1.Single-cell and spatial transcriptomic analysis reveals that an immune cell-related signature could predict clinical outcomes for microsatellite-stable colorectal cancer patients receiving immunotherapy.
Shijin YUAN ; Yan XIA ; Guangwei DAI ; Shun RAO ; Rongrong HU ; Yuzhen GAO ; Qing QIU ; Chenghao WU ; Sai QIAO ; Yinghua XU ; Xinyou XIE ; Haizhou LOU ; Xian WANG ; Jun ZHANG
Journal of Zhejiang University. Science. B 2025;26(4):371-392
Recent data suggest that vascular endothelial growth factor receptor inhibitor (VEGFRi) can enhance the anti-tumor activity of the anti-programmed cell death-1 (anti-PD-1) antibody in colorectal cancer (CRC) with microsatellite stability (MSS). However, the comparison between this combination and standard third-line VEGFRi treatment is not performed, and reliable biomarkers are still lacking. We retrospectively enrolled MSS CRC patients receiving anti-PD-1 antibody plus VEGFRi (combination group, n=54) or VEGFRi alone (VEGFRi group, n=32), and their efficacy and safety were evaluated. We additionally examined the immune characteristics of the MSS CRC tumor microenvironment (TME) through single-cell and spatial transcriptomic data, and an MSS CRC immune cell-related signature (MCICRS) that can be used to predict the clinical outcomes of MSS CRC patients receiving immunotherapy was developed and validated in our in-house cohort. Compared with VEGFRi alone, the combination of anti-PD-1 antibody and VEGFRi exhibited a prolonged survival benefit (median progression-free survival: 4.4 vs. 2.0 months, P=0.0024; median overall survival: 10.2 vs. 5.2 months, P=0.0038) and a similar adverse event incidence. Through single-cell and spatial transcriptomic analysis, we determined ten MSS CRC-enriched immune cell types and their spatial distribution, including naive CD4+ T, regulatory CD4+ T, CD4+ Th17, exhausted CD8+ T, cytotoxic CD8+ T, proliferated CD8+ T, natural killer (NK) cells, plasma, and classical and intermediate monocytes. Based on a systemic meta-analysis and ten machine learning algorithms, we obtained MCICRS, an independent risk factor for the prognosis of MSS CRC patients. Further analyses demonstrated that the low-MCICRS group presented a higher immune cell infiltration and immune-related pathway activation, and hence a significant relation with the superior efficacy of pan-cancer immunotherapy. More importantly, the predictive value of MCICRS in MSS CRC patients receiving immunotherapy was also validated with an in-house cohort. Anti-PD-1 antibody combined with VEGFRi presented an improved clinical benefit in MSS CRC with manageable toxicity. MCICRS could serve as a robust and promising tool to predict clinical outcomes for individual MSS CRC patients receiving immunotherapy.
Humans
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Colorectal Neoplasms/drug therapy*
;
Male
;
Female
;
Immunotherapy
;
Middle Aged
;
Aged
;
Tumor Microenvironment/immunology*
;
Retrospective Studies
;
Microsatellite Instability
;
Transcriptome
;
Single-Cell Analysis
;
Programmed Cell Death 1 Receptor/immunology*
;
Gene Expression Profiling
;
Immune Checkpoint Inhibitors/therapeutic use*
;
Adult
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Receptors, Vascular Endothelial Growth Factor/antagonists & inhibitors*
2.VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data.
Liang ZHANG ; Hua PANG ; Chenghao ZHANG ; Song LI ; Yang TAN ; Fan JIANG ; Mingchen LI ; Yuanxi YU ; Ziyi ZHOU ; Banghao WU ; Bingxin ZHOU ; Hao LIU ; Pan TAN ; Liang HONG
Acta Pharmaceutica Sinica B 2025;15(5):2454-2467
In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (DMS) experiments that use surrogate readouts, which may not adequately capture the complex biochemical properties of interest. Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties, and this is particularly true for the real industrial application scenario. Therefore, the desired testing datasets, will be small-size (∼10-100) experimental data for each protein, and involve as many proteins as possible and as many properties as possible, which is, however, lacking. Here, we present VenusMutHub, a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases, spanning 527 proteins across diverse functional properties including stability, activity, binding affinity, and selectivity. These datasets feature direct biochemical measurements rather than surrogate readouts, providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions. We evaluate 23 computational models across various methodological paradigms, such as sequence-based, structure-informed and evolutionary approaches. This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.
