1.Current status of proteomics research in diabetic retinopathy
Shun ZHOU ; Yan WANG ; Jing LENG ; Yong ZHAO
International Eye Science 2025;25(3):428-433
Diabetic retinopathy(DR)has emerged as the leading cause of vision loss among working-age people in many countries under the increasing prevalence of diabetes and the longevity of the population. The pathogenesis of DR is complicated and has not been fully elucidated at present, while the treatment methods of DR have not been greatly improved, mainly retinal laser photocoagulation, anti-vascular endothelial growth factor(VEGF)treatment and vitrectomy surgery. The current treatment methods not only have shortcomings, but also bring serious economic burden to patients. Therefore, new methods are needed to explore the pathogenesis of DR, discover new treatments or improve current treatments, and improve the satisfaction of DR patients. In recent years, the identification and quantification of proteins expressed in blood, retina, vitreous humor, aqueous humor, and tears of all observable DR patients and DR rats and differentially expressed proteins after drug intervention have provided new ideas for further exploring the pathogenesis, diagnosis and treatment of DR with the rise of proteomics, which put forward new insights into early detection and treatment.The proteomics of DR in recent years are reviewed, in order to provide new ideas for the diagnosis and treatment of DR.
2.Current status of proteomics research in diabetic retinopathy
Shun ZHOU ; Yan WANG ; Jing LENG ; Yong ZHAO
International Eye Science 2025;25(3):428-433
Diabetic retinopathy(DR)has emerged as the leading cause of vision loss among working-age people in many countries under the increasing prevalence of diabetes and the longevity of the population. The pathogenesis of DR is complicated and has not been fully elucidated at present, while the treatment methods of DR have not been greatly improved, mainly retinal laser photocoagulation, anti-vascular endothelial growth factor(VEGF)treatment and vitrectomy surgery. The current treatment methods not only have shortcomings, but also bring serious economic burden to patients. Therefore, new methods are needed to explore the pathogenesis of DR, discover new treatments or improve current treatments, and improve the satisfaction of DR patients. In recent years, the identification and quantification of proteins expressed in blood, retina, vitreous humor, aqueous humor, and tears of all observable DR patients and DR rats and differentially expressed proteins after drug intervention have provided new ideas for further exploring the pathogenesis, diagnosis and treatment of DR with the rise of proteomics, which put forward new insights into early detection and treatment.The proteomics of DR in recent years are reviewed, in order to provide new ideas for the diagnosis and treatment of DR.
3.In Vitro and in vivo Component Analysis of Total Phenolic Acids from Gei Herba and Its Effect on Promoting Acute Wound Healing and Inhibiting Scar Formation
Xixian KONG ; Guanghuan TIAN ; Tong WU ; Shaowei HU ; Jie ZHAO ; Fuzhu PAN ; Jingtong LIU ; Yong DENG ; Yi OUYANG ; Hongwei WU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(3):156-167
ObjectiveBased on ultra performance liquid chromatography-quadrupole-electrostatic field orbital trap high-resolution mass spectrometry(UPLC-Q-Orbitrap-MS), to identify the in vivo and in vitro chemical components of total phenolic acids in Gei Herba(TPAGH), and to clarify the pharmacological effects and potential mechanisms of the effective part in promoting acute wound healing and inhibiting scar formation. MethodsUPLC-Q-Orbitrap-MS was used to identify the chemical components of TPAGH and ingredients absorbed in vivo after topical administration. A total of 120 ICR mice were randomly divided into the model group, recombinant human epidermal growth factor(rhEGF) group(4 mg·kg-1), and low, medium, and high dose groups of TPAGH(3.5, 7, 14 mg·kg-1), with 24 mice in each group. A full-thickness skin excision model was constructed, and each administration group was coated with the drug at the wound site, and the model group was treated with an equal volume of normal saline, the treatment was continued for 30 days, during which 8 mice from each group were sacrificed on days 6, 12, and 30. The healing of the wounds in the mice was observed, and histopathological changes in the skin tissues were dynamically observed by hematoxylin-eosin(HE), Masson, and Sirius red staining, and enzyme-linked immunosorbent assay(ELISA) was used to dynamically measure the contents