1.Nucleic Acid-driven Protein Degradation: Frontiers of Lysosomal Targeted Degradation Technology
Han YIN ; Yu LI ; Yu-Chuan FAN ; Shuai GUO ; Yuan-Yu HUANG ; Yong LI ; Yu-Hua WENG
Progress in Biochemistry and Biophysics 2025;52(1):5-19
Distinct from the complementary inhibition mechanism through binding to the target with three-dimensional conformation of small molecule inhibitors, targeted protein degradation technology takes tremendous advantage of endogenous protein degradation pathway inside cells to degrade plenty of “undruggable” target proteins, which provides a novel route for the treatment of many serious diseases, mainly including proteolysis-targeting chimeras, lysosome-targeting chimeras, autophagy-targeting chimeras, antibody-based proteolysis-targeting chimeras, etc. Unlike proteolysis-targeting chimeras first found in 2001, which rely on ubiquitin-proteasome system to mainly degrade intracellular proteins of interest, lysosome-targeting chimeras identified in 2020, which was act as the fastly developing technology, utilize cellular lysosomal pathway through endocytosis mediated by lysosome-targeting receptor to degrade both extracellular and membrane proteins. As an emerging biomedical technology, nucleic acid-driven lysosome-targeting chimeras utilize nucleic acids as certain components of chimera molecule to replace with ligand to lysosome-targeting receptor or protein of interest, exhibiting broad application prospects and potential clinical value in disease treatment and drug development. This review mainly introduced present progress of nucleic acid-driven lysosome-targeting chimeras technology, including its basic composition, its advantages compared with antibody or glycopeptide-based lysosome-targeting chimeras, and focused on its chief application, in terms of the type of lysosome-targeting receptors. Most research about the development of nucleic acid-driven lysosome-targeting chimeras focused on those which utilized cation-independent mannose-6-phosphonate receptor as the lysosome-targeting receptor. Both mannose-6-phosphonate-modified glycopeptide and nucleic aptamer targeting cation-independent mannose-6-phosphonate receptor, even double-stranded DNA molecule moiety can be taken advantage as the ligand to lysosome-targeting receptor. The same as classical lysosome-targeting chimeras, asialoglycoprotein receptor can also be used for advance of nucleic acid-driven lysosome-targeting chimeras. Another new-found lysosome-targeting receptor, scavenger receptor, can bind dendritic DNA molecules to mediate cellular internalization of complex and lysosomal degradation of target protein, suggesting the successful application of scavenger receptor-mediated nucleic acid-driven lysosome-targeting chimeras. In addition, this review briefly overviewed the history of lysosome-targeting chimeras, including first-generation and second-generation lysosome-targeting chimeras through cation-independent mannose-6-phosphonate receptor-mediated and asialoglycoprotein receptor-mediated endocytosis respectively, so that a clear timeline can be presented for the advance of chimera technique. Meantime, current deficiency and challenge of lysosome-targeting chimeras was also mentioned to give some direction for deep progress of lysosome-targeting chimeras. Finally, according to faulty lysosomal degradation efficiency, more cellular mechanism where lysosome-targeting chimeras perform degradation of protein of interest need to be deeply explored. In view of current progress and direction of nucleic acid-driven lysosome-targeting chimeras, we discussed its current challenges and development direction in the future. Stability of natural nucleic acid molecule and optimized chimera construction have a great influence on the biological function of lysosome-targeting chimeras. Discovery of novel lysosome-targeting receptors and nucleic aptamer with higher affinity to the target will greatly facilitate profound advance of chimera technique. In summary, nucleic acid-driven lysosome-targeting chimeras have many superiorities, such as lower immunogenicity, expedient synthesis of chimera molecules and so on, in contrast to classical lysosome-targeting chimeras, making it more valuable. Also, the chimera technology provides new ideas and methods for biomedical research, drug development and clinical treatment, and can be used more widely through further research and optimization.
