1.Interplay Between Interferon Stimulatory Pathways and Organellar Dynamics
Jin-Ru LI ; Yu DUAN ; Xin-Gui DAI ; Yong-Ming YAO
Progress in Biochemistry and Biophysics 2025;52(7):1708-1727
Interferon stimulating factor STING, a transmembrane protein residing in the endoplasmic reticulum, is extensively involved in the sensing and transduction of intracellular signals and serves as a crucial component of the innate immune system. STING is capable of directly or indirectly responding to abnormal DNA originating from diverse sources within the cytoplasm, thereby fulfilling its classical antiviral and antitumor functions. Structurally, STING is composed of 4 transmembrane helices, a cytoplasmic ligand binding domain (LBD), and a C terminal tail structure (CTT). The transmembrane domain (TM), which is formed by the transmembrane helical structures, anchors STING to the endoplasmic reticulum, while the LBD is in charge of binding to cyclic dinucleotides (CDNs). The classical second messenger, cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), represents a key upstream molecule for STING activation. Once cGAMP binds to LBD, STING experiences conformational alterations, which subsequently lead to the recruitment of Tank-binding kinase 1 (TBK1) via the CTT domain. This, in turn, mediates interferon secretion and promotes the activation and migration of dendritic cells, T cells, and natural killer cells. Additionally, STING is able to activate nuclear factor-κB (NF-κB), thereby initiating the synthesis and release of inflammatory factors and augmenting the body’s immune response. In recent years, an increasing number of studies have disclosed the non-classical functions of STING. It has been found that STING plays a significant role in organelle regulation. STING is not only implicated in the quality control systems of organelles such as mitochondria and endoplasmic reticulum but also modulates the functions of these organelles. For instance, STING can influence key aspects of organelle quality control, including mitochondrial fission and fusion, mitophagy, and endoplasmic reticulum stress. This regulatory effect is not unidirectional; rather, it is subject to organelle feedback regulation, thereby forming a complex interaction network. STING also exerts a monitoring function on the nucleus and ribosomes, which further enhances the role of the cGAS-STING pathway in infection-related immunity. The interaction mechanism between STING and organelles is highly intricate, which, within a certain range, enhances the cells’ capacity to respond to external stimuli and survival pressure. However, once the balance of this interaction is disrupted, it may result in the occurrence and development of inflammatory diseases, such as aseptic inflammation and autoimmune diseases. Excessive activation or malfunction of STING may trigger an over-exuberant inflammatory response, which subsequently leads to tissue damage and pathological states. This review recapitulates the recent interactions between STING and diverse organelles, encompassing its multifarious functions in antiviral, antitumor, organelle regulation, and immune regulation. These investigations not only deepen the comprehension of molecular mechanisms underlying STING but also offer novel concepts for the exploration of human disease pathogenesis and the development of potential treatment strategies. In the future, with further probing into STING function and its regulatory mechanisms, it is anticipated to pioneer new approaches for the treatment of complex diseases such as inflammatory diseases and tumors.
