1.Analysis of thermal environment and students thermal comfort in primary and secondary school classrooms in winter
Chinese Journal of School Health 2026;47(2):168-172
Objective:
To evaluate the current situation of thermal environment in primary and secondary school classrooms during winter, and to analyze students thermal comfort needs, so as to provide a basis for improving classroom thermal environment.
Methods:
From December 16 to 26, 2024, a stratified cluster random sampling method was used to select 90 classrooms from 15 primary and secondary schools in centralized/air conditioned heating areas(Liaoning Province, Tianjin City, Shanghai City) and naturally ventilated areas(Anhui Province and Jiangxi Province)for on site environmental measurement. A questionnaire survey was conducted among 743 students. The differences between groups using the χ 2 test were compared. Based on actual measurement data, a predicted mean vote prepared percentage of dissatisfied (PMV-PPD) model for centralized/air conditioned classrooms and an adaptive model for naturally ventilated classrooms were established, and the thermal neutral temperature and comfort interval were calculated.
Results:
The average outdoor temperature during on site measurement was 4.00(0.20,7.00)℃. In classrooms with centralized or air conditioned heating systems, the measured average temperature was (19.33±2.59)℃, with a thermal comfort range of 20.35-25.35 ℃ and a thermal neutral temperature of 22.85 ℃. And 13.92% of students reported feeling cold, while 80.80% felt comfortable. In classrooms with natural ventilation, the measured average temperature was (12.26±1.83)℃, with a thermal neutral temperature of 19.67 ℃ and a thermal comfort range of 16.17-23.17 ℃. About 48.33% of students reported feeling cold, and 49.81 % felt comfortable.The results of univariate analysis showed that there were statistically significant differences in shoe thickness, temperature sensation, relative humidity sensation and wind speed sensation between centralized/air conditioned heating areas ( χ 2= 7.01 , 31.47, 13.57, 13.80,all P <0.05). There were also statistically significant differences in school stage for primary and secondary school students, body mass index, classroom location for seat, temperature sensation, relative humidity sensation and wind speed sensation between naturally ventilated areas ( χ 2=42.13, 11.13, 11.04, 60.39, 29.27, 38.46,all P <0.05).
Conclusions
There are differences in thermal environment and students subjective thermal comfort in primary and secondary schools under different ventilation modes in winter. The temperature standards for heated classrooms should be revised, and differentiated environmental regulation strategies should be adopted based on different ventilation methods to improve students health and comfort levels.
2.Mechanism and therapeutic targets of angiopoietin-like protein 4 in diabetic retinopathy
Jingrong FENG ; Yan LI ; Xiaocao REN ; Jixin LI ; Yu MA ; Wenfang ZHANG ; Yi YANG
International Eye Science 2026;26(5):785-791
Diabetic retinopathy(DR)remains the leading cause of vision loss in patients with diabetes. Current anti-vascular endothelial growth factor(VEGF)therapies are limited by inadequate response in some patients and the necessity for repeated intravitreal injections, underscoring the urgent need for novel therapeutic targets. Angiopoietin-like protein 4(ANGPTL4), a multifunctional secreted protein, has emerged as a critical regulator in the pathogenesis and progression of DR, positioning it as a promising interventional target. This review systematically elaborates the biological characteristics of ANGPTL4, with a focus on its expression dynamics, molecular mechanisms, and regulatory networks rolesin the development of DR. Furthermore, the prospects of ANGPTL4-targeted therapeutic strategies are discussed, aiming to offer new insights and directions for understanding DR pathogenesis, advancing multi-target drug development, and improving clinical management.
