1.Discovery of selective HDAC6 inhibitors driven by artificial intelligence and molecular dynamics simulation approaches.
Xingang LIU ; Hao YANG ; Xinyu LIU ; Minjie MOU ; Jie LIU ; Wenying YAN ; Tianle NIU ; Ziyang ZHANG ; He SHI ; Xiangdong SU ; Xuedong LI ; Yang ZHANG ; Qingzhong JIA
Journal of Pharmaceutical Analysis 2025;15(8):101338-101338
Increasing evidence showed that histone deacetylase 6 (HDAC6) dysfunction is directly associated with the onset and progression of various diseases, especially cancers, making the development of HDAC6-targeted anti-tumor agents a research hotspot. In this study, artificial intelligence (AI) technology and molecular simulation strategies were fully integrated to construct an efficient and precise drug screening pipeline, which combined Voting strategy based on compound-protein interaction (CPI) prediction models, cascade molecular docking, and molecular dynamic (MD) simulations. The biological potential of the screened compounds was further evaluated through enzymatic and cellular activity assays. Among the identified compounds, Cmpd.18 exhibited more potent HDAC6 enzyme inhibitory activity (IC50 = 5.41 nM) than that of tubastatin A (TubA) (IC50 = 15.11 nM), along with a favorable subtype selectivity profile (selectivity index ≈ 117.23 for HDAC1), which was further verified by the Western blot analysis. Additionally, Cmpd.18 induced G2/M phase arrest and promoted apoptosis in HCT-116 cells, exerting desirable antiproliferative activity (IC50 = 2.59 μM). Furthermore, based on long-term MD simulation trajectory, the key residues facilitating Cmpd.18's binding were identified by decomposition free energy analysis, thereby elucidating its binding mechanism. Moreover, the representative conformation analysis also indicated that Cmpd.18 could stably bind to the active pocket in an effective conformation, thus demonstrating the potential for in-depth research of the 2-(2-phenoxyethyl)pyridazin-3(2H)-one scaffold.
2.Identification of roots of Rubus parvifolius L. by UPLC-MS/MS and network pharmacology analysis
Xiaozhou JIA ; Han LIN ; Jiaying HE ; Chunlin ZHONG ; Yongxin LIANG ; Liye PAN ; Xiangdong CHEN
International Journal of Traditional Chinese Medicine 2025;47(1):75-81
Objective:The components of Rubus parvifolius L. were analyzed based on UPLC-MS/MS technology and combined with network pharmacology analysis to explore the mechanism of action of Rubi Parvifolii Radix in treating inflammation, cough, fever, influenza and sore throat. Method:The chemical constituents of Rubi Parvifolii Radix were identified according to the information of mass spectrometry. The network pharmacology was used to analyze the corresponding targets and related pathways of its chemical components, and the "component-target-pathway" interaction diagram was drawn. PyMOL 2.5.7 software wasused to perform molecular docking between active components and key targets.Results:Twenty chemical components were identified by UPLC-MS/MS, and 15 components were screened out by network pharmacology, which can be used as quality markers of Rubi Parvifolii Radix, namely Azelaic acid, Procyanidol B3, Caprolactam, Bis (2-ethylhexyl) adipate, Cryptochlorogenic acid, 3-O-Feruloylquinic, Ellagic acid, Aurantiamide acetate, 2 α,3 β,19 α,23-Tetrahydroxyurs-12-en-28-oic acid, L-Epicatechin, (E)-3-Indoleacrylic acid, Euscaphic acid, Suberic acid, Diisononyl phthalate and Prodelphinidin T4. Molecular docking showed that 5 compounds compared with the reference substance could bind to the target proteins of disease well. Conclusions:The 15 active ingredients in Rubi Parvifolii Radix, including Caprolactam and (E)-3-Indoleacrylic acid, may play a therapeutic role in treating colds, high fever, sore throat, and inflammation by acting on targets such as AKT1 and TNF. This provides a certain reference for the clinical application of Rubi Parvifolii Radix.