2.tRF Prospect: tRNA-derived Fragment Target Prediction Based on Neural Network Learning
Dai-Xi REN ; Jian-Yong YI ; Yong-Zhen MO ; Mei YANG ; Wei XIONG ; Zhao-Yang ZENG ; Lei SHI
Progress in Biochemistry and Biophysics 2025;52(9):2428-2438
ObjectiveTransfer RNA-derived fragments (tRFs) are a recently characterized and rapidly expanding class of small non-coding RNAs, typically ranging from 13 to 50 nucleotides in length. They are derived from mature or precursor tRNA molecules through specific cleavage events and have been implicated in a wide range of cellular processes. Increasing evidence indicates that tRFs play important regulatory roles in gene expression, primarily by interacting with target messenger RNAs (mRNAs) to induce transcript degradation, in a manner partially analogous to microRNAs (miRNAs). However, despite their emerging biological relevance and potential roles in disease mechanisms, there remains a significant lack of computational tools capable of systematically predicting the interaction landscape between tRFs and their target mRNAs. Existing databases often rely on limited interaction features and lack the flexibility to accommodate novel or user-defined tRF sequences. The primary goal of this study was to develop a machine learning based prediction algorithm that enables high-throughput, accurate identification of tRF:mRNA binding events, thereby facilitating the functional analysis of tRF regulatory networks. MethodsWe began by assembling a manually curated dataset of 38 687 experimentally verified tRF:mRNA interaction pairs and extracting seven biologically informed features for each pair: (1) AU content of the binding site, (2) site pairing status, (3) binding region location, (4) number of binding sites per mRNA, (5) length of the longest consecutive complementary stretch, (6) total binding region length, and (7) seed sequence complementarity. Using this dataset and feature set, we trained 4 distinct machine learning classifiers—logistic regression, random forest, decision tree, and a multilayer perceptron (MLP)—to compare their ability to discriminate true interactions from non-interactions. Each model’s performance was evaluated using overall accuracy, receiver operating characteristic (ROC) curves, and the corresponding area under the ROC curve (AUC). The MLP consistently achieved the highest AUC among the four, and was therefore selected as the backbone of our prediction framework, which we named tRF Prospect. For biological validation, we retrieved 3 high-throughput RNA-seq datasets from the gene expression omnibus (GEO) in which individual tRFs were overexpressed: AS-tDR-007333 (GSE184690), tRF-3004b (GSE197091), and tRF-20-S998LO9D (GSE208381). Differential expression analysis of each dataset identified genes downregulated upon tRF overexpression, which we designated as putative targets. We then compared the predictions generated by tRF Prospect against those from three established tools—tRFTar, tRForest, and tRFTarget—by quantifying the number of predicted targets for each tRF and assessing concordance with the experimentally derived gene sets. ResultsThe proposed algorithm achieved high predictive accuracy, with an AUC of 0.934. Functional validation was conducted using transcriptome-wide RNA-seq datasets from cells overexpressing specific tRFs, confirming the model’s ability to accurately predict biologically relevant downregulation of mRNA targets. When benchmarked against established tools such as tRFTar, tRForest, and tRFTarget, tRF Prospect consistently demonstrated superior performance, both in terms of predictive precision and sensitivity, as well as in identifying a higher number of true-positive interactions. Moreover, unlike static databases that are limited to precomputed results, tRF Prospect supports real-time prediction for any user-defined tRF sequence, enhancing its applicability in exploratory and hypothesis-driven research. ConclusionThis study introduces tRF Prospect as a powerful and flexible computational tool for investigating tRF:mRNA interactions. By leveraging the predictive strength of deep learning and incorporating a broad spectrum of interaction-relevant features, it addresses key limitations of existing platforms. Specifically, tRF Prospect: (1) expands the range of detectable tRF and target types; (2) improves prediction accuracy through multilayer perceptron model; and (3) allows for dynamic, user-driven analysis beyond database constraints. Although the current version emphasizes miRNA-like repression mechanisms and faces challenges in accurately capturing 5'UTR-associated binding events, it nonetheless provides a critical foundation for future studies aiming to unravel the complex roles of tRFs in gene regulation, cellular function, and disease pathogenesis.
