1.β-glucan attenuates intestinal ischemia-reperfusion injury in mice by promoting glucagon-like peptide-1 secretion
Wei WANG ; Ben HAN ; Lihua SUN ; Huichao XIE ; Xiong ZENG ; Weidong XIAO ; Jian WANG
Journal of Army Medical University 2025;47(2):112-121
Objective To investigate the protective effect of β-glucan(BG)against intestinal ischemia reperfusion(II/R)injury by regulating the secretion of glucagon-like peptide-1(GLP-1).Methods Male C57BL/6 mice(6~8 weeks old)were subjected,and finally,the experiments had sham group,II/R group,II/R+BG group(0.1 mg/mL BG in drinking water for 2 weeks before modeling),II/R+liraglutide(LLT,GLP-1 analogue)group(0.2 μg/g LLT injected every 12 hours for 3 consecutive days before modeling),and II/R+BG+Ex9-39(GLP-1 R antagonist)group(intraperitoneal injection of 2 μg/g Ex9-39 1 h before modeling).After modeling,HE staining was used to observe intestinal morphological changes,and RT-qPCR and Western blotting were employed to evaluate the molecules(Occludin,ZO-1 and Claudin-1)related to intestinal barrier damage.The effect of 0.1 mg/mL BG treatment on the GLP-1 level in the serum and intestinal tissues of normal mice was determined with ELISA and immunofluorescence assay,respectively,and RT-PCR for the molecules related to GLP-1 expression(Gcg,Pcsk1/2,GIP and Foxa2).The effects of LLT and Ex9-39 pretreatment on intestinal morphology and intestinal barrier damage were also determined by morphological observation and expression levels of related molecules.Results II/R induced significant decreases in the mRNA levels of Occludin,ZO-1 and Claudin-1 and increase in Chiu's score when compared with sham control mice(P<0.05).While,the mRNA levels of the 3 molecules were obviously higher and the Chiu's score was lower in the II/R+BG group than the II/R group(P<0.05).BG pretreatment induced notably enhanced secretion of GLP-1 in the serum and intestinal tract of normal mice,and improved the mRNA expression of GLP-1-related molecules(P<0.05).The intervention of GLP-1 analogue LLT could attenuate the II/R damage and decreased Chiu's score,with statistical difference in comparison with the II/R group(P<0.05).GLP-1 receptor antagonist Ex9-39 reversed the protective effects of BG pretreatment against II/R damage,with notably differences in the expression of Occludin,ZO-1 and Claudin-1 and Chiu's score(P<0.05).Conclusion BG can attenuate intestinal mucosal and functional injury after II/R by promoting intestinal GLP-1 secretion.
2.Efficacy of different doses of methylprednisolone on AECOPD mice induced by influenza A virus infection
Lei XUE ; Rui GUI ; Qiang ZENG ; Wu LI ; Cheng LIANG ; Weijia ZHOU ; Xiaotian DAI ; Guohong DENG ; Wei XIONG
Journal of Army Medical University 2025;47(10):1081-1091
Objective To investigate the efficacy of varying doses of methylprednisolone(MP)on mice with acute exacerbations of chronic obstructive pulmonary disease(AECOPD)induced with influenza A virus(IAV).Methods Mouse model of COPD was established using LPS combined with smoking for 12 weeks,and then these COPD mice were treated with administration of 40 μL IAV via nasal drip to establish a AECOPD model.A total of 15 AECOPD mice were randomly divided into low-,medium-and high-dose MP groups,oseltamivir group and blank group.The body weight and survival time were monitored within 10 d after IAV infection.On days 1,3,and 5 post-treatment,lung function was assessed using whole-body plethysmography(WBP),inflammatory factors in bronchoalveolar lavage fluid(BALF)were quantified with ELISA,viral titers in BALF were determined using plaque assays,and colony-forming units were evaluated with blood agar plates.Immunofluorescence analysis:① Pulmonary immunofluorescence assay:Mice were randomly categorized into(n=4):LPS 1-day group,LPS 3-day group,and LPS+MP treatment group.All groups received an initial dose of LPS via atomization;subsequently,the LPS+MP treatment group received a single gavage dose of MP.Lung tissues were harvested from the 1-day LPS group on 1 d post-treatment,and from the 3-day LPS and LPS+MP groups on 3 d for immunofluorescence staining.② Cellular immunofluorescence assay:Mouse bone marrow neutrophils were classified into blank control(no intervention),LPS stimulation(LPS group),MP intervention with LPS stimulation(LPS+MP group),and MP intervention alone(MP group).The above cells were collected in 4 h after corresponding interventions for subsequent cellular immunofluorescence analysis.Results ①The medium-dose MP group demonstrated the most significant improvement in survival rate,weight recovery,and lung function when compared to other groups(P<0.05).② Treatment of medium-dose MP obviously reduced the levels of IL-6 and neutrophil extracellular traps(NETs)(P<0.05),while,elevated inflammatory factors and NETs were observed in the high-dose MP group on day 5 post-treatment.③ Notable decline in the lung injury score was found in the medium-dose MP group than the other groups(P<0.05).④The high-dose MP group exhibited substantial bacterial proliferation and delayed viral clearance since day 5 after treatment.Conclusion Medium-dose MP shows best efficacy in treatment of IAV-induced AECOPD,and the dose neither delays viral clearance nor increases the risk of bacterial infection following viral infection.
