1.Da Chaihutang for Treatment of Sepsis with Yang Syndrome:A Randomized Controlled Trial
Na HUANG ; Guangmei CHEN ; Xingyu KAO ; Zhen YANG ; Weixian XU ; Kang YUAN ; Junna LEI ; Jingli CHEN ; Mingfeng HE
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(1):55-63
ObjectiveTo explore the clinical efficacy and safety of Da Chaihutang (DCH) for the treatment of sepsis with Yang syndrome. MethodsA total of 70 patients suffering from sepsis with Yang syndrome were randomly divided into an observation group and a control group, with 35 cases in each group. They both received standard Western medicine treatment. The observation group was additionally given a dose of DCH, which was boiled into 100 mL and taken twice. The control group was additionally given an equal volume and dosage of warm water. The intervention lasted for three days. The 28-day all-cause mortality and the changes in the following indicators before and after intervention were compared between the two groups, including sequential organ failure assessment (SOFA), acute physiology and chronic health evaluation Ⅱ (APACHE Ⅱ) score,white blood cell (WBC),the percentage of neutrophils (NEU%),C-reactive protein (CRP),procalcitonin (PCT),alanine transaminase (ALT),aspartate transaminase (AST),total bilirubin (TBil),creatinine (Cr),blood urea nitrogen (BUN),acute gastrointestinal injury (AGI) grade,gastrointestinal dysfunction score (GDS),serum intestinal fatty acid-binding protein (iFABP), citrulline (CR),platelet (PLT),prothrombin time(PT),activated partial thromboplastin time (APTT),fibrinogen (Fib),international normalized ratio (INR),and D-dimer (D-D). ResultsThere was no significant difference between the two groups regarding 28-day all-cause mortality. After the intervention,SOFA,WBC,PCT,and Cr were significantly decreased, and PLT was significantly increased in the control group (P<0.05). SOFA,APACHE Ⅱ,NEU%,CRP,PCT,ALT,AST,Cr,BUN,AGI grade,GDS,and serum iFABP and CR were significantly improved in the observation group (P<0.05). After the intervention,APACHE Ⅱ,PCT,AGI grade,GDS,and serum iFABP in the observation group were significantly lower than those in the control group ,while CR and PLT were higher (P<0.05,P<0.01). There were significant differences regarding the gap of SOFA,APACHE Ⅱ,AST,TBil,AGI grade,GDS,iFABP,CR, and PLT between the two groups (P<0.05,P<0.01). There were slight differences regarding PT,APTT,Fib,INR,and D-D between the two groups,which were in the clinical normal range. ConclusionOn the basis of Western medicine, DCH helped to reduce sepsis severity and improved multiple organ dysfunction with high clinical efficacy and safety, but further research on its impact on the prognosis of patients with sepsis is still required.
2.Untargeted Metabolomics Analysis of Demyelination in the Brain of Balb/c Mice Infected by Angiostrongylus cantonensis
Zhen NIU ; Xiaojie WU ; Liang YANG ; Zhixuan MA ; Junxiong YANG ; Ying FENG
Journal of Sun Yat-sen University(Medical Sciences) 2025;46(2):293-300
ObjectiveTo investigate the demyelination induced by Angiostrongylus cantonensis (AC) infection in the brain of Balb/c mice and analyze the untargeted metabolomic changes in the corpus callosum, aiming to elucidate the underlying mechanisms. MethodsBalb/c mice were randomly assigned to a control group (n=6) and an infection group (n=6). The infection group was orally administered 30 third-stage larvae of AC, while the control group received an equal volume of saline. Body weight, visual function, and behavioral scores were measured on post-infection 3, 6, 9, 12, 15, 18, and 21 days to assess neurological alterations. After 21 days, brain tissues were harvested for immunofluorescence staining, hematoxylin-eosin (HE) staining, and transmission electron microscopy to examine morphological changes in brain myelin and retina. Metabolomics analysis was performed, and differential metabolites were identified using volcano plots and heatmaps. The distribution of fold changes and bar charts were used to profile the key metabolites. These differential metabolites were then subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and regulatory network analysis. ResultsOn the 9th day after AC infection, Balb/c mice showed a decline in neurological behavioral scores (P<0.05). By day 15, visual scores decreased (P<0.05), and by day 21, significant weight loss (P<0.001) and mortality were observed. Concurrently, transmission electron microscopy and immunofluorescence staining revealed significant myelin damage in the corpus callosum and a marked reduction in oligodendrocytes (P<0.001). HE staining showed severe retinal ganglion cell damage. Metabolomic analysis revealed that glycerophospholipids were the most abundant differential metabolites, with steroids and sphingolipids being relatively less abundant. Cholesteryl ester CE (20:2) was significantly upregulated (P<0.001), while phosphatidylmethanol (18:0_18:1) was significantly downregulated (P<0.01). KEGG enrichment and regulatory network analyses demonstrated that the differential metabolites were mainly enriched in metabolic pathways like steroid biosynthesis, bile secretion, and cholesterol metabolism, and were involved in key metabolic pathways such as sphingolipid metabolism, neural signal regulation, and glycerophospholipid metabolism. ConclusionsAC infection affects the metabolic state of mice via multiple pathways, modifying the levels of metabolites crucial for myelination and myelin stability. Demyelination may be closely linked to the disruption of these key metabolic pathways, particularly the dysregulation of cholesterol and sphingolipid metabolism, potentially playing a central role in demyelination onset. Furthermore, alterations in phospholipid metabolism and abnormal nerve signaling regulation may exacerbate myelin damage.