3. Establishment and biological characterization of drug-resistant cells and identification of multidrug resistance in small-cell lung cancer
Yong-Qing HAN ; Zheng-Yuan WANG ; Xiu-Fen DAI ; Zi-Ran WANG ; Jing LI ; Xin QI ; Jing LI
Chinese Pharmacological Bulletin 2024;40(2):279-284
Aim To establish NCI-H446/EP for small cell lung cancer resistant cells resistant to cisplatin and etoposide, and to evaluate their biological characteristics and multidrug resistance. Methods Nude mice were subcutaneously inoculated with NCI-H446 cells of SCLC to construct an in vivo model of xenograft tumor, and were given first-line EP regimen treatment for SCLC, inducing drug resistance in vivo, and stripping tumor tissue in vitro culture to obtain drug-resistant cells. The resistance coefficient, cell doubling time, cell cycle distribution, expression of multidrug resistance gene (MDR1), and drug resistance-related protein were detected in vitro, and the drug resistance to cisplatin and etoposide in vivo were verified. Results Mice with NCI-H446 tumors acquired resistance after eight weeks' EP regimen treatment, and the drug-resistant cell line NCI-H446/EP was obtained by isolation and culture in vitro. The resistance factors of this cell line to cisplatin, etoposide, SN38 and doxorubicin were 12.01, 18.36, 65.4 and 10.12, respectively. Compared with parental cells, the proportion of NCIH446/EP cells in Q
4.Clinical effectiveness of endoscopic thyroidectomy via transoral submental approach vs.open surgery:a comparative study
Huilin LUO ; Mengqiao DAI ; Cao LIU ; Zhener LI ; Yang XIE ; Yong YING ; Xiangtai ZENG
The Journal of Practical Medicine 2024;40(3):384-388
Objective To compare endoscopic thyroidectomy via transoral submental approach with open surgery for treating thyroid tumors in terms of the clinical effectiveness.Methods We retrospectively reviewed and analyzed the clinical data and follow-up records of 154 patients in the study,who were hospitalized for thyroidectomy in our hospital from January 2021 to June 2022.Among them,74 cases undergoing endoscopic thyroidectomy via transoral submental approach were assigned to the endoscopic group and 80 cases undergoing traditional open thyroid surgery to the open surgery group.Results All operations were completed successfully and safely in both groups,with no intermediate openings in the endoscopic group.Compared with the open surgery group,the endoscopic group had significantly fewer intraoperative blood losses[(19.46±10.24)mL vs.(32.05±15.87)mL],significantly less incision length[(1.95±0.30)cm vs.(7.05±0.60)cm],significant shorter operative time[(136.66±22.44)min vs.(82.75±15.20)min],and significantly less total postoperative drainage[(111.35±38.92)mL vs.(95.45±36.73)mL](all P<0.05).Endoscopic patients had superior postoperative pain and cosmetic satisfaction compared to open patients,and the difference was statistically significant(P<0.05).The two groups had no significant differences in the number of lymph node dissections,parathyroid hormone,and postoperative morbidity between the two groups(P>0.05).Conclusion The endoscopic thyroidectomy via transoral submental approach can achieve the same clinical effectiveness as the traditional open surgery.However,it is advantageous in reducing intra-operative blood loss,relieving post-operative pain,and achieving a better cosmetic effects of neck incision,thus deserving clinical promotion and application.
5.Optimization and application of an automatic monitoring module for drug-induced arrhythmias based on population characteristics
Peng LI ; Dai-Hong GUO ; Man ZHU ; Ao GAO ; Hai-Li GUO ; An FU ; An-Qi ZHAO ; Ting-Yong SHI
The Chinese Journal of Clinical Pharmacology 2024;40(9):1345-1349
Objective To develop the functions and optimize the automatic monitoring module for arrhythmias of the adverse drug event active surveillance and assessment system-Ⅱ,in order to continuously improve the performance,enhance the monitoring efficiency,and explore the ways to optimize the module.Methods Expand and optimize the functions of the module,increase the customized configuration,and determine the optimal setting conditions;compare the optimized test data with the results of the evaluation studies on the automatic monitoring of drug-induced arrhythmias in large samples of medicated population previously,and verify the optimization extent as well as the accuracy of the module.Results In the new module optimized according to the characteristics of the monitoring population,the function of"mandatory medical order keywords"was added,and it was determined that the inclusion of 6 electrocardiogram examination-related medical order keywords with a frequency of not less than 2 occurrences was the optimal configuration condition for the optimization of the module;combining the results of the previous automatic monitoring and evaluation researches,the system functions were verified and compared under the conditions of using the whole drugs and 2 kinds of single drug.While there was no loss of true positive cases,the number of cases with system alarms decreased by 30.75%,80.13%and 90.82%,respectively,compared with that before the optimization of the module,and the positive predictive value was significantly improved.Conclusion After the function expansion and optimization,the automatic monitoring module of drug-induced arrhythmias significantly reduces the labor cost of case evaluation and keeps the accuracy of monitoring results constant;the new module can better adapt to the demands of different automatic monitoring modes and operates stably,which is more generalizable and flexible,and provides a new way of considering for the research and development of automatic monitoring modules.