2.Correlation between brain white matter lesions and insulin resistance in non-diabetic elderly individuals based on magnetic resonance imaging
Mei LI ; Fang YUAN ; Xizi XING ; Feng XIE ; Hua ZHANG
Chinese Journal of Radiological Health 2025;34(1):96-101
Objective To investigate the relationship between brain white matter lesions (WML) and triglyceride glucose (TyG) index in non-diabetic elderly individuals based on magnetic resonance imaging. Methods A total of 523 non-diabetic elderly individuals aged ≥ 60 years were selected from Jinan, Shandong Province, China from June 2018 to December 2019. According to the quartiles of TyG index, there were 133 participants in the first quartile (Q1) group, 127 in the second quartile (Q2) group, 132 in the third quartile (Q3) group, and 131 in the fourth quartile (Q4) group. All participants underwent brain magnetic resonance imaging to evaluate paraventricular, deep, and total WML volumes, as well as Fazekas scores. Results Compared with Q1, Q2, and Q3 groups, Q4 group showed significant increase in periventricular, deep, and total WML volumes (P < 0.05). The proportion of participants with a Fazekas score ≥ 2 in the periventricular, deep, and total WML was higher in the Q4 group compared with the Q1 and Q2 groups (P < 0.05). The proportion of participants with a Fazekas score ≥ 2 in deep WML was higher in Q4 group than in Q3 group (P < 0.05). TyG index was significantly positively correlated with periventricular, deep, and total WML volumes (r = 0.401, 0.405, and 0.445, P < 0.001). After adjusting for confounding factors, TyG index was still significantly positively correlated with periventricular, deep, and total WML volumes (P < 0.001). Logistic regression analysis showed that compared with Q1 group, the risk of Fazekas score ≥ 2 in periventricular WML was 1.950-fold (95% confidence interval [CI]: 1.154-3.294, P = 0.013) in Q3 group and 3.411-fold (95% CI: 1.984-5.863, P < 0.001) in Q4 group, the risk of Fazekas score ≥ 2 in total WML was 2.529-fold (95%CI: 1.444-4.430, P = 0.001) in Q3 group and 4.486-fold (95%CI: 2.314-8.696, P < 0.001) in Q4 group. The risk of Fazekas score ≥ 2 in deep WML was 2.953-fold (95%CI: 1.708-5.106, P < 0.001) in Q4 group compared with Q1 group. Conclusion Increased TyG index is an independent risk factor for WML in non-diabetic elderly individuals.
3.In situ Analytical Techniques for Membrane Protein Interactions
Zi-Yuan KANG ; Tong YU ; Chao LI ; Xue-Hua ZHANG ; Jun-Hui GUO ; Qi-Chang LI ; Jing-Xing GUO ; Hao XIE
Progress in Biochemistry and Biophysics 2025;52(5):1206-1218
Membrane proteins are integral components of cellular membranes, accounting for approximately 30% of the mammalian proteome and serving as targets for 60% of FDA-approved drugs. They are critical to both physiological functions and disease mechanisms. Their functional protein-protein interactions form the basis for many physiological processes, such as signal transduction, material transport, and cell communication. Membrane protein interactions are characterized by membrane environment dependence, spatial asymmetry, weak interaction strength, high dynamics, and a variety of interaction sites. Therefore, in situ analysis is essential for revealing the structural basis and kinetics of these proteins. This paper introduces currently available in situ analytical techniques for studying membrane protein interactions and evaluates the characteristics of each. These techniques are divided into two categories: label-based techniques (e.g., co-immunoprecipitation, proximity ligation assay, bimolecular fluorescence complementation, resonance energy transfer, and proximity labeling) and label-free techniques (e.g., cryo-electron tomography, in situ cross-linking mass spectrometry, Raman spectroscopy, electron paramagnetic resonance, nuclear magnetic resonance, and structure prediction tools). Each technique is critically assessed in terms of its historical development, strengths, and limitations. Based on the authors’ relevant research, the paper further discusses the key issues and trends in the application of these techniques, providing valuable references for the field of membrane protein research. Label-based techniques rely on molecular tags or antibodies to detect proximity or interactions, offering high specificity and adaptability for dynamic studies. For instance, proximity ligation assay combines the specificity of antibodies