1.Construction and Application of a Real-World Cohort of Community-Acquired Pneumonia Based on a Multimodal Large-Scale Traditional Chinese Medicine Big Data Platform
Zhichao WANG ; Xianmei ZHOU ; Fanchao FENG ; Mengqi WANG ; Xin WANG ; Bin KANG ; Xiaofan YU ; Xiaoxiao WANG ; Lei XIAO ; Juan LI ; Zhichao ZHANG ; Ye MA ; Yeqing JI ; Xin TONG ; Zhuoyue WU ; Jia LIU
Journal of Traditional Chinese Medicine 2026;67(9):961-965
This paper introduces a real-world cohort research model for community-acquired pneumonia (CAP) based on the Jiangsu Traditional Chinese Medicine (TCM) Dominant Diseases Diagnosis and Treatment Data Platform. Firstly, data cleaning is performed by standardizing diagnosis, symptoms, treatment and imaging, intelligently extracting unstructured information, and cleaning and constructing a standardized database. Secondly, for cohort establishment, CAP patients across the province are screened in accordance with CAP diagnostic criteria to build a high-quality disease-specific cohort. Lastly, in terms of protocol design, the characteristics of TCM research and the CAP disease profile are considered to determine appropriate inclusion and exclusion criteria, estimate sample size, define interventions, outcomes and economic evaluations, providing a reference for real-world TCM research on CAP.
2.Construction and Application of a Real-World Cohort of Community-Acquired Pneumonia Based on a Multimodal Large-Scale Traditional Chinese Medicine Big Data Platform
Zhichao WANG ; Xianmei ZHOU ; Fanchao FENG ; Mengqi WANG ; Xin WANG ; Bin KANG ; Xiaofan YU ; Xiaoxiao WANG ; Lei XIAO ; Juan LI ; Zhichao ZHANG ; Ye MA ; Yeqing JI ; Xin TONG ; Zhuoyue WU ; Jia LIU
Journal of Traditional Chinese Medicine 2026;67(9):961-965
This paper introduces a real-world cohort research model for community-acquired pneumonia (CAP) based on the Jiangsu Traditional Chinese Medicine (TCM) Dominant Diseases Diagnosis and Treatment Data Platform. Firstly, data cleaning is performed by standardizing diagnosis, symptoms, treatment and imaging, intelligently extracting unstructured information, and cleaning and constructing a standardized database. Secondly, for cohort establishment, CAP patients across the province are screened in accordance with CAP diagnostic criteria to build a high-quality disease-specific cohort. Lastly, in terms of protocol design, the characteristics of TCM research and the CAP disease profile are considered to determine appropriate inclusion and exclusion criteria, estimate sample size, define interventions, outcomes and economic evaluations, providing a reference for real-world TCM research on CAP.
3.Research progress on the relationship between early life obesogen exposure and childhood obesity
GAO Lei ; YE Zhen ; WANG Wei ; ZHAO Dong ; XU Peiwei ; ZHANG Ronghua
Journal of Preventive Medicine 2026;38(1):48-54
Childhood obesity has become a global public health issue. Current research indicates that early life obesogen exposure has emerged as a significant risk factor for childhood obesity. While obesogens have been confirmed to influence the development and progression of childhood obesity through mechanisms such as endocrine disruption and epigenetic programming, controversies remain regarding the establishment of causal relationships, assessment of combined exposures, and validation of transgenerational effects in humans. In recent years, novel approaches including multi-omics technologies, exposome-based analysis, and multigenerational cohort studies have integrated dynamic biomarker monitoring with analyses of social-environmental interactions, offering new perspectives and methodologies for constructing a systematic "exposure-mechanism-outcome" research framework. This article reviews literature from PubMed and Web of Science up to August 2025 on the association between early life obesogen exposure and childhood obesity, summarizing evidence on the health effects of early life obesogen exposure, major exposure pathways and internal exposure assessment, interactions and amplifying effects of social and environmental factors, as well as the biological mechanisms underlying obesogen action. It further examines current research frontiers and challenges, aiming to provide a theoretical foundation for early prevention and precision intervention of childhood obesity.