3.Bioinformatics-based identification of a disintegrin and metalloprotease 8 as a potential shared target for inflammatory bowel disease and colorectal cancer
ZHANG Hong1 ; YANG Lanjie2△ ; ZHEN Yuanyuan1 ; HUANG Yihua1 ; XIANG Feng2 ; ZHANG Yongzhen1 ; HAN Junling1
Chinese Journal of Cancer Biotherapy 2025;32(6):611-619
[摘 要] 目的:筛选炎症性肠病(IBD)和结直肠癌(CRC)的潜在共病基因,探讨关键基因去整合素-金属蛋白酶8(ADAM8)与IBD及CRC发生发展的关系及其潜在机制。方法:基于从GEO数据库和TCGA数据库下载IBD及CRC患者的转录组数据及对应临床资料,通过差异分析、预后基因筛选及交集分析鉴定同致共病基因。用多个数据集分析和验证关键基因ADAM8在IBD及CRC中的表达特征及其与临床病理指标的关系。生存分析探究ADAM8在CRC中的预后价值。功能和通路富集分析探究ADAM8影响CRC进展的潜在机制,进一步用肿瘤微环境算法评估ADAM8与肿瘤微环境的关系。用免疫组化(IHC)法检测中国人CRC组织中的表达验证数据库数据。结果: ADAM8为IBD和CRC的潜在关键共病基因。ADAM8在IBD和CRC组织中均呈高表达(均P < 0.01),且其高表达提示疾病病理进展(P < 0.01)。高表达ADAM8的CRC患者总生存期(OS)更短(P < 0.05或P < 0.01)。ADAM8在中国人CRC组中也呈高表达(P < 0.01)。免疫细胞迁移、细胞因子产生及免疫受体相互作用等通路与ADAM8表达密切关联,ADAM8表达与中性粒细胞、巨噬细胞等免疫细胞浸润水平呈正相关(P < 0.01或P < 0.001)。结论:ADAM8在IBD和CRC组织中呈高表达,与患者预后、疾病进展及免疫细胞浸润密切关联,有望成为2种疾病的共同干预靶点。
4.Analysis and prediction of global burden due to cystic echinococcosis from 1990 to 2035
Zhen LAI ; Gang LIU ; Haili ZHAO ; Miaomiao QIU ; Jian CHEN ; En LUO ; Junguo XIN ; Xiaohong YANG
Chinese Journal of Schistosomiasis Control 2025;37(3):255-267
Objective To investigate the trends in the global burden due to cystic echinococcosis from 1990 to 2021, and to predict the global burden of cystic echinococcosis from 2022 to 2035, so as to provide insights into formulation of the cystic echinococcosis control strategy. Methods The global age-standardized prevalence, mortality, disability-adjusted life years (DALYs) rates and their 95% uncertainty intervals (UI) of cystic echinococcosis from 1990 to 2021 were captured from the Global Burden of Disease Study 2021 (GBD 2021) database, and the trends in the global burden of cystic echinococcosis from 1990 to 2021 were analyzed using the Joinpoint regression model. The associations between the global burden of cystic echinococcosis and socio-demographic index (SDI) were examined using a smoothing spline model and frontier analysis, and the global burden of cystic echinococcosis was projected from 2022 to 2035 using the Bayesian age-period-cohort (BAPC) model. Results The global agestandardized prevalence, mortality and DALYs rates of cystic echinococcosis were 7.69/105 [95% UI: (6.27/105, 9.51/105)], 0.02/105 [95% UI: (0.01/105, 0.02/105)], and 1.32/105 [95% UI: (0.99/105, 1.69/105)] in 2021. The global age-standardized prevalence of cystic echinococcosis appeared a tendency towards a rise by 0.14% per year from 1990 to 2021, and the global age-standardized mortality and DALYs rates of cystic echinococcosis appeared a tendency towards a decline by 4.68% and 4.01% per year from 1990 to 2021, respectively. Joinpoint regression analysis showed that global age-standardized prevalence of cystic echinococcosis appeared a tendency towards a decline from 1990 to 2000 [annual percent change (APC) = −0.66%, 95% confidence interval (CI): (−0.70%, −0.61%)] and from 2005 to 2015 [APC = −0.88%, 95% CI: (−0.93%, −0.82%)], and towards a rise from 2000 to 2005 [APC = 3.68%, 95% CI: (3.49%, 3.87%)] and from 2015 to 2021 [APC=0.30%, 95%CI: (0.19%, 0.40%)].Theagestandardized prevalence (r = −0.17, P < 0.05), mortality (r = −0.67, P < 0.05) and DALYs rates of cystic echinococcosis (r = −0.60, P < 0.05) all correlated negatively with SDI across 21 geographical regions from 1990 to 2021, and the age-standardized mortality (r = −0.61, P < 0.05) and DALYs rates (r = −0.44, P < 0.05) both correlated