6.Research status of sodium-glucose co-transporter 2 inhibitors in the treatment of type 2 diabetes mellitus with heart failure with preserved ejection fraction
Ming-Yan LIU ; Bing-Qi ZHANG ; Hu-Hu LI ; Nai-Ru YUN ; Si-Miao FAN ; Rong-Rong YANG ; Rui-Ying GUO ; Yong-Na DAI
The Chinese Journal of Clinical Pharmacology 2024;40(13):1977-1981
Sodium-glucose co-transporter protein 2 inhibitor(SGLT2i)has steadily demonstrated benefits in the treatment of type 2 diabetes complicated with cardiovascular diseases based on evidence-based medicine,but its precise mechanism is yet unknown.We identified type 2 diabetes patients with HFpEF by searching PubMed,Web of Science,China knowledge network(CNKI),and other databases.We then summarized the pathological mechanism of HFpEF caused by type 2 diabetes.At the same time,to link to evidence-based medical,we explored the future of SGLT2i in clinical application.
7.Clinical trial of N-acetylcysteine in the treatment of children with respiratory tract infection
Jin-Tao SONG ; Yong ZHAO ; Hong-Chen DAI ; Gui-Tao LI
The Chinese Journal of Clinical Pharmacology 2024;40(20):2915-2919
Objective To observe the application effect of N-acetylcysteine in children with respiratory tract infection.Methods According to random number table method,children with respiratory tract infection were divided into control group and treatment group.The control group was given intravenous injection of ceftazidime(30-100 mg·kg-1,q12 h)on basis of routine symptomatic treatment,while treatment group was given aerosol inhalation of N-acetylcysteine solution(0.3 g∶3 mL,qd)on basis of control group.All patients were treated for 7 d.The clinical curative effect,remission time of symptoms,changes of chest X-ray,lung function[forced expiratory volume in 1 second(FEV1),tidal volume(VT),peak expiratory flow(PEF)],serum inflammatory factors,immune function and adverse drug reactions in the two groups were compared.Results In the trial,there were 28 cases excluded due to shedding and loss of follow-up,and there were 40 cases in treatment group and 52 cases in control group,respectively.After treatment,total clinical response rates in treatment group and control group were 92.50%(37 cases/40 cases)and 76.92%(40 cases/52 cases),the difference was statistically significant(P<0.05).After treatment,disappearance time of fever in treatment group and control group were(2.96±0.65)and(4.83±0.81)d;remission time of cough were(5.58±1.08)and(7.45±1.24)d;remission time of asthma were(3.23±0.54)and(4.72±0.75)d;disappearance time of lung rales were(4.66±0.72)and(5.94±0.87)d;FEV1 were(2.26±0.25)and(1.79±0.21)L;VT were(13.76±1.32)and(10.27±1.17)mL·kg-1;PEF were(5.78±0.68)%and(4.92±0.62)%;levels of serum C-reactive protein(CRP)were(7.68±1.18)and(9.41±1.29)mg·L-1;levels of interleukin-6(IL-6)were(18.76±3.24)and(22.75±3.85)ng·mL-1;levels of tumor necrosis factor α(TNF-α)were(8.93±1.51)and(15.46±2.24)ng·mL-1;CD4+/CD8+were 1.35±0.29 and 1.20±0.30.There were statistically significant differences in the above indexes between the treatment group and the control group(all P<0.05).In treatment group,there were 3 cases with nausea,1 case with vomiting and 1 case with diarrhea.In control group,there were 3 cases with vomiting and 2 cases with diarrhea.There was no significant difference in incidence of adverse drug reactions between treatment group and control group[12.50%(5 cases/40 cases)vs 9.62%(5 cases/52 cases),P>0.05].Conclusion Curative effect of N-acetylcysteine combined with ceftazidime is significant in children with respiratory tract infection,which can effectively improve lung function,relieve airway inflammation and enhance immune function,with good safety.