4.Mechanism of Yishen Huoxue Tongqiao Formula in Improving Unilateral Vestibular Labyrinth Destruction by Regulating Metabolism-neuroplasticity
Yu TIAN ; Hui LENG ; Rupeng QU ; Xianglong HAO ; Aiping WANG ; Lei SHI ; Zhongyuan QU ; Ye DONG ; Xiande MA ; Yangling HUANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(5):54-64
ObjectiveThis study aims to explore the mechanism by which Yishen Huoxue Tongqiao Formula improves metabolism-neuroplasticity and treats unilateral vestibular labyrinth destruction by regulating the metabolic balance of glutamate (Glu)/γ-aminobutyric acid (GABA). Methods48 Sprague-Dawley (SD) adult rats were randomly divided into the sham operation group, model group, Yishen Huoxue Tongqiao Formula groups with low, medium, and high doses (9.20, 18.39, 36.78 g·kg-1), and betahistine group (1.62 mg·kg-1). A unilateral vestibular labyrinth destruction (vestibular dysfunction) model was established by intratympanic injection of chloroform into the right ear, while the control group received intratympanic injection of normal saline. Drugs were administered once daily for seven consecutive days. During the period, behavioral tests were performed to evaluate the behaviors of rats after unilateral vestibular labyrinth destruction. Hematoxylin-eosin (HE) staining and Nissl staining were used to observe the neuronal morphology in the medial vestibular nucleus. Golgi staining was employed to assess the number of dendritic spines of neurons in the medial vestibular nucleus. Ultra-performance liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS) was utilized to detect Glu/GABA. Immunofluorescence and immunohistochemistry were used to detect the expressions of neuronal nuclei (NeuN), growth-associated protein 43 (GAP-43), and glial fibrillary acidic protein (GFAP). Western blot and real-time fluorescent quantitative polymerase chain reaction (Real-time PCR) were applied to determine the expressions of glutamate-immunoreactive (Glu-IR), GABA, GFAP, postsynaptic density protein 95 (PSD-95), and GAP-43. ResultsCompared with the sham operation group, the model group presented with head deviation, balance disorder, increased tail suspension score, nuclear consolidation of medial vestibular nerve neurons, and decreased Nissl bodies (P<0.01). The number of dendritic spines in neurons and NeuN-positive cells decreased. The content of Glu decreased. The content of GABA increased (Glu/GABA decreased). The expression of GAP-43 was down-regulated, and GFAP was up-regulated (P<0.05, P<0.01). The expressions of Glu-IR, PSD-95, and GAP-43 proteins, as well as Glu-IR mRNA decreased, while the expressions of GABA and GFAP proteins and mRNA increased (P<0.05, P<0.01). Compared with those in the model group, the head deviation, imbalanced behavior, and tail suspension scores in each treatment group decreased, with alleviated neuronal injury and recovered Nissl bodies (P<0.01). The number of dendritic spines of neurons increased, and the number of NeuN-positive cells rebounded. The content of Glu increased, and the content of GABA decreased (Glu/GABA increased). GFAP was down-regulated, and GAP-43 was up-regulated (P<0.05, P<0.01). The expressions of Glu-IR, PMD-95, and GAP-43 proteins, as well as Glu-IR mRNA increased, while the expressions of GABA and GFAP proteins and mRNA decreased. The effect was more significant in the high-dose group (P<0.01). ConclusionThe Yishen Huoxue Tongqiao Formula can alleviate vestibular dysfunction, and its mechanism may be associated with regulating the metabolic balance of Glu/GABA, mitigating neural damage, improving synaptic plasticity (promoting GAP-43 expression and inhibiting GFAP expression), and facilitating vestibular compensation.
