1.Advances and prospects of the integration of multi-omics and artificial intelligence in traditional Chinese medicine research
Guicheng Liu ; Xi Long ; Qinghua PENG ; Sainan Tian ; Shujuan Hu
Digital Chinese Medicine 2025;8(3):300-312
Objective:
To map the research hotspots, developmental trends, and existing challenges in the integration of artificial intelligence (AI) with multi-omics in traditional Chinese medicine (TCM) through comprehensive bibliometric analysis.
Methods:
China National Knowledge Infrastructure (CNKI), Wanfang Data, China Science and Technology Journal Database (VIP), Chaoxing Journal Database, PubMed, and Web of Science were searched to collect literature on the theme of AI in TCM multi-omics research from the inception of each database to December 31, 2024. Eligible records were required to simultaneously address AI, TCM, and multi-omics. Quantitative and visual analyses of publication growth, core authorship networks, institutional collaboration patterns, and keyword co-occurrence were performed using Microsoft Excel 2021, NoteExpress v4.0.0, and Cite Space 6.3.R1. AI application modes in TCM multi-omics research were also categorized and summarized.
Results:
A total of 1 106 articles were enrolled (932 Chinese and 174 English). Publication output has increased continuously since 2010 and accelerated after 2016. Region-specific collaboration clusters were identified, dominated by Beijing University of Chinese Medicine, China Academy of Chinese Medical Sciences, Shanghai University of Traditional Chinese Medicine, and Nanjing University of Chinese Medicine. Keyword co-occurrence analysis revealed that current AI applications predominantly centered on metabolomics and algorithms such as cluster analysis and data mining. Research foci mainly ranked as follows: single herbs, herbal formulae, and disease-syndrome differentiation.
Conclusion
Machine learning methods are the predominant integrative modality of AI in the realm of TCM multi-omics research at present, utilized for processing omics data and uncovering latent patterns therein. The domain of TCM, in addition to investigating omics information procured through high-throughput technologies, also integrates data on traditional Chinese medicinal substances and clinical phenotypes, progressing towards joint analysis of multi-omics, high-dimensionality of data, and multi-modality of information. Deep learning approaches represent an emerging trend in the field.
2.SYNJ2BP expression,role and regulatory mechanism in epithelial ovarian cancer
Meilin ZOU ; Zongli MA ; Zhijuan QIN ; Meiqin YIN ; Weihong XUE ; Qinghua XI
Chongqing Medicine 2025;54(7):1541-1551
Objective To analyze the expression,biological functions,and potential molecular regulatory mechanisms of synaptojanin-2 binding protein(SYNJ2BP)in epithelial ovarian cancer.Methods Clinical specimens from 73 patients treated at Rugao People's Hospital and Affiliated Hospital of Nantong University between September 2018 and September 2022 were collected,including 53 epithelial ovarian cancer tissues and 20 normal ovarian tissues.A retrospective analysis was performed to examine SYNJ2BP gene and protein ex-pression and its correlation with clinicopathological features.The effects of SYNJ2BP overexpression on pro-liferation,apoptosis,migration,and invasion abilities of epithelial ovarian cancer A2780 cells were assessed via CCK-8 assays,colony formation assays,cell cycle analysis,apoptosis assays,Transwell migration assays,and wound healing assays.Western blot was used to detect the impact of SYNJ2BP overexpression on ERK1/2 protein phosphorylation and c-Myc protein expression in A2780 cells.Results The expression of SYNJ2BP was significantly downregulated in epithelial ovarian cancer tissues,and its expression level was significantly correlated with FIGO stage,tumor grade,and histological type(P<0.05),but not with other clinicopatholog-ical features.CCK-8 and colony formation assays demonstrated that the proliferation level of A2780 cells in the pcDNA3.1-SYNJ2BP group was significantly lower than that in the pcDNA3.1-NC group(P<0.01).Flow cytometry with PI single staining revealed altered cell cycle distribution in A2780 cells of the pcDNA3.1-SYNJ2BP group,with cells arrested in the S phase and a significantly increased apoptosis ratio compared to the pcDNA3.1-NC group(P<0.05).Transwell assays showed that the number of A2780 cells invading through the artificial matrix membrane in the pcDNA3.1-SYNJ2BP group was approximately half that in the pcD-NA3.1-NC group(P<0.01).Western blot results indicated downregulated expression of ERK1/2 and c-Myc in A2780 cells of the pcDNA3.1-SYNJ2BP group compared to the pcDNA3.1-NC group.In nude mouse tumors of the pcDNA3.1-SYNJ2BP group,compared to the pcDNA3.1-NC group,SYNJ2BP expression was upregulated while ERK1/2 and c-Myc expression was downregulated,consistent with the cellular-level expres-sion results.Conclusion Low expression of SYNJ2BP is observed in epithelial ovarian cancer tissues,and overexpression of SYNJ2BP inhibits the proliferation and invasion abilities of epithelial ovarian cancer cells.This suggests that SYNJ2BP may serve as a potential tumor suppressor in epithelial ovarian cancer and could be considered as a prognostic typing marker or potential therapeutic target for ovarian cancer.