with the sensitivity of PCR amplification, while proximity labeling enables spatial mapping of interactomes. Conversely, label-free techniques, such as cryo-electron tomography, provide near-native structural insights, and Raman spectroscopy directly probes molecular interactions without perturbing the membrane environment. Despite advancements, these methods face several universal challenges: (1) indirect detection, relying on proximity or tagged proxies rather than direct interaction measurement; (2) limited capacity for continuous dynamic monitoring in live cells; and (3) potential artificial influences introduced by labeling or sample preparation, which may alter native conformations. Emerging trends emphasize the multimodal integration of complementary techniques to overcome individual limitations. For example, combining in situ cross-linking mass spectrometry with proximity labeling enhances both spatial resolution and interaction coverage, enabling high-throughput subcellular interactome mapping. Similarly, coupling fluorescence resonance energy transfer with nuclear magnetic resonance and artificial intelligence (AI) simulations integrates dynamic structural data, atomic-level details, and predictive modeling for holistic insights. Advances in AI, exemplified by AlphaFold’s ability to predict interaction interfaces, further augment experimental data, accelerating structure-function analyses. Future developments in cryo-electron microscopy, super-resolution imaging, and machine learning are poised to refine spatiotemporal resolution and scalability. In conclusion, in situ analysis of membrane protein interactions remains indispensable for deciphering their roles in health and disease. While current technologies have significantly advanced our understanding, persistent gaps highlight the need for innovative, integrative approaches. By synergizing experimental and computational tools, researchers can achieve multiscale, real-time, and perturbation-free analyses, ultimately unraveling the dynamic complexity of membrane protein networks and driving therapeutic discovery.
4.Adolescent Smoking Addiction Diagnosis Based on TI-GNN
Xu-Wen WANG ; Da-Hua YU ; Ting XUE ; Xiao-Jiao LI ; Zhen-Zhen MAI ; Fang DONG ; Yu-Xin MA ; Juan WANG ; Kai YUAN
Progress in Biochemistry and Biophysics 2025;52(9):2393-2405
ObjectiveTobacco-related diseases remain one of the leading preventable public health challenges worldwide and are among the primary causes of premature death. In recent years, accumulating evidence has supported the classification of nicotine addiction as a chronic brain disease, profoundly affecting both brain structure and function. Despite the urgency, effective diagnostic methods for smoking addiction remain lacking, posing significant challenges for early intervention and treatment. To address this issue and gain deeper insights into the neural mechanisms underlying nicotine dependence, this study proposes a novel graph neural network framework, termed TI-GNN. This model leverages functional magnetic resonance imaging (fMRI) data to identify complex and subtle abnormalities in brain connectivity patterns associated with smoking addiction. MethodsThe study utilizes fMRI data to construct functional connectivity matrices that represent interaction patterns among brain regions. These matrices are interpreted as graphs, where brain regions are nodes and the strength of functional connectivity between them serves as edges. The proposed TI-GNN model integrates a Transformer module to effectively capture global interactions across the entire brain network, enabling a comprehensive understanding of high-level connectivity patterns. Additionally, a spatial attention mechanism is employed to selectively focus on informative inter-regional connections while filtering out irrelevant or noisy features. This design enhances the model’s ability to learn meaningful neural representations crucial for classification tasks. A key innovation of TI-GNN lies in its built-in causal interpretation module, which aims to infer directional and potentially causal relationships among brain regions. This not only improves predictive performance but also enhances model interpretability—an essential attribute for clinical applications. The identification of causal links provides valuable insights into the neuropathological basis of addiction and contributes to the development of biologically