negatively with SDI across 204 countries and territories in 2021. Frontier analysis revealed that the age-standardized DALYs rate of cystic echinococcosis was still not in line with the frontier in some high-SDI countries or territories. In addition, the global age-standardized prevalence was projected with the BAPC model to appear a tendency towards a rise among both men [estimated annual percent change (EAPC) = 0.18%, 95% CI: (0.13%, 0.23%)] and women [EAPC = 0.29%, 95% CI: (0.24%, 0.34%)] from 2022 to 2035, and the global age-standardized mortality [men: EAPC = −4.71%, 95% CI: (−4.71%, −4.37%); women: EAPC = −4.74%, 95% CI: (−4.74%, −4.74%)] and DALYs rates [men: EAPC = −3.35%, 95% CI: (−3.36%, −3.34%); women: EAPC = −3.17%, 95% CI: (−3.18%, −3.16%)] were projected to appear a tendency towards a decline among both men and women. Conclusions The global burden of cystic echinococcosis appeared an overall tendency towards a decline from 1990 to 2021; however, the global prevalence of cystic echinococcosis is projected to appear a tendency towards a rise from 2022 to 2035. Intensified cystic echinococcosis control programmes are recommended.
5.Influenza vaccination on preventing the respiratory tract infection in preschool children
Mei LYU ; Zhen WANG ; Yu' ; e WANG ; Liyun FANG ; Yang YANG
Journal of Public Health and Preventive Medicine 2025;36(4):73-76
Objective To explore the effect of influenza vaccination on the prevention of respiratory tract infection in preschool children. Methods The clinical data of 400 preschool children (1-6 years old) who were diagnosed with respiratory tract infection for the first time in department of pediatrics of Xi'an Third Hospital and second department of respiratory medicine of Xi'an Children's Hospital were retrospectively analyzed from January 2023 to December 2023, including acute bronchitis, upper respiratory tract infection and pneumonia. According to the actual influenza vaccination status, the patients were divided into vaccination group (n=210) and non-vaccination group (n=190). The incidence of respiratory tract infection was compared between both groups. The fever duration, average course of disease, hospitalization rate, clinical symptoms scores (fever, cough, nasal congestion, sore throat), inflammation indicators [C-reactive protein (CRP), white blood cell count (WBC), neutrophil percentage (NE%)] and recurrence rate after 6 months of follow-up were compared. Results The incidence of respiratory tract infection in the vaccination group was significantly lower than that in the non-vaccination group (21.43% vs 43.16%, P<0.05), and the hospitalization rate was significantly lower compared with that in the non-vaccination group (P<0.05). The scores of fever, cough, nasal congestion and sore throat were lower in the vaccination group than those in the non-vaccination group (P<0.05), and the CRP, WBC and NE% were significantly lower compared to the non-vaccination group (P<0.05). After 6 months of follow-up, the recurrence rate in the vaccination group was 11.11% (5/45), which was significantly lower than 26.83% (22/82) in the non-vaccination group (χ2=0.038, P=4.288<0.05). Conclusion Influenza vaccination can effectively reduce the incidence of respiratory tract infection in preschool children, relieve the symptoms and shorten the disease course after infection. Its preventive effect on influenza is particularly significant, suggesting the importance of strengthening influenza vaccination in preschool children.
