1.Molecular Mechanisms of RNA Modification Interactions and Their Roles in Cancer Diagnosis and Treatment
Jia-Wen FANG ; Chao ZHE ; Ling-Ting XU ; Lin-Hai LI ; Bin XIAO
Progress in Biochemistry and Biophysics 2025;52(9):2252-2266
RNA modifications constitute a crucial class of post-transcriptional chemical alterations that profoundly influence RNA stability and translational efficiency, thereby shaping cellular protein expression profiles. These diverse chemical marks are ubiquitously involved in key biological processes, including cell proliferation, differentiation, apoptosis, and metastatic potential, and they exert precise regulatory control over these functions. A major advance in the field is the recognition that RNA modifications do not act in isolation. Instead, they participate in complex, dynamic interactions—through synergistic enhancement, antagonism, competitive binding, and functional crosstalk—forming what is now termed the “RNA modification interactome” or “RNA modification interaction network.” The formation and functional operation of this interactome rely on a multilayered regulatory framework orchestrated by RNA-modifying enzymes—commonly referred to as “writers,” “erasers,” and “readers.” These enzymes exhibit hierarchical organization within signaling cascades, often functioning in upstream-downstream sequences and converging at critical regulatory nodes. Their integration is further mediated through shared regulatory elements or the assembly into multi-enzyme complexes. This intricate enzymatic network directly governs and shapes the interdependent relationships among various RNA modifications. This review systematically elucidates the molecular mechanisms underlying both direct and indirect interactions between RNA modifications. Building upon this foundation, we introduce novel quantitative assessment frameworks and predictive disease models designed to leverage these interaction patterns. Importantly, studies across multiple disease contexts have identified core downstream signaling axes driven by specific constellations of interacting RNA modifications. These findings not only deepen our understanding of how RNA modification crosstalk contributes to disease initiation and progression, but also highlight its translational potential. This potential is exemplified by the discovery of diagnostic biomarkers based on interaction signatures and the development of therapeutic strategies targeting pathogenic modification networks. Together, these insights provide a conceptual framework for understanding the dynamic and multidimensional regulatory roles of RNA modifications in cellular systems. In conclusion, the emerging concept of RNA modification crosstalk reveals the extraordinary complexity of post-transcriptional regulation and opens new research avenues. It offers critical insights into the central question of how RNA-modifying enzymes achieve substrate specificity—determining which nucleotides within specific RNA transcripts are selectively modified during defined developmental or pathological stages. Decoding these specificity determinants, shaped in large part by the modification interactome, is essential for fully understanding the biological and pathological significance of the epitranscriptome.
2.Discovery of a normal-tension glaucoma-suspect rhesus macaque with craniocerebral injury: Hints of elevated translaminar cribrosa pressure difference.
Jian WU ; Qi ZHANG ; Xu JIA ; Yingting ZHU ; Zhidong LI ; Shu TU ; Ling ZHAO ; Yifan DU ; Wei LIU ; Jiaoyan REN ; Liangzhi XU ; Hanxiang YU ; Fagao LUO ; Wenru SU ; Ningli WANG ; Yehong ZHUO
Chinese Medical Journal 2024;137(4):484-486
3.Effects of Hedysarum polysaccharide on FXR-SHP-SREBP-1c signaling pathway in non-alcoholic fatty liver disease cell model
Lei ZHANG ; Zhi-Sheng JIN ; Xiao-Yi YANG ; Jia-Wei LI ; Ya-Ling LI ; Cai-Yun JIN ; Yan-Xu CHEN
The Chinese Journal of Clinical Pharmacology 2024;40(2):200-204