3.p300 promotes hepatic lipid accumulation in dyslipidemia by regulating SREBP-1c acetylation
Nyewneh Abdul-Rauf NUHU ; Xiaoli LI ; Lu FANG ; Yongqing CAI ; Fei CHEN ; Lie YUAN ; Xiong YANG ; Qingsong JIANG ; Yinbo LIU ; Chao LIU ; Peiling ZHONG ; Menghua ZENG
Journal of Army Medical University 2025;47(22):2735-2748
Objective To investigate the role of p300 in lipid metabolism disorders.Methods Bioinformatics analysis was performed to analyze the expression patterns of p300 in lipid metabolism disorder-related diseases and its correlation with SREBP-1c and downstream lipid metabolic enzymes.Immunofluorescence assay was used to detect the expression of p300 in the liver tissues of the patients with varying disease severity of non-alcoholic fatty liver disease(NAFLD).A mouse model of lipid metabolism disorder was established in male C57BL/6J mice by feeding high-fat diet(HFD)for 12 weeks.Western blotting was employed to assess p300 expression level in the liver tissues of HFD-fed mice.A cell model of lipid metabolism disorder was established in HepG2/AML-12 cells induced with free fatty acid(FFA).The effects of siRNA-mediated knockdown of p300 was observed to measure the levels of intracellular total cholesterol(TC)and triglyceride(TG),lipid deposition,and production of reactive oxygen species(ROS).Results Clinically,p300 was highly expressed in lipid metabolism disorders,and its level was positively correlated with NAFLD severity(P<0.05).Gene Set Enrichment Analysis(GSEA)revealed that p300 expression was significantly associated with fatty acid metabolism,cholesterol homeostasis,lipogenesis,PPAR signaling pathway,and peroxisome pathway.In vivo,p300 was significantly up-regulated in the livers of HFD-fed mice(P<0.01).In vitro,FFA stimulation markedly increased p300 expression in both HepG2 and AML-12 cells(P<0.01),whereas p300 knockdown significantly reduced intracellular TG and TC levels(P<0.01),attenuated lipid droplet accumulation,and reversed FFA-induced ROS elevation(P<0.01).Furthermore,p300 expression was positively correlated with the expression of SREBP-1c and its downstream key lipid synthesis enzymes.Conclusion p300 may promote hepatic lipid accumulation by acetylating and activating SREBP-1c and regulating downstream lipid metabolic enzymes,thereby affecting lipid synthesis and oxidative stress.These findings suggest that p300 may be a potential therapeutic target for lipid metabolism disorder-related diseases.
4.Intelligent cloud platform follow-up model improves joint range of motion and reduces follow-up costs after total knee arthroplasty:A retrospective cohort study
Shangwei YU ; Ke ZENG ; Ran XIONG ; Liming LIU ; Lin GUO
Journal of Army Medical University 2025;47(22):2763-2773
Objective To determine whether an intelligerct cloud platform follow-up model demonstrates superiority over conventional methods in enhancing follow-up quality,reducing costs,and improving functional recovery following total knee arthroplasty(TKA).Methods A retrospective cohort study was conducted on 260 patients undergoing TKA at our hospital from October 2022 to September 2023.According to the different postoperative follow-up methods,they were divided int a cloud platform group(n=130)and a traditional group(n=130).The baseline data,pre-and postoperative knee function scores,and follow-up costs were collected and compared between the 2 groups.Results The cloud platform group exhibited significantly higher rate of follow-up satisfaction,reduced resource utilization,shorter per-follow-up duration,fewer accompanying persons per visit,lower total follow-up expenditures,and decreased cumulative follow-up time when compared with the traditional group(P<0.05).At 6 weeks,3,6,and 12 months postoperatively,better range of motion(ROM)was observed in the cloud-based group than the traditional group(P<0.05),but no intergroup differences were seen in other knee function scores.Conclusion Cloud platform follow-up enhances early postoperative ROM(6 weeks to 12 months)and demonstrates marked cost-effectiveness when compared to the conventional mode.It represents a viable alternative for post-TKA rehabilitation surveillance.