6.Incidence rate and independent risk factors of synchronous multiple lesions in early gastric cancer
Yanqing ZHOU ; Yue YANG ; Yu XIAO ; Hongyong LI ; Zhen NI
Journal of Public Health and Preventive Medicine 2025;36(4):81-84
Objective To explore the incidence rate and independent risk factors of synchronous multiple early gastric cancer (SMEGC) in patients with early gastric cancer, and to provide evidence for early screening and intervention of high-risk population. Methods A retrospective analysis was performed on 308 patients with early gastric cancer who received treatment in the hospital from March 2019 to March 2024. The incidence rate of SMEGC was counted, and the risk factors were analyzed by univariate and multivariate Logistic regression analyses. Results Among the 308 patients with early gastric cancer in this study, 23 cases were SMEGC and 285 were single early gastric cancer, which were included in the SMEGC group and the single group respectively. The incidence rate of SMEGC was 7.47% (23/308). Compared with the single group, the proportions of male, smoking history, tumor diameter≤2 mm, chronic atrophic gastritis and intestinal metaplasia degree were higher in the SMEGC group (2=4.331、8.608、4.618、6.490、4.897,P=0.037、0.003、0.032、0.001、0.027). Logistic regression analysis suggested that chronic atrophic gastritis (OR=3.133, 95%CI: 1.240-7.918) and moderate-to-severe intestinal metaplasia (OR=3.171, 95%CI: 1.252-8.029) were independent risk factors for SMEGC (P<0.05). Conclusion Some patients with early gastric cancer are SMEGC. Chronic atrophic gastritis and moderate-to-severe intestinal metaplasia are independent risk factors affecting the occurrence of SMEGC. It is recommended to regularly screen high-risk patients and optimize management strategies to reduce the risk of SMEGC.
7.Renshentang Alleviates Atherosclerosis in Mice by Targeting TRPV1 to Regulate Foam Cell Cholesterol Metabolism
Yulu YUAN ; Ce CHU ; Xuguang TAO ; Zhen YANG ; Xiangyun CHEN ; Zhanzhan HE ; Yongqi XU ; Yuxin ZHANG ; Peizhang ZHAO ; Wanping CHEN ; Hongxia ZHAO ; Wenlai WANG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):11-19
ObjectiveTo explore the effects of Renshentang on atherosclerosis (AS) in mice based on the role of transient receptor potential vanilloid1 (TRPV1) in regulating cholesterol metabolism in foam cells. MethodsNine SPF-grade 8-week-old C57BL/6J mice were set as a normal group, and 60 ApoE-/- mice were randomized into model, positive drug (simvastatin, 0.02 g·kg-1·d-1), and low-, medium-, and high-dose (1.77, 3.54, 7.08 g·kg-1·d-1, respectively) Renshentang groups (n=12) according to body weight. The normal group was fed with a normal diet, and the other groups were fed with a high-fat diet and given corresponding drugs by oral gavage for the modeling of AS. The mice were administrated with corresponding drugs once a day for 12 weeks. After the last administration and fasting for 12 h, the aorta was collected. Plaque conditions, pathological changes, levels of total cholesterol (TC), triglcerides (TG), low-density lipoprotein-cholesterol (LDL-C), and high-density lipoprotein-cholesterol (HDL-C), and the expression of TRPV1, liver X receptor (LXR), inducible degrader of the low-density lipoprotein receptor (IDOL), and low-density lipoprotein receptor (LDLR) in the aortic tissue were observed and detected by gross oil red O staining, HE staining, Western blot, immunohistochemistry, and real-time PCR. ResultsCompared with the normal group, the model group presented obvious plaque deposition in the aorta, raised levels of TC, TG, and LDL-C in the serum (P<0.01), up-regulated expression level of LDLR in the aorta (P<0.01), lowered level of HDL-C in the serum, and down-regulated expression levels of TRPV1, LXR, and IDOL in the aorta (P<0.05, P<0.01). Compared with the model group, the positive drug and Renshentang at different doses alleviated AS, elevated the levels of HDL-C, TRPV1, LXR, and IDOL (P<0.05, P<0.01), while lowering the levels of TC, TG, LDL-C, and LDLR (P<0.05, P<0.01). ConclusionRenshentang has a lipid-lowering effect on AS mice. It can effectively reduce lipid deposition, lipid levels, and plaque area of AS mice by activating TRPV1 expression and regulating the LXR/IDOL/LDLR pathway.
