1.Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions.
Fang REN ; Jing WEI ; Qingxin CHEN ; Mengling HU ; Lu YU ; Jianing MI ; Xiaogang ZHOU ; Dalian QIN ; Jianming WU ; Anguo WU
Acta Pharmaceutica Sinica B 2025;15(9):4327-4385
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline and memory loss, with few effective treatments currently available. The multifactorial nature of AD, shaped by genetic, environmental, and biological factors, complicates both research and clinical management. Recent advances in artificial intelligence (AI) and multi-omics technologies provide new opportunities to elucidate the molecular mechanisms of AD and identify early biomarkers for diagnosis and prognosis. AI-driven approaches such as machine learning, deep learning, and network-based models have enabled the integration of large-scale genomic, transcriptomic, proteomic, metabolomic, and microbiomic datasets. These efforts have facilitated the discovery of novel molecular signatures and therapeutic targets. Methods including deep belief networks and joint deep semi-non-negative matrix factorization have contributed to improvements in disease classification and patient stratification. However, ongoing challenges remain. These include data heterogeneity, limited interpretability of complex models, a lack of large and diverse datasets, and insufficient clinical validation. The absence of standardized multi-omics data processing methods further restricts progress. This review systematically summarizes recent advances in AI-driven multi-omics research in AD, highlighting achievements in early diagnosis and biomarker discovery while discussing limitations and future directions needed to advance these approaches toward clinical application.
2.Single-cell transcriptomics identifies PDGFRA+ progenitors orchestrating angiogenesis and periodontal tissue regeneration.
Jianing LIU ; Junxi HE ; Ziqi ZHANG ; Lu LIU ; Yuan CAO ; Xiaohui ZHANG ; Xinyue CAI ; Xinyan LUO ; Xiao LEI ; Nan ZHANG ; Hao WANG ; Ji CHEN ; Peisheng LIU ; Jiongyi TIAN ; Jiexi LIU ; Yuru GAO ; Haokun XU ; Chao MA ; Shengfeng BAI ; Yubohan ZHANG ; Yan JIN ; Chenxi ZHENG ; Bingdong SUI ; Fang JIN
International Journal of Oral Science 2025;17(1):56-56
Periodontal bone defects, primarily caused by periodontitis, are highly prevalent in clinical settings and manifest as bone fenestration, dehiscence, or attachment loss, presenting a significant challenge to oral health. In regenerative medicine, harnessing developmental principles for tissue repair offers promising therapeutic potential. Of particular interest is the condensation of progenitor cells, an essential event in organogenesis that has inspired clinically effective cell aggregation approaches in dental regeneration. However, the precise cellular coordination mechanisms during condensation and regeneration remain elusive. Here, taking the tooth as a model organ, we employed single-cell RNA sequencing to dissect the cellular composition and heterogeneity of human dental follicle and dental papilla, revealing a distinct Platelet-derived growth factor receptor alpha (PDGFRA) mesenchymal stem/stromal cell (MSC) population with remarkable odontogenic potential. Interestingly, a reciprocal paracrine interaction between PDGFRA+ dental follicle stem cells (DFSCs) and CD31+ Endomucin+ endothelial cells (ECs) was mediated by Vascular endothelial growth factor A (VEGFA) and Platelet-derived growth factor subunit BB (PDGFBB). This crosstalk not only maintains the functionality of PDGFRA+ DFSCs but also drives specialized angiogenesis. In vivo periodontal bone regeneration experiments further reveal that communication between PDGFRA+ DFSC aggregates and recipient ECs is essential for effective angiogenic-osteogenic coupling and rapid tissue repair. Collectively, our results unravel the importance of MSC-EC crosstalk mediated by the VEGFA and PDGFBB-PDGFRA reciprocal signaling in orchestrating angiogenesis and osteogenesis. These findings not only establish a framework for deciphering and promoting periodontal bone regeneration in potential clinical applications but also offer insights for future therapeutic strategies in dental or broader regenerative medicine.
