1.External ocular manifestations among patients diagnosed with Coronavirus disease 2019 in a referral center in the Philippines.
Alyssa Louise B. Pejana-Paulino ; Aramis B. Torrefranca Jr. ; Nilo Vincent DG. Florcruz ; Ma. Dominga B. Padilla
Acta Medica Philippina 2026;60(1):69-77
BACKGROUND AND OBJECTIVES
data-mce-style="text-align: justify;">The global pandemic caused by Coronavirus Disease 2019 (COVID-19) has affected millions, with growing evidence of the potential role of ocular tissues in viral transmission. At the time of writing, local data regarding the phenomenon was limited. This study investigated external ocular manifestations in patients with COVID-19 at a referral center in the Philippines, examined correlations between demographics, systemic manifestations, and laboratory results with ocular manifestations, and determined their timing relative to systemic symptoms.
METHODSdata-mce-style="text-align: justify;">This single-center, descriptive cross-sectional study was carried out from December 8 to 18, 2020 at the adult COVID-19 wards of the Philippine General Hospital involving 72 participants. Data collection involved relevant clinical history taking and performing gross eye examination. The prevalence of ocular manifestations was described with 95% confidence intervals. Correlations between ocular manifestations and quantitative variables were analyzed with point-biserial correlation, and associations with qualitative variables were tested using chi-square or Fisher’s exact tests.
RESULTSdata-mce-style="text-align: justify;">Among participants, 31.9% presented with ocular manifestations with foreign body sensation as the most prevalent ocular symptom (11.1%) and conjunctival hyperemia as the most prevalent ocular finding (19.4%). The median age of patients with ocular manifestations was 41 years old with a higher prevalence in the male population (73.9%, CI=95%, p=0.001). No significant correlation was observed between presence of external ocular manifestations and the different systemic and ocular co-morbidities as well as with COVID-19 clinical classification. Among those who experienced symptoms, majority (29.2%) of the patients experienced systemic symptoms prior to the onset of ocular symptoms. Ocular complaints may present as the sole manifestation (13.9%). Several laboratory parameters were measured and only temperature and AST levels showed a low positive correlation with the presence of ocular manifestations.
CONCLUSIONdata-mce-style="text-align: justify;">Ocular manifestations occur in roughly one third of patients with COVID-19 based on this study population. With some individuals presenting with ocular signs or symptoms as the initial and sole manifestation, healthcare practitioners must exercise caution and remain vigilant in managing patients who present as such. At the time of writing, this is the first local study investigating the different external ocular manifestations in patients with COVID-19. There is a need to pursue more robust studies and conduct more local investigations which will guide both ophthalmologists and other practitioners in strengthening existing guidelines regarding precautionary practices, clinical diagnosis, and management of COVID-19 patients.
Human ; Sars-cov-2 ; Covid-19 ; Philippines ; Adult ; Association ; Classification ; Collection ; Confidence Intervals ; Coronavirus ; Cross-sectional Studies ; Data Collection ; Demography ; Diagnosis ; Disease ; Exercise ; Eye ; Foreign Bodies ; History ; Hospitals ; Hospitals, General ; Hyperemia ; Laboratories ; Male ; Morbidity ; Ophthalmologists ; Pandemics ; Patients ; Population ; Prevalence ; Referral And Consultation ; Role ; Sensation ; Temperature ; Time ; Tissues ; Volition ; World Health Organization ; Writing
2.Research on Classification of Medical Devices with Nanomaterials.
Qian DONG ; Li YI ; Liyin WEN ; Rui LIU ; Jinglong TANG ; Jiong ZHU
Chinese Journal of Medical Instrumentation 2025;49(3):336-339
The rapid development of nanomaterials has brought groundbreaking opportunities for high-quality innovation in medical devices, but it has also become a new challenge for regulatory authorities. How to scientifically and rationally evaluate the risks of medical device products with nanomaterials and establish appropriate regulatory classifications have become critical research priorities. To solve this problem, this study focuses on medical devices with nanomaterials, conducts a comparative analysis of domestic and international regulatory classification policies, reviews the current registration status of related products, and provides recommendations on key considerations for the classification and regulation of medical devices with nanomaterials, which aims at promoting high-quality advancement in China's medical device regulation.