3.Exploration on the material basis and mechanism of Prunus mume f. viridicalyx for anti-depression based on UPLC-QE-Orbitrap-MS combined with network pharmacology
Weisheng LYU ; Cuijie WEI ; Yueyi LIANG ; Tianrui XIA ; Dongmei SUN ; Xiangdong CHEN ; Xiaozhou JIA
International Journal of Traditional Chinese Medicine 2025;47(6):822-832
Objective:To identify the components of Prunus mume f. viridicalyx based on ultra performance liquid chromatography-QE-Orbitrap mass spectrometry (UPLC-QE-Orbitrap-MS); To predict and analyze its substances and mechanisms to exert anti-depression effects combined with network pharmacology.Methods:UPLC-QE Orbitrap MS technology was used to analyze the chemical components of Prunus mume f. viridicalyx. Based on ChemSpider, mzCloud online platform, orbitrap TCM library and existing literature research, the secondary mass spectra of target compounds were compared and confirmed to identify the chemical composition of Prunus mume f. viridicalyx. The active components of the Prunus mume f. viridicalyx were screened. The Swiss Target Prediction database was used to predict targets with high correlation to active components in Prunus mume f. viridicalyx, and obtaining depression related disease targets from GeneCards and DisGeNET databases. The intersection targets of constituents and diseases were obtained using Venny platform. Protein-protein interaction network (PPI) was constructed by using String database, and the core targets were screened. Gene ontology function and Kyoto encyclopedia of genes and genomes pathway enrichment analysis of potential core targets were performed by using David database, and "active component-core target-signal pathway" network was constructed. PyMOL software was used to perform molecular docking between active components and key targets.Results:A total of 54 components, including organic acids, flavonoids and their glycosides, alkaloid, amino acids and other compounds were identified from Prunus mume f. viridicalyx. A total of 22 active components were screened and 92 active components and disease intersection targets were identified. A total of 13 core targets were screened through PPI network, including tumor necrosis factor, albumin, amyloid beta-protein precursor, AKT serine/threonine kinase 1 and so on. Enrichment analysis showed that Prunus mume f. viridicalyx mainly participated in transcription from RNA polymerase Ⅱ promoter, gene expression, protein binding and other functions, and presented the effects of anti-depression through MAPK, Toll-like receptor signaling pathway and other pathways. 12 key targets and 7 key active components were further obtained through the analysis of the "active component-core target-signal pathway" network, three of them were confirmed as kaempferol, quercetin, and isorhamnetin by reference substance. Molecular docking showed that 3 compounds could bind to the target proteins of depression well.Conclusion:Prunus mume f. viridicalyx exerts antidepressant effects through multiple components, targets, and pathways, mainly through the MAPK signaling pathway.
4.Discovery of selective HDAC6 inhibitors driven by artificial intelligence and molecular dynamics simulation approaches
Xingang LIU ; Hao YANG ; Xinyu LIU ; Minjie MOU ; Jie LIU ; Wenying YAN ; Tianle NIU ; Ziyang ZHANG ; He SHI ; Xiangdong SU ; Xuedong LI ; Yang ZHANG ; Qingzhong JIA
Journal of Pharmaceutical Analysis 2025;15(8):1860-1872
Increasing evidence showed that histone deacetylase 6(HDAC6)dysfunction is directly associated with the onset and progression of various diseases,especially cancers,making the development of HDAC6-targeted anti-tumor agents a research hotspot.In this study,artificial intelligence(AI)technology and molecular simulation strategies were fully integrated to construct an efficient and precise drug screening pipeline,which combined Voting strategy based on compound-protein interaction(CPI)prediction models,cascade molecular docking,and molecular dynamic(MD)simulations.The biological potential of the screened compounds was further evaluated through enzymatic and cellular activity assays.Among the identified compounds,Cmpd.18 exhibited more potent HDAC6 enzyme inhibitory activity(IC50=5.41 nM)than that of tubastatin A(TubA)(IC50=15.11 nM),along with a favorable subtype selectivity profile(selectivity index ≈ 117.23 for HDAC1),which was further verified by the Western blot analysis.Additionally,Cmpd.18 induced G2/M phase arrest and promoted apoptosis in HCT-116 cells,exerting desirable antiproliferative activity(IC50=2.59 μM).Furthermore,based on long-term MD simulation trajectory,the key residues facilitating Cmpd.18's binding were identified by decomposition free energy analysis,thereby elucidating its binding mechanism.Moreover,the representative conformation analysis also indicated that Cmpd.18 could stably bind to the active pocket in an effective conformation,thus demonstrating the potential for in-depth research of the 2-(2-phenoxyethyl)pyridazin-3(2H)-one scaffold.