3.Expert consensus on classification and diagnosis of congenital orofacial cleft.
Chenghao LI ; Yang AN ; Xiaohong DUAN ; Yingkun GUO ; Shanling LIU ; Hong LUO ; Duan MA ; Yunyun REN ; Xudong WANG ; Xiaoshan WU ; Hongning XIE ; Hongping ZHU ; Jun ZHU ; Bing SHI
West China Journal of Stomatology 2025;43(1):1-14
Congenital orofacial cleft, the most common birth defect in the maxillofacial region, exhibits a wide range of prognosis depending on the severity of deformity and underlying etiology. Non-syndromic congenital orofacial clefts typically present with milder deformities and more favorable treatment outcomes, whereas syndromic congenital orofacial clefts often manifest with concomitant organ abnormalities, which pose greater challenges for treatment and result in poorer prognosis. This consensus provides an elaborate classification system for varying degrees of orofacial clefts along with corresponding diagnostic and therapeutic guidelines. Results serve as a crucial resource for families to navigate prenatal screening results or make informed decisions regarding treatment options while also contributing significantly to preventing serious birth defects within the development of population.
Humans
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Cleft Lip/diagnosis*
;
Cleft Palate/diagnosis*
;
Consensus
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Prenatal Diagnosis
;
Female
4.Factors influencing maxillary dental arch development in children after Sommerlad-Furlow palatoplasty.
Jue WANG ; Yuanyuan LI ; Ming WU ; Bing SHI ; Qian ZHENG ; Renkai LIU ; Chenghao LI
West China Journal of Stomatology 2025;43(2):197-203
OBJECTIVES:
This study aims to investigate factors influencing dental arch development in patients aged 0-6 years with cleft palate after Sommerlad-Furlow (SF) palatoplasty.
METHODS:
A total of 183 patients who underwent primary SF repair for cleft lip and palate before 18 months of age were included. Follow-ups were conducted at different ages, and digital dental casts of the maxillary dental arch were obtained using 3-matic Research 12.0 software. The length and width of the dental arch and palate were measured to explore developmental changes in the maxillary dental arch of the patients after the procedure. The study also investigated the influence of gender, age, cleft palate type, and relaxation incision on maxillary dental arch development.
RESULTS:
After SF, maxillary dental arch measurements showed statistically significant differences between children aged 0-2 years and those aged 3-6 years (P<0.05). However, no statistically significant differences were observed among different age groups within the 3-6 years range. Statistically significant differences were detected between males and females, with males having greater width of the posterior dental arch and palate (P=0.001) and shorter length of the anterior dental arch and entire dental arch (P<0.05). The unilateral cleft lip and palate group had shorter dental arch length (P<0.01) and wider posterior palate (P<0.01) than the cleft palate only group. Maxillary dental arch measurements had no statistically significant differences between groups with or without a relaxing incision.
CONCLUSIONS
Gender and age influence the width of the maxillary dental arch in children aged 0-6 years after SF, while age and cleft palate type affect dental arch length.