8.Renshentang Alleviates Atherosclerosis in Mice by Targeting TRPV1 to Regulate Foam Cell Cholesterol Metabolism
Yulu YUAN ; Ce CHU ; Xuguang TAO ; Zhen YANG ; Xiangyun CHEN ; Zhanzhan HE ; Yongqi XU ; Yuxin ZHANG ; Peizhang ZHAO ; Wanping CHEN ; Hongxia ZHAO ; Wenlai WANG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):11-19
ObjectiveTo explore the effects of Renshentang on atherosclerosis (AS) in mice based on the role of transient receptor potential vanilloid1 (TRPV1) in regulating cholesterol metabolism in foam cells. MethodsNine SPF-grade 8-week-old C57BL/6J mice were set as a normal group, and 60 ApoE-/- mice were randomized into model, positive drug (simvastatin, 0.02 g·kg-1·d-1), and low-, medium-, and high-dose (1.77, 3.54, 7.08 g·kg-1·d-1, respectively) Renshentang groups (n=12) according to body weight. The normal group was fed with a normal diet, and the other groups were fed with a high-fat diet and given corresponding drugs by oral gavage for the modeling of AS. The mice were administrated with corresponding drugs once a day for 12 weeks. After the last administration and fasting for 12 h, the aorta was collected. Plaque conditions, pathological changes, levels of total cholesterol (TC), triglcerides (TG), low-density lipoprotein-cholesterol (LDL-C), and high-density lipoprotein-cholesterol (HDL-C), and the expression of TRPV1, liver X receptor (LXR), inducible degrader of the low-density lipoprotein receptor (IDOL), and low-density lipoprotein receptor (LDLR) in the aortic tissue were observed and detected by gross oil red O staining, HE staining, Western blot, immunohistochemistry, and real-time PCR. ResultsCompared with the normal group, the model group presented obvious plaque deposition in the aorta, raised levels of TC, TG, and LDL-C in the serum (P<0.01), up-regulated expression level of LDLR in the aorta (P<0.01), lowered level of HDL-C in the serum, and down-regulated expression levels of TRPV1, LXR, and IDOL in the aorta (P<0.05, P<0.01). Compared with the model group, the positive drug and Renshentang at different doses alleviated AS, elevated the levels of HDL-C, TRPV1, LXR, and IDOL (P<0.05, P<0.01), while lowering the levels of TC, TG, LDL-C, and LDLR (P<0.05, P<0.01). ConclusionRenshentang has a lipid-lowering effect on AS mice. It can effectively reduce lipid deposition, lipid levels, and plaque area of AS mice by activating TRPV1 expression and regulating the LXR/IDOL/LDLR pathway.
9.Evaluation and prospect of clinical pharmacist instructor training reform oriented toward enhancing clinical teaching competence
Li YOU ; Jiancun ZHEN ; Jing BIAN ; Zhuo WANG ; Yunyun YANG ; Jin LU ; Jing LIU
China Pharmacy 2025;36(17):2085-2091
OBJECTIVE To summarize the implementation experiences of the China Hospital Association’s Clinical Pharmacist Instructor Training Program Reform, and to evaluate the effectiveness of the reform, thus continuously enhancing the quality and standards of clinical pharmacist instructor training. METHODS The study drew on project evaluation methodologies to summarize the main characteristics of the comprehensive system and new model for clinical pharmacist instructor training established through the reform by literature review. The “learning assessment” and “reaction assessment” were conducted by using Kirkpatrick’s four-level model of evaluation in order to evaluate the effectiveness of the clinical pharmacist instructor training reform through statistically processing and analyzing the performance data and teaching evaluation data of the instructor participants. Based on problem and trend analysis, the future development directions were anticipated for the reform of clinical pharmacist instructor training. RESULTS & CONCLUSIONS The latest round of clinical pharmacist instructor training reform initiated by the Chinese Hospital Association had initially established a four-pronged training system encompassing “recruitment, training, assessment, and management”. It had also forged a training 。 model “oriented towards enhancing clinical teaching competency, with practical learning and skill-based assessment conducted on clinical teaching sites as its core”. Following a period of over three years of gradual reform, the new training system and model became increasingly mature. In both 2023 and 2024, the participants achieved relatively high average total scores in their initial completion assessments [with scores of (84.05± 5.83) and (85.82±4.35) points, respectively]. They also reported a strong sense of gain from the training reform [with self- perceived gain scores of (4.80±0.44) and (4.85±0.39) points, respectively]. The operation and implementation effects of the reform were generally satisfactory. In the future, clinical pharmacist instructor training reforms should continue to address the issues remaining from the current phase, while aligning with global trends in pharmacy education and industry development. Additionally, sustained exploration and practice will be carried out around the core objective of “enhancing clinical teaching competence”.
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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