of interleukin-6(IL-6), tumor necrosis factor-α(TNF-α), vascular endothelial growth factor A(VEGFA), matrix metalloproteinase(MMP)-3 and MMP-9 in skin tissues. Network pharmacology was used to predict the targets related to the promotion of acute wound healing and the inhibition of scar formation by TPAGH, and molecular docking of key components and targets was performed. Gene Ontology(GO) biological process analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis were carried out for the related targets, so as to construct a network diagram of herbal material-compound-target-pathway-pharmacological effect-disease for further exploring its potential mechanisms. ResultsA total of 146 compounds were identified in TPAGH, including 28 phenylpropanoids, 31 tannins, 23 triterpenes, 49 flavonoids, and 15 others, and 16 prototype components were found in the serum of mice. Pharmacodynamic results showed that, compared with the model group, the TPAGH groups showed a significant increase in relative wound healing rate and relative scar inhibition rate(P<0.05), and the number of new capillaries, number of fibroblasts, number of new skin appendages, epidermal regeneration rate, collagen deposition ratio, and Ⅲ/Ⅰ collagen ratio in the tissue were significantly improved(P<0.05, 0.01), the levels of IL-6, TNF-α, MMP-3 and MMP-9 in the skin tissues were reduced to different degrees, while the level of VEGFA was increased. Network pharmacology analysis screened 10 core targets, including tumor protein 53(TP53), sarcoma receptor coactivator(SRC), protein kinase B(Akt)1, signal transducer and activator of transcription 3(STAT3), epidermal growth factor receptor(EGFR) and so on, participating in 75 signaling pathways such as advanced glycation end-products(AGE)-receptor for AGE(AGE/RAGE) signaling pathway, phosphatidylinositol 3-kinase(PI3K)/Akt signaling pathway, mitogen-activated protein kinase(MAPK) signaling pathway. Molecular docking confirmed that the key components genistein, geraniin, and casuariin had good binding ability to TP53, SRC, Akt1, STAT3 and EGFR. ConclusionThis study comprehensively reflects the chemical composition of TPAGH and the absorbed components after topical administration through UPLC-Q-Orbitrap-MS. TPAGH significantly regulates key indicators of skin healing and tissue reconstruction, thereby clarifying its role in promoting acute wound healing and inhibiting scar formation. By combining in vitro and in vivo component identification with network pharmacology, the study explores how key components may bind to targets such as TP53, Akt1 and EGFR, exerting therapeutic effects through related pathways such as immune inflammation and vascular regeneration.
4.Gushukang interferes with osteoclasts:activation of nuclear factor erythroid 2-related factor 2 regulates the c-Fos/NFATc1 pathway in the treatment of osteoporosis
Chengzhi HOU ; Jiatong HAN ; Guangcheng WEI ; Zechuan ZHUO ; Qiuyue LI ; Yong ZHAO ; Zhangjingze YU
Chinese Journal of Tissue Engineering Research 2025;29(2):279-285
BACKGROUND:It has been shown that Gushukang affects bone metabolism by regulating nucleotide and amino acid metabolism and immune mechanisms.Current research on the mechanism of Gushukang in the treatment of osteoporosis primarily focuses on osteoblast regulation and requires further improvement from the perspective of osteoclasts. OBJECTIVE:To investigate the mechanism by which Gushukang interferes with osteoclasts in the treatment of osteoporosis using RAW264.7 cells as the research model. METHODS:Twenty-four 8-week-old female Sprague-Dawley rats were randomly divided into four groups(n=6 per group):the three experimental groups were given 1,2 and 4 g/kg osteoporosis solution by gavage(2 times per day),and the control group was given an equal amount of distilled water by gavage(2 times per day).After 7 days of intragastric administration,aortic blood samples were extracted to collect serum samples using centrifugation,and serum samples from the same groups were combined to obtain the low-,medium-,and high-concentration Gushukang-containing and normal sera for the subsequent experiments.(1)RAW264.7 cells were cultured in six groups:normal serum was added to the control group;low,medium,and high concentration groups were added with low,medium,and high concentrations of Gushukang-containing serum,respectively;ML385,a nuclear factor erythroid 2-related factor 2(Nrf2)inhibitor was given in the Nrf2 inhibitor group;and t-BHQ,a Nrf2 activator,was added in the Nrf2 activator group.Cell viability was detected using the cell counting kit-8 assay.