1.Integrating Transcriptomics and 3D Organoids to Investigate Mechanism of Periplaneta americana Extract Against Lung Adenocarcinoma
Qiong MA ; Chunxia HUANG ; Jiawei HE ; Yuting BAI ; Xingyue LIU ; Yuxuan XIONG ; Yang ZHONG ; Hengzhou LAI ; Yuling JIANG ; Xueke LI ; Qian WANG ; Yifeng REN ; Xi FU ; Funeng GENG ; Taoqing WU ; Ping XIAO ; Fengming YOU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(11):124-132
ObjectiveTo evaluate the antitumor activity of Periplaneta americana extract(PAE) against human-derived lung adenocarcinoma organoids(LUAD-PDOs) and to elucidate its potential mechanism based on transcriptomics. MethodsFresh tumor and adjacent normal tissues from patients with LUAD were collected to construct LUAD-PDOs and normal lung organoid(Nor-PDOs) models using 3D organoid culture technology. The effective intervention concentration of PAE was determined using the cell counting kit-8(CCK-8) assay. Experimental groups included the model group(LUAD-PDOs), normal group, model administration group(LUAD-PDOs+PAE), and normal administration group(Nor-PDOs+PAE). Hematoxylin-eosin(HE) staining was used to observe the pathological structures of PDOs, immunohistochemistry(IHC) was performed to detect the expressions of the proliferation marker Ki-67 and lung adenocarcinoma differentiation markers cytokeratin-7(CK-7) and Napsin A, TUNEL staining was applied to detect cell apoptosis. RNA sequencing(RNA-Seq) was conducted to identify differentially expressed genes(DEGs), followed by Gene Ontology(GO), Kyoto Encyclopedia of Genes and Genomes(KEGG), and Gene Set Enrichment Analysis(GSEA), alongside protein-protein interaction(PPI) network analysis to screen core mechanisms. Finally, key targets were validated by integrating external database analysis with immunofluorescence(IF). ResultsNor-PDOs and LUAD-PDOs that highly recapitulated the pathological characteristics of the primary tissues were successfully established. The CCK-8 assay determined that the effective intervention concentration of PAE was 16 g·L-1. Morphological observation showed that Nor-PDOs exhibited lumen-forming structures, whereas LUAD-PDOs displayed dense, solid structures. CCK-8 and TUNEL assays revealed that, compared with the model group, PAE intervention inhibited the proliferation of LUAD-PDOs and promoted apoptosis in LUAD cells, while showing no significant effect on the viability of Nor-PDOs. Transcriptomic analysis identified 719 DEGs that were significantly reversed after PAE intervention(347 up-regulated and 372 down-regulated)(P<0.05). GO enrichment analysis indicated that DEGs in the model administration group were significantly enriched in biological processes related to cell cycle regulation compared to the model group. KEGG pathway analysis revealed that PAE affected pathways related to proliferation and metabolism, including pathways in cancer and the p53 signaling pathway. GSEA further confirmed that PAE significantly enhanced the activity of the p53 signaling pathway(P<0.05). PPI network analysis indicated that breast cancer type 1 susceptibility protein(BRCA1) and checkpoint kinase 1(CHEK1) were the core down-regulated targets in the p53 pathway. IF verified the high expression of BRCA1 and CHEK1 in LUAD-PDOs and their significant downregulation after PAE intervention(P<0.05). Furthermore, survival analysis based on The Cancer Genome Atlas(TCGA) database indicated that low expression of BRCA1 and CHEK1 was significantly associated with prolonged overall survival in patients with LUAD(P<0.05). ConclusionPAE effectively inhibits proliferation of LUAD-PDOs and promotes their apoptosis, its anti-tumor mechanism is potentially associated with the activation of the p53 signaling pathway, with BRCA1 and CHEK1 genes likely serving as key downstream targets for the effects of PAE.