plausible and trustworthy diagnostic tools. ResultsExperimental results demonstrate that the TI-GNN model achieves superior classification performance on the smoking addiction dataset, outperforming several state-of-the-art baseline models. Specifically, TI-GNN attains an accuracy of 0.91, an F1-score of 0.91, and a Matthews correlation coefficient (MCC) of 0.83, indicating strong robustness and reliability. Beyond performance metrics, TI-GNN identifies critical abnormal connectivity patterns in several brain regions implicated in addiction. Notably, it highlights dysregulations in the amygdala and the anterior cingulate cortex, consistent with prior clinical and neuroimaging findings. These regions are well known for their roles in emotional regulation, reward processing, and impulse control—functions that are frequently disrupted in nicotine dependence. ConclusionThe TI-GNN framework offers a powerful and interpretable tool for the objective diagnosis of smoking addiction. By integrating advanced graph learning techniques with causal inference capabilities, the model not only achieves high diagnostic accuracy but also elucidates the neurobiological underpinnings of addiction. The identification of specific abnormal brain networks and their causal interactions deepens our understanding of addiction pathophysiology and lays the groundwork for developing targeted intervention strategies and personalized treatment approaches in the future.
5.Multi-omics Analysis of NUDT19 Across Cancer Types and Its Functional Role in Leukemia
Xiao-Jin LI ; Shuai FENG ; Zhong-Tao YUAN ; Tong-Hua YANG
Progress in Biochemistry and Biophysics 2025;52(10):2627-2649
ObjectiveRecent studies have highlighted the critical role of NUDT19 in the initiation, progression, and prognosis of specific cancer types. However, its involvement in pan-cancer analysis has not been fully characterized. This study aims to systematically explore the expression patterns, clinical significance, and immune-related functions of NUDT19 in various cancer types through multi-omics analysis, further revealing its potential role in cancer, particularly its functional and therapeutic target value in leukemia. MethodsTo achieve this goal, various bioinformatics approaches were employed to evaluate the expression patterns, clinical significance, and immune-related functions of NUDT19 in tumors and normal tissues. Additionally, we analyzed the mutation characteristics of NUDT19 and its relationship with epigenetic modifications. Using the single-cell analysis tool SingleCellBase, we explored the distribution of NUDT19 across different cell subpopulations in tumors. To validate these findings, qRT-PCR was used to measure NUDT19 expression levels in specific tumor cell lines, and we established acute myeloid leukemia (AML) cell lines (HL-60 and THP-1) to conduct NUDT19 knockdown and overexpression experiments, assessing its effects on leukemia cell proliferation, apoptosis, and invasion. ResultsPan-cancer analysis revealed the dysregulated expression of NUDT19 across multiple cancer types, which was closely associated with poor prognosis, clinical staging, and diagnostic markers. Furthermore, NUDT19 was significantly correlated with tumor biomarkers, immune-related genes, and immune cell infiltration in different cancers. Mutation analysis showed that multiple mutations in NUDT19 were significantly associated with epigenetic changes. Single-cell analysis revealed the heterogeneity of NUDT19 expression in cancer cells, suggesting its potentially diverse functional roles in different cell subpopulations. qRT-PCR experiments confirmed the significant upregulation of NUDT19 in various tumor cell lines. In AML cell lines, NUDT19 knockdown led to reduced cell proliferation and invasion, with increased apoptosis, while NUDT19 overexpression significantly enhanced cell proliferation and invasion while reducing apoptosis. ConclusionThis study demonstrates the diverse roles of NUDT19 in various cancer types, with a particularly prominent functional role in leukemia. NUDT19 is not only associated with tumor initiation and progression but may also influence cancer progression through the regulation of immune microenvironment and epigenetic mechanisms. Our research highlights the potential of NUDT19 as a therapeutic target, particularly for targeted therapies in malignancies such as leukemia, with significant clinical application prospects.