3.Constructing a rat animal model of pelvic organ prolapse:a comparison of three modeling methods
Jing YANG ; Houmei WANG ; Yi WANG ; Min SONG ; Jie REN ; Lujun DAI ; Ziwen XIAO
Chinese Journal of Tissue Engineering Research 2026;30(4):864-872
BACKGROUND:Currently,there are many modeling methods for pelvic organ prolapse animal models,and the commonly used methods are vaginal balloon dilatation,oophorectomy and the combination of the two.There is no study comparing the three modeling methods in detail.OBJECTIVE:To construct and validate a rat animal model of pelvic organ prolapse using three different methods and to identify the advantages and disadvantages of various models.METHODS:Seventy-two 8-week SPF-grade female Sprague-Dawley rats were selected and randomly divided into four groups,namely,vaginal balloon dilatation group,ovariectomy group,ovariectomy combined with vaginal balloon dilatation group(the combined group),and the sham-operated group(no ovariectomy and no vaginal dilatation).The vaginal wall tissues of rats were collected at 4,8 and 12 weeks after the operation for hematoxylin-eosin staining,Masson staining,EVG staining and immunohistochemical staining of α-smooth muscle actin,Vimentin and matrix metalloproteinase 9 detection,and the pelvic floor muscle tissues were taken at 4,8 and 12 weeks after the operation for hematoxylin-eosin staining,Masson staining and EVG staining.RESULTS AND CONCLUSION:(1)Hematoxylin-eosi staining showed that there was no significant difference in the decrease of vaginal epithelial layer thickness in the vaginal balloon dilatation group compared with the sham-operated group,(P>0.05),while the thickness of the vaginal epithelial layer was significantly reduced in the ovariectomy group and the ovariectomy combined with vaginal balloon dilation group(P<0.001),and the reduction was more significant in the ovariectomy combined with vaginal balloon dilation group,remained stable at 8 weeks after surgery and lasted until 12 weeks.(2)The changes in the content of collagen fibers and elastic fibers in the vaginal wall stained by Masson and EVG staining were the same as the changes in the thickness of the vaginal epithelial layer stained by hematoxylin-eosin,and there were no changes in collagen fibers and elastic fibers in the pelvic floor muscle tissues of the treatment groups.(3)At 4,8 and 12 weeks after treatment,there was no significant difference in the expression levels of α-smooth muscle actin,Vimentin and matrix metalloproteinase 9 in the vaginal wall tissue of the balloon dilation group compared with the control group(P>0.05),whereas the expression levels of α-smooth muscle actin and Vimentin were significantly decreased in the ovariectomy group and ovariectomy combined with vaginal balloon dilation group(P<0.01)and the expression of matrix metalloproteinase 9 showed a significant increase(P<0.01),with a more pronounced increase in the ovariectomy combined with vaginal balloon dilation group,and the increase reached a stable state at 8 weeks after surgery and could persist up to 12 weeks.To conclude,vaginal balloon dilatation could not maintain the degeneration of pelvic organ prolapse formed by the vaginal wall for a long period,and both ovariectomy and the combined method can be used.Ovariectomy combined with vaginal balloon dilatation can significantly accelerate and aggravate the formation of typical histological features of pelvic organ prolapse in vaginal wall tissues,effectively shorten the experimental period,and improve the efficiency.These effects reach a stable state at 8 weeks after surgery and can be sustained up to 12 weeks,which is practical and convenient for the study of pelvic organ prolapse animal models.
4.Effect of macrophage polarization on osteogenesis-angiogenesis coupling in type 2 diabetic osteoporosis
Wenqi CAO ; Xiuzhi FENG ; Yi ZHAO ; Zhimin WANG ; Yiran CHEN ; Xiao YANG ; Yanling REN
Chinese Journal of Tissue Engineering Research 2026;30(4):917-925
BACKGROUND:Type 2 diabetes mellitus is a secondary causative factor for osteoporosis.As highly heterogeneous innate immune cells,macrophages may be polarized in a hyperglycemic environment,which affects osteogenesis-angiogenesis coupling.This may be a research target for improving bone quality in patients with type 2 diabetic osteoporosis.OBJECTIVE:To explore the role of modulating macrophage M1/M2 polarization to influence osteogenesis-angiogenesis coupling in type 2 diabetic osteoporosis and to summarize the effects of commonly used anti-glucose and anti-osteoporosis drugs and bone biorepair materials on bone osteogenesis-angiogenesis coupling by regulating macrophage M1/M2 polarization.METHODS:The keywords of"macrophage polarization,type 2 diabetes,osteoporosis,osteogenesis-angiogenesis coupling"in Chinese and"macrophages,macrophage polarization,osteogenesis-angiogenesis coupling"in English were used to search for relevant literature in CNKI and PubMed,respectively.Seventy-nine pieces of literature were screened and analyzed.RESULTS AND CONCLUSION:(1)Type 2 diabetes mellitus causes the body to be in a hyperglycemic environment and increases the secretion of inflammatory-related factors in the body,which promotes macrophage polarization towards M1 and decreases the number of M2 macrophages.(2)In type 2 diabetes,promoting M2 macrophage polarization is beneficial for osteogenesis-angiogenesis coupling.(3)Some anti-glycemic drugs,active ingredients in traditional Chinese medicine and bone biorepair materials can improve type 2 diabetic osteoporosis by regulating macrophage M1/M2 polarization,reducing M1/M2 ratio,and promoting osteogenesis-angiogenesis coupling.