8.Quality evaluation for Beidougen Formula Granules
Gui-Yun CAO ; Xue-Song ZHUANG ; Bo NING ; Yong-Qiang LIN ; Dai-Jie WANG ; Wei-Liang CUI ; Hong-Chao LIU ; Xiao-Di DONG ; Meng-Meng HUANG ; Zhao-Qing MENG
Chinese Traditional Patent Medicine 2024;46(3):717-723
AIM To evaluate the quality of Beidougen Formula Granules.METHODS Fifteen batches of standard decoctions and three batches of formula granules were prepared,after which paste rate and contents,transfer rates of magnoflorine,daurisoline,dauricine were determined.HPLC specific chromatograms were established,and cluster analysis was adopted in chemical pattern recognition.RESULTS For three batches of formula granules,the paste rates were 15.1%-16.6%,the contents of magnoflorine,daurisoline,dauricine were 18.93-19.39,9.42-9.60,6.79-6.85 mg/g with the transfer rates of 34.42%-35.25%,43.81%-44.65%,27.27%-27.51%from decoction pieces to formula granules,respectively,and there were seven characteristic peaks in the specific chromatograms with the similarities of more than 0.95,which demonstrated good consistence with those of standard decoctions and accorded with related limit requirements.Fifteen batches of standard decoctions were clustered into two types,and the medicinal materials produced from Jilin,Hebei,Shangdong could be used for the preparation of formula granules.CONCLUSION This reasonable and reliable method can provide references for the quality control and clinical application of Beidougen Formula Granules.
9.Early result of postoperative echocardiographic evaluation in 28 patients underwent left ventricular assist device implantation
Yong LIN ; Guican ZHANG ; Xiaofu DAI ; Qianzhen LI ; Guanhua FANG ; Zhihuang QIU ; Heng LU ; Yi DONG ; Liangwan CHEN
Chinese Journal of Thoracic and Cardiovascular Surgery 2024;40(1):7-11
Objective:To extract the early result of postoperative echocardiographic evaluation in patients underwent left ventricular assist device (LVAD) implantation, and to assess the efficacy of surgical treatment for end-staged heart failure.Methods:Between June 2019 and May 2023, the patients underwent left ventricular assist device implantation were enrolled in this study. Demographic baseline characteristics and perioperative echocardiographic parameters were collected and analyzed.Results:A total of 28 patients were included in the study. After LVAD implantation, the heart sizes of the patients obviously reduced and the left heart contractibility function improved. The right ventricular contractibility remained stable. The proportion of the patients with moderate to severe mitral regurgitation was significantly reduced, but patients with mild to moderate aortic insufficiency increased. No serious complications such as death, pericardial tamponade and thrombosis events were observed during the follow-up period.Conclusion:LVAD implantation improved the left cardiac function, while the right cardiac function remained stable. However, it should be paid attention that the aortic valve function was impaired after the surgery. Generally, the early results of LVAD implantation for the treatment of end-stage heart failure were satisfactory.