Receptor, Platelet-Derived Growth Factor alpha/metabolism*
;
Humans
;
Neovascularization, Physiologic/physiology*
;
Dental Sac/cytology*
;
Single-Cell Analysis
;
Transcriptome
;
Mesenchymal Stem Cells/metabolism*
;
Bone Regeneration
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Animals
;
Dental Papilla/cytology*
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Periodontium/physiology*
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Stem Cells/metabolism*
;
Regeneration
;
Angiogenesis
3.Mesalazine mediates TGF-β1/Smad signaling pathway to alleviate lipopolysac-charide-induced colonic epithelial cell inflammation and apoptosis
Jing HOU ; Jianing LIU ; Ru FENG ; Wei LU ; Yun WANG ; Feng SU
Chinese Journal of Immunology 2024;40(3):524-529,533
Objective:To investigate effects of mesalazine(MS)on proliferation,apoptosis and inflammatory injury of cell model of ulcerative colitis(UC)induced by lipopolysaccharide(LPS),as well as transforming growth factor-β1(TGF-β1)/Smad signaling pathway effect in this study.Methods:Human colonic epithelial cells NCM-460 cultured in vitro were induced UC model by LPS,and divided into Con group(no treatment),LPS group(1 mg/L LPS),MS group(0.1,0.2,0.4 mg/L MS+1 mg/L LPS)and inhibitor group(10 μmol/L TGF-β1/Smad signaling pathway inhibitor LY2109761+0.2 mg/L MS+1 mg/L LPS).Cell morphology,proliferation,apoptosis and levels of inflammatory factors and TGF-β1/Smad pathway-related markers were examined by inverted microscope,EdU assay,Hoechst 33258 staining,ELISA and Western blot.Results:LPS treatment highly induced cell proliferation rate and Smad7 pro-tein level compared with Con group,while apoptotic cells,inflammatory factors TNF-α and IL-6,soluble interleukin-2 receptor(sIL-2R)release,as well as TGF-β1,p-Smad2,p-Smad3 protein expressions were increased;the above effects induced by LPS was reversed by MS in a dose-dependent manner(P<0.05).Compared with 0.2 mg/L MS group,NCM-460 cells proliferation rate and Smad7 expression were increased,while apoptotic cells,TNF-α and IL-6,sIL-2R releases,and TGF-β1,p-Smad2,p-Smad3 protein expressions were decreased(P<0.05).Conclusion:MS can attenuate LPS-induced apoptosis and inflammatory injury in NCM-460 cells,and this protection was possibly through suppressing TGF-β1/Smad signaling pathway.
4.Single-cell level analysis of the immune microenvironment characteristics of dental follicle tissues from the human third molars
Jianing LIU ; Xiaohui ZHANG ; Yuan CAO ; Lu LIU ; Xiao LEI ; Jiongyi TIAN ; Junxi HE ; Fang JIN ; Bingdong SUI
Journal of Practical Stomatology 2024;40(6):747-752
Objective:To analyze the immune microenvironment characteristics of human dental follicle tissues from the third molars and to explore the mutual communication and the effects of innate immune cells and adaptive immune cells within the dental follicle.Methods:Sequencing data(GSA-Human:HRA008022)in the GSA database were analyzed.Bioinformatics tools were employed for gene identification and GO enrichment analysis was performed to define the biological function of innate and adaptive immune cells.CellChat analysis was used for explaining intercellular communication among immune cell populations.Results:Using t-SNE dimen-sionality reduction analysis for immune cell populations,innate immune cell populations were obtained,including innate lymphoid cells,dendritic cells,mast cells and macrophages,and adaptive immune cell populations including T cells and B cells.Pearson corre-lation analysis showed that innate immune cells,specifically innate lymphoid cells and macrophages,had a strong correlation with adap-tive immune cell populations.GO enrichment analysis revealed mutual coordination among innate immune cell populations and regulato-ry effects on adaptive immune cell populations.Further CellChat analysis indicated biological signal transmission between innate and a-daptive immune cell populations,with CLEC,MIF,ADGRE5,COLLAGEN and MIF signaling pathways is the most significant.Con-clusion:Dental follicle tissues are rich in immune cells and innate immune cell populations interact with adaptive immune cells to regulate immune responses and participate in maintaining the homeostasis of dental follicle.