3.Hypobaric hypoxia promotes macrophage necroptosis and atherosclerotic plaque in-stability in mice
Tao HU ; Yingrong HE ; Wushuai WANG ; Xi YANG ; Qinghua DUAN ; Xuan DU ; Qiang WANG
Chinese Journal of Arteriosclerosis 2025;33(3):219-226
Aim To investigate the effect of hypobaric hypoxia on macrophage necroptosis and atherosclerotic plaque instability and explore the underlying mechanisms.Methods Mouse bone marrow-derived macrophages were i-solated and cultured,and divided into control group(21%oxygen concentration)and hypoxia group(3%oxygen concen-tration).After 48 hours,cell necroptosis was detected,and the expression of cell necroptosis related proteins was deter-mined by Western blot.Healthy male ApoE-/-mice were randomly divided into control group and hypobaric hypoxia group.After the intervention for 16 weeks,the plasma lipids and inflammatory cytokines were measured,the areas of ath-erosclerotic plaque and necrotic core were evaluated by HE staining.The content of plaque collagen was detected by Mas-son staining.The number of macrophages in the plaque and the expression of necrotic apoptosis related proteins were de-tected by immunohistochemical staining and Western blot.Results Hypoxia induced increased necrotic apoptosis of macrophages(P<0.01),while necroptotic inhibitor necrostatin-1(Nec-1)reduced hypoxia induced cell death(P<0.05);hypoxia leads to a decrease in the expression of adenosine deaminase acting on RNA 1(ADAR1)in macrophages(P<0.01),and an increase in the expression of Z-DNA binding protein 1(ZBP1),phosphorylated receptor-interacting serine/threonine-protein kinase(p-RIPK3),and phosphorylated mixed lineage kinase domain-like protein(p-MLKL)(all P<0.01).Compared with the control group,the plasma lipid levels of ApoE-/-mice in the hypobaric hypoxia group did not change significantly(P>0.05),the plasma inflammatory cytokines(TNF-α,IL-1β,IL-6 and MCP-1)increased(all P<0.05),the area of atherosclerotic plaque increased(P<0.05),the area of plaque necrotic core increased,the content of plaque collagen decreased,the number of macrophages increased,the expression of ADAR1 decreased,and the expres-sion of ZBP1 and p-MLKL increased(all P<0.01).Conclusion Hypobaric hypoxia causes the imbalance of A-DAR1/ZBP1 expression in macrophages,activates RIPK3/MLKL signaling pathway,promotes macrophage necroptosis,in-creases the area of plaque necrosis core,and leads to increase instability of atherosclerotic plaque.
