1.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.
2.Mechanism of Liuwei dihuang pill promoting tendon-bone healing by regulating cell crosstalk through Wnt/β-catenin pathway
Peng ZHANG ; Honglüe TAN ; Xiaotao SHI ; Xiao WANG ; Peizhao WANG ; Yanhao YUAN ; Renkun ZHAO ; Guorui CAO
China Pharmacy 2026;37(13):1722-1727
OBJECTIVE To explore the mecha nism by which Liuwei dihuang pill promotes tendon-bone healing by regulating the interaction between bone marrow mesenchymal stem cells (BMSCs) and macrophages through Wnt/ β -catenin pathway. METHODS BMSCs were co-cultured with macrophages at a ratio of 1∶4 and divided into control group, 10% drug-containing serum group, 20% drug-containing serum group, Wnt/ β -catenin pathway inhibitor Dickkopf-related protein 1 (DKK-1) group, and 20% drug-containing serum+DKK-1 group. After 48 hours of cell co-culture and 14 days of osteogenic induction, the CD86 and CD206 positive cell rates in macrophages, the proportion of calcium nodule positive staining area in BMSCs, the levels of osteocalcin (OCN) and oncostatin M (OSM) and alkaline phosphatase (ALP) activity in cell supernatant, as well as the mRNA and protein expression levels of OCN, Runt-related transcription factor 2 (RUNX2), OSM, low-density lipoprotein receptor-related protein 5 (LRP5), β -catenin in cells were detected. Pearson correlation analysis was performed to assess the correlation between LRP5 and β -catenin protein expression with OCN, RUNX2, OSM protein expression, and CD206 positive cell rate, respectively. RESULTS Compared with the control group, the CD86 positive cell rates in the 10% drug-containing serum group and the 20% drug-containing serum group were significantly reduced, while the CD206 positive cell rate, proportion of calcium nodule positive staining area, OCN level, OSM level, ALP activity, and mRNA and protein expression levels of OCN, RUNX2, OSM, LRP5, β -catenin were significantly increased ( P <0.05). Compared with the 20% drug-containing serum group, the changes in the above indicators in the 20% drug-containing serum+DKK-1 group were significantly reversed ( P <0.05). The protein expression of LRP5 and β -catenin was positively correlated with the pro tein expression of OCN, RUNX2, OSM, and CD206 positive cell rate. CONCLUSIONS Liuwei dihuang pill can activate the Wnt/ β -catenin pathway, induce M2 polarization of macrophages and secretion of OSM, promote osteogenic differentiation and matrix mineralization of BMSCs, and synergistically promote tendon-bone healing.
3.Mechanism of Liuwei dihuang pill promoting tendon-bone healing by regulating cell crosstalk through Wnt/β-catenin pathway
Peng ZHANG ; Honglüe TAN ; Xiaotao SHI ; Xiao WANG ; Peizhao WANG ; Yanhao YUAN ; Renkun ZHAO ; Guorui CAO
China Pharmacy 2026;37(13):1722-1727
OBJECTIVE To explore the mecha nism by which Liuwei dihuang pill promotes tendon-bone healing by regulating the interaction between bone marrow mesenchymal stem cells (BMSCs) and macrophages through Wnt/ β -catenin pathway. METHODS BMSCs were co-cultured with macrophages at a ratio of 1∶4 and divided into control group, 10% drug-containing serum group, 20% drug-containing serum group, Wnt/ β -catenin pathway inhibitor Dickkopf-related protein 1 (DKK-1) group, and 20% drug-containing serum+DKK-1 group. After 48 hours of cell co-culture and 14 days of osteogenic induction, the CD86 and CD206 positive cell rates in macrophages, the proportion of calcium nodule positive staining area in BMSCs, the levels of osteocalcin (OCN) and oncostatin M (OSM) and alkaline phosphatase (ALP) activity in cell supernatant, as well as the mRNA and protein expression levels of OCN, Runt-related transcription factor 2 (RUNX2), OSM, low-density lipoprotein receptor-related protein 5 (LRP5), β -catenin in cells were detected. Pearson correlation analysis was performed to assess the correlation between LRP5 and β -catenin protein expression with OCN, RUNX2, OSM protein expression, and CD206 positive cell rate, respectively. RESULTS Compared with the control group, the CD86 positive cell rates in the 10% drug-containing serum group and the 20% drug-containing serum group were significantly reduced, while the CD206 positive cell rate, proportion of calcium nodule positive staining area, OCN level, OSM level, ALP activity, and mRNA and protein expression levels of OCN, RUNX2, OSM, LRP5, β -catenin were significantly increased ( P <0.05). Compared with the 20% drug-containing serum group, the changes in the above indicators in the 20% drug-containing serum+DKK-1 group were significantly reversed ( P <0.05). The protein expression of LRP5 and β -catenin was positively correlated with the pro tein expression of OCN, RUNX2, OSM, and CD206 positive cell rate. CONCLUSIONS Liuwei dihuang pill can activate the Wnt/ β -catenin pathway, induce M2 polarization of macrophages and secretion of OSM, promote osteogenic differentiation and matrix mineralization of BMSCs, and synergistically promote tendon-bone healing.