5.Mechanistic Study on Tougu Xiaotong Capsules in Regulating PANoptosis to Delay Degeneration of Chondrocytes in Knee Osteoarthritis
Jinxia YE ; Yixin LIN ; Xiaoqing LEI ; Yanfeng HUANG ; Changlong FU ; Desen LI ; Wenyi WANG ; Lan WANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):149-161
ObjectiveTo investigate the effect of Tougu Xiaotong capsules (TGXTC) on the regulation of chondrocyte PANoptosis, delay of chondrocyte degeneration, and improvement of the symptoms in knee osteoarthritis (KOA). MethodsIn vivo experiments: 50 male C57BL/6 mice were randomly assigned into five groups (n=10 per group): sham operation group, model group, low-dose TGXTC group (7.2 g·kg-1), high-dose TGXTC group (14.4 g·kg-1), and diclofenac sodium group (0.05 g·kg-1). Except for the sham group, KOA models were established in all other groups using the modified Hulth method. Following successful model induction, the TGXTC groups received daily oral gavage of 7.2 or 14.4 g·kg-1 for 6 weeks, while the diclofenac sodium group received 0.05 g·kg-1 solution daily over the same duration. Model evaluation was performed using Lequesne MG score; micro-computed tomography (micro-CT) was used to scan the knee, hematoxylin-eosin (HE) staining and safranin O-fast green staining were used to observe the morphology of cartilage, transmission electron microscopy (TEM) was used to determine ultrastructural changes of PANoptosis. Multiple immunofluorescence (IF) co-localization assays was performed to detect the co-localization of cleaved Caspase-3, receptor-interacting protein 3 (RlPK3), and the N-terminal domain of gasdermin D (GSDMD-N) in cartilage tissue, while western blot was employed to detect the expression levels of cleaved Caspase-3, RIPK3, and GSDMD-N. In vitro experiments: The knee cartilages of 4-week-old SD rats were isolated, and a chondrocyte in vitro culture system was established through mechanical digestion with 0.2% type Ⅱ collagenase. Second-generation chondrocytes were divided into three groups: the control group, the model group (pretreated with 10 mg·L-1 lipopolysaccharide (LPS) for 24 h followed by treatment with 1 μmol·L-1 nigericin for 4 h), and the TGXTC treatment group (pretreated with 10 mg·L-1 LPS for 24 h, followed by exposure to 1 μmol·L-1 nigericin for 4 h and subsequently treated with 100 mg·L-1 TGXTC for an additional 24 h). The levels of reactive oxygen species (ROS), apoptosis, necroptosis, and pyroptosis of chondrocytes were evaluated via fluorescence microscopy following staining with ROS detection, AO/EB and YO-PRO-1/PI staining kits. Transmission electron microscopy was utilized to investigate the ultrastructural changes associated with PANoptosis in cartilage tissue of KOA mice. Inflammatory cytokine levels (IL-1β and IL-18) were measured using ELISA. Western blot was conducted to assess protein expressions related to PANoptosis, including cleaved Caspase-3, cleaved Caspase-8, RIPK3, ZBP1, GSDMD-N, and NLRP3. ResultsCompared with the sham group, the Lequesne MG scores were significantly up-regulated(P<0.01) in the model group, and the pathological changes of cartilage were significantly, with joint spaces narrower, osteophyte formation increased, secere abrasion of cartilage surface. Ultrastructural analysis revealed pronounced chondrocyte apoptosis, necroptosis, and pyroptosis, along with markedly elevated expression of cleaved Caspase-3, RlPK3, and GSDMD-N in cartilage tissue (P<0.01). In addition, The mean fluorescence intensities of ROS, orange-red fluorescence in AO/EB staining, green fluorescence and red fluorescence in YO-PRO-1/PI staining were increased of chondrocyte in the model group (P<0.01) . The levels of inflammatory factors IL-1β and IL-18 in the supernatant were increased (P<0.01). The expression of PANoptosis related proteins (cleaved Caspase-3, cleaved Caspase-8, RIPK3, ZBP1, GSDMD-N, and NLRP3) were also significantly upregulated(P<0.05). Compared to the model group, the TGXTC group demonstrated a significant improvement in various parameters of mice. These included a reduction in the Lequesne MG score, an increase in joint space, a decrease in osteophyte formation, diminished cartilage damage, reduced release of ROS, and alleviation of apoptotic, necroptotic, and pyroptotic processes in chondrocytes. Additionally, mitochondrial swelling and endoplasmic reticulum dilation were also mitigated. The levels of ROS as well as IL-1β and IL-18 were significantly decreased (P<0.05). Furthermore, the expression levels of proteins associated with PANoptosis in cartilage tissue showed marked reductions (P<0.05). Similar results were observed in chondrocytes: cleaved Caspase-3, cleaved Caspase-8, RIPK3, ZBP1, GSDMD-N, and NLRP3 exhibited significant decreases as well (P<0.05). ConclusionTGXTC may mitigate chondrocytes degeneration and alleviate KOA symptoms by reducing oxidative stress and suppressing the activation of PANoptosis pathways.