Objective To study the effect of Hedysarum polysaccharides(HPS)on the farnisol X receptor(FXR)-small heterodimer chaperone(SHP)-sterol regulatory element-binding protein 1 c(SREBP-1c)signaling pathway in the non-alcoholic fatty liver disease cell model.Methods The cells were cultured with 1.2 mmol·L-1 fatty acids to construct the non-alcoholic fatty liver disease cell model.The cell were divided into normal group(complete medium),model group(1.2 mmol·L-1 fatty acid solution),positive control group(1.2 mmol·L-1 fatty acid solution+50 μmol·L-1 alpha-lipoic acid)and experimental group(1.2 mmol·L-1 fatty acid solution+80 mg·L-1 HPS),culture for 24 h.The content of triglyceride(TG)and total cholesterol(TC),the activity of glutamate transaminase(GOT)and glutamate transaminasewas(GPT)detected by GPO-PAP enzyme method;the apoptosis rate was detected by flow cytometry;the expressions of FXR,SHP,SREBP-1c protein and mRNA in hepatocytes were detected by Western blot and reverse transcription-polymerase chain reaction(RT-PCR).Results The contents of TG in hepatocytes of normal group,model group,positve control group and experimental group were(2.91±1.13),(6.81±1.32),(3.72±0.52)and(4.67±0.62)mmol·gprot-1;the contents of TC in these four groups were(23.66±4.92),(67.96±5.56),(29.41±4.22)and(54.34±3.96)mmol·gprot-1;the activity of GOT in these four groups were(249.10±11.59),(322.63±28.81),(288.89±19.14)and(266.91±8.77)U·gprot-1;the activity of GPT in these four groups were(58.83±16.88),(134.55±22.96),(89.63±15.81)and(77.37±7.25)U·gprot-1,respectively;FXR mRNA expression levels were 1.01±0.16,2.09±0.12,1.83±0.17 and 1.45±0.15,respectively;SHP mRNA expression levels were 1.00±0.11,0.51±0.15,0.64±0.14 and 0.70±0.14,respectively;SREBP-1c mRNA were 1.00±0.08,1.57±0.19,1.37±0.13 and 1.21±0.15;the expression levels of FXR protein were 1.00±0.02,1.63±0.03,1.42±0.02 and 1.25±0.03,respectively;the expression levels of SHP protein were 1.00±0.02,0.23±0.01,0.54±0.21 and 0.62±0.02;the expression levels of SREBP-1c protein were 1.00±0.03,4.08±0.05,1.99±0.02 and 1.48±0.01,respectively.Compared with the normal group,there were significant differences in the above indexes of model group(all P<0.05);compared with the model group,there were significant differences in the above indexes of experimental group(all P<0.05).Conclusion HPS may protect liver cells by regulating the FXR-SHP-SREBP-1 c signaling pathway,reducing lipid synthesis in liver cells.
4.Effects of dihydromyricetin on myocardial oxidative damage in exhaustive exercise mice
Ze-Hai SU ; Ling QIN ; Quan-Shui HAO ; Jia-Bao XU
The Chinese Journal of Clinical Pharmacology 2024;40(10):1443-1447
Objective To investigate the effect of dihydromyricetin(DMY)on myocardial oxidative damage in exhaustive exercise mice.Methods C57BL/6 mice were divided into control group,model group,positive control group and low,medium and high dose experimental groups and with 10 mice in each group.Mice in control group and model group were intragastricated with distilled water;20,40 and 80 mg·kg-1 dihydromyricetin were given by gavage in low,medium and high dose experimental groups,while mice in positive control group were intragastricated with 100 mg·kg-1 Vitamin C once a day for 4 weeks.After administration,superoxide dismutase(SOD),malondialdehyde(MDA)and lactate dehydrogenase(LDH)were detected by the kit.The expression of nuclear factor E2-related factor 2(Nrf2)and heme oxygenase-1(HO-1)protein were detected by Western blot.Results SOD levels in control group,model group and low,medium,high dose experimental groups and positive control group were(57.81±6.92),(26.85±2.74),(33.68±4.52),(39.74±3.95),(48.97±4.26)and(39.22±3.54)U·mg-1;MDA were(4.72±0.36),(10.48±1.68),(8.75±0.82),(6.43±0.71),(5.11±0.48)and(6.36±0.64)nmol·mg-1;LDH were(268.71±23.94),(726.58±81.26),(621.32±47.59),(479.12±50.24),(337.91±34.99)and(486.15±50.98)U·L-1;Nrf2 protein expression were 0.75±0.06,0.19±0.02,0.30±0.04,0.47±0.05,0.63±0.06 and 0.49±0.06;the protein expression of HO-1 were 0.83±0.08,0.27±0.05,0.39±0.04,0.52±0.03,0.77±0.07 and 0.55±0.06,respectively.There were statistically significant differences between control group and model group(all P<0.05);there were statistically significant differences in the above indexes between model group and positive control group,low dose experimental group,medium dose experimental group,high dose experimental group(all P<0.05).Conclusion Dihydromyricetin can delay myocardial oxidative injury in exhaustive exercise mice,which may be related to Nrf2/HO-1 pathway.