2.Thyroid Hormone Network Regulation in MASLD: Mechanisms and Targeted Therapies
Wen-Ping XIAO ; Yang MA ; Heng GUAN ; Sha WAN ; Wen HAN ; Bing-Bing LUO ; Wu-Feng WANG ; Fang LIU
Progress in Biochemistry and Biophysics 2026;53(3):643-661
Metabolic dysfunction-associated steatotic liver disease (MASLD) has become the most prevalent chronic liver disease worldwide, affecting approximately 32%-38% of the adult population and posing a growing public health burden. MASLD represents a continuous disease spectrum ranging from simple steatosis to metabolic dysfunction-associated steatohepatitis (MASH), progressive hepatic fibrosis, cirrhosis, and ultimately hepatocellular carcinoma (HCC). The pathological core of MASLD lies in disruption of hepatic lipid metabolic homeostasis, characterized by an imbalance among de novo lipogenesis, fatty acid β-oxidation, and very-low-density lipoprotein (VLDL)-mediated lipid export. This metabolic disequilibrium subsequently drives inflammatory injury and fibrotic progression. Among the multiple regulatory pathways involved, thyroid hormone (TH) signaling has emerged as a central regulator of hepatic metabolic homeostasis. The liver is a major peripheral target organ of TH action, where TH predominantly exerts its metabolic effects through thyroid hormone receptor β (TRβ). Large-scale epidemiological studies and meta-analyses have demonstrated that hypothyroidism is significantly associated with increased MASLD prevalence, more severe histological injury, and advanced hepatic fibrosis, suggesting that dysregulation of TH signaling may participate throughout the entire MASLD disease spectrum. At the molecular level, TH regulates hepatic lipid metabolism by coordinating suppression of lipogenesis, enhancement of mitochondrial fatty acid oxidation, and promotion of VLDL assembly and secretion through integrated genomic actions of the T3-TRβ axis and non-genomic signaling pathways. Across different stages of MASLD, TH signaling exerts stage-dependent protective effects. In the steatosis stage, TH improves metabolic flexibility by modulating insulin sensitivity, glucose metabolism, and lipid droplet clearance, thereby alleviating early lipotoxic stress. During progression to MASH, TH attenuates inflammatory amplification by improving mitochondrial homeostasis, suppressing activation of the NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome, and modulating the gut-liver axis microenvironment. In advanced stages, TH signaling influences hepatic stellate cell activation and extracellular matrix deposition, partly through interaction with the transforming growth factor-β (TGF-β)/SMAD pathway, while alterations in intrahepatic TH availability, mediated by dynamic changes in iodothyronine deiodinase 1 (DIO1), contribute to fibrosis progression and hepatocellular dedifferentiation. In hepatocellular carcinoma, coordinated downregulation of TRβ and DIO1 establishes a tumor-associated hypothyroid state that promotes metabolic reprogramming and tumor progression. The clinical relevance of TH signaling in MASLD has been underscored by the recent approval of Resmetirom, a liver-targeted TRβ‑selective agonist, for the treatment of non-cirrhotic MASH with moderate-to-severe fibrosis (F2-F3). This approval represents a landmark transition from mechanistic understanding to metabolism-centered precision therapy in MASLD. Clinical trials have demonstrated that Resmetirom not only improves key histological endpoints, including MASH resolution and fibrosis regression, but also favorably modulates atherogenic lipid profiles, highlighting the therapeutic potential of selectively targeting hepatic TH pathways. This review systematically summarizes the multidimensional regulatory roles of TH across the MASLD disease spectrum and discusses emerging diagnostic and therapeutic implications of TH-based interventions, aiming to inform future mechanistic research and optimize clinical management strategies.
3.Construction and Application of a Real-World Cohort of Community-Acquired Pneumonia Based on a Multimodal Large-Scale Traditional Chinese Medicine Big Data Platform
Zhichao WANG ; Xianmei ZHOU ; Fanchao FENG ; Mengqi WANG ; Xin WANG ; Bin KANG ; Xiaofan YU ; Xiaoxiao WANG ; Lei XIAO ; Juan LI ; Zhichao ZHANG ; Ye MA ; Yeqing JI ; Xin TONG ; Zhuoyue WU ; Jia LIU
Journal of Traditional Chinese Medicine 2026;67(9):961-965
This paper introduces a real-world cohort research model for community-acquired pneumonia (CAP) based on the Jiangsu Traditional Chinese Medicine (TCM) Dominant Diseases Diagnosis and Treatment Data Platform. Firstly, data cleaning is performed by standardizing diagnosis, symptoms, treatment and imaging, intelligently extracting unstructured information, and cleaning and constructing a standardized database. Secondly, for cohort establishment, CAP patients across the province are screened in accordance with CAP diagnostic criteria to build a high-quality disease-specific cohort. Lastly, in terms of protocol design, the characteristics of TCM research and the CAP disease profile are considered to determine appropriate inclusion and exclusion criteria, estimate sample size, define interventions, outcomes and economic evaluations, providing a reference for real-world TCM research on CAP.