Humans
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Child, Preschool
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Male
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Cleft Palate/surgery*
;
Female
;
Child
;
Infant
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Dental Arch/growth & development*
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Maxilla/growth & development*
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Cleft Lip/surgery*
;
Age Factors
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Sex Factors
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Palate/surgery*
;
Infant, Newborn
5.Shuxuetong Inhibits Bim-dependent Apoptosis of Cerebellar Granule Neurons
Shenhao PAN ; Dongfang CAO ; Fanyi ZHAO ; Sijie ZHAO ; Chenghao ZHANG ; Jianfeng LIANG ; Jianwei WU ; Zhongmin YUAN
Journal of Sun Yat-sen University(Medical Sciences) 2024;45(4):549-556
[Objective]To investigate the effect and mechanism of Shuxuetong and its main component hirudin on the apoptosis of cerebellar granule neurons(CGNs)in Sprague-Dawley(SD)rats.[Methods]CGNs incubated in vitro for 7 days were divided into survival control group or 25 K group(cultured in medium containing 25 mmol/L KCL)and apopto-sis group or 5 K group(cultured in medium containing 5 mmol/L KCL).CGNs were separately treated with proportionally diluted and different concentrations of Shuxuetong(1/50,1/40,1/30,1/20 and 1/10)and the corresponding different con-centrations of hirudin(2,2.5,3.34,5 and 10 U/mL).Hoechst staining was performed to analyze the apoptosis.Western blot was used to detect the expression levels of Cleaved Caspase-3,Bim and VEGF.[Results]Hoechst staining showed that 5 K group had a higher apoptosis rate than 25 K group.In 25 K group,there was no significant change in the apoptosis rate between neurons treated with different concentrations of Shuxuetong and hirudin,but significant changes was found in 5 K group and the higher the concentration,the lower the apoptosis rate.Western blot results revealed that,compared with control neurons in 5 K group,Shuxuetong injection and hirudin treatments resulted in a decrease of Cleaved Caspase-3 and Bim expression,but an increase of VEGF protein.[Conclusions]Shuxuetong and its main component hirudin inhibits the apoptosis of CGNs through suppressing proapoptotic BH3-only protein Bim.
6.Virtual shopping improves cognitive function of patients with mild cognitive impairment:a meta-analysis
Chenghao WU ; Qichao DING ; Xu SUN ; Xiaoying BI
Academic Journal of Naval Medical University 2024;45(9):1097-1106
Objective To systematically evaluate the effect of virtual shopping on cognitive function of patients with mild cognitive impairment. Methods PubMed,EMBASE,Cochrane Library,Web of Science,and CNKI were searched for literatures on virtual shopping,mild cognitive impairment,and cognitive function published from database inception to Sep. 2023. The literatures were screened and the data were extracted in strict accordance with the inclusion criteria,and the Review Manager 5.3 was used for meta-analysis. Results A total of 12 randomized controlled trials involving 382 patients with mild cognitive impairment were included. Meta analysis showed that compared with traditional cognitive rehabilitation training,virtual shopping could improve the comprehensive cognitive function,executive function,attention and abilities of daily living of patients with mild cognitive impairment (all P<0.05),but had no significant effects on the memory,language,or visuospatial ability (all P>0.05). Conclusion Virtual shopping is beneficial for improving the comprehensive cognitive function,executive function,attention and abilities of daily living of patients with mild cognitive impairment.
7.The preliminary experience of sandwich surgery in pectus carinatum repair
Jie YU ; Qi ZENG ; Chenghao CHEN ; Na ZHANG ; Yujia WU
Chinese Journal of Thoracic and Cardiovascular Surgery 2024;40(6):374-378
Objective:To determine the safety and efficacy of sandwich surgery in minimally invasive orthopedic surgery.Methods:A retrospective analysis was performed on 79 pectus carinatum patients undergoing minimally invasive orthopedic surgery admitted to the Department of Thoracic Surgery, Beijing Children's Hospital from July 2016 to July 2018, including 53 cases in the Abramson surgery group and 26 cases in the sandwich surgery group.Results:79 cases successfully completed the operation, the difference in complication rate between the two groups was not statistically significant. All cases were followed up to two years after bar removal, and no recurrence during the follow-up period. The excellent rate of orthopedic effect in sandwich surgery group was higher than that in Abramson surgery group.Conclusion:Sandwich surgery is safe, feasible and can achieve satisfactory postoperative results. It can be used as a surgical option for the treatment of pectus carinatum with depression or depression after orthosis.