(2)The 3rd generation RAW 264.7 cells were cultured and divided into five groups:the blank control group was added with normal serum,the osteoclast group was added with receptor activator of nuclear factor κB ligand(RANKL),and the low-,medium-,and high-concentration groups were added with low-,medium-,and high-concentration Gushukang-containing serum based on the addition of RANKL.Tartrate-resistant acid phosphate staining was performed after 5 days of culture.(3)RAW264.7 cells were cultured and divided into five groups:blank control group was cultured with normal serum,osteoclast group cultured with normal serum and RANKL,high concentration+osteoclast group cultured with RANKL+high concentration Gushukang-containing serum,osteoclast+Nrf2 agonist group cultured with RANKL+t-BHQ,and high concentration+osteoclast+Nrf2 inhibitor group cultured with RANKL+high concentration Gushukang-containing serum+ML385.Western blot assay and determination of reactive oxygen content were performed after 5 days of culture. RESULTS AND CONCLUSION:The cell counting kit-8 results indicated that Gushukang-containing serum,NRF2 inhibitor or agonist had no significant effect on RAW264.7 cell viability.Tartrate-resistant acid phosphate staining results demonstrated that Gushukang-containing serum exhibited a concentration-dependent inhibitory effect on osteoclast differentiation.Western blot analysis and determination of reactive oxygen species revealed that compared with the blank control group,Nrf2 protein expression was decreased in the osteoclast group(P<0.05),while c-Fos and NFATc1 protein expression and reactive oxygen species content were elevated(P<0.05);compared with the osteoclast group,Nrf2 protein expression was elevated and reactive oxygen species content was decreased in the high-concentration+osteoclast group,osteoclast+Nrf2 agonist group,and high-concentration+osteoclast+Nrf2 inhibitor group(P<0.05),while c-Fos and NFATc1 protein expression was decreased in the high concentration+osteoclast group and osteoclast+Nrf2 agonist group(P<0.05);compared with the high concentration+osteoclast group,Nrf2 protein expression was decreased(P<0.05)and reactive oxygen species content was elevated(P<0.05)in the high concentration+osteoclast+Nrf2 inhibitor group.To conclude,Gushukang reduces reactive oxygen species production by activating Nrf2,thereby inhibiting downstream of the c-Fos/NFATc1 pathway and suppressing osteoclast differentiation.
5.Wen-Shen-Tong-Du Decoction promoting spinal cord injury repair in mice
Ruihua ZHAO ; Sixian CHEN ; Yang GUO ; Lei SHI ; Chengjie WU ; Mao WU ; Guanglu YANG ; Haoheng ZHANG ; Yong MA
Chinese Journal of Tissue Engineering Research 2025;29(6):1118-1126
BACKGROUND:Previous studies have confirmed that Wen-Shen-Tong-Du Decoction can promote the recovery of spinal cord injury by inhibiting pyroptosis of splenic B cells,promoting the phagocytosis of myelin debris by microvascular endothelial cells,affecting the migration and infiltration of microglia,promoting the recovery of damaged neurons,and decreasing neuronal apoptosis after spinal cord injury,but the mechanism of this is still not clear. OBJECTIVE:To investigate the effect of Wen-Shen-Tong-Du Decoction on the triggering receptor expressed on myeloid cells 2(TREM2)and PI3K/Akt signaling pathways in mice following spinal cord injury. METHODS:Thirty-six C57BL/6 mice were selected and randomly divided into a sham-operation group,a model group and a Wen-Shen-Tong-Du Decoction group,with 12 mice in each group.In the model and Wen-Shen-Tong-Du Decoction groups,mouse models of T10 spinal cord injury were prepared by the modified Allen's method.On the 1st day after modeling,the Wen-Shen-Tong-Du Decoction group was given Wen-Shen-Tong-Du Decoction by gavage,and the sham-operation group and the model group were given saline by gavage once a day for 28 days.During the drug administration period,mouse motor function was evaluated by Basso Mouse Scale score and inclined plane test.On the 7th and 28th days after modeling,hematoxylin-eosin staining was used to observe the histopathological changes in the spinal cord tissue of the mice;immunofluorescence double staining was used to detect the protein expression of ionized calcium binding adaptor molecule 1(IBA1)and TREM2;and western blot assay was used to detect the expression of TREM2,PI3K,p-PI3K,Akt,p-Akt,Bcl2,Bax and Caspase3 in spinal cord tissue. RESULTS AND CONCLUSION:Basso Mouse Scale scores and inclined plane test results indicated that the motor function of the mouse hindlimbs was declined after spinal cord injury,and Wen-Shen-Tong-Du