5.Determination of Dilauryl Thiodipropionate in Fried Foods by Reverse Phase Liquid Chromatography-Tandem Mass Spectrometry
Jin-Can SHEN ; Yao LUO ; Feng-Qi WU ; Bei-Bei XIONG ; Zhang-Jie WU ; Ya-Mei LI ; Jun-Fa ZENG ; Chang-Xiong HUANG
Chinese Journal of Analytical Chemistry 2025;53(11):1860-1869
A method was developed for determination of dilauryl thiodipropionate(DLTDP)in fried foods by coupling solid-phase extraction(SPE)pretreatment with reverse-phase liquid chromatography-tandem mass spectrometry(RPLC-MS/MS)detection.Samples were extracted with n-hexane as the solvent,purified using a neutral alumina SPE cartridge,and finally analyzed by RPLC-MS/MS.Quantitative analysis was performed using matrix-matched calibration curves combined with an external standard method under optimal experimental conditions.The results showed that DLTDP exhibited good linearity in the range of 2.0-50.0 μg/L,with a correlation coefficient(R2)≥0.999.The limit of detection(LOD)and the limit of quantification(LOQ)of the method were 0.15 mg/kg and 0.5 mg/kg,respectively.The mean recoveries at three fortification levels(0.5,1.0,and 200 mg/kg)in different samples ranged from 84.8%to 96.8%,with the relative standard deviations(RSDs)all less than 8.0%.The developed method was highly sensitive,accurate and reliable,and easy to operate,making it well suited for the routine quantitative analysis of DLTDP in fried foods.
6.Efficacy of Shilian Powder Combined with Shumai Capsules in Promoting Wound Healing in Rats with Diabetic Foot Ulcers through Regulating the PI3K/Akt/Relaxin/Apelin Pathway
Yanping ZENG ; Zixin SHAO ; Wei MO ; Yang LIU ; Tianhao LI ; Xiong LYU ; Jianlu BI
Journal of Guangzhou University of Traditional Chinese Medicine 2025;42(2):461-468
Objective To observe the therapeutic effect and mechanism of external application with Shilian Powder combined with oral administration of Shumai Capsules for the treatment of rats with diabetic foot ulcer(DFU).Methods Eight male rats with successfully modeled foot ulcer(DF)were used as the control group.While 24 male rats with successfully modeled DFU were randomly divided into DFU group,Shumai Capsules group and Shilian Powder combined with Shumai Capsules group,with eight rats in each group.After the corresponding interventions,we determined the wound healing rate,histopathological changes of wound,levels of inflammatory factors such as interleukin(IL)-6,IL-1β and vascular endothelial growth factor(VEGF)in serum,levels of Apelin and Relaxin,and protein expressions of phosphatidylinositol 3-kinase(PI3K),protein kinase B(AKT)and VEGF in wound tissue,as well as mRNA expressions of PI3K,AKT,Relaxin and Apelin.Results Compared with the control group,the DFU group showed a significant decrease in wound healing rate,VEGF level in serum and wound,wound Relaxin level,protein and mRNA levels of wound AKT(P<0.05),and a significant increase in serum IL-6 and IL-1β levels,wound Apelin level,wound PI3K protein and mRNA levels(P<0.05),and the reduced wound granulation tissue and formation of new capillaries and increased inflammatory cell infiltration were seen under the microscope.Compared with the DFU group,the wound healing rate,VEGF level in serum and wound,wound Relaxin and Apelin levels,protein and mRNA levels of wound PI3K and AKT in the Shumai Capsules group and Shilian Powder combined with Shumai Capsules group were significantly increased(P<0.05),and serum IL-6 and IL-1β levels were significantly decreased(P<0.05),and the increased wound granulation tissue and formation of new capillaries and reduced inflammatory cell infiltration were seen under the microscope.Compared with the Shumai Capsules group,the wound healing rate,wound VEGF level,wound Relaxin and Apelin levels,protein and mRNA levels of wound PI3K and AKT in Shilian Powder combined with Shumai Capsules group were significantly increased(P<0.05),and the serum IL-6 and IL-1β levels were significantly decreased(P<0.05),and the increased wound granulation tissue and formation of new capillaries and reduced inflammatory cell infiltration were seen under the microscope.Conclusion External application with Shilian Powder combined with oral administration of Shumai Capsules can promote the wound healing in rats with DFU,its mechanism is related to the activation of PI3K/AKT/Relaxin/Apelin signaling pathway.