6.Mechanistic Study on Tougu Xiaotong Capsules in Regulating PANoptosis to Delay Degeneration of Chondrocytes in Knee Osteoarthritis
Jinxia YE ; Yixin LIN ; Xiaoqing LEI ; Yanfeng HUANG ; Changlong FU ; Desen LI ; Wenyi WANG ; Lan WANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):149-161
ObjectiveTo investigate the effect of Tougu Xiaotong capsules (TGXTC) on the regulation of chondrocyte PANoptosis, delay of chondrocyte degeneration, and improvement of the symptoms in knee osteoarthritis (KOA). MethodsIn vivo experiments: 50 male C57BL/6 mice were randomly assigned into five groups (n=10 per group): sham operation group, model group, low-dose TGXTC group (7.2 g·kg-1), high-dose TGXTC group (14.4 g·kg-1), and diclofenac sodium group (0.05 g·kg-1). Except for the sham group, KOA models were established in all other groups using the modified Hulth method. Following successful model induction, the TGXTC groups received daily oral gavage of 7.2 or 14.4 g·kg-1 for 6 weeks, while the diclofenac sodium group received 0.05 g·kg-1 solution daily over the same duration. Model evaluation was performed using Lequesne MG score; micro-computed tomography (micro-CT) was used to scan the knee, hematoxylin-eosin (HE) staining and safranin O-fast green staining were used to observe the morphology of cartilage, transmission electron microscopy (TEM) was used to determine ultrastructural changes of PANoptosis. Multiple immunofluorescence (IF) co-localization assays was performed to detect the co-localization of cleaved Caspase-3, receptor-interacting protein 3 (RlPK3), and the N-terminal domain of gasdermin D (GSDMD-N) in cartilage tissue, while western blot was employed to detect the expression levels of cleaved Caspase-3, RIPK3, and GSDMD-N. In vitro experiments: The knee cartilages of 4-week-old SD rats were isolated, and a chondrocyte in vitro culture system was established through mechanical digestion with 0.2% type Ⅱ collagenase. Second-generation chondrocytes were divided into three groups: the control group, the model group (pretreated with 10 mg·L-1 lipopolysaccharide (LPS) for 24 h followed by treatment with 1 μmol·L-1 nigericin for 4 h), and the TGXTC treatment group (pretreated with 10 mg·L-1 LPS for 24 h, followed by exposure to 1 μmol·L-1 nigericin for 4 h and subsequently treated with 100 mg·L-1 TGXTC for an additional 24 h). The levels of reactive oxygen species (ROS), apoptosis, necroptosis, and pyroptosis of chondrocytes were evaluated via fluorescence microscopy following staining with ROS detection, AO/EB and YO-PRO-1/PI staining kits. Transmission electron microscopy was utilized to investigate the ultrastructural changes associated with PANoptosis in cartilage tissue of KOA mice. Inflammatory cytokine levels (IL-1β and IL-18) were measured using ELISA. Western blot was conducted to assess protein expressions related to PANoptosis, including cleaved Caspase-3, cleaved Caspase-8, RIPK3, ZBP1, GSDMD-N, and NLRP3. ResultsCompared with the sham group, the Lequesne MG scores were significantly up-regulated(P<0.01) in the model group, and the pathological changes of cartilage were significantly, with joint spaces narrower, osteophyte formation increased, secere abrasion of cartilage surface. Ultrastructural analysis revealed pronounced chondrocyte apoptosis, necroptosis, and pyroptosis, along with markedly elevated expression of cleaved Caspase-3, RlPK3, and GSDMD-N in cartilage tissue (P<0.01). In addition, The mean fluorescence