5.Elucidating the Epigenetic Landscape of Type 2 Diabetes Mellitus: A Multi-Omics Analysis Revealing Novel CpG Sites and Their Association with Cardiometabolic Traits
Ren-Hua CHUNG ; Chun-Chao WANG ; Djeane Debora ONTHONI ; Ben-Yang LIAO ; Tzu-Sheng HSU ; Eden R. MARTIN ; Chao A. HSIUNG ; Wayne Huey-Herng SHEU ; Hung-Yi CHIOU
Diabetes & Metabolism Journal 2026;50(1):153-164
Background:
Type 2 diabetes mellitus (T2DM) is a complex, multifactorial disease with a significant global burden. Although genome-wide association studies (GWAS) have identified many T2DM-associated variants, most lie in non-coding regions, making it difficult to interpret their functional roles.
Methods:
We aimed to identify genetically regulated Cytosine–phosphate–Guanine (CpG) sites associated with T2DM by conducting a methylome-wide association study (MWAS), followed by Mendelian randomization (MR) and functional validation using human pancreatic cells and mouse models. MWAS was performed using summary statistics from large-scale GWAS and a DNA methylation (DNAm) prediction model to test associations between genetically predicted DNAm and T2DM.
Results:
We identified 111 CpG sites significantly associated with T2DM in Europeans, including 8 novel sites near genes not previously linked to T2DM. These findings were replicated in independent datasets. Many CpGs also showed associations with cardiometabolic traits, highlighting shared epigenetic mechanisms. Trans-ethnic MR analysis confirmed consistent effects for six CpGs in East Asians. Functional analysis revealed that several CpGs regulate gene expression in human pancreatic α- and β-cells. Among them, 2´-5´-oligoadenylate synthetase like (OASL) expression, regulated by a significant CpG, was differentially expressed in α-cells of T2DM cases compared to controls. Supporting evidence from mouse models suggests a role for OASL in glucose regulation.
Conclusion
Our study identifies novel genetically regulated CpG sites associated with T2DM risk and highlights OASL as a potential epigenetic regulator of glucose metabolism in α-cells. These findings provide mechanistic insights into the epigenetic architecture of T2DM and suggest potential targets for cross-ethnic biomarker development and therapeutic intervention.