8.Analysis of the efficacy of subretinal injection and intravitreal injection of conbercept in the treatment of polypoidal choroidal vasculopathy
Teng LIU ; Xiao YU ; Xiaojian WU ; Yuling ZOU ; Kangcheng LIU ; Hua ZOU ; Wei WU ; Chenghao XU ; Zhipeng YOU
Chinese Journal of Ocular Fundus Diseases 2024;40(6):421-428
Objective:To observe the clinical effect of subretinal injection and intravitreal injection of conbercept in the treatment of polypoid choroidal vasculopathy (PCV).Methods:A prospective, randomized double-blind controlled study. From June 2022 to January 2023, 35 patients of 35 eyes with PCV diagnosed at Affiliated Eye Hospital of Nanchang University were included in the study. All patients were first-time recipients of treatment. Best corrected visual acuity (BCVA), optical coherence tomography (OCT), and indocyanine green angiography (ICGA) were performed in all affected eyes. BCVA was performed using an international standard visual acuity chart and converted to logarithmic minimum resolved angle (logMAR) visual acuity for statistical purposes. Enhanced depth imaging with OCT instrument was used to measure the macular retinal thickness (MRT), subfoveal choroidal thickness (SFCT), and pigment epithelium detachment (PED) height. Randomized numerical table method was used to divide the patients into subretinal injection group (group A) and vitreous cavity injection group (Group B), 18 cases with 18 eyes and 17 cases with 17 eyes, respectively. Comparison of age ( t=0.090), disease duration ( t=-0.370), logMAR BCVA ( t=?0.190), MRT ( t=0.860), SFCT ( t=0.247), and PED height ( t=?0.520) between the two groups showed no statistically significant difference ( P>0.05). The eyes of group A were given one subretinal injection of 10 mg/ml conbercept 0.05 ml (containing conbercept 0.5 mg), and subsequently administered on demand (PRN); eyes in group B were given intravitreal injection of 10 mg/ml conbercept 0.05 ml (containing conbercept 0.5 mg). The treatment regimen was 3+PRN. Lesions were categorized into active and quiescent according to the results of post-treatment OCT and BCVA. Active lesions were treated with intravitreal injection of conbercept at the same dose as before; stationary lesions were followed up for observation. BCVA and OCT were performed at 1, 2, 3, 6 and 9 months after treatment; ICGA was performed at 3, 6 and 9 months. BCVA, MRT, SFCT, and PED height changes before and after treatment were compared and observed in the affected eyes of the two groups. Independent sample t-test was used to compare between the two groups. Results:With the prolongation of time after treatment, the BCVA of the affected eyes in groups A and B gradually increased, and the MRT, SFCT, and PED height gradually decreased. Compared with group B, at 2, 3, 6, and 9 months after treatment, the BCVA of group A was significantly improved, and the difference was statistically significant ( t=?2.215, ?2.820, ?2.559, ?4.051; P<0.05); at 1, 2, 3, 6, and 9 months after treatment, the MRT of the affected eyes in group A ( t=?2.439, ?3.091, ?3.099, ?3.665, ?5.494), SFCT ( t=?3.370, ?3.058, ?3.268, ?4.220, ?4.121), and PED height ( t=?3.460, ?4.678, ?4.956, ?5.368, ?6.396) were significantly reduced, and the differences were statistically significant ( P<0.05). No complications such as intraocular inflammation, high intraocular pressure, or vitreous hemorrhage occurred in any of the affected eyes during or after treatment. Conclusion:Compared with the intravitreal injection of conbercept, the subretinal injection of conbercept can more effectively reduce the height of MRT, SFCT, PED height, and improve the visual acuity of the affected eyes with PCV.