intensities of ROS, orange-red fluorescence in AO/EB staining, green fluorescence and red fluorescence in YO-PRO-1/PI staining were increased of chondrocyte in the model group (P<0.01) . The levels of inflammatory factors IL-1β and IL-18 in the supernatant were increased (P<0.01). The expression of PANoptosis related proteins (cleaved Caspase-3, cleaved Caspase-8, RIPK3, ZBP1, GSDMD-N, and NLRP3) were also significantly upregulated(P<0.05). Compared to the model group, the TGXTC group demonstrated a significant improvement in various parameters of mice. These included a reduction in the Lequesne MG score, an increase in joint space, a decrease in osteophyte formation, diminished cartilage damage, reduced release of ROS, and alleviation of apoptotic, necroptotic, and pyroptotic processes in chondrocytes. Additionally, mitochondrial swelling and endoplasmic reticulum dilation were also mitigated. The levels of ROS as well as IL-1β and IL-18 were significantly decreased (P<0.05). Furthermore, the expression levels of proteins associated with PANoptosis in cartilage tissue showed marked reductions (P<0.05). Similar results were observed in chondrocytes: cleaved Caspase-3, cleaved Caspase-8, RIPK3, ZBP1, GSDMD-N, and NLRP3 exhibited significant decreases as well (P<0.05). ConclusionTGXTC may mitigate chondrocytes degeneration and alleviate KOA symptoms by reducing oxidative stress and suppressing the activation of PANoptosis pathways.
7.Risk factors for postoperative delirium after pneumonectomy: A systematic review and meta-analysis
Lei YE ; Guanghong WU ; Jiefang DING ; Qin WANG ; Guanghui XIA
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(04):624-630
Objective To systematically evaluate the risk factors for postoperative delirium (POD) in patients undergoing pneumonectomy. Methods PubMed, Web of Science, Cochrane Library, CNKI, Wanfang, and VIP databases were searched from the inception to November 7, 2024 for cross-sectional studies, case-control studies, and cohort studies on POD in patients undergoing pneumonectomy. Two researchers independently screened the literature, extracted data, and evaluated the quality of the literature. RevMan 5.4.1 software was used for meta-analysis. The Newcastle-Ottawa Scale (NOS) was used to evaluate the quality of the literature. Results A total of 12 studies were included, with 5 574 patients. The NOS scores of the literature were all≥6 points. Meta-analysis results showed that age (≥60 years) [OR=2.43, 95%CI (2.01, 2.93), P<0.01], American Society of Anesthesiologists (ASA) classification (Ⅳ) [OR=8.74, 95%CI (5.23, 14.61), P<0.01], history of diabetes [OR=12.81, 95%CI (10.45, 15.71), P<0.01], history of cerebrovascular disease [OR=3.00, 95%CI (2.46, 3.67), P<0.01], depression [OR=7.27, 95%CI (5.46, 9.67), P<0.01], squamous cell carcinoma [OR=4.79, 95%CI (1.83, 12.51), P<0.01], malnutrition [OR=5.25, 95%CI (3.35, 8.25), P<0.01], sleep disorders [OR=2.79, 95%CI (2.28, 3.42), P<0.01], and duration of one-lung ventilation during surgery [OR=1.32, 95%CI (1.11, 1.57), P<0.01] were all risk factors for POD, while high body mass index (BMI) [OR=0.96, 95%CI (0.95, 0.97), P<0.01] was a protective factor for POD. Conclusion Age (≥60 years), ASA classification (Ⅳ), history of diabetes, history of cerebrovascular disease, depression, squamous cell carcinoma, malnutrition, sleep disorders, and duration of one-lung ventilation during surgery are independent risk factors for POD, while high BMI is a protective factor.