4.Hypobaric hypoxia promotes macrophage necroptosis and atherosclerotic plaque in-stability in mice
Tao HU ; Yingrong HE ; Wushuai WANG ; Xi YANG ; Qinghua DUAN ; Xuan DU ; Qiang WANG
Chinese Journal of Arteriosclerosis 2025;33(3):219-226
Aim To investigate the effect of hypobaric hypoxia on macrophage necroptosis and atherosclerotic plaque instability and explore the underlying mechanisms.Methods Mouse bone marrow-derived macrophages were i-solated and cultured,and divided into control group(21%oxygen concentration)and hypoxia group(3%oxygen concen-tration).After 48 hours,cell necroptosis was detected,and the expression of cell necroptosis related proteins was deter-mined by Western blot.Healthy male ApoE-/-mice were randomly divided into control group and hypobaric hypoxia group.After the intervention for 16 weeks,the plasma lipids and inflammatory cytokines were measured,the areas of ath-erosclerotic plaque and necrotic core were evaluated by HE staining.The content of plaque collagen was detected by Mas-son staining.The number of macrophages in the plaque and the expression of necrotic apoptosis related proteins were de-tected by immunohistochemical staining and Western blot.Results Hypoxia induced increased necrotic apoptosis of macrophages(P<0.01),while necroptotic inhibitor necrostatin-1(Nec-1)reduced hypoxia induced cell death(P<0.05);hypoxia leads to a decrease in the expression of adenosine deaminase acting on RNA 1(ADAR1)in macrophages(P<0.01),and an increase in the expression of Z-DNA binding protein 1(ZBP1),phosphorylated receptor-interacting serine/threonine-protein kinase(p-RIPK3),and phosphorylated mixed lineage kinase domain-like protein(p-MLKL)(all P<0.01).Compared with the control group,the plasma lipid levels of ApoE-/-mice in the hypobaric hypoxia group did not change significantly(P>0.05),the plasma inflammatory cytokines(TNF-α,IL-1β,IL-6 and MCP-1)increased(all P<0.05),the area of atherosclerotic plaque increased(P<0.05),the area of plaque necrotic core increased,the content of plaque collagen decreased,the number of macrophages increased,the expression of ADAR1 decreased,and the expres-sion of ZBP1 and p-MLKL increased(all P<0.01).Conclusion Hypobaric hypoxia causes the imbalance of A-DAR1/ZBP1 expression in macrophages,activates RIPK3/MLKL signaling pathway,promotes macrophage necroptosis,in-creases the area of plaque necrosis core,and leads to increase instability of atherosclerotic plaque.
5.Cong Rong San mitigates rat hippocampal neuronal apoptosis in an Al-zheimer disease model by inhibition of endoplasmic reticulum stress
Yuanqin CAI ; Qinghua LONG ; Xi WANG ; Chuhua ZENG
Chinese Journal of Pathophysiology 2024;40(7):1244-1252
AIM:To investigate the effects of Cong Rong San(CRS)on neuronal injury and endoplasmic re-ticulum stess(ERS)in rat models of Alzheimer disease.METHODS:Sixty male Sprague-Dawley rats(2 months old)were randomly divided into control(CON),model(MOD),low-dose CRS(CRSD),medium-dose CRS(CRSZ),high-dose CRS(CRSG),and memantine hydrochloride(MJG)groups.Morris water maze experiments were used to assess learning and memory in the rats.The morphology of neurons in the CA1 region of the hippocampus was examined using HE and Nissl staining,and the morphology of the endoplasmic reticulum in hippocampal cells was observed by transmission electron microscopy.Neuronal apoptosis in the CA1 region of the hippocampus was evaluated by TUNEL staining,while Western blot was used to assess the protein expression of glucose-regulated protein 78(GRP78),B-cell lymphoma-2(Bcl-2),Bcl-2-associated X protein(Bax),caspase-3,protein kinase R-like endoplasmic reticulum kinase(PERK),p-PERK,activating transcription factor 4(ATF4)and C/EBP homologous protein(CHOP)in rat hippocampal tissues.RE-SULTS:Compared with those in the MOD group,rats in the CRSZ and CRSG groups showed improved learning and mem-ory,together with reduced hippocampal neuronal loss,PERK-ATF4-CHOP activity,and the expression of the pro-apoptot-ic proteins Bax and caspase-3,while the expression of the anti-apoptotic protein Bcl-2 was increased.CONCLUSION:Treatment with Cong Rong San was found to mitigate cognitive impairment,as well as damage and apoptosis in hippocam-pal neurons,in rat models of Alzheimer disease,possibly by inhibition of endoplasmic reticulum stress.