4.Construction and Application of a Real-World Cohort of Community-Acquired Pneumonia Based on a Multimodal Large-Scale Traditional Chinese Medicine Big Data Platform
Zhichao WANG ; Xianmei ZHOU ; Fanchao FENG ; Mengqi WANG ; Xin WANG ; Bin KANG ; Xiaofan YU ; Xiaoxiao WANG ; Lei XIAO ; Juan LI ; Zhichao ZHANG ; Ye MA ; Yeqing JI ; Xin TONG ; Zhuoyue WU ; Jia LIU
Journal of Traditional Chinese Medicine 2026;67(9):961-965
This paper introduces a real-world cohort research model for community-acquired pneumonia (CAP) based on the Jiangsu Traditional Chinese Medicine (TCM) Dominant Diseases Diagnosis and Treatment Data Platform. Firstly, data cleaning is performed by standardizing diagnosis, symptoms, treatment and imaging, intelligently extracting unstructured information, and cleaning and constructing a standardized database. Secondly, for cohort establishment, CAP patients across the province are screened in accordance with CAP diagnostic criteria to build a high-quality disease-specific cohort. Lastly, in terms of protocol design, the characteristics of TCM research and the CAP disease profile are considered to determine appropriate inclusion and exclusion criteria, estimate sample size, define interventions, outcomes and economic evaluations, providing a reference for real-world TCM research on CAP.
5.Progress in artificial intelligence for predicting therapeutic efficacy of intravitreal injection
Xiaofeng WU ; Jiayi ZHANG ; Chunyan XIAO ; Yanshuang GENG ; Yonggang LIU ; Boxuan SONG ; Jiawei WANG
International Eye Science 2026;26(4):687-693
Intravitreal anti-vascular endothelial growth factor(anti-VEGF)therapy has been widely used, but the variability in its therapeutic efficacy limits individualized treatment. In recent years, the application of artificial intelligence(AI)has opened up new avenues for personalized treatment response prediction, and its core branches include machine learning(ML)and deep learning(DL). This review systematically retrieved and analyzed 41 relevant studies published up to April 2025. Comprehensive analysis reveals that AI predictive models are evolving from forecasting single endpoints(such as visual acuity or central retinal thickness)to integrating multi-dimensional endpoints(encompassing anatomical, functional, and treatment demand parameters)and generating predictive imaging outputs. In terms of technical approaches, DL models(28 studies, accounting for 68.3%)dominate this field due to their robust image interpretation capabilities, while ML models(10 studies, 24.4%)retain significant value in the analysis of structured clinical data. Cross-disease comparisons indicate that research efforts are most concentrated on age-related macular degeneration(ARMD)and diabetic macular edema(DME), with shared conceptual frameworks for model construction, yet distinct anatomical and functional indicators are prioritized for each disease. Currently, the field confronts several key challenges, including insufficient prospective clinical validation, limited model interpretability(the “black box problem”), and a scarcity of high-quality multi-center datasets. Moving forward, it is imperative to advance real-world validation and develop explainable AI techniques to expedite the clinical translation of these predictive models.