5.Resveratrol alleviates the immune response and proliferation of macrophages induced by homocysteine
Xue-Sen ZHANG ; Kai-Yue QIN ; Xiao-Han LI ; Yan-Jia WANG ; Xi XU ; Xiao-Ling YANG
The Chinese Journal of Clinical Pharmacology 2024;40(14):2038-2042
Objective To explore the role of resveratrol in the immune response and proliferation of macrophages induced by homocysteine(Hcy).Methods ANA-1 cells were divided into control group(conventional culture),model group(100 μmol·L-1 Hcy),experimental-L,-M,-H groups(adding 25,50 and 100 μmol·L-1 resveratrol to model group,respectively),Hcy+Ad-SIRT1 group(100 μmol·L-1 Hcy+Ad-SIRT1),Hcy+si-FOXO1 group(100 μmol·L-1 Hcy+si-FOXO1),Hcy+Res-L+Ad-SIRT1+si-FOXO1 group(100 μmol·L-1 Hcy+25 μmol·L-1 Resveratrol transfected with Ad-SIRT1+si-FOXO1).The cell proliferation was detected by methyl thiazolyl tetrazolium(MTT),and the concentration of interleukin-6(IL-6)and tumor necrosis factor-α(TNF-α)in the supernatant of cell culture medium was detected by enzyme-linked immunosorbent assay.The gene and protein expression of silencing information regulator 1(SIRT1)and forkhead protein 01(FOXO1)were detected by Western blot.Results The optical density of 450 nm in control group,model group and experimental-L,-M,-H groups were 0.25±0.02,0.36±0.02,0.33±0.01,0.30±0.02 and 0.29±0.01,respectively.Compared with the control group,the cell proliferation in the model group was significantly increased(P<0.05).Cell proliferation in experimental-L,-M,-H groups was significantly decreased compared with model group(all P<0.05).IL-6 in the supernatant of cell culture medium of control group,model group and experimental-L group were(394.04±20.06),(614.23±21.09)and(501.53±16.52)pg·mL-1,respectively;TNF-α were(516.54±18.96),(717.22±24.81)and(632.74±19.11)pg·mL-1,respectively;SIRT1 relative protein expression were(1.00±0.05),(0.57±0.05)and(0.77±0.04),respectively;the relative protein expression of FOXO1 were 1.00±0.05,2.31±0.18 and 1.58±0.11,respectively.Compared with the control group,the above indexes in the experimental-L group had statistical significance(all P<0.05).The contents of IL-6 and TNF-α in cell culture fluid supernatant in model group,experimental-L group,Hcy+Ad-SIRT1 group and Hcy+si-FOXO1 group were significantly lower than those in model group,with statistical significance(all P<0.05).After co-transfection with Ad-SIRT1 and si-FOXO1,the contents of IL-6 and TNF-α in cell culture medium superserum of experimental-L group were significantly lower than those of Ad-SIRT1 group and si-FOXO1 group(all P<0.05).Conclusion Resveratrol can attenuate the immune response and proliferation of macrophages induced by Hcy,which may be related to the alteration of SIRT1/FOXO1 pathway.
6.Identification of TEAD1 Transcripts and Functional Analysis in Chicken Preadipocytes
Min PENG ; Hu XU ; Zi-Qiu JIA ; Qing-Zhu YANG ; Lin PAN ; Wei-Yu WANG ; Ling-Zhe KONG ; Ying-Ning SUN
Progress in Biochemistry and Biophysics 2024;51(1):215-229
ObjectiveAlthough expression of the TEAD1 protein in preadipocytes has been established, its function remains unclear. In this study, we sought to detect transcripts of TEAD1 in chicken and to examine the effects of this protein on the proliferation, migration, apoptosis, and differentiation of immortalized chicken preadipocyte cell lines (ICP1). MethodsThe full-length sequence of the TEAD1 gene was cloned and the two transcripts were subjected to bioinformatics analysis. The subcellsular localization of TEAD1 transcripts was determined based on indirect immunofluorescence. The effects of TEAD1 transcripts overexpression on the proliferation of ICP1 cells were examined by RT-qPCR, CCK-8, and EdU assays; the effects of TEAD1 transcripts on ICP1 cells migration were examined based on the scratch test; and the effects of TEAD1 transcripts overexpression on ICP1 cells apoptosis were analyzed using apoptosis-Hoechst staining and RT-qPCR. The expression of TEAD1 transcripts in different tissues, cells lines, and ICP1 at different periods of differentiation was analyzed by RT-qPCR. The effects of TEAD1 transcripts overexpression on lipid droplet accumulation and adipogenic-related gene expression in ICP1 cells were analyzed based on Oil Red O and BODIPY staining, RT-qPCR, Western blot, and dual-luciferase reporter gene assays. Finally, the content of triglyceride (TG) was measured in TEAD1 overexpressed ICP1 cells. ResultsThe full-length TEAD1 was cloned and two TEAD1 transcripts were identified. The TEAD1-V1 protein was found to be localized primarily in the cell nucleus, whereas the TEAD1-V2 protein is localized in the cell cytoplasm and nucleus. The overexpression of both TEAD1-V1 and TEAD1-V2 significantly inhibited the proliferation of ICP1 cells. Whereas the overexpression of TEAD1-V1 promoted ICP1 cell migration, the overexpression of TEAD1-V2 had no significant effects on ICP1 migration; the overexpression