6.Borneol attenuates inflammation and inhibits cardiac remodeling after myocardial infarction in mice via TRPM8
Yingrong HE ; Tao HU ; Wushuai WANG ; Xi YANG ; Qinghua DUAN ; Xuan DU ; Qiang WANG
Chinese Journal of Pathophysiology 2024;40(3):456-464
AIM:To examine the effects of borneol on inflammation and myocardial remodeling after myocar-dial infarction(MI)in mice,and to investigate the underlying mechanisms.METHODS:Eight-week-old wild-type(WT)C57BL/6 mice and transient receptor potential cation channel subfamily M member 8(TRPM8)gene knockout(TRPM8-/-)mice were randomly divided into sham and MI groups,and were subsequently treated with normal saline(control group)or borneol(borneol group)via gavage.Survival curves were plotted for WT and TRPM8-/-mice with MI treated with or with-out borneol.After 28 d,cardiac function of the mice was assessed through echocardiography,and haemodynamic indexes were evaluated using a multi-channel physiological instrument.Infarct size,myocardial hypertrophy and interstitial fibro-sis were assessed via pathological staining.In addition,inflammatory response in the peri-infarct region was detected.RE-SULTS:The TRPM8 expression was up-regulated in the peri-infarct region of the mice with MI(P<0.05),and borneol had no effect on TRPM8 expression(P>0.05).Borneol increased the survival rate,reduced the infarct size,inhibited car-diac remodeling and improved cardiac function in WT mice with MI(P<0.05 or P<0.01).However,it did not affect the survival rate,infarct size,myocardial hypertrophy,myocardial fibrosis or cardiac function in TRPM8-/-mice(P>0.05).Furthermore,borneol reduced inflammatory cell infiltration and the expression of inflammatory cytokines,tumor necrosis factor-α(TNF-α),interleukin-1β(IL-1β),IL-6 and monocyte chemotactic protein-1(MCP-1),in WT mice(P<0.05 or P<0.01)but not in TRPM8-/-mice(P>0.05).CONCLUSION:Borneol attenuates inflammation,inhibits cardiac re-modeling and improves cardiac function in mice with MI via TRPM8.
7.Application of DDPM in artificial intelligence image data augmentation of medical device
Pengfei HAO ; Qingyu LI ; Rui CHAI ; Xi CHEN ; Qinghua SONG ; Naishui HAN ; Ke ZHANG
China Medical Equipment 2024;21(3):154-158
Medical device imaging data augmentation is a method of expanding existing datasets by generating new data samples,which is of great significance for improving the performance of artificial intelligence(AI)medical device-related models and clinical application effects.However,traditional data augmentation methods are usually limited by the quality,realism,and diversity of generated samples.Denoising diffusion probabilistic model(DDPM)is a generative model based on the noise diffusion process,and its main idea is to generate samples with high quality by modelling the sampling process of the target distribution as a process of progressive denoising from the noise distribution.The basic principles and working mechanisms of DDPM were reviewed,the application scenarios of this method in AI medical device data augmentation were analyzed,and its advantages,challenges,and future development directions were explored to provide a reference for the field of AI medical device data augmentation.
8.Clinical treatment guideline for pulmonary blast injury (version 2023)
Zhiming SONG ; Junhua GUO ; Jianming CHEN ; Jing ZHONG ; Yan DOU ; Jiarong MENG ; Guomin ZHANG ; Guodong LIU ; Huaping LIANG ; Hezhong CHEN ; Shuogui XU ; Yufeng ZHANG ; Zhinong WANG ; Daixing ZHONG ; Tao JIANG ; Zhiqiang XUE ; Feihu ZHOU ; Zhixin LIANG ; Yang LIU ; Xu WU ; Kaican CAI ; Yi SHEN ; Yong SONG ; Xiaoli YUAN ; Enwu XU ; Yifeng ZHENG ; Shumin WANG ; Erping XI ; Shengsheng YANG ; Wenke CAI ; Yu CHEN ; Qingxin LI ; Zhiqiang ZOU ; Chang SU ; Hongwei SHANG ; Jiangxing XU ; Yongjing LIU ; Qianjin WANG ; Xiaodong WEI ; Guoan XU ; Gaofeng LIU ; Junhui LUO ; Qinghua LI ; Bin SONG ; Ming GUO ; Chen HUANG ; Xunyu XU ; Yuanrong TU ; Liling ZHENG ; Mingke DUAN ; Renping WAN ; Tengbo YU ; Hai YU ; Yanmei ZHAO ; Yuping WEI ; Jin ZHANG ; Hua GUO ; Jianxin JIANG ; Lianyang ZHANG ; Yunfeng YI
Chinese Journal of Trauma 2023;39(12):1057-1069
Pulmonary blast injury has become the main type of trauma in modern warfare, characterized by externally mild injuries but internally severe injuries, rapid disease progression, and a high rate of early death. The injury is complicated in clinical practice, often with multiple and compound injuries. Currently, there is a lack of effective protective materials, accurate injury detection instrument and portable monitoring and transportation equipment, standardized clinical treatment guidelines in various medical centers, and evidence-based guidelines at home and abroad, resulting in a high mortality in clinlcal practice. Therefore, the Trauma Branch of Chinese Medical Association and the Editorial Committee of Chinese Journal of Trauma organized military and civilian experts in related fields such as thoracic surgery and traumatic surgery to jointly develop the Clinical treatment guideline for pulmonary blast injury ( version 2023) by combining evidence for effectiveness and clinical first-line treatment experience. This guideline provided 16 recommended opinions surrounding definition, characteristics, pre-hospital diagnosis and treatment, and in-hospital treatment of pulmonary blast injury, hoping to provide a basis for the clinical treatment in hospitals at different levels.