4.Epidemiological characteristics of other infectious diarrheal diseases and their pathogens in Yangpu District of Shanghai from 2005 to 2024
Shen CAO ; Lu ZHOU ; Qiaoli SUN ; Zhengxi ZHANG ; Zhiping XIAO ; Yihan LU
Shanghai Journal of Preventive Medicine 2026;38(6):432-439
ObjectiveTo elucidate the epidemiological characteristics, evolution of the pathogen spectrum, and spatial distribution patterns of other infectious diarrheal diseases (excluding cholera, typhoid fever, paratyphoid fever, and bacillary dysentery) in Yangpu District of Shanghai from 2005 to 2024, thereby providing a scientific basis for the formulation of targeted prevention and control strategies. MethodsInformation on other infectious diarrhea cases with a current address in Yangpu District of Shanghai, and onset dates from January 1, 2005 to December 31, 2024, was extracted from the Chinese Center for Disease Control and Prevention Information System. Data on cases, including gender, age, occupation, and pathogen testing results, were collected. Descriptive epidemiological methods were employed to analyze the temporal, spatial, and demographic distribution of reported incidence rates and the epidemiological characteristics of pathogens for other infectious diarrheal diseases in Yangpu District from 2005 to 2024. Spatial autocorrelation analyses of reported incidence rates for viral and bacterial diarrhea were conducted using Moran’s Index (Moran’s I). Local spatial autocorrelation analyses were performed using local indicators of spatial association (LISA), with a first-order Queen contiguity spatial weight matrix, and significance was tested via 999 random permutations. Time-series and radar chart analyses were used to examine the temporal patterns of other infectious diarrhea cases caused by major pathogens. ResultsFrom 2005 to 2024, a total of 5 211 cases of other infectious diarrhea were reported in Yangpu District. The cases were predominantly males (2 714 cases, accounting for 52.08%) and children under 5 years of age (1 639 cases, accounting for 31.45%). The primary occupational groups were scattered children (1 433 cases, accounting for 27.50%) and retired personnel (1 403 cases, accounting for 26.92%). The annual average reported incidence rate was 20.36/100 000, showing an overall fluctuating trend with peaks around 2009 and 2024. Peak incidence occurred in summer and autumn (July‒September), with the highest reported incidence rate observed in summer (June‒August) (7.31/100 000). Children under 5 years of age (116.00/100 000) and adults aged 60 and older (21.39/100 000) were the top two age groups in terms of reported incidence. Global spatial autocorrelation analyses showed that the reported incidence rates of viral diarrhea across the sub-districts in Yangpu District in 2020 exhibited a significant positive spatial correlation (Moran’s I =0.30, P=0.016). The spatial autocorrelation of reported incidence rates of viral diarrhea in each sub-district for the periods 2008‒2019 and 2021‒2024 was not statistically significant (all P>0.05). Local spatial autocorrelation analyses of viral diarrhea incidence in 2020 revealed that Xinjiangwancheng Sub-district exhibited a low‑low clustering trend (local Moran’s I =0.49, P=0.018), while Dinghai Road Sub-district exhibited a high‑high clustering trend (local Moran’s I =1.33, P=0.024). The global spatial autocorrelation of reported incidence rates of bacterial diarrhea across the sub-districts of Yangpu District from 2005 to 2024 was not statistically significant (all P>0.05). Among the 5 211 cases, 4 049 had definitive pathogen test results. Bacterial diarrhea accounted for a relatively high proportion (55.52%, 2 248/4 049). The pathogens with the highest proportions were rotavirus (32.33%, 1 309/4 049), Vibrio spp. (31.69%, 1 283/4 049), Salmonella spp. (19.63%, 795/4 049), and norovirus (9.16%, 371/4 049). The radar chart showed that diarrhea cases caused by norovirus had no obvious seasonality, rotavirus cases were mainly concentrated in winter, and cases caused by Salmonella spp. and Vibrio spp. were mainly concentrated in summer and autumn. Among cases under 20 years of age, rotavirus accounted for a relatively high proportion, especially in children under 5 years of age. Among cases aged 20 years and older, Vibrio spp. and Salmonella spp. accounted for relatively high proportions. ConclusionFrom 