7.Clinical Observation of Long's Spinal Manipulation Therapy Combined with Four Postures of Rotational Tendon-Releasing Maneuver for Lumbar Disc Herniation
Shiyuan XIONG ; Manguang LIANG ; Guoqing ZENG ; Dihao WU ; Ying LIN ; Meiyi SU ; Dehui FAN
Journal of Guangzhou University of Traditional Chinese Medicine 2025;42(8):1963-1969
Objective To evaluate the clinical efficacy of Long's spinal manipulation therapy combined with four postures of rotational tendon-releasing maneuver in treating lumbar disc herniation(LDH).Methods Sixty-eight patients diagnosed with LDH were enrolled from the Department of Acupuncture and Rehabilitation at Guangdong Second Traditional Chinese Medicine Hospital between July 2024 and December 2024.Patients were randomly divided into an observation group and a control group using a random number table,with 34 cases in each group.The control group received Long's spinal manipulation therapy,while the observation group received additional training in four postures of rotational tendon-releasing maneuver.Both groups were treated for 2 weeks,with a 1-month follow-up.Clinical efficacy was evaluated after treatment by comparing Visual Analogue Scale(VAS)scores,Oswestry Disability Index(ODI)scores,and Japanese Orthopaedic Association(JOA)scores before and after intervention.Spinal parameters including maximum lumbar curvature angle,pelvic tilt angle,and maximum vertebral rotation angle were assessed using the DIERS formetric 3D evaluation system.Results(1)The total effective rate was 94.12%(32/34)in the observation group and 91.18%(31/34)in the control group,and both groups achieved ideal therapeutic efficacy,but the difference was not statistically significant(P>0.05).(2)After treatment,the VAS scores of patients in the two groups significantly improved(P<0.05),and the observation group was significantly superior to the control group in improving VAS scores,with statistically significant differences(P<0.05).At the 1-month follow-up after treatment,the VAS score of the observation group significantly improved(P<0.05),and the observation group was significantly superior to the control group,and the difference was statistically significant(P<0.05).(3)After treatment,the JOA and ODI scores of the patients in the two groups significantly improved(P<0.05),and the observation group was significantly superior to the control group in improving the JOA and ODI scores,and the difference was statistically significant(P<0.05).At 1-month follow-up after treatment,JOA and ODI scores of the observation group significantly improved(P<0.05),and the observation group was significantly superior to the control group,with statistically significant differences(P<0.05).(4)After treatment,the maximum angle of lumbar flexion,pelvic torsion angle,and maximum rotation angle of the vertebral body of the two groups of patients were significantly improved(P<0.05),and the observation group was significantly better than the control group,and the difference was statistically significant(P<0.05).At the 1-month follow-up after treatment,the maximum angle of lumbar flexion,pelvic torsion angle,and maximum vertebral rotation angle of the observation group were significantly improved(P<0.05),and the observation group was significantly superior to the control group,and the difference was statistically significant(P<0.05).Conclusion The combination of Long's spinal manipulation therapy and four postures of rotational tendon-releasing maneuve significantly improves spinal alignment,reduces pain and disability,and enhances quality of life in patients with LDH,demonstrating notable clinical efficacy.
8.Working practices in eliminating the public health crisis caused by viral hepatitis in Hainan Province of China
Weihua LI ; Changfu XIONG ; Taifan CHEN ; Bin HE ; Dapeng YIN ; Xuexia ZENG ; Feng LIN ; Biyu CHEN ; Xiaomei ZENG ; Biao WU ; Juan JIANG ; Lu ZHONG ; Yuhui ZHANG
Journal of Clinical Hepatology 2025;41(2):228-233
In 2022, Hainan provincial government launched the project for the prevention and control of viral hepatitis with the goals of a hepatitis B screening rate of 90%, a diagnostic rate of 90%, and a treatment rate of 80% among people aged 18 years and above by the year 2025, and the main intervention measures include population-based prevention, case screening, antiviral therapy, and health management. As of December 31, 2024, a total of 6.875 million individuals in the general population had been screened for hepatitis B, with a screening rate of 95.6%. A total of 184 710 individuals with positive HBsAg were identified, among whom 156 772 were diagnosed through serological reexamination, resulting in a diagnostic rate of 84.9%. A total of 50 742 patients with chronic hepatitis B were identified, among whom 42 921 had hepatitis B-specific health records established for health management, with a file establishment rate of 84.6%. A total of 31 553 individuals received antiviral therapy, with a treatment rate of 62.2%. A total of 2.503 million individuals at a high risk of hepatitis C were screened, among whom 4 870 tested positive for HCV antibody and 3 858 underwent HCV RNA testing, resulting in a diagnostic rate of 79.2%, and 1 824 individuals with positive HCV RNA were identified, among whom 1 194 received antiviral therapy, with a treatment rate of 65.5%. In addition, 159 301 individuals with negative HBsAg and anti-HBs and an age of 20 — 40 years were inoculated with hepatitis B vaccine free of charge. Through the implementation of the project for the prevention and control of viral hepatitis, a large number of hepatitis patients have been identified, treated, and managed in the province within a short period of time, which significantly accelerates the efforts to eliminate the crisis of viral hepatitis.