Decoction significantly improved motor function in mice with spinal cord injury.Hematoxylin-eosin staining results revealed that Wen-Shen-Tong-Du Decoction significantly ameliorated the pathological structure of spinal cord tissue compared with the model group,manifesting as reduced degrees of dorsal white matter and neuronal atrophy,decreased cytoplasmic vacuolization,and reduced inflammatory cell infiltration.Immunofluorescence double staining results showed that on the 7th day after modeling,the protein expression of IBA1 and TREM2 in the model group was lower than that in the sham-operation group(P<0.05),and the protein expression of IBA1 and TREM2 in the Wen-Shen-Tong-Du Decoction group was higher than that in the model group(P<0.05);on the 28th day after modeling,the protein expression of TREM2 in the model group was lower than that in the sham-operation group(P<0.05),and the protein expression of TREM2 in the spinal cord tissue of the mice in the Wen-Shen-Tong-Du Decoction group was higher than that in the model group(P<0.05).Western blot results analysis demonstrated that on the 7th day after modeling,compared with the sham-operation group,the model group exhibited a significant reduction in TREM2,PI3K,and Bcl2/Bax(P<0.05),as well as a significant increase in p-Akt,Bax and p-Akt/Aktp-PI3K(P<0.05);compared with the model group,the Wen-Shen-Tong-Du Decoction group showed a significant increase in TREM2,PI3K,p-PI3K,Akt,p-Akt,Bcl2,p-PI3K/PI3K,p-Akt/Ak,and Bcl2/Bax(P<0.05),as well as a significant decrease in Bax and Caspase3 protein expression(P<0.05).On the 28th day after modeling,compared with the sham-operation group,the model group exhibited a significant reduction in TREM2,PI3K,p-PI3K,Akt,p-Akt,Bcl2 and Bcl2/Bax(P<0.05),as well as a significant increase in Bax protein expression(P<0.05);compared with the model group,the Wen-Shen-Tong-Du Decoction group showed a significant increase in TREM2,PI3K,Akt,p-Akt,Bcl2,and Bcl2/Bax(P<0.05),as well as a significant decrease in Bax protein expression(P<0.05).To conclude,Wen-Shen-Tong-Du Decoction may activate the PI3K/Akt signaling pathway by up-regulating the expression of TREM2 protein in microglia,and then inhibit neuronal apoptosis,thus exerting neuroprotective effects and promoting the repair of spinal cord injury.
6.Differences in dynamic stability across different height barriers between obese and average men
Wenli ZHANG ; Ziqi ZHAO ; Leichao LIANG ; Yunqi TANG ; Yong WANG
Chinese Journal of Tissue Engineering Research 2025;29(11):2319-2326
BACKGROUND:Obesity negatively affects dynamic balance during walking,and crossing barriers is a more routine functional activity that requires more stability in controlling body posture. OBJECTIVE:To investigate the differences in dynamic stability between obese and average males,and to assess the balance ability of obese males using a relatively more challenging obstacle crossing. METHODS:A total of 24 male youths(12 each in the obese and normal groups)were recruited to complete the tests of walking on level ground and crossing obstacles of different heights(4 cm,11 cm,15 cm)in random order.Kinematic and dynamic data were collected using the Qualisys motion capture system and Kistler force stage.Statistical analysis was performed using two-factor(2 groups * 4 movement types)repeated measures analysis of variance. RESULTS AND CONCLUSION:The obese group had a lower step speed than the normal group(P<0.05),the proportion of the first single support period decreased and the proportion of the second double support period increased when crossing the 11 cm versus 15 cm hurdles(P<0.05).When walking on level ground,the margin of stability in the internal and external directions in the normal group was greater than that of the obese group(P<0.05).When crossing the 4 cm hurdles,the margin of stability in the obese group was less than that in the normal group(P<0.05).When crossing the 11 cm hurdles,there was no significant difference between the two groups in the anterior-posterior direction(P>0.05),while there was a significant difference in the internal-external direction(P<0.05).When crossing the 15 cm hurdles,the margin of stability in the obese group was lower than that in the normal group(P<0.05).Overall,obesity decreases the body's ability to control the body,reduces dynamic stability during crossing the barrier,and increases the risk of falls compared with the general population.In addition,compared with level ground walking,the decrease in the dynamic stability when crossing barriers is more significant in the obese group than the general population.