5.Prenatal diagnosis and analysis of fetuses with false-positive NIPT results caused by sex chromosomal abnormalities in pregnant women.
Tingting BAI ; Fengni FAN ; Lihui YANG ; Xiangdong LIN ; Rong QIANG ; Ting JIA ; Rui WANG
Chinese Journal of Medical Genetics 2025;42(5):525-531
OBJECTIVE:
To analyze the results of prenatal diagnosis for fetuses with a high risk for sex chromosome aneuploidies (SCAs) indicated by non-invasive prenatal testing (NIPT), and to assess the influence of maternal chromosomal factors on the results of NIPT.
METHODS:
A retrospective analysis was conducted on the clinical data of 454 pregnant women with a high risk for SCAs indicated by NIPT undergoing invasive prenatal diagnosis at the Medical Genetics Center of Northwest Women's and Children's Hospital from January 2022 to September 2024. The data has included prenatal diagnosis indications, results, pregnancy outcomes, and the chromosomal results of pregnant women.
RESULTS:
Among the 454 women (including 10 with twin pregnancy) with a high risk for SCAs indicated by NIPT, 149 (including 4 twin cases) were diagnosed with SCAs through invasive prenatal diagnosis. These had included 47,XXX (37 cases), 47,XXY (56 cases), 47,XYY (29 cases), 45,X (1 case), 48,XXYY (1 case), mosaicism (20 cases), sex chromosome structural abnormalities (6 cases), and small-scale pathogenic copy number variations (3 cases). 383 pregnant women (including 7 with twin pregnancy) had accepted chromosomal karyotyping analysis. In total 49 cases of SCAs abnormalities were detected. Among them, 41 cases were pregnant women with SCAs but normal fetal chromosomes, which yielded a false positive rate for NIPT caused by maternal factors by 10.7%. In addition, 8 cases (including 1 twin case) had SCAs abnormalities in both the pregnant woman and the fetus. Among the 383 pregnant women, 129 cases (including 3 twin cases) of fetal SCAs were diagnosed, which yielded an overall positive predictive value (PPV) of NIPT for SCAs by 33.7% (129/383). With the 41 false positive cases caused by maternal SCAs abnormalities excluded, the PPV of NIPT for SCAs will be increased to 37.7% (129/342). Among the 454 pregnant women, twin pregnancies have accounted for 2.2% (10/454). Among the confirmed cases of SCAs abnormalities, twin cases accounted for 2.7% (4/149). Among the 383 pregnant women undergoing chromosomal karyotyping, twin cases accounted for 1.8% (7/383). Among the detected cases of chromosomal abnormalities, twin cases accounted for 2.0% (1/49). By calculation, the proportion of singleton pregnant women with a high risk for SCAs indicated by NIPT was approximately 32.1%, and the proportion of twin pregnant women was approximately 38.6%, indicating that twin pregnancies could increase the positive rate of NIPT.
CONCLUSION
NIPT can improve the screening efficiency for SCAs, but its PPV is limited. Therefore, pregnant women with a high risk for SCAs indicated by NIPT need to undergo invasive prenatal diagnosis for a definite diagnosis, and twin pregnancies can increase the positive rate of NIPT. The study confirmed that chromosomal abnormalities in pregnant women can significantly affect the accuracy of NIPT in detecting fetal SCAs. Therefore, when NIPT indicates SCAs abnormalities, it is recommended to simultaneously conduct chromosomal testing on the pregnant women. The combined application of chromosomal karyotyping analysis, fluorescence in situ hybridization, and copy number variation detection techniques can significantly improve the diagnostic accuracy for SCAs, especially for the detection of mosaicisms.
