGE, and HMGB1 in the collected samples using enzyme-linked immunosorbent kits. Immunohistochemical staining was also performed to assess the expression of S100A8/9, CD11b, and CD8 in lung cancer tissues. The correlation between the expression of these proteins and the clinical characteristics of patients with NSCLC was also explored.
    RESULTS: The expression of S100A8/A9, RAGE, and HMGB was significantly correlated with smoking status and was higher in people with a history of smoking or who were currently smoking. There was a positive correlation between serum and BAL fluid S100A8/9 levels. The expression of S100A8/A9 and CD8 in lung tumor tissues was significantly correlated with smoking history in patients with NSCLC. Ever-smokers, non-adenocarcinoma histology, and high PD-L1 expression were significant factors predicting high serum S100A8/9 levels in multivariate analysis.
    CONCLUSION: The S100A8/9-RAGE pathway and CD8 expression were increased in smoking-related NSCLC patients. The S100A8/9-RAGE pathway could be a promising biomarker for chronic airway inflammation and carcinogenesis in smoking-related lung diseases.
    Keywords:  Lung cancer; RAGE; S100A8/A9; inflammation; smoke
    DOI:  https://doi.org/10.21873/invivo.13462
  52. Front Genet. 2023 ;14 1293393
    Methylation and transcriptomic expression profiles of HUVEC in the oxygen and glucose deprivation model and its clinical implications in AMI patients.
    Yuning Tang, Yongxiang Wang, Shengxiang Wang, Runqing Wang, Jin Xu, Yu Peng, Liqiong Ding, Jing Zhao, Gang Zhou, Shougang Sun, Zheng Zhang.
      The obstructed coronary artery undergoes a series of pathological changes due to ischemic-hypoxic shocks during acute myocardial infarction (AMI). However, the altered DNA methylation levels in endothelial cells under these conditions and their implication for the etiopathology of AMI have not been investigated in detail. This study aimed to explore the relationship between DNA methylation and pathologically altered gene expression profile in human umbilical vein endothelial cells (HUVECs) subjected to oxygen-glucose deprivation (OGD), and its clinical implications in AMI patients. The Illumina Infinium MethylationEPIC BeadChip assay was used to explore the genome-wide DNA methylation profile using the Novaseq6000 platform for mRNA sequencing in 3 pairs of HUVEC-OGD and control samples. GO and KEGG pathway enrichment analyses, as well as correlation, causal inference test (CIT), and protein-protein interaction (PPI) analyses identified 22 hub genes that were validated by MethylTarget sequencing as well as qRT-PCR. ELISA was used to detect four target molecules associated with the progression of AMI. A total of 2,524 differentially expressed genes (DEGs) and 22,148 differentially methylated positions (DMPs) corresponding to 6,642 differentially methylated genes (DMGs) were screened (|Δβ|>0.1 and detection p < 0.05). After GO, KEGG, correlation, CIT, and PPI analyses, 441 genes were filtered. qRT-PCR confirmed the overexpression of VEGFA, CCL2, TSP-1, SQSTM1, BCL2L11, and TIMP3 genes, and downregulation of MYC, CD44, BDNF, GNAQ, RUNX1, ETS1, NGFR, MME, SEMA6A, GNAI1, IFIT1, and MEIS1. DNA fragments BDNF_1_ (r = 0.931, p < 0.0001) and SQSTM1_2_NEW (r = 0.758, p = 0.0043) were positively correlated with the expressions of corresponding genes, and MYC_1_ (r = -0.8245, p = 0.001) was negatively correlated. Furthermore, ELISA confirmed TNFSF10 and BDNF were elevated in the peripheral blood of AMI patients (p = 0.0284 and p = 0.0142, respectively). Combined sequencing from in vitro cellular assays with clinical samples, aiming to establish the potential causal chain of the causal factor (DNA methylation) - mediator (mRNA)-cell outcome (endothelial cell ischemic-hypoxic injury)-clinical outcome (AMI), our study identified promising OGD-specific genes, which provided a solid basis for screening fundamental diagnostic and prognostic biomarkers of coronary endothelial cell injury of AMI. Moreover, it furnished the first evidence that during ischemia and hypoxia, the expression of BNDF was regulated by DNA methylation in endothelial cells and elevated in peripheral blood.
    Keywords:  DNA methylation; acute myocardial infarction; brain-derived neurotrophic factor; mRNA sequence; oxygen-glucose deprivation; tumor necrosis factor superfamily member 10
    DOI:  https://doi.org/10.3389/fgene.2023.1293393
  53. Prostate. 2023 Dec 25.
    PrLZ regulates EMT and invasion in prostate cancer via the TGF-β1/p-smad2/miR-200 family/ZEB1 axis.
    Hongjun Xie, Jiaqi Chen, Zhenkun Ma, Yang Gao, Jin Zeng, Yule Chen, Zhao Yang, Shan Xu.
       BACKGROUND: Prostate leucine zipper (PrLZ) is a prostate-specific protein, and our previous study demonstrated that PrLZ enhances the malignant progression of prostate cancer (Pca). However, the roles of PrLZ in epithelial to mesenchymal transition (EMT) remain unknown.
    METHODS: Quantitative real-time PCR (qRT-PCR), immunohistochemical (IHC) staining, hematoxylin-eosin (HE) staining, and western blotting were used to analyze the expression of protein and genes level in human PCa cell lines. Invasion assay was used to examine the effect of PrLZ, miR-200a, miR-200b, miR-200c, miR-141, miR-429, miR-205, and ZEB1 on PCa cell line invasion in vitro. Prostate cancer metastasis animal model was designed to assess the effect of PrLZ on PCa cell line invasion in vivo.
    RESULTS: We proved that high PrLZ expression initiates EMT, which was shown by the downregulation of E-cadherin and upregulation of vimentin in PC-3/PrLZ and ARCaP-E/PrLZ cells. Mechanistic analysis revealed that PrLZ regulates EMT by activating TGF-β1/p-smad2 signaling and further inhibiting the expression of miR-200 family members, which negatively regulates ZEB1 expression and causes EMT in Pca. Moreover, using two of orthotopic mouse model and tail vein injection of human prostate cancer cells mouse model, we observed that PC-3/PrLZ cells led to the development of distant organ metastases in vivo.
    CONCLUSIONS: Our results show the mechanism by which PrLZ regulates EMT and metastasis and suggest that PrLZ may be a potential therapeutic target for Pca metastasis.
    Keywords:  EMT; PrLZ; ZEB1; miR-200 family; prostate cancer
    DOI:  https://doi.org/10.1002/pros.24647
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