9.A novel nomogram-based model to predict the postoperative overall survival in patients with gastric and colorectal cancer
Siwen WANG ; Kangjing XU ; Xuejin GAO ; Tingting GAO ; Guangming SUN ; Yaqin XIAO ; Haoyang WANG ; Chenghao ZENG ; Deshuai SONG ; Yupeng ZHANG ; Lingli HUANG ; Bo LIAN ; Jianjiao CHEN ; Dong GUO ; Zhenyi JIA ; Yong WANG ; Fangyou GONG ; Junde ZHOU ; Zhigang XUE ; Zhida CHEN ; Gang LI ; Mengbin LI ; Wei ZHAO ; Yanbing ZHOU ; Huanlong QIN ; Xiaoting WU ; Kunhua WANG ; Qiang CHI ; Jianchun YU ; Yun TANG ; Guoli LI ; Li ZHANG ; Xinying WANG
Chinese Journal of Clinical Nutrition 2024;32(3):138-149
Objective:We aimed to develop a novel visualized model based on nomogram to predict postoperative overall survival.Methods:This was a multicenter, retrospective, observational cohort study, including participants with histologically confirmed gastric and colorectal cancer who underwent radical surgery from 11 medical centers in China from August 1, 2015 to June 30, 2018. Baseline characteristics, histopathological data and nutritional status, as assessed using Nutrition Risk Screening 2002 (NRS 2002) score and the scored Patient-Generated Subjective Global Assessment, were collected. The least absolute shrinkage and selection operator regression and Cox regression were used to identify variables to be included in the predictive model. Internal and external validations were performed.Results:There were 681 and 127 patients in the training and validation cohorts, respectively. A total of 188 deaths were observed over a median follow-up period of 59 (range: 58 to 60) months. Two independent predictors of NRS 2002 and Tumor-Node-Metastasis (TNM) stage were identified and incorporated into the prediction nomogram model together with the factor of age. The model's concordance index for 1-, 3- and 5-year overall survival was 0.696, 0.724, and 0.738 in the training cohort and 0.801, 0.812, and 0.793 in the validation cohort, respectively.Conclusions:In this study, a new nomogram prediction model based on NRS 2002 score was developed and validated for predicting the overall postoperative survival of patients with gastric colorectal cancer. This model has good differentiation, calibration and clinical practicability in predicting the long-term survival rate of patients with gastrointestinal cancer after radical surgery.
10.Development and validation of a risk-prediction model for immune-related adverse events in patients with non-small-cell lung cancer receiving PD-1/PD-L1 inhibitors.
Qing QIU ; Chenghao WU ; Wenxiao TANG ; Longfei JI ; Guangwei DAI ; Yuzhen GAO ; Enguo CHEN ; Hanliang JIANG ; Xinyou XIE ; Jun ZHANG
Journal of Zhejiang University. Science. B 2023;24(10):935-942
Lung cancer remains the leading cause of cancer deaths worldwide and is the most common cancer in males. Immune-checkpoint inhibitors (ICIs) that target programmed cell death protein-1 (PD-1) or programmed cell death-ligand 1 (PD-L1) have achieved impressive efficacy in the treatment of non-small-cell lung cancer (NSCLC) (Pardoll, 2012; Champiat et al., 2016; Gao et al., 2022). Although ICIs are usually well tolerated, they are often accompanied by immune-related adverse events (irAEs) (Doroshow et al., 2019). Non-specific activation of the immune system produces off-target immune and inflammatory responses that can affect virtually any organ or system (O'Kane et al., 2017; Puzanov et al., 2017). Compared with adverse events caused by chemotherapy, irAEs are often characterized by delayed onset and prolonged duration and can occur in any organ at any stage of treatment, including after cessation of treatment (Puzanov et al., 2017; von Itzstein et al., 2020). They range from rash, pneumonitis, hypothyroidism, enterocolitis, and autoimmune hepatitis to cardiovascular, hematological, renal, neurological, and ophthalmic irAEs (Nishino et al., 2016; Kumar et al., 2017; Song et al., 2020). Hence, we conducted a retrospective study to identify validated factors that could predict the magnitude of the risk of irAEs in patients receiving PD-1/PD-L1 inhibitors; our approach was to analyze the correlation between the clinical characteristics of patients at the start of treatment and relevant indicators such as hematological indices and the risk of developing irAEs. Then, we developed an economical, practical, rapid, and simple model to assess the risk of irAEs in patients receiving ICI treatment, as early as possible.
Male
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Humans
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Carcinoma, Non-Small-Cell Lung/drug therapy*
;
Lung Neoplasms/drug therapy*
;
Immune Checkpoint Inhibitors/adverse effects*
;
Programmed Cell Death 1 Receptor
;
Retrospective Studies
;
Apoptosis

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