2005 to 2024, other infectious diarrhea in Yangpu District of Shanghai was most prevalent in summer and autumn. Children under 5 years of age and adults aged 60 years and older were high-risk groups. In 2020, Dinghai Road Sub-district was a high-risk area for viral diarrhea. Rotavirus, Vibrio spp., Salmonella spp., and norovirus were the dominant pathogens. Prevention and control efforts for other infectious diarrhea should be strengthened among key populations (e.g., children under 5 years of age and adults aged 60 years and older) and in high-risk areas such as Dinghai Road Sub-district. During summer and autumn, priority should be given to the prevention and control of bacterial diarrhea caused by Salmonella spp. and Vibrio spp., especially among individuals aged 20 years and older (particularly those aged 60 and above). During winter, priority should be given to the prevention and control of diarrhea caused by rotavirus infection among individuals under 20 years of age, particularly children under 5 years of age.
5.Mechanism of Gancao Fuzitang Improving Knee Osteoarthritis in Rats via Regulating PI3K/Akt/mTOR Signaling Pathway and Promoting Autophagy
Xiaochao WANG ; Mange LIU ; Jiacong XIAO ; Zehui LI ; Da GUO ; Yulin CAI ; Chunjian ZI ; Xuewei CAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(17):46-58
ObjectiveThis paper aims to investigate the intervention effect and molecular mechanism of Gancao Fuzitang (GCFZT) in knee osteoarthritis (KOA). MethodsNetwork pharmacology was employed to predict the key targets and signaling pathways of GCFZT. Fifty SD rats were randomly divided into a sham group, a model group (KOA), a low-dose GCFZT group (GCFZT-L, 2.8 g·kg-1), a high-dose GCFZT group (GCFZT-H, 5.6 g·kg-1), and a positive drug celecoxib group (Celecoxib, 20 mg·kg-1), with 10 rats in each group. The rats in the sham group and the model group were given an equal volume of distilled water. Except for the sham group, the other four groups underwent anterior cruciate ligament transection to establish the KOA rat model. After successful modeling, the rats in each group received intragastric administration once a day for eight consecutive weeks. The structural changes of cartilage and subchondral bone were assessed via micro-computed tomography (micro-CT) and histological staining. The levels of inflammatory factors in the serum, such as interleukin-1β (IL-1β), IL-6, and tumor necrosis factor-α (TNF-α) were measured using an enzyme linked immunosorbent assay (ELISA) kit. Real-time quantitative polymerase chain reaction (Real-time PCR), Western blot, and immunohistochemistry were used to detect changes in the expression of autophagy-related proteins such as microtubule-associated protein 1 light chain 3B (LC3B), selective autophagy junction protein 62 (p62), and autophagy key molecule yeast Atg6 homolog (Beclin-1) in articular cartilage, as well as key molecules of the phosphatidylinositol 3 kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway. ResultsNetwork pharmacology analysis suggests that GCFZT may exert anti-osteoarthritic effects through regulating the PI3K/Akt/mTOR pathway. In vivo experiment shows that GCFZT can significantly improve cartilage degeneration and attenuate subchondral bone destruction in KOA rats. Detection results of inflammatory factors in the serum reveal that, compared with those in the sham group, the levels of IL-6, IL-1β, and TNF-α in the serum of rats in the KOA group are significantly increased (P<0.05). Compared with those in the KOA group, the levels of these three inflammatory factors in the GCFZT-L, GCFZT-H, and Celecoxib groups were significantly decreased (P<0.05). However, there was no statistically significant difference in these three inflammatory factor levels between the GCFZT-H group and the celecoxib group. These findings suggest that GCFZT can effectively inhibit the systemic inflammatory response in KOA rats. Mechanism research indicates that GCFZT inhibits activation of the PI3K/Akt/mTOR pathway, thereby enhancing autophagic activity and improving chondrocyte function and matrix degeneration. ConclusionGCFZT improves cartilage and subchondral bone damage in KOA rats by inhibiting the PI3K/Akt/mTOR signaling pathway and promoting autophagy. These findings provide theoretical evidence for the application of GCFZT in the prevention and treatment of osteoarthritis.