of both TEAD1-V1 and TEAD1-V2 significantly promoted the apoptosis of ICP1 cells. We found that the different transcripts of TEAD1 have similar expression pattern in different tissues and cells lines. During induced preadipocyte differentiation, the expression of these genes initially declined, although subsequently increased. Overexpression of TEAD1-V1 promoted a significant reduction in lipid droplet formation and inhibited C/EBPα expression during the differentiation of ICP1 cells (P<0.05). However, the overexpression of TEAD1-V2 had no significant effect on lipid droplet accumulation or the expression of adipogenic-related proteins (P>0.05). Overexpression of TEAD1-V1 significantly decreased triglyceride content in ICP1 cells (P<0.05), while overexpression of TEAD1-V2 had no effect on triglyceride content in ICP1 cells (P>0.05). ConclusionIn this study, for the first time, identified two TEAD1 transcripts. Overexpressed transcripts TEAD1-V1 and TEAD1-V2 both inhibited the proliferation of chicken preadipocytes and promoted apoptosis of chicken preadipocytes. TEAD1-V1 inhibited the differentiation of preadipocytes and promoted the migration of preadipocytes, while TEAD1-V2 had no effect on the differentiation and migration of preadipocytes.
7.Anti-glioblastoma study of YHP-836, a novel PARP1/2 inhibitor, in combination with temozolomide
Jia-ling DENG ; Ting-ting DU ; Jie ZHOU ; Bai-ling XU ; Xiao-guang CHEN ; Ming JI
Acta Pharmaceutica Sinica 2024;59(6):1656-1663
The aim of this study was to investigate and evaluate the antitumor effects of a novel poly(ADP-ribose) polymerase (PARP) 1/2 inhibitor, YHP-836, in combination with temozolomide (TMZ) for the treatment of glioblastoma (GBM). The cytotoxicity of YHP-836 was tested alone or in combination with TMZ using MTT assay. Immunoblotting and flow cytometry were also employed to assess the combination activity of YHP-836 and TMZ in multiply GBM cell lines. Further, the antitumor activity of YHP-836 and TMZ was evaluated using subcutaneous and orthotopic mice xenograft tumor models. All procedures were approved by the Ethics Committee for Animal Experiments of the Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College and conducted under the Guidelines for Animal Experiments of Peking Union Medical College. The approval number is 00009138. It was demonstrated that the combination of YHP-836 and TMZ increased the cytotoxicity against GBM cells and upregulated histone H2AX phosphorylation (
8.Mechanism of salvianolic acid B protecting H9C2 from OGD/R injury based on mitochondrial fission and fusion
Zi-xin LIU ; Gao-jie XIN ; Yue YOU ; Yuan-yuan CHEN ; Jia-ming GAO ; Ling-mei LI ; Hong-xu MENG ; Xiao HAN ; Lei LI ; Ye-hao ZHANG ; Jian-hua FU ; Jian-xun LIU
Acta Pharmaceutica Sinica 2024;59(2):374-381
This study aims to investigate the effect of salvianolic acid B (Sal B), the active ingredient of Salvia miltiorrhiza, on H9C2 cardiomyocytes injured by oxygen and glucose deprivation/reperfusion (OGD/R) through regulating mitochondrial fission and fusion. The process of myocardial ischemia-reperfusion injury was simulated by establishing OGD/R model. The cell proliferation and cytotoxicity detection kit (cell counting kit-8, CCK-8) was used to detect cell viability; the kit method was used to detect intracellular reactive oxygen species (ROS), total glutathione (t-GSH), nitric oxide (NO) content, protein expression levels of mitochondrial fission and fusion, apoptosis-related detection by Western blot. Mitochondrial permeability transition pore (MPTP) detection kit and Hoechst 33342 fluorescence was used to observe the opening level of MPTP, and molecular docking technology was used to determine the molecular target of Sal B. The results showed that relative to control group, OGD/R injury reduced cell viability, increased the content of ROS, decreased the content of t-GSH and NO. Furthermore, OGD/R injury increased the protein expression levels of dynamin-related protein 1 (Drp1), mitofusions 2 (Mfn2), Bcl-2 associated X protein (Bax) and cysteinyl aspartate specific proteinase 3 (caspase 3), and decreased the protein expression levels of Mfn1, increased MPTP opening level. Compared with the OGD/R group, it was observed that Sal B had a protective effect at concentrations ranging from 6.25 to 100 μmol·L-1. Sal B decreased the content of ROS, increased the content of t-GSH and NO, and Western blot showed that Sal B decreased the protein expression levels of Drp1, Mfn2, Bax and caspase 3, increased the protein expression level of Mfn1, and decreased the opening level of MPTP. In summary, Sal B may inhibit the opening of MPTP, reduce cell apoptosis and reduce OGD/R damage in H9C2 cells by regulating the balance of oxidation and anti-oxidation, mitochondrial fission and fusion, thereby providing a scientific basis for the use of Sal B in the treatment of myocardial ischemia reperfusion injury.