8.Association between screen behaviors with overweight and obesity among children and adolescents
Chinese Journal of School Health 2026;47(4):486-489
Objective:
To investigate the prevalence of overweight and obesity among children and adolescents in Yangzhou City, and its association with screen behaviors, so as to provide scientific evidence for weight management among students.
Methods:
In May 2025, an electronic questionnaire survey was conducted among children and adolescents in Yangzhou City. A total of 3 722 participants were selected from grades 4 to 12 in 18 primary and secondary schools (108 classes) by using stratified cluster random sampling. The Chi square test was used to compare the differences in the detection rates of overweight and obesity among children and adolescents with 5 types of screen behaviors (watching TV, playing electronic games, scrolling short videos, screen based learning, electronic socializing) in different time groups each day (never, >0~<2 h, ≥2 h). Multivariate Logistic regression analysis was performed to examine the associations of five types of screen behaviors, presence of electronic devices in the bedroom, and screen use during meals on the weight status of children and adolescents.
Results:
The prevalence of overweight and obesity among children and adolescents was 37.3%. For all five types of screen behaviors, the differences in the distribution of overweight and obesity detection rates among children and adolescents across the three time spent categories were statistically significant ( χ 2=30.76- 70.78 , all P <0.01). After adjusting for confounding factors, multivariate Logistic regression analysis revealed that frequent or always using screens during meals( OR =1.63, 95% CI =1.14~2.31), playing video games ( OR =1.28, 95% CI =1.11-1.48), browsing short videos ( OR =1.29, 95% CI=1.09-1.54), and screen based learning ( OR =1.26, 95% CI =1.10-1.44) were significantly associated with overweight and obesity among children and adolescents (all P <0.05).
Conclusions
Excessive screen use is positively correlated with the incidence of overweight and obesity in children and adolescents. Targeted interventions on screen behaviors among children and adolescents are therefore warranted.
9.Plasma miRNA testing in the differential diagnosis of very early-stage hepatocellular carcinoma: a multicenter real-world study
Jie HU ; Ying XU ; Ao HUANG ; Lei YU ; Zheng WANG ; Xiaoying WANG ; Xinrong YANG ; Zhenbin DING ; Qinghai YE ; Yinghong SHI ; Shuangjian QIU ; Huichuan SUN ; Qiang GAO ; Jia FAN ; Jian ZHOU
Chinese Journal of Clinical Medicine 2025;32(3):350-354
Objective To explore the application of plasma 7 microRNA (miR7) testing in the differential diagnosis of very early-stage hepatocellular carcinoma (HCC). Methods This study is a multicenter real-world study. Patients with single hepatic lesion (maximum diameter≤2 cm) who underwent plasma miR7 testing at Zhongshan Hospital, Fudan University, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Anhui Provincial Hospital, and Peking University People’s Hospital between January 2019 and December 2024 were retrospectively enrolled. Patients were divided into very early-stage HCC group and non-HCC group, and the clinical pathological characteristics of the two groups were compared. The value of plasma miR7 levels, alpha-fetoprotein (AFP), and des-gamma-carboxy prothrombin (DCP) in the differential diagnosis of very early-stage HCC was evaluated using receiver operating characteristic (ROC) curves and area under the curve (AUC). In patients with both negative AFP and DCP (AFP<20 ng/mL, DCP<40 mAU/mL), the diagnostic value of plasma miR7 for very early-stage HCC was analyzed. Results A total of 64 528 patients from 4 hospitals underwent miR7 testing, and 1 682 were finally included, of which 1 073 were diagnosed with very early-stage HCC and 609 were diagnosed with non-HCC. The positive rate of miR7 in HCC patients was significantly higher than that in non-HCC patients (67.9% vs 24.3%, P<0.001). ROC curves showed that the AUCs for miR7, AFP, and DCP in distinguishing HCC patients from the non-HCC individuals were 0.718, 0.682, and 0.642, respectively. The sensitivities were 67.85%, 43.71%, and 44.45%, and the specificities were 75.70%, 92.78%, and 83.91%, respectively. The pairwise comparison of AUCs showed that the diagnostic efficacy of plasma miR7 detection was significantly better than that of AFP or DCP (P<0.05). Although its specificity was slightly lower than AFP and DCP, the sensitivity was significantly higher. Among patients negative for both AFP and DCP, miR7 maintained an AUC of 0.728 for diagnosing very early-stage HCC, with 67.82% sensitivity and 77.73% specificity. Conclusions Plasma miR7 testing is a potential molecular marker with high sensitivity and specificity for the differential diagnosis of small hepatic nodules. In patients with very early-stage HCC lacking effective molecular markers (negative for both AFP and DCP), miR7 can serve as a novel and effective molecular marker to assist diagnosis.