6.Exploring on Processing Mechanism of Enhanced "Invigorating Spleen and Stopping Diarrhea" Effect of Soil-fried Atractylodis Macrocephalae Rhizoma Based on "Microscopic Characterization, Chemical Analysis and Pharmacodynamic Evaluation" Trinity
Guoshun SHAN ; Yuyan XIAO ; Chu YUAN ; Xiuai CHEN ; Qimiao ZHAO ; Xiang LIU ; Hao WU ; Ke ZHANG ; Siqi LIU ; Yongduo YU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):182-193
ObjectiveTo analyze the processing mechanism underlying the enhanced effect of invigorating spleen and stopping diarrhea of soil-fried Atractylodis Macrocephalae Rhizoma(AMR) by analyzing the changes of microstructure, chemical composition and anti-ulcerative colitis(UC) activity before and after soil stir-frying. MethodsThe microstructure and elemental composition of AMR before and after soil stir-frying were analyzed by scanning electron microscopy-energy dispersive spectroscopy(SEM-EDS), to investigate the differences in microstructure and the underlying causes. Ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS) coupled with UNIFI 1.9.2 natural product analysis platform were used to analyze and identify the chemical constituents in raw and soil-fried products, and multivariate statistical methods including principal component analysis(PCA) and orthogonal partial least squares-discriminant analysis(OPLS-DA) were used to explore the differences and sources of chemical constituents between them. A dextran sulfate sodium(DSS)-induced UC mouse model was established. The method of disease activity index(DAI) was used to evaluate the severity of intestinal inflammation. Hematoxylin-eosin(HE) staining was used to observe the pathological changes of colon tissue, enzyme-linked immunosorbent assay(ELISA) was used to detect the levels of inflammatory factors, Real-time quantitative polymerase chain reaction(Real-time PCR) and Western blot were used to analyze the expressions of key genes and proteins involved in the intestinal mucosal barrier. The 16S rRNA sequencing was used to evaluate the diversity of intestinal flora, headspace gas chromatography-mass spectrometry(HS-GC-MS) was used to explore the levels of short-chain fatty acids(SCFAs) in feces. Base on the above findings, this paper investigated the effects of raw and soil-fried AMR on the biological, chemical, mechanical and immune barriers of model animals, and the differences in pharmacological effects and underlying mechanisms from the perspective of regulating the intestinal mucosal barrier in UC mice. ResultsSEM observation revealed numerous hearth soil particles on the surface of soil-fried AMR, accompanied by bubble-like bulges. At the same time, there were many cracks and folds on the surface of the hearth soil. EDS analysis revealed that the contents of Si, Al, Mg and Ca in soil-fried AMR were significantly higher than those of raw products, and these elements constituted the primary components of hearth soil. UPLC-Q-TOF-MS combined with database comparison was used to identify the chemical constituents of raw and soil-fried AMR. In positive ion mode, a total of 132 components were identified, primarily comprising three categories of terpenoids, polyphenols and amino acids. In negative ion mode, a total of 40 components were identified, primarily polyphenolic and glycoside compounds. Among them, the contents of sesquiterpenes and polyphenolic acids were changed significantly before and after processing. Soil-fried AMR could reduce the DAI score of UC mice, alleviate the shortening of colon length, reduce the levels of pro-inflammatory factors such as interleukin(IL)-17, IL-18, γ-interferon(IFN-γ) and tumor necrosis factor(TNF)-α in serum, increase the levels of anti-inflammatory factors such as secretory immunoglobulin A(sIgA), IL-10, IL-4 and transforming growth factor-β(TGF-β) in serum, increase the expressions of key genes and proteins of intestinal mucosal barrier such as tight junction protein-1(ZO-1), Occludin, Claudin-1 and mucin 2(MUC2) in colonic mucosa, and improve the disorders of intestinal flora diversity and the levels of SCFAs(P<0.05, P<0.01). The raw and stir-fried products of AMR also exhibited the aforementioned effects, but they were weaker than the soil-fried products. Additionally, the auxiliary material hearth soil also had a certain pharmacodynamic effect. ConclusionSoil-fried AMR can enhance the protective effect on intestinal mucosal barrier in UC mice. These changes or heating-induced alterations in the microscopic structure and chemical composition of AMR may be attributed to the dual effects of adsorption of hearth soil.
7.Impact of birth weight on the trajectory of blood pressure among primary school students
CUI Chengpeng, YE Siyan, FANG Yanfei, LI Yan, PENG Zeqin, XIAO Yuqing, WU Meng, LIU Qin
Chinese Journal of School Health 2026;47(3):309-313
Objective:
To explore the early effects of birth weight at different gestational ages on blood pressure trajectory among primary school students, so as to provide evidence for incorporating gestational age birth weight into individualized early warning and intervention strategies for childhood hypertension.