Nanostructures/classification*
;
Equipment and Supplies/classification*
3.Network Pharmacology and in vitro Experimental Verification on Intervention of Oridonin on Non-Small Cell Lung Cancer.
Ke CHANG ; Li-Fei ZHU ; Ting-Ting WU ; Si-Qi ZHANG ; Zi-Cheng YU
Chinese journal of integrative medicine 2025;31(4):347-356
OBJECTIVE:
To explore the key target molecules and potential mechanisms of oridonin against non-small cell lung cancer (NSCLC).
METHODS:
The target molecules of oridonin were retrieved from SEA, STITCH, SuperPred and TargetPred databases; target genes associated with the treatment of NSCLC were retrieved from GeneCards, DisGeNET and TTD databases. Then, the overlapping target molecules between the drug and the disease were identified. The protein-protein interaction (PPI) was constructed using the STRING database according to overlapping targets, and Cytoscape was used to screen for key targets. Molecular docking verification were performed using AutoDockTools and PyMOL software. Using the DAVID database, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted. The impact of oridonin on the proliferation and apoptosis of NSCLC cells was assessed using cell counting kit-8, cell proliferation EdU image kit, and Annexin V-FITC/PI apoptosis kit respectively. Moreover, real-time quantitative PCR and Western blot were used to verify the potential mechanisms.
RESULTS:
Fifty-six target molecules and 12 key target molecules of oridonin involved in NSCLC treatment were identified, including tumor protein 53 (TP53), Caspase-3, signal transducer and activator of transcription 3 (STAT3), mitogen-activated protein kinase kinase 8 (MAPK8), and mammalian target of rapamycin (mTOR). Molecular docking showed that oridonin and its key target molecules bind spontaneously. GO and KEGG enrichment analyses revealed cancer, apoptosis, phosphoinositide-3 kinase/protein kinase B (PI3K/Akt), and other signaling pathways. In vitro experiments showed that oridonin inhibited the proliferation, induced apoptosis, downregulated the expression of Bcl-2 and Akt, and upregulated the expression of Caspase-3.
CONCLUSION
Oridonin can act on multiple targets and pathways to exert its inhibitory effects on NSCLC, and its mechanism may be related to upregulating the expression of Caspase-3 and downregulating the expressions of Akt and Bcl-2.
Diterpenes, Kaurane/chemistry*
;
Carcinoma, Non-Small-Cell Lung/pathology*
;
Humans
;
Network Pharmacology
;
Lung Neoplasms/pathology*
;
Cell Proliferation/drug effects*
;
Apoptosis/drug effects*
;
Molecular Docking Simulation
;
Protein Interaction Maps/drug effects*
;
Cell Line, Tumor
;
Signal Transduction/drug effects*
;
Gene Expression Regulation, Neoplastic/drug effects*
;
Reproducibility of Results
;
Gene Ontology
4.Identification of prognosis-related key genes in hepatocellular carcinoma based on bioinformatics analysis.
Qian XIE ; Yingshan ZHU ; Ge HUANG ; Yue ZHAO
Journal of Central South University(Medical Sciences) 2025;50(2):167-180
OBJECTIVES:
Hepatocellular carcinoma is one of the most common primary malignant tumors with the third highest mortality rate worldwide. This study aims to identify key genes associated with hepatocellular carcinoma prognosis using the Gene Expression Omnibus (GEO) database and provide a theoretical basis for discovering novel prognostic biomarkers for hepatocellular carcinoma.
METHODS:
Hepatocellular carcinoma-related datasets were retrieved from the GEO database. Differentially expressed genes (DEGs) were identified using the GEO2R tool. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), and key genes were identified using Cytoscape software. The University of Alabama at Birmingham Cancer Data Analysis Resource (UALCAN) was used to analyze the expression levels of key genes in normal and hepatocellular carcinoma tissues, as well as their associations with pathological grade, clinical stage, and patient survival. The Human Protein Atlas (THPA) was used to further validate the impact of key genes on overall survival. Expression levels of key genes in the blood of hepatocellular carcinoma patients were evaluated using the expression atlas of blood-based biomarkers in the early diagnosis of cancers (BBCancer).