9.Clinical Effect of Pedicled Pericardial Fat Flap in Prevention of Bronchial Pleural Fistula in Bronchial Sleeve Lobectomy.
Xiaoyun LI ; Hanyu DENG ; Xi ZHENG ; Daxing ZHU ; Qinghua ZHOU ; Xiaojun TANG
Chinese Journal of Lung Cancer 2020;23(5):360-364
BACKGROUND:
Bronchial sleeve lobectomy is essential surgical approach to treat centralized lung cancer. It is the best reflected the principle of lung cancer surgery, "remove tumor completely while minimize pulmonary function loss". Bronchial pleural fistula (BPF) is not common but very severe complication of bronchial sleeve lobectomy, that is usually fatal. Present article is to explore clinical effect on prevention of bronchial pleural fistula (BPF) in bronchial sleeve lobectomy, by wrapping brachial anastomosis with pedicled pericardial fat flap.
METHODS:
Clinical data of 39 non-small cell lung cancer (NSCLC) patients who underwent surgical resection during January 2016 to May 2019 in Lung Cancer Center of West China Hospital, Sichuan University were collected and retrospectively analyzed. All of the patients underwent bronchial sleeve lobectomy and a brachial anastomosis wrapping with pedicled pericardial fat flap.
RESULTS:
All patients recovered well and were discharged within 6 d-14 d after operation. No BPF occurred, nor other severe complications, such as reoperation needing intrathoracic bleeding, several pneumonia and respiratory failure, and life threatening cardiac arrhythmia. Only one patient (1/39) had several anastomotic stenosis and consequential atelectasis of residual lung in operative side 6 months after surgery.
CONCLUSIONS
Wrapping bronchial anastomosis with pedicled pericardial fat flap in bronchial lobectomy for centralized NSCLC is a simple and effective approach to prevent BPF, thus safety of the operation could be significantly improved.
10.Application of serum N -glycan profiling diagnostic model in evaluation of liver fibrosis in patients with hepatitis C
Xi CAO ; Ying ZHANG ; Yuemin NAN ; Zongnan TAN ; Cuiying CHEN ; Qinghua SHANG ; Xueen LIU ; Hui ZHUANG
Chinese Journal of Hepatology 2020;28(12):1023-1029
Objective:To study the changes of serum N-glycan abundance in patients with liver fibrosis at different stages of hepatitis C, and to establish and evaluate the diagnostic model for clinical application value.Methods:Data of 169 hepatitis C virus-infected cases with liver fibrosis were enrolled. Nine kinds of serum N-glycans were detected and analyzed using DNA sequencer-assisted fluorophore-assisted capillary electrophoresis technology. A binary logistics regression method was used to establish a diagnostic model based on the changes in the relative content of N-glycans in each stage of liver fibrosis. Receiver operating characteristic curve was used to evaluate and compare the diagnostic efficacy with other liver fibrosis diagnostic models.Results:N-glycan diagnostic model (B and C) had highest AUROC= 0.776, 0.827 for distinguishing fibrosis S1~S2 to S3~S4 and S1~S3 to S4 than GlycoFibroTest (AUROC = 0.760, 0.807), GlycoCirrhoTest (AUROC = 0.722, 0.787), aspartate aminotransferase to platelet ratio index (AUROC = 0.755, 0.751), FIB-4 index (AUROC = 0.730, 0.774), and S-index (AUROC = 0.707, 0.744). However, the diagnostic efficacy of model A (AUROC = 0.752) for distinguishing fibrosis S1 with S2~S4 had lower diagnostic potency than that of the aspartate aminotransferase to platelet ratio index (AUROC = 0.807). Diagnostic efficiency was improved when the N-glycan profiling and the aspartate aminotransferase to platelet ratio index were combined to diagnose liver fibrosis in each stage, and the area under the receiver operating characteristic curve was 0.839, 0.825, and 0.837, respectively.Conclusion:The serum N-glycan profiling diagnostic model has potential clinical application value in the diagnosis of liver fibrosis in patients with hepatitis C.

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