6.Constructing a rat animal model of pelvic organ prolapse:a comparison of three modeling methods
Jing YANG ; Houmei WANG ; Yi WANG ; Min SONG ; Jie REN ; Lujun DAI ; Ziwen XIAO
Chinese Journal of Tissue Engineering Research 2026;30(4):864-872
BACKGROUND:Currently,there are many modeling methods for pelvic organ prolapse animal models,and the commonly used methods are vaginal balloon dilatation,oophorectomy and the combination of the two.There is no study comparing the three modeling methods in detail.OBJECTIVE:To construct and validate a rat animal model of pelvic organ prolapse using three different methods and to identify the advantages and disadvantages of various models.METHODS:Seventy-two 8-week SPF-grade female Sprague-Dawley rats were selected and randomly divided into four groups,namely,vaginal balloon dilatation group,ovariectomy group,ovariectomy combined with vaginal balloon dilatation group(the combined group),and the sham-operated group(no ovariectomy and no vaginal dilatation).The vaginal wall tissues of rats were collected at 4,8 and 12 weeks after the operation for hematoxylin-eosin staining,Masson staining,EVG staining and immunohistochemical staining of α-smooth muscle actin,Vimentin and matrix metalloproteinase 9 detection,and the pelvic floor muscle tissues were taken at 4,8 and 12 weeks after the operation for hematoxylin-eosin staining,Masson staining and EVG staining.RESULTS AND CONCLUSION:(1)Hematoxylin-eosi staining showed that there was no significant difference in the decrease of vaginal epithelial layer thickness in the vaginal balloon dilatation group compared with the sham-operated group,(P>0.05),while the thickness of the vaginal epithelial layer was significantly reduced in the ovariectomy group and the ovariectomy combined with vaginal balloon dilation group(P<0.001),and the reduction was more significant in the ovariectomy combined with vaginal balloon dilation group,remained stable at 8 weeks after surgery and lasted until 12 weeks.(2)The changes in the content of collagen fibers and elastic fibers in the vaginal wall stained by Masson and EVG staining were the same as the changes in the thickness of the vaginal epithelial layer stained by hematoxylin-eosin,and there were no changes in collagen fibers and elastic fibers in the pelvic floor muscle tissues of the treatment groups.(3)At 4,8 and 12 weeks after treatment,there was no significant difference in the expression levels of α-smooth muscle actin,Vimentin and matrix metalloproteinase 9 in the vaginal wall tissue of the balloon dilation group compared with the control group(P>0.05),whereas the expression levels of α-smooth muscle actin and Vimentin were significantly decreased in the ovariectomy group and ovariectomy combined with vaginal balloon dilation group(P<0.01)and the expression of matrix metalloproteinase 9 showed a significant increase(P<0.01),with a more pronounced increase in the ovariectomy combined with vaginal balloon dilation group,and the increase reached a stable state at 8 weeks after surgery and could persist up to 12 weeks.To conclude,vaginal balloon dilatation could not maintain the degeneration of pelvic organ prolapse formed by the vaginal wall for a long period,and both ovariectomy and the combined method can be used.Ovariectomy combined with vaginal balloon dilatation can significantly accelerate and aggravate the formation of typical histological features of pelvic organ prolapse in vaginal wall tissues,effectively shorten the experimental period,and improve the efficiency.These effects reach a stable state at 8 weeks after surgery and can be sustained up to 12 weeks,which is practical and convenient for the study of pelvic organ prolapse animal models.
7.Effect of macrophage polarization on osteogenesis-angiogenesis coupling in type 2 diabetic osteoporosis
Wenqi CAO ; Xiuzhi FENG ; Yi ZHAO ; Zhimin WANG ; Yiran CHEN ; Xiao YANG ; Yanling REN
Chinese Journal of Tissue Engineering Research 2026;30(4):917-925
BACKGROUND:Type 2 diabetes mellitus is a secondary causative factor for osteoporosis.As highly heterogeneous innate immune cells,macrophages may be polarized in a hyperglycemic environment,which affects osteogenesis-angiogenesis coupling.This may be a research target for improving bone quality in patients with type 2 diabetic osteoporosis.OBJECTIVE:To explore the role of modulating macrophage M1/M2 polarization to influence osteogenesis-angiogenesis coupling in type 2 diabetic osteoporosis and to summarize the effects of commonly used anti-glucose and anti-osteoporosis drugs and bone biorepair materials on bone osteogenesis-angiogenesis coupling by regulating macrophage M1/M2 polarization.METHODS:The keywords of"macrophage polarization,type 2 diabetes,osteoporosis,osteogenesis-angiogenesis coupling"in Chinese and"macrophages,macrophage polarization,osteogenesis-angiogenesis coupling"in English were used to search for relevant literature in CNKI and PubMed,respectively.Seventy-nine pieces of literature were screened and analyzed.RESULTS AND CONCLUSION:(1)Type 2 diabetes mellitus causes the body to be in a hyperglycemic environment and increases the secretion of inflammatory-related factors in the body,which promotes macrophage polarization towards M1 and decreases the number of M2 macrophages.(2)In type 2 diabetes,promoting M2 macrophage polarization is beneficial for osteogenesis-angiogenesis coupling.(3)Some anti-glycemic drugs,active ingredients in traditional Chinese medicine and bone biorepair materials can improve type 2 diabetic osteoporosis by regulating macrophage M1/M2 polarization,reducing M1/M2 ratio,and promoting osteogenesis-angiogenesis coupling.