RESULTS:
A total of 78 DEGs were identified from the GEO database. GO and KEGG analyses indicated that these genes may contribute to hepatocellular carcinoma progression by promoting cell division and regulating protein kinase activity. Sixteen key genes were screened via Cytoscape and validated using UALCAN and THPA. These genes were overexpressed in hepatocellular carcinoma tissues and were associated with disease progression and poor prognosis. Finally, BBCancer analysis showed that ASPM and NCAPG were also elevated in the blood of hepatocellular carcinoma patients.
CONCLUSIONS
This study identified 16 key genes as potential prognostic biomarkers for hepatocellular carcinoma, among which ASPM and NCAPG may serve as promising blood-based markers for hepatocellular carcinoma.
Humans
;
Carcinoma, Hepatocellular/mortality*
;
Liver Neoplasms/pathology*
;
Prognosis
;
Computational Biology/methods*
;
Protein Interaction Maps/genetics*
;
Biomarkers, Tumor/genetics*
;
Gene Expression Regulation, Neoplastic
;
Gene Expression Profiling
;
Gene Ontology
;
Databases, Genetic
5.Identification of shared key genes and pathways in osteoarthritis and sarcopenia patients based on bioinformatics analysis.
Yuyan SUN ; Ziyu LUO ; Huixian LING ; Sha WU ; Hongwei SHEN ; Yuanyuan FU ; Thainamanh NGO ; Wen WANG ; Ying KONG
Journal of Central South University(Medical Sciences) 2025;50(3):430-446
OBJECTIVES:
Osteoarthritis (OA) and sarcopenia are significant health concerns in the elderly, substantially impacting their daily activities and quality of life. However, the relationship between them remains poorly understood. This study aims to uncover common biomarkers and pathways associated with both OA and sarcopenia.
METHODS:
Gene expression profiles related to OA and sarcopenia were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between disease and control groups were identified using R software. Common DEGs were extracted via Venn diagram analysis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify biological processes and pathways associated with shared DEGs. Protein-protein interaction (PPI) networks were constructed, and candidate hub genes were ranked using the maximal clique centrality (MCC) algorithm. Further validation of hub gene expression was performed using 2 independent datasets. Receiver operating characteristic (ROC) curve analysis was used to evaluate the predictive value of key genes for OA and sarcopenia. Mouse models of OA and sarcopenia were established. Hematoxylin-eosin and Safranin O/Fast Green staining were used to validate the OA model. The sarcopenia model was validated via rotarod testing and quadriceps muscle mass measurement. Real-time reverse transcription PCR (real-time RT-PCR) was employed to assess the mRNA expression levels of candidate key genes in both models. Gene set enrichment analysis (GSEA) was conducted to identify pathways associated with the selected shared key genes in both diseases.
RESULTS:
A total of 89 common DEGs were identified in the gene expression profiles of OA and sarcopenia, including 76 upregulated and 13 downregulated genes. These 89 DEGs were significantly enriched in protein digestion and absorption, the PI3K-Akt signaling pathway, and extracellular matrix-receptor interaction. PPI network analysis and MCC algorithm analysis of the 89 common DEGs identified the top 17 candidate hub genes. Based on the differential expression analysis of these 17 candidate hub genes in the validation datasets, AEBP1 and COL8A2 were ultimately selected as the common key genes for both diseases, both of which showed a significant upregulation trend in the disease groups (all P<0.05). The value of area under the curve (AUC) for AEBP1 and COL8A2 in the OA and sarcopenia datasets were all greater than 0.7, indicating that both genes have potential value in predicting OA and sarcopenia. Real-time RT-PCR results showed that the mRNA expression levels of AEBP1 and COL8A2 were significantly upregulated in the disease groups (all P<0.05), consistent with the results observed in the bioinformatics analysis. GSEA revealed that AEBP1 and COL8A2 were closely related to extracellular matrix-receptor interaction, ribosome, and oxidative phosphorylation in OA and sarcopenia.
CONCLUSIONS
AEBP1 and COL8A2 have the potential to serve as common biomarkers for OA and sarcopenia. The extracellular matrix-receptor interaction pathway may represent a potential target for the prevention and treatment of both OA and sarcopenia.