9.Epidemiological Investigation of Dampness Syndrome Manifestations in the Population at Risk of Cerebrovascular Disease
Xiao-Jia NI ; Hai-Yan HUANG ; Qing SU ; Yao XU ; Ling-Ling LIU ; Zhuo-Ran KUANG ; Yi-Hang LI ; Yi-Kai ZHANG ; Miao-Miao MENG ; Yi-Xin GUO ; Xiao-Bo YANG ; Ye-Feng CAI
Journal of Guangzhou University of Traditional Chinese Medicine 2024;41(3):531-539
Objective To make an epidemiological investigation on traditional Chinese medicine(TCM)dampness syndrome manifestations in the population at risk of cerebrovascular diseases in Guangdong area.Methods A cross-sectional study was conducted to analyze the clinical data related to the risk of cerebrovascular diseases in 330 Guangdong permanent residents.The diagnosis of dampness syndrome,quantitative scoring of dampness syndrome and rating of the risk of stroke were performed for the investigation of the distribution pattern of dampness syndrome and its influencing factors.Results(1)A total of 306(92.73%)study subjects were diagnosed as dampness syndrome.The percentage of dampness syndrome in the risk group was 93.82%(258/275),which was slightly higher than that of the healthy group(48/55,87.27%),but the difference was not statistically significant(χ2 = 2.91,P = 0.112).The quantitative score of dampness syndrome in the risk group was higher than that of the healthy group,and the difference was statistically significance(Z =-2.24,P = 0.025).(2)Among the study subjects at risk of cerebrovascular disease,evaluation time(χ2 = 26.11,P = 0.001),stroke risk grading(χ2= 8.85,P = 0.031),and history of stroke or transient ischemic attack(TIA)(χ2 = 9.28,P = 0.015)were the factors influencing the grading of dampness syndrome in the population at risk of cerebrovascular disease.Conclusion Dampness syndrome is the common TCM syndrome in the population of Guangdong area.The manifestations of dampness syndrome are more obvious in the population with risk factors of cerebrovascular disease,especially in the population at high risk of stroke,and in the population with a history of stroke or TIA.The assessment and intervention of dampness syndrome should be taken into account for future project of stroke prevention in Guangdong.
10.Bonding strength of metal brackets to polished and glazed zirconia ceramics with 3 adhesives respectively
Yu CAO ; Jia LIU ; Huichao ZHANG ; Jingyu XU ; Ling YU ; Surong YE ; Luyi YANG
Journal of Practical Stomatology 2024;40(1):53-57
Objective:To investigate the effects of 3 adhesives on the bond force and durability of polished and glazed zirconia ceram-ics to orthodontic metal brackets respectively.Methods:Universal adhesives,Single Bond Universal(SBU)and Prime&Bond Universal(PBU)were respectively used to bond polished and glazed zirconia to metal braces of maxillary central incisors using TransbondTM MIP(TM)as the control.The shear bond strength(SBS),the fracture morphology and adhesive residual index(ARI)were examed after wa-ter bath or water bath-thermal cycling storage.Results:The adhesive(P<0.001)and storage conditions(P<0.001)significantly af-fected the shear bond strength of zirconia to brackets.There was no significant difference between the polished or glazed groups(P=0.09).SBU showed the stronger SBS and lower ABI,there were significant differences in ARI scores among the 3 cements(P<0.001).Conclusion:SBU may have better bonding performance than PBU and TM in the orthodontic bonding of polished or glazed zir-conia surfaces to the zirconia ceramics.

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