6.Current status of cognition and skin care behavior in adolescent patients with acne: A survey in China.
Jing TIAN ; Hong SHU ; Qiufang QIAN ; Zhong SHEN ; Chunyu ZHAO ; Li SONG ; Ping LI ; Xiuping HAN ; Hua QIAN ; Jinping CHEN ; Hua WANG ; Lin MA ; Yuan LIANG
Chinese Medical Journal 2024;137(4):476-477
7.Mechanism of salvianolic acid B protecting H9C2 from OGD/R injury based on mitochondrial fission and fusion
Zi-xin LIU ; Gao-jie XIN ; Yue YOU ; Yuan-yuan CHEN ; Jia-ming GAO ; Ling-mei LI ; Hong-xu MENG ; Xiao HAN ; Lei LI ; Ye-hao ZHANG ; Jian-hua FU ; Jian-xun LIU
Acta Pharmaceutica Sinica 2024;59(2):374-381
This study aims to investigate the effect of salvianolic acid B (Sal B), the active ingredient of Salvia miltiorrhiza, on H9C2 cardiomyocytes injured by oxygen and glucose deprivation/reperfusion (OGD/R) through regulating mitochondrial fission and fusion. The process of myocardial ischemia-reperfusion injury was simulated by establishing OGD/R model. The cell proliferation and cytotoxicity detection kit (cell counting kit-8, CCK-8) was used to detect cell viability; the kit method was used to detect intracellular reactive oxygen species (ROS), total glutathione (t-GSH), nitric oxide (NO) content, protein expression levels of mitochondrial fission and fusion, apoptosis-related detection by Western blot. Mitochondrial permeability transition pore (MPTP) detection kit and Hoechst 33342 fluorescence was used to observe the opening level of MPTP, and molecular docking technology was used to determine the molecular target of Sal B. The results showed that relative to control group, OGD/R injury reduced cell viability, increased the content of ROS, decreased the content of t-GSH and NO. Furthermore, OGD/R injury increased the protein expression levels of dynamin-related protein 1 (Drp1), mitofusions 2 (Mfn2), Bcl-2 associated X protein (Bax) and cysteinyl aspartate specific proteinase 3 (caspase 3), and decreased the protein expression levels of Mfn1, increased MPTP opening level. Compared with the OGD/R group, it was observed that Sal B had a protective effect at concentrations ranging from 6.25 to 100 μmol·L-1. Sal B decreased the content of ROS, increased the content of t-GSH and NO, and Western blot showed that Sal B decreased the protein expression levels of Drp1, Mfn2, Bax and caspase 3, increased the protein expression level of Mfn1, and decreased the opening level of MPTP. In summary, Sal B may inhibit the opening of MPTP, reduce cell apoptosis and reduce OGD/R damage in H9C2 cells by regulating the balance of oxidation and anti-oxidation, mitochondrial fission and fusion, thereby providing a scientific basis for the use of Sal B in the treatment of myocardial ischemia reperfusion injury.