7.Effect of oxymatrine on expression of stem markers and osteogenic differentiation of periodontal ligament stem cells
Jing LUO ; Min YONG ; Qi CHEN ; Changyi YANG ; Tian ZHAO ; Jing MA ; Donglan MEI ; Jinpeng HU ; Zhaojun YANG ; Yuran WANG ; Bo LIU
Chinese Journal of Tissue Engineering Research 2025;29(19):3992-3999
BACKGROUND:Human periodontal ligament stem cells are potential functional cells for periodontal tissue engineering.However,long-term in vitro culture may lead to reduced stemness and replicative senescence of periodontal ligament stem cells,which may impair the therapeutic effect of human periodontal ligament stem cells. OBJECTIVE:To investigate the effect of oxymatrine on the stemness maintenance and osteogenic differentiation of periodontal ligament stem cells in vitro,and to explore the potential mechanism. METHODS:Periodontal ligament stem cells were isolated from human periodontal ligament tissues by tissue explant enzyme digestion and cultured.The surface markers of mesenchymal cells were identified by flow cytometry.Periodontal ligament stem cells were incubated with 0,2.5,5,and 10 μg/mL oxymatrine.The effect of oxymatrine on the proliferation activity of periodontal ligament stem cells was detected by CCK8 assay.The appropriate drug concentration for subsequent experiments was screened.Western blot assay was used to detect the expression of stem cell non-specific proteins SOX2 and OCT4 in periodontal ligament stem cells.qRT-PCR and western blot assay were used to detect the expression levels of related osteogenic genes and proteins in periodontal ligament stem cells. RESULTS AND CONCLUSION:(1)The results of CCK8 assay showed that 2.5 μg/mL oxymatrine significantly enhanced the proliferative activity of periodontal stem cells,and the subsequent experiment selected 2.5 μg/mL oxymatrine to intervene.(2)Compared with the blank control group,the protein expression level of SOX2,a stem marker of periodontal ligament stem cells in the oxymatrine group did not change significantly(P>0.05),and the expression of OCT4 was significantly up-regulated(P<0.05).(3)Compared with the osteogenic induction group,the osteogenic genes ALP,RUNX2 mRNA expression and their osteogenic associated protein ALP protein expression of periodontal ligament stem cells were significantly down-regulated in the oxymatrine+osteogenic induction group(P<0.05).(4)The oxymatrine up-regulated the expression of stemness markers of periodontal ligament stem cells and inhibited the bone differentiation of periodontal ligament stem cells,and the results of high-throughput sequencing showed that it may be associated with WNT2,WNT16,COMP,and BMP6.