Humans
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Female
;
Pregnancy
;
Sex Chromosome Aberrations
;
Adult
;
Retrospective Studies
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False Positive Reactions
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Prenatal Diagnosis/methods*
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Noninvasive Prenatal Testing/methods*
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Aneuploidy
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Male
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Sex Chromosome Disorders/genetics*
6.Prenatal diagnosis and analysis of fetuses with false-positive NIPT results caused by sex chromosomal abnormalities in pregnant women
Tingting BAI ; Fengni FAN ; Xiangdong LIN ; Lihui YANG ; Rong QIANG ; Ting JIA ; Rui WANG
Chinese Journal of Medical Genetics 2025;42(5):525-531
Objective:To analyze the results of prenatal diagnosis for fetuses with a high risk for sex chromosome aneuploidies (SCAs) indicated by non-invasive prenatal testing (NIPT), and to assess the influence of maternal chromosomal factors on the results of NIPT.Methods:A retrospective analysis was conducted on the clinical data of 454 pregnant women with a high risk for SCAs indicated by NIPT undergoing invasive prenatal diagnosis at the Medical Genetics Center of Northwest Women′s and Children′s Hospital from January 2022 to September 2024. The data has included prenatal diagnosis indications, results, pregnancy outcomes, and chromosomal results of the pregnant women. This study has been approved by the Ethics Committe of Northwest Women′s and Children′s Hospital(Ethics No.2024-132)Results:Among the 454 women (including 10 with twin pregnancy) with a high risk for SCAs indicated by NIPT, 149 (including 4 twin cases) were diagnosed with SCAs through invasive prenatal diagnosis. These had included 47, XXX (37 cases), 47, XXY (56 cases), 47, XYY (29 cases), 45, X (1 case), 48, XXYY (1 case), mosaicism (20 cases), sex chromosome structural abnormalities (6 cases), and small-scale pathogenic copy number variations (3 cases). 383 pregnant women (including 7 with twin pregnancy) had accepted chromosomal karyotyping analysis. In total 49 cases(including 1 twih case) of SCAs were detected. Among them, 41 cases were pregnant women with SCAs but normal fetal chromosomes, which yielded a false positive rate for NIPT caused by maternal factors by 10.7%. In addition, 9 cases (including 1 twin case) had SCAs in both the pregnant woman and the fetus. Among the 383 pregnant women, 129 cases (including 3 twin cases) of fetal SCAs were diagnosed, which yielded an overall positive predictive value (PPV) of NIPT for SCAs by 33.7% (129/383). With the 41 false positive cases caused by maternal SCAs excluded, the PPV of NIPT for SCAs will be increased to 37.7% (129/342). Among the 454 pregnant women, twin pregnancies have accounted for 2.2% (10/454). Among the confirmed cases of SCAs, twin cases accounted for 2.7% (4/149). Among the 383 pregnant women undergoing chromosomal karyotyping, twin cases accounted for 1.8% (7/383). Among the detected cases of chromosomal abnormalities, twin cases accounted for 2.0% (1/49). Among singleton pregnancies, the positive predictive value (PPV) of NIPT for sex chromosome aneuploidies (SCAs) was 32.7% (145/444), in twin pregnancies, the PPV was 40.0% (4/10).Conclusion:NIPT can improve the screening efficiency for SCAs, but its PPV is limited. Therefore, pregnant women with a high risk for SCAs indicated by NIPT need to undergo invasive prenatal diagnosis for a definite diagnosis, while the PPV in twin pregnancies may be higher than in singletons, this observation is limited by the small sample size of twins in our study. The study confirmed that chromosomal abnormalitpies in pregnant women can significantly affect the accuracy of NIPT in detecting fetal SCAs. Therefore, when NIPT indicates SCAs, it is recommended to simultaneously conduct chromosomal karyotyping for the pregnant women. The combined application of chromosomal karyotyping analysis, fluorescence in situ hybridization, and copy number variation detection techniques can significantly improve the diagnostic accuracy for SCAs, especially for the detection of mosaicisms.