Methods:
From May to November 2023, a purposeful sampling method was used to recruit 1 676 students in grade 1-3 from three primary schools in a certain urban district of Chongqing. Follow up assessments were conducted in May 2024(T1), November 2024(T2), and May 2025(T3). General demographic and birth related information were collected via self administered questionnaires, while height, weight and blood pressure were obtained through physical examinations. Linear mixed effects model was used to analyze the associations between birth weight at different gestational ages and blood pressure trajectories.
Results:
During the T1-T3 period, the systolic blood pressure of boys were 98.5 (93.0, 104.5 ),98.5 (93.5, 105.0), and 97.5 (92.5, 103.5)mmHg, respectively, while the diastolic blood pressure were 60.5 (56.5, 65.0), 61.5 ( 57.0 , 65.5), and 60.0 (56.0, 64.0)mmHg, respectively. For girls, the systolic blood pressure were 95.5 (90.0, 102.0),95.5 (90.5, 101.5), and 96.0 (90.5, 101.5)mmHg, respectively, and the diastolic blood pressure were 60.5 (56.0, 64.5 ),61.5 (57.5, 65.5), and 59.5 (56.0, 63.0)mmHg, respectively. Through Friedman test within both boys and girls, diostolic blood pressure were statistically significant across three measurements( χ 2=48.85,81.54,both P <0.01). The proportion of normal blood pressure increased , and the proportion of prehypertension and hypertension decreased with time( χ 2=39.72,25.62,both P < 0.01 ). Linear mixed effects model analysis revealed that after adjusting for age, sex, household income monthly, parental education, family history of hypertension and maternal pregnancy complications, large for gestational age had significantly higher trajectories of systolic ( β = 1.50) and diastolic( β =0.94) blood pressure compared to appropriate for gestational age(both P <0.01).
Conclusion
Large for gestational age is associated with elevated blood pressure trajectories during school age, and it may be considered as an early indicator for individualized screening and intervention for childhood hypertension.
8.Exploring on Processing Mechanism of Enhanced "Invigorating Spleen and Stopping Diarrhea" Effect of Soil-fried Atractylodis Macrocephalae Rhizoma Based on "Microscopic Characterization, Chemical Analysis and Pharmacodynamic Evaluation" Trinity
Guoshun SHAN ; Yuyan XIAO ; Chu YUAN ; Xiuai CHEN ; Qimiao ZHAO ; Xiang LIU ; Hao WU ; Ke ZHANG ; Siqi LIU ; Yongduo YU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):182-193
ObjectiveTo analyze the processing mechanism underlying the enhanced effect of invigorating spleen and stopping diarrhea of soil-fried Atractylodis Macrocephalae Rhizoma(AMR) by analyzing the changes of microstructure, chemical composition and anti-ulcerative colitis(UC) activity before and after soil stir-frying. MethodsThe microstructure and elemental composition of AMR before and after soil stir-frying were analyzed by scanning electron microscopy-energy dispersive spectroscopy(SEM-EDS), to investigate the differences in microstructure and the underlying causes. Ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS) coupled with UNIFI 1.9.2 natural product analysis platform were used to analyze and identify the chemical constituents in raw and soil-fried products, and multivariate statistical methods including principal component analysis(PCA) and orthogonal partial least squares-discriminant analysis(OPLS-DA) were used to explore the differences and sources of chemical constituents between them. A dextran sulfate sodium(DSS)-induced UC mouse model was established. The method of disease activity index(DAI) was used to evaluate the severity of intestinal inflammation. Hematoxylin-eosin(HE) staining was used to observe the pathological changes of colon tissue, enzyme-linked immunosorbent assay(ELISA) was used to detect the levels of inflammatory factors, Real-time quantitative polymerase chain reaction(Real-time PCR) and Western blot were used to analyze the expressions of key genes and proteins involved in the intestinal mucosal barrier. The 16S rRNA sequencing was used to evaluate the diversity of intestinal flora, headspace gas chromatography-mass spectrometry(HS-GC-MS) was used to explore the levels of short-chain fatty acids(SCFAs) in feces. Base on the above findings, this paper investigated the effects of raw and soil-fried AMR on the biological, chemical, mechanical and immune barriers of model animals, and the differences in pharmacological effects and underlying mechanisms from the perspective of regulating the intestinal mucosal barrier in UC mice. ResultsSEM