Sarcopenia/genetics*
;
Osteoarthritis/genetics*
;
Computational Biology/methods*
;
Humans
;
Protein Interaction Maps/genetics*
;
Animals
;
Mice
;
Gene Expression Profiling
;
Gene Ontology
;
Transcriptome
;
Male
;
Signal Transduction/genetics*
;
Gene Regulatory Networks
6.Roles of PANoptosis and related genes in acute liver failure: neoteric insight from bioinformatics analysis and animal experiment verification.
Tiantian GE ; Yao CHEN ; Lantian PANG ; Junwei SHAO ; Zhi CHEN
Journal of Zhejiang University. Science. B 2025;26(4):353-370
BACKGROUND: PANoptosis has the features of pyroptosis, apoptosis, and necroptosis. Numerous studies have confirmed the diverse roles of various types of cell death in acute liver failure (ALF), but limited attention has been given to the crosstalk among them. In this study, we aimed to explore the role of PANoptosis in ALF and uncover new targets for its prevention or treatment. METHODS: Three ALF-related datasets (GSE14668, GSE62029, and GSE74000) were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs). Hub genes were identified through intersecting DEGs, genes obtained from weighted gene co-expression network analysis (WGCNA), and genes related to PANoptosis. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein‒protein interaction (PPI) analyses and gene set enrichment analysis (GSEA) were performed to determine functional roles. Verification was performed using an ALF mouse model. RESULTS: Our results showed that expression of seven hub genes (B-cell lymphoma-2-modifying factor (BMF), B-cell lymphoma-2-interacting protein 3-like (BNIP3L), Caspase-1 (CASP1), receptor-interacting protein kinase 3 (RIPK3), uveal autoantigen with coiled-coil domains and ankyrin repeats protein (UACA), uncoordinated-5 homolog B receptor (UNC5B), and Z-DNA-binding protein 1 (ZBP1)) was up-regulated in liver samples of patients. However, in the ALF mouse model, the expression of BNIP3L, RIPK3, phosphorylated RIPK3 (P-RIPK3), UACA, and cleaved caspase-1 was up-regulated, while the expression of CASP1 and UNC5B was down-regulated. The expression of ZBP1 and BMF increased only during the development of ALF, and there was no significant change in the end stage. Immunofluorescence of mouse liver tissue showed that macrophages expressed all seven markers. Western blot results showed that pyroptosis, apoptosis, and necroptosis were always involved in lipopolysaccharide (LPS)/ d-galactosamine (d-gal)-induced ALF mice. The ALF cell model showed that bone marrow-derived macrophages (BMDMs) form PANoptosomes after LPS stimulation. CONCLUSIONS: Our results suggest that PANoptosis of macrophages promotes the development of ALF. The seven new ALF biomarkers identified and validated in this study may contribute to further investigation of diagnostic markers or novel therapeutic targets of ALF.
Animals
;
Liver Failure, Acute/genetics*
;
Computational Biology
;
Mice
;
Pyroptosis/genetics*
;
Humans
;
Protein Interaction Maps
;
Apoptosis/genetics*
;
Necroptosis/genetics*
;
Gene Regulatory Networks
;
Gene Ontology
;
Gene Expression Profiling
;
Disease Models, Animal
7.Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.
Jinyou LI ; Yue WU ; Yichen YANG ; Lufang CHEN ; Caihong HE ; Shixian ZHOU ; Shunmei HUANG ; Xia ZHANG ; Yuming WANG ; Qifeng GUI ; Haifeng LU ; Qin ZHANG ; Yunmei YANG
Journal of Zhejiang University. Science. B 2025;26(5):477-492
Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.
Aged
;
Aged, 80 and over
;
Female
;
Humans
;
Male
;
Middle Aged
;
Bacteroides
;
China
;
Diabetes Mellitus, Type 2/microbiology*
;
Escherichia coli/classification*
;
Gastrointestinal Microbiome/genetics*
;
Metagenomics
;
East Asian People
8.Characteristics of the subtype of vestibular migraine with ear fullness: association with early onset age and low-frequency hearing loss.