10.Development of an Analytical Software for Forensic Proteomic SAP Typing
Feng HU ; Meng-Jiao WANG ; Jia-Lei WU ; Dong-Sheng DING ; Zhi-Yuan YANG ; An-Quan JI ; Lei FENG ; Jian YE
Progress in Biochemistry and Biophysics 2025;52(9):2406-2416
ObjectiveThe proteome of biological evidence contains rich genetic information, namely single amino acid polymorphisms (SAPs) in protein sequences. However, due to the lack of efficient and convenient analysis tools, the application of SAP in public security still faces many challenges. This paper aims to meet the application requirements of SAP analysis for forensic biological evidence’s proteome data. MethodsThe software is divided into three modules. First, based on a built-in database of common non-synonymous single nucleotide polymorphisms (nsSNPs) and SAPs in East Asian populations, the software integrates and annotates newly identified exonic nsSNPs as SAPs, thereby constructing a customized SAP protein sequence database. It then utilizes a pre-installed search engine—either pFind or MaxQuant—to perform analysis and output SAP typing results, identifying both reference and variant types, along with their corresponding imputed nsSNPs. Finally, SAPTyper compares the proteome-based typing results with the individual’s exome-derived nsSNP profile and outputs the comparison report. ResultsSAPTyper accepts proteomic DDA mass spectrometry raw data (DDA acquisition mode) and exome sequencing results of nsSNPs as input and outputs the report of SAPs result. The pFind and Maxquant search engines were used to test the proteome data of 2 hair shafts of2 individuals, and both obtained SAP results. It was found that the results of the Maxquant search engine were slightly less than those of pFind. This result shows that SAPTyper can achieve SAP fingding function. Moreover, the pFind search engine was used to test the proteome data of 3 hair shafts from 1 European person and 1 African person in the literature. Among the sites fully matched by the literature method, sites detected by SAPTyper are also included; for semi-matching sites, that is, nsSNPs are heterozygous, both literature method and SAPTyper method had the risk of missing detection for one type of the allele. Comparing the analysis results of SAPTyper with the SAP test results reported in the literature, it was found that some imputed nsSNP sites identified by the literature method but not detected by SAPTyper had a MAF of less than 0.1% in East Asian populations, and therefore they were not included in the common nsSNP database of East Asian populations constructed by this software. Since the database construction of this software is based on the genetic variation information of East Asian populations, it is currently unable to effectively identify representative unique common variation sites in European or African populations, but it can still identify SAP sites shared by these populations and East Asian populations. ConclusionAn automated SAP analysis algorithm was developed for East Asian populations, and the software named SAPTyper was developed. This software provides a convenient and efficient analysis tool for the research and application of forensic proteomic SAP and has important application prospects in individual identification and phenotypic inference based on SAP.


Result Analysis
Print
Save
E-mail