8.Fangji Fulingtang Attenuates Myocardial Fibrosis by Regulating Mitochondrial Function Through AMPK/PGC-1α/MFN2-PKM2 Signaling Pathway
Xuqin DU ; Yixuan LI ; Yuxia JIN ; Hongding LI ; Ruogu YANG ; Lipeng SHI ; Yi REN
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(20):1-10
ObjectiveTo investigate the effects and mechanisms of Fangji Fulingtang (FFD) on mitochondrial function in the mouse model of myocardial fibrosis (MF). MethodsSixty SPF-grade male C57BL/6J mice were randomly allocated into six groups (n=10 per group): control, model, low-dose, medium-dose, and high-dose (3.315, 6.63, and 13.26 g·kg-1, respectively) FFD, and captopril (20 mg·kg-1). MF was induced by subcutaneous injection of isoproterenol (10 mg·kg-1·d-1) in other groups except the control group for 14 consecutive days, with simultaneous gavage of corresponding drugs. Left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) were measured by echocardiography. Serum levels of creatine kinase-MB (CK-MB), cardiac troponin I (cTnI), N-terminal pro-brain natriuretic peptide (NT-pro BNP), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) were determined by enzyme-linked immunosorbent assay (ELISA). Malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione (GSH) levels were measured by biochemical assays. Reactive oxygen species (ROS) were detected by dihydroethidium (DHE) fluorescence staining. Hematoxylin-eosin (HE), Masson's trichrome, and wheat germ agglutinin (WGA) staining were performed to evaluate myocardial structure and fibrosis. Mitochondrial ultrastructure and function were assessed by transmission electron microscopy, adenosine triphosphate (ATP) colorimetric assay, and JC-1 fluorescence staining. The protein levels of phosphorylated adenosine monophosphate-activated protein kinase α subunit (p-AMPKα), AMPKα, peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), mitofusin 2 (MFN2), pyruvate kinase M2 isoform (PKM2), lactate dehydrogenase A (LDHA), and hypoxia-inducible factor 1 alpha (HIF-1α) were analyzed by Western blot. ResultsCompared with the control group, the model group exhibited decreased LVEF and LVFS, increased heart weight index and heart weight-to-tibia length ratio (P<0.01), elevated levels of myocardial injury markers (CK-MB, cTnI, and NT-pro BNP), inflammatory cytokines (TNF-α, IL-1β, and IL-6), and MDA, along with reduced SOD and GSH levels (P<0.01). Enhanced interstitial collagen deposition and cardiomyocyte hypertrophy were observed in the model group (P<0.01). Transmission electron microscopy and JC-1 staining revealed mitochondrial swelling, crista disruption, decreased ATP content, and reduced red/green fluorescence ratio in the model group (P<0.01). Western blot analysis demonstrated downregulation of p-AMPKα, PGC-1α, and MFN2 and upregulation of PKM2, LDHA, and HIF-1α in the model group (P<0.01). Compared with the model group, treatment with FFD or captopril improved LVEF and LVFS, reduced heart weight index and heart weight-to-tibia length ratio (P<0.05, P<0.01), lowered the serum levels of CK-MB, cTnI, NT-pro BNP, TNF-α, IL-1β, IL-6, and MDA, increased the SOD and GSH levels (P<0.05, P<0.01), attenuated the myocardial fibrosis and cardiomyocyte hypertrophy (P<0.01), and restored the mitochondrial ultrastructure. The medium and high-dose FFD groups as well as the captopril group showed increased ATP production and red/green fluorescence ratio (P<0.05, P<0.01). Furthermore, FFD upregulated the expression of p-AMPKα and PGC-1α while downregulating the expression of LDHA and HIF-1α (P<0.05, P<0.01). ConclusionFFD activates the AMPK/PGC-1α/MFN2 signaling pathway and inhibits the PKM2/LDHA/HIF-1α axis to restore mitochondrial function and energy metabolic homeostasis, thereby attenuating isoproterenol-induced myocardial fibrosis.