observation revealed numerous hearth soil particles on the surface of soil-fried AMR, accompanied by bubble-like bulges. At the same time, there were many cracks and folds on the surface of the hearth soil. EDS analysis revealed that the contents of Si, Al, Mg and Ca in soil-fried AMR were significantly higher than those of raw products, and these elements constituted the primary components of hearth soil. UPLC-Q-TOF-MS combined with database comparison was used to identify the chemical constituents of raw and soil-fried AMR. In positive ion mode, a total of 132 components were identified, primarily comprising three categories of terpenoids, polyphenols and amino acids. In negative ion mode, a total of 40 components were identified, primarily polyphenolic and glycoside compounds. Among them, the contents of sesquiterpenes and polyphenolic acids were changed significantly before and after processing. Soil-fried AMR could reduce the DAI score of UC mice, alleviate the shortening of colon length, reduce the levels of pro-inflammatory factors such as interleukin(IL)-17, IL-18, γ-interferon(IFN-γ) and tumor necrosis factor(TNF)-α in serum, increase the levels of anti-inflammatory factors such as secretory immunoglobulin A(sIgA), IL-10, IL-4 and transforming growth factor-β(TGF-β) in serum, increase the expressions of key genes and proteins of intestinal mucosal barrier such as tight junction protein-1(ZO-1), Occludin, Claudin-1 and mucin 2(MUC2) in colonic mucosa, and improve the disorders of intestinal flora diversity and the levels of SCFAs(P<0.05, P<0.01). The raw and stir-fried products of AMR also exhibited the aforementioned effects, but they were weaker than the soil-fried products. Additionally, the auxiliary material hearth soil also had a certain pharmacodynamic effect. ConclusionSoil-fried AMR can enhance the protective effect on intestinal mucosal barrier in UC mice. These changes or heating-induced alterations in the microscopic structure and chemical composition of AMR may be attributed to the dual effects of adsorption of hearth soil.
9.Clinical Advantages of Traditional Chinese Medicine in Treatment of Childhood Simple Obesity: Insights from Expert Consensus
Qi ZHANG ; Yingke LIU ; Xiaoxiao ZHANG ; Guichen NI ; Heyin XIAO ; Junhong WANG ; Liqun WU ; Zhanfeng YAN ; Kundi WANG ; Jiajia CHEN ; Hong ZHENG ; Xinying GAO ; Liya WEI ; Qiang HE ; Qian ZHAO ; Huimin SU ; Zhaolan LIU ; Dafeng LONG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(6):238-245
Childhood simple obesity has become a significant public health issue in China. Modern medicine primarily relies on lifestyle interventions and often suffers from poor long-term compliance, while pharmacological options are limited and associated with potential adverse effects. Traditional Chinese Medicine (TCM) has a long history in the prevention and management of this condition, demonstrating eight distinct advantages, including systematic theoretical foundation, diversified therapeutic approaches, definite therapeutic efficacy, high safety profile, good patient compliance, comprehensive intervention strategies, emphasis on prevention, and stepwise treatment protocols. Additionally, TCM is characterized by six distinctive features: the use of natural medicinal substances, non-invasive external therapies, integration of medicinal dietetics, simple exercise regimens, precise syndrome differentiation, and diverse dosage forms. By combining internal and external treatments, TCM facilitates individualized regimen adjustment and holistic regulation, demonstrating remarkable effects in improving obesity-related metabolic indicators, regulating constitutional imbalance, and promoting healthy behaviors. However, challenges remain, such as inconsistent operational standards, insufficient high-quality clinical evidence, and a gap between basic research and clinical application. Future efforts should focus on accelerating the standardization of TCM diagnosis and treatment, conducting multicenter randomized controlled trials, and fostering interdisciplinary integration, so as to enhance the scientific validity and international recognition of TCM in the prevention and treatment of childhood obesity.
10.A Computational Perspective on Differences Between MHC-I and MHC-II in TCR-pMHC Structure Prediction Resources: Review and Benchmarking
Xiao-Qin WU ; Da-Wei LIU ; Bin-Yu LI ; Yang LIU ; Yang CAO ; Wen-Tao DAI
Progress in Biochemistry and Biophysics 2026;53(5):1376-1399
The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.


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