9.Immune function regulation and tumor-suppressive effects of Shenqi Erpi Granules on S_(180) tumor-bearing mice.
Xiong-Wei ZHANG ; Yan-Ning JIANG ; Hu QI ; Bin LI ; Yuan-Lin GAO ; Ze-Yang ZHANG ; Jian-An FENG ; Xi LI ; Nan ZENG
China Journal of Chinese Materia Medica 2025;50(13):3753-3764
This study aims to establish the S_(180) tumor-bearing mice model, and to investigate the influence of Shenqi Erpi Granules(SQEPG) on immune function, as well as the drug's tumor-suppressive effect and mechanism. SPF grade KM mice(half male and half female) were randomly divided into 6 groups: a control group, a model group, a cyclophosphamide group(50 mg·kg~(-1)), as well as SQEPG groups in low-, medium-, and high-dose(5.25, 10.5, 21 g·kg~(-1)). The control group and the model group were given distilled water, and the other 4 groups were given the corresponding drugs by gavage. The administration continued for 10 days before the mice were sacrificed. The antitumor and immune regulation effects of SQEPG were evaluated. The effect of SQEPG on delayed type hypersensitivity reaction(DTH), carbon clearance index, and serum hemolysin antibody level was observed to reflect the effect on the immune function of tumor-bearing mice. Tumor weight was recorded to calculate the tumor suppression rate and the immune organ index. Hematoxylin-eosin(HE) staining was used to detect morphological changes in tumor tissues. Flow cytometry was employed to detect the percentage of CD4~+ and CD8~+ T-cells in the spleen tissues and the tumor tissue apoptosis levels. Immunohistochemistry was conducted to detect the KI67 protein expression level of tumor tissues. ELISA resorted to the detection of the following expression levels in tumor tissues: tumor necrosis factor-α(TNF-α), interleukin-2(IL-2), interferon-γ(IFN-γ). Western blot was performed to detect the expression levels of caspase-3, B-cell lymphoma-2(Bcl-2), Bcl-2-associated X protein(Bax), cyclin-dependent kinases 4(CDK4), G_1/S-specific cyclin D1(cyclin D1), and vascular endothelial growth factor A(VEGFA). The results showed that, compared with the model group, the SQEPG could increase the swelling of the auricle of the tumor-bearing mice; significantly increase the phagocytic index of carbon granule contour(P<0.05 or P<0.01), and the middle dose of SQEPG could significantly increase the antibody level of hemolysin(P<0.05); different doses of SQEPG significantly inhibit the growth of the tumor, and decrease the mass of the tumor tissues(P<0.05 or P<0.01); the low dose of SQEPG significantly decreased spleen index(P<0.05), low and high doses of SQEPG increased thymus index, while medium doses of SQEPG decreased thymus index. High doses of SQEPG significantly elevated the levels of CD4~+ and CD8~+ T-cells in the spleens of the homozygous mice(P<0.01 or P<0.001), and increased the apoptosis rate of the cells of the tumor tissues(P<0.05); Meanwhile, high-dose SQEPG elevated the levels of immunity factors such as IL-2, IFN-γ and TNF-α in the serum of tumor-bearing mice(P<0.01); medium-and high-dose SQEPG significantly lowered the rate of positive expression of KI67 protein in tumor tissues(P<0.01). Compared with the model group, high-dose SQEPG significantly up-regulated the expression of caspase-3 and Bax proteins in tumor tissues(P<0.05), and significantly down-regulated the expression of CDK4, cyclin D1, and VEGFA proteins(P<0.05 or P<0.01). In conclusion, SQEPG has the effect of improving immune function and inhibiting tumor growth in tumor-bearing mice. Its mechanism of tumor-suppressive effects may be related to apoptosis promotion, cell cycle progression block, and tumor cell proliferation inhibition.
Animals
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Mice
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Drugs, Chinese Herbal/pharmacology*
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Male
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Female
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Apoptosis/drug effects*
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Sarcoma 180/genetics*
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Humans
10.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.

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