5.Gallbladder polypoid lesions: Current practices and future prospects
Kun WANG ; Qingpeng XU ; Lu XIA ; Jianing SUN ; Kanger SHEN ; Haoran LIU ; Linning XU ; Rui LI
Chinese Medical Journal 2024;137(14):1674-1683
Gallbladder polypoid lesions (GPLs) refer to any elevated lesion of the mucosal surface of the gallbladder wall, and the prevalence is estimated to be between 0.9% and 12.1%. GPLs include benign polyps and malignant polyps. Benign polyps are further classified as non-neoplastic polyps and neoplastic polyps. Cholesterol polyps are the most common benign polyps and adenocarcinoma is the main type of malignant polyp. Hepatitis B virus infection, liver function abnormalities, dyslipidemia, and obesity are the main risk factors for GPLs. Studies of biological mechanisms have focused on malignant gallbladder polyps, the development of which is regulated by hormone levels in vivo, gut microbiota, inflammation, oxidative stress, Salmonella typhimurium, and related molecules. Diagnostic modalities include chemical examination and imaging examination, with imaging examination currently being the mainstay. Treatment of patients with GPLs is based on the presence or absence of symptoms, age, size of the polyps, tendency of the polyp to increase, and risk factors for symptomatic malignancy to determine whether surgery should be performed.
6.Construction and Testing of Health LifeStyle Evidence (HLSE)
Chen TIAN ; Yong WANG ; Yilong YAN ; Yafei LIU ; Yao LU ; Mingyao SUN ; Jianing LIU ; Yan MA ; Jinling NING ; Ziying YE ; Qianji CHENG ; Ying LI ; Jiajie HUANG ; Shuihua YANG ; Yiyun WANG ; Bo TONG ; Jiale LU ; Long GE
Medical Journal of Peking Union Medical College Hospital 2024;15(6):1413-1421
Healthy lifestyles and good living habits are effective strategies and important approaches to prevent chronic non-communicable diseases. With the development of evidence-based medicine, the evidence translation system has made some achievements in clinical practice. There is, however, no comprehensive, professional and efficient system for translating lifestyle evidence globally. Therefore, the Health Lifestyle Evidence (HLSE) Group of Lanzhou University constructed the HLSE Evidence Translation System (
7.Method for Developing Patient Decision Aid in China
Yao LU ; Qian ZHANG ; Qianji CHENG ; Jianing LIU ; Mingyao SUN ; Jinling NING ; Jiajie HUANG ; Simeng REN ; Wenzheng ZHANG ; Yajie LIU ; Xiyuan DENG ; Jinhui TIAN ; Jie LIU ; Long GE
Medical Journal of Peking Union Medical College Hospital 2024;15(6):1422-1431
To systematically construct a guideline to provide a methodological guide for researchers to develop patient decision aids. Through a literature review of international methodological guidance for developing patient decision aids, sorting out the similarities and differences in the processes and methods for developing patient decision aids, and combining them with the topic discussion of the working group, the initial guideline was drafted. A total of 13 guidances was included, with the initial version containing 3 phases, 13 steps, and 48 points. We invited 19 multidisciplinary domain experts for forming consensus. The final version of the guideline contains 3 phases, 11 steps, and 24 points. The guideline has great potential to guide the development of patient decision aids in China and is expected to fill the methodological gap in the field. In the future, several rounds of pilot testing of the guideline based on specific decision issues will be conducted, and the guideline will be further revised and improved.