7.Prenatal diagnosis and analysis of fetuses with false-positive NIPT results caused by sex chromosomal abnormalities in pregnant women
Tingting BAI ; Fengni FAN ; Xiangdong LIN ; Lihui YANG ; Rong QIANG ; Ting JIA ; Rui WANG
Chinese Journal of Medical Genetics 2025;42(5):525-531
Objective:To analyze the results of prenatal diagnosis for fetuses with a high risk for sex chromosome aneuploidies (SCAs) indicated by non-invasive prenatal testing (NIPT), and to assess the influence of maternal chromosomal factors on the results of NIPT.Methods:A retrospective analysis was conducted on the clinical data of 454 pregnant women with a high risk for SCAs indicated by NIPT undergoing invasive prenatal diagnosis at the Medical Genetics Center of Northwest Women′s and Children′s Hospital from January 2022 to September 2024. The data has included prenatal diagnosis indications, results, pregnancy outcomes, and chromosomal results of the pregnant women. This study has been approved by the Ethics Committe of Northwest Women′s and Children′s Hospital(Ethics No.2024-132)Results:Among the 454 women (including 10 with twin pregnancy) with a high risk for SCAs indicated by NIPT, 149 (including 4 twin cases) were diagnosed with SCAs through invasive prenatal diagnosis. These had included 47, XXX (37 cases), 47, XXY (56 cases), 47, XYY (29 cases), 45, X (1 case), 48, XXYY (1 case), mosaicism (20 cases), sex chromosome structural abnormalities (6 cases), and small-scale pathogenic copy number variations (3 cases). 383 pregnant women (including 7 with twin pregnancy) had accepted chromosomal karyotyping analysis. In total 49 cases(including 1 twih case) of SCAs were detected. Among them, 41 cases were pregnant women with SCAs but normal fetal chromosomes, which yielded a false positive rate for NIPT caused by maternal factors by 10.7%. In addition, 9 cases (including 1 twin case) had SCAs in both the pregnant woman and the fetus. Among the 383 pregnant women, 129 cases (including 3 twin cases) of fetal SCAs were diagnosed, which yielded an overall positive predictive value (PPV) of NIPT for SCAs by 33.7% (129/383). With the 41 false positive cases caused by maternal SCAs excluded, the PPV of NIPT for SCAs will be increased to 37.7% (129/342). Among the 454 pregnant women, twin pregnancies have accounted for 2.2% (10/454). Among the confirmed cases of SCAs, twin cases accounted for 2.7% (4/149). Among the 383 pregnant women undergoing chromosomal karyotyping, twin cases accounted for 1.8% (7/383). Among the detected cases of chromosomal abnormalities, twin cases accounted for 2.0% (1/49). Among singleton pregnancies, the positive predictive value (PPV) of NIPT for sex chromosome aneuploidies (SCAs) was 32.7% (145/444), in twin pregnancies, the PPV was 40.0% (4/10).Conclusion:NIPT can improve the screening efficiency for SCAs, but its PPV is limited. Therefore, pregnant women with a high risk for SCAs indicated by NIPT need to undergo invasive prenatal diagnosis for a definite diagnosis, while the PPV in twin pregnancies may be higher than in singletons, this observation is limited by the small sample size of twins in our study. The study confirmed that chromosomal abnormalitpies in pregnant women can significantly affect the accuracy of NIPT in detecting fetal SCAs. Therefore, when NIPT indicates SCAs, it is recommended to simultaneously conduct chromosomal karyotyping for the pregnant women. The combined application of chromosomal karyotyping analysis, fluorescence in situ hybridization, and copy number variation detection techniques can significantly improve the diagnostic accuracy for SCAs, especially for the detection of mosaicisms.
8.Monitoring results and analysis of key endemic disease prevention and control projects in Shanxi Province in 2021
Man HE ; Jianlyu YANG ; Qingzhen JIA ; Yongping WANG ; Zhenghui WANG ; Xiangdong ZHANG ; Fengfeng ZHANG
Chinese Journal of Endemiology 2024;43(8):643-646
Objective:To investigate the current situation of key endemic disease prevention and control in Shanxi Province, and provide a scientific basis for further strengthening the implementation of prevention and control measures.Methods:In 2021, monitoring of key endemic disease prevention and control projects in Shanxi Province was carried out in accordance with the current national monitoring plans for iodine deficiency disorders and water source high iodine areas, for endemic fluorosis, endemic arsenic poisoning, Kashin-Beck disease, and Keshan disease. The effect of prevention and control measures was evaluated in accordance with the "Evaluation Measures for Key Endemic Disease Control and Elimination (2019 Edition)". Patient management services and treatment subsidy projects were carried out in accordance with the "Management Service Standards for Endemic Disease Patients" and the "Management Measures for Treatment of Endemic Disease Patients".Results:All 117 counties (cities, districts, hereinafter referred to as counties) in Shanxi Province had reached the national elimination standards for iodine deficiency disorders, and the overall iodine nutrition of the population was generally suitable. However, the consumption rate of qualified iodine salt in 8 counties was ≤90%, and the iodine nutrition of pregnant women in 13 counties was insufficient. The water improvement rate in 295 villages in 12 counties across the province with high water iodine level was 80.68% (238/295), and the proportion of villages with qualified water iodine after water improvement was 38.31% (113/295). The prevention and control measures of 93.55% (58/62) of the counties in the province with endemic fluorosis caused through drinking water reached the national control standards. Totally 20 counties ravaged by coal-burning borne endemic fluorosis, 16 counties ravaged by drinking water borne endemic arsenicosis (high arsenic areas), 35 counties ravaged by Kashin-Beck disease, and 11 counties ravaged by Keshan disease met the national elimination standards. In 2021, 11 197 patients with endemic diseases were followed up and managed in Shanxi Province, and drug treatment programs were carried out on 3 413 patients with skeletal fluorosis, 2 088 patients with Kashin-Beck disease, and 10 patients with chronic Keshan disease.Conclusions:The overall prevention and control of key endemic diseases in Shanxi Province remains under control or elimination. However, the water improvement in some drinking water borne endemic fluorosis areas still needs to be further strengthened. Measures for water improvement and supply of non-iodized salt in water source high iodine areas still need to be coordinated and promoted. Key endemic disease patients in Shanxi Province have basically achieved standardized management.