8.Three 2,3-diketoquinoxaline alkaloids with hepatoprotective activity from Heterosmilax yunnanensis
Rong-rong DU ; Xin-yi GUO ; Wen-jie QIN ; Hua SUN ; Xiu-mei DUAN ; Xiang YUAN ; Ya-nan YANG ; Kun LI ; Pei-cheng ZHANG
Acta Pharmaceutica Sinica 2024;59(2):413-417
Three 2,3-diketoquinoxaline alkaloids were isolated from
9.The relationship between activities of daily living and mental health in community elderly people and the mediating role of sleep quality
Heng-Yi ZHOU ; Jing LI ; Dan-Hua DAI ; Yang LI ; Bin ZHANG ; Rong DU ; Rui-Long WU ; Jia-Yan JIANG ; Yuan-Man WEI ; Jing-Rong GAO ; Qi ZHAO
Fudan University Journal of Medical Sciences 2024;51(2):143-150
Objective To explore the relationship and internal path between activities of daily living(ADL),sleep quality and mental health of community elderly people in Shanghai.Methods A questionnaire survey was conducted among community residents aged 60 years and older seeing doctors in community health care center of five streets in Shanghai during Sept to Dec,2021 using convenience sampling.Activities of Daily Living(ADL),Pittsburgh Sleep Quality Index(PSQI)and 10-item Kessler Psychological Distress Scale(K10)were adopted in the survey.Single factor analysis,correlation analysis and multiple linear regression were used to analyze the data.The effect relationship between the variables was tested using Bootstrap's mediated effects test.Results A total of 1 864 participants were included in the study.The average score was 15.53±4.47 for ADL,5.60±3.71 for PSQI and 15.50±6.28 for K10.The rate of ADL impairment,poor sleep quality,poor and very poor mental health of the elderly were 23.6%,27.3%,11.9%and 4.9%,respectively.ADL and sleep quality were all positively correlated with mental health(r=0.321,P<0.001;r=0.466,P<0.001);ADL was positively correlated with sleep quality(r=0.294,P<0.001).Multiple linear results of factors influencing mental health showed that ADL(β= 0.457,95%CI:0.341-0.573),sleep quality(β =0.667,95%CI:0.598-0.737)and mental health were positively correlated(P<0.001).Sleep quality partially mediated the relationship between ADL and mental health(95%CI:0.078-0.124)with an effect size of 33.0%.Conclusion Sleep quality is a mediator between ADL and mental health among community elderly people.Improving ADL and sleep quality may improve mental health in the population.
10.Survival analysis of patients with diffuse large B-cell lymphoma after chemotherapy using Fuzheng Jiedu Formula and its mechanism of action on lymphocyte subsets
Xi LI ; Wenyi ZHOU ; Shiya ZHUANSUN ; Xinbei YUAN ; Yijie YANG ; Hua FU ; Wei SHEN ; Min XU ; Xinjin GAN ; Jiahui LU
Journal of Beijing University of Traditional Chinese Medicine 2024;47(11):1603-1611
Objective To evaluate the survival of patients with diffuse large B-cell lymphoma(DLBCL)after chemotherapy using Fuzheng Jiedu Formula and to explore the intrinsic correlation between the lymphocyte subset level and the survival of patients with DLBCL.Methods A total of 234 patients with DLBCL who had completed chemotherapy and achieved complete or partial response in the Department of Hematology,Longhua Hospital Shanghai University of Traditional Chinese Medicine and Shanghai East Hospital,Tongji University from January 1,2013,to December 31,2023,were recruited.A cohort study design was adopted,with"whether to receive continuous Fuzheng Jiedu Formula treatment for≥6 months after chemotherapy"as the exposed factor.Patients meeting this exposed factor were divided into the traditional Chinese medicine(TCM)cohort,whereas those who did not meet this exposed factor were divided into the observation cohort.The 1-and 2-year progression-free survival(PFS)rate,overall survival(OS)rate,and duration of response(DOR)of the two cohorts were compared.The survival curves of PFS and OS of the two cohorts were drawn,and subgroup survival analysis was performed to determine factors affecting disease progression.The effect of Fuzheng Jiedu Formula on lymphocyte subset count level was observed.Results The study included 126 and 108 patients in the TCM and observation cohorts,respectively.Compared with the observation cohort,the 2-year PFS rate,2-year OS rate,and DOR were increased in the TCM cohort(P<0.05).The PFS in the TCM cohort was higher than that in the observation cohort[HR=0.542,95%CI(0.345-0.853),P<0.01].The result of subgroup analysis showed that PFS in the TCM cohort was higher than that in the observation cohort in the age≥60 years,AA stage Ⅲ-Ⅳ,CD4+

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