8.Construction and Testing of Health LifeStyle Evidence (HLSE)
Chen TIAN ; Yong WANG ; Yilong YAN ; Yafei LIU ; Yao LU ; Mingyao SUN ; Jianing LIU ; Yan MA ; Jinling NING ; Ziying YE ; Qianji CHENG ; Ying LI ; Jiajie HUANG ; Shuihua YANG ; Yiyun WANG ; Bo TONG ; Jiale LU ; Long GE
Medical Journal of Peking Union Medical College Hospital 2024;15(6):1413-1421
Healthy lifestyles and good living habits are effective strategies and important approaches to prevent chronic non-communicable diseases. With the development of evidence-based medicine, the evidence translation system has made some achievements in clinical practice. There is, however, no comprehensive, professional and efficient system for translating lifestyle evidence globally. Therefore, the Health Lifestyle Evidence (HLSE) Group of Lanzhou University constructed the HLSE Evidence Translation System (
9.Method for Developing Patient Decision Aid in China
Yao LU ; Qian ZHANG ; Qianji CHENG ; Jianing LIU ; Mingyao SUN ; Jinling NING ; Jiajie HUANG ; Simeng REN ; Wenzheng ZHANG ; Yajie LIU ; Xiyuan DENG ; Jinhui TIAN ; Jie LIU ; Long GE
Medical Journal of Peking Union Medical College Hospital 2024;15(6):1422-1431
To systematically construct a guideline to provide a methodological guide for researchers to develop patient decision aids. Through a literature review of international methodological guidance for developing patient decision aids, sorting out the similarities and differences in the processes and methods for developing patient decision aids, and combining them with the topic discussion of the working group, the initial guideline was drafted. A total of 13 guidances was included, with the initial version containing 3 phases, 13 steps, and 48 points. We invited 19 multidisciplinary domain experts for forming consensus. The final version of the guideline contains 3 phases, 11 steps, and 24 points. The guideline has great potential to guide the development of patient decision aids in China and is expected to fill the methodological gap in the field. In the future, several rounds of pilot testing of the guideline based on specific decision issues will be conducted, and the guideline will be further revised and improved.
10.Effect of sling exercise with Tuina therapy on kinesiophobia in old patients with lumbar disc herniation:a ran-domized controlled trial based on concept of brain-bone axis
Yuqin DAN ; Jianing SU ; Yi DING ; Xueyan WANG ; Danghan XU ; Jinghua WANG ; Yujing WU ; Mengyuan ZHANG ; Meng YIN ; Haifeng LU ; Gongchang YU ; Li LI
Chinese Journal of Rehabilitation Theory and Practice 2024;30(7):861-868
Objective To explore the effect of sling exercise with Tuina therapy on kinesiophobia in old patients with lumbar disc herniation,and analyze the mechanism based on brain-bone axis. Methods A total of 56 old patients with chronic lumbar disc herniation and kinesiophobia were selected from the Reha-bilitation Hospital of the Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine from September,2022 to December,2023;and randomly divided into control group(n=28)and experimental group(n=28).The control group accepted conventional exercise therapy,while the experimental group accepted sling exercise with Tuina therapy,for four weeks.They were assessed with simplified Chinese version of Tampa Scale of Kinesiophobia(TSK),Japanese Orthopaedic Association score(JOA)and Visual Analogue Scale for pain(VAS)before and after treatment,while the bone mineral density(BMD)was tested,the levels of osteoprote-gerin(OPG),norepinephrine(NE)and corticosteroids(Cor)in serum were measured,and the median frequency(MF)of weak-link erector spinae was detected with surface electromyography. Results Two cases dropped off in the control group,and one in the experimental group.The scores of all the assessment improved in both groups after treatment(|t|>14.168,P<0.001),as well as the serum levels of OPG,NE and Cor(|t|>2.103,P<0.05),BMD(|t|>2.726,P<0.05),and MF of erector spinae(|t|>14.736,P<0.001);all of them were better in the experimental group than in the control group(|t|>2.154,P<0.05). Conclusion Sling exercise with Tuina therapy can improve the pain and kinesiophobia of lumbar disc herniation in the old adults,which may promote the recovery of physical and mental function through regulating the levels of hor-mones and neurotransmitters related to the brain-bone axis.

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