6.Pre-operative risk assessment of hepatocellular carcinoma recurrence in liver transplant recipients by non-invasive detection of pre-existing genetic lesions
Suqin YANG ; Sunbin LING ; Jianhua LI ; Yan WANG ; Jiapei WANG ; Qiwei HUANG ; Fanming LIU ; Yiqi ZHUANG ; Yingyu ZHENG ; Rui WANG ; Zhe YANG ; Xiaoping ZHENG ; Kai WANG ; Zhikun LIU ; Jun CHEN ; Jianguo WANG ; Haiyang XIE ; Lin ZHOU ; Leiming CHEN ; Guoqiang CAO ; Dandan CHEN ; Junfang JI ; Bin ZHAO ; Chao JIANG ; Di LU ; Xuyong WEI ; Hangjin JIANG ; Qiaonan SHAN ; Hengbo SHI ; Yong-Zhen XU ; Shusen ZHENG ; Zhengxin WANG ; Shengda LIN ; Xiao XU
Clinical and Molecular Hepatology 2026;32(2):884-903
Background/Aims:
Liver transplantation (LT) following total hepatectomy is a life-saving treatment for hepatocellular carcinoma (HCC). The HCC recurrence after LT hinders the effectiveness of the procedure. The objective of this study is to develop a pre-operative risk stratification model based on a liquid biopsy.
Methods:
We conducted a comprehensive multi-omics study of 260 HCC patients from three centers, including clinical data, low-coverage whole-genome sequencing of cell-free DNA (cfDNA) from plasma, as well as whole-exome, single-nucleus RNA, and spatial transcriptomics from matched tumor and non-tumor tissues.
Results:
We identified cfDNA-derived copy number alteration (CNA) signatures associated with post-transplant recurrence. By integrating cfDNA-derived CNA profiles with single-cell transcriptomic data, we traced recurrence-associated cfDNA to a distinct subpopulation of malignant cells within the primary tumor. These cells were embedded in a pro-metastatic microenvironment of specialized endothelial subtypes and cancer-associated fibroblasts. Notably, most recurrence-associated lesions were detectable in cfDNA prior to liver transplantation (LT). Building on these insights, we developed the ZJU Criteria based on CNA fragments and tumor markers, a pre-LT risk prediction tool that integrates conventional clinical factors with cfDNA-derived CNA signatures, and validated it using internal and independent external cohorts.
Conclusion
Our findings suggest that post-transplant recurrence commonly originates from advanced subclones that emerge late during tumor evolution. The ZJU Criteria provides an accurate, non-invasive strategy that significantly improves pre-LT risk stratification and clinical decision-making for patients with HCC.