10.Construction of a model based on multipoint full-layer puncture biopsy for predicting pathological complete response after neoadjuvant therapy for locally advanced rectal cancer
Ying JIN ; Zhiwei ZHAI ; Liting SUN ; Pingdian XIA ; Hang HU ; Chongqiang JIANG ; Baocheng ZHAO ; Hao QU ; Qun QIAN ; Yong DAI ; Hongwei YAO ; Zhenjun WANG ; Jiagang HAN
Chinese Journal of Gastrointestinal Surgery 2024;27(4):403-411
Objective:To investigate the value of transanal multipoint full-layer puncture biopsy (TMFP) in predicting pathological complete response (pCR) after neoadjuvant radiotherapy and chemotherapy (nCRT) in patients with locally advanced rectal cancer (LARC) and to establish a predictive model for providing clinical guidance regarding the treatment of LARC.Methods:In this multicenter, prospective, cohort study, we collected data on 110 LARC patients from four hospitals between April 2020 and March 2023: Beijing Chaoyang Hospital of Capital Medical University (50 patients), Beijing Friendship Hospital of Capital Medical University (41 patients), Qilu Hospital of Shandong University (16 patients), and Zhongnan Hospital of Wuhan University (three patients). The patients had all received TMFP after completing standard nCRT. The variables studied included (1) clinicopathological characteristics; (2) clinical complete remission (cCR) and efficacy of TMFP in determining pCR after NCRT in LARC patients; and (3) hospital attended, sex, age, clinical T- and N-stages, distance between the lower margin of the tumor and the anal verge, baseline and post-radiotherapy serum carcinoembryonic antigen (CEA) and carbohydrate antigen (CA)19-9 concentrations, chemotherapy regimen, use of immunosuppressants with or without radiotherapy, radiation therapy dosage, interval between surgery and radiotherapy, surgical procedure, clinical T/N stage after radiotherapy, cCR, pathological results of TMFP, puncture method (endoscopic or percutaneous), and number and timing of punctures. Single-factor and multifactorial logistic regression analysis were used to determine the factors affecting pCR after NCRT in LARC patients. A prediction model was constructed based on the results of multivariat analysis and the performance of this model evaluated by analyzing subject work characteristics (ROC), calibration, and clinical decision-making (DCA) curves. pCR was defined as complete absence of tumor cells on microscopic examination of the surgical specimens of rectal cancer (including lymph node dissection) after NCRT, that is, ypT0+N0. cCR was defined according to the Chinese Neoadjuvant Rectal Cancer Waiting Watch Database Study Collaborative Group criteria after treatment, which specify an absence of ulceration and nodules on endoscopy; negative rectal palpation; no tumor signals on rectal MRI T2 and DWI sequences; normal serum CEA concentrations, and no evidence of recurrence on pelvic computed tomography/magnetic resonance imaging.Results:Of the 110 patients, 45 (40.9%) achieved pCR after nCRT, which was combined with immune checkpoint inhibitors in 34 (30.9%). cCR was diagnosed before puncture in 38 (34.5%) patients, 43 (39.1%) of the punctures being endoscopic. There were no complications of puncture such as enterocutaneous fistulae, vaginal injury, prostatic injury, or presacral bleeding . Only one (2.3%) patient had a small amount of blood in the stools, which was relieved by anal pressure. cCR had a sensitivity of 57.8% (26/45) for determining pCR, specificity of 81.5% (53/65), accuracy of 71.8% (79/110), positive predictive value 68.4% (26/38), and negative predictive value of 73.6% (53/72). In contrast, the sensitivity of TMFP pathology in determining pCR was 100% (45/45), specificity 66.2% (43/65), accuracy 80.0% (88/110), positive predictive value 67.2% (45/67), and negative predictive value 100.0% (43/43). In this study, the sensitivity of TMFP for pCR (100.0% vs. 57.8%, χ 2=24.09, P<0.001) was significantly higher than that for cCR. However, the accuracy of pCR did not differ significantly (80.0% vs. 71.8%, χ 2=2.01, P=0.156). Univariate and multivariate logistic regression analyses showed that a ≥4 cm distance between the lower edge of the tumor and the anal verge (OR=7.84, 95%CI: 1.48-41.45, P=0.015), non-cCR (OR=4.81, 95%CI: 1.39-16.69, P=0.013), and pathological diagnosis by TMFP (OR=114.29, the 95%CI: 11.07-1180.28, P<0.001) were risk factors for pCR after NCRT in LARC patients. Additionally, endoscopic puncture (OR=0.02, 95%CI: 0.05-0.77, P=0.020) was a protective factor for pCR after NCRT in LARC patients. The area under the ROC curve of the established prediction model was 0.934 (95%CI: 0.892-0.977), suggesting that the model has good discrimination. The calibration curve was relatively close to the ideal 45° reference line, indicating that the predicted values of the model were in good agreement with the actual values. A decision-making curve showed that the model had a good net clinical benefit. Conclusion:Our predictive model, which incorporates TMFP, has considerable accuracy in predicting pCR after nCRT in patients with locally advanced rectal cancer. This may provide a basis for more precisely selecting individualized therapy.

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