9.Study on quality evaluation of Buddleja officinalis from different habitats based on HPLC fingerprint and content determination
Cuijie WEI ; Xiaoxia LIU ; Zhiwen DUAN ; Yongwei FENG ; Xiaozhou JIA ; Yueyi LIANG ; Xiangdong CHEN ; Dongmei SUN ; Zhenyu LI
International Journal of Traditional Chinese Medicine 2024;46(2):215-221
Objective:To establish UPLC fingerprint method and 2 contents determination methods of Buddleja officinalis; To provide a reference for improving the quality control standard and evaluation of Buddleja officinalis from different habitats.Methods:UPLC method was used to establish the fingerprints of 17 batches of Buddleja officinalis. The similarity evaluation, clustering analysis, principal component analysis and orthogonal partial least squares discriminant analysis were used to compare the quality differences of Buddleja officinalis from different habitats. The contents of acteoside and linarin in Buddleja officinalis were determined.Results:There were 12 common peaks in UPLC fingerprints of Buddleja officinalis, six of which were identified as echinacoside, acteoside, cynaroside, isoacteoside, linarin, and apigenin. The fingerprint similarity of 17 batches of Buddleja officinalis was more than 0.9; Buddleja officinalis from different habitats were classified into 2 groups. Five differential markers were determined by OPLS-DA analysis. The order of significance was acteoside > peak 3 > echinacoside > isoacteoside > linarin. Edgeworthia chrysantha was identified by the method of fingerprint as counterfeit. The results of content determination showed that the content of Buddleja officinalis in Hubei and Sichuan was the high and stable.Conclusion:The method can effectively analyze the differences of Buddleja officinalis from different habitats, and provide reference for the quality control of Buddleja officinalis.
10.Clinical and translational mode of single-cell measurements:clinical artificial intelligent single-cell
Xiangdong WANG ; A.Powell CHARLES ; Qin MA ; Jia FAN
Chinese Journal of Clinical Medicine 2024;31(5):691-695
With rapid development and maturity of single-cell measurements,single-cell biology and pathology has become an emerging discipline to understand the disease.However,it is important to address concerns raised by clinicians as to how to apply single-cell measurements for clinical practice,translate the signals of single-cell systems biology into determination of clinical phenotype,and predict patient response to therapies.This paper proposes a new system coined as the clinical artificial intelligent single-cell(caiSC)with the dynamic generator of clinical single-cell informatics,artificial intelligent analyzers,molecular multimodal reference boxes,clinical inputs and outputs,and AI-based computerization.This system provides reliable and rapid information for impacting clinical diagnoses,monitoring,and prediction of the disease at the single-cell level.The caiSC represents an important step and milestone to translate the single-cell measurement into clinical application,assist clinicians'decision-making,and improve the quality of medical services.There is increasing evidence to support the possibility of the caiSC proposal,since the corresponding biotechnologies associated with caiSCs are rapidly developed.Therefore,we call the special attention and efforts from various scientists and clinicians on the caiSCs and believe that the appearance of the caiSCs can shed light on the future of clinical molecular medicine.

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