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.Construction of the Diagnosis and Treatment System of "Sinew Prescription Correspondence" under the Guidance of Systematic Dialectical Sphygmology
Feng ZHANG ; Baoqiang DONG ; Xingxing LIN ; Yapeng LIU ; Lujia XIAO ; Bodong XING ; Yiyun CAO ; Wenhui ZHANG ; Wenqian QI
Journal of Traditional Chinese Medicine 2026;67(10):1038-1043
"Sinew prescription correspondence" is the principle of selecting prescriptions for channel sinew diseases. On the basis of the theory of syndrome differentiation and treatment, the pulse manifestation corresponds to the channel sinew syndrome, which can improve the flexibility and standardization of clinical prescriptions. From the perspective of systematic dialectical sphygmology, this paper explains the dialectical relationship between channel sinew theory and pulse body elements, pulse wall elements, pulse elements and blood flow elements, and clarifies the internal relationship between pulse manifestation and prescriptions at the level of channel sinew disease. The prescription is derived from the method, while the method is established with the syndrome, and the prescription is unified by the method. According to the theory of "sinew prescription correspondence", the treatment ideas of channel sinew diseases were analyzed from the perspective of channel sinew distribution, functional characteristics and structural changes. On this basis, the diagnosis of channel sinew disease and the application of prescriptions are expanded, and the research on the internal treatment and diagnosis mode of "pulse manifestation-channel sinew-zang fu (脏腑)" is prospected, so as to expand the differentiation and treatment methods of channel sinew theory.
9.Effect of Acupuncture at Neiguan (PC6) on Improving Autism by Promoting Myelination Through The METTL14/m⁶A/PTEN Axis Based on “Xuanfu-Suiqiao” Theory
Wei-Li DANG ; Lü-Yuan LIANG ; Yu-Xin LI ; Zhi-Yao LI ; Sai-Dan LIU ; Jia-Lei CAO ; Rong-Ze MA ; Yun-Kai WANG ; Xiao-Qing YANG ; Bing-Qi WEI ; Bing-Xiang MA
Progress in Biochemistry and Biophysics 2026;53(5):1165-1177
ObjectiveTo clarify whether METTL14 mediates the core role of acupuncture at Neiguan (PC6) in promoting myelination and improving behavior in young autistic rats through gene intervention technology. MethodsThe ASD model was established by intraperitoneal injection of valproic acid (VPA) in pregnant rats. Male offspring were intracerebroventricularly injected with adenovirus-packaged METTL14 shRNA (sh-METTL14) or its control (sh-NC) on postnatal day 1, with a model group set as well. Subsequently, the juvenile rats were divided into model group, acupuncture group, acupuncture+sh-NC group, and acupuncture+sh-METTL14 group. The acupuncture group received acupuncture at Neiguan (PC6) from postnatal day 7, once daily for 21 consecutive days. Neurobehavioral changes were evaluated by behavioral tests; METTL14 knockdown efficiency and the expression of METTL14, METTL3, and PTEN were detected by quantitative real-time PCR (qRT-PCR) and Western blot (WB); PTEN m6A levels were measured by RNA immunoprecipitation-qPCR (RIP-qPCR); myelin ultrastructure, expression of myelin basic protein (MBP) and neurofascin 155 (NF155), and dendritic spine density were observed using transmission electron microscopy (TEM), enzyme-linked immunosorbent assay (ELISA), immunofluorescence, qRT-PCR, and primary neuron culture. ResultsBehaviorally, knockdown of METTL14 significantly counteracted the beneficial effects of acupuncture in improving self-grooming, open field exploration, three-chamber social interaction, and Morris water maze learning and memory (P<0.05, P<0.01). Compared with the acupuncture+sh-NC group, the acupuncture+sh-METTL14 group showed significantly decreased mRNA and protein expression of hippocampal METTL14 (P<0.01), and the upregulating effects of acupuncture on METTL3 and PTEN expression were reversed (P<0.01). Meanwhile, knockdown of METTL14 significantly inhibited the acupuncture-induced increase in PTEN m6A levels (P<0.01). Morphologically, knockdown of METTL14 attenuated the improvement of myelin structure by acupuncture, reversed the downregulation of MBP and upregulation of NF155 induced by acupuncture, and blocked the increase in dendritic spine density (P<0.05, P<0.01). ConclusionMETTL14 is a key molecule mediating the therapeutic effect of acupuncture at Neiguan. Acupuncture at Neiguan upregulates METTL14, thereby enhancing m6A methylation modification of PTEN mRNA to stabilize its expression, ultimately promoting myelin development and improving behavioral symptoms in ASD juvenile rats. This preliminarily reveals the modern biological connotation of “opening Xuanfu and dredging myelin”.
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.

Result Analysis
Print
Save
E-mail