9.Fangji Fulingtang Attenuates Myocardial Fibrosis by Regulating Mitochondrial Function Through AMPK/PGC-1α/MFN2-PKM2 Signaling Pathway
Xuqin DU ; Yixuan LI ; Yuxia JIN ; Hongding LI ; Ruogu YANG ; Lipeng SHI ; Yi REN
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(20):1-10
ObjectiveTo investigate the effects and mechanisms of Fangji Fulingtang (FFD) on mitochondrial function in the mouse model of myocardial fibrosis (MF). MethodsSixty SPF-grade male C57BL/6J mice were randomly allocated into six groups (n=10 per group): control, model, low-dose, medium-dose, and high-dose (3.315, 6.63, and 13.26 g·kg-1, respectively) FFD, and captopril (20 mg·kg-1). MF was induced by subcutaneous injection of isoproterenol (10 mg·kg-1·d-1) in other groups except the control group for 14 consecutive days, with simultaneous gavage of corresponding drugs. Left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) were measured by echocardiography. Serum levels of creatine kinase-MB (CK-MB), cardiac troponin I (cTnI), N-terminal pro-brain natriuretic peptide (NT-pro BNP), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) were determined by enzyme-linked immunosorbent assay (ELISA). Malondialdehyde (MDA), superoxide dismutase (SOD), and glutathione (GSH) levels were measured by biochemical assays. Reactive oxygen species (ROS) were detected by dihydroethidium (DHE) fluorescence staining. Hematoxylin-eosin (HE), Masson's trichrome, and wheat germ agglutinin (WGA) staining were performed to evaluate myocardial structure and fibrosis. Mitochondrial ultrastructure and function were assessed by transmission electron microscopy, adenosine triphosphate (ATP) colorimetric assay, and JC-1 fluorescence staining. The protein levels of phosphorylated adenosine monophosphate-activated protein kinase α subunit (p-AMPKα), AMPKα, peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), mitofusin 2 (MFN2), pyruvate kinase M2 isoform (PKM2), lactate dehydrogenase A (LDHA), and hypoxia-inducible factor 1 alpha (HIF-1α) were analyzed by Western blot. ResultsCompared with the control group, the model group exhibited decreased LVEF and LVFS, increased heart weight index and heart weight-to-tibia length ratio (P<0.01), elevated levels of myocardial injury markers (CK-MB, cTnI, and NT-pro BNP), inflammatory cytokines (TNF-α, IL-1β, and IL-6), and MDA, along with reduced SOD and GSH levels (P<0.01). Enhanced interstitial collagen deposition and cardiomyocyte hypertrophy were observed in the model group (P<0.01). Transmission electron microscopy and JC-1 staining revealed mitochondrial swelling, crista disruption, decreased ATP content, and reduced red/green fluorescence ratio in the model group (P<0.01). Western blot analysis demonstrated downregulation of p-AMPKα, PGC-1α, and MFN2 and upregulation of PKM2, LDHA, and HIF-1α in the model group (P<0.01). Compared with the model group, treatment with FFD or captopril improved LVEF and LVFS, reduced heart weight index and heart weight-to-tibia length ratio (P<0.05, P<0.01), lowered the serum levels of CK-MB, cTnI, NT-pro BNP, TNF-α, IL-1β, IL-6, and MDA, increased the SOD and GSH levels (P<0.05, P<0.01), attenuated the myocardial fibrosis and cardiomyocyte hypertrophy (P<0.01), and restored the mitochondrial ultrastructure. The medium and high-dose FFD groups as well as the captopril group showed increased ATP production and red/green fluorescence ratio (P<0.05, P<0.01). Furthermore, FFD upregulated the expression of p-AMPKα and PGC-1α while downregulating the expression of LDHA and HIF-1α (P<0.05, P<0.01). ConclusionFFD activates the AMPK/PGC-1α/MFN2 signaling pathway and inhibits the PKM2/LDHA/HIF-1α axis to restore mitochondrial function and energy metabolic homeostasis, thereby attenuating isoproterenol-induced myocardial fibrosis.
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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