8.Application and clinical efficacy of red blood cell therapeutic apheresis in erythropoietic protoporphyria and hereditary hemochromatosis
Haoqiang LIU ; Caihan ZHAO ; Qing YUAN ; Lixia XIE ; Yong ZOU ; Ying LU
Chinese Journal of Blood Transfusion 2025;38(7):915-921
Objective: To explore the application and clinical efficacy of red blood cell therapeutic apheresis in erythropoietic protoporphyria (EPP) and hereditary hemochromatosis (HH). Methods: 1) The EPP patient was hospitalized twice for "abdominal pain, nausea, vomiting, and brown urine". One and two sessions of red blood cell exchange/therapeutic plasma exchange (RCE/TPE) were respectively performed during the two hospitalizations. During each session, one RCE with 6-8 units of leukoreduced RBCs and 3-4 TPE procedures with 1 800-2 000 mL of frozen plasma was conducted. Biochemical parameters were monitored before and after treatment. 2) The HH patient was hospitalized for “repeatedly elevated aminotransferases”. Erythrocytapheresis was performed once, removing 550 mL of red blood cells, and venous phlebotomy was conducted once every 2 months subsequently. Blood routine and ferritin levels were assessed before and after treatment. Results: 1) During the first hospitalization, the EPP patient was relieved of the abdominal pain and brown urine after therapeutic apheresis. The total bilirubin level decreased from 141.8 μmol/L on admission to 68.6 μmol/L at discharge, with a symptom remission duration of 10 months. During the second hospitalization, the EPP patient still had recurrent abdominal pain after therapeutic apheresis. He developed psychiatric symptoms and gastrointestinal bleeding subsequently, accompanied by elevated bilirubin levels. Liver function deteriorated and the patient went into the state of the end-stage liver disease (ESLD). 2) For the HH patient, the hemoglobin level prior to erythrocytapheresis and vein phlebotomy was 150-160 g/L, with the lowest value occurring two days after erythrocytapheresis, decreasing to 107 g/L. The ferritin level before erythrocytapheresis was 2 428.08 ng/mL and it declined gradually after theraphy, with the lowest value occurring two months after erythrocytapheresis, decreasing to 1 094 ng/mL. The ferritin level was 1 114 ng/mL two months following the first vein phlebotomy, however it increased to 1 472 ng/mL two months after the second vein phlebotomy. Conclusion: RCE/TPE may alleviate protoporphyrin liver disease and help patients with bridging liver transplantation before EPP developments to ESLD. For HH patients with significantly elevated ferritin levels, erythrocytapheresis reduces serum ferritin more quickly and maintains its level longer relative to phlebotomy.
9.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.
10.LIU Fengbin's Experience in Treating Autoimmune Liver Disease with the Method of Nourishing Yin and Removing Stasis Based on Stage
Xiling YANG ; Qiuhong YONG ; Chaoyuan HUANG ; Lina ZHAO ; Yiyuan ZHENG ; Chong PENG ; Kunhai ZHUANG ;
Journal of Traditional Chinese Medicine 2025;66(7):674-679
This paper summarizes Professor LIU Fengbin's clinical experience in treating autoimmune liver disease (AILD) using the method of nourishing yin and removing stasis based on stage differentiation. He believes that the pathogenesis of AILD generally involves both deficiency in essence and excess in manifestation, with essence deficiency often presenting as liver and kidney yin deficiency, which may progress to spleen deficiency and yang deficiency over time. The excess manifestation commonly includes qi stagnation, blood stasis, damp-heat, and phlegm toxicity. Clinically, he advocates for the treatment principle of nourishing yin and removing stasis. On the foundation of nourishing liver and kidney yin, different pathological factors causing stasis are eliminated according to their nature. Treatment is also tailored to different stages of AILD. In the early and asymptomatic stages, liver qi stagnation and spleen deficiency are prominent, warranting a therapeutic approach of soothing the liver, regulating qi and strengthening the spleen. The modified Chaishao Qizhi Decoction (柴芍气滞汤) is used. During the symptomatic stage, pathogenic factors become more pronounced, often accompanied by a significant deficiency of vital qi, with damp-heat, water retention, and phlegm toxicity as key pathological features. The treatment should focus on strengthening the spleen and dispelling dampness, using modified Sijunzi Decoction (四君子汤) combined with Yinchen Wuling Powder (茵陈五苓散). In the liver function decompensation stage, vital qi is severely deficient while pathogenic factors persist, with damp-heat, phlegm toxicity, and blood stasis obstructing the liver collaterals. Treatment should focus on nourishing blood, softening the liver, strengthening the spleen, and resolving stasis, using the modified Ruangan Yangxue Decoction (软肝养血汤). Throughout the treatment process, emphasis is placed on tonifying the liver and kidneys while protecting yin fluids.

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