Lizhu JIANG ; Shiqi YU ; Yan LEI ; Xiaofang ZONG ; Shixun ZHONG ; Wenqi ZUO
Journal of Clinical Otorhinolaryngology Head and Neck Surgery 2025;39(10):918-922
Objective:The clinical significance of aural fullness in patients with vestibular migraine(VM) remains unclear, and it is yet to be determined whether VM with aural fullness represents a distinct subtype of VM; this study aimed to compare differences in demographic characteristics, clinical manifestations, audiological findings, and vestibular function tests between VM patients with and without aural fullness, and explore whether the former is a subtype of VM and whether it requires differentiated treatment. Methods:A total of 174 VM patients were enrolled, including 75 with aural fullness(aural fullness group) and 99 without aural fullness(non-aural fullness group); demographic data, vertigo characteristics, medical history, family history, pure-tone audiometry, and vestibular function tests were thoroughly recorded, and independent samples t-test and chi-square test were used for inter-group comparisons. Results:①Regarding demographic characteristics, the age of the aural fullness group was significantly lower than that of the non-aural fullness group[(44.08±13.97) years vs. (49.45±16.05) years, P=0.020), while the two groups showed consistent gender distribution(more females than males) with no statistically significant difference. ②For aural fullness characteristics, unilateral aural fullness accounted for 65.0% in the aural fullness group, significantly higher than bilateral aural fullness(35.0%, P<0.001). ③In terms of vertigo characteristics, there were no statistically significant inter-group differences in the nature of attacks(rotational vertigo: 36.0% vs. 41.4%, P=0.463; dizziness: 21.3% vs. 11.1%, P=0.064; rotational vertigo or dizziness: 29.3% vs. 25.3%, P=0.548; dizziness with unsteady gait: 9.3% vs. 11.1%, Fisher P=0.806; visual oscillation with unsteady gait: 4.0% vs. 11.1%, Fisher P=0.086), duration(several hours: 34.7% vs. 33.3%, P=0.841; several minutes: 22.7% vs. 21.2%, P=0.808; several seconds: 5.3% vs. 8.1%, Fisher P=0.557; several days: 9.3% vs. 9.1%, Fisher P=1.000; multiple combined patterns: 17.3% vs. 15.2%, P=0.686), or incidence of nausea and vomiting(84.0% vs. 72.7%, P=0.071, no statistical significance). ④No statistically significant inter-group differences were found in medical history and family history, including motion sickness history(8.0% vs. 4.0%, Fisher P=0.337), headache history(22.7% vs. 34.3%, P=0.084), and family history of dizziness(12.0% vs. 14.1%, P=0.666). ⑤For audiological characteristics, 21.3%(16/75) of patients in the aural fullness group had low-frequency hearing loss, significantly higher than 5.1% in the non-aural fullness group(χ²=10.66, P=0.001); among patients with unilateral aural fullness, 28.6%(14/49) had ipsilateral low-frequency hearing loss, significantly higher than 7.7%(2/26) of those with bilateral aural fullness(χ²=4.41, P=0.036); however, there was no statistically significant difference in the rate of bilateral high-frequency hearing loss between the two groups(54.7%[41/75]vs. 50.5%[50/99], χ²=0.30, P=0.586). ⑥In vestibular function tests, no statistically significant inter-group differences were observed in smooth pursuit type Ⅲ/Ⅳ(12.5% vs. 13.1%, P=0.913), caloric test with CP>25%(31.2% vs. 37.4%, P=0.411), abnormal video head impulse test(vHIT) rate(30.8% vs. 32.6%, P=0.865), or abnormal vestibular evoked myogenic potential(VEMP) rate(53.8% vs. 38.9%, Fisher P=0.484). Conclusion:VM patients with aural fullness have an earlier age of onset, with nearly 1/4 accompanied by low-frequency hearing loss; VM patients with and without aural fullness are highly consistent in gender distribution, nature/duration of vertigo, vestibular function impairment, and presence of bilateral high-frequency hearing loss, suggesting that the core clinical phenotypes of the two groups are consistent, while the former has an earlier age of onset and a higher proportion of unilateral hearing loss, which may be related to the pathological mechanism of VM and inner ear microcirculation disorders.
Humans
;
Female
;
Male
;
Middle Aged
;
Adult
;
Migraine Disorders/classification*
;
Young Adult
;
Vertigo
;
Age of Onset
;
Aged
;
Hearing Loss
9.Expert consensus on early orthodontic treatment of class III malocclusion.
Xin ZHOU ; Si CHEN ; Chenchen ZHOU ; Zuolin JIN ; Hong HE ; Yuxing BAI ; Weiran LI ; Jun WANG ; Min HU ; Yang CAO ; Yuehua LIU ; Bin YAN ; Jiejun SHI ; Jie GUO ; Zhihua LI ; Wensheng MA ; Yi LIU ; Huang LI ; Yanqin LU ; Liling REN ; Rui ZOU ; Linyu XU ; Jiangtian HU ; Xiuping WU ; Shuxia CUI ; Lulu XU ; Xudong WANG ; Songsong ZHU ; Li HU ; Qingming TANG ; Jinlin SONG ; Bing FANG ; Lili CHEN
International Journal of Oral Science 2025;17(1):20-20
The prevalence of Class III malocclusion varies among different countries and regions. The populations from Southeast Asian countries (Chinese and Malaysian) showed the highest prevalence rate of 15.8%, which can seriously affect oral function, facial appearance, and mental health. As anterior crossbite tends to worsen with growth, early orthodontic treatment can harness growth potential to normalize maxillofacial development or reduce skeletal malformation severity, thereby reducing the difficulty and shortening the treatment cycle of later-stage treatment. This is beneficial for the physical and mental growth of children. Therefore, early orthodontic treatment for Class III malocclusion is particularly important. Determining the optimal timing for early orthodontic treatment requires a comprehensive assessment of clinical manifestations, dental age, and skeletal age, and can lead to better results with less effort. Currently, standardized treatment guidelines for early orthodontic treatment of Class III malocclusion are lacking. This review provides a comprehensive summary of the etiology, clinical manifestations, classification, and early orthodontic techniques for Class III malocclusion, along with systematic discussions on selecting early treatment plans. The purpose of this expert consensus is to standardize clinical practices and improve the treatment outcomes of Class III malocclusion through early orthodontic treatment.
Humans
;
Malocclusion, Angle Class III/classification*
;
Orthodontics, Corrective/methods*
;
Consensus
;
Child
10.Gene print-based cell subtypes annotation of human disease across heterogeneous datasets with gPRINT.
Ruojin YAN ; Chunmei FAN ; Shen GU ; Tingzhang WANG ; Zi YIN ; Xiao CHEN
Protein & Cell 2025;16(8):685-704
Identification of disease-specific cell subtypes (DSCSs) has profound implications for understanding disease mechanisms, preoperative diagnosis, and precision therapy. However, achieving unified annotation of DSCSs in heterogeneous single-cell datasets remains a challenge. In this study, we developed the gPRINT algorithm (generalized approach for cell subtype identification with single cell's voicePRINT). Inspired by the principles of speech recognition in noisy environments, gPRINT transforms gene position and gene expression information into voiceprints based on ordered and clustered gene expression phenomena, obtaining unique "gene print" patterns for each cell. Then, we integrated neural networks to mitigate the impact of background noise on cell identity label mapping. We demonstrated the reproducibility of gPRINT across different donors, single-cell sequencing platforms, and disease subtypes, and its utility for automatic cell subtype annotation across datasets. Moreover, gPRINT achieved higher annotation accuracy of 98.37% when externally validated based on the same tissue, surpassing other algorithms. Furthermore, this approach has been applied to fibrosis-associated diseases in multiple tissues throughout the body, as well as to the annotation of fibroblast subtypes in a single tissue, tendon, where fibrosis is prevalent. We successfully achieved automatic prediction of tendinopathy-specific cell subtypes, key targets, and related drugs. In summary, gPRINT provides an automated and unified approach for identifying DSCSs across datasets, facilitating the elucidation of specific cell subtypes under different disease states and providing a powerful tool for exploring therapeutic targets in diseases.
Humans
;
Algorithms
;
Single-Cell Analysis
;
Databases, Genetic
;
Molecular Sequence Annotation


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